1
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Li Y, Grotewold E, Dudareva N. Enough is enough: feedback control of specialized metabolism. Trends Plant Sci 2024; 29:514-523. [PMID: 37625949 DOI: 10.1016/j.tplants.2023.07.012] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Recent advances in our understanding of plant metabolism have highlighted the significance of specialized metabolites in the regulation of gene expression associated with biosynthetic networks. This opinion article focuses on the molecular mechanisms of small-molecule-mediated feedback regulation at the transcriptional level and its potential modes of action, including metabolite signal perception, the nature of the sensor, and the signaling transduction mechanisms leading to transcriptional and post-transcriptional regulation, based on evidence available from plants and other kingdoms of life. We also discuss the challenges associated with identifying the occurrences, effects, and localization of small molecule-protein interactions. Further understanding of small-molecule-controlled metabolic fluxes will enable rational design of transcriptional regulation systems in metabolic engineering to produce high-value specialized metabolites.
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Affiliation(s)
- Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA; Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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2
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Marathe S, Grotewold E, Otegui MS. Should I stay or should I go? Trafficking of plant extra-nuclear transcription factors. Plant Cell 2024; 36:1524-1539. [PMID: 38163635 PMCID: PMC11062434 DOI: 10.1093/plcell/koad277] [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: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 01/03/2024]
Abstract
At the heart of all biological processes lies the control of nuclear gene expression, which is primarily achieved through the action of transcription factors (TFs) that generally contain a nuclear localization signal (NLS) to facilitate their transport into the nucleus. However, some TFs reside in the cytoplasm in a transcriptionally inactive state and only enter the nucleus in response to specific signals, which in plants include biotic or abiotic stresses. These extra-nuclear TFs can be found in the cytosol or associated with various membrane systems, including the endoplasmic reticulum and plasma membrane. They may be integral proteins with transmembrane domains or associate peripherally with the lipid bilayer via acylation or membrane-binding domains. Although over 30 plant TFs, most of them involved in stress responses, have been experimentally shown to reside outside the nucleus, computational predictions suggest that this number is much larger. Understanding how extra-nuclear TFs are trafficked into the nucleus is essential for reconstructing transcriptional regulatory networks that govern major cellular pathways in response to biotic and abiotic signals. Here, we provide a perspective on what is known on plant extranuclear-nuclear TF retention, nuclear trafficking, and the post-translational modifications that ultimately enable them to regulate gene expression upon entering the nucleus.
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Affiliation(s)
- Sarika Marathe
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, 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
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Ying S, Webster B, Gomez-Cano L, Shivaiah KK, Wang Q, Newton L, Grotewold E, Thompson A, Lundquist PK. Multiscale physiological responses to nitrogen supplementation of maize hybrids. Plant Physiol 2024; 195:879-899. [PMID: 37925649 PMCID: PMC11060684 DOI: 10.1093/plphys/kiad583] [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: 06/05/2023] [Revised: 09/15/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Maize (Zea mays) production systems are heavily reliant on the provision of managed inputs such as fertilizers to maximize growth and yield. Hence, the effective use of nitrogen (N) fertilizer is crucial to minimize the associated financial and environmental costs, as well as maximize yield. However, how to effectively utilize N inputs for increased grain yields remains a substantial challenge for maize growers that requires a deeper understanding of the underlying physiological responses to N fertilizer application. We report a multiscale investigation of five field-grown maize hybrids under low or high N supplementation regimes that includes the quantification of phenolic and prenyl-lipid compounds, cellular ultrastructural features, and gene expression traits at three developmental stages of growth. Our results reveal that maize perceives the lack of supplemented N as a stress and, when provided with additional N, will prolong vegetative growth. However, the manifestation of the stress and responses to N supplementation are highly hybrid-specific. Eight genes were differentially expressed in leaves in response to N supplementation in all tested hybrids and at all developmental stages. These genes represent potential biomarkers of N status and include two isoforms of Thiamine Thiazole Synthase involved in vitamin B1 biosynthesis. Our results uncover a detailed view of the physiological responses of maize hybrids to N supplementation in field conditions that provides insight into the interactions between management practices and the genetic diversity within maize.
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Affiliation(s)
- Sheng Ying
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Brandon Webster
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Lina Gomez-Cano
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kiran-Kumar Shivaiah
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Qianjie Wang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Linsey Newton
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Erich Grotewold
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Addie Thompson
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Peter K Lundquist
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
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4
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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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5
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Sugimoto K, Irani N, Grotewold E, Howe GA. Catalytically impaired chalcone isomerase retains flavonoid biosynthetic capacity. Plant Physiol 2024:kiae096. [PMID: 38386294 DOI: 10.1093/plphys/kiae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
Catalytically impaired chalcone isomerases having no appreciable activity in vitro retain the ability to robustly promote flavonoid biosynthesis in planta.
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Affiliation(s)
- Koichi Sugimoto
- Tsukuba-Plant Innovation Center, University of Tsukuba, Tsukuba, Japan
| | - Niloufer Irani
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Erich Grotewold
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing MI, USA
| | - Gregg A Howe
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing MI, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing MI, USA
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6
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Sudhakaran M, Navarrete TG, Mejía-Guerra K, Mukundi E, Eubank TD, Grotewold E, Arango D, Doseff AI. Transcriptome reprogramming through alternative splicing triggered by apigenin drives cell death in triple-negative breast cancer. Cell Death Dis 2023; 14:824. [PMID: 38092740 PMCID: PMC10719380 DOI: 10.1038/s41419-023-06342-6] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized by its aggressiveness and resistance to cancer-specific transcriptome alterations. Alternative splicing (AS) is a major contributor to the diversification of cancer-specific transcriptomes. The TNBC transcriptome landscape is characterized by aberrantly spliced isoforms that promote tumor growth and resistance, underscoring the need to identify approaches that reprogram AS circuitry towards transcriptomes, favoring a delay in tumorigenesis or responsiveness to therapy. We have previously shown that flavonoid apigenin is associated with splicing factors, including heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2). Here, we showed that apigenin reprograms TNBC-associated AS transcriptome-wide. The AS events affected by apigenin were statistically enriched in hnRNPA2 substrates. Comparative transcriptomic analyses of human TNBC tumors and non-tumor tissues showed that apigenin can switch cancer-associated alternative spliced isoforms (ASI) to those found in non-tumor tissues. Apigenin preferentially affects the splicing of anti-apoptotic and proliferation factors, which are uniquely observed in cancer cells, but not in non-tumor cells. Apigenin switches cancer-associated aberrant ASI in vivo in TNBC xenograft mice by diminishing proliferation and increasing pro-apoptotic ASI. In accordance with these findings, apigenin increased apoptosis and reduced tumor proliferation, thereby halting TNBC growth in vivo. Our results revealed that apigenin reprograms transcriptome-wide TNBC-specific AS, thereby inducing apoptosis and hindering tumor growth. These findings underscore the impactful effects of nutraceuticals in altering cancer transcriptomes, offering new options to influence outcomes in TNBC treatments.
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Affiliation(s)
- Meenakshi Sudhakaran
- Molecular, Cellular, and Integrative Physiology Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Eric Mukundi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Timothy D Eubank
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Daniel Arango
- Department of Pharmacology and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Andrea I Doseff
- Department of Physiology and Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA.
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7
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Ellison EL, Zhou P, Hermanson P, Chu YH, Read A, Hirsch CN, Grotewold E, Springer NM. Mutator transposon insertions within maize genes often provide a novel outward reading promoter. Genetics 2023; 225:iyad171. [PMID: 37815810 DOI: 10.1093/genetics/iyad171] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/04/2023] [Indexed: 10/11/2023] Open
Abstract
The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles that result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu-suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5' UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and does not depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlight a strategy for transposons to co-exist with their host.
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Affiliation(s)
- Erika L Ellison
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peter Hermanson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Andrew Read
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
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8
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Arias CL, García Navarrete LT, Mukundi E, Swanson T, Yang F, Hernandez J, Grotewold E, Alonso AP. Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement. Plant Biotechnol J 2023; 21:1887-1903. [PMID: 37335591 PMCID: PMC10440992 DOI: 10.1111/pbi.14101] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co-expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.
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Affiliation(s)
- Cintia Lucía Arias
- Department of Biological Sciences & BioDiscovery InstituteUniversity of North TexasDentonTexasUSA
| | | | - Eric Mukundi
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Tyler Swanson
- Department of Biological Sciences & BioDiscovery InstituteUniversity of North TexasDentonTexasUSA
| | - Fan Yang
- Center for Applied Plant SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Jonathan Hernandez
- Department of Biological Sciences & BioDiscovery InstituteUniversity of North TexasDentonTexasUSA
| | - Erich Grotewold
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Ana Paula Alonso
- Department of Biological Sciences & BioDiscovery InstituteUniversity of North TexasDentonTexasUSA
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9
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Lee YS, Shiu SH, Grotewold E. Evolution and diversification of the ACT-like domain associated with plant basic helix-loop-helix transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2219469120. [PMID: 37126718 PMCID: PMC10175843 DOI: 10.1073/pnas.2219469120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/21/2023] [Indexed: 05/03/2023] Open
Abstract
Basic helix-loop-helix (bHLH) proteins are one of the largest families of transcription factor (TF) in eukaryotes, and ~30% of all flowering plants' bHLH TFs contain the aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain at variable distances C-terminal from the bHLH. However, the evolutionary history and functional consequences of the bHLH/ACT-like domain association remain unknown. Here, we show that this domain association is unique to the plantae kingdom with green algae (chlorophytes) harboring a small number of bHLH genes with variable frequency of ACT-like domain's presence. bHLH-associated ACT-like domains form a monophyletic group, indicating a common origin. Indeed, phylogenetic analysis results suggest that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT (ACR) genes by an ancestral bHLH gene. We determined the functional significance of this association by showing that Chlamydomonas reinhardtii ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. We show that, while ACT-like domains have experienced faster selection than the associated bHLH domain, their rates of evolution are strongly and positively correlated, suggesting that the evolution of the ACT-like domains was constrained by the bHLH domains. This study proposes an evolutionary trajectory for the association of ACT-like and bHLH domains with the experimental characterization of the functional consequence in the regulation of plant-specific processes, highlighting the impacts of functional domain coevolution.
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Affiliation(s)
- Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI48824
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI48824
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10
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Gavgani HN, Grotewold E, Gray J. Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information. Methods Mol Biol 2023; 2698:277-300. [PMID: 37682481 DOI: 10.1007/978-1-0716-3354-0_17] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The amount of biological data is growing at a rapid pace as many high-throughput omics technologies and data pipelines are developed. This is resulting in the growth of databases for DNA and protein sequences, gene expression, protein accumulation, structural, and localization information. The diversity and multi-omics nature of such bioinformatic data requires well-designed databases for flexible organization and presentation. Besides general-purpose online bioinformatic databases, users need narrowly focused online databases to quickly access a meaningful collection of related data for their research. Here, we describe the methodology used to implement a plant gene regulatory knowledgebase, with data, query, and tool features, as well as the ability to expand to accommodate future datasets. We exemplify this methodology for the GRASSIUS knowledgebase, but it is applicable to developing and updating similar plant gene regulatory knowledgebases. GRASSIUS organizes and presents gene regulatory data from grass species with a central focus on maize (Zea mays). The main class of data presented include not only the families of transcription factors (TFs) and co-regulators (CRs) but also protein-DNA interaction data, where available.
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Affiliation(s)
- Hadi Nayebi Gavgani
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Dandelions Therapeutics Inc., San Francisco, CA, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA.
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11
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Johnston C, García Navarrete LT, Ortiz E, Romsdahl TB, Guzha A, Chapman KD, Grotewold E, Alonso AP. Effective Mechanisms for Improving Seed Oil Production in Pennycress ( Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics. Front Plant Sci 2022; 13:943585. [PMID: 35909773 PMCID: PMC9330397 DOI: 10.3389/fpls.2022.943585] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Pennycress is a potentially lucrative biofuel crop due to its high content of long-chain unsaturated fatty acids, and because it uses non-conventional pathways to achieve efficient oil production. However, metabolic engineering is required to improve pennycress oilseed content and make it an economically viable source of aviation fuel. Research is warranted to determine if further upregulation of these non-conventional pathways could improve oil production within the species even more, which would indicate these processes serve as promising metabolic engineering targets and could provide the improvement necessary for economic feasibility of this crop. To test this hypothesis, we performed a comparative biomass, metabolomic, and transcriptomic analyses between a high oil accession (HO) and low oil accession (LO) of pennycress to assess potential factors required to optimize oil content. An evident reduction in glycolysis intermediates, improved oxidative pentose phosphate pathway activity, malate accumulation in the tricarboxylic acid cycle, and an anaplerotic pathway upregulation were noted in the HO genotype. Additionally, higher levels of threonine aldolase transcripts imply a pyruvate bypass mechanism for acetyl-CoA production. Nucleotide sugar and ascorbate accumulation also were evident in HO, suggesting differential fate of associated carbon between the two genotypes. An altered transcriptome related to lipid droplet (LD) biosynthesis and stability suggests a contribution to a more tightly-packed LD arrangement in HO cotyledons. In addition to the importance of central carbon metabolism augmentation, alternative routes of carbon entry into fatty acid synthesis and modification, as well as transcriptionally modified changes in LD regulation, are key aspects of metabolism and storage associated with economically favorable phenotypes of the species.
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Affiliation(s)
- Christopher Johnston
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | | | - Emmanuel Ortiz
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Trevor B. Romsdahl
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Athanas Guzha
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Kent D. Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Ana Paula Alonso
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
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12
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Rodriguez J, Gomez-Cano L, Grotewold E, de Leon N. Normalizing and Correcting Variable and Complex LC-MS Metabolomic Data with the R Package pseudoDrift. Metabolites 2022; 12:435. [PMID: 35629939 PMCID: PMC9144304 DOI: 10.3390/metabo12050435] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
In biological research domains, liquid chromatography-mass spectroscopy (LC-MS) has prevailed as the preferred technique for generating high quality metabolomic data. However, even with advanced instrumentation and established data acquisition protocols, technical errors are still routinely encountered and can pose a significant challenge to unveiling biologically relevant information. In large-scale studies, signal drift and batch effects are how technical errors are most commonly manifested. We developed pseudoDrift, an R package with capabilities for data simulation and outlier detection, and a new training and testing approach that is implemented to capture and to optionally correct for technical errors in LC-MS metabolomic data. Using data simulation, we demonstrate here that our approach performs equally as well as existing methods and offers increased flexibility to the researcher. As part of our study, we generated a targeted LC-MS dataset that profiled 33 phenolic compounds from seedling stem tissue in 602 genetically diverse non-transgenic maize inbred lines. This dataset provides a unique opportunity to investigate the dynamics of specialized metabolism in plants.
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Affiliation(s)
- Jonas Rodriguez
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; (L.G.-C.); (E.G.)
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; (L.G.-C.); (E.G.)
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA;
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13
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García Navarrete T, Arias C, Mukundi E, Alonso AP, Grotewold E. Natural variation and improved genome annotation of the emerging biofuel crop field pennycress ( Thlaspi arvense). G3 Genes|Genomes|Genetics 2022; 12:6568017. [PMID: 35416986 PMCID: PMC9157065 DOI: 10.1093/g3journal/jkac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/02/2022] [Indexed: 11/25/2022]
Abstract
The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.
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Affiliation(s)
- Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Cintia Arias
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ana Paula Alonso
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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14
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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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15
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Ding X, Zhang X, Paez-Valencia J, McLoughlin F, Reyes FC, Morohashi K, Grotewold E, Vierstra RD, Otegui MS. Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells. Front Plant Sci 2022; 13:833612. [PMID: 35251104 PMCID: PMC8894768 DOI: 10.3389/fpls.2022.833612] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The molecular machinery orchestrating microautophagy, whereby eukaryotic cells sequester autophagic cargo by direct invagination of the vacuolar/lysosomal membrane, is still largely unknown, especially in plants. Here, we demonstrate microautophagy of storage proteins in the maize aleurone cells of the endosperm and analyzed proteins with potential regulatory roles in this process. Within the cereal endosperm, starchy endosperm cells accumulate storage proteins (mostly prolamins) and starch whereas the peripheral aleurone cells store oils, storage proteins, and specialized metabolites. Although both cell types synthesize prolamins, they employ different pathways for their subcellular trafficking. Starchy endosperm cells accumulate prolamins in protein bodies within the endoplasmic reticulum (ER), whereas aleurone cells deliver prolamins to vacuoles via an autophagic mechanism, which we show is by direct association of ER prolamin bodies with the tonoplast followed by engulfment via microautophagy. To identify candidate proteins regulating this process, we performed RNA-seq transcriptomic comparisons of aleurone and starchy endosperm tissues during seed development and proteomic analysis on tonoplast-enriched fractions of aleurone cells. From these datasets, we identified 10 candidate proteins with potential roles in membrane modification and/or microautophagy, including phospholipase-Dα5 and a possible EUL-like lectin. We found that both proteins increased the frequency of tonoplast invaginations when overexpressed in Arabidopsis leaf protoplasts and are highly enriched at the tonoplast surface surrounding ER protein bodies in maize aleurone cells, thus supporting their potential connections to microautophagy. Collectively, this candidate list now provides useful tools to study microautophagy in plants.
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Affiliation(s)
- Xinxin Ding
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Xiaoguo Zhang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Julio Paez-Valencia
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Francisca C. Reyes
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Kengo Morohashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Marisa S. Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
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16
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Moore BM, Lee YS, Wang P, Azodi C, Grotewold E, Shiu SH. Modeling temporal and hormonal regulation of plant transcriptional response to wounding. Plant Cell 2022; 34:867-888. [PMID: 34865154 PMCID: PMC8824630 DOI: 10.1093/plcell/koab287] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 11/18/2021] [Indexed: 06/02/2023]
Abstract
Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.
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Affiliation(s)
| | | | - Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Christina Azodi
- St. Vincent’s Institute of Medical Research, Fitzroy 3065, Victoria, Australia
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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17
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Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. Plant Cell 2022; 34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
Abstract
The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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18
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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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19
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Jiang N, Dillon FM, Silva A, Gomez-Cano L, Grotewold E. Corrigendum to "Rhamnose in plants - from biosynthesis to diverse functions" [Plant Sci. 302 (2021) 110687]. Plant Sci 2021; 307:110897. [PMID: 33902856 DOI: 10.1016/j.plantsci.2021.110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Nan Jiang
- 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
| | - Alexander Silva
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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20
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Lee YS, Herrera-Tequia A, Silwal J, Geiger JH, Grotewold E. A hydrophobic residue stabilizes dimers of regulatory ACT-like domains in plant basic helix-loop-helix transcription factors. J Biol Chem 2021; 296:100708. [PMID: 33901489 PMCID: PMC8202348 DOI: 10.1016/j.jbc.2021.100708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
About a third of the plant basic helix–loop–helix (bHLH) transcription factors harbor a C-terminal aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain, which was originally identified in the maize R regulator of anthocyanin biosynthesis, where it modulates the ability of the bHLH to dimerize and bind DNA. Characterization of other bHLH ACT-like domains, such as the one in the Arabidopsis R ortholog, GL3, has not definitively confirmed dimerization, raising the question of the overall role of this potential regulatory domain. To learn more, we compared the dimerization of the ACT-like domains of R (RACT) and GL3 (GL3ACT). We show that RACT dimerizes with a dissociation constant around 100 nM, over an order of magnitude stronger than GL3ACT. Structural predictions combined with mutational analyses demonstrated that V568, located in a hydrophobic pocket in RACT, is important: when mutated to the Ser residue present in GL3ACT, dimerization affinity dropped by almost an order of magnitude. The converse S595V mutation in GL3ACT significantly increased the dimerization strength. We cloned and assayed dimerization for all identified maize ACT-like domains and determined that 12 of 42 formed heterodimers in yeast two-hybrid assays, irrespective of whether they harbored V568, which was often replaced by other aliphatic amino acids. Moreover, we determined that the presence of polar residues at that position occurs only in a small subset of anthocyanin regulators. The combined results provide new insights into possibly regulatory mechanisms and suggest that many of the other plant ACT-like domains associate to modulate fundamental cellular processes.
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Affiliation(s)
- Yun Sun Lee
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Andres Herrera-Tequia
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jagannath Silwal
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Erich Grotewold
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
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21
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Jiang N, Dillon FM, Silva A, Gomez-Cano L, Grotewold E. Rhamnose in plants - from biosynthesis to diverse functions. Plant Sci 2021; 302:110687. [PMID: 33288005 DOI: 10.1016/j.plantsci.2020.110687] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 06/26/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 05/27/2023]
Abstract
In plants, the deoxy sugar l-rhamnose is widely present as rhamnose-containing polymers in cell walls and as part of the decoration of various specialized metabolites. Here, we review the current knowledge on the distribution of rhamnose, highlighting the differences between what is known in dicotyledoneuos compared to commelinid monocotyledoneous (grasses) plants. We discuss the biosynthesis and transport of UDP-rhamnose, as well as the transfer of rhamnose from UDP-rhamnose to various primary and specialized metabolites. This is carried out by rhamnosyltransferases, enzymes that can use a large variety of substrates. Some unique characteristics of rhamnose synthases, the multifunctional enzymes responsible for the conversion of UDP-glucose into UDP-rhamnose, are considered, particularly from the perspective of their ability to convert glucose present in flavonoids. Finally, we discuss how little is still known with regards to how plants rescue rhamnose from the many compounds to which it is linked, or how rhamnose is catabolized.
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Affiliation(s)
- Nan Jiang
- 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
| | - Alexander Silva
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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22
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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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23
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Jiang N, Gutierrez-Diaz A, Mukundi E, Lee YS, Meyers BC, Otegui MS, Grotewold E. Author Correction: Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism. Nat Commun 2020; 11:5276. [PMID: 33057182 PMCID: PMC7560853 DOI: 10.1038/s41467-020-19223-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Nan Jiang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Aimer Gutierrez-Diaz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri, Columbia, MO, 65201, USA
| | - Marisa S Otegui
- Department of Botany, Laboratory of Molecular and Cell Biology, University of Wisconsin-Madison, Wisconsin-Madison, WI, 53706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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24
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Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research & Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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Zhou P, Li Z, Magnusson E, Gomez Cano F, Crisp PA, Noshay JM, Grotewold E, Hirsch CN, Briggs SP, Springer NM. Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. Plant Cell 2020; 32:1377-1396. [PMID: 32184350 PMCID: PMC7203921 DOI: 10.1105/tpc.20.00080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 05/22/2023]
Abstract
The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including >6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.
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Affiliation(s)
- Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Erika Magnusson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Fabio Gomez Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Steven P Briggs
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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26
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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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27
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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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28
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Springer N, de León N, Grotewold E. Challenges of Translating Gene Regulatory Information into Agronomic Improvements. Trends Plant Sci 2019; 24:1075-1082. [PMID: 31377174 DOI: 10.1016/j.tplants.2019.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 03/27/2019] [Revised: 06/26/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
Improvement of agricultural species has exploited the genetic variation responsible for complex quantitative traits. Much of the functional variation is regulatory, in cis-regulatory elements and trans-acting factors that ultimately contribute to gene expression differences. However, the identification of gene regulatory network components that, when modulated, will increase plant productivity or resilience, is challenging, yet essential to provide increased predictive power for genome engineering approaches that are likely to benefit useful traits. Here, we discuss the opportunities and limitations of using data obtained from gene coexpression, transcription factor binding, and genome-wide association mapping analyses to predict regulatory interactions that impact crop improvement. It is apparent that a combination of information from these data types is necessary for the reliable identification and utilization of important regulatory interactions that underlie complex agronomic traits.
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Affiliation(s)
- Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA.
| | - Natalia de León
- Department of Agronomy, University of Wisconsin, Madison, WI 56706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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29
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Milutinovic M, Lindsey BE, Wijeratne A, Hernandez JM, Grotewold N, Fernández V, Grotewold E, Brkljacic J. Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation. Plant Sci 2019; 285:99-109. [PMID: 31203898 DOI: 10.1016/j.plantsci.2019.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 02/01/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Seed development is a complex regulatory process that includes a transition from gametophytic to sporophytic program. The synchronized development of different seed compartments (seed coat, endosperm and embryo) depends on a balance in parental genome contributions. In the most severe cases, the disruption of the balance leads to seed abortion. This represents one of the main obstacles for the engineering of asexual reproduction through seeds (apomixis), and for generating new interspecies hybrids. The repression of auxin synthesis by the Polycomb Repressive Complex 2 (PRC2) is a major mechanism contributing to sensing genome balance. However, current efforts focusing on decreasing PRC2 or elevating auxin levels have not yet resulted in the production of apomictic seed. Here, we show that EMSY-Like Tudor/Agenet H3K36me3 histone readers EML1 and EML3 are necessary for early stages of seed development to proceed at a normal rate in Arabidopsis. We further demonstrate that both EML1 and EML3 are required to prevent the initiation of seed development in the absence of fertilization. Based on the whole genome expression analysis, we identify auxin transport and signaling genes as the most enriched downstream targets of EML1 and EML3. We hypothesize that EML1 and EML3 function to repress and soften paternal gene expression by fine-tuning auxin responses. Discovery of this pathway may contribute to the engineering of apomixis and interspecies hybrids.
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Affiliation(s)
- Milica Milutinovic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Benson E Lindsey
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Asela Wijeratne
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - J Marcela Hernandez
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolas Grotewold
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Virginia Fernández
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Erich Grotewold
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA.
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30
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Righini S, Rodriguez EJ, Berosich C, Grotewold E, Casati P, Falcone Ferreyra ML. Apigenin produced by maize flavone synthase I and II protects plants against UV-B-induced damage. Plant Cell Environ 2019; 42:495-508. [PMID: 30160312 DOI: 10.1111/pce.13428] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 04/23/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 05/20/2023]
Abstract
Flavones, one of the largest groups of flavonoids, have beneficial effects on human health and are considered of high nutritional value. Previously, we demonstrated that maize type I flavone synthase (ZmFNSI) is one of the enzymes responsible for the synthesis of O-glycosyl flavones in floral tissues. However, in related species such as rice and sorghum, type II FNS enzymes also contribute to flavone biosynthesis. In this work, we provide evidence that maize has both one FNSI and one FNSII flavone synthases. Arabidopsis transgenic plants expressing each FNS enzyme were generated to validate the role of flavones in protecting plants against UV-B radiation. Here, we demostrate that ZmCYP93G7 (FNSII) has flavone synthase activity and is able to complement the Arabidopsis dmr6 mutant, restoring the susceptibility to Pseudomonas syringae. ZmFNSII expression is controlled by the C1/PL1 + R/B anthocyanin transcriptional complexes, and both ZmFNSI and ZmFNSII are regulated by UV-B. Arabidopsis transgenic plants expressing ZmFNSI or ZmFNSII that accumulate apigenin exhibit less UV-B-induced damage than wild-type plants. Together, we show that maize has two FNS-type enzymes that participate in the synthesis of apigenin, conferring protection against UV-B radiation.
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Affiliation(s)
- Silvana Righini
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo José Rodriguez
- Instituto de Biología Molecular y Celular de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carla Berosich
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
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31
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Silva GFF, Silva EM, Correa JPO, Vicente MH, Jiang N, Notini MM, Junior AC, De Jesus FA, Castilho P, Carrera E, López-Díaz I, Grotewold E, Peres LEP, Nogueira FTS. Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA-controlled modules. New Phytol 2019; 221:1328-1344. [PMID: 30238569 DOI: 10.1111/nph.15492] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/07/2018] [Indexed: 05/18/2023]
Abstract
Age-regulated microRNA156 (miR156) and targets similarly control the competence to flower in diverse species. By contrast, the diterpene hormone gibberellin (GA) and the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote flowering in the facultative long-day Arabidopsis thaliana, but suppress it in the day-neutral tomato (Solanum lycopersicum). We combined genetic and molecular studies and described a new interplay between GA and two unrelated miRNA-associated pathways that modulates tomato transition to flowering. Tomato PROCERA/DELLA activity is required to promote flowering along with the miR156-targeted SQUAMOSA PROMOTER BINDING-LIKE (SPL/SBP) transcription factors by activating SINGLE FLOWER TRUSS (SFT) in the leaves and the MADS-Box gene APETALA1(AP1)/MC at the shoot apex. Conversely, miR319-targeted LANCEOLATE represses floral transition by increasing GA concentrations and inactivating SFT in the leaves and AP1/MC at the shoot apex. Importantly, the combination of high GA concentrations/responses with the loss of SPL/SPB function impaired canonical meristem maturation and flower initiation in tomato. Our results reveal a cooperative regulation of tomato floral induction and flower development, integrating age cues (miR156 module) with GA responses and miR319-controlled pathways. Importantly, this study contributes to elucidate the mechanisms underlying the effects of GA in controlling flowering time in a day-neutral species.
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Affiliation(s)
- Geraldo F F Silva
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Eder M Silva
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Joao P O Correa
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Mateus H Vicente
- Laboratory of Hormonal Control of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Nan Jiang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Marcela M Notini
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Airton C Junior
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Frederico A De Jesus
- Laboratory of Hormonal Control of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Pollyanna Castilho
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ingeniero Fausto Elío s/n, 46022, Valencia, Spain
| | - Isabel López-Díaz
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ingeniero Fausto Elío s/n, 46022, Valencia, Spain
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Lazaro E P Peres
- Laboratory of Hormonal Control of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo (USP), 13418-900, Piracicaba, Sao Paulo, Brazil
| | - Fabio T S Nogueira
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), University of Sao Paulo, 13418-900, Piracicaba, Sao Paulo, Brazil
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32
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Jones MA, Morohashi K, Grotewold E, Harmer SL. Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation. Front Plant Sci 2019; 10:57. [PMID: 30774641 PMCID: PMC6367231 DOI: 10.3389/fpls.2019.00057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/16/2019] [Indexed: 05/08/2023]
Abstract
The circadian system ensures that plants respond appropriately to environmental change by predicting regular transitions that occur during diel cycles. In order to be most useful, the circadian system needs to be compensated against daily and seasonal changes in temperature that would otherwise alter the pace of this biological oscillator. We demonstrate that an evening-phased protein, the putative histone demethylase JMJD5, contributes to temperature compensation. JMJD5 is co-expressed with components of the Evening Complex, an agglomeration of proteins including EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHYMO (LUX), which also integrates temperature changes into the molecular clockwork. One role of the Evening Complex is to regulate expression of PSEUDORESPONSE REGULATOR9 (PRR9) and PRR7, important components of the temperature compensation mechanism. Surprisingly we find that LUX, but not other Evening Complex components, is dispensable for clock function at low temperatures. Further genetic analysis suggests JMJD5 acts in a parallel pathway to LUX within the circadian system. Although an intact JMJD5 catalytic domain is required for its function within the clock, our findings suggest JMJD5 does not directly regulate H3K36 methylation at circadian loci. Such data refine our understanding of how JMDJ5 acts within the Arabidopsis circadian system.
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Affiliation(s)
- Matthew A. Jones
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Kengo Morohashi
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
- *Correspondence: Stacey L. Harmer,
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33
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34
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Cocuron JC, Casas MI, Yang F, Grotewold E, Alonso AP. Beyond the wall: High-throughput quantification of plant soluble and cell-wall bound phenolics by liquid chromatography tandem mass spectrometry. J Chromatogr A 2018; 1589:93-104. [PMID: 30626504 DOI: 10.1016/j.chroma.2018.12.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/20/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
Abstract
Plants accumulate several thousand of phenolic compounds, including lignins and flavonoids, which are mainly synthesized through the phenylpropanoid pathway, and play important roles in plant growth and adaptation. A novel high-throughput ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method was established to quantify the levels of 19 flavonoids and 15 other phenolic compounds, including acids, aldehydes, and alcohols. The chromatographic separation was performed in 10 min, allowing for the resolution of isomers such as 3-, 4-, and 5-chlorogenic acids, 4-hydroxybenzoic and salicylic acids, isoorientin and orientin, and luteolin and kaempferol. The linearity range for each compound was found to be in the low fmol to the high pmol. Furthermore, this UHPLC-MS/MS approach was shown to be very sensitive with limits of detection between 1.5 amol to 300 fmol, and limits of quantification between 5 amol to 1000 fmol. Extracts from maize seedlings were used to assess the robustness of the method in terms of recovery efficiency, matrix effect, and accuracy. The biological matrix did not suppress the signal for 32 out of the 34 metabolites under investigation. Additionally, the majority of the analytes were recovered from the biological samples with an efficiency above 75%. All flavonoids and other phenolic compounds had an intra- and inter-day accuracy within a ±20% range, except for coniferyl alcohol and vanillic acid. Finally, the quantification of flavonoids, free and cell wall-bound phenolics in seedlings from two maize lines with contrasting phenolic content was successfully achieved using this methodology.
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Affiliation(s)
- Jean-Christophe Cocuron
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | | | - Fan Yang
- Benson Hill Biosystems, St. Louis, MO, 63132, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Ana Paula Alonso
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
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35
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Kovinich N, Wang Y, Adegboye J, Chanoca AA, Otegui MS, Durkin P, Grotewold E. Arabidopsis MATE45 antagonizes local abscisic acid signaling to mediate development and abiotic stress responses. Plant Direct 2018; 2:e00087. [PMID: 31245687 PMCID: PMC6508792 DOI: 10.1002/pld3.87] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 09/22/2018] [Accepted: 09/26/2018] [Indexed: 05/11/2023]
Abstract
Anthocyanins provide ideal visual markers for the identification of mutations that disrupt molecular responses to abiotic stress. We screened Arabidopsis mutants of ABC (ATP-Binding Cassette) and MATE (Multidrug And Toxic compound Extrusion) transporter genes under nutritional stress and identified four genes (ABCG25,ABCG9,ABCG5, and MATE45) required for normal anthocyanin pigmentation. ABCG25 was previously demonstrated to encode a vascular-localized cellular exporter of abscisic acid (ABA). Our results show that MATE45 encodes an aerial meristem- and a vascular-localized transporter associated with the trans-Golgi, and that it plays an important role in controlling the levels and distribution of ABA in growing aerial meristems and non-meristematic tissues. MATE45 promoter-GUS reporter fusions revealed the activity localized to the leaf and influorescence meristems and the vasculature. Loss-of-function mate45 mutants exhibited accelerated rates of aerial organ initiation suggesting at least partial functional conservation with the maize ortholog bige1. The aba2-1 mutant, which is deficient in ABA biosynthesis, exhibited a number of phenotypes that were rescued in the mate45-1 aba2-1 double mutant. mate45 exhibited enhanced the seed dormancy, and germination was hypersensitive to ABA. Enhanced frequency of leaf primordia growth in mate45 seedlings grown in nutrient imbalance stress was ABA-dependent. The ABA signaling reporter construct pRD29B::GUS revealed elevated levels of ABA signaling in the true leaf primordia of mate45 seedlings grown under nutritional stress, and gradually reduced signaling in surrounding cotyledon and hypocotyl tissues concomitant with reduced expressions of ABCG25. Our results suggest a role of MATE45 in reducing meristematic ABA and in maintaining ABA distribution in adjacent non-meristematic tissues.
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Affiliation(s)
- Nik Kovinich
- Center for Applied Plant Sciences and Department of Molecular GeneticsThe Ohio State UniversityColumbusOhio
- Davis College of Agriculture, Natural Resources and DesignWest Virginia UniversityMorgantownWest Virginia
- Present address:
Davis College of Agriculture, Natural Resources and DesignWest Virginia UniversityMorgantownWest Virginia
| | - Yiqun Wang
- Center for Applied Plant Sciences and Department of Molecular GeneticsThe Ohio State UniversityColumbusOhio
- Present address:
Department of Molecular and Cellular BiologyHarvard UniversityCambridgeMassachusetts
| | - Janet Adegboye
- Center for Applied Plant Sciences and Department of Molecular GeneticsThe Ohio State UniversityColumbusOhio
- Present address:
Cleveland Clinic Lerner College of MedicineClevelandOhio
| | - Alexandra A. Chanoca
- Davis College of Agriculture, Natural Resources and DesignWest Virginia UniversityMorgantownWest Virginia
- Department of Botany and Department of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsin
- Present address:
VIB‐UGENT Center for Plant Systems BiologyZwijnaardeBelgium
| | - Marisa S. Otegui
- Department of Botany and Department of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsin
- Laboratory of Molecular and Cellular BiologyUniversity of Wisconsin‐MadisonMadisonWisconsin
| | - Paige Durkin
- Davis College of Agriculture, Natural Resources and DesignWest Virginia UniversityMorgantownWest Virginia
- Present address:
West Virginia University School of DentistryMorgantownWest Virginia
| | - Erich Grotewold
- Center for Applied Plant Sciences and Department of Molecular GeneticsThe Ohio State UniversityColumbusOhio
- Present address:
Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichigan
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36
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Ouma WZ, Pogacar K, Grotewold E. Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties. PLoS Comput Biol 2018; 14:e1006098. [PMID: 29708965 PMCID: PMC5945062 DOI: 10.1371/journal.pcbi.1006098] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/10/2018] [Accepted: 03/20/2018] [Indexed: 11/30/2022] Open
Abstract
Understanding complexity in physical, biological, social and information systems is predicated on describing interactions amongst different components. Advances in genomics are facilitating the high-throughput identification of molecular interactions, and graphs are emerging as indispensable tools in explaining how the connections in the network drive organismal phenotypic plasticity. Here, we describe the architectural organization and associated emergent topological properties of gene regulatory networks (GRNs) that describe protein-DNA interactions (PDIs) in several model eukaryotes. By analyzing GRN connectivity, our results show that the anticipated scale-free network architectures are characterized by organism-specific power law scaling exponents. These exponents are independent of the fraction of the GRN experimentally sampled, enabling prediction of properties of the complete GRN for an organism. We further demonstrate that the exponents describe inequalities in transcription factor (TF)-target gene recognition across GRNs. These observations have the important biological implication that they predict the existence of an intrinsic organism-specific trans and/or cis regulatory landscape that constrains GRN topologies. Consequently, architectural GRN organization drives not only phenotypic plasticity within a species, but is also likely implicated in species-specific phenotype.
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Affiliation(s)
- Wilberforce Zachary Ouma
- Molecular and Cellular Imaging Center (MCIC), Ohio Agricultural and Research Development Center (OARDC), Ohio State University, Wooster, OH, United States of America
| | - Katja Pogacar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
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37
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Abstract
Anthocyanins are intrinsically fluorescent pigments that accumulate in plant vacuoles. We have developed a platform to analyze the fluorescence decay of anthocyanins by fluorescence lifetime imaging microscopy (FLIM), under in vitro and in vivo conditions. Fluorescence lifetime of a fluorophore can be influenced by temperature, pH, oxygen concentration, and other environmental conditions. Within plant cells, the anthocyanin fluorescence lifetime correlates with distinct subcellular compartments. Vacuolar anthocyanins exhibit shorter fluorescence lifetime than the cytoplasmic pool. Consistent with these observations, lower pH of anthocyanins solutions correlated with shorter fluorescence lifetimes. We discuss here the use of FLIM as a tool for analyzing the subcellular distribution of anthocyanins and estimating variation in vacuolar pH in intact cells.
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Affiliation(s)
- Alexandra Chanoca
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.,Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian Burkel
- Laboratory for Optical and Computational Instrumentation (LOCI), University of Wisconsin-Madison, Madison, WI, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin W Eliceiri
- Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, Madison, WI, USA.,Laboratory for Optical and Computational Instrumentation (LOCI), University of Wisconsin-Madison, Madison, WI, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA. .,Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
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38
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Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol 2017; 175:1499-1509. [PMID: 29208732 PMCID: PMC5717721 DOI: 10.1104/pp.17.01490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 05/20/2023]
Abstract
Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development.
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Affiliation(s)
- Joanna Friesner
- Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, University of California, Davis, California 95616
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802
| | - Ruth Bastow
- GARNet, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Volker Brendel
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana 47405
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Alexander Bucksch
- Department of Plant Biology, Warnell School of Forestry and Natural Resources, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Jose R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Pascal Falter-Braun
- Institute of Network Biology, Department of Environmental Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Rodrigo Gutierrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile 8331150
| | - Ute Kramer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, CNRS, INRA, Montpellier SupAgro, Université Montpellier, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier cedex, France
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, California 95616
| | - Molly Megraw
- Department of Botany and Plant Pathology, Department of Computer Science, and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132; Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A H Murray
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, United Kingdom
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Sue Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Roger Smith
- Syngenta Crop Protection, Research Triangle Park, North Carolina 27709
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, Maryland 20855
| | | | - Keiko U Torii
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, Washington 98195
| | - Chris Town
- J. Craig Venter Institute, Rockville, Maryland 20850
| | - Matthew Vaughn
- Life Sciences Computing, Texas Advanced Computing Center, Austin, Texas 78758
| | - Richard Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; U.S. Department of Agriculture Agricultural Research Service, Ithaca, New York 14853
| | - Olivia Wilkins
- Department of Plant Science, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Siobhan M Brady
- Department of Plant Biology, Genome Center, University of California, Davis, California 95616
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Abstract
Arabidopsis thaliana (Arabidopsis) seedlings often need to be grown on sterile media. This requires prior seed sterilization to prevent the growth of microbial contaminants present on the seed surface. Currently, Arabidopsis seeds are sterilized using two distinct sterilization techniques in conditions that differ slightly between labs and have not been standardized, often resulting in only partially effective sterilization or in excessive seed mortality. Most of these methods are also not easily scalable to a large number of seed lines of diverse genotypes. As technologies for high-throughput analysis of Arabidopsis continue to proliferate, standardized techniques for sterilizing large numbers of seeds of different genotypes are becoming essential for conducting these types of experiments. The response of a number of Arabidopsis lines to two different sterilization techniques was evaluated based on seed germination rate and the level of seed contamination with microbes and other pathogens. The treatments included different concentrations of sterilizing agents and times of exposure, combined to determine optimal conditions for Arabidopsis seed sterilization. Optimized protocols have been developed for two different sterilization methods: bleach (liquid-phase) and chlorine (Cl2) gas (vapor-phase), both resulting in high seed germination rates and minimal microbial contamination. The utility of these protocols was illustrated through the testing of both wild type and mutant seeds with a range of germination potentials. Our results show that seeds can be effectively sterilized using either method without excessive seed mortality, although detrimental effects of sterilization were observed for seeds with lower than optimal germination potential. In addition, an equation was developed to enable researchers to apply the standardized chlorine gas sterilization conditions to airtight containers of different sizes. The protocols described here allow easy, efficient, and inexpensive seed sterilization for a large number of Arabidopsis lines.
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Affiliation(s)
- Benson E Lindsey
- Arabidopsis Biological Resource Center, Center for Applied Plant Sciences, The Ohio State University
| | - Luz Rivero
- Arabidopsis Biological Resource Center, Center for Applied Plant Sciences, The Ohio State University
| | - Chistopher S Calhoun
- Arabidopsis Biological Resource Center, Center for Applied Plant Sciences, The Ohio State University
| | - Erich Grotewold
- Arabidopsis Biological Resource Center, Center for Applied Plant Sciences, The Ohio State University; Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, Center for Applied Plant Sciences, The Ohio State University;
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40
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Feller A, Yuan L, Grotewold E. The BIF Domain in Plant bHLH Proteins Is an ACT-Like Domain. Plant Cell 2017; 29:1800-1802. [PMID: 28747421 PMCID: PMC5590504 DOI: 10.1105/tpc.17.00356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/09/2017] [Accepted: 07/26/2017] [Indexed: 05/16/2023]
Affiliation(s)
- Antje Feller
- Center for Plant Molecular Biology-ZMBP,Developmental Genetics,University of Tuebingen,72076 Tuebingen, Germany
| | - Ling Yuan
- Department of Plant and Soil Sciences,University of Kentucky,Lexington, Kentucky 40546
- South China Botanical Garden,Guangzhou, China 510650
| | - Erich Grotewold
- Center for Applied Plant Sciences andDepartment of Molecular Genetics,The Ohio State University,Columbus, Ohio 43210
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41
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Francis D, Finer JJ, Grotewold E. Challenges and opportunities for improving food quality and nutrition through plant biotechnology. Curr Opin Biotechnol 2017; 44:124-129. [DOI: 10.1016/j.copbio.2016.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022]
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42
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McCluskey K, Boundy-Mills K, Dye G, Ehmke E, Gunnell GF, Kiaris H, Polihronakis Richmond M, Yoder AD, Zeigler DR, Zehr S, Grotewold E. The challenges faced by living stock collections in the USA. eLife 2017; 6. [PMID: 28266913 PMCID: PMC5376150 DOI: 10.7554/elife.24611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/06/2017] [Indexed: 12/16/2022] Open
Abstract
Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the need for repetitive calibration. While collections differ in many ways, they all require expertise in maintaining living organisms and good logistical systems for keeping track of stocks and fulfilling requests for specimens. Here, we review some of the contributions made by living stock collections to research across all branches of the tree of life, and outline the challenges they face. DOI:http://dx.doi.org/10.7554/eLife.24611.001
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Affiliation(s)
- Kevin McCluskey
- Department of Plant Pathology, Fungal Genetics Stock Center, Kansas State University, Manhattan, United States
| | - Kyria Boundy-Mills
- Phaff Yeast Culture Collection, Food Science and Technology, University of California, Davis, Davis, United States
| | - Greg Dye
- Duke Lemur Center, Duke University, Durham, United States
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, United States
| | | | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences and Peromyscus Genetic Stock Center, University of South Carolina, Columbia, United States
| | | | - Anne D Yoder
- Duke Lemur Center, Duke University, Durham, United States
| | - Daniel R Zeigler
- Bacillus Genetics Stock Center, The Ohio State University, Columbus, United States
| | - Sarah Zehr
- Duke Lemur Center, Duke University, Durham, United States
| | - Erich Grotewold
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, United States
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43
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Yang F, Li W, Jiang N, Yu H, Morohashi K, Ouma WZ, Morales-Mantilla DE, Gomez-Cano FA, Mukundi E, Prada-Salcedo LD, Velazquez RA, Valentin J, Mejía-Guerra MK, Gray J, Doseff AI, Grotewold E. A Maize Gene Regulatory Network for Phenolic Metabolism. Mol Plant 2017; 10:498-515. [PMID: 27871810 DOI: 10.1016/j.molp.2016.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 07/28/2016] [Revised: 09/20/2016] [Accepted: 10/31/2016] [Indexed: 05/23/2023]
Abstract
The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.
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Affiliation(s)
- Fan Yang
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Li
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Nan Jiang
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Haidong Yu
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Kengo Morohashi
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Wilberforce Zachary Ouma
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel E Morales-Mantilla
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Fabio Andres Gomez-Cano
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Mukundi
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Luis Daniel Prada-Salcedo
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Roberto Alers Velazquez
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jasmin Valentin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Maria Katherine Mejía-Guerra
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH 43560, USA
| | - Andrea I Doseff
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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44
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Iwase A, Harashima H, Ikeuchi M, Rymen B, Ohnuma M, Komaki S, Morohashi K, Kurata T, Nakata M, Ohme-Takagi M, Grotewold E, Sugimoto K. WIND1 Promotes Shoot Regeneration through Transcriptional Activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis. Plant Cell 2017; 29:54-69. [PMID: 28011694 PMCID: PMC5304349 DOI: 10.1105/tpc.16.00623] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/14/2016] [Accepted: 12/22/2016] [Indexed: 05/20/2023]
Abstract
Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown. We previously identified an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION1 (WIND1) as a central regulator of wound-induced cellular reprogramming in plants. In this study, we demonstrate that WIND1 promotes callus formation and shoot regeneration by upregulating the expression of the ENHANCER OF SHOOT REGENERATION1 (ESR1) gene, which encodes another AP2/ERF transcription factor in Arabidopsis thaliana The esr1 mutants are defective in callus formation and shoot regeneration; conversely, its overexpression promotes both of these processes, indicating that ESR1 functions as a critical driver of cellular reprogramming. Our data show that WIND1 directly binds the vascular system-specific and wound-responsive cis-element-like motifs within the ESR1 promoter and activates its expression. The expression of ESR1 is strongly reduced in WIND1-SRDX dominant repressors, and ectopic overexpression of ESR1 bypasses defects in callus formation and shoot regeneration in WIND1-SRDX plants, supporting the notion that ESR1 acts downstream of WIND1. Together, our findings uncover a key molecular pathway that links wound signaling to shoot regeneration in plants.
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Affiliation(s)
- Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | | | - Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Bart Rymen
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Mariko Ohnuma
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Shinichiro Komaki
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kengo Morohashi
- Center for Applied Plant Sciences and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Masaru Nakata
- National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8562, Japan
| | - Masaru Ohme-Takagi
- National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8562, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Erich Grotewold
- Center for Applied Plant Sciences and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
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45
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Chanoca A, Burkel B, Kovinich N, Grotewold E, Eliceiri KW, Otegui MS. Using fluorescence lifetime microscopy to study the subcellular localization of anthocyanins. Plant J 2016; 88:895-903. [PMID: 27500780 DOI: 10.1111/tpj.13297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 03/25/2016] [Revised: 07/28/2016] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Anthocyanins are flavonoid pigments that accumulate in most seed plants. They are synthesized in the cytoplasm but accumulate inside the vacuoles. Anthocyanins are pigmented at the lower vacuolar pH, but in the cytoplasm they can be visualized based on their fluorescence properties. Thus, anthocyanins provide an ideal system for the development of new methods to investigate cytoplasmic pools and association with other molecular components. We have analyzed the fluorescence decay of anthocyanins by fluorescence lifetime imaging microscopy (FLIM), in both in vitro and in vivo conditions, using wild-type and mutant Arabidopsis thaliana seedlings. Within plant cells, the amplitude-weighted mean fluorescence lifetime (τm ) correlated with distinct subcellular localizations of anthocyanins. The vacuolar pool of anthocyanins exhibited shorter τm than the cytoplasmic pool. Consistently, lowering the pH of anthocyanins in solution shortened their fluorescence decay. We propose that FLIM is a useful tool for understanding the trafficking of anthocyanins and, potentially, for estimating vacuolar pH inside intact plant cells.
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Affiliation(s)
- Alexandra Chanoca
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
- Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI, 53706, USA
| | - Brian Burkel
- Laboratory for Optical and Computational Instrumentation (LOCI), University of Wisconsin-Madison, 1675 Observatory Drive, Madison, WI, 53706, USA
| | - Nik Kovinich
- Center for Applied Plant Sciences (CAPS), Department of Molecular Genetics and Department of Horticulture and Crop Science, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Rd, Columbus, OH, 43210, USA
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS), Department of Molecular Genetics and Department of Horticulture and Crop Science, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Rd, Columbus, OH, 43210, USA
| | - Kevin W Eliceiri
- Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI, 53706, USA
- Laboratory for Optical and Computational Instrumentation (LOCI), University of Wisconsin-Madison, 1675 Observatory Drive, Madison, WI, 53706, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
- Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI, 53706, USA
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA
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46
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Affiliation(s)
- Erich Grotewold
- Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA.
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
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47
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Brkljacic J, Grotewold E. Combinatorial control of plant gene expression. Biochim Biophys Acta Gene Regul Mech 2016; 1860:31-40. [PMID: 27427484 DOI: 10.1016/j.bbagrm.2016.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 01/02/2023]
Abstract
Combinatorial gene regulation provides a mechanism by which relatively small numbers of transcription factors can control the expression of a much larger number of genes with finely tuned temporal and spatial patterns. This is achieved by transcription factors assembling into complexes in a combinatorial fashion, exponentially increasing the number of genes that they can target. Such an arrangement also increases the specificity and affinity for the cis-regulatory sequences required for accurate target gene expression. Superimposed on this transcription factor combinatorial arrangement is the increasing realization that histone modification marks expand the regulatory information, which is interpreted by histone readers and writers that are part of the regulatory apparatus. Here, we review the progress in these areas from the perspective of plant combinatorial gene regulation, providing examples of different regulatory solutions and comparing them to other metazoans. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Jelena Brkljacic
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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48
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Casas MI, Falcone-Ferreyra ML, Jiang N, Mejía-Guerra MK, Rodríguez E, Wilson T, Engelmeier J, Casati P, Grotewold E. Identification and Characterization of Maize salmon silks Genes Involved in Insecticidal Maysin Biosynthesis. Plant Cell 2016; 28:1297-309. [PMID: 27221383 PMCID: PMC4944406 DOI: 10.1105/tpc.16.00003] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/23/2016] [Indexed: 05/02/2023]
Abstract
The century-old maize (Zea mays) salmon silks mutation has been linked to the absence of maysin. Maysin is a C-glycosyl flavone that, when present in silks, confers natural resistance to the maize earworm (Helicoverpa zea), which is one of the most damaging pests of maize in America. Previous genetic analyses predicted Pericarp Color1 (P1; R2R3-MYB transcription factor) to be epistatic to the sm mutation. Subsequent studies identified two loci as being capable of conferring salmon silks phenotypes, salmon silks1 (sm1) and sm2 Benefitting from available sm1 and sm2 mapping information and from knowledge of the genes regulated by P1, we describe here the molecular identification of the Sm1 and Sm2 gene products. Sm2 encodes a rhamnosyl transferase (UGT91L1) that uses isoorientin and UDP-rhamnose as substrates and converts them to rhamnosylisoorientin. Sm1 encodes a multidomain UDP-rhamnose synthase (RHS1) that converts UDP-glucose into UDP-l-rhamnose. Here, we demonstrate that RHS1 shows unexpected substrate plasticity in converting the glucose moiety in rhamnosylisoorientin to 4-keto-6-deoxy glucose, resulting in maysin. Both Sm1 and Sm2 are direct targets of P1, as demonstrated by chromatin immunoprecipitation experiments. The molecular characterization of Sm1 and Sm2 described here completes the maysin biosynthetic pathway, providing powerful tools for engineering tolerance to maize earworm in maize and other plants.
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Affiliation(s)
- María Isabel Casas
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | | | - Nan Jiang
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - María Katherine Mejía-Guerra
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - Eduardo Rodríguez
- Instituto de Biología Molecular y Celular de Rosario, Rosario, Santa Fe S2002LRK, Argentina
| | - Tyler Wilson
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - Jacob Engelmeier
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Santa Fe S2002LRK, Argentina
| | - Erich Grotewold
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
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49
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Cardenas H, Arango D, Nicholas C, Duarte S, Nuovo GJ, He W, Voss OH, Gonzalez-Mejia ME, Guttridge DC, Grotewold E, Doseff AI. Dietary Apigenin Exerts Immune-Regulatory Activity in Vivo by Reducing NF-κB Activity, Halting Leukocyte Infiltration and Restoring Normal Metabolic Function. Int J Mol Sci 2016; 17:323. [PMID: 26938530 PMCID: PMC4813185 DOI: 10.3390/ijms17030323] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [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: 01/20/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 12/31/2022] Open
Abstract
The increasing prevalence of inflammatory diseases and the adverse effects associated with the long-term use of current anti-inflammatory therapies prompt the identification of alternative approaches to reestablish immune balance. Apigenin, an abundant dietary flavonoid, is emerging as a potential regulator of inflammation. Here, we show that apigenin has immune-regulatory activity in vivo. Apigenin conferred survival to mice treated with a lethal dose of Lipopolysaccharide (LPS) restoring normal cardiac function and heart mitochondrial Complex I activity. Despite the adverse effects associated with high levels of splenocyte apoptosis in septic models, apigenin had no effect on reducing cell death. However, we found that apigenin decreased LPS-induced apoptosis in lungs, infiltration of inflammatory cells and chemotactic factors’ accumulation, re-establishing normal lung architecture. Using NF-κB luciferase transgenic mice, we found that apigenin effectively modulated NF-κB activity in the lungs, suggesting the ability of dietary compounds to exert immune-regulatory activity in an organ-specific manner. Collectively, these findings provide novel insights into the underlying immune-regulatory mechanisms of dietary nutraceuticals in vivo.
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Affiliation(s)
- Horacio Cardenas
- Department of Physiology and Cell Biology, the Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA.
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
| | - Daniel Arango
- Department of Physiology and Cell Biology, the Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA.
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
- Molecular Cellular and Developmental Biology Graduate Program, the Ohio State University, Columbus, OH 43210, USA.
| | - Courtney Nicholas
- Department of Physiology and Cell Biology, the Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA.
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
- Molecular Cellular and Developmental Biology Graduate Program, the Ohio State University, Columbus, OH 43210, USA.
| | - Silvia Duarte
- Department of Physiology and Cell Biology, the Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA.
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
- Nutrition Graduate Program, the Ohio State University, Columbus, OH 43210, USA.
| | - Gerard J Nuovo
- Comprehensive Cancer Center, the Ohio State University, Columbus, OH 43210, USA.
| | - Wei He
- Molecular Cellular and Developmental Biology Graduate Program, the Ohio State University, Columbus, OH 43210, USA.
- Comprehensive Cancer Center, the Ohio State University, Columbus, OH 43210, USA.
| | - Oliver H Voss
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
| | - M Elba Gonzalez-Mejia
- Department of Physiology and Cell Biology, the Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA.
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
| | - Denis C Guttridge
- Comprehensive Cancer Center, the Ohio State University, Columbus, OH 43210, USA.
| | - Erich Grotewold
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
- Center for Applied Plant Sciences, the Ohio State University, Columbus, OH 43210, USA.
| | - Andrea I Doseff
- Department of Physiology and Cell Biology, the Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA.
- Department of Molecular Genetics, the Ohio State University, Columbus, OH 43210, USA.
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50
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Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. New Phytol 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
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