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Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. Plant Cell 2024; 36:812-828. [PMID: 38231860 PMCID: PMC10980355 DOI: 10.1093/plcell/koae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 01/19/2024]
Abstract
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.
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Affiliation(s)
- Carolin Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
- VIB Single Cell Core Facility, Ghent 9052, Belgium
| | - Dongbo Shi
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Manuel Neumann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Lea S Berg
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Yuji Ke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Fabio Gomez-Cano
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Jan U Lohmann
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Olivier C Martin
- Universities of Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette 91192, France
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Michael T Raissig
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Gergo Palfalvi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marc Libault
- Division of Plant Science and Technology, Interdisciplinary Plant Group, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65201, USA
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
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2
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Gomez-Cano F, Rodriguez J, Zhou P, Chu YH, Magnusson E, Gomez-Cano L, Krishnan A, Springer NM, de Leon N, Grotewold E. Prioritizing Metabolic Gene Regulators through Multi-Omic Network Integration in Maize. bioRxiv 2024:2024.02.26.582075. [PMID: 38464086 PMCID: PMC10925184 DOI: 10.1101/2024.02.26.582075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elucidating gene regulatory networks (GRNs) is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. In this study, we integrated publicly available co-expression networks derived from more than 6,000 RNA-seq samples, 283 protein-DNA interaction assays, and 16 million of SNPs used to identify expression quantitative loci (eQTL), to construct TF-target networks. In total, we analyzed ~4.6M interactions to generate four distinct types of TF-target networks: co-expression, protein-DNA interaction (PDI), trans-expression quantitative loci (trans-eQTL), and cis-eQTL combined with PDIs. To improve the functional annotation of TFs based on its target genes, we implemented three different strategies to integrate these four types of networks. We subsequently evaluated the effectiveness of our method through loss-of function mutant and random networks. The multi-network integration allowed us to identify transcriptional regulators of hormone-, metabolic- and development-related processes. Finally, using the topological properties of the fully integrated network, we identified potentially functional redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
- Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jonas Rodriguez
- Department of Plant and Agroecosystem Sciences, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Erika Magnusson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Arjun Krishnan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
- Current address: Global Breeding, Bayer Crop Sciences, Chesterfield MO 63017, USA
| | - Natalia de Leon
- Department of Plant and Agroecosystem Sciences, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
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3
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Gomez-Cano F, Chu YH, Cruz-Gomez M, Abdullah HM, Lee YS, Schnell DJ, Grotewold E. Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses. Plant J 2022; 110:589-606. [PMID: 35064997 DOI: 10.1111/tpj.15682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Mariel Cruz-Gomez
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Hesham M Abdullah
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
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4
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Zhou P, Enders TA, Myers ZA, Magnusson E, Crisp PA, Noshay JM, Gomez-Cano F, Liang Z, Grotewold E, Greenham K, Springer NM. Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information. Plant Cell 2022; 34:514-534. [PMID: 34735005 PMCID: PMC8773969 DOI: 10.1093/plcell/koab267] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes in transcript abundance. We used comparisons of expression responses in multiple genotypes to identify alleles with variable responses to heat or cold stress and to distinguish examples of cis- or trans-regulatory variation for stress-responsive expression changes. We used motifs enriched near the transcription start sites (TSSs) for thermal stress-responsive genes to develop predictive models of gene expression responses. Prediction accuracies can be improved by focusing only on motifs within unmethylated regions near the TSS and vary for genes with different dynamic responses to stress. Models trained on expression responses in a single genotype and promoter sequences provided lower performance when applied to other genotypes but this could be improved by using models trained on data from all three genotypes tested. The analysis of genes with cis-regulatory variation provides evidence for structural variants that result in presence/absence of transcription factor binding sites in creating variable responses. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and defines a framework for developing models to predict expression responses across multiple genotypes.
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Affiliation(s)
- Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Tara A Enders
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Zachary A Myers
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Erika Magnusson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kathleen Greenham
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
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5
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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Gomez-Cano F, Carey L, Lucas K, García Navarrete T, Mukundi E, Lundback S, Schnell D, Grotewold E. CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa. Database (Oxford) 2020; 2020:6031001. [PMID: 33306801 PMCID: PMC7731927 DOI: 10.1093/database/baaa075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/03/2022]
Abstract
Camelina is an annual oilseed plant from the Brassicaceae family that is gaining momentum as a biofuel winter cover crop. However, a significant limitation in further enhancing its utility as a producer of oils that can be used as biofuels, jet fuels or bio-based products is the absence of a repository for all the gene expression and regulatory information that is being rapidly generated by the community. Here, we provide CamRegBase (https://camregbase.org/) as a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide orthologs in the close-relative reference plant Arabidopsis. We envision this as a resource of curated information for users, as well as a repository of new gene regulation information.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Lisa Carey
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI 48824-1312, USA
| | - Kevin Lucas
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Steve Lundback
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Danny Schnell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI 48824-1312, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
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7
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Gomez-Cano L, Gomez-Cano F, Dillon FM, Alers-Velazquez R, Doseff AI, Grotewold E, Gray J. Discovery of modules involved in the biosynthesis and regulation of maize phenolic compounds. Plant Sci 2020; 291:110364. [PMID: 31928683 DOI: 10.1016/j.plantsci.2019.110364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Phenolic compounds are among the most diverse and widespread of specialized plant compounds and underly many important agronomic traits. Our comprehensive analysis of the maize genome unraveled new aspects of the genes involved in phenylpropanoid, monolignol, and flavonoid production in this important crop. Remarkably, just 19 genes accounted for 70 % of the overall mRNA accumulation of these genes across 95 tissues, indicating that these are the main contributors to the flux of phenolic metabolites. Eighty genes with intermediate to low expression play minor and more specialized roles. Remaining genes are likely undergoing loss of function or are expressed in limited cell types. Phylogenetic and expression analyses revealed which members of gene families governing metabolic entry and branch points exhibit duplication, subfunctionalization, or loss of function. Co-expression analysis applied to genes in sequential biosynthetic steps revealed that certain isoforms are highly co-expressed and are candidates for metabolic complexes that ensure metabolite delivery to correct cellular compartments. Co-expression of biosynthesis genes with transcription factors discovered connections that provided candidate components for regulatory modules governing this pathway. Our study provides a comprehensive analysis of maize phenylpropanoid related genes, identifies major pathway contributors, and novel candidate enzymatic and regulatory modules of the metabolic network.
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Affiliation(s)
- Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Francisco M Dillon
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Andrea I Doseff
- Department of Physiology, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, 43606, USA.
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8
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Jiang N, Lee YS, Mukundi E, Gomez-Cano F, Rivero L, Grotewold E. Diversity of genetic lesions characterizes new Arabidopsis flavonoid pigment mutant alleles from T-DNA collections. Plant Sci 2020; 291:110335. [PMID: 31928687 DOI: 10.1016/j.plantsci.2019.110335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 05/22/2023]
Abstract
The visual phenotypes afforded by flavonoid pigments have provided invaluable tools for modern genetics. Many Arabidopsis transparent testa (tt) mutants lacking the characteristic proanthocyanidin (PA) seed coat pigmentation and often failing to accumulate anthocyanins in vegetative tissues have been characterized. These mutants have significantly contributed to our understanding of flavonoid biosynthesis, regulation, and transport. A comprehensive screening for tt mutants in available large T-DNA collection lines resulted in the identification of 16 independent lines lacking PAs and anthocyanins, or with seed coat pigmentation clearly distinct from wild type. Segregation analyses and the characterization of second alleles in the genes disrupted by the indexed T-DNA insertions demonstrated that all the lines contained at least one additional mutation responsible for the tt phenotypes. Using a combination of RNA-Seq and whole genome re-sequencing and confirmed through complementation, we show here that these mutations correspond to novel alleles of ttg1 (two alleles), tt3 (two alleles), tt5 (two alleles), ban (two alleles), tt1 (two alleles), and tt8 (six alleles), which harbored additional T-DNA insertions, indels, missense mutations, and large genomic deletion. Several of the identified alleles offer interesting perspectives on flavonoid biosynthesis and regulation.
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Affiliation(s)
- Nan Jiang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Luz Rivero
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA.
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9
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Muñoz-Bodnar A, Perez-Quintero AL, Gomez-Cano F, Gil J, Michelmore R, Bernal A, Szurek B, Lopez C. RNAseq analysis of cassava reveals similar plant responses upon infection with pathogenic and non-pathogenic strains of Xanthomonas axonopodis pv. manihotis. Plant Cell Rep 2014; 33:1901-12. [PMID: 25120000 DOI: 10.1007/s00299-014-1667-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 05/28/2023]
Abstract
An RNAseq-based analysis of the cassava plants inoculated with Xam allowed the identification of transcriptional upregulation of genes involved in jasmonate metabolism, phenylpropanoid biosynthesis and putative targets for a TALE. Cassava bacterial blight, a disease caused by the gram-negative bacterium Xanthomonas axonopodis pv. manihotis (Xam), is a major limitation to cassava production worldwide and especially in developing countries. The molecular mechanisms underlying cassava susceptibility to Xam are currently unknown. To identify host genes and pathways leading to plant susceptibility, we analyzed the transcriptomic responses occurring in cassava plants challenged with either the non-pathogenic Xam strain ORST4, or strain ORST4(TALE1 Xam ) which is pathogenic due to the major virulence transcription activator like effector TALE1 Xam . Both strains triggered similar responses, i.e., induction of genes related to photosynthesis and phenylpropanoid biosynthesis, and repression of genes related to jasmonic acid signaling. Finally, to search for TALE1 Xam virulence targets, we scanned the list of cassava genes induced upon inoculation of ORST4(TALE1 Xam ) for candidates harboring a predicted TALE1 Xam effector binding element in their promoter. Among the six genes identified as potential candidate targets of TALE1 Xam a gene coding for a heat shock transcription factor stands out as the best candidate based on their induction in presence of TALE1 Xam and contain a sequence putatively recognized by TALE1 Xam .
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Affiliation(s)
- Alejandra Muñoz-Bodnar
- Manihot Biotec Group, Department of Biology, Universidad Nacional de Colombia, Bogotá, Colombia
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