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Yuan P, Cai Q, Hu Z. Arabidopsis DEAD-box RNA helicase 12 is required for salt tolerance during seed germination. Biochem Biophys Res Commun 2024; 725:150228. [PMID: 38936167 DOI: 10.1016/j.bbrc.2024.150228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
The DEAD-box family is the largest family of RNA helicases (RHs), playing crucial roles in RNA metabolism and plant stress resistance. In this study, we report that an RNA helicase, RH12, positively regulates plant salt tolerance, as rh12 knockout mutants exhibit heightened sensitivity to salt stress. Further analysis indicates that RH12 is involved in the abscisic acid (ABA) response, as rh12 knockout mutants show increased sensitivity to ABA. Examination of reactive oxygen species (ROS) revealed that RH12 helps inhibit ROS accumulation under salt stress during seed germination. Additionally, RH12 accelerates the degradation of specific germination-related transcripts. In conclusion, our results demonstrate that RH12 plays multiple roles in the salt stress response in Arabidopsis.
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Affiliation(s)
- Penglai Yuan
- College of Life Sciences, Nanjing Agricultural University, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qingsheng Cai
- College of Life Sciences, Nanjing Agricultural University, China.
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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2
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Zuo Z, Roux ME, Dagdas YF, Rodriguez E, Petersen M. PAT mRNA decapping factors are required for proper development in Arabidopsis. FEBS Lett 2024; 598:1008-1021. [PMID: 38605280 DOI: 10.1002/1873-3468.14872] [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: 02/27/2024] [Revised: 04/10/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize posttranscriptional reprogramming. Here, we generated multiple mutants of pat1, pat1 homolog 1 (path1), and pat1 homolog 2 (path2) and discovered that pat triple mutants exhibit extremely stunted growth and all mutants with pat1 exhibit leaf serration while mutants with pat1 and path1 display short petioles. All three PATs can be found localized to processing bodies and all PATs can target ASYMMETRIC LEAVES 2-LIKE 9 transcripts for decay to finely regulate apical hook and lateral root development. In conclusion, PATs exhibit both specific and redundant functions during different plant growth stages and our observations underpin the selective regulation of the mRNA decay machinery for proper development.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Yasin F Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Austria
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
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3
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Zuo Z, Roux ME, Chevalier JR, Dagdas YF, Yamashino T, Højgaard SD, Knight E, Østergaard L, Rodriguez E, Petersen M. The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development. Life Sci Alliance 2023; 6:e202302090. [PMID: 37385753 PMCID: PMC10310928 DOI: 10.26508/lsa.202302090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Multicellular organisms perceive and transduce multiple cues to optimize development. Key transcription factors drive developmental changes, but RNA processing also contributes to tissue development. Here, we report that multiple decapping deficient mutants share developmental defects in apical hook, primary and lateral root growth. More specifically, LATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3)/ASYMMETRIC LEAVES 2-LIKE 9 (ASL9) transcripts accumulate in decapping deficient plants and can be found in complexes with decapping components. Accumulation of ASL9 inhibits apical hook and lateral root formation. Interestingly, exogenous auxin application restores lateral roots formation in both ASL9 over-expressors and mRNA decay-deficient mutants. Likewise, mutations in the cytokinin transcription factors type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs) ARR10 and ARR12 restore the developmental defects caused by over-accumulation of capped ASL9 transcript upon ASL9 overexpression. Most importantly, loss-of-function of asl9 partially restores apical hook and lateral root formation in both dcp5-1 and pat triple decapping deficient mutants. Thus, the mRNA decay machinery directly targets ASL9 transcripts for decay, possibly to interfere with cytokinin/auxin responses, during development.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Milena E Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan R Chevalier
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Yasin F Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Takafumi Yamashino
- Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Nagoya, Japan
| | - Søren D Højgaard
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Knight
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Lars Østergaard
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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Pan J, Zhou Q, Wang H, Chen Y, Wang Z, Zhang J. Genome-wide identification and characterization of abiotic stress responsive GRAS family genes in oat ( Avena sativa). PeerJ 2023; 11:e15370. [PMID: 37187518 PMCID: PMC10178225 DOI: 10.7717/peerj.15370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Background GRAS transcription factors play a variety of functions in plant growth and development and are named after the first three transcription factors GAI (GIBBERRELLICACIDINSENSITIVE), RGA (REPRESSOROFGAI), and SCR (SCARECROW) found in this family. Oat (Avena sativa) is one of the most important forage grasses in the world. However, there are few reports on the GRAS gene family in oat. Methods In order to understand the information and expression pattern of oat GRAS family members, we identified the GRAS members and analyzed their phylogenetic relationship, gene structure, and expression pattern in oat by bioinformatics technology. Results The results showed that the oat GRAS family consists of 30 members, and most of the AsGRAS proteins were neutral or acidic proteins. The phylogenetic tree divided the oat GRAS members into four subfamilies, and each subfamily has different conservative domains and functions. Chromosome location analysis suggested that 30 GRAS genes were unevenly distributed on five chromosomes of oat. The results of real-time quantitative reverse transcription-PCR (qRT-PCR) showed that some AsGRAS genes (AsGRAS12, AsGRAS14, AsGRAS21, and AsGRAS24) were all up-regulated with increasing stress treatment time.The results of this study provide a theoretical basis for further research into the corresponding stress of oat. Therefore, further studies concentrating on these AsGRAS genes might reveal the many roles played by GRAS genes in oat.
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Affiliation(s)
- Jing Pan
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Qingping Zhou
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Hui Wang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Youjun Chen
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Zhiqiang Wang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Junchao Zhang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
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5
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Peng H, Phung J, Stowe EC, Dhingra A, Neff MM. The NAC transcription factor ATAF2 promotes ethylene biosynthesis and response in Arabidopsis thaliana seedlings. FEBS Lett 2022; 596:1586-1599. [PMID: 35170054 DOI: 10.1002/1873-3468.14317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/10/2022]
Abstract
Arabidopsis thaliana ACTIVATING FACTOR 2 (ATAF2) plays extensive regulatory roles in pathogenesis, seedling development, and stress responses. Here, we performed transcriptome analysis on ATAF2 loss- and gain-of-function mutants to identify differentially expressed genes (DEGs). Gene ontology analyses on DEGs reveal that ATAF2 enhances seedling responses to multiple hormone and stress signals. In particular, our transcriptome analysis suggests that ATAF2 promotes ethylene biosynthesis and responses via activating relevant genes. This novel role of ATAF2 was further demonstrated by using multiple ATAF2 null and overexpression lines for reverse transcription quantitative PCR verification, ethylene production measurements, and assays of seedlings growth responses to the ethylene immediate biosynthetic precursor 1-aminocyclopropane-1-carboxylic acid (ACC). ACC suppresses ATAF2 expression to form a negative feedback regulation loop.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.,Chemical and Hop Laboratory, Department of Agriculture, Washington State, Yakima, WA, 98902, USA
| | - Jessica Phung
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Evan C Stowe
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA.,Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michael M Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
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Zuo Z, Roux M, Rodriguez E, Petersen M. mRNA Decapping Factors LSM1 and PAT Paralogs Are Involved in Turnip Mosaic Virus Viral Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:125-130. [PMID: 35100808 DOI: 10.1094/mpmi-09-21-0220-sc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Turnip mosaic virus is a devastating potyvirus infecting many economically important brassica crops. In response to this, the plant host engages its RNA silencing machinery, involving AGO proteins, as a prominent strategy to restrain turnip mosaic virus (TuMV) infection. It has also been shown that the mRNA decay components DCP2 and VCS partake in viral infection suppression. Here, we report that the mRNA decapping components LSM1, PAT1, PATH1, and PATH2 are essential for TuMV infection. More specifically, lsm1a/lsm1b double mutants and pat1/path1/path2 triple mutants in summ2 background exhibit resistance to TuMV. Concurrently, we observed that TuMV interferes with the decapping function of LSM1 and PAT proteins as the mRNA-decay target genes UGT87A2 and ASL9 accumulate during TuMV infection. Moreover, as TuMV coat protein can be specifically found in complexes with PAT proteins but not LSM1, this suggests that TuMV "hijacks" decapping components via PAT proteins to support viral infection.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Milena Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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Yang N, Nesme J, Røder HL, Li X, Zuo Z, Petersen M, Burmølle M, Sørensen SJ. Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis. NPJ Biofilms Microbiomes 2021; 7:82. [PMID: 34795326 PMCID: PMC8602335 DOI: 10.1038/s41522-021-00253-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/08/2021] [Indexed: 01/04/2023] Open
Abstract
Drought severely restricts plant production and global warming is further increasing drought stress for crops. Much information reveals the ability of individual microbes affecting plant stress tolerance. However, the effects of emergent bacterial community properties on plant drought tolerance remain largely unexplored. Here, we inoculated Arabidopsis plants in vivo with a four-species bacterial consortium (Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans, and Paenibacillus amylolyticus, termed as SPMX), which is able to synergistically produce more biofilm biomass together than the sum of the four single-strain cultures, to investigate its effects on plant performance and rhizo-microbiota during drought. We found that SPMX remarkably improved Arabidopsis survival post 21-day drought whereas no drought-tolerant effect was observed when subjected to the individual strains, revealing emergent properties of the SPMX consortium as the underlying cause of the induced drought tolerance. The enhanced drought tolerance was associated with sustained chlorophyll content and endogenous abscisic acid (ABA) signaling. Furthermore, our data showed that the addition of SPMX helped to stabilize the diversity and structure of root-associated microbiomes, which potentially benefits plant health under drought. These SPMX-induced changes jointly confer an increased drought tolerance to plants. Our work may inform future efforts to engineer the emergent bacterial community properties to improve plant tolerance to drought.
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Affiliation(s)
- Nan Yang
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Lyng Røder
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xuanji Li
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhangli Zuo
- grid.5254.60000 0001 0674 042XDepartment of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- grid.5254.60000 0001 0674 042XDepartment of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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