Trends Plant Sci , IF:18.313 , 2022 Oct doi: 10.1016/j.tplants.2022.08.016
PANOMICS at the interface of root-soil microbiome and BNI.
Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.; Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: palak.chaturvedi@univie.ac.at.; Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan.; Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: wolfram.weckwerth@univie.ac.at.
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N(2)O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
PMID: 36229336
Trends Plant Sci , IF:18.313 , 2022 Dec , V27 (12) : P1209-1217 doi: 10.1016/j.tplants.2022.06.002
Towards a hierarchical gene regulatory network underlying somatic embryogenesis.
National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; University of Chinese Academy of Sciences (UCAS), Shanghai 200032, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; ShanghaiTech University, Shanghai 200031, PR China. Electronic address: jwwang@sippe.ac.cn.
Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics.
PMID: 35810071
Trends Microbiol , IF:17.079 , 2022 Oct , V30 (10) : P922-924 doi: 10.1016/j.tim.2022.06.006
Synthetic plant microbiota challenges in nonmodel species.
Department of Biology, University of Florence, Florence, Italy.; Department of Biology, University of Florence, Florence, Italy. Electronic address: alessio.mengoni@unifi.it.
Plant-associated microbiota are becoming central in the development of ways to improve plant productivity and health. However, most research has focussed mainly on a few model plant species. It is essential to translate discoveries to the many nonmodel crops, allowing the design and application of effective synthetic microbiota.
PMID: 35843854
Biotechnol Adv , IF:14.227 , 2022 Oct , V59 : P107969 doi: 10.1016/j.biotechadv.2022.107969
Current status, and the developments of hosts and expression systems for the production of recombinant human cytokines.
Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.; Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India. Electronic address: veeranki@iitg.ac.in.
Cytokines consist of peptides, proteins and glycoproteins, which are biological signaling molecules, and boost cell-cell communication in immune reactions to stimulate cellular movements in the place of trauma, inflammation and infection. Recombinant cytokines are designed in such a way that they have generalized immunostimulation action or stimulate specific immune cells when the body encounters immunosuppressive signals from exogenous pathogens or other tumor microenvironments. Recombinant cytokines have improved the treatment processes for numerous diseases. They are also beneficial against novel toxicities that arise due to pharmacologic immunostimulators that lead to an imbalance in the regulation of cytokine. So, the production and use of recombinant human cytokines as therapeutic proteins are significant for medical treatment purposes. For the improved production of recombinant human cytokines, the development of host cells such as bacteria, yeast, fungi, insect, mammal and transgenic plants, and the specific expression systems for individual hosts is necessary. The recent advancements in the field of genetic engineering are beneficial for easy and efficient genetic manipulations for hosts as well as expression cassettes. The use of metabolic engineering and systems biology approaches have tremendous applications in recombinant protein production by generating mathematical models, and analyzing complex biological networks and metabolic pathways via simulations to understand the interconnections between metabolites and genetic behaviors. Further, the bioprocess developments and the optimization of cell culture conditions would enhance recombinant cytokines productivity on large scales.
PMID: 35525478
Genome Biol , IF:13.583 , 2022 Nov , V23 (1) : P233 doi: 10.1186/s13059-022-02801-z
Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.; Hubei Hongshan Laboratory, Wuhan, China.; Department of Plant Breeding, Justus Liebig University, Giessen, Germany.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. weibo.xie@mail.hzau.edu.cn.; Hubei Hongshan Laboratory, Wuhan, China. weibo.xie@mail.hzau.edu.cn.; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China. weibo.xie@mail.hzau.edu.cn.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. guoliang@mail.hzau.edu.cn.; Hubei Hongshan Laboratory, Wuhan, China. guoliang@mail.hzau.edu.cn.; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China. guoliang@mail.hzau.edu.cn.; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. guoliang@mail.hzau.edu.cn.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. zhaohu@mail.hzau.edu.cn.; Hubei Hongshan Laboratory, Wuhan, China. zhaohu@mail.hzau.edu.cn.
BACKGROUND: Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) is an important source for the vegetable oil in the world, and the seed oil content is an important trait of B. napus. RESULTS: We perform a comprehensive analysis of the transcriptional variability in the seeds of B. napus at two developmental stages, 20 and 40 days after flowering (DAF). We detect 53,759 and 53,550 independent expression quantitative trait loci (eQTLs) for 79,605 and 76,713 expressed genes at 20 and 40 DAF, respectively. Among them, the local eQTLs are mapped to the adjacent genes more frequently. The adjacent gene pairs are regulated by local eQTLs with the same open chromatin state and show a stronger mode of expression piggybacking. Inter-subgenomic analysis indicates that there is a feedback regulation for the homoeologous gene pairs to maintain partial expression dosage. We also identify 141 eQTL hotspots and find that hotspot87-88 co-localizes with a QTL for the seed oil content. To further resolve the regulatory network of this eQTL hotspot, we construct the XGBoost model using 856 RNA-seq datasets and the Basenji model using 59 ATAC-seq datasets. Using these two models, we predict the mechanisms affecting the seed oil content regulated by hotspot87-88 and experimentally validate that the transcription factors, NAC13 and SCL31, positively regulate the seed oil content. CONCLUSIONS: We comprehensively characterize the gene regulatory features in the seeds of B. napus and reveal the gene networks regulating the seed oil content of B. napus.
PMID: 36345039
Mol Plant , IF:13.164 , 2022 Nov , V15 (11) : P1807-1824 doi: 10.1016/j.molp.2022.10.016
MINI-EX: Integrative inference of single-cell gene regulatory networks in plants.
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium. Electronic address: klaas.vandepoele@psb.vib-ugent.be.
Multicellular organisms, such as plants, are characterized by highly specialized and tightly regulated cell populations, establishing specific morphological structures and executing distinct functions. Gene regulatory networks (GRNs) describe condition-specific interactions of transcription factors (TFs) regulating the expression of target genes, underpinning these specific functions. As efficient and validated methods to identify cell-type-specific GRNs from single-cell data in plants are lacking, limiting our understanding of the organization of specific cell types in both model species and crops, we developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type-specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. Next, regulons are assigned to different cell types, leveraging cell-specific expression, and candidate regulators are prioritized using network centrality measures, functional annotations, and expression specificity. This embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell types controlling a biological process of interest. We demonstrate the stability of MINI-EX toward input data sets with low number of cells and its robustness toward missing data, and show that it infers state-of-the-art networks with a better performance compared with other related single-cell network tools. MINI-EX successfully identifies key regulators controlling root development in Arabidopsis and rice, leaf development in Arabidopsis, and ear development in maize, enhancing our understanding of cell-type-specific regulation and unraveling the roles of different regulators controlling the development of specific cell types in plants.
PMID: 36307979
New Phytol , IF:10.151 , 2022 Oct doi: 10.1111/nph.18564
Defining the scope for altering rice leaf anatomy to improve photosynthesis: a modelling approach.
Center of Excellence for Molecular Plant Science, Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China.; Plants, Photosynthesis and Soil, Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.; Division of Agriculture and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.; Pacific Northwest National Laboratory, Richland, WA, 99354, USA.; Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Malaysia.
Leaf structure plays an important role in photosynthesis. However, the causal relationship and the quantitative importance of any single structural parameter to the overall photosynthetic performance of a leaf remains open to debate. In this paper, we report on a mechanistic model, eLeaf, which successfully captures rice leaf photosynthetic performance under varying environmental conditions of light and CO(2) . We developed a 3D reaction-diffusion model for leaf photosynthesis parameterised using a range of imaging data and biochemical measurements from plants grown under ambient and elevated CO(2) and then interrogated the model to quantify the importance of these elements. The model successfully captured leaf-level photosynthetic performance in rice. Photosynthetic metabolism underpinned the majority of the increased carbon assimilation rate observed under elevated CO(2) levels, with a range of structural elements making positive and negative contributions. Mesophyll porosity could be varied without any major outcome on photosynthetic performance, providing a theoretical underpinning for experimental data. eLeaf allows quantitative analysis of the influence of morphological and biochemical properties on leaf photosynthesis. The analysis highlights a degree of leaf structural plasticity with respect to photosynthesis of significance in the context of attempts to improve crop photosynthesis.
PMID: 36271620
New Phytol , IF:10.151 , 2022 Oct doi: 10.1111/nph.18567
AabHLH113 integrates JA and ABA signalling to positively regulate artemisinin biosynthesis in Artemisia annua.
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & Southwest University, School of Life Sciences, Southwest University, Chongqing, 400715, China.; Chongqing Academy of Science and Technology, Chongqing, 401123, China.; College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China.; College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
Artemisinin, a sesquiterpene lactone isolated from Artemisia annua L., is in huge market demand due to its efficient anti-malarial action, especially after the COVID-19 pandemic. Many researchers have elucidated that phytohormones jasmonic acid (JA) and abscisic acid (ABA) positively regulate artemisinin biosynthesis via kinds of transcription factors (TFs). However, the crosstalk between JA and ABA in regulating artemisinin biosynthesis remains unclear. Here, we identified a novel ABA- and JA- induced bHLH TF, AabHLH113, which positively regulated artemisinin biosynthesis by directly binding to the promoters of artemisinin biosynthetic genes, DBR2 and ALDH1. The contents of artemisinin and dihydroartemisinic acid increased by 1.71- to 2.06-fold and 1.47- to 2.23-fold, respectively, in AabHLH1113 overexpressed Artemisia annua, whereas they decreased by 14-36% and 26-53%, respectively, in RNAi-AabHLH113 plants. Furthermore, we demonstrated that the AabZIP1 and AabHLH112, which respectively participate in ABA and JA signalling pathway to regulate artemisinin biosynthesis, directly bind to and activate the promoter of AabHLH113. Collectively, we revealed a complex network in which AabHLH113 plays a key interrelation role to integrate ABA- and JA-mediated regulating artemisinin biosynthesis.
PMID: 36271612
Plant Biotechnol J , IF:9.803 , 2022 Oct doi: 10.1111/pbi.13944
Multi-stress resilience in plants recovering from submergence.
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.; Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.
PMID: 36217562
Plant Biotechnol J , IF:9.803 , 2022 Dec , V20 (12) : P2372-2388 doi: 10.1111/pbi.13918
Single-cell RNA-seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum).
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei Province, China.; Department of Biosciences, Durham University, Durham, UK.
Cotton fibre is a unicellular seed trichome, and lint fibre initials per seed as a factor determines fibre yield. However, the mechanisms controlling fibre initiation from ovule epidermis are not understood well enough. Here, with single-cell RNA sequencing (scRNA-seq), a total of 14 535 cells were identified from cotton ovule outer integument of Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis and the day of anthesis). Three major cell types, fibre, non-fibre epidermis and outer pigment layer were identified and then verified by RNA in situ hybridization. A comparative analysis on scRNA-seq data between Xu142 and its fibreless mutant Xu142 fl further confirmed fibre cluster definition. The developmental trajectory of fibre cell was reconstructed, and fibre cell was identified differentiated at 1 day before anthesis. Gene regulatory networks at four stages revealed the spatiotemporal pattern of core transcription factors, and MYB25-like and HOX3 were demonstrated played key roles as commanders in fibre differentiation and tip-biased diffuse growth respectively. A model for early development of a single fibre cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fibre yield.
PMID: 36053965
Environ Pollut , IF:8.071 , 2022 Dec , V314 : P120344 doi: 10.1016/j.envpol.2022.120344
Effects of manure fertilization on human pathogens in endosphere of three vegetable plants.
Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. Electronic address: ygzhu@rcees.ac.cn.
Pathogens can colonize plant endosphere and, be transferred into human beings through the food chain. However, our understanding of the influences of agricultural activities, such as fertilization, on endophytic microbial communities and human pathogens is still limited. Here, we conducted a microcosm experiment using the combination of 16 S rRNA gene amplicon sequencing and high-throughput qPCR array to reveal the effects of manure fertilization on microbiomes of soils and plants and how such impact is translated into endophytic pathogens. Our results showed that manure fertilization significantly altered soil microbiomes, whereas with less influence on endophytic microbial communities. Soil is a vital source of both bacterial communities and human pathogens for the plant endosphere. The abundance of pathogens was increased both in soils and endosphere under manure fertilization. These findings provide an integrated understanding of the impact of manure fertilization on endophytic pathogens.
PMID: 36206891
Sci Total Environ , IF:7.963 , 2022 Nov , V846 : P157496 doi: 10.1016/j.scitotenv.2022.157496
Temperature drives the assembly of Bacillus community in mangrove ecosystem.
Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China.; Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China. Electronic address: liwenjun3@mail.sysu.edu.cn.; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province 350002, PR China. Electronic address: sgzhou@soil.gd.cn.
Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO(3)-N and NH(4)-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.
PMID: 35870580
Genomics Proteomics Bioinformatics , IF:7.691 , 2022 Oct doi: 10.1016/j.gpb.2022.10.005
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China.; College of Life Science, Northeast Forestry University, Harbin 150040, China.; College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China. Electronic address: ghwang@nefu.edu.cn.
Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular bases underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated for humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB) from 649 samples of 37 species. These samples are abiotic stress-related (159 samples, such as heat, cold, drought, and salt), development-related (232 samples), and/or tissue-specific (376 samples). Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factor footprint, motif, and single nucleotide polymorphisms (SNPs). Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility resource, which can aid in better understanding genetic regulatory networks underlying development, important traits, stress adaptations, and evolution.PlantCADB is freely available at https://bioinfor.nefu.edu.cn/PlantCADB/.
PMID: 36328151
Food Chem , IF:7.514 , 2023 Mar , V404 (Pt A) : P134545 doi: 10.1016/j.foodchem.2022.134545
Controlled mechanical stimuli reveal novel associations between basil metabolism and sensory quality.
School of Science and Technology, Man-Technology-Environment Research Centre, Orebro University, 701 82 Orebro, Sweden.; School of Hospitality, Culinary Arts and Meal Science, Sweden. Electronic address: anders.herdenstam@oru.se.; School of Science and Technology, Centre for Applied Autonomous Sensor Systems, Orebro University, 701 82 Orebro, Sweden; Department of Radiation Sciences, Radiation Physics, Umea University, 901 87 Umea, Sweden.; School of Science and Technology, Centre for Applied Autonomous Sensor Systems, Orebro University, 701 82 Orebro, Sweden.; School of Science and Technology, Man-Technology-Environment Research Centre, Orebro University, 701 82 Orebro, Sweden. Electronic address: victor.castro-alves@oru.se.
There is an increasing interest in the use of automation in plant production settings. Here, we employed a robotic platform to induce controlled mechanical stimuli (CMS) aiming to improve basil quality. Semi-targeted UHPLC-qToF-MS analysis of organic acids, amino acids, phenolic acids, and phenylpropanoids revealed changes in basil secondary metabolism under CMS, which appear to be associated with changes in taste, as revealed by different means of sensory evaluation (overall liking, check-all-that-apply, and just-about-right analysis). Further network analysis combining metabolomics and sensory data revealed novel links between plant metabolism and sensory quality. Amino acids and organic acids including maleic acid were negatively associated with basil quality, while increased levels of secondary metabolites, particularly linalool glucoside, were associated with improved basil taste. In summary, by combining metabolomics and sensory analysis we reveal the potential of automated CMS on crop production, while also providing new associations between plant metabolism and sensory quality.
PMID: 36252376
BMC Biol , IF:7.431 , 2022 Nov , V20 (1) : P252 doi: 10.1186/s12915-022-01450-9
Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula.
Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, 53715, USA.; School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA.; Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA.; Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA.; School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA. mkirst@ufl.edu.; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA. mkirst@ufl.edu.; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, 53715, USA. sroy@biostat.wisc.edu.; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, 53792, USA. sroy@biostat.wisc.edu.; Department of Computer Sciences, University of Wisconsin, Madison, WI, 53792, USA. sroy@biostat.wisc.edu.
BACKGROUND: Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules. RESULTS: We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. CONCLUSIONS: Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.
PMID: 36352404
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6307-6333 doi: 10.1093/jxb/erac300
Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Rua do Matao, Sao Paulo, Brazil.; VIB Center for Plant Systems Biology, Ghent, Belgium.; VIB Metabolomics Core, Ghent, Belgium.; Joint BioEnergy Institute, Emeryville, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, Sao Paulo, Brazil.
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
PMID: 35788296
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6089-6102 doi: 10.1093/jxb/erac270
Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals.
National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China.; Sanya Institute of China Agricultural University, Sanya, Hainan, China.
Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.
PMID: 35724645
J Environ Manage , IF:6.789 , 2022 Oct , V319 : P115694 doi: 10.1016/j.jenvman.2022.115694
Optimization of vegetable waste composting and the exploration of microbial mechanisms related to fungal communities during composting.
Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. Electronic address: wangweiping119@126.com.
The application of additives to regulate the microbial functional composition during composting has attracted much research attention. However, little is known about the succession and role of the fungal community in the laboratory-scale composting of vegetable waste supplemented with pig manure and microbial agents. The purpose of this study was to identify effective additives for improving vegetable waste composting performance and product quality, and to analyze the microbial community succession during composting. The results showed that the combined addition of pig manure and microbial agents (T2 treatment) accelerated the pile temperature increase, enhanced total organic carbon degradation (23.36%), and promoted the maturation of the compost. Furthermore, the T2 treatment increased the activities of most enzymes, reshaped the microbial community, and reduced the relative abundance of potential animal (1.60%) and plant (0.095%) pathogens. The relative abundance of Firmicutes (71.23%) increased with the combined addition of pig manure and microbial agents in the thermophilic stage. In the middle and late stages, Saccharomonospora, Aspergillus, and Thermomyces, which were related to C/N and total phosphorus, were enriched in the T2 treatment. Network analysis demonstrated that the complexity and stability of the fungal network were more evidently increased in the T2 treatment, and Saccharomonospora, Aspergillus, and Microascus were identified as keystone taxa. The keystone taxa associated with extracellular enzymes contributed significantly to compost maturation. These results provide a reference for the application of additives to improve compost safety in pilot-scale composting.
PMID: 35841778
Cells , IF:6.6 , 2022 Oct , V11 (20) doi: 10.3390/cells11203250
Melatonin and Indole-3-Acetic Acid Synergistically Regulate Plant Growth and Stress Resistance.
Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, College of Pharmacy, BaoTou Medical College, Baotou 014040, China.; University Engineering Research Center of Chinese (Mongolia) Ecological Planting Medicinal Materials (Nurture) in Inner Mongolia Autonomous Region, College of agronomy, Inner Mongolia Minzu University, Tongliao 028000, China.; School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.; College of Pharmacy, Inner Mongolia Medical University, Hohhot 010110, China.; Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot 010020, China.; Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China.
Plant growth and development exhibit plasticity, and plants can adapt to environmental changes and stress. Various phytohormones interact synergistically or antagonistically to regulate these responses. Melatonin and indole-3-acetic acid (IAA) are widespread across plant kingdom. Melatonin, an important member of the neuroendocrine immune regulatory network, can confer autoimmunity and protect against viral invasion. Melatonin functions as a plant growth regulator and biostimulant, with an important role in enhancing plant stress tolerance. IAA has a highly complex stress response mechanism, which participates in a series of stress induced physiological changes. This article reviews studies on the signaling pathways of melatonin and IAA, focusing on specific regulatory mechanisms. We discuss how these hormones coordinate plant growth and development and stress responses. Furthermore, the interactions between melatonin and IAA and their upstream and downstream transcriptional regulation are discussed from the perspective of modulating plant development and stress adaptation. The reviewed studies suggest that, at low concentrations, melatonin promotes IAA synthesis, whereas at high levels it reduces IAA levels. Similarly to IAA, melatonin promotes plant growth and development. IAA suppresses the melatonin induced inhibition of germination. IAA signaling plays an important role in plant growth and development, whereas melatonin signaling plays an important role in stress responses.
PMID: 36291118
Environ Res , IF:6.498 , 2022 Dec , V215 (Pt 1) : P114238 doi: 10.1016/j.envres.2022.114238
The emerging potential of natural and synthetic algae-based microbiomes for heavy metal removal and recovery from wastewaters.
Sustainable Resources Laboratory, Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod, Kerala, 671 316, India.; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 34113, Daejeon, Republic of Korea.; Sustainable Resources Laboratory, Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod, Kerala, 671 316, India; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, Republic of Korea. Electronic address: rishi@cukerala.ac.in.
Heavy Metal (HM) bioremoval by microbes is a successful, environment-friendly technique, particularly at low concentrations of HMs. Studies using algae, bacteria, and fungi reveal promising capabilities in isolation and when used in consortia. Yet, few reviews have emphasized individual and collective HM removal rates and the associated mechanisms in natural or synthetic microbiomes. Besides discussing the limitations of conventional and synthetic biology approaches, this review underscores the utility of indigenous microbial taxon, i.e., algae, fungi, and bacteria, in HM removal with adsorption capacities and their synergistic role in microbiome-led studies. The detoxification mechanisms studied for certain HMs indicate distinctive removal pathways in each taxon which points to an enhanced effect when used as a microbiome. The role and higher efficacies of the designer microbiomes with complementing and mutualistic taxa are also considered, followed by recovery options for a circular bioeconomy. The citation network analysis further validates the multi-metal removal ability of microbiomes and the restricted capabilities of the individual counterparts. In precis, the study reemphasizes increased metal removal efficiencies of inter-taxon microbiomes and the mechanisms for synergistic and improved removal, eventually drawing attention to the benefits of ecological engineering approaches compared to other alternatives.
PMID: 36108721
Food Res Int , IF:6.475 , 2022 Nov , V161 : P111491 doi: 10.1016/j.foodres.2022.111491
Comparative proteomic analysis of wild-type and a SlETR-3 (Nr) mutant reveals an ethylene-induced physiological regulatory network in fresh-cut tomatoes.
Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Department of Food Science and Engineering, College of Biological Sciences and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing 100083, China.; Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China.; Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing 402160, China. Electronic address: jialiu1983@163.com.; Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China. Electronic address: wangqing@nercv.org.
Ethylene plays a crucial role in regulating fruit ripening, quality, and defense response. However, the mechanism(s) responsible for wound-induced ethylene regulation of fruit physiology at a network level is unclear. We used mass spectrometry (MS) to identify differences in the physiological response between fresh-cut fruits of wild-type (WT) tomato and an ethylene receptor mutant (SlETR-3) (also referred to as Nr) during storage. We found that Nr mutants exhibited better appearance and quality, as well as higher ethylene levels during the first 3 d of storage at 4 degrees C. Thirty-seven (0 h), eighty-two (12 h) and twelve (24 h) differentially abundant proteins were identified between the fresh-cut slices of the two genotypes during storage at the designated timepoints. In particular, antioxidant enzymes, such as ascorbate peroxidase, glutathione S-transferase, and peroxiredoxin were highly expressed in WT fruit, which was associated with higher H(2)O(2) production, and high levels of transcription of cell-wall degrading enzymes. Leucine aminopeptidase, a marker enzyme for response to wounding exhibited higher levels in the Nr mutant, which is consistent with its higher production of ethylene. Collectively, our results provide a deeper insight into the ethylene-induced physiological regulatory network that is activated in fresh-cut tomatoes.
PMID: 36192866
Plant J , IF:6.417 , 2022 Oct , V112 (1) : P68-83 doi: 10.1111/tpj.15928
A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid.
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F(2) s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.
PMID: 35912411
J Fungi (Basel) , IF:5.816 , 2022 Oct , V8 (10) doi: 10.3390/jof8101073
Identification of Key Regulatory Pathways of Basidiocarp Formation in Pleurotus spp. Using Modeling, Simulation and System Biology Studies.
ICAR-Directorate of Mushroom Research, Solan 173 213, India.; Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA.; ICAR-Indian Institute of Soil and Water Conservation, Research Center, Udhagamandalam 643 006, India.; National Institute of Agricultural Extension Management (MANAGE), Hyderabad 500 030, India.; Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu 180 009, India.; Department of Plant Pathology, College of Horticulture, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan 173 230, India.; Division of Biochemistry, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Tech-nology of Jammu, Jammu 180 009, India.; Division of Microbiology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Tech-nology of Jammu, Jammu 180 009, India.
Pleurotus (Oyster mushroom) is an important cultivated edible mushroom across the world. It has several therapeutic effects as it contains various useful bio-molecules. The cultivation and crop management of these basidiomycete fungi depends on many extrinsic and intrinsic factors such as substrate composition, growing environment, enzymatic properties, and the genetic makeup, etc. Moreover, for efficient crop production, a comprehensive understanding of the fundamental properties viz. intrinsic-extrinsic factors and genotype-environment interaction analysis is required. The present study explores the basidiocarp formation biology in Pleurotus mushroom using an in silico response to the environmental factors and involvement of the major regulatory genes. The predictive model developed in this study indicates involvement of the key regulatory pathways in the pinhead to fruit body development process. Notably, the major regulatory pathways involved in the conversion of mycelium aggregation to pinhead formation and White Collar protein (PoWC1) binding flavin-chromophore (FAD) to activate respiratory enzymes. Overall, cell differentiation and higher expression of respiratory enzymes are the two important steps for basidiocarp formation. PoWC1 and pofst genes were participate in the structural changes process. Besides this, the PoWC1 gene is also involved in the respiratory requirement, while the OLYA6 gene is the triggering point of fruiting. The findings of the present study could be utilized to understand the detailed mechanism associated with the basidiocarp formation and to cultivate mushrooms at a sustainable level.
PMID: 36294638
Front Plant Sci , IF:5.753 , 2022 , V13 : P1019709 doi: 10.3389/fpls.2022.1019709
An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean.
Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.; Department of Resource and Environment, Faculty of Science at Sriracha, Kasetsart University, Sriracha, Thailand.; Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.
PMID: 36247545
Front Plant Sci , IF:5.753 , 2022 , V13 : P1013412 doi: 10.3389/fpls.2022.1013412
Weighted gene co-expression network analysis reveals key module and hub genes associated with the anthocyanin biosynthesis in maize pericarp.
Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.; School of Life Sciences, Anhui Agricultural University, Hefei, China.
Anthocyanins are the visual pigments that present most of the colors in plants. Its biosynthesis requires the coordinated expression of structural genes and regulatory genes. Pericarps are the rich sources of anthocyanins in maize seeds. In the experiment, the transcriptomes of transparent and anthocyanins-enriched pericarps at 15, 20, and 25 DAP were obtained. The results output 110.007 million raw reads and 51407 genes' expression matrix. Using data filtration in R language, 2057 genes were eventually identified for weighted gene co-expression network analysis. The results showed that 2057 genes were classified into ten modules. The cyan module containing 183 genes was confirmed to be the key module with the highest correlation value of 0.98 to the anthocyanins trait. Among 183 genes, seven structural genes were mapped the flavonoid biosynthesis pathway, and a transcription factor Lc gene was annotated as an anthocyanin regulatory gene. Cluster heatmap and gene network analysis further demonstrated that Naringenin, 2-oxoglutarate 3-dioxygenase (Zm00001d001960), Dihydroflavonol 4-reductase (Zm00001d044122), Leucoanthocyanidin dioxygenase (Zm00001d014914), anthocyanin regulatory Lc gene (Zm00001d026147), and Chalcone synthase C2 (Zm00001d052673) participated in the anthocyanins biosynthesis. And the transcription factor anthocyanin regulatory Lc gene Zm00001d026147 may act on the genes Chalcone synthase C2 (Zm00001d052673) and Dihydroflavonol 4-reductase (Zm00001d044122). The yeast one-hybrid assays confirmed that the Lc protein could combine with the promoter region of C2 and directly regulate the anthocyanin biosynthesis in the pericarp. These results may provide a new sight to uncover the module and hub genes related to anthocyanins biosynthesis in plants.
PMID: 36388502
Front Plant Sci , IF:5.753 , 2022 , V13 : P941338 doi: 10.3389/fpls.2022.941338
Transcriptional deregulation of stress-growth balance in Nicotiana benthamiana biofactories producing insect sex pheromones.
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.; Jozef Stefan International Postgraduate School, Ljubljana, Slovenia.; Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Cientificas (CSIC), Universidad Politecnica de Valencia (UPV), Valencia, Spain.
Plant biofactories are a promising platform for sustainable production of high-value compounds, among which are insect sex pheromones, a green alternative to conventional insecticides in agriculture. Recently, we have constructed transgenic Nicotiana benthamiana plants ("Sexy Plants", SxP) that successfully produce a blend of moth (Lepidoptera) sex pheromone compounds (Z)-11-hexadecen-1-ol and (Z)-11-hexadecenyl acetate. However, efficient biosynthesis of sex pheromones resulted in growth and developmental penalty, diminishing the potential for commercial use of SxP in biomanufacturing. To gain insight into the underlying molecular responses, we analysed the whole-genome transcriptome and evaluated it in relation to growth and pheromone production in low- and high-producing transgenic plants of v1.0 and v1.2 SxP lines. In our study, high-producing SxPv1.2 plants accumulated the highest amounts of pheromones but still maintained better growth compared to v1.0 high producers. For an in-depth biological interpretation of the transcriptomic data, we have prepared a comprehensive functional N. benthamiana genome annotation as well as gene translations to Arabidopsis thaliana, enabling functional information transfer by using Arabidopsis knowledge networks. Differential gene expression analysis, contrasting pheromone producers to wild-type plants, revealed that while only a few genes were differentially regulated in low-producing plants, high-producing plants exhibited vast transcriptional reprogramming. They showed signs of stress-like response, manifested as downregulation of photosynthesis-related genes and significant differences in expression of hormonal signalling and secondary metabolism-related genes, the latter presumably leading to previously reported volatilome changes. Further network analyses confirmed stress-like response with activation of jasmonic acid and downregulation of gibberellic acid signalling, illuminating the possibility that the observed growth penalty was not solely a consequence of a higher metabolic burden imposed upon constitutive expression of a heterologous biosynthetic pathway, but rather the result of signalling pathway perturbation. Our work presents an example of comprehensive transcriptomic analyses of disadvantageous stress signalling in N. benthamiana biofactory that could be applied to other bioproduction systems.
PMID: 36388501
Front Plant Sci , IF:5.753 , 2022 , V13 : P1005077 doi: 10.3389/fpls.2022.1005077
Histone methyltransferases SDG33 and SDG34 regulate organ-specific nitrogen responses in tomato.
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States.; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States.; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States.
Histone posttranslational modifications shape the chromatin landscape of the plant genome and affect gene expression in response to developmental and environmental cues. To date, the role of histone modifications in regulating plant responses to environmental nutrient availability, especially in agriculturally important species, remains largely unknown. We describe the functions of two histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen (N) responses of shoots and roots in tomato. By comparing the transcriptomes of CRISPR edited tomato lines sdg33 and sdg34 with wild-type plants under N-supplied and N-starved conditions, we uncovered that SDG33 and SDG34 regulate overlapping yet distinct downstream gene targets. In response to N level changes, both SDG33 and SDG34 mediate gene regulation in an organ-specific manner: in roots, SDG33 and SDG34 regulate a gene network including Nitrate Transporter 1.1 (NRT1.1) and Small Auxin Up-regulated RNA (SAUR) genes. In agreement with this, mutations in sdg33 or sdg34 abolish the root growth response triggered by an N-supply; In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and photosynthetic parameters in response to N. Our analysis thus revealed that SDG33 and SDG34 regulate N-responsive gene expression and physiological changes in an organ-specific manner, thus presenting previously unknown candidate genes as targets for selection and engineering to improve N uptake and usage in crop plants.
PMID: 36311072
Front Plant Sci , IF:5.753 , 2022 , V13 : P1035233 doi: 10.3389/fpls.2022.1035233
MbHY5-MbYSL7 mediates chlorophyll synthesis and iron transport under iron deficiency in Malus baccata.
State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China.
Iron (Fe) plays an important role in cellular respiration and catalytic reactions of metalloproteins in plants and animals. Plants maintain iron homeostasis through absorption, translocation, storage, and compartmentalization of iron via a cooperative regulative network. Here, we showed different physiological characteristics in the leaves and roots of Malus baccata under Fe sufficiency and Fe deficiency conditions and propose that MbHY5 (elongated hypocotyl 5), an important transcription factor for its function in photomorphogenesis, participated in Fe deficiency response in both the leaves and roots of M. baccata. The gene co-expression network showed that MbHY5 was involved in the regulation of chlorophyll synthesis and Fe transport pathway under Fe-limiting conditions. Specifically, we found that Fe deficiency induced the expression of MbYSL7 in root, which was positively regulated by MbHY5. Overexpressing or silencing MbYSL7 influenced the expression of MbHY5 in M. baccata.
PMID: 36340415
Front Plant Sci , IF:5.753 , 2022 , V13 : P976371 doi: 10.3389/fpls.2022.976371
A comprehensive map of preferentially located motifs reveals distinct proximal cis-regulatory sequences in plants.
Universite Paris-Saclay, CNRS, INRAE, Universite Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France.; Universite de Paris Cite, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France.; Universite Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.; Universite Paris-Saclay, INRAE, AgroParisTech, UMR MIA-Paris-Saclay, Palaiseau, France.
Identification of cis-regulatory sequences controlling gene expression is an arduous challenge that is being actively explored to discover key genetic factors responsible for traits of agronomic interest. Here, we used a genome-wide de novo approach to investigate preferentially located motifs (PLMs) in the proximal cis-regulatory landscape of Arabidopsis thaliana and Zea mays. We report three groups of PLMs in both the 5'- and 3'-gene-proximal regions and emphasize conserved PLMs in both species, particularly in the 3'-gene-proximal region. Comparison with resources from transcription factor and microRNA binding sites shows that 79% of the identified PLMs are unassigned, although some are supported by MNase-defined cistrome occupancy analysis. Enrichment analyses further reveal that unassigned PLMs provide functional predictions that differ from those derived from transcription factor and microRNA binding sites. Our study provides a comprehensive map of PLMs and demonstrates their potential utility for future characterization of orphan genes in plants.
PMID: 36311095
Front Plant Sci , IF:5.753 , 2022 , V13 : P985088 doi: 10.3389/fpls.2022.985088
Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with drought tolerance in Tartary buckwheat.
Key Laboratory of High-Quality Crops Cultivation and Safety Control of Yunnan Province, Honghe University, Honghe, China.; Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, China.; College of Life Science, Guizhou Normal University, Guiyang, China.; Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region of Ministry of Education, Guizhou University, Guiyang, China.
Drought stress is one of the major abiotic stress factors that affect plant growth and crop productivity. Tartary buckwheat is a nutritionally balanced and flavonoid-rich pseudocereal crop and also has strong adaptability to different adverse environments including drought. However, little is known about its drought tolerance mechanism. In this study, we performed comparative physiological and transcriptomic analyses of two contrasting drought-resistant Tartary buckwheat genotypes under nature drought treatment in the reproductive stage. Under drought stress, the drought-tolerant genotype XZSN had significantly higher contents of relative water, proline, and soluble sugar, as well as lower relative electrolyte leakage in the leaves than the drought-susceptible LK3. A total of 5,058 (2,165 upregulated and 2,893 downregulated) and 5,182 (2,358 upregulated and 2,824 downregulated) potential drought-responsive genes were identified in XZSN and LK3 by transcriptome sequencing analysis, respectively. Among the potential drought-responsive genes of XZSN, 1,206 and 1,274 genes were identified to be potential positive and negative contributors for XZSN having higher drought resistance ability than LK3. Furthermore, 851 out of 1,206 positive drought-resistant genes were further identified to be the core drought-resistant genes of XZSN based on WGCNA analysis, and most of them were induced earlier and quicker by drought stress than those in LK3. Functional annotation of the 851 core drought-resistant genes found that a large number of stress-responsive genes were involved in TFs, abscisic acid (ABA) biosynthesis, signal transduction and response, non-ABA signal molecule biosynthesis, water holding, oxygen species scavenging, osmotic adjustment, cell damage prevention, and so on. Transcriptional regulatory network analyses identified the potential regulators of these drought-resistant functional genes and found that the HD-ZIP and MYB TFs might be the key downstream TFs of drought resistance in Tartary buckwheat. Taken together, these results indicated that the XZSN genotype was more drought-tolerant than the LK3 genotype as evidenced by triggering the rapid and dramatic transcriptional reprogramming of drought-resistant genes to reduce water loss, prevent cell damage, and so on. This research expands our current understanding of the drought tolerance mechanisms of Tartary buckwheat and provides important information for its further drought resistance research and variety breeding.
PMID: 36262653
Front Plant Sci , IF:5.753 , 2022 , V13 : P1001357 doi: 10.3389/fpls.2022.1001357
Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress.
Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China.; National Engineering Research Center for Oil Tea Camellia, Changsha, China.
Camellia oleifera Abel. (C. oleifera) is an edible oil tree species that provide an important guarantee for targeted poverty alleviation strategy in China. Severe difficulties in irrigation leading to drought stress have become a major obstacle to the development of the C. oleifera planting industry. Breeding of drought-tolerant cultivars is the main idea for solving the problem of water shortage stress in C. oleifera cultivation. The photosynthetic physiology traits of C. oleifera cultivars 'Xianglin No.1' and 'Hengdong No.2' were affected by drought stress to different degrees, which demonstrated that the two cultivars suffered different degrees of damage. In the present study, we applied mRNA-seq and miRNA-seq to analyze the difference in molecular responses between drought stress and control, drought-tolerant and -sensitive cultivars, at mRNA and miRNA levels. The differentially expressed genes (DEGs) involved in photosynthesis-related, porphyrin, and chlorophyll metabolism, circadian rhythm system, and plant hormone signal transduction pathways were identified that might be candidates for drought stress tolerance genes. Subsequently, the miRNA-mRNA regulatory networks connected the differentially expressed miRNAs (DEMs) to their predicted target genes were established. miR398 and miR408-3p in C. oleifera showed that associated with the response to drought stress by negatively regulating genes encoding Downy Mildew Resistance 6 (DMR6) and Enhanced Disease Resistance 2 (EDR2), respectively, which might further improve drought tolerance via crosstalk between different stress-responsive pathways. The quantitation results of miRNA and mRNA were validated by quantitative real-time PCR (qRT-PCR). In summary, the integrated mRNA-seq and miRNA-seq analysis deepen our understanding of the regulatory network response to drought stress and variety-specific responses improving drought tolerance in C. oleifera.
PMID: 36247533
Genomics , IF:5.736 , 2022 Oct , V114 (6) : P110513 doi: 10.1016/j.ygeno.2022.110513
Integrated metabolite profiling and transcriptome analysis reveal candidate genes involved in the formation of yellow Nelumbo nucifera.
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: wuyanyan@webmail.hzau.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: wsh_chin@webmail.hzau.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: shiyan@webmail.hzau.edu.cn.; College of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China. Electronic address: libojiang@sdut.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: juicy.yang@webmail.hzau.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: wangxueqin@webmail.hzau.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: zhukaijie@mail.hzau.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: zhanghy@mail.hzau.edu.cn.; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: flybebrave@mail.hzau.edu.cn.
As a worldwide major ornamental flower and a edible plant, lotus (Nelumbo nucifera) is also used as medicine and tea beverage. Here, transcriptome and metabolites of yellow (MLQS) and white (YGB) lotus cultivars during five key flower coloration stages were profiled. 2014 differentially expressed genes were detected with 11 carotenoids in lotus were identified for the first time. Then, regulatory networks between and within functional modules was reconstructed, and the correlation between module-metabolites and gene-metabolites was conducted within 3 core modules. 18 candidate genes related to the formation of yellow flower were screened out and a gene regulatory model for the flower color difference between MLQS and YGB were speculated as follows: The substrate competition between F3'H and F3'5'H and substrate specificity of FLS, together with differential expression of CCD4a and CCD4b were contribute to the differences in flavonoids and carotenoids. Besides, UGT73C2, UGT91C1-2 and SGTase, and regulation of UGTs by transcription factors PLATZ, MADS, NAC031, and MYB308 may also play a role in the upstream regulation. The following verification results indicated that functional differences existed in the coding sequences of NnCCD4b and promoters of NnCCD4a of MLQS and YGB. In all, this study preliminarily reveals the mechanism of yellow flower coloration in lotus and provides new ideas for the study of complex ornamental characters of other plants.
PMID: 36309147
Front Microbiol , IF:5.64 , 2022 , V13 : P1019023 doi: 10.3389/fmicb.2022.1019023
Soil pqqC-harboring bacterial community response to increasing aridity in semi-arid grassland ecosystems: Diversity, co-occurrence network, and assembly process.
College of Grassland Science, Xinjiang Agricultural University, Urumqi, China.; School of Life Science, Shaoxing University, Shaoxing, China.; Inner Mongolia Autonomous Region Water Conservancy and Hydropower Survey and Design Institute Co., Ltd., Hohhot, China.; Inner Mongolia Institute of Water Conservancy Science Research, Hohhot, China.; Xilin Gol League Bureau of Agriculture and Animal Husbandry, Xilinhot, China.; Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China.
Aridity is increasing in several regions because of global climate change, which strongly affects the soil microbial community. The soil pqqC-harboring bacterial community plays a vital role in soil P cycling and P availability. However, the effect of shifts in aridity on the pqqC community is largely unknown. Here, based on high-throughput sequencing technology, we investigated the response patterns of the diversity, co-occurrence networks, and assembly mechanisms of the soil pqqC communities along a natural aridity gradient in adjacent pairs of natural and disturbed grasslands in Inner Mongolia, China. The results showed that the alpha-diversity of the pqqC community first increased and then decreased with increasing aridity in the natural grassland, while it linearly increased as aridity increased in the disturbed grassland. The pqqC community dissimilarity significantly increased with increased aridity, exhibiting a steeper change rate in the disturbed grassland than in the natural grassland. Increased aridity altered the pqqC community composition, leading to increases in the relative abundance of Actinobacteria but decreases in Proteobacteria. The composition and structure of the pqqC community showed significant differences between natural and disturbed grasslands. In addition, the network analysis revealed that aridity improved the interactions among pqqC taxa and promoted the interspecific competition of pqqC microorganisms. The pqqC community assembly was primarily governed by stochastic processes, and the relative contribution of stochastic processes increased with increasing aridity. Furthermore, disturbances could affect pqqC-harboring bacterial interactions and assembly processes. Overall, our findings fill an important knowledge gap in our understanding of the influence of aridity on the diversity and assembly mechanism of the soil pqqC community in grassland ecosystems, and this work is thus conducive to predicting the pqqC community and its ecological services in response to future climate change.
PMID: 36338099
Front Microbiol , IF:5.64 , 2022 , V13 : P947678 doi: 10.3389/fmicb.2022.947678
Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network.
Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico.; Division of Oncology, Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden.; Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico.
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of co-expression of transcriptional regulators (TF's) in the profiles, by selection of genes whose matrices were clustered with matrices of TF's, Transcriptional Regulatory networks (TRN s) were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF's and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene-target relationships for bases to construct a TRN.
PMID: 36312930
Ambio , IF:5.129 , 2022 Oct , V51 (10) : P2137-2154 doi: 10.1007/s13280-022-01733-z
Trees as brokers in social networks: Cascades of rights and benefits from a Cultural Keystone Species.
Jalan CIFOR Situ Gede, Bogor Barat, Bogor, 16115, Indonesia. h.djoudi@cgiar.org.; Jalan CIFOR Situ Gede, Bogor Barat, Bogor, 16115, Indonesia.; Cirad, UPR Forets et Societes, Univ Montpellier, TA C105-D, 34398, Montpellier Cedex5, France.; Center for International Forestry Research (CIFOR), 06 BP 9478, Ouagadougou, Burkina Faso.; Fenner School of Environment and Society, Australian National University, Bldg, 141, Linnaeus Way, Canberra, ACT, 2601, Australia.; The Alliance of Bioversity International and International Center for Tropical Agriculture, Via di San Domenico, 1, 00153, Rome, Italy.; CSIRO Land and Water, Ngunnawal Country GPO, Box 1700, Canberra, ACT, 2601, Australia.
Indigenous trees play key roles in West African landscapes, such as the nere tree (Parkia biglobosa (Jacq.) R.Br. ex G.Don). We applied social-ecological network analysis to understand the social-ecological interactions around nere. We documented the benefits nere provides and the multiple social interactions it creates amongst a large range of actors. The flows of rights over the trees and benefits from them formed two hierarchical networks, or cascades, with different actors at the top. The two forms of power revealed by the two cascades of rights and benefits suggest possible powers and counter-powers across gender, ethnicity, and age. We documented how the tree catalyses social interactions across diverse groups to sustain vital social connections, and co-constitute places, culture, and relationships. We argue that a paradigm shift is urgently needed to leverage the remarkable untapped potential of indigenous trees and Cultural Keystone Species in current global restoration and climate change agendas.
PMID: 35737271
Plant Cell Physiol , IF:4.927 , 2022 Nov doi: 10.1093/pcp/pcac161
Molecular mechanisms underlying the establishment and maintenance of vascular stem cells in Arabidopsis thaliana.
Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe 657-8501, Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.; College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan.
The vascular system plays pivotal roles in transporting water and nutrients throughout the plant body. Primary vasculature is established as a continuous strand, which subsequently initiates secondary growth through cell division. Key factors regulating primary and secondary vascular development have been identified in numerous studies, and the regulatory networks including these factors have been elucidated through omics-based approaches. However, the vascular system is composed of a variety of cells such as xylem and phloem cells, which are commonly generated from vascular stem cells. In addition, the vasculature is located deep inside the plant body, which makes it difficult to investigate the vascular development while distinguishing between vascular stem cells and developing xylem and phloem cells. Recent technical advances in tissue clearing method, RNA-seq analysis and tissue culture system overcome these problems by enabling the cell type-specific analysis during vascular development, especially with a special focus on stem cells. In this review, we summarize the recent findings on the establishment and maintenance of vascular stem cells.
PMID: 36398989
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111459 doi: 10.1016/j.plantsci.2022.111459
ZmDWF1 regulates leaf angle in maize.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China; Henan Academy of Agricultural Science, Zhengzhou, Henan 450002, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China. Electronic address: kulixia0371@163.com.
Leaf angle (LA) is a critical agronomic trait enhancing grain yield under high-density planting in maize. A number of researches have been conducted in recent years to investigate the quantitative trait loci/genes responsible for LA variation, while only a few genes were identified through map-based cloning. Here we cloned the ZmDWF1 gene, which was previously reported to encode Delta24-sterol reductase in the brassinosteroids (BRs) biosynthesis pathway. Overexpression of ZmDWF1 resulted in enlarged LA, indicating that ZmDWF1 is a positive regulator of LA in maize. To reveal the regulatory framework of ZmDWF1, we conducted RNA-Sequencing and yeast-two hybrid (Y2H) screening analysis. RNA-Sequencing analyzing results indicate ZmDWF1 mainly affected expression level of genes involved in cell wall associated metabolism and hormone metabolism including BR, gibberellin, and auxin. Y2H screening with Bi-FC assay confirmed three proteins (ZmPP2C-1, ZmROF1, and ZmTWD1) interacting with ZmDWF1. We revealed a new regulatory network of ZmDWF1 gene in controlling plant architecture in maize.
PMID: 36113675
J Proteome Res , IF:4.466 , 2022 Nov doi: 10.1021/acs.jproteome.2c00559
Susceptibility of Rice Crop to Salt Threat: Proteomic, Metabolomic, and Physiological Inspections.
Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Mangalore 575018, India.
Rice is a staple food crop worldwide; however, salinity stress is estimated to reduce its global production by 50%. Knowledge about initial molecular signaling and proteins associated with sensing salinity among crop plants is limited. We characterized early salt effects on the proteome and metabolome of rice tissues. Omics results were validated by western blotting and multiple reaction monitoring assays and integrated with physiological changes. We identified 8160 proteins and 2045 metabolites in rice tissues. Numerous signaling pathways were induced rapidly or partially by salinity. Combined data showed the most susceptible proteins or metabolites in each pathway that likely affected the sensitivity of rice to salinity, such as PLA1, BON3 (involved in sensing stress), SnRK2, pro-resilin, GDT1, G-proteins, calmodulin activators (Ca(2+) and abscisic acid signaling), MAPK3/5, MAPKK1/3 (MAPK pathway), SOS1, ABC F/D, PIP2-7, and K(+) transporter-23 (transporters), OPR1, JAR1, COL1, ABA2, and MAPKK3 (phytohormones). Additionally, our results expanded the stress-sensing function of receptor-like kinases, phosphatidylinositols, and Na(+) sensing proteins (IPUT1). Combined analyses revealed the most sensitive components of signaling pathways causing salt-susceptibility in rice and suggested potential targets for crop improvement.
PMID: 36417662
Environ Sci Pollut Res Int , IF:4.223 , 2022 Nov , V29 (53) : P80532-80548 doi: 10.1007/s11356-022-21387-4
Spatial-temporal characteristics and driving factors of the chemical fertilizer supply/demand correlation network in China.
Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Anhui Agricultural University, Hefei, 230036, China.; College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China.; Wuhan Geomatics Institute, Wuhan, 430022, China.; Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Anhui Agricultural University, Hefei, 230036, China. lijunli866@whu.edu.cn.; College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China. lijunli866@whu.edu.cn.
The rational allocation of chemical fertilizer resources is of strategic importance in mitigating agricultural source pollution and achieving agricultural green development. The spatiotemporal correlation of chemical fertilizer supply/demand and its determinants remains unclear. In this study, based on the inter-provincial chemical fertilizer supply/demand panel data of China from 1994 to 2018, an improved gravity model was employed to determine provincial chemical fertilizer supply/demand correlations. Finally, the chemical fertilizer supply/demand evolution and its driving factors were analyzed using social network analysis and a quadratic assignment procedure. The results indicated that (1) the intensity of the spatial relationship of inter-provincial chemical fertilizer supply/demand increased in a fluctuating fashion, but there was still room for improvement. The network structure presented good stability, and the spillover effect exhibited multiple superposition characteristics; (2) the spatial correlation network of inter-provincial chemical fertilizer supply/demand presented a "core-periphery" distribution pattern of the supply, demand, and balance areas. The division of blocks in the network changed in time and space, and some provinces changed their roles and positions in the network during development; (3) chemical fertilizer-related policies (e.g., Exemption Agricultural Tax, Notice on the resumption of value added tax policy on fertilizers, and Rural Revitalization Strategy) have played a positive role in the formation and development of the interprovincial spatial correlation network of chemical fertilizer supply/demand in China; (4) natural conditions and socioeconomic factors interact to promote the formation of the spatial correlation network of chemical fertilizer supply/demand. The differences in the scale of the rural labor force, the scale of agricultural mechanization, the agricultural planting structure, the populations, and urbanization levels all had a significant impact on it. The identification of the spatial characteristics of chemical fertilizer supply/demand correlation networks offers a new perspective on taking various measures to realize the cross-regional coordination of chemical fertilizer resources, strengthen the protection and utilization of agricultural resources, and promote green agricultural development.
PMID: 35718849
Mol Plant Microbe Interact , IF:4.171 , 2022 Nov , V35 (11) : P1056-1059 doi: 10.1094/MPMI-07-22-0148-A
Complete Genome Sequence Resource of Bacillus cereus Gsicc 30237, Isolated from Cabbage Planting Soil.
Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China.; State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430000, China.; College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China.
PMID: 36306438
Genes (Basel) , IF:4.096 , 2022 Oct , V13 (10) doi: 10.3390/genes13101851
Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine.
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.; University of Chinese Academy of Sciences, Beijing 100049, China.
Grapevine (Vitisvinifera L.) fruit ripening is a complex biological process involving a phase transition from immature to mature. Understanding the molecular mechanism of fruit ripening is critical for grapevine fruit storage and quality improvement. However, the regulatory mechanism for the critical phase transition of fruit ripening from immature to mature in grapevine remains poorly understood. In this work, to identify the key molecular events controlling the critical phase transition of grapevine fruit ripening, we performed an integrated dynamic network analysis on time-series transcriptomic data of grapevine berry development and ripening. As a result, we identified the third time point as a critical transition point in grapevine fruit ripening, which is consistent with the onset of veraison reported in previous studies. In addition, we detected 68 genes as being key regulators involved in controlling fruit ripening. The GO (Gene Ontology) analysis showed that some of these genes participate in fruit development and seed development. This study provided dynamic network biomarkers for marking the initial transcriptional events that characterizes the transition process of fruit ripening, as well as new insights into fruit development and ripening.
PMID: 36292736
Genes (Basel) , IF:4.096 , 2022 Sep , V13 (10) doi: 10.3390/genes13101767
Mining Candidate Genes Related to Heavy Metals in Mature Melon (Cucumis melo L.) Peel and Pulp Using WGCNA.
Xinjiang Key Laboratory of Agricultural Product Quality and Safety/Agricultural Product Quality and Safety Risk Assessment Laboratory of the Ministry of Rural Agriculture/Institute of Agricultural Quality Standards and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.; School of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830091, China.; New Plant Variety Testing (Urumqi) Branch Center of the Ministry of Agriculture and Rural Affairs, Crop Variety Resources Institute, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.; Xinjiang Key Laboratory of Agricultural Product Quality and Safety/Agricultural Product Quality and Safety Risk Assessment Laboratory of the Ministry of Rural Agriculture, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
The content of metal ions in fruits is inseparable from plant intake of trace elements and health effects in the human body. To understand metal ion content in the fruit and pericarp of melon (Cucumis melo L.) and the candidate genes responsible for controlling this process, we analyzed the metal ion content in distinct parts of melon fruit and pericarp and performed RNA-seq. The results showed that the content of metal ions in melon fruit tissue was significantly higher than that in the pericarp. Based on transcriptome expression profiling, we found that the fruit and pericarp contained elevated levels of DEGs. GO functional annotations included cell surface receptor signaling, signal transduction, organic substance metabolism, carbohydrate derivative binding, and hormone-mediated signaling pathways. KEGG pathways included pectate lyase, pentose and glucuronate interconversions, H+-transporting ATPase, oxidative phosphorylation, plant hormone signal transduction, and MAPK signaling pathways. We also analyzed the expression patterns of genes and transcription factors involved in hormone biosynthesis and signal transduction. Using weighted gene co-expression network analysis (WGCNA), a co-expression network was constructed to identify a specific module that was significantly correlated with the content of metal ions in melon, after which the gene expression in the module was measured. Connectivity and qRT-PCR identified five candidate melon genes, LOC103501427, LOC103501539, LOC103503694, LOC103504124, and LOC107990281, associated with metal ion content. This study provides a theoretical basis for further understanding the molecular mechanism of heavy metal ion content in melon fruit and peel and provides new genetic resources for the study of heavy metal ion content in plant tissues.
PMID: 36292652
Genes (Basel) , IF:4.096 , 2022 Oct , V13 (11) doi: 10.3390/genes13111963
Differences in the Chloroplast Genome and Its Regulatory Network among Cathaya argyrophylla Populations from Different Locations in China.
Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, China.
Cathaya argyrophylla Chun et Kuang is a severely endangered, tertiary relict plant unique to China whose high physiological sensitivity to the environment, including photosensitivity, is likely closely related to its endangered status; however, the exact mechanism responsible has remained unknown due to the rarity of the plant and the difficulties involved in performing physiological studies on the molecular level. In this study, the chloroplast genomes of six C. argyrophylla populations sampled from different locations in China were characterized and compared. In addition, a gene regulatory network of the polymorphic chloroplast genes responsible for regulating genes found elsewhere in the plant genome was constructed. The result of the genome characterization and comparison showed that the genome characteristics, the gene composition, and the gene sequence of the chloroplast genes varied by location, and the gene regulatory network showed that the differences in growth location may have led to variations in the protein-coding chloroplast gene via various metabolic processes. These findings provide new insights into the relationship between chloroplasts and the sensitive metabolism of C. argyrophylla and provide additional reference materials for the conservation of this endangered plant.
PMID: 36360200
Plants (Basel) , IF:3.935 , 2022 Oct , V11 (19) doi: 10.3390/plants11192614
Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.
UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia.; Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia.; Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia.
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
PMID: 36235479
J Plant Physiol , IF:3.549 , 2022 Nov , V278 : P153827 doi: 10.1016/j.jplph.2022.153827
MicroRNA miR1118 contributes to wheat (Triticum aestivum L.) salinity tolerance by regulating the Plasma Membrane Intrinsic Proteins1;5 (PIP1;5) gene.
Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran. Electronic address: shamloor@gmail.com.; Department of Plant Production and Genetics, College of Agricultural Engineering, Isfahan University of Technology, Isfahan, Iran.; Institute of Biotechnology, Shiraz University, Shiraz, Iran.
microRNAs (miRNAs) are important regulators of various adaptive stress responses in crops; however, many details about associations among miRNAs, their target genes and physiochemical responses of crops under salinity stress remain poorly understood. We designed this study in a systems biology context and used a collection of computational, experimental and statistical procedures to uncover some regulatory functions of miRNAs in the response of the important crop, wheat, to salinity stress. Accordingly, under salinity conditions, wheat roots' Expressed Sequence Tag (EST) libraries were computationally mined to identify the most reliable differentially expressed miRNA and its related target gene(s). Then, molecular and physiochemical evaluations were carried out in a separate salinity experiment using two contrasting wheat genotypes. Finally, the association between changes in measured characteristics and wheat salinity tolerance was determined. From the results, miR1118 was assigned as a reliable salinity-responsive miRNA in wheat roots. The expression profiles of miR1118 and its predicted target gene, Plasma Membrane Intrinsic Proteins1,5 (PIP1;5), significantly differed between wheat genotypes. Moreover, results revealed that expression profiles of miR1118 and PIP1;5 significantly correlate to Relative Water Content (RWC), root hydraulic conductance (Lp), photosynthetic activities, plasma membrane damages, osmolyte accumulation and ion homeostasis of wheat. Our results suggest a plausible regulatory node through miR1118 adjusting the wheat water status, maintaining ion homeostasis and mitigating membrane damages, mainly through the PIP1;5 gene, under salinity conditions. To our knowledge, this is the first report on the role of miR1118 and PIP1;5 in wheat salinity response.
PMID: 36206620
Funct Integr Genomics , IF:3.41 , 2022 Dec , V22 (6) : P1403-1410 doi: 10.1007/s10142-022-00899-9
"KRiShI": a manually curated knowledgebase on rice sheath blight disease.
Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.; Department of Plant Pathology, Assam Agricultural University, Assam, 785013, India.; University of Horticultural Sciences, Karnataka, 587315, India.; Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India. barah@tezu.ernet.in.
Knowledgebase for rice sheath blight information (KRiShI) is a manually curated user-friendly knowledgebase for rice sheath blight (SB) disease that allows users to efficiently mine, visualize, search, benchmark, download, and update meaningful data and information related to SB using its easy and interactive interface. KRiShI collects and integrates widely scattered and unstructured information from various scientific literatures, stores it under a single window, and makes it available to the community in a user-friendly manner. From basic information, best management practices, host resistance, differentially expressed genes, proteins, metabolites, resistance genes, pathways, and OMICS scale experiments, KRiShI presents these in the form of easy and comprehensive tables, diagrams, and pictures. The "Search" tab allows users to verify if their input rice gene id(s) are Rhizoctonia solani (R. solani) responsive and/or resistant. KRiShI will serve as a valuable resource for easy and quick access to data and information related to rice SB disease for both the researchers and the farmers. To encourage community curation a submission facility is made available. KRiShI can be found at http://www.tezu.ernet.in/krishi .
PMID: 36109405
BMC Pulm Med , IF:3.317 , 2022 Nov , V22 (1) : P437 doi: 10.1186/s12890-022-02240-3
Comparative proteomic analysis of mustard lung as a complicated disease using systems biology approach.
Education Office, Pasteur Institute of Iran, Tehran, Iran.; Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.; Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran. najafi74@bmsu.ac.ir.
During Iraq-Iran conflict, chemical weapons, particularly SM gas, were used numerous times, whose aftereffects are still present. This study aimed to compare serum proteome in the chronic ML (n = 10) and HC (n = 10). TMT label-based quantitative proteomics was used to examine serums from two groups. Among total significant proteins, 14 proteins were upregulated (log(2) >/= FC 0.5, p 0.05), and 6 proteins were downregulated (log(2)
PMID: 36419000
J Appl Genet , IF:3.24 , 2022 Dec , V63 (4) : P771-782 doi: 10.1007/s13353-022-00722-y
Genome-wide post-transcriptional regulation of bovine mammary gland response to Streptococcus uberis.
Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran.; Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran. ss.sharifi2015@gmail.com.; Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran. pakdel@iut.ac.ir.; Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, 3391653755, Iran.; Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, 84156-83111, Iran.; Institute of Biotechnology, Shiraz University, Shiraz, 71946-84334, Iran.; Novocraft Technologies Sdn Bhd, Petaling Jaya, Malaysia.
MicroRNAs (miRNAs) as post-transcriptionally regulators of gene expression have been shown to be critical regulators to fine-tuning immune responses, besides their criteria for being an ideal biomarker. The regulatory role of miRNAs in responses to most mastitis-causing pathogens is not well understood. Gram-positive Streptococcus uberis (Str. uberis), the leading pathogen in dairy herds, cause both clinical and subclinical infections. In this study, a system biology approach was used to better understand the main post-transcriptional regulatory functions and elements of bovine mammary gland response to Str. uberis infection. Publicly available miRNA-Seq data containing 50 milk samples of the ten dairy cows (five controls and five infected) were retrieved for this current research. Functional enrichment analysis of predicted targets revealed that highly confident responsive miRNAs (4 up- and 19 downregulated) mainly regulate genes involved in the regulation of transcription, apoptotic process, regulation of cell adhesion, and pro-inflammatory signaling pathways. Time series analysis showed that six gene clusters significantly differed in comparisons between Str. uberis-induced samples with controls. Additionally, other bioinformatic analysis, including upstream network analysis, showed essential genes, including TP53 and TGFB1 and some small molecules, including glucose, curcumin, and LPS, commonly regulate most of the downregulated miRNAs. Upregulated miRNAs are commonly controlled by the most important genes, including IL1B, NEAT1, DICER1 enzyme and small molecules including estradiol, tamoxifen, estrogen, LPS, and epigallocatechin. Our study used results of next-generation sequencing to reveal key miRNAs as the main regulator of gene expression responses to a Gram-positive bacterial infection. Furthermore, by gene regulatory network (GRN) analysis, we can introduce the common upregulator transcription factor of these miRNAs. Such milk-based miRNA signature(s) would facilitate risk stratification for large-scale prevention programs and provide an opportunity for early diagnosis and therapeutic intervention.
PMID: 36066834
R Soc Open Sci , IF:2.963 , 2022 Oct , V9 (10) : P220953 doi: 10.1098/rsos.220953
Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.).
Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of China.; Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China.
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
PMID: 36249327
Biomed Pharmacother , 2022 Nov , V155 : P113798 doi: 10.1016/j.biopha.2022.113798
Therapeutic efficacy of Scutellaria baicalensis Georgi against psoriasis-like lesions via regulating the responses of keratinocyte and macrophage.
Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.; Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan.; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.; Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Taoyuan, Taiwan.; National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan.; School of Traditional Chinese Medicine, Chang Gung University, Taoyuan, Taiwan; Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan. Electronic address: pan@mail.cgu.edu.tw.
Psoriasis is a chronic and recurrent skin problem that affects 3% of the global population. Nowadays, most medicines may not promise a complete cure for patients with psoriasis because of the development of pharmacoresistance and the side effects of drugs due to the microenvironment impact in the context of skin imbalance. Herein, we attempt to explore the pharmaceutical efficacy of Scutellaria baicalensis (S. baicalensis) in modulating the microenvironment created by macrophages and keratinocytes in psoriasis. The results indicated that treatment of S. baicalensis extract significantly reduced the thickness of epidermis and attenuated psoriatic lesions. Moreover, S. baicalensis extract obviously inhibited the activation and infiltration of macrophages by alleviating inflammatory factors such as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappaB) and cyclooxygenase-2 (COX-2). The administration of S. baicalensis extract also remarkably abolished oxidative damage upon DNA and proteins, which attributed to the activation of nuclear factor erythroid 2-related factor-2 (Nrf2) and heme oxygenase-1 (HO-1). The network analysis of redox proteomics and cytokine profiles suggested that S. baicalensis administration regulated the specific pathways associated with oxidative stress, inflammation and cytokine signaling cascades to ameliorate the macrophage-targeted responses and subsequently arrest proliferation of keratinocytes. Collectively, our findings highlighted the importance of S. baicalensis application in reprogramming microenvironment to provide an alternative and complementary intervention for long-term psoriatic therapy.
PMID: 36271574
Huan Jing Ke Xue , 2022 Oct , V43 (10) : P4755-4764 doi: 10.13227/j.hjkx.202201210
[Effects of Long-term Straw Returning on Fungal Community, Enzyme Activity and Wheat Yield in Fluvo-aquic Soil].
Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Ji'nan 250100, China.; Dezhou Academy of Agricultural Sciences, Dezhou 253015, China.
To illustrate the effects of long-term straw returning on the fungal community, soil enzyme activity, and crop yield in a fluvo-aquic soil area typical of the Huang-Huai-Hai Plain, a 10-year field experiment (established in 2010) located in Dezhou City, Shandong province, was performed, including three fertilization regimes (NF, no fertilization control; NPK, fertilization with chemical N, P, and K fertilizers; NPKS, straw returning combined with chemical N, P, and K fertilizers). This study aimed to explore the regulation mechanisms of fungal communities on soil fertility, enzyme activities, and crop yield by employing co-occurrence network and structural equation model analyses. Our results showed that long-term straw returning significantly improved soil nutrients, enzyme activity, and wheat yield. Compared with the NPK and NF treatments, soil organic matter (SOM) increased by 9.20% and 34.75%, alkali-hydrolyzed nitrogen (AN) increased by 12.03% and 39.17%, dehydrogenase (DHA) increased by 37.21% and 50.91%, beta-glucosidase (beta-GC) increased by 17.29% and 73.48%, and wheat production increased by 16.22% and 125.53%, respectively. Different long-term fertilization regimes did not significantly change soil fungal alpha-diversity but resulted in significant differences in beta-diversity. Available phosphorus (AP), SOM, and AN were the main driving factors of fungal community differentiation based on redundancy analysis and hierarchical partitioning analysis. Different abundance analyses revealed significantly different fungal community compositions among fertilization regimes. The long-term NF treatment resulted in a significant enrichment of phosphate/potassium-solubilizing species (i.e., Mortierella, Aspergillus, Ceriporia, and Acremonium) and symbiotic species (i.e., Leohumicola and Hyalodendriella). The relative abundance of pathogenic fungi, namely Sarocladium, Fusarium, and Fusicolla, increased significantly in the NPK treatment. Long-term straw returning in the NPKS treatment significantly stimulated the growth of plant growth-promoting species (i.e., Pseudogymnoascus and Schizothecium) and straw-degrading species (i.e., Trichocladium and Lobulomyces). Co-occurrence network analysis showed that the fungal network was composed of four main modules; the cumulative relative abundance of module 2 was significantly increased under the NPKS treatment and showed a positive linear correlation with DHA and beta-GC. The structural equation model further indicated that the wheat yield was mainly regulated by SOM, whereas species of module 2 could indirectly affect SOM and wheat yield by positively regulating DHA and beta-GC. Taken together, long-term straw returning to the fluvo-aquic soil area of the Huang-Huai-Hai Plain could regulate fungal interspecific interactions, stimulate the growth of specific species groups, inhibit the activity of pathogens, increase the activity of soil enzymes, promote the accumulation of SOM, and achieve high crop yield.
PMID: 36224161
Huan Jing Ke Xue , 2022 Oct , V43 (10) : P4536-4544 doi: 10.13227/j.hjkx.202201136
[Historical Antibiotic Stress Changed the Effects of Sulfamethoxazole and Trimethoprim on Activated Sludge: ARGs and Potential Hosts].
Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing 100124, China.
The co-exposure of antibiotics has important effects on antibiotic resistance genes (ARGs) and microbial community aggregation in wastewater treatment plants (WWTPs). However, it is unclear whether differences in historical antibiotic exposure stress can determine responses of microbes and ARGs to combined antibiotics. By selecting a high concentration (30 mg.L(-1)) of sulfamethoxazole (SMX) and trimethoprim (TMP) as historical exposure stress conditions, the effects of SMX and TMP-combined pollution on ARGs, bacterial communities, and their interactions were explored in short-term experiments. Based on high-throughput quantitative PCR, a total of 13 ARGs were detected, and the absolute abundance was 2.21-5.42 copies.muL(-1) (logarithm, DNA, the same below). Among them, sul2, ermB, mefA, and tetM-01 were the main subtypes in the samples, and the absolute abundance was between 2.95 and 5.40 copies.muL(-1). The combined contamination of SMX and TMP could cause the enrichment of ARGs and mobile genetic elements (MGEs); however, their effects on each subtype were different, and the historical legacy effect of SMX was higher than that of TMP. Under the different exposure histories, the co-occurrence and co-exclusion patterns existed between ARGs. Moreover, MGEs (especially intI-1) were significantly correlated with sulfonamides (sul1 and sul2), tetracyclines[tet(32)], and macrolide-lincosamide-streptogramin (MLSB) resistance genes (ermB). Based on the full-scale classification of microorganisms, it was found that the microbial community structure of various groups responded differently to combined pollution, and the conditionally abundant taxa (CAT) were obviously enriched. Thauera, Pseudoxanthomonas, and Paracoccus were the dominant resistant bacterial genera. Furthermore, a total of 31 potential hosts of ARGs were identified with network analysis, which were dominated with conditionally rare taxa (CRT). Particularly, Candidatus_Alysiosphaera and Fusibacter were positively correlated with most of the ARGs, being the common protentional hosts. Importantly, some rare genera (RT, Variibacter, Aeromonas, Cloacibacterium, etc.) were potential hosts of transposon IS613, which played an important role in the proliferation and spread of ARGs. In conclusion, this study revealed the legacy effects of historical antibiotic stress on ARGs and their hosts, which could provide new ideas and theoretical basis for reducing ARGs pollution in WWTPs.
PMID: 36224139
Methods Mol Biol , 2023 , V2594 : P217-223 doi: 10.1007/978-1-0716-2815-7_16
Identification of Plant Co-regulatory Modules Using CoReg.
Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA. sqsq3178@gmail.com.; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
Regulatory network is often characterized by complex interactions between transcription factors (TFs) and target genes. The synergistic regulations among multiple TFs may co-induce/co-suppress the expressions of the similar target genes. Such information is important for understanding stress response signaling pathways in plants. In this chapter, we present a computational tool, CoReg, for mining co-regulatory gene modules from network topology. The analysis results can be used to interpret co-regulation effects in regulatory networks generated by high-through TF-DNA interaction screenings such as yeast-one-hybrid, ChIP-seq, and DAP-seq.
PMID: 36264499
Methods Mol Biol , 2023 , V2594 : P205-215 doi: 10.1007/978-1-0716-2815-7_15
Modeling Plant Transcription Factor Networks Using ConSReg.
Computational Biology Department, Carnegie Mellon University, Pittsburgh,, PA, USA. sqsq3178@gmail.com.; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
Plants have developed complex regulatory programs to respond to various environmental stress such as heat, drought, and cold. Systematic understanding of these biological processes depends on robust construction of regulatory networks which encodes interactions between transcription factors and target genes. In this chapter, we present a computational tool ConSReg, which predicts regulatory interactions using ATAC-seq, DAP-seq, and expression data. By using expression data generated under a specific environmental stress, ConSReg can reconstruct an interpretable, weighted, and stress response-specific regulatory network.
PMID: 36264498
Methods Mol Biol , 2023 , V2594 : P173-183 doi: 10.1007/978-1-0716-2815-7_13
Database for Plant Transcription Factor Binding Sites.
Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan. sarah321@mail.ncku.edu.tw.; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan.
Reconstruction of gene regulatory networks is a very important but difficult issue in plant sciences. Recently, numerous high-throughput techniques, such as chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq), have been developed to identify the genomic binding landscapes of regulatory factors. To understand the relationships among transcription factors (TFs) and their corresponding binding sites on target genes is usually the first step for elucidating gene regulatory mechanisms. Therefore, a good database for plant TFs and transcription factor binding sites (TFBSs) will be useful for starting a series of complex experiments. In this chapter, PlantPAN (version 3.0) is utilized as an example to explain how bioinformatics systems advance research on gene regulation.
PMID: 36264496
Methods Mol Biol , 2023 , V2594 : P1-12 doi: 10.1007/978-1-0716-2815-7_1
The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells.
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.; USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA.; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.; BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France.; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. bastiaan@vt.edu.
The TARGET system allows for the rapid identification of direct regulated gene targets of transcription factors (TFs). It employs the transient transformation of plant protoplasts with inducible nuclear entry of the TF and subsequent transcriptomic and/or ChIP-seq analysis. The ability to separate direct TF-target gene regulatory interactions from indirect downstream responses and the significantly shorter amount of time required to perform the assay, compared to the generation of transgenics, make this plant cell-based approach a valuable tool for a higher throughput approach to identify the genome-wide targets of multiple TFs, to build validated transcriptional networks in plants. Here, we describe the use of the TARGET system in Arabidopsis seedling root protoplasts to map the gene regulatory network downstream of transcription factors-of-interest.
PMID: 36264484