1
|
Hu Y, Li C, Zhou R, Song Y, Lv Z, Wang Q, Dong X, Liu S, Feng C, Zhou Y, Zeng X, Zhang L, Wang Z, Di H. The Transcription Factor ZmNAC89 Gene Is Involved in Salt Tolerance in Maize ( Zea mays L.). Int J Mol Sci 2023; 24:15099. [PMID: 37894780 PMCID: PMC10606073 DOI: 10.3390/ijms242015099] [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: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The NAC gene family has transcription factors specific to plants, which are involved in development and stress response and adaptation. In this study, ZmNAC89, an NAC gene in maize that plays a role in saline-alkaline tolerance, was isolated and characterized. ZmNAC89 was localized in the nucleus and had transcriptional activation activity during in vitro experiments. The expression of ZmNAC89 was strongly upregulated under saline-alkaline, drought and ABA treatments. Overexpression of the ZmNAC89 gene in transgenic Arabidopsis and maize enhanced salt tolerance at the seedling stage. Differentially expressed genes (DEGs) were then confirmed via RNA-sequencing analysis with the transgenic maize line. GO analyses showed that oxidation-reduction process-regulated genes were involved in ZmNAC89-mediated salt-alkaline stress. ZmNAC89 may regulate maize saline-alkali tolerance through the REDOX pathway and ABA signal transduction pathway. From 140 inbred maize lines, 20 haplotypes and 16 SNPs were found in the coding region of the ZmNAC89 gene, including the excellent haplotype HAP20. These results contribute to a better understanding of the response mechanism of maize to salt-alkali stress and marker-assisted selection during maize breeding.
Collapse
Affiliation(s)
- Yingying Hu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chunxiang Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Runyu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yongfeng Song
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhichao Lv
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Qi Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xiaojie Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
- Institute of Crop Resources Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Shan Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chenchen Feng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| |
Collapse
|
2
|
Sybilska E, Daszkowska-Golec A. Alternative splicing in ABA signaling during seed germination. FRONTIERS IN PLANT SCIENCE 2023; 14:1144990. [PMID: 37008485 PMCID: PMC10060653 DOI: 10.3389/fpls.2023.1144990] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Seed germination is an essential step in a plant's life cycle. It is controlled by complex physiological, biochemical, and molecular mechanisms and external factors. Alternative splicing (AS) is a co-transcriptional mechanism that regulates gene expression and produces multiple mRNA variants from a single gene to modulate transcriptome diversity. However, little is known about the effect of AS on the function of generated protein isoforms. The latest reports indicate that alternative splicing (AS), the relevant mechanism controlling gene expression, plays a significant role in abscisic acid (ABA) signaling. In this review, we present the current state of the art about the identified AS regulators and the ABA-related changes in AS during seed germination. We show how they are connected with the ABA signaling and the seed germination process. We also discuss changes in the structure of the generated AS isoforms and their impact on the functionality of the generated proteins. Also, we point out that the advances in sequencing technology allow for a better explanation of the role of AS in gene regulation by more accurate detection of AS events and identification of full-length splicing isoforms.
Collapse
|
3
|
Wyrzykowska A, Bielewicz D, Plewka P, Sołtys‐Kalina D, Wasilewicz‐Flis I, Marczewski W, Jarmolowski A, Szweykowska‐Kulinska Z. The MYB33, MYB65, and MYB101 transcription factors affect Arabidopsis and potato responses to drought by regulating the ABA signaling pathway. PHYSIOLOGIA PLANTARUM 2022; 174:e13775. [PMID: 36050907 PMCID: PMC9828139 DOI: 10.1111/ppl.13775] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the main climate threats limiting crop production. Potato is one of the four most important food crop species worldwide and is sensitive to water shortage. The CBP80 gene was shown to affect Arabidopsis and potato responses to drought by regulating the level of microRNA159 and, consequently, the levels of the MYB33 and MYB101 transcription factors (TFs). Here, we show that three MYB TFs, MYB33, MYB65, and MYB101, are involved in plant responses to water shortage. Their downregulation in Arabidopsis causes stomatal hyposensitivity to abscisic acid (ABA), leading to reduced tolerance to drought. Transgenic Arabidopsis and potato plants overexpressing these genes, with a mutated recognition site in miR159, show hypersensitivity to ABA and relatively high tolerance to drought conditions. Thus, the MYB33, MYB65, and MYB101 genes may be potential targets for innovative breeding to obtain crops with relatively high tolerance to drought.
Collapse
Affiliation(s)
- Anna Wyrzykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Dorota Sołtys‐Kalina
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Iwona Wasilewicz‐Flis
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Zofia Szweykowska‐Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| |
Collapse
|
4
|
Bieker VC, Battlay P, Petersen B, Sun X, Wilson J, Brealey JC, Bretagnolle F, Nurkowski K, Lee C, Barreiro FS, Owens GL, Lee JY, Kellner FL, van Boheeman L, Gopalakrishnan S, Gaudeul M, Mueller-Schaerer H, Lommen S, Karrer G, Chauvel B, Sun Y, Kostantinovic B, Dalén L, Poczai P, Rieseberg LH, Gilbert MTP, Hodgins KA, Martin MD. Uncovering the genomic basis of an extraordinary plant invasion. SCIENCE ADVANCES 2022; 8:eabo5115. [PMID: 36001672 PMCID: PMC9401624 DOI: 10.1126/sciadv.abo5115] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/11/2022] [Indexed: 05/31/2023]
Abstract
Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.
Collapse
Affiliation(s)
- Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100 Kedah, Malaysia
| | - Xin Sun
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - François Bretagnolle
- UMR CNRS/uB 6282 Biogéosciences, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Kristin Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Chris Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fátima Sánchez Barreiro
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jacqueline Y. Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fabian L. Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Myriam Gaudeul
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, National Herbarium (P), 57 rue Cuvier, CP39, 75005 Paris, France
| | | | - Suzanne Lommen
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA Leiden, Netherlands
- Koppert Biological Systems, Department R&D Macrobiology, Veilingweg 14, 2651 BE Berkel en Rodenrijs, Netherlands
| | - Gerhard Karrer
- Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bruno Chauvel
- UMR Agroécologie, Institut Agro, INRAE, Univ. Bourgogne, Univ. Bourgogne-Franche-Comté, F-21000 Dijon, France
| | - Yan Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Bojan Kostantinovic
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), Kőszeg, Hungary
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - M. Thomas P. Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
5
|
Chen Y, Weng X, Zhou X, Gu J, Hu Q, Luo Q, Wen M, Li C, Wang ZY. Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153574. [PMID: 34890846 DOI: 10.1016/j.jplph.2021.153574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.
Collapse
Affiliation(s)
- Yanhang Chen
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Xun Weng
- College of Life Sciences, South China Agricultural University, Guangdong, 510642, China
| | - Xiaoxia Zhou
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Jinbao Gu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qing Hu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qingwen Luo
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Mingfu Wen
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Cong Li
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
| |
Collapse
|
6
|
Marondedze C. The increasing diversity and complexity of the RNA-binding protein repertoire in plants. Proc Biol Sci 2020; 287:20201397. [PMID: 32962543 PMCID: PMC7542812 DOI: 10.1098/rspb.2020.1397] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Post-transcriptional regulation has far-reaching implications on the fate of RNAs. It is gaining increasing momentum as a critical component in adjusting global cellular transcript levels during development and in response to environmental stresses. In this process, RNA-binding proteins (RBPs) are indispensable chaperones that naturally bind RNA via one or multiple globular RNA-binding domains (RBDs) changing the function or fate of the bound RNAs. Despite the technical challenges faced in plants in large-scale studies, several hundreds of these RBPs have been discovered and elucidated globally over the past few years. Recent discoveries have more than doubled the number of proteins implicated in RNA interaction, including identification of RBPs lacking classical RBDs. This review will discuss these new emerging classes of RBPs, focusing on the current state of the RBP repertoire in Arabidopsis thaliana, including the diverse functional roles derived from quantitative studies implicating RBPs in abiotic stress responses. Notably, this review highlights that 836 RBPs are enriched as Arabidopsis RBPs while 1865 can be classified as candidate RBPs. The review will also outline outstanding areas within this field that require addressing to advance our understanding and potential biotechnological applications of RBPs.
Collapse
Affiliation(s)
- C. Marondedze
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Biochemistry, Midlands State University, P. Bag 9055, Gweru, Zimbabwe
| |
Collapse
|
7
|
Li Y, Liu X, Guo Y, Xie J, Wang L, Chen Q, Wang G, Wang Z, Gao H. Secondary Mutation-Induced Alternative Splicing Suppresses RNA Splicing Defect of the jhs1 Mutant. PLANT PHYSIOLOGY 2020; 182:2025-2034. [PMID: 32054782 PMCID: PMC7140918 DOI: 10.1104/pp.19.01571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
jing he sheng1 (jhs1) is a mutant of the DNA2 homolog in Arabidopsis (Arabidopsis thaliana), which was previously identified as being involved in DNA damage repair, cell cycle regulation, and meristem maintenance. A mutation at the 3' intron splice site of the 11th intron causes alternative splicing of this intron at two other sites, which results in frame shifts and premature stop codons. Here, we screened suppressors of jhs1 to further study the function and regulatory networks of JHS1 Three suppressors with wild-type-like phenotypes were obtained. Sequencing analysis results showed that each of the suppressors has a second mutation in jhs1 that causes further alternative splicing of the intron and corrects the shifted reading frame with small insertions. Precursor mRNA sequence analysis and intron splice site evaluation results suggested that intron splicing was disturbed in the suppressors, and this switched the splice site, resulting in small insertions in the coding regions of JHS1. Structural analysis of JHS1 suggested that the insertions are in a disordered loop region of the DNA2 domain and do not seem to have much deleterious effect on the function of the protein. This work not only has implications for the evolution of protein sequences at exon junctions but also provides a strategy to study the mechanism of precursor mRNA splicing.
Collapse
Affiliation(s)
- Yiqiong Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaomin Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuxuan Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Lulu Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Qiankuo Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Guangshuai Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Zefeng Wang
- Chinese Academy of Sciences and the German Max Planck Society, Partner Institute for Computational Biology, Shanghai 20031, China
| | - Hongbo Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
8
|
Baek D, Shin G, Kim MC, Shen M, Lee SY, Yun DJ. Histone Deacetylase HDA9 With ABI4 Contributes to Abscisic Acid Homeostasis in Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:143. [PMID: 32158458 PMCID: PMC7052305 DOI: 10.3389/fpls.2020.00143] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/30/2020] [Indexed: 05/18/2023]
Abstract
Drought stress, a major environmental factor, significantly affects plant growth and reproduction. Plants have evolved complex molecular mechanisms to tolerate drought stress. In this study, we investigated the function of the Arabidopsis thaliana RPD3-type HISTONE DEACETYLASE 9 (HDA9) in response to drought stress. The loss-of-function mutants hda9-1 and hda9-2 were insensitive to abscisic acid (ABA) and sensitive to drought stress. The ABA content in the hda9-1 mutant was reduced in wild type (WT) plant. Most histone deacetylases in animals and plants form complexes with other chromatin-remodeling components, such as transcription factors. In this study, we found that HDA9 interacts with the ABA INSENSITIVE 4 (ABI4) transcription factor using a yeast two-hybrid assay and coimmunoprecipitation. The expression of CYP707A1 and CYP707A2, which encode (+)-ABA 8'-hydroxylases, key enzymes in ABA catabolic pathways, was highly induced in hda9-1, hda9-2, abi4, and hda9-1 abi4 mutants upon drought stress. Chromatin immunoprecipitation and quantitative PCR showed that the HDA9 and ABI4 complex repressed the expression of CYP707A1 and CYP707A2 by directly binding to their promoters in response to drought stress. Taken together, these data suggest that HDA9 and ABI4 form a repressive complex to regulate the expression of CYP707A1 and CYP707A2 in response to drought stress in Arabidopsis.
Collapse
Affiliation(s)
- Dongwon Baek
- Division of Applied Life Science (BK21plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Gilok Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Min Chul Kim
- Division of Applied Life Science (BK21plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea
| | - Mingzhe Shen
- Division of Applied Life Science (BK21plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- *Correspondence: Dae-Jin Yun,
| |
Collapse
|
9
|
Auge GA, Penfield S, Donohue K. Pleiotropy in developmental regulation by flowering-pathway genes: is it an evolutionary constraint? THE NEW PHYTOLOGIST 2019; 224:55-70. [PMID: 31074008 DOI: 10.1111/nph.15901] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/28/2019] [Indexed: 05/11/2023]
Abstract
Pleiotropy occurs when one gene influences more than one trait, contributing to genetic correlations among traits. Consequently, it is considered a constraint on the evolution of adaptive phenotypes because of potential antagonistic selection on correlated traits, or, alternatively, preservation of functional trait combinations. Such evolutionary constraints may be mitigated by the evolution of different functions of pleiotropic genes in their regulation of different traits. Arabidopsis thaliana flowering-time genes, and the pathways in which they operate, are among the most thoroughly studied regarding molecular functions, phenotypic effects, and adaptive significance. Many of them show strong pleiotropic effects. Here, we review examples of pleiotropy of flowering-time genes and highlight those that also influence seed germination. Some genes appear to operate in the same genetic pathways when regulating both traits, whereas others show diversity of function in their regulation, either interacting with the same genetic partners but in different ways or potentially interacting with different partners. We discuss how functional diversification of pleiotropic genes in the regulation of different traits across the life cycle may mitigate evolutionary constraints of pleiotropy, permitting traits to respond more independently to environmental cues, and how it may even contribute to the evolutionary divergence of gene function across taxa.
Collapse
Affiliation(s)
- Gabriela A Auge
- Fundación Instituto Leloir, IIBBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1405BWE3, Argentina
| | - Steven Penfield
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kathleen Donohue
- Department of Biology, Duke University, Box 90338, Durham , NC 27708-0338, USA
| |
Collapse
|
10
|
Matsui A, Nakaminami K, Seki M. Biological Function of Changes in RNA Metabolism in Plant Adaptation to Abiotic Stress. PLANT & CELL PHYSIOLOGY 2019; 60:1897-1905. [PMID: 31093678 DOI: 10.1093/pcp/pcz068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved various sophisticated mechanisms for adaptation to nonoptimal environments. Recent studies using RNA metabolism-related mutants have revealed that RNA processing, RNA decay and RNA stability play an important role in regulating gene expression at a post-transcriptional level in response to abiotic stresses. Studies indicate that RNA metabolism is a unified network, and modification of stress adaptation-related transcripts at multiple steps of RNA metabolism is necessary to control abiotic stress-related gene expression. Recent studies have also demonstrated the important role of noncoding RNAs (ncRNAs) in regulating abiotic stress-related gene expression and revealed their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications and RNA-RNA interactions. ncRNAs regulate mRNA transcription and their synthesis is affected by mRNA processing and degradation. In the present review, recent findings pertaining to the role of the metabolic regulation of mRNAs and ncRNAs in abiotic stress adaptation are summarized and discussed.
Collapse
Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, Japan
| |
Collapse
|
11
|
Marondedze C, Thomas L, Gehring C, Lilley KS. Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms. BMC PLANT BIOLOGY 2019; 19:139. [PMID: 30975080 PMCID: PMC6460520 DOI: 10.1186/s12870-019-1750-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 03/31/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND RNA-binding proteins (RBPs) are increasingly recognized as regulatory component of post-transcriptional gene expression. RBPs interact with mRNAs via RNA-binding domains and these interactions affect RNA availability for translation, RNA stability and turn-over thus affecting both RNA and protein expression essential for developmental and stimulus specific responses. Here we investigate the effect of severe drought stress on the RNA-binding proteome to gain insights into the mechanisms that govern drought stress responses at the systems level. RESULTS Label-free mass spectrometry enabled the identification 567 proteins of which 150 significantly responded to the drought-induced treatment. A gene ontology analysis revealed enrichment in the "RNA binding" and "RNA processing" categories as well as biological processes such as "response to abscisic acid" and "response to water deprivation". Importantly, a large number of the stress responsive proteins have not previously been identified as RBPs and include proteins in carbohydrate metabolism and in the glycolytic and citric acid pathways in particular. This suggests that RBPs have hitherto unknown roles in processes that govern metabolic changes during stress responses. Furthermore, a comparative analysis of RBP domain architectures shows both, plant specific and common domain architectures between plants and animals. The latter could be an indication that RBPs are part of an ancient stress response. CONCLUSION This study establishes mRNA interactome capture technique as an approach to study stress signal responses implicated in environmental changes. Our findings denote RBP changes in the proteome as critical components in plant adaptation to changing environments and in particular drought stress protein-dependent changes in RNA metabolism.
Collapse
Affiliation(s)
- Claudius Marondedze
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Kingdom of Saudi Arabia.
- Present Address: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CEA/DRF/BIG, INRA UMR1417, CNRS UMR5168, 38054, Grenoble Cedex 9, France.
| | - Ludivine Thomas
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Present Address: HM.Clause, rue Louis Saillant, 26802, Portes-lès-Valence, France
| | - Chris Gehring
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 74 Borgo XX Giugno, 06121, Perugia, Italy
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| |
Collapse
|
12
|
Expression Patterns of MYB (V-myb Myeloblastosis Viral Oncogene Homolog) Gene Family in Resistant and Susceptible Tung Trees Responding to Fusarium Wilt Disease. FORESTS 2019. [DOI: 10.3390/f10020193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Vernicia fordii (tung oil tree) is famous in the world for its production of tung oil. Unfortunately, it was infected by the soil-borne fungus Fusarium oxysporum f. sp. fordii 1 (Fof-1) and suffered serious wilt disease. Conversely, its sister species V. montana is highly resistant to Fof-1. The MYB (v-myb myeloblastosis viral oncogene homolog) transcription factors were activated during the pathogen Fof-1 infection according to our previous comparative transcriptomic results. Depending on whether the sequence has a complete MYB-DNA-binding domain, a total of 75 VfMYB and 77 VmMYB genes were identified in susceptible V. fordii and resistant V. montana, respectively. In addition, we detected 49 pairs of one-to-one orthologous Vf/VmMYB genes with the reciprocal-best BLAST-hits (RBH)method. In order to investigate the expression modes and the internal network of MYB transcription factors in the two species responding to Fusarium wilt disease, the expressions of Vf/VmMYBs were then investigated and we found that most orthologous Vf/VmMYB genes exhibited similar expression patterns during the Fof-1 infection. However, four pairs of Vf/VmMYB genes, annotated as unknown proteins and mediator of root architecture, demonstrated absolute opposite expression patterns in the two Vernicia species responding to Fof-1. The interaction network of VmMYB genes were further constructed using weighted gene co-expression network analysis (WGCNA) method and four hub genes showing extremely high interaction with the other 1157 genes were identified. RT-qPCR result verified the opposite expression pattern of the hub gene VmMYB011 and VmMYB041 in two Vernicia species. In summary, co-expression network of the Vf/VmMYBs and significantly opposite related pairs of genes in resistant and susceptible Vernicia species provided knowledge for understanding the molecular basis of Vernicia responding to Fusarium wilt disease.
Collapse
|
13
|
Daszkowska-Golec A. Emerging Roles of the Nuclear Cap-Binding Complex in Abiotic Stress Responses. PLANT PHYSIOLOGY 2018; 176:242-253. [PMID: 29142023 PMCID: PMC5761810 DOI: 10.1104/pp.17.01017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/23/2017] [Indexed: 05/26/2023]
Abstract
Plant nuclear CBC consisted of two subunits (CBP20 and CBP80) is involved in both conserved processes related to RNA metabolism and simultaneously in extremely dynamic plant stress response.
Collapse
Affiliation(s)
- Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| |
Collapse
|
14
|
Papacek M, Christmann A, Grill E. Interaction network of ABA receptors in grey poplar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:199-210. [PMID: 28746755 DOI: 10.1111/tpj.13646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
The plant hormone abscisic acid (ABA) is a key player in responses to abiotic stress. ABA regulates a plant's water status and mediates drought tolerance by controlling stomatal gas exchange, water conductance and differential gene expression. ABA is recognized and bound by the Regulatory Component of ABA Receptors (RCARs)/PYR1/PYL (Pyrabactin Resistance 1/PYR1-like). Ligand binding stabilizes the interaction of RCARs with type 2C protein phosphatases (PP2C), which are ABA co-receptors. While the core pathway of ABA signalling has been elucidated, the large number of different ABA receptors and co-receptors within a plant species generates a complexity of heteromeric receptor complexes that has not functionally been resolved in any plant species to date. In this study, we characterized ABA receptors and co-receptors of grey poplar (Populus x canescens [Ait.] Sm.) and their capacity to regulate ABA responses. We observed a high number of regulatory combinations of holo-receptor complexes, but also some preferential and selective RCAR-PP2C interactions. Poplar and Arabidopsis ABA receptor components revealed a strong structural and functional conservation. Heterologous receptor complexes of poplar and Arabidopsis components showed functionality in vitro and regulated ABA-responsive gene expression in cells of both species. ABA-responsive promoters of Arabidopsis were also active in poplar, which was explored to generate poplar reporter lines expressing green fluorescent protein in response to ABA. The study presents a detailed analysis of receptor complexes of a tree species and shows high conservation of ABA receptor components between an annual and a perennial plant.
Collapse
Affiliation(s)
- Michael Papacek
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| | - Alexander Christmann
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| |
Collapse
|
15
|
Daszkowska-Golec A, Skubacz A, Marzec M, Slota M, Kurowska M, Gajecka M, Gajewska P, Płociniczak T, Sitko K, Pacak A, Szweykowska-Kulinska Z, Szarejko I. Mutation in HvCBP20 ( Cap Binding Protein 20) Adapts Barley to Drought Stress at Phenotypic and Transcriptomic Levels. FRONTIERS IN PLANT SCIENCE 2017; 8:942. [PMID: 28626467 PMCID: PMC5454077 DOI: 10.3389/fpls.2017.00942] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/19/2017] [Indexed: 05/20/2023]
Abstract
CBP20 (Cap-Binding Protein 20) encodes a small subunit of the cap-binding complex (CBC), which is involved in the conserved cell processes related to RNA metabolism in plants and, simultaneously, engaged in the signaling network of drought response, which is dependent on ABA. Here, we report the enhanced tolerance to drought stress of barley mutant in the HvCBP20 gene manifested at the morphological, physiological, and transcriptomic levels. Physiological analyses revealed differences between the hvcbp20.ab mutant and its WT in response to a water deficiency. The mutant exhibited a higher relative water content (RWC), a lower stomatal conductance and changed epidermal pattern compared to the WT after drought stress. Transcriptome analysis using the Agilent Barley Microarray integrated with observed phenotypic traits allowed to conclude that the hvcbp20.ab mutant exhibited better fitness to stress conditions by its much more efficient and earlier activation of stress-preventing mechanisms. The network hubs involved in the adjustment of hvcbp20.ab mutant to the drought conditions were proposed. These results enabled to make a significant progress in understanding the role of CBP20 in the drought stress response.
Collapse
Affiliation(s)
- Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Anna Skubacz
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Michal Slota
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Marzena Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Monika Gajecka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Patrycja Gajewska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Tomasz Płociniczak
- Department of Microbiology, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Krzysztof Sitko
- Department of Plant Physiology, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Faculty of Biology, Adam Mickiewicz University in PoznanPoznań, Poland
| | | | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| |
Collapse
|
16
|
Yu X, Willmann MR, Anderson SJ, Gregory BD. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis. THE PLANT CELL 2016; 28:2385-2397. [PMID: 27758893 PMCID: PMC5134982 DOI: 10.1105/tpc.16.00456] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/02/2016] [Accepted: 10/07/2016] [Indexed: 05/19/2023]
Abstract
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome.
Collapse
Affiliation(s)
- Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Matthew R Willmann
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Stephen J Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
17
|
Dolata J, Bajczyk M, Bielewicz D, Niedojadlo K, Niedojadlo J, Pietrykowska H, Walczak W, Szweykowska-Kulinska Z, Jarmolowski A. Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels. PLANT PHYSIOLOGY 2016; 172:297-312. [PMID: 27385819 PMCID: PMC5074614 DOI: 10.1104/pp.16.00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/02/2016] [Indexed: 05/03/2023]
Abstract
Plants as sessile organisms have developed prompt response mechanisms to react to rapid environmental changes. In addition to the transcriptional regulation of gene expression, microRNAs (miRNAs) are key posttranscriptional regulators of the plant stress response. We show here that the expression levels of many miRNAs were regulated under salt stress conditions. This regulation occurred at the transcriptional and posttranscriptional levels. During salinity stress, the levels of miRNA161 and miRNA173 increased, while the expression of pri-miRNA161 and pri-miRNA173 was down-regulated. Under salt stress conditions, miRNA161 and miRNA173 were stabilized in the cytoplasm, and the expressions of MIR161 and MIR173 were negatively regulated in the nucleus. ARGONAUTE1 (AGO1) participated in both processes. We demonstrated that AGO1 cotranscriptionally controlled the expression of MIR161 and MIR173 in the nucleus. Our results suggests that AGO1 interacts with chromatin at MIR161 and MIR173 loci and causes the disassembly of the transcriptional complex, releasing short and unpolyadenylated transcripts.
Collapse
Affiliation(s)
- Jakub Dolata
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Mateusz Bajczyk
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Katarzyna Niedojadlo
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Janusz Niedojadlo
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Halina Pietrykowska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Weronika Walczak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland (J.D., M.B., D.B., H.P., W.W., Z.S.-K., A.J.); andDepartment of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, 87-100 Torun, Poland (K.N., J.N.)
| |
Collapse
|
18
|
Skubacz A, Daszkowska-Golec A, Szarejko I. The Role and Regulation of ABI5 (ABA-Insensitive 5) in Plant Development, Abiotic Stress Responses and Phytohormone Crosstalk. FRONTIERS IN PLANT SCIENCE 2016; 7:1884. [PMID: 28018412 PMCID: PMC5159420 DOI: 10.3389/fpls.2016.01884] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/29/2016] [Indexed: 05/18/2023]
Abstract
ABA Insensitive 5 (ABI5) is a basic leucine zipper transcription factor that plays a key role in the regulation of seed germination and early seedling growth in the presence of ABA and abiotic stresses. ABI5 functions in the core ABA signaling, which is composed of PYR/PYL/RCAR receptors, PP2C phosphatases and SnRK2 kinases, through the regulation of the expression of genes that contain the ABSCISIC ACID RESPONSE ELEMENT (ABRE) motif within their promoter region. The regulated targets include stress adaptation genes, e.g., LEA proteins. However, the expression and activation of ABI5 is not only dependent on the core ABA signaling. Many transcription factors such as ABI3, ABI4, MYB7 and WRKYs play either a positive or a negative role in the regulation of ABI5 expression. Additionally, the stability and activity of ABI5 are also regulated by other proteins through post-translational modifications such as phosphorylation, ubiquitination, sumoylation and S-nitrosylation. Moreover, ABI5 also acts as an ABA and other phytohormone signaling integrator. Components of auxin, cytokinin, gibberellic acid, jasmonate and brassinosteroid signaling and metabolism pathways were shown to take part in ABI5 regulation and/or to be regulated by ABI5. Monocot orthologs of AtABI5 have been identified. Although their roles in the molecular and physiological adaptations during abiotic stress have been elucidated, knowledge about their detailed action still remains elusive. Here, we describe the recent advances in understanding the action of ABI5 in early developmental processes and the adaptation of plants to unfavorable environmental conditions. We also focus on ABI5 relation to other phytohormones in the abiotic stress response of plants.
Collapse
|
19
|
Zielezinski A, Dolata J, Alaba S, Kruszka K, Pacak A, Swida-Barteczka A, Knop K, Stepien A, Bielewicz D, Pietrykowska H, Sierocka I, Sobkowiak L, Lakomiak A, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM. mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs. BMC PLANT BIOLOGY 2015; 15:144. [PMID: 26141515 PMCID: PMC4490709 DOI: 10.1186/s12870-015-0533-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/23/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. DESCRIPTION The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation (e.g., tooltips, exemplary videos and presentations). All data contained within the mirEX 2.0 database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page. CONCLUSIONS The mirEX 2.0 portal provides the plant research community with easily accessible data and powerful tools for application in multi-conditioned analyses of miRNA expression from important plant species in different biological and developmental backgrounds.
Collapse
Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Sylwia Alaba
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Lukasz Sobkowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Alicja Lakomiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| |
Collapse
|
20
|
Towards the identification of new genes involved in ABA-dependent abiotic stresses using Arabidopsis suppressor mutants of abh1 hypersensitivity to ABA during seed germination. Int J Mol Sci 2013; 14:13403-32. [PMID: 23807502 PMCID: PMC3742194 DOI: 10.3390/ijms140713403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/20/2013] [Accepted: 06/06/2013] [Indexed: 01/23/2023] Open
Abstract
Abscisic acid plays a pivotal role in the abiotic stress response in plants. Although great progress has been achieved explaining the complexity of the stress and ABA signaling cascade, there are still many questions to answer. Mutants are a valuable tool in the identification of new genes or new alleles of already known genes and in elucidating their role in signaling pathways. We applied a suppressor mutation approach in order to find new components of ABA and abiotic stress signaling in Arabidopsis. Using the abh1 (ABA hypersensitive 1) insertional mutant as a parental line for EMS mutagenesis, we selected several mutants with suppressed hypersensitivity to ABA during seed germination. Here, we present the response to ABA and a wide range of abiotic stresses during the seed germination and young seedling development of two suppressor mutants—soa2 (suppressor of abh1 hypersensitivity to ABA 2) and soa3 (suppressor of abh1 hypersensitivity to ABA 3). Generally, both mutants displayed a suppression of the hypersensitivity of abh1 to ABA, NaCl and mannitol during germination. Both mutants showed a higher level of tolerance than Columbia-0 (Col-0—the parental line of abh1) in high concentrations of glucose. Additionally, soa2 exhibited better root growth than Col-0 in the presence of high ABA concentrations. soa2 and soa3 were drought tolerant and both had about 50% fewer stomata per mm2 than the wild-type but the same number as their parental line—abh1. Taking into account that suppressor mutants had the same genetic background as their parental line—abh1, it was necessary to backcross abh1 with Landsberg erecta four times for the map-based cloning approach. Mapping populations, derived from the cross of abh1 in the Landsberg erecta background with each suppressor mutant, were created. Map based cloning in order to identify the suppressor genes is in progress.
Collapse
|
21
|
Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. Proc Natl Acad Sci U S A 2013; 110:10866-71. [PMID: 23754415 DOI: 10.1073/pnas.1301647110] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Freshly matured seeds exhibit primary dormancy, which prevents germination until environmental conditions are favorable. The establishment of dormancy occurs during seed development and involves both genetic and environmental factors that impact on the ratio of two antagonistic phytohormones: abscisic acid (ABA), which promotes dormancy, and gibberellic acid, which promotes germination. Although our understanding of dormancy breakage in mature seeds is well advanced, relatively little is known about the mechanisms involved in establishing dormancy during seed maturation. We previously showed that the SPATULA (SPT) transcription factor plays a key role in regulating seed germination. Here we investigate its role during seed development and find that, surprisingly, it has opposite roles in setting dormancy in Landsberg erecta and Columbia Arabidopsis ecotypes. We also find that SPT regulates expression of five transcription factor encoding genes: ABA-INSENSITIVE4 (ABI4) and ABI5, which mediate ABA signaling; REPRESSOR-OF-GA (RGA) and RGA-LIKE3 involved in gibberellic acid signaling; and MOTHER-OF-FT-AND-TFL1 (MFT) that we show here promotes Arabidopsis seed dormancy. Although ABI4, RGA, and MFT are repressed by SPT, ABI5 and RGL3 are induced. Furthermore, we show that RGA, MFT, and ABI5 are direct targets of SPT in vivo. We present a model in which SPT drives two antagonistic "dormancy-repressing" and "dormancy-promoting" routes that operate simultaneously in freshly matured seeds. Each of these routes has different impacts and this in turn explains the opposite effect of SPT on seed dormancy of the two ecotypes analyzed here.
Collapse
|