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
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.; 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: penghuiru@cau.edu.cn.
Gene regulation is central to all aspects of organism growth, and understanding it using 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 is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and 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 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 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 power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, 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 Feb , V237 (3) : P885-899 doi: 10.1111/nph.18567
AabHLH113 integrates jasmonic acid and abscisic acid signaling to positively regulate artemisinin biosynthesis in Artemisia annua.
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & Southwest University, School of Life Sciences, Southwest University, Chongqing, 400715, China.; Chongqing Academy of Science and Technology, Chongqing, 401123, China.; College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China.; College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
Artemisinin, a sesquiterpene lactone isolated from Artemisia annua, is in huge market demand due to its efficient antimalarial action, especially after the COVID-19 pandemic. Many researchers have elucidated that phytohormones jasmonic acid (JA) and abscisic acid (ABA) positively regulate artemisinin biosynthesis via types of transcription factors (TFs). However, the crosstalk between JA and ABA in regulating artemisinin biosynthesis remains unclear. Here, we identified a novel ABA- and JA-induced bHLH TF, AabHLH113, which positively regulated artemisinin biosynthesis by directly binding to the promoters of artemisinin biosynthetic genes, DBR2 and ALDH1. The contents of artemisinin and dihydroartemisinic acid increased by 1.71- to 2.06-fold and 1.47- to 2.23-fold, respectively, in AabHLH1113 overexpressed A. annua, whereas they decreased by 14-36% and 26-53%, respectively, in RNAi-AabHLH113 plants. Furthermore, we demonstrated that AabZIP1 and AabHLH112, which, respectively, participate in ABA and JA signaling pathway to regulate artemisinin biosynthesis, directly bind to and activate the promoter of AabHLH113. Collectively, we revealed a complex network in which AabHLH113 plays a key interrelational role to integrate ABA- and JA-mediated regulation of artemisinin biosynthesis.
PMID: 36271612
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 , 2023 Jan , V12 doi: 10.7554/eLife.82819
Transformer-based deep learning for predicting protein properties in the life sciences.
Department of Computing Science, Umea University, Umea, Sweden.; Umea Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umea, Sweden.
Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model-the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.
PMID: 36651724
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
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
Chemosphere , IF:7.086 , 2023 Feb , V313 : 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 have 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 the 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 concepts like, gene manipulation andediting, expression and regulation of catabolic enzymes, implementation of whole-cell based and enzyme based biosensor systems 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 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 the simultaneous implementation of more than one remediation strategy or a combinational approach creating an advantageous hybrid technique for OPP bioremediation.
PMID: 36526134
Int J Biol Macromol , IF:6.953 , 2023 Feb , V227 : P1098-1118 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 , 2023 Jan , V163 : P112287 doi: 10.1016/j.foodres.2022.112287
Identification of the key metabolites and related genes network modules highly associated with the nutrients and taste components among different Pepino (Solanum muricatum) cultivars.
Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China; College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100, China.; Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China.; Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China. Electronic address: zhongqiwen@qhu.edu.cn.
There is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.
PMID: 36596193
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, 4030, Philippines.
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, 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, was used. We identified 109 candidate genes with 5-20% phenotypic variation explained for the 12 micronutrients and identified epistatic interactions with multiple micronutrients. Pooling all candidate genes per micronutrient exhibited phenotypic variation explained 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 genome-wide association studies. 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 Dec , V24 (1) doi: 10.3390/ijms24010384
Construction of a Hierarchical Gene Regulatory Network to Reveal the Drought Tolerance Mechanism of Shanxin Poplar.
College of Forestry, Shenyang Agricultural University, Shenyang 110866, China.; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China.
Drought stress is a common adverse environment that plants encounter, and many drought-tolerant genes have been characterized. The gene regulatory network (GRN) is important in revealing the drought tolerance mechanism. Here, to investigate the regulatory mechanism of Shanxin poplar (Populus davidiana x P. bolleana) responding to drought stress, a three-layered GRN was built, and the regulatory relationship between genes in the GRN were predicted from expression correlation using a partial correlation coefficient-based algorithm. The GRN contains 1869 regulatory relationships, and includes 11 and 19 transcription factors (TFs) in the first and second layers, respectively, and 158 structural genes in the bottom layers involved in eight enriched biological processes. ChIP-PCR and qRT-PCR based on transient transformation were performed to validate the reliability of the GRN. About 88.0% of predicted interactions between the first and second layers, and 82.0% of predicted interactions between the second and third layers were correct, suggesting that the GRN is reliable. Six TFs were randomly selected from the top layer for characterizing their function in drought, and all of these TFs can confer drought tolerance. The important biological processes related to drought tolerance were identified, including "response to jasmonic acid", "response to oxidative stress", and "response to osmotic stress". In this GRN, PdbERF3 is predicted to play an important role in drought tolerance. Our data revealed the key regulators, TF-DNA interactions, and the main biological processes involved in adaption of drought stress in Shanxin poplar.
PMID: 36613845
Front Plant Sci , IF:5.753 , 2022 , V13 : P1086335 doi: 10.3389/fpls.2022.1086335
Full-length transcriptome and metabolite analysis reveal reticuline epimerase-independent pathways for benzylisoquinoline alkaloids biosynthesis in Sinomenium acutum.
State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.; Haihe Laboratory of Modern Chinese Medicine, Tianjin, China.; WuXi AppTec (Tianjin) Co., Ltd., Tianjin, China.; College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.; School of Medicine, Foshan University, Foshan, Guangdong, China.; Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua, Hunan, China.
Benzylisoquinoline alkaloids (BIAs) are a large family of plant natural products with important pharmaceutical applications. Sinomenium acutum is a medicinal plant from the Menispermaceae family and has been used to treat rheumatoid arthritis for hundreds of years. Sinomenium acutum contains more than 50 BIAs, and sinomenine is a representative BIA from this plant. Sinomenine was found to have preventive and curative effects on opioid dependence. Despite the broad applications of S. acutum, investigation on the biosynthetic pathways of BIAs from S. acutum is limited. In this study, we comprehensively analyzed the transcriptome data and BIAs in the root, stem, leaf, and seed of S. acutum. Metabolic analysis showed a noticeable difference in BIA contents in different tissues. Based on the study of the full-length transcriptome, differentially expressed genes, and weighted gene co-expression network, we proposed the biosynthetic pathways for a few BIAs from S. acutum, such as sinomenine, magnoflorine, and tetrahydropalmatine, and screened candidate genes involved in these biosynthesis processes. Notably, the reticuline epimerase (REPI/STORR), which converts (S)-reticuline to (R)-reticuline and plays an essential role in morphine and codeine biosynthesis, was not found in the transcriptome data of S. acutum. Our results shed light on the biogenesis of the BIAs in S. acutum and may pave the way for the future development of this important medicinal plant.
PMID: 36605968
Front Plant Sci , IF:5.753 , 2022 , V13 : P1047452 doi: 10.3389/fpls.2022.1047452
Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.
College of Landscape Architecture, Beijing University of Agriculture, Beijing, China.; Laboratory of Urban and Rural Ecological Environment, Beijing University of Agriculture, Beijing, China.
Acer pictum subsp. mono is a colorful tree species with considerable ornamental and economic value. However, little is known about the metabolism and regulatory mechanism of leaf color change in A. p. subsp. mono. To reveal the molecular mechanism of leaf color change in A. p. subsp. mono, the present study examined the bud mutation branches and compared the metabolites of the red leaves (AR) of the bud mutation branches of A. p. subsp. mono with those of the green leaves (AG) of the wild-type branches. It was found that the chlorophyll and carotenoids content of the red leaves decreased significantly, while anthocyanins, and various antioxidant enzymes increased significantly compared with the green leaves. The glycosides cyanidin, pelargonidin, malvidin, petunidin, delphinidin, and peonidin were detected in AR by liquid chromatography-mass spectrometry. The cyanidin glycosides increased, and cyanidin 3-O-glycoside was significantly upregulated. We analyzed the transcriptome and small RNA of A. p. subsp. mono leaves and detected 4061 differentially expressed mRNAs and 116 differentially expressed miRNAs. Through miRNA-mRNA association analysis, five differentially expressed modules were found; one miRNA targeted three genes, and four miRNAs targeted a single gene. Among them, miR160b, miR6300, and miR396g were found to be the key miRNAs regulating stable anthocyanin accumulation in A. p. subsp. mono leaves. By revealing the physiological response of leaf color change and the molecular regulatory mechanism of the miRNA, this study provides new insight into the molecular regulatory mechanism of leaf color change, thereby offering a foundation for future studies.
PMID: 36714704
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 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 , 2023 Jan , V63 (12) : P2008-2026 doi: 10.1093/pcp/pcac133
The Alteration of Tomato Chloroplast Vesiculation Positively Affects Whole-Plant Source-Sink Relations and Fruit Metabolism under Stress Conditions.
School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel.; Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel.; Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Muhlenberg, Golm, Potsdam 14476, Germany.; Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria.; Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA.
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato chloroplast vesiculation (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/CAS9) knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the l-glutamine and l-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
PMID: 36161338
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 , 2023 Jan , V22 (1) : P152-169 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
BMC Plant Biol , IF:4.215 , 2023 Jan , V23 (1) : P16 doi: 10.1186/s12870-023-04037-w
Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch).
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.; Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China. yphan@wbgcas.cn.; Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China. yphan@wbgcas.cn.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China. zhangxj@wbgcas.cn.; Center of Economic Botany, Core Botanical Gardens, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China. zhangxj@wbgcas.cn.
BACKGROUND: Organic acids are important components that determine the fruit flavor of peach (Prunus persica L. Batsch). However, the dynamics of organic acid diversity during fruit ripening and the key genes that modulate the organic acids metabolism remain largely unknown in this kind of fruit tree which yield ranks sixth in the world. RESULTS: In this study, we used 3D transcriptome data containing three dimensions of information, namely time, phenotype and gene expression, from 5 different varieties of peach to construct gene co-expression networks throughout fruit ripening of peach. With the network inferred, the time-ordered network comparative analysis was performed to select high-acid specific gene co-expression network and then clarify the regulatory factors controlling organic acid accumulation. As a result, network modules related to organic acid synthesis and metabolism under high-acid and low-acid comparison conditions were identified for our following research. In addition, we obtained 20 candidate genes as regulatory factors related to organic acid metabolism in peach. CONCLUSIONS: The study provides new insights into the dynamics of organic acid accumulation during fruit ripening, complements the results of classical co-expression network analysis and establishes a foundation for key genes discovery from time-series multiple species transcriptome data.
PMID: 36617558
BMC Plant Biol , IF:4.215 , 2023 Jan , V23 (1) : P11 doi: 10.1186/s12870-022-04012-x
Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice.
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China.; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China. huaanxie@163.com.; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China. huaanxie@163.com.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China. jianfzhang@163.com.; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China. jianfzhang@163.com.
BACKGROUND: The sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma. RESULTS: In the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas. CONCLUSION: The regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.
PMID: 36604645
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
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 , 2023 Jan , V12 (2) doi: 10.3390/plants12020408
Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory.
Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor 43600, Malaysia.
Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
PMID: 36679121
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (24) doi: 10.3390/plants11243473
Transcriptome and Gene Regulatory Network Analyses Reveal New Transcription Factors in Mature Fruit Associated with Harvest Date in Prunus persica.
Escuela de Agronomia, Facultad de Ciencias Agronomicas y de los Alimentos, Pontificia Universidad Catolica de Valparaiso, Quillota 2260000, Chile.; Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile.; Departamento de Fruticultura y Enologia, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile.; Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago 8331150, Chile.; ANID-Millennium Science Initiative Program, Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile.; Millennium Institute Center for Genome Regulation (CRG), Santiago 8331150, Chile.; Departamento de Produccion Agricola, Facultad de Ciencias Agronomicas, Universidad de Chile, Santiago 8820808, Chile.
Harvest date is a critical parameter for producers and consumers regarding agro-industrial performance. It involves a pleiotropic effect controlling the development of other fruit quality traits through finely controlling regulatory mechanisms. Fruit ripening is a process in which various signals and biological events co-occur and are regulated by hormone signaling that produces the accumulation/degradation of multiple compounds. However, the regulatory mechanisms that control the hormone signaling involved in fruit development and ripening are still unclear. To investigate the issue, we used individuals with early, middle and late harvest dates from a peach segregating population to identify regulatory candidate genes controlling fruit quality traits at the harvest stage and validate them in contrasting peach varieties for this trait. We identified 467 and 654 differentially expressed genes for early and late harvest through a transcriptomic approach. In addition, using the Arabidopsis DAP-seq database and network analysis, six transcription factors were selected. Our results suggest significant hormonal balance and cell wall composition/structure differences between early and late harvest samples. Thus, we propose that higher expression levels of the transcription factors HB7, ERF017 and WRKY70 in early harvest individuals would induce the expression of genes associated with the jasmonic acid pathway, photosynthesis and gibberellins inhibition. While on the other hand, the high expression levels of LHY, CDF3 and NAC083 in late harvest individuals would promote the induction of genes associated with abscisic acid biosynthesis, auxins and cell wall remodeling.
PMID: 36559585
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
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
OMICS , IF:3.374 , 2023 Jan , V27 (1) : P2-5 doi: 10.1089/omi.2022.0107
Systems Biology of COVID-19 and Human Diseases: Beyond a Bird's Eye View, and Toward One Health.
Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad, India.
As we gaze into the future beyond the current coronavirus disease 2019 (COVID-19) pandemic, there is a need to rethink our priorities in planetary health, research funding, and, importantly, the concepts and unchecked assumptions by which we attempt to understand health and prevent illness. Next-generation quantitative omics technologies promise a more profound and panoptic understanding of the dynamic pathophysiological processes and their aberrations in diverse diseased conditions. Systems biology research is highly relevant for COVID-19, a systemic disease affecting multiple organs and biological pathways. In addition, expanding the concept of health beyond humans so as to capture the importance of ecosystem health and recognizing the interdependence of human, animal, and plant health are enormously relevant and timely in the current historical moment of the pandemic. Notably, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, can affect our body clock, and the circadian aspects of this viral infection and host immunity need to be considered for its effective clinical management. Finally, we need to rethink and expand beyond the false binaries such as humans versus nature, and deploy multiomics systems biology research if we intend to design effective, innovative, and socioecological planetary health interventions to prevent future pandemics and ecological crises. We argue here that juxtaposing ecology and human health sciences scholarship is one of the key emerging tenets of 21st-century integrative biology.
PMID: 36095163
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
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