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Molecular cloning and characterization of two novel genes from hexaploid wheat that encode double PR-1 domains coupled with a receptor-like protein kinase. Mol Genet Genomics 2017; 292:435-452. [DOI: 10.1007/s00438-017-1287-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/03/2017] [Indexed: 11/26/2022]
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Song J, Liu H, Zhuang H, Zhao C, Xu Y, Wu S, Qi J, Li J, Hettenhausen C, Wu J. Transcriptomics and Alternative Splicing Analyses Reveal Large Differences between Maize Lines B73 and Mo17 in Response to Aphid Rhopalosiphum padi Infestation. FRONTIERS IN PLANT SCIENCE 2017; 8:1738. [PMID: 29067035 PMCID: PMC5641392 DOI: 10.3389/fpls.2017.01738] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/22/2017] [Indexed: 05/20/2023]
Abstract
Maize (Zea mays L.) is a staple crop worldwide with extensive genetic variations. Various insects attack maize plants causing large yield loss. Here, we investigated the responses of maize B73, a susceptible line, and Mo17, a resistant line, to the aphid Rhopalosiphum padi on metabolite and transcriptome levels. R. padi feeding had no effect on the levels of the defensive metabolites benzoxazinoids (Bxs) in either line, and Mo17 contained substantially greater levels of Bxs than did B73. Profiling of the differentially expressed genes revealed that B73 and Mo17 responded to R. padi infestation specifically, and importantly, these two lines showed large gene expression differences even without R. padi herbivory. Correlation analysis identified four transcription factors (TFs) that might account for the high Bx levels in Mo17. Similarly, genome-wide alternative splicing (AS) analyses indicated that both B73 and Mo17 had temporally specific responses to R. padi infestation, and these two lines also exhibited large differences of AS regulation under normal condition, and 340 genes, including 10 TFs, were constantly differentially spliced. This study provides large-scale resource datasets for further studies on the mechanisms underlying maize-aphid interactions, and highlights the phenotypic divergence in defense against aphids among maize varieties.
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Affiliation(s)
- Juan Song
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hui Liu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Huifu Zhuang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chunxia Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Yuxing Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shibo Wu
- Yunnan Academy of Science and Technology Development, Kunming, China
| | - Jinfeng Qi
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Christian Hettenhausen
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Christian Hettenhausen
| | - Jianqiang Wu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Jianqiang Wu
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John R, Anjum NA, Sopory SK, Akram NA, Ashraf M. Some key physiological and molecular processes of cold acclimation. BIOLOGIA PLANTARUM 2016; 60:603-618. [PMID: 0 DOI: 10.1007/s10535-016-0648-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
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Brkljacic J, Grotewold E. Combinatorial control of plant gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:31-40. [PMID: 27427484 DOI: 10.1016/j.bbagrm.2016.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 01/02/2023]
Abstract
Combinatorial gene regulation provides a mechanism by which relatively small numbers of transcription factors can control the expression of a much larger number of genes with finely tuned temporal and spatial patterns. This is achieved by transcription factors assembling into complexes in a combinatorial fashion, exponentially increasing the number of genes that they can target. Such an arrangement also increases the specificity and affinity for the cis-regulatory sequences required for accurate target gene expression. Superimposed on this transcription factor combinatorial arrangement is the increasing realization that histone modification marks expand the regulatory information, which is interpreted by histone readers and writers that are part of the regulatory apparatus. Here, we review the progress in these areas from the perspective of plant combinatorial gene regulation, providing examples of different regulatory solutions and comparing them to other metazoans. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Jelena Brkljacic
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun 2016; 7:11708. [PMID: 27339440 DOI: 10.1038/ncomms11708] [Citation(s) in RCA: 325] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/20/2016] [Indexed: 12/31/2022] Open
Abstract
Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 transcripts from 6 tissues capturing ∼70% of the genes annotated in maize RefGen_v3 genome. A large proportion of transcripts (57%) represent novel, sometimes tissue-specific, isoforms of known genes and 3% correspond to novel gene loci. In other cases, the identified transcripts have improved existing gene models. Averaging across all six tissues, 90% of the splice junctions are supported by short reads from matched tissues. In addition, we identified a large number of novel long non-coding RNAs and fusion transcripts and found that DNA methylation plays an important role in generating various isoforms. Our results show that characterization of the maize B73 transcriptome is far from complete, and that maize gene expression is more complex than previously thought.
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Affiliation(s)
- Bo Wang
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Elizabeth Tseng
- Pacific Biosciences, 1380 Willow Road, Menlo Park, California 94025, USA
| | - Michael Regulski
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Tyson A Clark
- Pacific Biosciences, 1380 Willow Road, Menlo Park, California 94025, USA
| | - Ting Hon
- Pacific Biosciences, 1380 Willow Road, Menlo Park, California 94025, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Joshua C Stein
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA.,USDA ARS NEA Robert W. Holley Center for Agriculture and Health Cornell University, Ithaca, New York 14853, USA
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Wang W, Sun Q, Cai C, Yang C, Liu X, He X, Jiang H, Mo J, Cai Y. Molecular characterization and alternative splicing of a MYB transcription factor gene in tumourous stem mustard and its response to abiotic stresses. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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57
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Sun M, Jia B, Cui N, Wen Y, Duanmu H, Yu Q, Xiao J, Sun X, Zhu Y. Functional characterization of a Glycine soja Ca(2+)ATPase in salt-alkaline stress responses. PLANT MOLECULAR BIOLOGY 2016; 90:419-434. [PMID: 26801329 DOI: 10.1007/s11103-015-0426-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/24/2015] [Indexed: 06/05/2023]
Abstract
It is widely accepted that Ca(2+)ATPase family proteins play important roles in plant environmental stress responses. However, up to now, most researches are limited in the reference plants Arabidopsis and rice. The function of Ca(2+)ATPases from non-reference plants was rarely reported, especially its regulatory role in carbonate alkaline stress responses. Hence, in this study, we identified the P-type II Ca(2+)ATPase family genes in soybean genome, determined their chromosomal location and gene architecture, and analyzed their amino acid sequence and evolutionary relationship. Based on above results, we pointed out the existence of gene duplication for soybean Ca(2+)ATPases. Then, we investigated the expression profiles of the ACA subfamily genes in wild soybean (Glycine soja) under carbonate alkaline stress, and functionally characterized one representative gene GsACA1 by using transgenic alfalfa. Our results suggested that GsACA1 overexpression in alfalfa obviously increased plant tolerance to both carbonate alkaline and neutral salt stresses, as evidenced by lower levels of membrane permeability and MDA content, but higher levels of SOD activity, proline concentration and chlorophyll content under stress conditions. Taken together, for the first time, we reported a P-type II Ca(2+)ATPase from wild soybean, GsACA1, which could positively regulate plant tolerance to both carbonate alkaline and neutral salt stresses.
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Affiliation(s)
- Mingzhe Sun
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Bowei Jia
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Na Cui
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Yidong Wen
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Huizi Duanmu
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Qingyue Yu
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Jialei Xiao
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Yanming Zhu
- Key Laboratory of Agricultural Biological Functional Gene, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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Kim JY, Ryu JY, Baek K, Park CM. High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. THE NEW PHYTOLOGIST 2016; 209:265-279. [PMID: 26256266 DOI: 10.1111/nph.13602] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
In higher plants, gravitropism proceeds through three sequential steps in the responding organs: perception of gravity signals, signal transduction and asymmetric cell elongation. Light and temperature also influence the gravitropic orientation of plant organs. A series of Arabidopsis shoot gravitropism (sgr) mutants has been shown to exhibit disturbed shoot gravitropism. SGR5 is functionally distinct from other SGR members in that it mediates the early events of gravitropic responses in inflorescence stems. Here, we demonstrated that SGR5 alternative splicing produces two protein variants (SGR5α and SGR5β) in modulating the gravitropic response of inflorescence stems at high temperatures. SGR5β inhibits SGR5α function by forming non-DNA-binding heterodimers. Transgenic plants overexpressing SGR5β (35S:SGR5β) exhibit reduced gravitropic growth of inflorescence stems, as observed in the SGR5-deficient sgr5-5 mutant. Interestingly, SGR5 alternative splicing is accelerated at high temperatures, resulting in the high-level accumulation of SGR5β transcripts. When plants were exposed to high temperatures, whereas gravitropic curvature was reduced in Col-0 inflorescence stems, it was uninfluenced in the inflorescence stems of 35S:SGR5β transgenic plants and sgr5-5 mutant. We propose that the thermoresponsive alternative splicing of SGR5 provides an adaptation strategy by which plants protect the shoots from hot air under high temperature stress in natural habitats.
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Affiliation(s)
- Joo-Young Kim
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Kon Baek
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
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MAF2 Is Regulated by Temperature-Dependent Splicing and Represses Flowering at Low Temperatures in Parallel with FLM. PLoS One 2015; 10:e0126516. [PMID: 25955034 PMCID: PMC4425511 DOI: 10.1371/journal.pone.0126516] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/03/2015] [Indexed: 11/19/2022] Open
Abstract
Plants enter their reproductive phase when the environmental conditions are favourable for the successful production of progeny. The transition from vegetative to reproductive phase is influenced by several environmental factors including ambient temperature. In the model plant Arabidopsis thaliana, SHORT VEGETATIVE PHASE (SVP) is critical for this pathway; svp mutants cannot modify their flowering time in response to ambient temperature. SVP encodes a MADS-box transcription factor that directly represses genes that promote flowering. SVP binds DNA in complexes with other MADS-box transcription factors, including FLOWERING LOCUS M (FLM), which acts with SVP to repress the floral transition at low temperatures. Small temperature changes post-transcriptionally regulate FLM through temperature-dependent alternative splicing (TD-AS). As ambient temperature increases, the predominant FLM splice isoform shifts to encode a protein incapable of exerting a repressive effect on flowering. Here we characterize a closely related MADS-box transcription factor, MADS AFFECTING FLOWERING2 (MAF2), which has independently evolved TD-AS. At low temperatures the most abundant MAF2 splice variant encodes a protein that interacts with SVP to repress flowering. At increased temperature the relative abundance of splice isoforms shifts in favour of an intron-retaining variant that introduces a premature termination codon. We show that this isoform encodes a protein that cannot interact with SVP or repress flowering. At lower temperatures MAF2 and SVP repress flowering in parallel with FLM and SVP, providing an additional input to sense ambient temperature for the control of flowering.
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Rosales R, Romero I, Escribano MI, Merodio C, Sanchez-Ballesta MT. The crucial role of Φ- and K-segments in the in vitro functionality of Vitis vinifera dehydrin DHN1a. PHYTOCHEMISTRY 2014; 108:17-25. [PMID: 25457499 DOI: 10.1016/j.phytochem.2014.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 05/07/2023]
Abstract
Dehydrins (DHNs), group II LEA (Late Embryogenesis Abundant) proteins, are among the most commonly observed proteins which accumulate in plants in response to cold and any other environmental factors, causing the dehydration of cells. In previous studies, we isolated a YSK2-type VvcDHN1a gene from table grapes (Vitis vinifera cv. Cardinal) which presented two spliced variants (the spliced, DHN1a_s and the unspliced, DHN1a_u). Their expression was induced by low temperature storage and CO2, although with different accumulation patterns. DHN1a_u codifies for a truncated YS protein lacking Ф- and K-segments, which might affect its functionality. In this work, we expressed both DHN1a_s and DHN1a_u recombinant proteins in Escherichia coli. We carried out a number of in vitro assays to analyze the implications that Ф- and K-segments have in the protective role of VvcDHN1 against different abiotic stresses and their antifungal activity against the fungal pathogen Botrytis cinerea. Our results showed that unlike DHN1a_u, DHN1a_s has a potent cryoprotective effect on lactate dehydrogenase activity, protects malate dehydrogenase against dehydration and partially inhibits B. cinerea growth. Moreover, the DHN1a promoter presented cis-regulatory elements related to cold and drought, as well as biotic stress-related elements. We also observed that both spliced variants interact weakly with DNA, suggesting that K-segments are not involved in DNA binding. Overall, this work highlights the crucial role of Ф- and K-segments in DHNs function in plant response to abiotic stress showing for the first time, the potential role of the V. vinifera DHN1a_s in the protection against freezing and dehydration as well as inhibiting B. cinerea growth.
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Arendsee ZW, Li L, Wurtele ES. Coming of age: orphan genes in plants. TRENDS IN PLANT SCIENCE 2014; 19:698-708. [PMID: 25151064 DOI: 10.1016/j.tplants.2014.07.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/27/2014] [Accepted: 07/17/2014] [Indexed: 05/19/2023]
Abstract
Sizable minorities of protein-coding genes from every sequenced eukaryotic and prokaryotic genome are unique to the species. These so-called ‘orphan genes’ may evolve de novo from non-coding sequence or be derived from older coding material. They are often associated with environmental stress responses and species-specific traits or regulatory patterns. However, difficulties in studying genes where comparative analysis is impossible, and a bias towards broadly conserved genes, have resulted in underappreciation of their importance. We review here the identification, possible origins, evolutionary trends, and functions of orphans with an emphasis on their role in plant biology. We exemplify several evolutionary trends with an analysis of Arabidopsis thaliana and present QQS as a model orphan gene.
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Kong X, Ma L, Yang L, Chen Q, Xiang N, Yang Y, Hu X. Quantitative proteomics analysis reveals that the nuclear cap-binding complex proteins arabidopsis CBP20 and CBP80 modulate the salt stress response. J Proteome Res 2014; 13:2495-510. [PMID: 24689873 DOI: 10.1021/pr4012624] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cap-binding proteins CBP20 and CBP80 have well-established roles in RNA metabolism and plant growth and development. Although these proteins are thought to be involved in the plant's response to environmental stress, their functions in this process are unclear. Here we demonstrated that Arabidopsis cbp20 and cbp80 null mutants had abnormal leaves and flowers and exhibited increased sensitivity to salt stress. The aberrant phenotypes were more pronounced in the cbp20/80 double mutant. Quantification by iTRAQ (isobaric tags for relative and absolute quantification) identified 77 differentially expressed proteins in the cbp20 and cbp80 lines compared with the wild-type Col-0 under salt stress conditions. Most of these differentially expressed proteins were synergistically expressed in cbp20 and cbp80, suggesting that CBP20 and CBP80 have synergistic roles during the salt stress response. Biochemical analysis demonstrated that CBP20 and CBP80 physically interacted with each other. Further analysis revealed that CBP20/80 regulated the splicing of genes involved in proline and sugar metabolism and that the epigenetic and post-translational modifications of these genes were involved in salt stress tolerance. Our data suggest a link between CBP20/80-dependent protein ubiquitination/sumoylation and the salt stress response.
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Affiliation(s)
- Xiangxiang Kong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, ‡Plant Germplasm and Genomics Center, the Germplasm Bank of Wild Species, and §Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Science , No. 132 Lanhei Road, Heilongtan, Kunming 650204, China
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Hemsley PA, Hurst CH, Kaliyadasa E, Lamb R, Knight MR, De Cothi EA, Steele JF, Knight H. The Arabidopsis mediator complex subunits MED16, MED14, and MED2 regulate mediator and RNA polymerase II recruitment to CBF-responsive cold-regulated genes. THE PLANT CELL 2014; 26:465-84. [PMID: 24415770 PMCID: PMC3963590 DOI: 10.1105/tpc.113.117796] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The Mediator16 (MED16; formerly termed SENSITIVE TO FREEZING6 [SFR6]) subunit of the plant Mediator transcriptional coactivator complex regulates cold-responsive gene expression in Arabidopsis thaliana, acting downstream of the C-repeat binding factor (CBF) transcription factors to recruit the core Mediator complex to cold-regulated genes. Here, we use loss-of-function mutants to show that RNA polymerase II recruitment to CBF-responsive cold-regulated genes requires MED16, MED2, and MED14 subunits. Transcription of genes known to be regulated via CBFs binding to the C-repeat motif/drought-responsive element promoter motif requires all three Mediator subunits, as does cold acclimation-induced freezing tolerance. In addition, these three subunits are required for low temperature-induced expression of some other, but not all, cold-responsive genes, including genes that are not known targets of CBFs. Genes inducible by darkness also required MED16 but required a different combination of Mediator subunits for their expression than the genes induced by cold. Together, our data illustrate that plants control transcription of specific genes through the action of subsets of Mediator subunits; the specific combination defined by the nature of the stimulus but also by the identity of the gene induced.
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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Transcriptomic characterization of cold acclimation in larval zebrafish. BMC Genomics 2013; 14:612. [PMID: 24024969 PMCID: PMC3847098 DOI: 10.1186/1471-2164-14-612] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 09/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background Temperature is one of key environmental parameters that affect the whole life of fishes and an increasing number of studies have been directed towards understanding the mechanisms of cold acclimation in fish. However, the adaptation of larvae to cold stress and the cold-specific transcriptional alterations in fish larvae remain largely unknown. In this study, we characterized the development of cold-tolerance in zebrafish larvae and investigated the transcriptional profiles under cold stress using RNA-seq. Results Pre-exposure of 96 hpf zebrafish larvae to cold stress (16°C) for 24 h significantly increased their survival rates under severe cold stress (12°C). RNA-seq generated 272 million raw reads from six sequencing libraries and about 92% of the processed reads were mapped to the reference genome of zebrafish. Differential expression analysis identified 1,431 up- and 399 down-regulated genes. Gene ontology enrichment analysis of cold-induced genes revealed that RNA splicing, ribosome biogenesis and protein catabolic process were the most highly overrepresented biological processes. Spliceosome, proteasome, eukaryotic ribosome biogenesis and RNA transport were the most highly enriched pathways for genes up-regulated by cold stress. Moreover, alternative splicing of 197 genes and promoter switching of 64 genes were found to be regulated by cold stress. A shorter isoform of stk16 that lacks 67 amino acids at the N-terminus was specifically generated by skipping the second exon in cold-treated larvae. Alternative promoter usage was detected for per3 gene under cold stress, which leading to a highly up-regulated transcript encoding a truncated protein lacking the C-terminal domains. Conclusions These findings indicate that zebrafish larvae possess the ability to build cold-tolerance under mild low temperature and transcriptional and post-transcriptional regulations are extensively involved in this acclimation process.
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