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
Mol Plant , IF:13.164 , 2023 Feb , V16 (2) : P393-414 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 Hazard Mater , IF:10.588 , 2023 Feb , V449 : P131026 doi: 10.1016/j.jhazmat.2023.131026
Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus.
Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China.; Centre for Environmental Policy, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.; Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.; College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310032, China. Electronic address: hfqian@zjut.edu.cn.; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, China.
Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter's microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.
PMID: 36812731
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 doi: 10.1111/nph.18840
A comprehensive metabolic map reveals major quality regulations in red flesh kiwifruit (Actinidia chinensis).
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.; Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, 610213, Sichuan, China.; GBF Laboratory, Universite de Toulouse, INRA, Castanet-Tolosan, 31320, France.; School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.; School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK.; Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
Kiwifruit (Actinidia chinensis) is one of the popular fruits worldwide, and its quality is mainly determined by key metabolites (sugars, flavonoids and vitamins). Previous works on kiwifruit are mostly done via a single omics approach or involve only limited metabolites. Consequently, the dynamic metabolomes during kiwifruit development and ripening and the underlying regulatory mechanisms are poorly understood. In this study, using high-resolution metabolomic and transcriptomic analyses, we investigated kiwifruit metabolic landscapes at 11 different developmental and ripening stages and revealed a parallel classification of 515 metabolites and their co-expressed genes into 10 distinct metabolic vs gene modules (MM vs GM). Through integrative bioinformatics coupled with functional genomic assays, we constructed a global map and uncovered essential transcriptomic and transcriptional regulatory networks for all major metabolic changes that occurred throughout the kiwifruit growth cycle. Apart from known MM vs GM for metabolites such as soluble sugars, we identified novel transcription factors that regulate the accumulation of procyanidins, vitamin C and other important metabolites. Our findings thus shed light on the kiwifruit metabolic regulatory network and provide a valuable resource for the designed improvement of kiwifruit quality.
PMID: 36843264
New Phytol , IF:10.151 , 2023 Feb doi: 10.1111/nph.18788
A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO(2).
IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France.; IMAG, Univ. Montpellier, CNRS, 34000, Montpellier, France.; Universite Paul-Valery-Montpellier 3, 34000, Montpellier, France.
The elevation of CO(2) in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO(2) on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO(2) , nitrate, and iron. We demonstrated that elevated CO(2) has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO(2) negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO(2) . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO(2) . Our approach identified key features and regulators of the plant response to elevated CO(2) , with the objective of developing crops resilient to climate change.
PMID: 36727308
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 , 2023 Mar , V21 (3) : P466-481 doi: 10.1111/pbi.13944
Multi-stress resilience in plants recovering from submergence.
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.; Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.
PMID: 36217562
Elife , IF:8.14 , 2023 Feb , V12 doi: 10.7554/eLife.84379
Dynamics of co-substrate pools can constrain and regulate metabolic fluxes.
School of Life Sciences, University of Warwick, Warwick, United Kingdom.; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.; Department of Mathematics, University of Copenhagen, Copenhagen, Denmark.
Cycling of co-substrates, whereby a metabolite is converted among alternate forms via different reactions, is ubiquitous in metabolism. Several cycled co-substrates are well known as energy and electron carriers (e.g. ATP and NAD(P)H), but there are also other metabolites that act as cycled co-substrates in different parts of central metabolism. Here, we develop a mathematical framework to analyse the effect of co-substrate cycling on metabolic flux. In the cases of a single reaction and linear pathways, we find that co-substrate cycling imposes an additional flux limit on a reaction, distinct to the limit imposed by the kinetics of the primary enzyme catalysing that reaction. Using analytical methods, we show that this additional limit is a function of the total pool size and turnover rate of the cycled co-substrate. Expanding from this insight and using simulations, we show that regulation of these two parameters can allow regulation of flux dynamics in branched and coupled pathways. To support these theoretical insights, we analysed existing flux measurements and enzyme levels from the central carbon metabolism and identified several reactions that could be limited by the dynamics of co-substrate cycling. We discuss how the limitations imposed by co-substrate cycling provide experimentally testable hypotheses on specific metabolic phenotypes. We conclude that measuring and controlling co-substrate dynamics is crucial for understanding and engineering metabolic fluxes in cells.
PMID: 36799616
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
Sci Total Environ , IF:7.963 , 2023 Feb , V871 : P162034 doi: 10.1016/j.scitotenv.2023.162034
Biodegradable mulch films significantly affected rhizosphere microbial communities and increased peanut yield.
Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China.; Hebei Province Key Laboratory of Sustained Utilization and Development of Water Recourse, School of Water Resources and Environment, Hebei GEO University, Shijiazhuang 050031, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing 100125, China.; Liaoning Academy of Agricultural Sciences, Shenyang 110161, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: dcjin@rcees.ac.cn.
Biodegradable mulch films are widely used to replace conventional plastic films in agricultural fields. However, their ecological effects on different microbial communities that naturally inhabit agricultural fields are scarcely explored. Herein, differences in bacterial communities recovered from biofilms, bulk soil, and rhizosphere soil were comparatively assessed for polyethylene film (PE) and biodegradable mulch film (BDM) application in peanut planted fields. The results showed that the plastic film type significantly influenced the bacterial community in different ecological niches of agricultural fields (P < 0.001). Specifically, BDMs significantly increased the diversity and abundance of bacteria in the rhizosphere soil. The bacterial communities in each ecological niche were distinguishable from each other; bacterial communities in the rhizosphere soil showed the most pronounced response among different treatments. Acidobacteria and Pseudomonas were significantly enriched in the rhizosphere soil when BDMs were used. BDMs also increased the rhizosphere soil bacterial network complexity and stability. The enrichment of beneficial bacteria in the rhizosphere soil under BDMs may also have implications for the observed increase in peanut yield. Deepening analyses indicated that Pseudoxanthomonas and Glutamicibacter are biomarkers in biofilms of PE and BDMs respectively. Our study provides new insights into the consequences of the application of different types of plastic films on microbial communities in different ecological niches of agricultural fields.
PMID: 36754316
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
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 , 2023 Feb , V113 (4) : P749-771 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 , 2023 Jan , V24 (3) doi: 10.3390/ijms24032526
From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology.
Departament de Biologia, Bioquimica i Ciencies Naturals, Universitat Jaume I, 12071 Castello de la Plana, Spain.; Instituto de Bioingenieria, Universidad Miguel Hernandez, 03202 Elche, Spain.
The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy and processivity due to the implementation of molecular biology techniques, particularly genomics, Next Generation Sequencing and other omics such as proteomics and metabolomics. In this regard, the identification of interesting variants before they develop the phenotype trait of interest with molecular markers has advanced the breeding process of new varieties. Moreover, the correlation of phenotype or biochemical traits with gene expression or protein abundance has boosted the identification of potential new regulators of the traits of interest, using a relatively low number of variants. These important breakthrough technologies, built on top of classical approaches, will be improved in the future by including the spatial variable, allowing the identification of gene(s) involved in key processes at the tissue and cell levels.
PMID: 36768850
Int J Mol Sci , IF:5.923 , 2023 Feb , V24 (4) doi: 10.3390/ijms24043878
Alternative Splicing in the Regulatory Circuit of Plant Temperature Response.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xi'an 712100, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, Institute of Future Agriculture, Northwest A&F University, Xi'an 712100, China.
As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled.
PMID: 36835290
Front Plant Sci , IF:5.753 , 2022 , V13 : P1067076 doi: 10.3389/fpls.2022.1067076
Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco.
Hunan Tobacco Research Institute, Changsha, Hunan, China.; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China.; Hu'nan Tobacco Company Changde Company, Changde, Hunan, China.; College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China.; Siberian Institute of Plant Physiology and Biochemistry Siberian Branch of Russian Academy of Sciences (SB RAS) Irkutsk, Lermontova, Russia.
Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.
PMID: 36743571
Front Plant Sci , IF:5.753 , 2022 , V13 : P1094459 doi: 10.3389/fpls.2022.1094459
miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses.
Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.; School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China.; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
PMID: 36714724
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 Microbiol , IF:5.64 , 2023 , V14 : P1120679 doi: 10.3389/fmicb.2023.1120679
Soil fungal community characteristics vary with bamboo varieties and soil compartments.
Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China.; Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.; Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China.; School of Life Science, Hebei University, Baoding, China.; Sanya Research Base, International Centre for Bamboo and Rattan, Sanya, China.
Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal alpha diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities.
PMID: 36814565
Front Mol Biosci , IF:5.246 , 2023 , V10 : P1122201 doi: 10.3389/fmolb.2023.1122201
Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance.
Universite Paris-Saclay, Gif-sur-Yvette, France.; Ecole Nationale Superieure d'Informatique pour l'Industrie et l'Entreprise, Evry-Courcouronnes, France.; Department of Botany, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil.; Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom.
To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant's inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.
PMID: 36818043
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
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
Foods , IF:4.35 , 2023 Jan , V12 (2) doi: 10.3390/foods12020290
Widely Targeted Metabolomics Was Used to Reveal the Differences between Non-Volatile Compounds in Different Wines and Their Associations with Sensory Properties.
Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130117, China.
In this study, metabolites from six varieties of wines, including 'Haasan' (A1), 'Zuoshaner' (A2), 'Beibinghong' (A3), 'Shuanghong' (A4), 'Zijingganlu' (A5), and 'Cabernet Sauvignon' (A6), were identified and quantified using widely targeted metabolomics analysis techniques. Based on the test results, 1172 metabolites were detected and classified into 18 categories. These include 62 amino acids, 178 alkaloids, 189 flavonoids, 106 phenols, 148 terpenoids, etc. Comparing the differential metabolites between the comparison groups of each variety, differences between varieties based on P-values and VIP values were shown. Among these differential metabolites, Trimethoprim and Crotonoside were screened out as core differential metabolites. Multiple comparisons also screened the biomarkers for each species. We used widely targeted metabolomics to reveal the differences between non-volatile compounds in different wines and their associations with sensory properties. We also used the simultaneous weighted gene co-expression network analysis (WGCNA) to correlate metabolites with sensory traits, including color difference values and taste characteristics. Two of the six key modules were screened by WGCNA for relevance to sensory traits (brown module and turquoise module). This study provides a high-throughput method for linking compounds to various sensory characteristics of food, opening up new avenues for explaining differences in different varieties of wine.
PMID: 36673382
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 Feb , V23 (1) : P85 doi: 10.1186/s12870-023-04094-1
Integrated transcriptomics and metabolomics analysis reveals key regulatory network that response to cold stress in common Bean (Phaseolus vulgaris L.).
Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150000, China.; Horticulture Department, College of Life Sciences, Heilongjiang University, Harbin, 150000, China.; Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150000, China. feng998@126.com.; Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150000, China. jianlongedu@163.com.
Cold temperatures can be detrimental to crop survival and productivity. Breeding progress can be improved by understanding the molecular basis of low temperature tolerance. We investigated the key routes and critical metabolites related to low temperature resistance in cold-tolerant and -sensitive common bean cultivars 120 and 093, respectively. Many potential genes and metabolites implicated in major metabolic pathways during the chilling stress response were identified through transcriptomics and metabolomics research. Under chilling stress, the expression of many genes involved in lipid, amino acid, and flavonoid metabolism, as well as metabolite accumulation increased in the two bean types. Malondialdehyde (MDA) content was lower in 120 than in 093. Regarding amino acid metabolism, 120 had a higher concentration of acidic amino acids than 093, whereas 093 had a higher concentration of basic amino acids. Methionine accumulation was clearly higher in 120 than in 093. In addition, 120 had a higher concentration of many types of flavonoids than 093. Flavonoids, methionine and malondialdehyde could be used as biomarkers of plant chilling injury. Transcriptome analysis of hormone metabolism revealed considerably greater, expression of abscisic acid (ABA), gibberellin (GA), and jasmonic acid (JA) in 093 than in 120 during chilling stress, indicating that hormone regulation modes in 093 and 120 were different. Thus, chilling stress tolerance is different between 093 and 120 possibly due to transcriptional and metabolic regulation.
PMID: 36759761
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
Genes (Basel) , IF:4.096 , 2023 Jan , V14 (2) doi: 10.3390/genes14020282
A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites in Arabidopsis thaliana.
Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA.; Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA.
Transcription factors are an integral component of the cellular machinery responsible for regulating many biological processes, and they recognize distinct DNA sequence patterns as well as internal/external signals to mediate target gene expression. The functional roles of an individual transcription factor can be traced back to the functions of its target genes. While such functional associations can be inferred through the use of binding evidence from high-throughput sequencing technologies available today, including chromatin immunoprecipitation sequencing, such experiments can be resource-consuming. On the other hand, exploratory analysis driven by computational techniques can alleviate this burden by narrowing the search scope, but the results are often deemed low-quality or non-specific by biologists. In this paper, we introduce a data-driven, statistics-based strategy to predict novel functional associations for transcription factors in the model plant Arabidopsis thaliana. To achieve this, we leverage one of the largest available gene expression compendia to build a genome-wide transcriptional regulatory network and infer regulatory relationships among transcription factors and their targets. We then use this network to build a pool of likely downstream targets for each transcription factor and query each target pool for functionally enriched gene ontology terms. The results exhibited sufficient statistical significance to annotate most of the transcription factors in Arabidopsis with highly specific biological processes. We also perform DNA binding motif discovery for transcription factors based on their target pool. We show that the predicted functions and motifs strongly agree with curated databases constructed from experimental evidence. In addition, statistical analysis of the network revealed interesting patterns and connections between network topology and system-level transcriptional regulation properties. We believe that the methods demonstrated in this work can be extended to other species to improve the annotation of transcription factors and understand transcriptional regulation on a system level.
PMID: 36833209
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 , 2023 Jan , V12 (3) doi: 10.3390/plants12030538
Metabolomics and Transcriptomics Provide Insights into Lipid Biosynthesis in the Embryos of Walnut (Juglans regia L.).
College of Forestry, Hebei Agricultural University, Baoding 071001, China.; Technology Innovation Center of Hebei Province, Xingtai 054000, China.; Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China.
Walnut (Juglans regia L.) is an important woody oilseed tree species due to its commercial value. However, the regulation mechanism of walnut oil accumulation is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. In order to explore the metabolic mechanism that regulates the synthesis of walnut oil, we used transcriptome sequencing technology and metabolome technology to comprehensively analyze the key genes and metabolites involved in oil synthesis of the walnut embryo at 60, 90, and 120 days after pollination (DAP). The results showed that the oil and protein contents increased gradually during fruit development, comprising 69.61% and 18.32% of the fruit, respectively, during ripening. Conversely, the contents of soluble sugar and starch decreased gradually during fruit development, comprising 2.14% and 0.84%, respectively, during ripening. Transcriptome sequencing generated 40,631 unigenes across 9 cDNA libraries. We identified 51 and 25 candidate unigenes related to the biosynthesis of fatty acid and the biosynthesis of triacylglycerol (TAG), respectively. The expression levels of the genes encoding Acetyl-CoA carboxylase (ACCase), long-chain acyl-CoA synthetases (LACS), 3-oxoacyl-ACP synthase II (KASII), and glycerol-3-phosphate acyl transfer (GPAT) were upregulated at 60 DAP relative to the levels at 90 and 120 DAP, while the stearoyl-ACP-desaturase (SAD) and fatty acid desaturase 2 (FAD2) genes were highly abundantly expressed during all walnut developmental periods. We found that ABSCISIC ACID INSENSEITIVE3 (ABI3), WRINKLEDl (WRI1), LEAFY COTYLEDON1 (LEC1), and FUSCA3 (FUS3) may be key transcription factors involved in lipid synthesis. Additionally, the metabolomics analysis detected 706 metabolites derived from 18 samples, among which, 4 are implicated in the TAG synthesis, 2 in the glycolysis pathway, and 5 in the tricarboxylic acid cycle (TCA cycle) pathway. The combined analysis of the related genes and metabolites in TAG synthesis showed that phospholipid:diacylglycerol acyltransferase (PDAT) genes were highly abundantly expressed across walnut fruit developmental periods, and their downstream metabolite TAG gradually accumulated with the progression of fruit development. The FAD2 gene showed consistently higher expression during fruit development, and its downstream metabolites 18:2-PC and 18:3-PC gradually accumulated. The ACCase, LACS, SAD, FAD2, and PDAT genes may be crucial genes required for walnut oil synthesis. Our data will enrich public databases and provide new insights into functional genes related to lipid metabolism in walnut.
PMID: 36771622
Life (Basel) , IF:3.817 , 2023 Feb , V13 (2) doi: 10.3390/life13020559
Orthologs of Human-Disease-Associated Genes in Plants Are Involved in Regulating Leaf Senescence.
National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
As eukaryotes, plants and animals have many commonalities on the genetic level, although they differ greatly in appearance and physiological habits. The primary goal of current plant research is to improve the crop yield and quality. However, plant research has a wider aim, exploiting the evolutionary conservatism similarities between plants and animals, and applying discoveries in the field of botany to promote zoological research that will ultimately serve human health, although very few studies have addressed this aspect. Here, we analyzed 35 human-disease-related gene orthologs in plants and characterized the genes in depth. Thirty-four homologous genes were found to be present in the herbaceous annual plant Arabidopsis thaliana and the woody perennial plant Populus trichocarpa, with most of the genes having more than two exons, including the ATM gene with 78 exons. More surprisingly, 27 (79.4%) of the 34 homologous genes in Arabidopsis were found to be senescence-associated genes (SAGs), further suggesting a close relationship between human diseases and cellular senescence. Protein-protein interaction network analysis revealed that the 34 genes formed two main subnetworks, and genes in the first subnetwork interacted with 15 SAGs. In conclusion, our results show that most of the 34 homologs of human-disease-associated genes in plants are involved in the leaf senescence process, suggesting that leaf senescence may offer a means to study the pathogenesis of human diseases and to screen drugs for the treat of diseases.
PMID: 36836919
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
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