Trends Plant Sci , IF:18.313 , 2023 Jan , V28 (1) : P106-122 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
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
Mol Plant , IF:13.164 , 2022 Dec doi: 10.1016/j.molp.2022.12.019
A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement.
Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: guoweilong@cau.edu.cn.
Gene regulation is central to all aspects of organism growth, and understanding it from large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement still lacks. Here, we constructed a wheat integrative gene regulatory network (wGRN) by using an updated genome annotation and combining diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5,947 TFs and 127,439 target genes and was further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3,891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the predictive power of spike phenotypic traits using the machine learning method and contribute to the spike phenotypic differences among modern wheat accessions. An interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), was finally developed for the community to explore gene regulations and discover trait-associated genes. Overall, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.
PMID: 36575796
J Adv Res , IF:10.479 , 2022 Dec , V42 : P17-28 doi: 10.1016/j.jare.2022.07.014
Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions.
Department of Biotechnology, Panjab University, Chandigarh, India.; Department of Biotechnology, Panjab University, Chandigarh, India; Department of Biology, University of Pennsylvania, Philadelphia, USA(1).; Department of Biotechnology, Panjab University, Chandigarh, India. Electronic address: kashmirbio@pu.ac.in.
INTRODUCTION: Duplication events are fundamental to co-evolution in host-pathogen interactions. Pseudogenes (Psis) are dysfunctional paralogs of functional genes and resistance genes (Rs) in plants are the key to disarming pathogenic invasions. Thus, deciphering the roles of pseudo-R genes in plant defense is momentous. OBJECTIVES: This study aimed to functionally characterize diverse roles of the resistance Psis as novel gene footprints and as significant gene regulators in the grapevine genome. METHODS: PlantPseudo pipeline and HMM-profiling identified whole-genome duplication-derived (WGD) Psis associated with resistance genes (Psi-Rs). Further, novel antifungal and antimicrobial peptides were characterized for fungal associations using protein-protein docking with Erysiphe necator proteins. miRNA and tasiRNA target sites and transcription factor (TF) binding sites were predicted in Psi-Rs. Finally, differential co-expression patterns in Psi-Rs-lncRNAs-coding genes were identified using the UPGMA method. RESULTS: 2,746 Psi-Rs were identified from 31,032 WGD Psis in the genome of grapevine. 69-antimicrobial and 81-antifungal novel peptides were generated from Psi-Rs. The putative genic potential was predicted for five novel antifungal peptides which were further characterized by docking against E. necator proteins. 395 out of 527 resistance loci-specific Psi-Rs were acting as parental gene mimics. Further, to explore the diverse roles of Psi-Rs in plant-defense, we identified 37,026 TF-binding sites, 208 miRNA, and 99 tasiRNA targeting sites on these Psi-Rs. 194 Psi-Rs were exhibiting tissue-specific expression patterns. The co-expression network analysis between Psis-lncRNA-genes revealed six out of 79 pathogen-responsive Psi-Rs as significant during pathogen invasion. CONCLUSIONS: Our study provides pathogen responsive Psi-Rs integral for pathogen invasion, which will offer a useful resource for future experimental validations. In addition, our findings on novel peptide generations from Psi-Rs offer valuable insights which can serve as a useful resource for predicting novel genes with the futuristic potential of being investigated for their bioactivities in the plant system.
PMID: 35933092
J Adv Res , IF:10.479 , 2022 Dec doi: 10.1016/j.jare.2022.12.003
Chilling-induced peach flavor loss is associated with expression and DNA methylation of functional genes.
Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.; Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China.; Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Shandong (Linyi) Institute of Morden Agriculture, Zhejiang University, Linyin 276000, China. Electronic address: bozhang@zju.edu.cn.
INTRODUCTION: Flavor is a major contributor to consumer preference. Despite being effective at extending the fruit's commercial life, cold storage also results in a significant loss of flavor volatiles. To date, there has been few studies on the metabolic dynamics and the mechanism underlying the regulatory networks that modulate flavor loss during cold storage for fruit. METHODS: The volatile contents were detected by Gas Chromatography-Mass Spectrometer (GC-MS). Weighted gene co-expression network analysis (WGCNA) was used to identify structure genes and transcription factors (TFs). DNA methylation was analyzed by whole-genome methylation sequencing during cold storage. RESULTS: We generated a temporal map, over hourly to weekly timescales, for the effects of chilling on flavor volatiles by combining metabolome, transcriptome, and DNA methylome in peach fruit. Based on the big data analysis, we developed a regulatory network for volatile formation and found that a decrease in volatiles during cold storage was significantly correlated with a decrease in the expression of synthesis genes. Moreover, TFs associated with these structure genes were identified. Expression of genes involved in ethylene biosynthesis was reduced while cold tolerance pathway was activated in response to low temperature. Functions of those genes were confirmed through transgenic experiments and across peach cultivars, suggesting our dataset is a useful tool for elucidating regulatory factors that have not yet been clarified in relation to flavor and cold tolerance. Genome wide DNA methylation was induced by chilling and peaked at 7 d followed by a decline during 28 d cold storage. Reduction of gene expression was accompanied by major changes in the methylation status of their promoters, including PpACS1, PpAAT1, PpTPS3 and PpMADS2. CONCLUSION: Our study revealed the mechanism for chilling-induced flavor loss of peach fruit through time-course transcriptome and DNA methylome analysis.
PMID: 36496174
New Phytol , IF:10.151 , 2023 Jan , V237 (2) : P441-453 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 , 2023 Jan , V237 (1) : P310-322 doi: 10.1111/nph.18486
To stripe or not to stripe: the origin of a novel foliar pigmentation pattern in monkeyflowers (Mimulus).
Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT, 06269-3043, USA.; Institute for Systems Genomics, University of Connecticut, 67 North Eagleville Road, Storrs, CT, 06269-3197, USA.
The origin of phenotypic novelty is one of the most challenging problems in evolutionary biology. Although genetic regulatory network rewiring or co-option has been widely recognised as a major contributor, in most cases how such genetic rewiring/co-option happens is completely unknown. We have studied a novel foliar pigmentation pattern that evolved recently in the monkeyflower species Mimulus verbenaceus. Through genome-wide association tests using wild-collected samples, experimental crosses of laboratory inbred lines, gene expression analyses, and functional assays, we identified an anthocyanin-activating R2R3-MYB gene, STRIPY, as the causal gene triggering the emergence of the discrete, mediolateral anthocyanin stripe in the M. verbenaceus leaf. Chemical mutagenesis revealed the existence of upstream activators and repressors that form a 'hidden' prepattern along the leaf proximodistal axis, potentiating the unique expression pattern of STRIPY. Population genomics analyses did not reveal signatures of positive selection, indicating that nonadaptive processes may be responsible for the establishment of this novel trait in the wild. This study demonstrates that the origin of phenotypic novelty requires at least two separate phases, potentiation and actualisation. The foliar stripe pattern of M. verbenaceus provides an excellent platform to probe the molecular details of both processes in future studies.
PMID: 36101514
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
Plant Physiol , IF:8.34 , 2022 Dec doi: 10.1093/plphys/kiac564
Living with high potassium: balance between nutrient acquisition and K-induced salt stress signaling.
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
High potassium (K) in the growth medium induces salinity stress in plants. However, the molecular mechanisms underlying plant responses to K-induced salt stress are virtually unknown. We examined Arabidopsis (Arabidopsis thaliana) and its extremophyte relative Schrenkiella parvula using a comparative multi-omics approach to identify cellular processes affected by excess K and understand which deterministic regulatory pathways are active to avoid tissue damages while sustaining growth. Arabidopsis showed limited capacity to curb excess K accumulation and prevent nutrient depletion, contrasting to S. parvula which could limit excess K accumulation without restricting nutrient uptake. A targeted transcriptomic response in S. parvula promoted nitrogen uptake along with other key nutrients followed by uninterrupted N assimilation into primary metabolites during excess K-stress. This resulted in larger antioxidant and osmolyte pools and corresponded with sustained growth in S. parvula. Antithetically, Arabidopsis showed increased reactive oxygen species levels, reduced photosynthesis, and transcriptional responses indicative of a poor balance between stress signaling, subsequently leading to growth limitations. Our results indicate that the ability to regulate independent nutrient uptake and a coordinated transcriptomic response to avoid non-specific stress signaling are two main deterministic steps towards building stress resilience to excess K + -induced salt stress.
PMID: 36493387
Plant Physiol , IF:8.34 , 2022 Dec doi: 10.1093/plphys/kiac600
GROWTH REGULATING FACTOR 15-mediated gene regulatory network enhances salt tolerance in poplar.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China.; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China.; CSIRO Agriculture and Food, Black Mountain, Canberra ACT 2601, Australia.; Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Soil salinity is an important determinant of crop productivity and triggers salt stress response pathways in plants. The salt stress response is controlled by transcriptional regulatory networks that maintain regulatory homeostasis through combinations of transcription factor (TF)-DNA and TF-TF interactions. We investigated the transcriptome of poplar 84 K (Populus alba x Populus glandulosa) under salt stress using samples collected at 4 or 6 h intervals within 2 days of salt stress treatment. We detected 24,973 differentially expressed genes, including 2,231 TFs that might be responsive to salt stress. To explore these interactions and targets of TFs in perennial woody plants, we combined gene regulatory network, DNA affinity purification sequencing (DAP-seq), yeast two-hybrid-sequencing (Y2H-seq), and multi-gene association approaches. Growth-regulating factor 15 (PagGRF15) and its target, high-affinity K+ transporter 6 (PagHAK6), were identified as an important regulatory module in the salt stress response. Overexpression of PagGRF15 and PagHAK6 in transgenic lines improved salt tolerance by enhancing Na+ transport and modulating H2O2 accumulation in poplar. Yeast two-hybrid (Y2H) assays identified more than 420 PagGRF15-interacting proteins, including ETHYLENE RESPONSE FACTOR (ERF) TFs and a zinc finger protein (C2H2) that are produced in response to a variety of phytohormones and environmental signals and are likely involved in abiotic stress. Therefore, our findings demonstrate that PagGRF15 is a multifunctional TF involved in growth, development and salt stress tolerance, highlighting the capability of a multifaceted approach in identifying regulatory nodes in plants.
PMID: 36567515
Elife , IF:8.14 , 2022 Nov , V11 doi: 10.7554/eLife.79224
Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis.
Universite Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France.; Universite Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France.
Noise plays a major role in cellular processes and in the development of tissues and organs. Several studies have examined the origin, the integration or the accommodation of noise in gene expression, cell growth and elaboration of organ shape. By contrast, much less is known about variability in cell division plane positioning, its origin and links with cell geometry, and its impact on tissue organization. Taking advantage of the first-stereotyped-then-variable division patterns in the embryo of the model plant Arabidopsis thaliana, we combined 3D imaging and quantitative cell shape and cell lineage analysis together with mathematical and computer modeling to perform a large-scale, systematic analysis of variability in division plane orientation. Our results reveal that, paradoxically, variability in cell division patterns of Arabidopsis embryos is accompanied by a progressive reduction of heterogeneity in cell shape topology. The paradox is solved by showing that variability operates within a reduced repertoire of possible division plane orientations that is related to cell geometry. We show that in several domains of the embryo, a recently proposed geometrical division rule recapitulates observed variable patterns, suggesting that variable patterns emerge from deterministic principles operating in a variable geometrical context. Our work highlights the importance of emerging patterns in the plant embryo under iterated division principles, but also reveal domains where deviations between rule predictions and experimental observations point to additional regulatory mechanisms.
PMID: 36444654
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
Free Radic Biol Med , IF:7.376 , 2022 Nov , V193 (Pt 2) : P764-778 doi: 10.1016/j.freeradbiomed.2022.11.019
Plant thiol peroxidases as redox sensors and signal transducers in abiotic stress acclimation.
Biochemistry and Physiology of Plants, W5-134, Bielefeld University, 33615, Bielefeld, Germany.; Biochemistry and Physiology of Plants, W5-134, Bielefeld University, 33615, Bielefeld, Germany. Electronic address: karl-josef.dietz@uni-bielefeld.de.
The temporal and spatial patterns of reactive oxygen species (ROS) in cells and tissues decisively determine the plant acclimation response to diverse abiotic and biotic stresses. Recent progress in developing dynamic cell imaging probes provides kinetic information on changes in parameters like H(2)O(2), glutathione (GSH/GSSG) and NAD(P)H/NAD(P)(+), that play a crucial role in tuning the cellular redox state. Central to redox-based regulation is the thiol-redox regulatory network of the cell that integrates reductive information from metabolism and oxidative ROS signals. Sensitive proteomics allow for monitoring changes in redox-related posttranslational modifications. Thiol peroxidases act as sensitive peroxide and redox sensors and play a central role in this signal transduction process. Peroxiredoxins (PRX) and glutathione peroxidases (GPX) are the two main thiol peroxidases and their function in ROS sensing and redox signaling in plants is emerging at present and summarized in this review. Depending on their redox state, PRXs and GPXs act as redox-dependent binding partners, direct oxidants of target proteins and oxidants of thiol redox transmitters that in turn oxidize target proteins. With their versatile functions, the multiple isoforms of plant thiol peroxidases play a central role in plant stress acclimation, e.g. to high light or osmotic stress, but also in ROS-mediated immunity and development.
PMID: 36403735
Chemosphere , IF:7.086 , 2022 Dec : P137506 doi: 10.1016/j.chemosphere.2022.137506
A systematic review on the implementation of advanced and evolutionary biotechnological tools for efficient bioremediation of organophosphorus pesticides.
Department of Bioscience School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.; Department of Bioscience School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India. Electronic address: jabez.vit@gmail.com.
Ever since the concept of bioremediation was introduced, microorganisms, microbial enzymes and plants have been used as principal elements for Organophosphate pesticide (OPP) bioremediation. The enzyme systems and genetic profile of these microbes has been studied deeply in past years. Plant growth promoting rhizobacteria (PGPR) are considered as one of the potential candidates for OPP bioremediation and has been widely used to stimulate phytoremediation potential of plants. Constructed wetlands (CWs) in OPP biodegradation have brought new prospects to microcosm and mesocosm based remediation strategies. Application of synthetic biology has provided a new dimension to the field of OPP bioremediation by introducing concept like, gene manipulation and editing, expression and regulation of catabolic enzymes, implementation of whole-cell based and enzyme based biosensor system for the detection and monitoring of OPP pollution in both terrestrial and aquatic environment. System biology and bioinformatics tools have rendered significant knowledge regarding the genetic, enzymatic and biochemical aspects of microbes and plants thereby helping researchers to analyze the mechanism of OPP biodegradation. Structural biology has provided significant conceptual information regarding OPP biodegradation pathways, structural and functional characterization of metabolites and enzymes, enzyme-pollutant interactions etc. Therefore, this review discussed about the prospects and challenges of most advanced and high throughput strategies implemented for OPP biodegradation. The review also established a comparative analysis of various bioremediation techniques and highlighted the interdependency among them. The review highly suggested simultaneous implementation of more than one remediation strategy or a combinational approach to create an advantageous hybrid technique for OPP bioremediation.
PMID: 36526134
Int J Biol Macromol , IF:6.953 , 2022 Nov doi: 10.1016/j.ijbiomac.2022.11.290
Identification and expression profiles of xylogen-like arabinogalactan protein (XYLP) gene family in Phyllostachys edulis in different developmental tissues and under various abiotic stresses.
Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: ymiao@fafu.edu.cn.; Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: ryj@fafu.edu.cn.
Xylogen-like arabinogalactan protein (XYLP) is an atypical lipid transport protein. In this study, 23 Phyllostachys edulis XYLPs were identified, and their proteins contain characteristic structures of AGP and nsLTP domain. All PeXYLPs can be divided into four clades, and their genes were unevenly distributed on 11 chromosome scaffolds. Collinear analysis revealed that segmental duplication was the main driver for PeXYLP family expansion. The cis-acting elements presented in the promoter are involved in various regulations of PeXYLPs expression. G.O. annotation revealed that PeXYLPs are mainly interested in lipid transport and synthesis and primarily function at the plasma membrane. Transcriptome analysis revealed that PeXYLPs were spatiotemporally expressed and displayed significant variability during various tissue development. Besides that, some PeXYLPs also respond to multiple phytohormones and abiotic stresses. By semi-quantitative RT-PCR, the response of some PeXYLPs to MeJA was confirmed, and the proteins were shown to localize to the plasma membrane mainly. WGCNA in defined regions of fast-growing bamboo shoots revealed that 5 PeXYLPs in 4 gene co-expression modules showed a positive module-trait relationship with three fast-growing regions. This systematic analysis of the PeXYLP family will provide a foundation for further insight into the functions of individual PeXYLP in a specific tissue or organ development, phytohormone perception, and stress responses in the future.
PMID: 36462591
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 Dec doi: 10.1111/tpj.16080
Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages.
International Rice Research Institute, Los Banos, Laguna, Philippines, 4030.
Rice (Oryza sativa) is an important staple crop to address the Hidden Hunger problem not only in Asia but also in Africa where rice is fast becoming an important source of calories. The brown rice (whole grain with bran) is known to be more nutritious due to elevated mineral composition. The genetics underlying brown rice ionome (sum-total of such mineral composition) remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies (GWAS), gene-set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms (SNPs), was used. We identified 109 candidate genes with 5 to 20% phenotypic variation explained (PVE) for the 12 micronutrients and identified epistatic interactions with multiple micronutrients. Pooling all candidate genes per micronutrient exhibited PVE values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through GWAS. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships and on the molecular mechanisms underlying micronutrient signatures.
PMID: 36573652
Int J Mol Sci , IF:5.923 , 2022 Nov , V23 (23) doi: 10.3390/ijms232314783
Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean.
Genetica del Desarrollo de Plantas, Mision Biologica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain.; Centro de Investigacion en Biotecnologia Agroalimentaria (CIAIMBITAL), Universidad de Almeria, 04120 Almeria, Spain.; Departamento de Genetica, Facultad de Ciencias & Laboratorio de Bioinformatica, Centro de Investigacion Biomedica, Universidad de Granada, 18071 Granada, Spain.
The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.
PMID: 36499112
Front Plant Sci , IF:5.753 , 2022 , V13 : P1035712 doi: 10.3389/fpls.2022.1035712
Comparative metabolomics provides novel insights into correlation between dominant habitat factors and constituents of Stellaria Radix (Stellaria dichotoma L. var. lanceolata Bge.).
School of Life Sciences, Ningxia University, Yinchuan, China.; State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, Shandong, China.; Ningxia Institute of Meteorological Sciences, Yinchuan, China.
Stellaria dichotoma L. var. lanceolata Bge. (SDL) is the original plant of the traditional Chinese medicine Yinchaihu (Stellaria Radix). It is mainly distributed in the arid desert areas of northwest China, which is the genuine medicinal material and characteristic cultivated crop in Ningxia. This study aims to analyze the effects of different origins on SDL metabolites and quality, as well as to screen the dominant habitat factors affecting SDL in different origins. In this study, metabolites of SDL from nine different production areas were analyzed by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS) based metabolomics. And field investigations were conducted to record thirteen habitat-related indicators. Results showed that 1586 metabolites were identified in different origins, which were classified as thirteen categories including lipids, organic acids and organic heterocyclic compounds derivatives. Multivariate statistical analysis showed that the metabonomic spectra of SDL from different origins had various characteristics. What's more, co-expression network correlation analysis revealed that three metabolites modules (MEturquoise, MEbrown and MEblue) were more closely with the habitat factors and 104 hub metabolites were further screened out as the habitat-induced metabolite indicators. Besides, soil texture, soil pH value and soil total salt content were found as the dominant habitat factors which affect SDL metabolites. In conclusion, the study showed different habitat factors had various effects on SDL's quality and established relationship between them, which provide reference for revealing SDL's genuineness formation mechanism and guiding industrial crops practical production by habitat factors selection.
PMID: 36507406
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 : P1018991 doi: 10.3389/fpls.2022.1018991
Analysis of the response regulatory network of pepper genes under hydrogen peroxide stress.
College of Horticulture, Hunan Agricultural University, Changsha, Hunan, China.; Longping Branch, Graduate School of Hunan University, Changsha, Hunan, China.; Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China.; Laboratory of Lingnan Modern Agriculture, Guangzhou, Guangdong, China.
Hydrogen peroxide (H(2)O(2)) is a regulatory component related to plant signal transduction. To better understand the genome-wide gene expression response to H(2)O(2) stress in pepper plants, a regulatory network of H(2)O(2) stress-gene expression in pepper leaves and roots was constructed in the present study. We collected the normal tissues of leaves and roots of pepper plants after 40 days of H(2)O(2) treatment and obtained the RNA-seq data of leaves and roots exposed to H(2)O(2) for 0.5-24 h. By comparing the gene responses of pepper leaves and roots exposed to H(2)O(2) stress for different time periods, we found that the response in roots reached the peak at 3 h, whereas the response in leaves reached the peak at 24 h after treatment, and the response degree in the roots was higher than that in the leaves. We used all datasets for K-means analysis and network analysis identified the clusters related to stress response and related genes. In addition, CaEBS1, CaRAP2, and CabHLH029 were identified through a co-expression analysis and were found to be strongly related to several reactive oxygen species-scavenging enzyme genes; their homologous genes in Arabidopsis showed important functions in response to hypoxia or iron uptake. This study provides a theoretical basis for determining the dynamic response process of pepper plants to H(2)O(2) stress in leaves and roots, as well as for determining the critical time and the molecular mechanism of H(2)O(2) stress response in leaves and roots. The candidate transcription factors identified in this study can be used as a reference for further experimental verification.
PMID: 36570911
Front Plant Sci , IF:5.753 , 2022 , V13 : P1038109 doi: 10.3389/fpls.2022.1038109
Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics.
School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China.; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China.
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
PMID: 36570898
Front Plant Sci , IF:5.753 , 2022 , V13 : P1023696 doi: 10.3389/fpls.2022.1023696
Integrated metabolomic and transcriptomic analysis reveals the role of phenylpropanoid biosynthesis pathway in tomato roots during salt stress.
College of Life Science and Technology, Xinjiang University, Urumqi, China.; Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.; College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China.
As global soil salinization continues to intensify, there is a need to enhance salt tolerance in crops. Understanding the molecular mechanisms of tomato (Solanum lycopersicum) roots' adaptation to salt stress is of great significance to enhance its salt tolerance and promote its planting in saline soils. A combined analysis of the metabolome and transcriptome of S. lycopersicum roots under different periods of salt stress according to changes in phenotypic and root physiological indices revealed that different accumulated metabolites and differentially expressed genes (DEGs) associated with phenylpropanoid biosynthesis were significantly altered. The levels of phenylpropanoids increased and showed a dynamic trend with the duration of salt stress. Ferulic acid (FA) and spermidine (Spd) levels were substantially up-regulated at the initial and mid-late stages of salt stress, respectively, and were significantly correlated with the expression of the corresponding synthetic genes. The results of canonical correlation analysis screening of highly correlated DEGs and construction of regulatory relationship networks with transcription factors (TFs) for FA and Spd, respectively, showed that the obtained target genes were regulated by most of the TFs, and TFs such as MYB, Dof, BPC, GRAS, and AP2/ERF might contribute to the regulation of FA and Spd content levels. Ultimately, FA and Spd attenuated the harm caused by salt stress in S. lycopersicum, and they may be key regulators of its salt tolerance. These findings uncover the dynamics and possible molecular mechanisms of phenylpropanoids during different salt stress periods, providing a basis for future studies and crop improvement.
PMID: 36570882
Front Plant Sci , IF:5.753 , 2022 , V13 : P1006044 doi: 10.3389/fpls.2022.1006044
Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice.
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States.; Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan.; Global Change and Photosynthesis Research Unit, United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Urbana, IL, United States.; Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.; Agencia Nacional de Investigacion y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile.; Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Santiago, Chile.; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States.; Rice Breeding Innovations Platform, International Rice Research Institute, Los Banos, Laguna, Philippines.
Nitrogen (N) and Water (W) - two resources critical for crop productivity - are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF-->target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta. This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF-->target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils.
PMID: 36507422
Genomics , IF:5.736 , 2022 Nov , 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 : P1041314 doi: 10.3389/fmicb.2022.1041314
In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection.
Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.; Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany.; Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada.; Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran.; Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan.; Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran.; Halal Research Center of IRI, FDA, Tehran, Iran.; Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.; Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.; Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.; Regional Department of Bioengineering, Tecnologico de Monterrey, Monterrey, Mexico.
OBJECTIVE: Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS: RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS: As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION: The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
PMID: 36532492
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
Biomolecules , IF:4.879 , 2022 Nov , V12 (12) doi: 10.3390/biom12121731
Chromosome-Level Genome Assembly and Multi-Omics Dataset Provide Insights into Isoflavone and Puerarin Biosynthesis in Pueraria lobata (Wild.) Ohwi.
School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China.; National R&D Center for Se-Rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China.; College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, China.
Pueraria lobata (wild.) Ohwi is a leguminous plant and one of the traditional Chinese herbal medicines. Its puerarin extract is widely used in the pharmaceutical industry. This study reported a chromosome-level genome assembly for P. lobata and its characteristics. The genome size was ~939.2 Mb, with a contig N50 of 29.51 Mbp. Approximately 97.82% of the assembled sequences were represented by 11 pseudochromosomes. We identified that the repetitive sequences accounted for 63.50% of the P. lobata genome. A total of 33,171 coding genes were predicted, of which 97.34% could predict the function. Compared with other species, P. lobata had 757 species-specific gene families, including 1874 genes. The genome evolution analysis revealed that P. lobata was most closely related to Glycine max and underwent two whole-genome duplication (WGD) events. One was in a gamma event shared by the core dicotyledons at around 65 million years ago, and another was in the common ancestor shared by legume species at around 25 million years ago. The collinearity analysis showed that 61.45% of the genes (54,579 gene pairs) in G. max and P. lobata had collinearity. In this study, six unique PlUGT43 homologous genes were retrieved from the genome of P. lobata, and no 2-hydroxyisoflavanone 8-C-glucoside was found in the metabolites. This also revealed that the puerarin synthesis was mainly from the glycation of daidzein. The combined transcriptome and metabolome analysis suggested that two bHLHs, six MYBs and four WRKYs were involved in the expression regulation of puerarin synthesis structural genes. The genetic information obtained in this study provided novel insights into the biological evolution of P. lobata and leguminous species, and it laid the foundation for further exploring the regulatory mechanism of puerarin synthesis.
PMID: 36551157
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
BMC Plant Biol , IF:4.215 , 2022 Dec , V22 (1) : P616 doi: 10.1186/s12870-022-03970-6
A systematical genome-wide analysis and screening of WRKY transcription factor family engaged in abiotic stress response in sweetpotato.
Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, Jiangsu Province, China.; Agricultural Bureau of Linyi City, 276000, Linyi, Shandong Province, China.; Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, Jiangsu Province, China.; Jiangsu Xuzhou Sweetpotato Research Center, 221131, Xuzhou, Jiangsu Province, China.; Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, Jiangsu Province, China. xiaoqingmeng008@126.com.; Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, Jiangsu Province, China. xiaoqingmeng008@126.com.; Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, Jiangsu Province, China. mingkuzhu007@126.com.; Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, Jiangsu Province, China. mingkuzhu007@126.com.
BACKGROUND: WRKY transcription factors play pivotal roles in regulating plant multiple abiotic stress tolerance, however, a genome-wide systematical analysis of WRKY genes in sweetpotato is still missing. RESULTS: Herein, 84 putative IbWRKYs with WRKY element sequence variants were identified in sweetpotato reference genomes. Fragment duplications, rather than tandem duplications, were shown to play prominent roles in IbWRKY gene expansion. The collinearity analysis between IbWRKYs and the related orthologs from other plants further depicted evolutionary insights into IbWRKYs. Phylogenetic relationships displayed that IbWRKYs were divided into three main groups (I, II and III), with the support of the characteristics of exon-intron structures and conserved protein motifs. The IbWRKY genes, mainly from the group Ib, displayed remarkable and diverse expression profiles under multiple abiotic stress (NaCl, PEG6000, cold and heat) and hormone (ABA, ACC, JA and SA) treatments, which were determined by RNA-seq and qRT-PCR assays, suggesting their potential roles in mediating particular stress responses. Moreover, IbWRKY58L could interact with IbWRKY82 as revealed by yeast two-hybrid based on the protein interaction network screening. And abiotic stress-remarkably induced IbWRKY21L and IbWRKY51 were shown to be localized in the nucleus and had no transactivation activities. CONCLUSION: These results provide valuable insights into sweetpotato IbWRKYs and will lay a foundation for further exploring functions and possible regulatory mechanisms of IbWRKYs in abiotic stress tolerance.
PMID: 36575404
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
BMC Genomics , IF:3.969 , 2022 Dec , V23 (1) : P814 doi: 10.1186/s12864-022-09039-w
A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.).
Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China.; Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.; School of Tropical Crops, Hainan University, Haikou, China.; State Key Laboratory of Grassland Agro-ecosystems, China, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.; Grassland Technology Experiment and Extension Station, Guiyang, China.; College of Agriculture, Guizhou University, Guiyang, China. hejin0811@163.com.
BACKGROUND: Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown. RESULTS: We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance. CONCLUSION: This study identifies specific genes involved in Ca(2+) signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.
PMID: 36482290
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (23) doi: 10.3390/plants11233401
The TaGSK1, TaSRG, TaPTF1, and TaP5CS Gene Transcripts Confirm Salinity Tolerance by Increasing Proline Production in Wheat (Triticum aestivum L.).
Graduate School of Natural and Applied Sciences, Ankara University, Ankara 06110, Turkiye.; Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.; Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara 06110, Turkiye.
Salinity is an abiotic stress factor that reduces yield and threatens food security in the world's arid and semi-arid regions. The development of salt-tolerant genotypes is critical for mitigating yield losses, and this journey begins with the identification of sensitive and tolerant plants. Numerous physiologic and molecular markers for detecting salt-tolerant wheat genotypes have been developed. One of them is proline, which has been used for a long time but has received little information about proline-related genes in wheat genotypes. In this study, proline content and the expression levels of proline-related genes (TaPTF1, TaDHN, TaSRG, TaSC, TaPIMP1, TaMIP, TaHKT1;4, TaGSK, TaP5CS, and TaMYB) were examined in sensitive, moderate, and tolerant genotypes under salt stress (0, 50, 150, and 250 mM NaCl) for 0, 12, and 24 h. Our results show that salt stress increased the proline content in all genotypes, but it was found higher in salt-tolerant genotypes than in moderate and sensitive genotypes. The salinity stress increased gene expression levels in salt-tolerant and moderate genotypes. While salt-stress exposure for 12 and 24 h had a substantial effect on gene expression in wheat, TaPTF1, TaPIMP1, TaMIP, TaHKT1;4, and TaMYB genes were considerably upregulated in 24 h. The salt-tolerant genotypes showed a higher positive interaction than a negative interaction. The TaPTF1, TaP5CS, TaGSK1, and TaSRG genes were found to be more selective than the other analyzed genes under salt-stress conditions. Despite each gene's specific function, increasing proline biosynthesis functioned as a common mechanism for separating salt tolerance from sensitivity.
PMID: 36501443
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
Biosci Biotechnol Biochem , IF:2.043 , 2022 Dec , V87 (1) : P21-27 doi: 10.1093/bbb/zbac191
Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.; BioResource Research Center, RIKEN, Tsukuba, Ibaraki, Japan.; Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, Japan.
In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.
PMID: 36416843
STAR Protoc , 2022 Dec , V4 (1) : P101934 doi: 10.1016/j.xpro.2022.101934
Deep learning based protocol to construct an immune-related gene network of host-pathogen interactions in plants.
Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.; Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. Electronic address: vishal@ihbt.res.in.
Investigating network behavior from host-pathogen interactions is challenging. Here, we present the deep-learning-based protocol to construct an immune-related gene network and list the genes involved in the defense response of host to specific biotic stress. The protocol includes the steps to pre-process the interaction pairs and expression profile of plants treated with pathogen/control, feed as input for DLNet algorithm to rank genes based on their contribution to data classification. The top-ranked genes are subjected to module and enrichment analysis. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2022).(1).
PMID: 36525344
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
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