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Voichek Y, Hristova G, Mollá-Morales A, Weigel D, Nordborg M. Widespread position-dependent transcriptional regulatory sequences in plants. Nat Genet 2024:10.1038/s41588-024-01907-3. [PMID: 39266765 DOI: 10.1038/s41588-024-01907-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 08/13/2024] [Indexed: 09/14/2024]
Abstract
Much of what we know about eukaryotic transcription stems from animals and yeast; however, plants evolved separately for over a billion years, leaving ample time for divergence in transcriptional regulation. Here we set out to elucidate fundamental properties of cis-regulatory sequences in plants. Using massively parallel reporter assays across four plant species, we demonstrate the central role of sequences downstream of the transcription start site (TSS) in transcriptional regulation. Unlike animal enhancers that are position independent, plant regulatory elements depend on their position, as altering their location relative to the TSS significantly affects transcription. We highlight the importance of the region downstream of the TSS in regulating transcription by identifying a DNA motif that is conserved across vascular plants and is sufficient to enhance gene expression in a dose-dependent manner. The identification of a large number of position-dependent enhancers points to fundamental differences in gene regulation between plants and animals.
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Affiliation(s)
- Yoav Voichek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| | - Gabriela Hristova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Almudena Mollá-Morales
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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2
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Macgregor SR, Beronilla PKS, Goring DR. The Arabidopsis SNARE complex genes regulate the early stages of pollen-stigma interactions. PLANT REPRODUCTION 2024; 37:309-320. [PMID: 38038738 DOI: 10.1007/s00497-023-00488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023]
Abstract
KEY MESSAGE The VAMP721, VAMP722, SYP121, SYP122 and SNAP33 SNAREs are required in the Arabidopsis stigma for pollen hydration, further supporting a role for vesicle trafficking in the stigma's pollen responses. In the Brassicaceae, the process of accepting compatible pollen is a key step in successful reproduction and highly regulated following interactions between the pollen and the stigma. Central to this is the initiation of secretion in the stigma, which is proposed to provide resources to the pollen for hydration and germination and pollen tube growth. Previously, the eight exocyst subunit genes were shown to be required in the Arabidopsis stigma to support these pollen responses. One of the roles of the exocyst is to tether secretory vesicles at the plasma membrane for membrane fusion by the SNARE complex to enable vesicle cargo release. Here, we investigate the role of Arabidopsis SNARE genes in the stigma for pollen responses. Using a combination of different knockout and knockdown SNARE mutant lines, we show that VAMP721, VAMP722, SYP121, SYP122 and SNAP33 are involved in this process. Significant disruptions in pollen hydration were observed following pollination of wildtype pollen on the mutant SNARE stigmas. Overall, these results place the Arabidopsis SNARE complex as a contributor in the stigma for pollen responses and reaffirm the significance of secretion in the stigma to support the pollen-stigma interactions.
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Affiliation(s)
- Stuart R Macgregor
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2, Canada
- Faculty of Science, York University, Toronto, Canada
| | - Paula K S Beronilla
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Daphne R Goring
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2, Canada.
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, M5S 3B2, Canada.
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3
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Joshi K, Ahmed S, Ge L, Avestakh A, Oloyede B, Phuntumart V, Kalinoski A, Morris PF. Spatial organization of putrescine synthesis in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112232. [PMID: 39214468 DOI: 10.1016/j.plantsci.2024.112232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Three plant pathways for the synthesis of putrescine have been described to date. These are the synthesis of putrescine from ornithine, by ornithine decarboxylase (ODC); the synthesis of putrescine from arginine by arginine decarboxylase, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (NLP1); and arginine decarboxylase and agmatinase. To address how these pathways are organized in plants, we have used transient expression analysis of these genes in the leaves of Nicotiana benthamiana. Brassicas do not have ODC, but the single ODC gene from rice and one of the soybean genes, were localized to the ER. Transient expression of the rice agmatinase gene showed that it was localized to the mitochondria. In A. thaliana there are five isoforms of AIH and three isoforms of NLP1. Stable GFP-tagged transformants of the longest isoforms of AIH and NLP1 showed that both proteins were localized to the ER, but in tissues with chloroplasts, the localization was concentrated to lamellae adjacent to chloroplasts. Transient expression analyses showed that four of the isoforms of AIH and all of the isoforms of NLP1 were localized to the ER. However, AIH.4 was localized to the chloroplast. Combining these results with other published data, reveal that putrescine synthesis is excluded from the cytoplasm and is spatially localized to the chloroplast, ER, and likely the mitochondria. Synthesis of putrescine in the ER may facilitate cell to cell transport via plasmodesmata, or secretion via vesicles. Differential expression of these pathways may enable putrescine-mediated activation of hormone-responsive genes.
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Affiliation(s)
- Kumud Joshi
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Sheaza Ahmed
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Lingxiao Ge
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Arefeh Avestakh
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Babatunde Oloyede
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Andrea Kalinoski
- Department of Surgery, University of Toledo, 3000 Arlington Ave., Toledo, USA
| | - Paul F Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
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4
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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. THE PLANT CELL 2024; 36:2512-2530. [PMID: 38635902 PMCID: PMC11218782 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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5
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Kulesza E, Thomas P, Prewitt SF, Shalit-Kaneh A, Wafula E, Knollenberg B, Winters N, Esteban E, Pasha A, Provart N, Praul C, Landherr L, dePamphilis C, Maximova SN, Guiltinan MJ. The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L. BMC PLANT BIOLOGY 2024; 24:601. [PMID: 38926852 PMCID: PMC11201900 DOI: 10.1186/s12870-024-05171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/19/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RESULTS We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues. CONCLUSION The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
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Affiliation(s)
- Evelyn Kulesza
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Patrick Thomas
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah F Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- USDA Animal and Plant Health Inspection Service (APHIS), Riverdale, MD, 20737, USA
| | - Akiva Shalit-Kaneh
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Plant Sciences, Volcani-ARO (Agricultural and Rural Organization), Gilat, Israel
| | - Eric Wafula
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Benjamin Knollenberg
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Mars Inc, Davis, CA, 95616, USA
| | - Noah Winters
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Eddi Esteban
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Nicholas Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Craig Praul
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lena Landherr
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Claude dePamphilis
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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Lee HK, Canales Sanchez LE, Bordeleau SJ, Goring DR. Arabidopsis leucine-rich repeat malectin receptor-like kinases regulate pollen-stigma interactions. PLANT PHYSIOLOGY 2024; 195:343-355. [PMID: 38270530 DOI: 10.1093/plphys/kiae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Flowering plants contain tightly controlled pollen-pistil interactions required for promoting intraspecific fertilization and preventing interspecific hybridizations. In Arabidopsis (Arabidopsis thaliana), several receptor kinases (RKs) are known to regulate the later stages of intraspecific pollen tube growth and ovular reception in the pistil, but less is known about RK regulation of the earlier stages. The Arabidopsis RECEPTOR-LIKE KINASE IN FLOWERS1 (RKF1)/RKF1-LIKE (RKFL) 1-3 cluster of 4 leucine-rich repeat malectin (LRR-MAL) RKs was previously found to function in the stigma to promote intraspecific pollen hydration. In this study, we tested additional combinations of up to 7 Arabidopsis LRR-MAL RK knockout mutants, including RKF1, RKFL1-3, LysM RLK1-INTERACTING KINASE1, REMORIN-INTERACTING RECEPTOR1, and NEMATODE-INDUCED LRR-RLK2. These LRR-MAL RKs were discovered to function in the female stigma to support intraspecific Arabidopsis pollen tube growth and to establish a prezygotic interspecific barrier against Capsella rubella pollen. Thus, this study uncovered additional biological functions for this poorly understood group of RKs in regulating the early stages of Arabidopsis sexual reproduction.
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Affiliation(s)
- Hyun Kyung Lee
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | | | - Stephen J Bordeleau
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Daphne R Goring
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada
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7
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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Smolko A, Repar J, Matković M, Pavlović I, Pěnčík A, Novák O, Ludwig-Müller J, Salopek-Sondi B. Application of Long-Chained Auxin Conjugates Influenced Auxin Metabolism and Transcriptome Response in Brassica rapa L. ssp. pekinensis. Int J Mol Sci 2023; 25:447. [PMID: 38203617 PMCID: PMC10778880 DOI: 10.3390/ijms25010447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Auxin amino acid conjugates are considered to be storage forms of auxins. Previous research has shown that indole-3-acetyl-L-alanine (IAA-Ala), indole-3-propionyl-L-alanine (IPA-Ala) and indole-3-butyryl-L-alanine (IBA-Ala) affect the root growth of Brassica rapa seedlings. To elucidate the potential mechanism of action of the conjugates, we treated B. rapa seedlings with 0.01 mM IAA-, IPA- and IBA-Ala and investigated their effects on the auxin metabolome and transcriptome. IBA-Ala and IPA-Ala caused a significant inhibition of root growth and a decrease in free IAA compared to the control and IAA-Ala treatments. The identification of free auxins IBA and IPA after feeding experiments with IBA-Ala and IPA-Ala, respectively, confirms their hydrolysis in vivo and indicates active auxins responsible for a stronger inhibition of root growth. IBA-Ala caused the induction of most DEGs (807) compared to IPA-Ala (417) and IAA-Ala (371). All treatments caused similar trends in transcription profile changes when compared to control treatments. The majority of auxin-related DEGs were found after IBA-Ala treatment, followed by IPA-Ala and IAA-Ala, which is consistent with the apparent root morphology. In addition to most YUC genes, which showed a tendency to be downregulated, transcripts of auxin-related DEGs that were identified (UGT74E2, GH3.2, SAUR, IAA2, etc.) were more highly expressed after all treatments. Our results are consistent with the hypothesis that the hydrolysis of conjugates and the release of free auxins are responsible for the effects of conjugate treatments. In conclusion, free auxins released by the hydrolysis of all auxin conjugates applied affect gene regulation, auxin homeostasis and ultimately root growth inhibition.
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Affiliation(s)
- Ana Smolko
- Department for Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.S.); (J.R.)
| | - Jelena Repar
- Department for Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.S.); (J.R.)
| | - Marija Matković
- Department for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Iva Pavlović
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (I.P.); (A.P.); (O.N.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (I.P.); (A.P.); (O.N.)
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (I.P.); (A.P.); (O.N.)
| | - Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany;
| | - Branka Salopek-Sondi
- Department for Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.S.); (J.R.)
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9
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Kileeg Z, Haldar A, Khan H, Qamar A, Mott GA. Differential expansion and retention patterns of LRR-RLK genes across plant evolution. PLANT DIRECT 2023; 7:e556. [PMID: 38145254 PMCID: PMC10739070 DOI: 10.1002/pld3.556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/03/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
Abstract
To maximize overall fitness, plants must accurately respond to a host of growth, developmental, and environmental signals throughout their life. Many of these internal and external signals are perceived by the leucine-rich repeat receptor-like kinases, which play roles in regulating growth, development, and immunity. This largest family of receptor kinases in plants can be divided into subfamilies based on the conservation of the kinase domain, which demonstrates that shared evolutionary history often indicates shared molecular function. Here we investigate the evolutionary history of this family across the evolution of 112 plant species. We identify lineage-specific expansions of the malectin-domain containing subfamily LRR subfamily I primarily in the Brassicales and bryophytes. Most other plant lineages instead show a large expansion in LRR subfamily XII, which in Arabidopsis is known to contain key receptors in pathogen perception. This striking asymmetric expansion may reveal a dichotomy in the evolutionary history and adaptation strategies employed by plants. A greater understanding of the evolutionary pressures and adaptation strategies acting on members of this receptor family offers a way to improve functional predictions for orphan receptors and simplify the identification of novel stress-related receptors.
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Affiliation(s)
- Zachary Kileeg
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Aparna Haldar
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Hasna Khan
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Arooj Qamar
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
| | - G. Adam Mott
- Department of Biological SciencesUniversity of Toronto ‐ ScarboroughTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
- Centre for the Analysis of Genome Evolution & FunctionUniversity of TorontoTorontoCanada
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10
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Chao H, Zhang S, Hu Y, Ni Q, Xin S, Zhao L, Ivanisenko VA, Orlov YL, Chen M. Integrating omics databases for enhanced crop breeding. J Integr Bioinform 2023; 20:jib-2023-0012. [PMID: 37486120 PMCID: PMC10777369 DOI: 10.1515/jib-2023-0012] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Crop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes underlying plant traits and their interactions. This review highlights the importance of integrating omics databases in crop plant breeding, discusses available omics data and databases, describes integration challenges, and highlights recent developments and potential benefits. Taken together, the integration of omics databases is a critical step towards enhancing crop plant breeding and improving global food security.
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Affiliation(s)
- Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Shilong Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Saige Xin
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Liang Zhao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk630090, Russia
| | - Yuriy L. Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk630090, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, Moscow117198, Russia
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow119991, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
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11
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Bakshi A, Choi WG, Kim SH, Gilroy S. The vacuolar Ca 2+ transporter CATION EXCHANGER 2 regulates cytosolic calcium homeostasis, hypoxic signaling, and response to flooding in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2023; 240:1830-1847. [PMID: 37743731 DOI: 10.1111/nph.19274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
Flooding represents a major threat to global agricultural productivity and food security, but plants are capable of deploying a suite of adaptive responses that can lead to short- or longer-term survival to this stress. One cellular pathway thought to help coordinate these responses is via flooding-triggered Ca2+ signaling. We have mined publicly available transcriptomic data from Arabidopsis subjected to flooding or low oxygen stress to identify rapidly upregulated, Ca2+ -related transcripts. We then focused on transporters likely to modulate Ca2+ signals. Candidates emerging from this analysis included AUTOINHIBITED Ca2+ ATPASE 1 and CATION EXCHANGER 2. We therefore assayed mutants in these genes for flooding sensitivity at levels from growth to patterns of gene expression and the kinetics of flooding-related Ca2+ changes. Knockout mutants in CAX2 especially showed enhanced survival to soil waterlogging coupled with suppressed induction of many marker genes for hypoxic response and constitutive activation of others. CAX2 mutants also generated larger and more sustained Ca2+ signals in response to both flooding and hypoxic challenges. CAX2 is a Ca2+ transporter located on the tonoplast, and so these results are consistent with an important role for vacuolar Ca2+ transport in the signaling systems that trigger flooding response.
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Affiliation(s)
- Arkadipta Bakshi
- Department of Botany, University of Wisconsin, Birge Hall, 430 Lincoln Dr., Madison, WI, 53706, USA
| | - Won-Gyu Choi
- Department of Biochemistry and Molecular Biology, 1664 N. Virginia St, Reno, NV, 89557, USA
| | - Su-Hwa Kim
- Department of Biochemistry and Molecular Biology, 1664 N. Virginia St, Reno, NV, 89557, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Birge Hall, 430 Lincoln Dr., Madison, WI, 53706, USA
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12
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Kerbler SML, Armijos-Jaramillo V, Lunn JE, Vicente R. The trehalose 6-phosphate phosphatase family in plants. PHYSIOLOGIA PLANTARUM 2023; 175:e14096. [PMID: 38148193 DOI: 10.1111/ppl.14096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/15/2023] [Accepted: 11/12/2023] [Indexed: 12/28/2023]
Abstract
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signalling metabolite linking plant growth and development to carbon metabolism. While recent work has focused predominantly on the enzymes that produce Tre6P, little is known about the proteins that catalyse its degradation, the trehalose 6-phosphate phosphatases (TPPs). Often occurring in large protein families, TPPs exhibit cell-, tissue- and developmental stage-specific expression patterns, suggesting important regulatory functions in controlling local levels of Tre6P and trehalose as well as Tre6P signalling. Furthermore, growing evidence through gene expression studies and transgenic approaches shows that TPPs play an important role in integrating environmental signals with plant metabolism. This review highlights the large diversity of TPP isoforms in model and crop plants and identifies how modulating Tre6P metabolism in certain cell types, tissues, and at different developmental stages may promote stress tolerance, resilience and increased crop yield.
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Affiliation(s)
- Sandra Mae-Lin Kerbler
- Leibniz-Institute für Gemüse- und Zierpflanzenbau, Groβbeeren, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Vinicio Armijos-Jaramillo
- Grupo de Bio-Quimioinformática, Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rubén Vicente
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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13
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Williams CJ, Dai D, Tran KA, Monroe JG, Williams BP. Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants. Genome Biol 2023; 24:227. [PMID: 37828516 PMCID: PMC10571256 DOI: 10.1186/s13059-023-03059-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear. RESULTS We report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range in drdd mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity. CONCLUSIONS We propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.
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Affiliation(s)
- Clara J Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Dawei Dai
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Kevin A Tran
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California, Davis, USA
| | - Ben P Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA.
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14
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Wang J, Eulgem T. The Arabidopsis RRM domain proteins EDM3 and IBM2 coordinate the floral transition and basal immune responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:128-143. [PMID: 37347678 DOI: 10.1111/tpj.16364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
The transition from vegetative to reproductive development (floral transition) is a costly process in annual plants requiring increased investments in metabolic resources. The Arabidopsis thaliana (Arabidopsis) PHD finger protein EDM2 and RRM domain proteins EDM3 and IBM2 are known to form chromatin-associated complexes controlling transcript processing. We are reporting that distinct splice isoforms of EDM3 and IBM2 cooperate in the coordination of the floral transition with basal immune responses. These cooperating splice isoforms, termed EDM3L and IBM2L, control the intensity of basal immunity and, via a separate pathway, the timing of the floral transition. During the developmental phase prior to the floral transition expression of EDM3L and IBM2L strongly and gradually increases, while these isoforms simultaneously down-regulate expression of the floral suppressor gene FLC and promote the transition to reproductive growth. At the same time these accumulating EDM3 and IBM2 splice isoforms gradually suppress basal immunity against the virulent Noco2 isolate of the pathogenic oomycete Hyaloperonospora arabidopsidis and down-regulate expression of a set of defense-associated genes and immune receptor genes. We are providing clear evidence for a functional link between the floral transition and basal immunity in the annual plant Arabidopsis. Coordination of these two biological processes, which compete for metabolic resources, is likely critical for plant survival and reproductive success.
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Affiliation(s)
- Jianqiang Wang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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15
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Devendrakumar KT, Copeland C, Adamchek C, Zhong X, Huang X, Gendron JM, Li X. Arabidopsis Tubby domain-containing F-box proteins positively regulate immunity by modulating PI4Kβ protein levels. THE NEW PHYTOLOGIST 2023; 240:354-371. [PMID: 37571862 PMCID: PMC11114105 DOI: 10.1111/nph.19187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/30/2023] [Indexed: 08/13/2023]
Abstract
The Tubby domain, named after the TUBBY protein in mice, binds to phosphatidylinositol 4,5-bisphosphate. Arabidopsis has 11 Tubby domain-containing proteins referred to as Tubby-Like Proteins (TLPs). Of the 11 TLPs, 10 possess the N-terminal F-box domain, which can interact with SKP-like proteins and form SKP1-Cullin-F-box E3 ligase complexes. Although mice TUBBY has been extensively studied, plant TLPs' functions are scarcely detailed. In this study, we show that the Arabidopsis Tubby-like protein 6 (TLP6) and its redundant homologs, TLP1, TLP2, TLP5, and TLP10, positively regulate Arabidopsis immune responses. Furthermore, in an immunoprecipitation mass spectrometry analysis to search for ubiquitination substrates of the TLPs, we identified two redundant phosphoinositide biosynthesis enzymes, phosphatidylinositol 4-kinase β proteins (PI4Kβs), PI4Kβ1 and PI4Kβ2, as TLP interactors. Importantly, TLP6 overexpression lines fully phenocopy the phenotypes of the pi4kβ1,2 mutant, while TLP6 overexpression also leads to increased PI4Kβ2 ubiquitination and reduction in its protein level in a proteasome-dependent manner. Most significantly, TLP6 overexpression does not further enhance the autoimmunity of the pi4kβ1,2 double mutant, supporting the hypothesis that TLP6 targets the PI4Kβs for ubiquitination and degradation. Thus, our study reveals a novel mechanism where TLPs promote plant immune responses by modulating the PI4Kβs protein levels.
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Affiliation(s)
- Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Charles Copeland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christopher Adamchek
- Yale Science Building, Yale University, 260 Whitney Ave, New Haven, CT 06511, USA
| | - Xionghui Zhong
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xingchuan Huang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Joshua M. Gendron
- Yale Science Building, Yale University, 260 Whitney Ave, New Haven, CT 06511, USA
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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16
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Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1486-1499. [PMID: 37309871 PMCID: PMC10598807 DOI: 10.1111/tpj.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Advances in single-cell epigenomics have revolutionized the field of identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single-cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges, and common pitfalls in the analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.
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Affiliation(s)
| | - Ankush Sangra
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Mark A A Minow
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
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17
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Chen YL, Lin FW, Cheng KT, Chang CH, Hung SC, Efferth T, Chen YR. XCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis. Nat Commun 2023; 14:4697. [PMID: 37542077 PMCID: PMC10403534 DOI: 10.1038/s41467-023-40406-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Proteolytic activation of cytokines regulates immunity in diverse organisms. In animals, cysteine-dependent aspartate-specific proteases (caspases) play central roles in cytokine maturation. Although the proteolytic production of peptide cytokines is also essential for plant immunity, evidence for cysteine-dependent aspartate-specific proteases in regulating plant immunity is still limited. In this study, we found that the C-terminal proteolytic processing of a caspase-like substrate motif "CNYD" within Pathogenesis-related protein 1 (PR1) generates an immunomodulatory cytokine (CAPE9) in Arabidopsis. Salicylic acid enhances CNYD-targeted protease activity and the proteolytic release of CAPE9 from PR1 in Arabidopsis. This process involves a protease exhibiting caspase-like enzyme activity, identified as Xylem cysteine peptidase 1 (XCP1). XCP1 exhibits a calcium-modulated pH-activity profile and a comparable activity to human caspases. XCP1 is required to induce systemic immunity triggered by pathogen-associated molecular patterns. This work reveals XCP1 as a key protease for plant immunity, which produces the cytokine CAPE9 from the canonical salicylic acid signaling marker PR1 to activate systemic immunity.
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Affiliation(s)
- Ying-Lan Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Fan-Wei Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Kai-Tan Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chi-Hsin Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Taiwan Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Sheng-Chi Hung
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Taiwan Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 402, Taiwan.
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
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18
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Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M. Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107895. [PMID: 37478728 DOI: 10.1016/j.plaphy.2023.107895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Glutamate dehydrogenase (GDH) is an enzyme at the crossroad of plant nitrogen and carbon metabolism. GDH catalyzes the conversion of 2-oxoglutarate into glutamate (2OG → Glu), utilizing ammonia as cosubstrate and NADH as coenzyme. The GDH reaction is reversible, meaning that the NAD+-dependent reaction (Glu → 2OG) releases ammonia. In Arabidopsis thaliana, three GDH isoforms exist, AtGDH1, AtGDH2, and AtGDH3. The subject of this work is AtGDH2. Previous reports have suggested that enzymes homologous to AtGDH2 contain a calcium-binding EF-hand motif located in the coenzyme binding domain. Here, we show that while AtGDH2 indeed does bind calcium, the binding occurs elsewhere and the region predicted to be the EF-hand motif has a completely different structure. As the true calcium binding site is > 20 Å away from the active site, it seems to play a structural, rather than catalytic role. We also performed comparative kinetic characterization of AtGDH1 and AtGDH2 using spectroscopic methods and isothermal titration calorimetry, to note that the isoenzymes generally exhibit similar behavior, with calcium having only a minor effect. However, the spatial and temporal changes in the gene expression profiles of the three AtGDH genes point to AtGDH2 as the most prevalent isoform.
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Affiliation(s)
- Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Joanna Sliwiak
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Mariusz Jaskolski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland; Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland.
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19
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Cui M, Gupta SK, Bauer P. Role of the plant-specific calcium-binding C2-DOMAIN ABSCISIC ACID-RELATED (CAR) protein family in environmental signaling. Eur J Cell Biol 2023; 102:151322. [PMID: 37211005 DOI: 10.1016/j.ejcb.2023.151322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
Many signaling processes rely on information decoding at the plasma membrane, and membrane-associated proteins and their complexes are fundamental for regulating this process. Still many questions exist as to how protein complexes are assembled and function at membrane sites to change identity and dynamics of membrane systems. Peripheral membrane proteins containing a calcium and phospholipid-binding C2-domain can act in membrane-related signaling by providing a tethering function so that protein complexes form. C2 domain proteins termed C2-DOMAIN ABSCISIC ACID-RELATED (CAR) proteins are plant-specific, and the functional relevance of this C2 domain protein subgroup is just emerging. The ten Arabidopsis CAR proteins CAR1 to CAR10 have a single C2 domain with a plant-specific insertion, the so-called "CAR-extra-signature" or also termed "sig domain". Via this "sig domain" CAR proteins can bind signaling protein complexes of different kinds and act in biotic and abiotic stress, blue light and iron nutrition. Interestingly, CAR proteins can oligomerize in membrane microdomains, and their presence in the nucleus can be linked with nuclear protein regulation. This shows that CAR proteins may play unprecedented roles in coordinating environmental responses and assembling required protein complexes to transmit information cues between plasma membrane and nucleus. The aim of this review is to summarize structure-function characteristics of the CAR protein family and assemble findings from CAR protein interactions and physiological functions. From this comparative investigation we extract common principles about the molecular operations that CAR proteins may fulfill in the cell. We also deduce functional properties of the CAR protein family based on its evolution and gene expression profiles. We highlight open questions and suggest novel avenues to prove and understand the functional networks and roles played by this protein family in plants.
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Affiliation(s)
- Mingming Cui
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Shishir K Gupta
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany; Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany; Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany.
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20
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Jiang Y, N'Diaye A, Koh CS, Quilichini TD, Shunmugam ASK, Kirzinger MW, Konkin D, Bekkaoui Y, Sari E, Pasha A, Esteban E, Provart NJ, Higgins JD, Rozwadowski K, Sharpe AG, Pozniak CJ, Kagale S. The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:209-224. [PMID: 36710629 DOI: 10.1111/tpj.16125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.
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Affiliation(s)
- Yunfei Jiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Arun S K Shunmugam
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Morgan W Kirzinger
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Ehsan Sari
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Kevin Rozwadowski
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Pl., Saskatoon, SK, S7N 0X2, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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21
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Ferela A, Debernardi JM, Rosatti S, Liebsch D, Schommer C, Palatnik JF. Interplay among ZF-HD and GRF transcription factors during Arabidopsis leaf development. PLANT PHYSIOLOGY 2023; 191:1789-1802. [PMID: 36652435 PMCID: PMC10022616 DOI: 10.1093/plphys/kiad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The growth-regulating factor (GRF) family of transcriptional factors are involved in the control of leaf size and senescence, inflorescence and root growth, grain size, and plant regeneration. However, there is limited information about the genes regulated by these transcriptional factors, which are in turn responsible for their functions. Using a meta-analysis approach, we identified genes encoding Arabidopsis (Arabidopsis thaliana) zinc-finger homeodomain (ZF-HD) transcriptional factors, as potential targets of the GRFs. We further showed that GRF3 binds to the promoter of one of the members of the ZF-HD family, HOMEOBOX PROTEIN 33 (HB33), and activates its transcription. Increased levels of HB33 led to different modifications in leaf cell number and size that were dependent on its expression levels. Furthermore, we found that expression of HB33 for an extended period during leaf development increased leaf longevity. To cope with the functional redundancy among ZF-HD family members, we generated a dominant repressor version of HB33, HB33-SRDX. Expression of HB33-SRDX from HB33 regulatory regions was seedling-lethal, revealing the importance of the ZF-HD family in plant development. Misexpression of HB33-SRDX in early leaf development caused a reduction in both cell size and number. Interestingly, the loss-of-function of HB33 in lines carrying a GRF3 allele insensitive to miR396 reverted the delay in leaf senescence characteristic of these plants. Our results revealed functions for ZF-HDs in leaf development and linked them to the GRF pathway.
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Affiliation(s)
- Antonella Ferela
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Juan Manuel Debernardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Santiago Rosatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Daniela Liebsch
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Carla Schommer
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina
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22
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Fahlgren N, Kapoor M, Yordanova G, Papatheodorou I, Waese J, Cole B, Harrison P, Ware D, Tickle T, Paten B, Burdett T, Elsik CG, Tuggle CK, Provart NJ. Toward a data infrastructure for the Plant Cell Atlas. PLANT PHYSIOLOGY 2023; 191:35-46. [PMID: 36200899 PMCID: PMC9806565 DOI: 10.1093/plphys/kiac468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.
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Affiliation(s)
- Noah Fahlgren
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132, USA
| | - Muskan Kapoor
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | | | | | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, 1, Cyclotron Road, Berkeley, California 94720, USA
| | - Peter Harrison
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Doreen Ware
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Timothy Tickle
- Data Sciences Platform, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, Baskin School of Engineering, 1156 High Street, Santa Cruz, California 95064, USA
| | - Tony Burdett
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christine G Elsik
- Division of Animal Sciences/Division of Plant Science & Technology/Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Christopher K Tuggle
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - 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
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23
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Lau V, Provart NJ. AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis. Methods Mol Biol 2023; 2698:351-360. [PMID: 37682484 DOI: 10.1007/978-1-0716-3354-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Gene regulatory networks (GRNs) are important for determining how an organism develops and how it responds to external stimuli. In the case of Arabidopsis thaliana, several GRNs have been identified covering many important biological processes. We present AGENT, the Arabidopsis GEne Network Tool, for exploring and analyzing published GRNs. Using tools in AGENT, regulatory motifs such as feed-forward loops can be easily identified. Nodes with high centrality-and hence importance-can likewise be identified. Gene expression data can also be overlaid onto GRNs to help discover subnetworks acting in specific tissues or under certain conditions.
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Affiliation(s)
- Vincent Lau
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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24
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Gouesbet G. Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis. Methods Mol Biol 2023; 2642:257-294. [PMID: 36944884 DOI: 10.1007/978-1-0716-3044-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Plant functioning and responses to abiotic stresses largely involve regulations at the transcriptomic level via complex interactions of signal molecules, signaling cascades, and regulators. Nevertheless, all the signaling networks involved in responses to abiotic stresses have not yet been fully established. The in-depth analysis of transcriptomes in stressed plants has become a relevant state-of-the-art methodology to study these regulations and signaling pathways that allow plants to cope with or attempt to survive abiotic stresses. The plant science and molecular biology community has developed databases about genes, proteins, protein-protein interactions, protein-DNA interactions and ontologies, which are valuable sources of knowledge for deciphering such regulatory and signaling networks. The use of these data and the development of bioinformatics tools help to make sense of transcriptomic data in specific contexts, such as that of abiotic stress signaling, using functional biological approaches. The aim of this chapter is to present and assess some of the essential online tools and resources that will allow novices in bioinformatics to decipher transcriptomic data in order to characterize the cellular processes and functions involved in abiotic stress responses and signaling. The analysis of case studies further describes how these tools can be used to conceive signaling networks on the basis of transcriptomic data. In these case studies, particular attention was paid to the characterization of abiotic stress responses and signaling related to chemical and xenobiotic stressors.
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Affiliation(s)
- Gwenola Gouesbet
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Evolution)] - UMR 6553, Rennes, France.
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25
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Castro PH, Santos MÂ, Magalhães AP, Tavares RM, Azevedo H. Bioinformatic Tools for Exploring the SUMO Gene Network: An Update. Methods Mol Biol 2023; 2581:367-383. [PMID: 36413331 DOI: 10.1007/978-1-0716-2784-6_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plant sumoylation research has seen significant advances in recent years, particularly since high-throughput proteomic strategies have enabled the discovery of more than one thousand SUMO targets. In the present chapter, we update the previously reported SUMO (small ubiquitin-related modifier) gene network (SGN) to its v4 iteration. SGN is a curated assembly of Arabidopsis thaliana genes that have been functionally associated with sumoylation, from SUMO pathway components to targets and interactors. The enclosed tutorial helps interpret and manage these datasets and details bioinformatic tools that can be used for in silico-based hypothesis generation. The latter include tools for sumoylation site prediction, comparative genomics, and gene network analysis.
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Affiliation(s)
- Pedro Humberto Castro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal.
| | - Miguel Ângelo Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal
- Crops Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alexandre Papadopoulos Magalhães
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal
- Max-Planck Institute for Molecular Genetics, Department of Genome Regulation, Ihnestr, Berlin, Germany
| | - Rui Manuel Tavares
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal
- Centre of Molecular and Environmental Biology (CBMA), School of Sciences, University of Minho, Braga, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
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Isolation of Salvia miltiorrhiza Kaurene Synthase-like ( KSL) Gene Promoter and Its Regulation by Ethephon and Yeast Extract. Genes (Basel) 2022; 14:genes14010054. [PMID: 36672795 PMCID: PMC9859234 DOI: 10.3390/genes14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The presented study describes the regulation of the promoter region of the Salvia miltiorrhiza kaurene synthase-like gene (SmKSL) by ethylene and yeast extract. The isolated fragment is 897 bp and is composed of a promoter (763 bp), 5'UTR (109 bp), and a short CDS (25 bp). The initial in silico analysis revealed the presence of numerous putative cis-active sites for trans-factors responding to different stress conditions. However, this study examines the influence of ethylene and yeast extract on SmKSL gene expression and tanshinone biosynthesis regulation. The results of 72h RT-PCR indicate an antagonistic interaction between ethylene, provided as ethephon (0.05, 0.10, 0.25, and 0.50 mM), and yeast extract (0.5%) on SmKSL gene expression in callus cultures of S. miltiorrhiza. A similar antagonistic effect was observed on total tanshinone concentration for up to 60 days. Ethylene provided as ethephon (0.05, 0.10, 0.25, and 0.50 mM) is a weak inducer of total tanshinone biosynthesis, increasing them only up to the maximum value of 0.67 ± 0.04 mg g-1 DW (60-day induction with 0.50 mM ethephon). Among the tanshinones elicited by ethephon, cryptotanshinone (52.21%) dominates, followed by dihydrotanshinone (45.00%) and tanshinone IIA (3.79%). In contrast, the 0.5% yeast extract strongly increases the total tanshinone concentration up to a maximum value of 13.30 ± 1.09 mg g-1 DW, observed after 50 days of induction. Yeast extract and ethylene appear to activate different fragments of the tanshinone biosynthesis route; hence the primary tanshinones induced by yeast extract were cryptotanshinone (81.42%), followed by dihydrotanshinone (17.06%) and tanshinone IIA (1.52%).
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27
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Nogués I, Sekula B, Angelaccio S, Grzechowiak M, Tramonti A, Contestabile R, Ruszkowski M. Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 187:37-49. [PMID: 35947902 DOI: 10.1016/j.plaphy.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Serine hydroxymethyltransferase (SHM) is one of the hallmarks of one-carbon metabolism. In plants, isoforms of SHM participate in photorespiration and/or transfer the one-carbon unit from L-serine to tetrahydrofolate (THF), hence producing 5,10-CH2-THF that is needed, e.g., for biosynthesis of methionine, thymidylate, and purines. These links highlight the importance of SHM activity in DNA biogenesis, its epigenetic methylations, and in stress responses. Plant genomes encode several SHM isoforms that localize to cytosol, mitochondria, plastids, and nucleus. In this work, we present a thorough functional and structural characterization of all seven SHM isoforms from Arabidopsis thaliana (AtSHM1-7). In particular, we analyzed tissue-specific expression profiles of the AtSHM genes. We also compared catalytic properties of the active AtSHM1-4 in terms of catalytic efficiency in both directions and inhibition by the THF substrate. Despite numerous attempts to rescue the SHM activity of AtSHM5-7, we failed, which points towards different physiological functions of these isoforms. Comparative analysis of experimental and predicted three-dimensional structures of AtSHM1-7 proteins indicated differences in regions that surround the entrance to the active site cavity.
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Affiliation(s)
- Isabel Nogués
- Research Institute on Terrestrial Ecosystems, Italian National Research Council, Monterotondo Scalo, Rome, Italy
| | - Bartosz Sekula
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA; Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
| | - Sebastiana Angelaccio
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA; Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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28
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Kudjordjie EN, Hooshmand K, Sapkota R, Darbani B, Fomsgaard IS, Nicolaisen M. Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots. Microbiol Spectr 2022; 10:e0122622. [PMID: 35766498 PMCID: PMC9430778 DOI: 10.1128/spectrum.01226-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Kourosh Hooshmand
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Rumakanta Sapkota
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Behrooz Darbani
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Inge S. Fomsgaard
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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29
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Bello Bello E, Rico Cambron TY, Ortiz Ramírez LA, Rellán Álvarez R, Herrera-Estrella L. ROOT PENETRATION INDEX 3, a major quantitative trait locus associated with root system penetrability in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4716-4732. [PMID: 35512438 PMCID: PMC9366324 DOI: 10.1093/jxb/erac188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/03/2022] [Indexed: 05/07/2023]
Abstract
Soil mechanical impedance precludes root penetration, confining root system development to shallow soil horizons where mobile nutrients are scarce. Using a two-phase-agar system, we characterized Arabidopsis responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show a significant reduction in leaf area, root length, and elongation zone and an increment in root diameter, while those capable of penetrating show only minor morphological effects. Analyses using different auxin-responsive reporter lines, exogenous auxins, and inhibitor treatments suggest that auxin responsiveness and PIN-mediated auxin distribution play an important role in regulating root responses to mechanical impedance. The assessment of 21 Arabidopsis accessions revealed that primary root penetrability varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population derived from Landsberg erecta (Ler-0, with a high primary root penetrability) and Shahdara (Sha, with a low primary root penetrability) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3, ROOT PENETRATION INDEX 3 (q-RPI3), which accounted for 29.98% (logarithm of odds=8.82) of the total phenotypic variation. Employing an introgression line (IL-321) with a homozygous q-RPI3 region from Sha in the Ler-0 genetic background, we demonstrated that q-RPI3 plays a crucial role in root penetrability. This multiscale study reveals new insights into root plasticity during the penetration process in hard agar layers, natural variation, and genetic architecture behind primary root penetrability in Arabidopsis.
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Affiliation(s)
- Elohim Bello Bello
- Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México
| | - Thelma Y Rico Cambron
- Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México
| | - Lesly Abril Ortiz Ramírez
- Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México
| | - Rubén Rellán Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
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30
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Loudya N, Maffei DPF, Bédard J, Ali SM, Devlin PF, Jarvis RP, López-Juez E. Mutations in the chloroplast inner envelope protein TIC100 impair and repair chloroplast protein import and impact retrograde signaling. THE PLANT CELL 2022; 34:3028-3046. [PMID: 35640571 PMCID: PMC9338805 DOI: 10.1093/plcell/koac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/19/2022] [Indexed: 05/16/2023]
Abstract
Chloroplast biogenesis requires synthesis of proteins in the nucleocytoplasm and the chloroplast itself. Nucleus-encoded chloroplast proteins are imported via multiprotein translocons in the organelle's envelope membranes. Controversy exists around whether a 1-MDa complex comprising TIC20, TIC100, and other proteins constitutes the inner membrane TIC translocon. The Arabidopsis thaliana cue8 virescent mutant is broadly defective in plastid development. We identify CUE8 as TIC100. The tic100cue8 mutant accumulates reduced levels of 1-MDa complex components and exhibits reduced import of two nucleus-encoded chloroplast proteins of different import profiles. A search for suppressors of tic100cue8 identified a second mutation within the same gene, tic100soh1, which rescues the visible, 1 MDa complex-subunit abundance, and chloroplast protein import phenotypes. tic100soh1 retains but rapidly exits virescence and rescues the synthetic lethality of tic100cue8 when retrograde signaling is impaired by a mutation in the GENOMES UNCOUPLED 1 gene. Alongside the strong virescence, changes in RNA editing and the presence of unimported precursor proteins show that a strong signaling response is triggered when TIC100 function is altered. Our results are consistent with a role for TIC100, and by extension the 1-MDa complex, in the chloroplast import of photosynthetic and nonphotosynthetic proteins, a process which initiates retrograde signaling.
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Affiliation(s)
- Naresh Loudya
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Douglas P F Maffei
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Jocelyn Bédard
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Sabri Mohd Ali
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Paul F Devlin
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Enrique López-Juez
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
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31
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Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters. PLANTS 2022; 11:plants11141861. [PMID: 35890495 PMCID: PMC9318348 DOI: 10.3390/plants11141861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. These compounds have a complex biosynthetic pathway, whose first rate limiting enzyme is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). In the present study, a new 1646 bp fragment of the S. miltiorrhiza HMGR4 gene consisting of a promoter, 5′ untranslated region and part of a coding sequence was isolated and characterised in silico using bioinformatics tools. The results indicate the presence of a TATA box, tandem repeat and pyrimidine-rich sequence, and the absence of CpG islands. The sequence was rich in motifs recognised by specific transcription factors sensitive mainly to light, salicylic acid, bacterial infection and auxins; it also demonstrated many binding sites for microRNAs. Moreover, our results suggest that HMGR4 expression is possibly regulated during flowering, embryogenesis, organogenesis and the circadian rhythm. The obtained data were verified by comparison with microarray co-expression results obtained for Arabidopsis thaliana. Alignment of the isolated HMGR4 sequence with other plant HMGRs indicated the presence of many common binding sites for transcription factors, including conserved ones. Our findings provide valuable information for understanding the mechanisms that direct transcription of the S. miltiorrhiza HMGR4 gene.
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32
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Lim PK, Zheng X, Goh JC, Mutwil M. Exploiting plant transcriptomic databases: Resources, tools, and approaches. PLANT COMMUNICATIONS 2022; 3:100323. [PMID: 35605200 PMCID: PMC9284291 DOI: 10.1016/j.xplc.2022.100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 05/11/2023]
Abstract
There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data. Because gene expression provides essential clues to where and when a gene is active, the data provide powerful tools for predicting gene function, and comparative analyses allow us to study plant evolution from a new perspective. This review describes how we can gain new knowledge from gene expression profiles, expression specificities, co-expression networks, differential gene expression, and experiment correlation. We also introduce and demonstrate databases that provide user-friendly access to these tools.
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Affiliation(s)
- Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xinghai Zheng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jong Ching Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Lewsey MG, Yi C, Berkowitz O, Ayora F, Bernado M, Whelan J. scCloudMine: A cloud-based app for visualization, comparison, and exploration of single-cell transcriptomic data. PLANT COMMUNICATIONS 2022; 3:100302. [PMID: 35605202 PMCID: PMC9284053 DOI: 10.1016/j.xplc.2022.100302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 06/12/2023]
Abstract
scCloudMine is a cloud-based application for visualization, comparison, and exploration of single-cell transcriptome data. It does not require an on-site, high-power computing server, installation, or associated expertise and expense. Users upload their own or publicly available scRNA-seq datasets after pre-processing for visualization using a web browser. The data can be viewed in two color modes-Cluster, representing cell identity, and Values, showing levels of expression-and data can be queried using keywords or gene identification number(s). Using the app to compare studies, we determined that some genes frequently used as cell-type markers are in fact study specific. The apparent cell-specific expression of PHO1;H3 differed between GFP-tagging and scRNA-seq studies. Some phosphate transporter genes were induced by protoplasting, but they retained cell specificity, suggesting that cell-specific responses to stress (i.e., protoplasting) can occur. Examination of the cell specificity of hormone response genes revealed that 132 hormone-responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells, in contrast to previous reports. It also appears that JAZ repressors have cell-type-specific functions. These features identified using scCloudMine highlight the need for resources to enable biological researchers to compare their datasets of interest under a variety of parameters. scCloudMine enables researchers to form new hypotheses and perform comparative studies and allows for the easy re-use of data from this emerging technology by a wide variety of users who may not have access or funding for high-performance on-site computing and support.
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Affiliation(s)
- Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Changyu Yi
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Felipe Ayora
- BizData, Level 9/278, Collins Street, Melbourne, VIC 3000, Australia; Research and Advanced Computing, BizData, Level 31, 2-6, Gilmer Terrace, Wellington, 6011, New Zealand.
| | - Maurice Bernado
- BizData, Level 9/278, Collins Street, Melbourne, VIC 3000, Australia
| | - James Whelan
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Department of Animal, Plant and Soil Sciences, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia.
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Biswas S, Mondal R, Srivastava A, Trivedi M, Singh SK, Mishra Y. In silico characterization, molecular phylogeny, and expression profiling of genes encoding legume lectin-like proteins under various abiotic stresses in Arabidopsis thaliana. BMC Genomics 2022; 23:480. [PMID: 35768782 PMCID: PMC9241310 DOI: 10.1186/s12864-022-08708-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
Background Lectin receptor-like kinases (Lec-RLKs), a subfamily of RLKs, have been demonstrated to play an important role in signal transduction from cell wall to the plasma membrane during biotic stresses. Lec-RLKs include legume lectin-like proteins (LLPs), an important group of apoplastic proteins that are expressed in regenerating cell walls and play a role in immune-related responses. However, it is unclear whether LLPs have a function in abiotic stress mitigation and related signaling pathways. Therefore, in this study, we examined the possible role of LLPs in Arabidopsis thaliana (AtLLPs) under various abiotic stresses. Results The study was initiated by analyzing the chromosomal localization, gene structure, protein motif, peptide sequence, phylogeny, evolutionary divergence, and sub-cellular localization of AtLLPs. Furthermore, the expression profiling of these AtLLPs was performed using publicly accessible microarray datasets under various abiotic stresses, which indicated that all AtLLPs were differently expressed in both root and shoot tissues in response to abiotic stresses. The cis-regulatory elements (CREs) analysis in 500 bp promoter sequences of AtLLPs suggested the presence of multiple important CREs implicated for regulating abiotic stress responses, which was further supported by expressional correlation analysis between AtLLPs and their CREs cognate transcription factors (TFs). qRT-PCR analysis of these AtLLPs after 2, 6, and 12 h of cold, high light, oxidative (MV), UV-B, wound, and ozone stress revealed that all AtLLPs displayed differential expression patterns in most of the tested stresses, supporting their roles in abiotic stress response and signaling again. Out of these AtLLPs, AT1g53070 and AT5g03350 appeared to be important players. Furthermore, the mutant line of AT5g03350 exhibited higher levels of ROS than wild type plants till 12 h of exposure to high light, MV, UV-B, and wound, whereas its overexpression line exhibited comparatively lower levels of ROS, indicating a positive role of this gene in abiotic stress response in A. thaliana. Conclusions This study provides basic insights in the involvement of two important representative AtLLPs, AT1g53070 and AT5g03350, in abiotic stress response. However, further research is needed to determine the specific molecular mechanism of these AtLLPs in abiotic stress mitigation and related signaling pathways in A. thaliana. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08708-0.
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Affiliation(s)
- Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, 221005, Varanasi, Uttar Pradesh, India
| | - Raju Mondal
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, 221005, Varanasi, Uttar Pradesh, India.,Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Center, Central Silk Board-Ministry of Textiles (GoI), 635109, Hosur, Tamil Nadu, India
| | - Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, 221005, Varanasi, Uttar Pradesh, India
| | - Maitri Trivedi
- Plant Cell and Molecular Biology Lab, Department of Botany, Faculty of Science, The Maharaja Sayajirao University of Baroda, 390 002, Vadodara, Gujarat, India
| | - Sunil Kumar Singh
- Plant Cell and Molecular Biology Lab, Department of Botany, Faculty of Science, The Maharaja Sayajirao University of Baroda, 390 002, Vadodara, Gujarat, India
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, 221005, Varanasi, Uttar Pradesh, India.
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Mechanisms Regulating Energy Homeostasis in Plant Cells and Their Potential to Inspire Electrical Microgrids Models. Biomimetics (Basel) 2022; 7:biomimetics7020083. [PMID: 35735599 PMCID: PMC9221007 DOI: 10.3390/biomimetics7020083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
In this paper, the main features of systems that are required to flexibly modulate energy states of plant cells in response to environmental fluctuations are surveyed and summarized. Plant cells possess multiple sources (chloroplasts and mitochondria) to produce energy that is consumed to drive many processes, as well as mechanisms that adequately provide energy to the processes with high priority depending on the conditions. Such energy-providing systems are tightly linked to sensors that monitor the status of the environment and inside the cell. In addition, plants possess the ability to efficiently store and transport energy both at the cell level and at a higher level. Furthermore, these systems can finely tune the various mechanisms of energy homeostasis in plant cells in response to the changes in environment, also assuring the plant survival under adverse environmental conditions. Electrical power systems are prone to the effects of environmental changes as well; furthermore, they are required to be increasingly resilient to the threats of extreme natural events caused, for example, by climate changes, outages, and/or external deliberate attacks. Starting from this consideration, similarities between energy-related processes in plant cells and electrical power grids are identified, and the potential of mechanisms regulating energy homeostasis in plant cells to inspire the definition of new models of flexible and resilient electrical power grids, particularly microgrids, is delineated. The main contribution of this review is surveying energy regulatory mechanisms in detail as a reference and helping readers to find useful information for their work in this research field.
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Mondal R, Madhurya K, Saha P, Chattopadhyay SK, Antony S, Kumar A, Roy S, Roy D. Expression profile, transcriptional and post-transcriptional regulation of genes involved in hydrogen sulphide metabolism connecting the balance between development and stress adaptation in plants: a data-mining bioinformatics approach. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:602-617. [PMID: 34939301 DOI: 10.1111/plb.13378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Recent research focused on novel aspects of sulphur and sulphur-containing molecules in fundamental plant processes has highlighted the importance of these compounds. Currently, the focus has shifted to the efficacy of hydrogen sulphide (H2 S) as signalling compounds that regulate different development and stress mitigation in plants. Accordingly, we used an in silico approach to study the differential expression patterns of H2 S metabolic genes at different growth/development stages and their tissue-specific expression patterns under a range of abiotic stresses. Moreover, to understand the multilevel regulation of genes involved in H2 S metabolism, we performed computation-based promoter analysis, alternative splice variant analysis, prediction of putative miRNA targets and co-expression network analysis. Gene expression analysis suggests that H2 S biosynthesis is highly influenced by developmental and stress stimuli. The functional annotation of promoter structures reveales a wide range of plant hormone and stress responsive cis-regulatory elements (CREs) that regulate H2 S metabolism. Co-expression analysis suggested that genes involved in H2 S metabolism are also associated with different metabolic processes. In this data-mining study, the primary focus was to understand the genetic architecture governing pathways of H2 S metabolism in different cell compartments under various developmental and stress signalling cascades. The present study will help to understand the genetic architecture of H2 S metabolism via cysteine metabolism and the functional roles of these genes in development and stress tolerance mechanisms.
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Affiliation(s)
- R Mondal
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, India
| | - K Madhurya
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, India
| | - P Saha
- Department of Botany, Durgapur Government College, Durgapur, India
| | - S K Chattopadhyay
- Directorate of Distance Education, Vidyasagar University Midnapore (West), Midnapore, India
| | - S Antony
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, India
| | - A Kumar
- Host Plant Division, Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textile, Govt. of India, Jorhat, India
| | - S Roy
- Department of Botany, Santipur College, Nadia, India
| | - D Roy
- Department of Botany, Seth Anandram Jaipuria College, Kolkata, India
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Vonapartis E, Mohamed D, Li J, Pan W, Wu J, Gazzarrini S. CBF4/DREB1D represses XERICO to attenuate ABA, osmotic and drought stress responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:961-977. [PMID: 35199890 DOI: 10.1111/tpj.15713] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 01/29/2022] [Accepted: 02/12/2022] [Indexed: 05/22/2023]
Abstract
Water stress can severely impact plant growth, productivity and yield. Consequently, plants have evolved various strategies through which they can respond and adapt to their environment. XERICO (XER) is a stress-responsive RING E3 ubiquitin ligase that modulates abscisic acid (ABA) levels and promotes drought tolerance when overexpressed. To better understand the biological role of XER in stress responses, we characterized a xer-1 hypomorphic mutant and a CRISPR/Cas9-induced xer-2 null mutant in Arabidopsis. Both xer mutant alleles exhibited increased drought sensitivity, supporting the results from overexpression studies. Furthermore, we discovered that both xer mutants have greater stomatal indices and that XER is expressed in epidermal cells, indicating that XER functions in the epidermis to repress stomatal development. To explore XER spatiotemporal and stress-dependent regulation, we conducted a yeast one-hybrid screen and found that CBF4/DREB1D associates with the XER 5' untranslated region (5'-UTR). We generated three cbf4 null mutants with CRISPR/Cas9 and showed that CBF4 negatively regulates ABA responses, promotes stomatal development and reduces drought tolerance, in contrast to the roles shown for XER. CBF4 is induced by ABA and osmotic stress, and localizes to the nucleus where it downregulates XER expression via the DRE element in its 5'-UTR. Lastly, genetic interaction studies confirmed that xer is epistatic to cbf4 in stomatal development and in ABA, osmotic and drought stress responses. We propose that the repression of XER by CBF4 functions to attenuate ABA signaling and stress responses to maintain a balance between plant growth and survival under adverse environmental conditions.
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Affiliation(s)
- Eliana Vonapartis
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Deka Mohamed
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Jian Wu
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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Cheng X, Gao C, Liu X, Xu D, Pan X, Gao W, Yan S, Yao H, Cao J, Min X, Lu J, Chang C, Zhang H, Ma C. Characterization of the wheat VQ protein family and expression of candidate genes associated with seed dormancy and germination. BMC PLANT BIOLOGY 2022; 22:119. [PMID: 35291943 PMCID: PMC8925178 DOI: 10.1186/s12870-022-03430-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/07/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Seed dormancy and germination determine wheat resistance to pre-harvest sprouting and thereby affect grain yield and quality. Arabidopsis VQ genes have been shown to influence seed germination; however, the functions of wheat VQ genes have not been characterized. RESULTS We identified 65 TaVQ genes in common wheat and named them TaVQ1-65. We identified 48 paralogous pairs, 37 of which had Ka/Ks values greater than 1, suggesting that most TaVQ genes have experienced positive selection. Chromosome locations, gene structures, promoter element analysis, and gene ontology annotations of the TaVQs showed that their structures determined their functions and that structural changes reflected functional diversity. Transcriptome-based expression analysis of 62 TaVQ genes and microarray analysis of 11 TaVQ genes indicated that they played important roles in diverse biological processes. We compared TaVQ gene expression and seed germination index values among wheat varieties with contrasting seed dormancy and germination phenotypes and identified 21 TaVQ genes that may be involved in seed dormancy and germination. CONCLUSIONS Sixty-five TaVQ proteins were identified for the first time in common wheat, and bioinformatics analyses were used to investigate their phylogenetic relationships and evolutionary divergence. qRT-PCR data showed that 21 TaVQ candidate genes were potentially involved in seed dormancy and germination. These findings provide useful information for further cloning and functional analysis of TaVQ genes and introduce useful candidate genes for the improvement of PHS resistance in wheat.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chang Gao
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xue Liu
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Dongmei Xu
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xu Pan
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Wei Gao
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Shengnan Yan
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Hui Yao
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiaoyu Min
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Cheng Chang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Haiping Zhang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Chuanxi Ma
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
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Szymczyk P, Szymańska G, Kuźma Ł, Jeleń A, Balcerczak E. Methyl Jasmonate Activates the 2C Methyl-D-erithrytol 2,4-cyclodiphosphate Synthase Gene and Stimulates Tanshinone Accumulation in Salvia miltiorrhiza Solid Callus Cultures. Molecules 2022; 27:molecules27061772. [PMID: 35335134 PMCID: PMC8950807 DOI: 10.3390/molecules27061772] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 01/25/2023] Open
Abstract
The present study characterizes the 5′ regulatory region of the SmMEC gene. The isolated fragment is 1559 bp long and consists of a promoter, 5′UTR and 31 nucleotide 5′ fragments of the CDS region. In silico bioinformatic analysis found that the promoter region contains repetitions of many potential cis-active elements. Cis-active elements associated with the response to methyl jasmonate (MeJa) were identified in the SmMEC gene promoter. Co-expression studies combined with earlier transcriptomic research suggest the significant role of MeJa in SmMEC gene regulation. These findings were in line with the results of the RT-PCR test showing SmMEC gene expression induction after 72 h of MeJa treatment. Biphasic total tanshinone accumulation was observed following treatment of S. miltiorrhiza solid callus cultures with 50–500 μM methyl jasmonate, with peaks observed after 10–20 and 50–60 days. An early peak of total tanshinone concentration (0.08%) occurred after 20 days of 100 μM MeJa induction, and a second, much lower one, was observed after 50 days of 50 μM MeJa stimulation (0.04%). The dominant tanshinones were cryptotanshinone (CT) and dihydrotanshinone (DHT). To better understand the inducing effect of MeJa treatment on tanshinone biosynthesis, a search was performed for methyl jasmonate-responsive cis-active motifs in the available sequences of gene proximal promoters associated with terpenoid precursor biosynthesis. The results indicate that MeJa has the potential to induce a significant proportion of the presented genes, which is in line with available transcriptomic and RT-PCR data.
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Affiliation(s)
- Piotr Szymczyk
- Department of Biology and Pharmaceutical Botany, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland;
- Correspondence:
| | - Grażyna Szymańska
- Department of Pharmaceutical Biotechnology, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland;
| | - Łukasz Kuźma
- Department of Biology and Pharmaceutical Botany, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland;
| | - Agnieszka Jeleń
- Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland; (A.J.); (E.B.)
| | - Ewa Balcerczak
- Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland; (A.J.); (E.B.)
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Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism. Life (Basel) 2022; 12:life12030326. [PMID: 35330077 PMCID: PMC8953324 DOI: 10.3390/life12030326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/24/2022] Open
Abstract
Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana, the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting of 1267 nodes and 14,308 edges. In addition, 1151 co-expressed genes were annotated, integrated, and visualised using relevant bioinformatic tools. Based on three criteria, 21 potential GSL genes encoding TPs were selected. The AST68 and ABCG40 potential GSL TPs were chosen for further investigation because their subcellular localisation is similar to that of known GSL TPs (SULTR1;1 and SULTR1;2) and ABCG36, respectively. However, AST68 was selected for a molecular-docking analysis using AutoDOCK Vina and AutoDOCK 4.2 with the generated 3D model, showing that both domains were well superimposed on the homologs. Both molecular-docking tools calculated good binding-energy values between the sulphate ion and Ser419 and Val172, with the formation of hydrogen bonds and van der Waals interactions, respectively, suggesting that AST68 was one of the sulphate transporters involved in GSL biosynthesis. This finding illustrates the ability to use computational analysis on gene co-expression data to screen and characterise plant TPs on a large scale to comprehensively elucidate GSL metabolism in A. thaliana. Most importantly, newly identified potential GSL transporters can serve as molecular tools in improving the nutritional value of crops.
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Hartmann A, Berkowitz O, Whelan J, Narsai R. Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment. BMC PLANT BIOLOGY 2022; 22:62. [PMID: 35120438 PMCID: PMC8815143 DOI: 10.1186/s12870-021-03406-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/14/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND For translational genomics, a roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species. This knowledge is invaluable for the selection of target genes and pathways to alter downstream in response to the same stimuli. Here, the transcriptomic responses to six treatments including hormones (abscisic acid - ABA and salicylic acid - SA); treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - MV); inhibit respiration (antimycin A - AA) or induce genetic damage (ultraviolet radiation -UV) were analysed and compared between Arabidopsis (Arabidopsis thaliana), barley (Hordeum vulgare) and rice (Oryza sativa). RESULTS Common and opposite responses were identified between species, with the number of differentially expressed genes (DEGs) varying greatly between treatments and species. At least 70% of DEGs overlapped with at least one other treatment within a species, indicating overlapping response networks. Remarkably, 15 to 34% of orthologous DEGs showed opposite responses between species, indicating diversity in responses, despite orthology. Orthologous DEGs with common responses to multiple treatments across the three species were correlated with experimental data showing the functional importance of these genes in biotic/abiotic stress responses. The mitochondrial dysfunction response was revealed to be highly conserved in all three species in terms of responsive genes and regulation via the mitochondrial dysfunction element. CONCLUSIONS The orthologous DEGs that showed a common response between species indicate conserved transcriptomic responses of these pathways between species. However, many genes, including prominent salt-stress responsive genes, were oppositely responsive in multiple-stresses, highlighting fundamental differences in the responses and regulation of these genes between species. This work provides a resource for translation of knowledge or functions between species.
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Affiliation(s)
- Andreas Hartmann
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe Institute for Agriculture and Food (LIAF), La Trobe University, 5 Ring Road Bundoora, Victoria, 3083, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe Institute for Agriculture and Food (LIAF), La Trobe University, 5 Ring Road Bundoora, Victoria, 3083, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe Institute for Agriculture and Food (LIAF), La Trobe University, 5 Ring Road Bundoora, Victoria, 3083, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe Institute for Agriculture and Food (LIAF), La Trobe University, 5 Ring Road Bundoora, Victoria, 3083, Australia.
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Sanden NC, Schulz A. Identification of new proteins in mature sieve elements. PHYSIOLOGIA PLANTARUM 2022; 174:e13634. [PMID: 35060148 DOI: 10.1111/ppl.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
The phloem enables vascular plants to transport photoassimilates from source tissues to heterotrophic sink tissues. In the phloem, unbroken strings of enucleated sieve elements, which lose the majority of their cellular contents upon maturation, provide a low resistance path for mass flow. The protein machinery in mature sieve elements performs vital functions to maintain the flow, transmit systemic signals and defend the sugar stream against pests. However, our knowledge of this particular protein population is very limited since mature sieve elements are difficult to isolate and not amenable to transcriptomic analysis due to their enucleate nature. Here, we used co-expression analysis and published gene clusters from transcriptomic studies to generate a list of sieve element proteins that potentially survive the enucleation process to reside in mature sieve elements. We selected seven candidates and show that they all localize in sieve elements in Arabidopsis roots and six of them in bolting stems. Our results support the idea that nascent sieve elements prior to enucleation translate part of the protein machinery found in mature sieve elements. Our co-expression list and the publicly available gene clusters expressed in late proto- and meta-phloem sieve elements are valuable resources for uncharacterized genes that may function in mature sieve elements.
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Affiliation(s)
- Niels Christian Sanden
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section for Transport biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section for Transport biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Fang Y, Gu Y. Regulation of Plant Immunity by Nuclear Membrane-Associated Mechanisms. Front Immunol 2021; 12:771065. [PMID: 34938291 PMCID: PMC8685260 DOI: 10.3389/fimmu.2021.771065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/18/2021] [Indexed: 12/25/2022] Open
Abstract
Unlike animals, plants do not have specialized immune cells and lack an adaptive immune system. Instead, plant cells rely on their unique innate immune system to defend against pathogens and coordinate beneficial interactions with commensal and symbiotic microbes. One of the major convergent points for plant immune signaling is the nucleus, where transcriptome reprogramming is initiated to orchestrate defense responses. Mechanisms that regulate selective transport of nuclear signaling cargo and chromatin activity at the nuclear boundary play a pivotal role in immune activation. This review summarizes the current knowledge of how nuclear membrane-associated core protein and protein complexes, including the nuclear pore complex, nuclear transport receptors, and the nucleoskeleton participate in plant innate immune activation and pathogen resistance. We also discuss the role of their functional counterparts in regulating innate immunity in animals and highlight potential common mechanisms that contribute to nuclear membrane-centered immune regulation in higher eukaryotes.
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Affiliation(s)
- Yiling Fang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, CA, United States
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, CA, United States
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Christie N, Mannapperuma C, Ployet R, van der Merwe K, Mähler N, Delhomme N, Naidoo S, Mizrachi E, Street NR, Myburg AA. qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). BMC Bioinformatics 2021; 22:595. [PMID: 34911434 PMCID: PMC8672637 DOI: 10.1186/s12859-021-04514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. RESULTS We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. CONCLUSIONS qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.
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Affiliation(s)
- Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Karen van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Niklas Mähler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden.
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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Mondal R, Kumar A, Chattopadhyay SK. Structural property, molecular regulation, and functional diversity of glutamine synthetase in higher plants: a data-mining bioinformatics approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1565-1584. [PMID: 34628690 DOI: 10.1111/tpj.15536] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 05/26/2023]
Abstract
Glutamine synthetase (GS; E.C.6.3.1.2) is a key enzyme in higher plants with two isozymes, cytosolic GS1 and plastidic GS2, and involves in the assimilation and recycling of NH4+ ions and maintenance of complex traits such as crop nitrogen-use efficiency and yield. Our present understanding of crop nitrogen-use efficiency and its correlation with the functional role of the GS family genes is inadequate, which delays harnessing the benefit of this key enzyme in crop improvement. In this report, we performed a comprehensive investigation on the phylogenetic relationship, structural properties, complex multilevel gene regulation, and expression patterns of the GS genes to enrich present understanding about the enzyme. Our Gene Ontology and protein-protein interactions analysis revealed the functional aspects of GS isozymes in stress mitigation, aging, nucleotide biosynthesis/transport, DNA repair and response to metals. The insight gained here contributes to the future research strategies in developing climate-smart crops for global sustainability.
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Affiliation(s)
- Raju Mondal
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, 635109, India
| | - Amit Kumar
- Host Plant Section, Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textile, Govt. of India, Lahdoigarh, Jorhat, Assam, 785700, India
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Cantó-Pastor A, Mason GA, Brady SM, Provart NJ. Arabidopsis bioinformatics: tools and strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1585-1596. [PMID: 34695270 DOI: 10.1111/tpj.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The sequencing of the Arabidopsis thaliana genome 21 years ago ushered in the genomics era for plant research. Since then, an incredible variety of bioinformatic tools permit easy access to large repositories of genomic, transcriptomic, proteomic, epigenomic and other '-omic' data. In this review, we cover some more recent tools (and highlight the 'classics') for exploring such data in order to help formulate quality, testable hypotheses, often without having to generate new experimental data. We cover tools for examining gene expression and co-expression patterns, undertaking promoter analyses and gene set enrichment analyses, and exploring protein-protein and protein-DNA interactions. We will touch on tools that integrate different data sets at the end of the article.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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Cheng X, Tian B, Gao C, Gao W, Yan S, Yao H, Wang X, Jiang Y, Hu L, Pan X, Cao J, Lu J, Ma C, Chang C, Zhang H. Identification and expression analysis of candidate genes related to seed dormancy and germination in the wheat GATA family. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:343-359. [PMID: 34837867 DOI: 10.1016/j.plaphy.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/21/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
GATA transcription factors have been reported to function in plant growth and development and during various biotic/abiotic stresses in Arabidopsis and rice. However, the functions of wheat GATAs, particularly in the regulation of seed dormancy and germination, remain unclear. Here, we identified 78 TaGATAs in wheat and divided them into five subfamilies. Sixty-four paralogous pairs and 52 orthologous pairs were obtained, and Ka/Ks ratios showed that the TaGATAs had undergone strong purifying election during the evolutionary process. Triplet analysis indicated that a high homologue retention rate could explain the large number of TaGATAs in wheat. Gene structure analysis revealed that most members of the same subfamily had similar structures, and subcellular localization prediction indicated that most TaGATAs were located in the nucleus. Gene ontology annotation results showed that most TaGATAs had molecular functions in DNA and zinc binding, and promoter analysis suggested that they may play important roles in growth, development, and biotic/abiotic stress response. We combined three microarray datasets with qRT-PCR expression data from wheat varieties of contrasting dormancy and pre-harvest sprouting resistance levels during imbibition in order to identify ten candidate genes (TaGATA17/-25/-34/-37/-40/-46/-48/-51/-72/-73) that may be involved in the regulation of seed dormancy and germination in wheat. These findings provide valuable information for further dissection of TaGATA functions in the regulation of seed dormancy and germination, thereby enabling the improvement of wheat pre-harvest sprouting resistance by gene pyramiding.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China; National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingbing Tian
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Chang Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Wei Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Shengnan Yan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Hui Yao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xuyang Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Yating Jiang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Leixue Hu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xu Pan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
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Mondal R, Biswas S, Srivastava A, Basu S, Trivedi M, Singh SK, Mishra Y. In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana. BMC Genomics 2021; 22:817. [PMID: 34772363 PMCID: PMC8590313 DOI: 10.1186/s12864-021-08133-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. RESULTS This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. CONCLUSIONS To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.
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Affiliation(s)
- Raju Mondal
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.,Current address: Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Center, Central Silk Board-Ministry of Textiles (GoI), Hosur, Tamil Nadu, 635109, India
| | - Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Suvajit Basu
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Maitri Trivedi
- Plant Cell and Molecular Biology Lab, Department of Botany, Faculty of Science, The MS University of Baroda, Vadodara, Gujarat, 390 002, India
| | - Sunil Kumar Singh
- Plant Cell and Molecular Biology Lab, Department of Botany, Faculty of Science, The MS University of Baroda, Vadodara, Gujarat, 390 002, India
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Bonea D, Noureddine J, Gazzarrini S, Zhao R. Oxidative and salt stresses alter the 26S proteasome holoenzyme and associated protein profiles in Arabidopsis thaliana. BMC PLANT BIOLOGY 2021; 21:486. [PMID: 34696730 PMCID: PMC8543921 DOI: 10.1186/s12870-021-03234-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/29/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND The 26S proteasome, canonically composed of multi-subunit 19S regulatory (RP) and 20S core (CP) particles, is crucial for cellular proteostasis. Proteasomes are re-modeled, activated, or re-localized and this regulation is critical for plants in response to environmental stresses. The proteasome holoenzyme assembly and dissociation are therefore highly dynamic in vivo. However, the stoichiometric changes of the plant proteasomes and how proteasome associated chaperones vary under common abiotic stresses have not been systematically studied. RESULTS Here, we studied the impact of abiotic stresses on proteasome structure, activity, and interacting partners in Arabidopsis thaliana. We analyzed available RNA expression data and observed that expressions of proteasome coding genes varied substantially under stresses; however, the protein levels of a few key subunits did not change significantly within 24 h. Instead, a switch in the predominant proteasome complex, from 26S to 20S, occurs under oxidative or salt stress. Oxidative stress also reduced the cellular ATP content and the association of HSP70-family proteins to the 20S proteasome, but enhanced the activity of cellular free form CP. Salt stress, on the other hand, did not affect cellular ATP level, but caused subtle changes in proteasome subunit composition and impacted bindings of assembly chaperones. Analyses of an array of T-DNA insertional mutant lines highlighted important roles for several putative assembly chaperones in seedling establishment and stress sensitivity. We also observed that knockout of PBAC1, one of the α-ring assembly chaperones, resulted in reduced germination and tearing of the seed coat following sterilization. CONCLUSIONS Our study revealed an evolutionarily conserved mechanism of proteasome regulation during oxidative stress, involving dynamic regulation of the holoenzyme formation and associated regulatory proteins, and we also identified a novel role of the PBAC1 proteasome assembly chaperone in seed coat development.
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Affiliation(s)
- Diana Bonea
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
| | - Jenan Noureddine
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
| | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5 Canada
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Ambastha V, Matityahu I, Tidhar D, Leshem Y. RabA2b Overexpression Alters the Plasma-Membrane Proteome and Improves Drought Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:738694. [PMID: 34691115 PMCID: PMC8526897 DOI: 10.3389/fpls.2021.738694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 06/07/2023]
Abstract
Rab proteins are small GTPases that are important in the regulation of vesicle trafficking. Through data mining, we identified RabA2b to be stress responsive, though little is known about the involvement of RabA in plant responses to abiotic stresses. Analysis of the RabA2b native promoter showed strong activity during osmotic stress, which required the stress hormone Abscisic acid (ABA) and was restricted to the vasculature. Sequence analysis of the promoter region identified predicted binding motifs for several ABA-responsive transcription factors. We cloned RabA2b and overexpressed it in Arabidopsis. The resulting transgenic plants were strikingly drought resistant. The reduced water loss observed in detached leaves of the transgenic plants could not be explained by stomatal aperture or density, which was similar in all the genotypes. Subcellular localization studies detected strong colocalization between RabA2b and the plasma membrane (PM) marker PIP2. Further studies of the PM showed, for the first time, a distinguished alteration in the PM proteome as a result of RabA2b overexpression. Proteomic analysis of isolated PM fractions showed enrichment of stress-coping proteins as well as cell wall/cuticle modifiers in the transgenic lines. Finally, the cuticle permeability of transgenic leaves was significantly reduced compared to the wild type, suggesting that it plays a role in its drought resistant properties. Overall, these data provide new insights into the roles and modes of action of RabA2b during water stresses, and indicate that increased RabA2b mediated PM trafficking can affect the PM proteome and increase drought tolerance.
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Affiliation(s)
- Vivek Ambastha
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
| | - Ifat Matityahu
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
| | - Dafna Tidhar
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
| | - Yehoram Leshem
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
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