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Zhang Y, Mo Y, Li J, Liu L, Gao Y, Zhang Y, Huang Y, Ren L, Zhu H, Jiang X, Ling Y. Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress. Sci Rep 2024; 14:8743. [PMID: 38627506 PMCID: PMC11021534 DOI: 10.1038/s41598-024-59341-8] [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: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The IVa subfamily of glycine-rich proteins (GRPs) comprises a group of glycine-rich RNA binding proteins referred to as GR-RBPa here. Previous studies have demonstrated functions of GR-RBPa proteins in regulating stress response in plants. However, the mechanisms responsible for the differential regulatory functions of GR-RBPa proteins in different plant species have not been fully elucidated. In this study, we identified and comprehensively studied a total of 34 GR-RBPa proteins from five plant species. Our analysis revealed that GR-RBPa proteins were further classified into two branches, with proteins in branch I being relatively more conserved than those in branch II. When subjected to identical stresses, these genes exhibited intensive and differential expression regulation in different plant species, corresponding to the enrichment of cis-acting regulatory elements involving in environmental and internal signaling in these genes. Unexpectedly, all GR-RBPa genes in branch I underwent intensive alternative splicing (AS) regulation, while almost all genes in branch II were only constitutively spliced, despite having more introns. This study highlights the complex and divergent regulations of a group of conserved RNA binding proteins in different plants when exposed to identical stress conditions. These species-specific regulations may have implications for stress responses and adaptations in different plant species.
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Affiliation(s)
- Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yanhu Gao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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Mukherjee A, Maheshwari U, Sharma V, Sharma A, Kumar S. Functional insight into multi-omics-based interventions for climatic resilience in sorghum (Sorghum bicolor): a nutritionally rich cereal crop. PLANTA 2024; 259:91. [PMID: 38480598 DOI: 10.1007/s00425-024-04365-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION The article highlights omics-based interventions in sorghum to combat food and nutritional scarcity in the future. Sorghum with its unique ability to thrive in adverse conditions, has become a tremendous highly nutritive, and multipurpose cereal crop. It is resistant to various types of climatic stressors which will pave its way to a future food crop. Multi-omics refers to the comprehensive study of an organism at multiple molecular levels, including genomics, transcriptomics, proteomics, and metabolomics. Genomic studies have provided insights into the genetic diversity of sorghum and led to the development of genetically improved sorghum. Transcriptomics involves analysing the gene expression patterns in sorghum under various conditions. This knowledge is vital for developing crop varieties with enhanced stress tolerance. Proteomics enables the identification and quantification of the proteins present in sorghum. This approach helps in understanding the functional roles of specific proteins in response to stress and provides insights into metabolic pathways that contribute to resilience and grain production. Metabolomics studies the small molecules, or metabolites, produced by sorghum, provides information about the metabolic pathways that are activated or modified in response to environmental stress. This knowledge can be used to engineer sorghum varieties with improved metabolic efficiency, ultimately leading to better crop yields. In this review, we have focused on various multi-omics approaches, gene expression analysis, and different pathways for the improvement of Sorghum. Applying omics approaches to sorghum research allows for a holistic understanding of its genome function. This knowledge is invaluable for addressing challenges such as climate change, resource limitations, and the need for sustainable agriculture.
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Affiliation(s)
- Ananya Mukherjee
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Uma Maheshwari
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Vishal Sharma
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, Crop and Soil Science, University of Georgia, 111 Riverbend Road, Athens, GA, 30605, USA
| | - Satish Kumar
- Department of Food Science and Technology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, HP, 173230, India
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3
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Li J, Zhao R, Liu J, Yao J, Ma S, Yin K, Zhang Y, Liu Z, Yan C, Zhao N, Zhou X, Chen S. Populus euphratica GRP2 Interacts with Target mRNAs to Negatively Regulate Salt Tolerance by Interfering with Photosynthesis, Na +, and ROS Homeostasis. Int J Mol Sci 2024; 25:2046. [PMID: 38396725 PMCID: PMC10888501 DOI: 10.3390/ijms25042046] [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: 12/18/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The transcription of glycine-rich RNA-binding protein 2 (PeGRP2) transiently increased in the roots and shoots of Populus euphratica (a salt-resistant poplar) upon initial salt exposure and tended to decrease after long-term NaCl stress (100 mM, 12 days). PeGRP2 overexpression in the hybrid Populus tremula × P. alba '717-1B4' (P. × canescens) increased its salt sensitivity, which was reflected in the plant's growth and photosynthesis. PeGRP2 contains a conserved RNA recognition motif domain at the N-terminus, and RNA affinity purification (RAP) sequencing was developed to enrich the target mRNAs that physically interacted with PeGRP2 in P. × canescens. RAP sequencing combined with RT-qPCR revealed that NaCl decreased the transcripts of PeGRP2-interacting mRNAs encoding photosynthetic proteins, antioxidative enzymes, ATPases, and Na+/H+ antiporters in this transgenic poplar. Specifically, PeGRP2 negatively affected the stability of the target mRNAs encoding the photosynthetic proteins PETC and RBCMT; antioxidant enzymes SOD[Mn], CDSP32, and CYB1-2; ATPases AHA11, ACA8, and ACA9; and the Na+/H+ antiporter NHA1. This resulted in (i) a greater reduction in Fv/Fm, YII, ETR, and Pn; (ii) less pronounced activation of antioxidative enzymes; and (iii) a reduced ability to maintain Na+ homeostasis in the transgenic poplars during long-term salt stress, leading to their lowered ability to tolerate salinity stress.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Rui Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Jian Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China;
| | - Siyuan Ma
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Kexin Yin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Ying Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Zhe Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Caixia Yan
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Nan Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Xiaoyang Zhou
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Shaoliang Chen
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
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Liu Z, Zhang T, Xu R, Liu B, Han Y, Dong W, Xie Q, Tang Z, Lei X, Wang C, Fu Y, Gao C. BpGRP1 acts downstream of BpmiR396c/BpGRF3 to confer salt tolerance in Betula platyphylla. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:131-147. [PMID: 37703500 PMCID: PMC10754015 DOI: 10.1111/pbi.14173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/22/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023]
Abstract
Glycine-rich RNA-binding proteins (GRPs) have been implicated in the responses of plants to environmental stresses, but the function of GRP genes involved in salt stress and the underlying mechanism remain unclear. In this study, we identified BpGRP1 (glycine-rich RNA-binding protein), a Betula platyphylla gene that is induced under salt stress. The physiological and molecular responses to salt tolerance were investigated in both BpGRP1-overexpressing and suppressed conditions. BpGRF3 (growth-regulating factor 3) was identified as a regulatory factor upstream of BpGRP1. We demonstrated that overexpression of BpGRF3 significantly increased the salt tolerance of birch, whereas the grf3-1 mutant exhibited the opposite effect. Further analysis revealed that BpGRF3 and its interaction partner, BpSHMT, function upstream of BpGRP1. We demonstrated that BpmiR396c, as an upstream regulator of BpGRF3, could negatively regulate salt tolerance in birch. Furthermore, we uncovered evidence showing that the BpmiR396c/BpGRF3 regulatory module functions in mediating the salt response by regulating the associated physiological pathways. Our results indicate that BpmiR396c regulates the expression of BpGRF3, which plays a role in salt tolerance by targeting BpGRP1.
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Affiliation(s)
- Zhongyuan Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
- Key Laboratory of Forest Plant EcologyMinistry of EducationNortheast Forestry UniversityHarbinChina
- College of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbinChina
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Ruiting Xu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Baichao Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Yating Han
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Wenfang Dong
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Qingjun Xie
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Zihao Tang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Xiaojin Lei
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Chao Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Yujie Fu
- Key Laboratory of Forest Plant EcologyMinistry of EducationNortheast Forestry UniversityHarbinChina
- College of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbinChina
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
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5
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Corre M, Boehm V, Besic V, Kurowska A, Viry A, Mohammad A, Sénamaud-Beaufort C, Thomas-Chollier M, Lebreton A. Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection. Nucleic Acids Res 2023; 51:12459-12475. [PMID: 37941135 PMCID: PMC10711537 DOI: 10.1093/nar/gkad1033] [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: 03/22/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Cell autonomous responses to intracellular bacteria largely depend on reorganization of gene expression. To gain isoform-level resolution of these modes of regulation, we combined long- and short-read transcriptomic analyses of the response of intestinal epithelial cells to infection by the foodborne pathogen Listeria monocytogenes. Among the most striking isoform-based types of regulation, expression of the cellular stress response regulator CIRBP (cold-inducible RNA-binding protein) and of several SRSFs (serine/arginine-rich splicing factors) switched from canonical transcripts to nonsense-mediated decay-sensitive isoforms by inclusion of 'poison exons'. We showed that damage to host cell membranes caused by bacterial pore-forming toxins (listeriolysin O, perfringolysin, streptolysin or aerolysin) led to the dephosphorylation of SRSFs via the inhibition of the kinase activity of CLK1, thereby driving CIRBP alternative splicing. CIRBP isoform usage was found to have consequences on infection, since selective repression of canonical CIRBP reduced intracellular bacterial load while that of the poison exon-containing isoform exacerbated it. Consistently, CIRBP-bound mRNAs were shifted towards stress-relevant transcripts in infected cells, with increased mRNA levels or reduced translation efficiency for some targets. Our results thus generalize the alternative splicing of CIRBP and SRSFs as a common response to biotic or abiotic stresses by extending its relevance to the context of bacterial infection.
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Affiliation(s)
- Morgane Corre
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Vinko Besic
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anna Kurowska
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anouk Viry
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Ammara Mohammad
- GenomiqueENS, Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Catherine Sénamaud-Beaufort
- GenomiqueENS, Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Morgane Thomas-Chollier
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- GenomiqueENS, Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alice Lebreton
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
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Ma L, Tao X, Wang W, Jiao J, Pu Y, Yang G, Liu L, Fang Y, Wu J, Sun W. Genome-wide identification of RNA recognition motif (RRM1) in Brassica rapa and functional analysis of RNA-binding protein (BrRBP) under low-temperature stress. BMC PLANT BIOLOGY 2023; 23:621. [PMID: 38057714 DOI: 10.1186/s12870-023-04639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND The RNA recognition motif (RRM) is primarily engaged in the processing of mRNA and rRNA following gene transcription as well as the regulation of RNA transport; it is critical in preserving RNA stability. RESULTS In this study, we identified 102 members of the RRM1 gene family in Brassica rapa, which were dispersed across 10 chromosomes with the ninth chromosome being the most extensively distributed. The RRM1 gene family members of Brassica rapa and Arabidopsis thaliana were grouped into 14 subclades (I-XIV) using phylogenetic analysis. Moreover, the results of transcriptome analysis and RT-qPCR indicated that the expression of Brapa05T000840 was upregulated in the cultivars 'Longyou 7' and 'Longyou 99' following exposure to cold stress at a temperature of 4 °C for 24 h. The levels of expression in the leaves and growth cones of the 'Longyou 7' variety were found to be significantly higher than those observed in the 'Longyou 99' variety under conditions of low temperature and NaCl stress. It illustrates the involvement of the RRM1 gene in the physiological response to both low temperature and salt stress. In addition, it was observed that the survival rate of transgenic BrRBP (Brapa05T000840) Arabidopsis thaliana plants was notably higher compared to that of wild-type plants when subjected to varying durations of low temperature treatment. Furthermore, the expression of the BrRBP gene in transgenic plants exhibited an upward trend as the duration of low temperature treatment increased, reaching its peak at 24 h. The in-vivo enzymatic activity of reactive oxygen species-scavenging enzymes were found to be significantly elevated in comparison to wild-type plants, suggesting that the BrRBP gene may enhance the cold tolerance of Arabidopsis thaliana. CONCLUSIONS This study offers a significant foundation for comprehending the regulation mechanism of the RRM1 gene family in winter Brassica rapa subjected to cold stress, as well as for finding key genes associated with cold resistance.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaolei Tao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jintang Jiao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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Duan M, Zong M, Guo N, Han S, Wang G, Miao L, Liu F. Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea. PLANTS (BASEL, SWITZERLAND) 2023; 12:3706. [PMID: 37960062 PMCID: PMC10649936 DOI: 10.3390/plants12213706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants.
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Affiliation(s)
- Mengmeng Duan
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Mei Zong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Ning Guo
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Shuo Han
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Guixiang Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Liming Miao
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
| | - Fan Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
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8
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Cheng K, Zhang C, Lu Y, Li J, Tang H, Ma L, Zhu H. The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3504. [PMID: 37836244 PMCID: PMC10575402 DOI: 10.3390/plants12193504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
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Affiliation(s)
- Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hui Tang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
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Kim S, Huh SM, Han HJ, Lee GS, Hwang YS, Cho MH, Kim BG, Song JS, Chung JH, Nam MH, Ji H, Kim KH, Yoon IS. A rice seed-specific glycine-rich protein OsDOR1 interacts with GID1 to repress GA signaling and regulates seed dormancy. PLANT MOLECULAR BIOLOGY 2023; 111:523-539. [PMID: 36973492 DOI: 10.1007/s11103-023-01343-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Seed dormancy is an important agronomic trait under the control of complex genetic and environmental interactions, which have not been yet comprehensively understood. From the field screening of rice mutant library generated by a Ds transposable element, we identified a pre-harvest sprouting (PHS) mutant dor1. This mutant has a single insertion of Ds element at the second exon of OsDOR1 (LOC_Os03g20770), which encodes a novel seed-specific glycine-rich protein. This gene successfully complemented the PHS phenotype of dor1 mutant and its ectopic expression enhanced seed dormancy. Here, we demonstrated that OsDOR1 protein binds to the GA receptor protein, OsGID1 in rice protoplasts, and interrupts with the formation OsGID1-OsSLR1 complex in yeast cells. Co-expression of OsDOR1 with OsGID1 in rice protoplasts attenuated the GA-dependent degradation of OsSLR1, the key repressor of GA signaling. We showed the endogenous OsSLR1 protein level in the dor1 mutant seeds is significantly lower than that of wild type. The dor1 mutant featured a hypersensitive GA-response of α-amylase gene expression during seed germination. Based on these findings, we suggest that OsDOR1 is a novel negative player of GA signaling operated in the maintenance of seed dormancy. Our findings provide a novel source of PHS resistance.
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Affiliation(s)
- Sooyeon Kim
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Sun Mi Huh
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
- Department of Medical and Biological Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Hay Ju Han
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Gang Seob Lee
- Biosafety Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Yong-Sic Hwang
- Department of Systems Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mi Hyun Cho
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Beom-Gi Kim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Ji Sun Song
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Joo Hee Chung
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul, 02841, Republic of Korea
| | - Myung Hee Nam
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul, 02841, Republic of Korea
| | - Hyeonso Ji
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - Kyung-Hwan Kim
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea
| | - In Sun Yoon
- Gene Engineering Division, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 55365, Republic of Korea.
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Lu X, Yang Z, Song W, Miao J, Zhao H, Ji P, Li T, Si J, Yin Z, Jing M, Shen D, Dou D. The Phytophthora sojae effector PsFYVE1 modulates immunity-related gene expression by targeting host RZ-1A protein. PLANT PHYSIOLOGY 2023; 191:925-945. [PMID: 36461945 PMCID: PMC9922423 DOI: 10.1093/plphys/kiac552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Oomycete pathogens secrete numerous effectors to manipulate plant immunity and promote infection. However, relatively few effector types have been well characterized. In this study, members of an FYVE domain-containing protein family that are highly expanded in oomycetes were systematically identified, and one secreted protein, PsFYVE1, was selected for further study. PsFYVE1 enhanced Phytophthora capsici infection in Nicotiana benthamiana and was necessary for Phytophthora sojae virulence. The FYVE domain of PsFYVE1 had PI3P-binding activity that depended on four conserved amino acid residues. Furthermore, PsFYVE1 targeted RNA-binding proteins RZ-1A/1B/1C in N. benthamiana and soybean (Glycine max), and silencing of NbRZ-1A/1B/1C genes attenuated plant immunity. NbRZ-1A was associated with the spliceosome complex that included three important components, glycine-rich RNA-binding protein 7 (NbGRP7), glycine-rich RNA-binding protein 8 (NbGRP8), and a specific component of the U1 small nuclear ribonucleoprotein complex (NbU1-70K). Notably, PsFYVE1 disrupted NbRZ-1A-NbGRP7 interaction. RNA-seq and subsequent experimental analysis demonstrated that PsFYVE1 and NbRZ-1A not only modulated pre-mRNA alternative splicing (AS) of the necrotic spotted lesions 1 (NbNSL1) gene, but also co-regulated transcription of hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (NbHCT), ethylene insensitive 2 (NbEIN2), and sucrose synthase 4 (NbSUS4) genes, which participate in plant immunity. Collectively, these findings indicate that the FYVE domain-containing protein family includes potential uncharacterized effector types and also highlight that plant pathogen effectors can regulate plant immunity-related genes at both AS and transcription levels to promote disease.
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Affiliation(s)
- Xinyu Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zitong Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Song
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hanqing Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyun Ji
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jierui Si
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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11
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Ma L, Yang Y, Wang Y, Cheng K, Zhou X, Li J, Zhang J, Li R, Zhang L, Wang K, Zeng N, Gong Y, Zhu D, Deng Z, Qu G, Zhu B, Fu D, Luo Y, Zhu H. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato. THE PLANT CELL 2022; 34:2747-2764. [PMID: 35385118 PMCID: PMC9252502 DOI: 10.1093/plcell/koac104] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/05/2022] [Indexed: 06/01/2023]
Abstract
Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Yuqiu Wang
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiwen Zhou
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingyu Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Lingling Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ni Zeng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yanyan Gong
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Danmeng Zhu
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Xu W, Dou Y, Geng H, Fu J, Dan Z, Liang T, Cheng M, Zhao W, Zeng Y, Hu Z, Huang W. OsGRP3 Enhances Drought Resistance by Altering Phenylpropanoid Biosynthesis Pathway in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms23137045. [PMID: 35806050 PMCID: PMC9266740 DOI: 10.3390/ijms23137045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/07/2023] Open
Abstract
As a sessile organism, rice often faces various kinds of abiotic stresses, such as drought stress. Drought stress seriously harms plant growth and damages crop yield every year. Therefore, it is urgent to elucidate the mechanisms of drought resistance in rice. In this study, we identified a glycine-rich RNA-binding protein, OsGRP3, in rice. Evolutionary analysis showed that it was closely related to OsGR-RBP4, which was involved in various abiotic stresses. The expression of OsGRP3 was shown to be induced by several abiotic stress treatments and phytohormone treatments. Then, the drought tolerance tests of transgenic plants confirmed that OsGRP3 enhanced drought resistance in rice. Meanwhile, the yeast two-hybrid assay, bimolecular luminescence complementation assay and bimolecular fluorescence complementation assay demonstrated that OsGRP3 bound with itself may affect the RNA chaperone function. Subsequently, the RNA-seq analysis, physiological experiments and histochemical staining showed that OsGRP3 influenced the phenylpropanoid biosynthesis pathway and further modulated lignin accumulation. Herein, our findings suggested that OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid biosynthesis pathway and further increasing lignin accumulation.
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Affiliation(s)
- Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangfan Dou
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han Geng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jinmei Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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Cui H, Fan C, Ding Z, Wang X, Tang L, Bi Y, Luan F, Gao P. CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in Melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1209-1222. [PMID: 34989827 DOI: 10.1007/s00122-021-04025-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Two genes for resistance to Podosphaera xanthii race 1 in melon were identified on chromosomes 10 and 12 of the Cucumis melo cultivar MR-1. Cucumis melo L. is an economically important crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P1; resistant to PM) and M4-7 (P2; susceptible to PM) accessions to assess the heritability of PM (race 1) resistance in these melon plants. PM resistance in MR-1 leaves was linked to a dominant gene (CmPMRl), whereas stem resistance was under the control of a recessive gene (CmPMrs), with the dominant gene having an epistatic effect on the recessive gene. The CmPMRl gene was mapped to a 50 Kb interval on chromosome 12, while CmPMrs was mapped to an 89 Kb interval on chromosome 10. The CmPMRl candidate gene MELO3C002441 and the CmPMrs candidate gene MELO3C012438 were identified through sequence alignment, functional annotation, and expression pattern analyzes of all genes within these respective intervals. MELO3C002441 and MELO3C012438 were both localized to the cellular membrane and were contained conserved NPR gene-like and MLO domains, respectively, which were linked to PM resistance. In summary, we identified patterns of PM resistance in the disease-resistant MR-1 melon cultivar and identified two putative genes linked to resistance. Our results offer new genetic resources and markers to guide future marker-assisted breeding for PM resistance in melon.
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Affiliation(s)
- Haonan Cui
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China
| | - Chao Fan
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150030, Heilongjiang, China
| | - Zhuo Ding
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China
| | - Lili Tang
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150030, Heilongjiang, China
| | - Yingdong Bi
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150030, Heilongjiang, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China.
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China.
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14
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Singh G, Singh V, Singh V. Systems scale characterization of circadian rhythm pathway in Camellia sinensis. Comput Struct Biotechnol J 2022; 20:598-607. [PMID: 35116135 PMCID: PMC8790616 DOI: 10.1016/j.csbj.2021.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 11/29/2022] Open
Abstract
Tea (Camellia sinensis) is among the most valuable commercial crops being a non-alcoholic beverage having antioxidant properties. Like in other plants, circadian oscillator in tea modulates several biological processes according to earth's revolution dependent variations in environmental cues like light and temperature. In the present study, we report genome wide identification and characterization of circadian oscillator (CO) proteins in tea. We first mined the genes (24, in total) involved in circadian rhythm pathway in the 56 plant species having available genomic information and then built their hidden Markov models (HMMs). Using these HMMs, 24 proteins were identified in tea and were further assessed for their functional annotation. Expression analysis of all these 24 CO proteins was then performed in 3 abiotic (A) and 3 biotic conditions (B) stress conditions and co-expressed as well as differentially expressed genes in the selected 6 stress conditions were elaborated. A methodology to identify the differentially expressed genes in specific types of stresses (A or B) is proposed and novel markers among CO proteins are presented. By mapping the identified CO proteins against the recently reported genome wide interologous protein-protein interaction network of tea (TeaGPIN), an interaction sub-network of tea CO proteins (TeaCO-PIN) is developed and analysed. Out of 24 CO proteins, structures of 4 proteins could be successfully predicted and validated using consensus of three structure prediction algorithms and their stability was further assessed using molecular dynamic simulations at 100 ns. Phylogenetic analysis of these proteins is performed to examine their molecular evolution.
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Affiliation(s)
| | | | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
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15
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Du C, Bai HY, Chen JJ, Wang JH, Wang ZF, Zhang ZH. Alternative Splicing Regulation of Glycine-Rich Proteins via Target of Rapamycin-Reactive Oxygen Species Pathway in Arabidopsis Seedlings Upon Glucose Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:830140. [PMID: 35498646 PMCID: PMC9051487 DOI: 10.3389/fpls.2022.830140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/16/2022] [Indexed: 05/05/2023]
Abstract
Glucose can serve as both the source of energy and regulatory signaling molecule in plant. Due to the environmental and metabolic change, sugar levels could affect various developmental processes. High glucose environment is hardly conductive to the plant growth but cause development arrest. Increasing evidence indicate that alternative splicing (AS) plays a pivotal role in sugar signaling. However, the regulatory mechanism upon glucose stress remains unclear. The full-length transcriptomes were obtained from the samples of Arabidopsis seedlings with 3% glucose and mock treatment, using Oxford Nanopore sequencing technologies. Further analysis indicated that many genes involved in photosynthesis were significantly repressed and many genes involved in glycolysis, mitochondrial function, and the response to oxidative stress were activated. In total, 1,220 significantly differential alternative splicing (DAS) events related to 619 genes were identified, among which 75.74% belong to intron retention (IR). Notably, more than 20% of DAS events come from a large set of glycine-rich protein (GRP) family genes, such as GRP7, whose AS types mostly belong to IR. Besides the known productive GRP transcript isoforms, we identified a lot of splicing variants with diverse introns spliced in messenger RNA (mRNA) region coding the glycine-rich (GR) domain. The AS pattern of GRPs changed and particularly, the productive GRPs increased upon glucose stress. These ASs of GRP pre-mRNAs triggered by glucose stress could be abolished by AZD-8055, which is an ATP competitive inhibitor for the target of rapamycin (TOR) kinase but could be mimicked by H2O2. Additionally, AS pattern change of arginine/serine-rich splicing factor 31(RS31) via TOR pathway, which was previously described in response to light and sucrose signaling, was also induced in a similar manner by both glucose stress and reactive oxygen species (ROS). Here we conclude that (i) glucose stress suppresses photosynthesis and activates the glycolysis-mitochondria energy relay and ROS scavenging system; (ii) glucose stress triggers transcriptome-wide AS pattern changes including a large set of splicing factors, such as GRPs and RS31; (iii) high sugars regulate AS pattern change of both GRPs and RS31 via TOR-ROS pathway. The results from this study will deepen our understanding of the AS regulation mechanism in sugar signaling.
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Yan Y, Gan J, Tao Y, Okita TW, Tian L. RNA-Binding Proteins: The Key Modulator in Stress Granule Formation and Abiotic Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:882596. [PMID: 35783947 PMCID: PMC9240754 DOI: 10.3389/fpls.2022.882596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
To cope with abiotic environmental stress, plants rapidly change their gene expression transcriptionally and post-transcriptionally, the latter by translational suppression of selected proteins and the assembly of cytoplasmic stress granules (SGs) that sequester mRNA transcripts. RNA-binding proteins (RBPs) are the major players in these post-transcriptional processes, which control RNA processing in the nucleus, their export from the nucleus, and overall RNA metabolism in the cytoplasm. Because of their diverse modular domain structures, various RBP types dynamically co-assemble with their targeted RNAs and interacting proteins to form SGs, a process that finely regulates stress-responsive gene expression. This review summarizes recent findings on the involvement of RBPs in adapting plants to various abiotic stresses via modulation of specific gene expression events and SG formation. The relationship of these processes with the stress hormone abscisic acid (ABA) is discussed.
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Affiliation(s)
- Yanyan Yan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jianghuang Gan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Yilin Tao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- *Correspondence: Thomas W. Okita,
| | - Li Tian
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
- Li Tian,
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17
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Abreha KB, Enyew M, Carlsson AS, Vetukuri RR, Feyissa T, Motlhaodi T, Ng'uni D, Geleta M. Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress. PLANTA 2021; 255:20. [PMID: 34894286 PMCID: PMC8665920 DOI: 10.1007/s00425-021-03799-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/19/2021] [Indexed: 05/10/2023]
Abstract
Droughts negatively affect sorghum's productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.
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Affiliation(s)
- Kibrom B Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden.
| | - Muluken Enyew
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
- Institute of Biotechnology, Addis Ababa University, Box 1176, Addis Ababa, Ethiopia
| | - Anders S Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Box 1176, Addis Ababa, Ethiopia
| | - Tiny Motlhaodi
- Department of Agricultural Research, Private Bag, 0033, Gaborone, Botswana
| | - Dickson Ng'uni
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/B 7, Chilanga, Zambia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
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18
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The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator. EPIGENOMES 2021; 5:epigenomes5040024. [PMID: 34968248 PMCID: PMC8715473 DOI: 10.3390/epigenomes5040024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.
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Tang Y, Huang C, Li Y, Wang Y, Zhang C. Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes ( Vitis vinifera). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2231-2243. [PMID: 34744363 PMCID: PMC8526680 DOI: 10.1007/s12298-021-01082-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Glycine-rich RNA-binding proteins (GRPs) are essential for many physiological and biochemical processes in plants, especially the response to environmental stresses. GRPs exist widely in angiosperms and gymnosperms plant species; however, their roles in Vitis vinifera are still poorly understood. To characterize VviGRP gene family, we performed a genomic survey, bioinformatics and expression analysis of VviGRPs in grape. We identified nineteen VviGRPs gene family members. The result of bioinformatics analysis showed their motif distribution, gene structure characteristics and chromosomal locations. Then we carried out synteny and phylogenetic analysis to study the origin and evolutionary relationship of GRPs. Tissue-specific expression analysis showed that VviGRPs have different expression patterns. Meanwhile, we studied expression profiles of seventeen ovule-expressed genes during seed development of stenospermocarpic seedless and seeded grapes, and the result showed that most of them have much higher relative expression levels in stenospermocarpic seedless grapes than that of seeded one before 25 days after full bloom (DAFB). It is suggested that VviGRPs may involve in the seed development process. Taken together, our research indicated that VviGRPs are related to seed development and will be beneficial for further investigations into the seed abortion mechanism under stenospermocarpic grapes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01082-3.
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Affiliation(s)
- Yujin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Congbo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Yan Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
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Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview. Int J Mol Sci 2021; 22:ijms22136731. [PMID: 34201749 PMCID: PMC8269355 DOI: 10.3390/ijms22136731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.
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21
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Ma L, Cheng K, Li J, Deng Z, Zhang C, Zhu H. Roles of Plant Glycine-Rich RNA-Binding Proteins in Development and Stress Responses. Int J Mol Sci 2021; 22:ijms22115849. [PMID: 34072567 PMCID: PMC8198583 DOI: 10.3390/ijms22115849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
In recent years, much progress has been made in elucidating the functional roles of plant glycine-rich RNA-binding proteins (GR-RBPs) during development and stress responses. Canonical GR-RBPs contain an RNA recognition motif (RRM) or a cold-shock domain (CSD) at the N-terminus and a glycine-rich domain at the C-terminus, which have been associated with several different RNA processes, such as alternative splicing, mRNA export and RNA editing. However, many aspects of GR-RBP function, the targeting of their RNAs, interacting proteins and the consequences of the RNA target process are not well understood. Here, we discuss recent findings in the field, newly defined roles for GR-RBPs and the actions of GR-RBPs on target RNA metabolism.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Zhiqi Deng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
- Correspondence:
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22
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Slaby P, Körner M, Albert M. A cell wall-localized glycine-rich protein of dodder acts as pathogen-associated molecular pattern. Commun Integr Biol 2021; 14:111-114. [PMID: 33995821 PMCID: PMC8096328 DOI: 10.1080/19420889.2021.1918369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Cuscuta reflexa (giant dodder) is an obligate stem holoparasite withdrawing water, nutrients, and carbohydrates from its hosts. For a broad spectrum of host plants, C. reflexa usually stays unrecognized. The cultivated tomato Solanum lycopersicum, as one notable exception, possesses a leucine-rich repeat receptor protein (LRR-RP), Cuscuta receptor 1 (CuRe1), which enables tomato to recognize C. reflexa as a dangerous parasitic invader and to respond with plant immune responses. During the infection process, a glycine-rich protein (GRP) is freed from C. reflexa and gets detected by CuRe1. Here, we focus on the subcellular localization of the GRP within plant cell walls using a fluorescence based co-localization.
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Affiliation(s)
- Peter Slaby
- Department of Biology, Molecular Plant Physiology, Erlangen, Germany
| | - Max Körner
- Department of Biology, Molecular Plant Physiology, Erlangen, Germany
| | - Markus Albert
- Department of Biology, Molecular Plant Physiology, Erlangen, Germany
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23
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Shim JS, Park SH, Lee DK, Kim YS, Park SC, Redillas MCFR, Seo JS, Kim JK. The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes. RICE (NEW YORK, N.Y.) 2021; 14:31. [PMID: 33742286 PMCID: PMC7979854 DOI: 10.1186/s12284-021-00473-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant glycine-rich proteins are categorized into several classes based on their protein structures. The glycine-rich RNA binding proteins (GRPs) are members of class IV subfamily possessing N-terminus RNA-recognition motifs (RRMs) and proposed to be involved in post-transcriptional regulation of its target transcripts. GRPs are involved in developmental process and cellular stress responses, but the molecular mechanisms underlying these regulations are still elusive. RESULTS Here, we report the functional characterization of rice GLYCINE-RICH PROTEIN 3 (OsGRP3) and its physiological roles in drought stress response. Both drought stress and ABA induce the expression of OsGRP3. Transgenic plants overexpressing OsGRP3 (OsGRP3OE) exhibited tolerance while knock-down plants (OsGRP3KD) were susceptible to drought compared to the non-transgenic control. In vivo, subcellular localization analysis revealed that OsGRP3-GFP was transported from cytoplasm/nucleus into cytoplasmic foci following exposure to ABA and mannitol treatments. Comparative transcriptomic analysis between OsGRP3OE and OsGRP3KD plants suggests that OsGRP3 is involved in the regulation of the ROS related genes. RNA-immunoprecipitation analysis revealed the associations of OsGRP3 with PATHOGENESIS RELATED GENE 5 (PR5), METALLOTHIONEIN 1d (MT1d), 4,5-DOPA-DIOXYGENASE (DOPA), and LIPOXYGENASE (LOX) transcripts. The half-life analysis showed that PR5 transcripts decayed slower in OsGRP3OE but faster in OsGRP3KD, while MT1d and LOX transcripts decayed faster in OsGRP3OE but slower in OsGRP3KD plants. H2O2 accumulation was reduced in OsGRP3OE and increased in OsGRP3KD plants compared to non-transgenic plants (NT) under drought stress. CONCLUSION OsGRP3 plays a positive regulator in rice drought tolerance and modulates the transcript level and mRNA stability of stress-responsive genes, including ROS-related genes. Moreover, OsGRP3 contributes to the reduction of ROS accumulation during drought stress. Our results suggested that OsGRP3 alleviates ROS accumulation by regulating ROS-related genes' mRNA stability under drought stress, which confers drought tolerance.
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Affiliation(s)
- Jae Sung Shim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Hyun Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Dong-Keun Lee
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- E GREEN GLOBAL, Gunpo, 15843, South Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, South Korea
| | - Soo-Chul Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, South Korea
| | | | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
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Tawab F, Munir I, Nasim Z, Khan MS, Tawab S, Nasim A, Iqbal A, Ahmad MA, Ali W, Munir R, Munir M, Asim N. Identification and characterization of a novel multi-stress responsive gene in Arabidopsis. PLoS One 2020; 15:e0244030. [PMID: 33332435 PMCID: PMC7746274 DOI: 10.1371/journal.pone.0244030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/01/2020] [Indexed: 12/04/2022] Open
Abstract
Abiotic stresses especially salinity, drought and high temperature result in considerable reduction of crop productivity. In this study, we identified AT4G18280 annotated as a glycine-rich cell wall protein-like (hereafter refer to as GRPL1) protein as a potential multistress-responsive gene. Analysis of public transcriptome data and GUS assay of pGRPL1::GUS showed a strong induction of GRPL1 under drought, salinity and heat stresses. Transgenic plants overexpressing GRPL1-3HA showed significantly higher germination, root elongation and survival rate under salt stress. Moreover, the 35S::GRPL1-3HA transgenic lines also showed higher survival rates under drought and heat stresses. GRPL1 showed similar expression patterns with Abscisic acid (ABA)-pathway genes under different growth and stress conditions, suggesting a possibility that GRPL1 might act in the ABA pathway that is further supported by the inability of ABA-deficient mutant (aba2-1) to induce GRPL1 under drought stress. Taken together, our data presents GRPL1 as a potential multi-stress responsive gene working downstream of ABA.
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Affiliation(s)
- Faiza Tawab
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Iqbal Munir
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
- * E-mail:
| | - Zeeshan Nasim
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Mohammad Sayyar Khan
- Genomics and Bioinformatics Division, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Saleha Tawab
- Agriculture Research System, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Adnan Nasim
- Agriculture Research System, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Aqib Iqbal
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Mian Afaq Ahmad
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Waqar Ali
- Department of Biotechnology, University of Malakand, Chakdara, Lower Dir, Khyber Pakhtunkhwa, Pakistan
| | - Raheel Munir
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Maria Munir
- Division of Biochemistry, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Noreen Asim
- Genomics and Bioinformatics Division, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
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Sun S, Yi C, Ma J, Wang S, Peirats-Llobet M, Lewsey MG, Whelan J, Shou H. Analysis of Spatio-Temporal Transcriptome Profiles of Soybean ( Glycine max) Tissues during Early Seed Development. Int J Mol Sci 2020; 21:E7603. [PMID: 33066688 PMCID: PMC7589660 DOI: 10.3390/ijms21207603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 01/17/2023] Open
Abstract
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.
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Affiliation(s)
- Shuo Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Changyu Yi
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Jing Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Shoudong Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China;
| | - Marta Peirats-Llobet
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia;
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
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26
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Lou L, Ding L, Wang T, Xiang Y. Emerging Roles of RNA-Binding Proteins in Seed Development and Performance. Int J Mol Sci 2020; 21:ijms21186822. [PMID: 32957608 PMCID: PMC7555721 DOI: 10.3390/ijms21186822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 02/01/2023] Open
Abstract
Seed development, dormancy, and germination are key physiological events that are not only important for seed generation, survival, and dispersal, but also contribute to agricultural production. RNA-binding proteins (RBPs) directly interact with target mRNAs and fine-tune mRNA metabolism by governing post-transcriptional regulation, including RNA processing, intron splicing, nuclear export, trafficking, stability/decay, and translational control. Recent studies have functionally characterized increasing numbers of diverse RBPs and shown that they participate in seed development and performance, providing significant insight into the role of RBP-mRNA interactions in seed processes. In this review, we discuss recent research progress on newly defined RBPs that have crucial roles in RNA metabolism and affect seed development, dormancy, and germination.
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Lee K, Kang H. Roles of Organellar RNA-Binding Proteins in Plant Growth, Development, and Abiotic Stress Responses. Int J Mol Sci 2020; 21:ijms21124548. [PMID: 32604726 PMCID: PMC7352785 DOI: 10.3390/ijms21124548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation of post-transcriptional RNA metabolism in organelles. Although the functional roles of nCMRBPs have been studied in plants, their cellular and physiological functions remain largely unknown. Nevertheless, existing studies that have characterized the functions of nCMRBP families, such as chloroplast ribosome maturation and splicing domain (CRM) proteins, pentatricopeptide repeat (PPR) proteins, DEAD-Box RNA helicase (DBRH) proteins, and S1-domain containing proteins (SDPs), have begun to shed light on the role of nCMRBPs in plant growth, development, and stress responses. Here, we review the latest research developments regarding the functional roles of organellar RBPs in RNA metabolism during growth, development, and abiotic stress responses in plants.
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Affiliation(s)
- Kwanuk Lee
- Plant Molecular Biology (Botany), Department of Biology I, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
- Correspondence: (K.L.); (H.K.); Tel.: +49-157-8852-8990 (K.L.); +82-62-530-2181 (H.K.); Fax: +82-62-530-2079 (H.K.)
| | - Hunseung Kang
- Department of Applied Biology and AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (K.L.); (H.K.); Tel.: +49-157-8852-8990 (K.L.); +82-62-530-2181 (H.K.); Fax: +82-62-530-2079 (H.K.)
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Chen Z, Xu J, Wang F, Wang L, Xu Z. Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties. Sci Rep 2019; 9:18523. [PMID: 31811189 PMCID: PMC6898209 DOI: 10.1038/s41598-019-54995-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
To gain insight into the molecular mechanisms underpinning tobacco (Nicotiana tabacum) tolerance to drought stress, we integrated anatomical, physiological, and proteomic analyses of drought-tolerant (Yuyan6, [Y6]) and -sensitive (Yunyan87 [Y87]) varieties. In comparison to Y87, Y6 exhibited higher water retention capability, improved photosynthetic performance, delayed leaf-senescence, stable leaf ultrastructure, a stronger antioxidant defense, and lesser ROS accumulation when subjected to water stress. Using an iTRAQ-based proteomics approach, 405 and 1,560 differentially accumulated proteins (DAPs) were identified from Y6 and Y87 plants, respectively, of which 114 were found to be present in both cultivars. A subsequent functional characterization analysis revealed that these DAPs were significantly enriched in eight biological processes, six molecular functions, and six cellular components and displayed differential expression patterns in Y6 and Y87 plants, suggesting that the response to water stress between both varieties differed at the proteomic level. Furthermore, we constructed protein coexpression networks and identified hub proteins regulating tobacco defenses to water stress. Additionally, qPCR analysis indicated that the majority of genes encoding selected proteins showed consistency between mRNA levels and their corresponding protein expression levels. Our results provide new insights into the genetic regulatory mechanisms associated with drought response in tobacco plants.
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Affiliation(s)
- Zheng Chen
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiayang Xu
- Agronomy and Biotechnology College, China Agricultural University, Beijing, 100193, China
| | - Fazhan Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lin Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zicheng Xu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
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Single-nucleotide polymorphism markers within MVA and MEP pathways among Hevea brasiliensis clones through transcriptomic analysis. 3 Biotech 2019; 9:388. [PMID: 31656726 DOI: 10.1007/s13205-019-1921-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022] Open
Abstract
In this study, RNA sequencing of several Hevea brasiliensis clones grown in Malaysia with different annual rubber production yields and disease resistance was performed on the Illumina platform. A total of 29,862,548 reads were generated, resulting in 101,269 assembled transcripts that were used as the reference transcripts. A similarity search against the non-redundant (nr) protein databases presented 83,771 (83%) positive BLASTx hits. The transcriptome was annotated using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Pfam database. A search for putative molecular markers was performed to identify single-nucleotide polymorphisms (SNPs). Overall, 3,210,629 SNPs were detected and a total of 1314 SNPs associated with the genes involved in MVA and MEP pathways were identified. A total of 176 SNP primer pairs were designed from sequences that were related to the MVA and MEP pathways. The transcriptome of RRIM 3001 and RRIM 712 were subjected to pairwise comparison and the results revealed that there were 1262 significantly differentially expressed genes unique to RRIM 3001, 1499 significantly differentially expressed genes unique to RRIM 712 and several genes related to the MVA and MEP pathways such as AACT, HMGS, PMK, MVD, DXS and HDS were included. The results will facilitate the characterization of H. brasiliensis transcriptomes and the development of a new set of molecular markers in the form of SNPs from transcriptome assembly for the genotype identification of various rubber varieties with superior traits in Malaysia.
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Chen MX, Sun C, Zhang KL, Song YC, Tian Y, Chen X, Liu YG, Ye NH, Zhang J, Qu S, Zhu FY. SWATH-MS-facilitated proteomic profiling of fruit skin between Fuji apple and a red skin bud sport mutant. BMC PLANT BIOLOGY 2019; 19:445. [PMID: 31651235 PMCID: PMC6813987 DOI: 10.1186/s12870-019-2018-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. RESULTS Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin bud mutation and a total of 451 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substantial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected, indicating a promising role for the red skin color development in the mutant. Furthermore, we also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. CONCLUSION Our work provides important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributing for the molecular breeding of fruit skin color.
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Affiliation(s)
- Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Chao Sun
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 8210095 China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Yu-Chen Song
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Yuan Tian
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Xi Chen
- Medical Research Institute, Wuhan University and SpecAlly Life Technology Co., Ltd, Wuhan, China
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong China
| | - Neng-Hui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128 China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Shenchun Qu
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 8210095 China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
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Liu C, Schläppi MR, Mao B, Wang W, Wang A, Chu C. The bZIP73 transcription factor controls rice cold tolerance at the reproductive stage. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1834-1849. [PMID: 30811812 PMCID: PMC6686130 DOI: 10.1111/pbi.13104] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 05/19/2023]
Abstract
Cold temperature during the reproductive stage often causes great yield loss of grain crops in subtropical and temperate regions. Previously we showed that the rice transcription factor bZIP73Jap plays an important role in cold adaptation at the seedling stage. Here we further demonstrate that bZIP73Jap also confers cold stress tolerance at the reproductive stage. bZIP73Jap was up-regulated under cold treatment and predominately expressed in panicles at the early binucleate and flowering stages. bZIP73Jap forms heterodimers with bZIP71, and co-expression of bZIP73Jap and bZIP71 transgenic lines significantly increased seed-setting rate and grain yield under natural cold stress conditions. bZIP73Jap :bZIP71 not only repressed ABA level in anthers, but also enhanced soluble sugar transport from anthers to pollens and improved pollen grain fertility, seed-setting rate, and grain yield. Interestingly, bZIP73Jap :bZIP71 also regulated the expression of qLTG3-1Nip , and qLTG3-1Nip overexpression lines greatly improved rice tolerance to cold stress during the reproductive stage. Therefore, our work establishes a framework for rice cold stress tolerance through the bZIP71-bZIP73Jap -qLTG3-1Nip -sugar transport pathway. Together with our previous work, our results provide a powerful tool for improving rice cold stress tolerance at both the seedling and the reproductive stages.
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Affiliation(s)
- Citao Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | | | - Bigang Mao
- State Key Laboratory of Hybrid RiceChina National Hybrid Rice Research and Development CenterChangshaChina
| | - Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Aiju Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Castaño E, Rodríguez-Zapata LC. Global Dynamics in Protein Disorder during Maize Seed Development. Genes (Basel) 2019; 10:genes10070502. [PMID: 31262071 PMCID: PMC6678312 DOI: 10.3390/genes10070502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco. División de Biotecnología Industrial. Camino Arenero 1227, El Bajío, Zapopan, Jalisco. C.P. 45019
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México.
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Yang W, Yu M, Zou C, Lu C, Yu D, Cheng H, Jiang P, Feng X, Zhang Y, Wang Q, Zhang H, Song G, Zhou Z. Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii. PLoS One 2019; 14:e0218938. [PMID: 31242257 PMCID: PMC6594650 DOI: 10.1371/journal.pone.0218938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/12/2019] [Indexed: 11/18/2022] Open
Abstract
RB-GRP (RNA-binding Glycine-rich protein gene) family belongs to the fourth subfamily of the GRP (Glycine-rich protein gene) superfamily, which plays a great role in plant growth and development, as well as in abiotic stresses response, while it has not been identified in cotton. Here, we identified 37 and 32 RB-GRPs from two cotton species (Gossypium arboreum and Gossypium raimondii, respectively), which were divided into four distinct subfamilies based on the presence of additional motifs and the arrangement of the glycine repeats. The distribution of RB-GRPs was nonrandom and uneven among the chromosomes both in two cotton species. The expansion of RB-GRP gene family between two cultivars was mainly attributed to segmental and tandem duplication events indicated by synteny analysis, and the tandem duplicated genes were mapped into homologous collinear blocks, indicated that they shared a common ancestral gene in both species. Furthermore, most RB-GRPs in two cotton species undergone stronger negative selective pressure by evolutionary analysis of RB-GRP orthologous genes. Meanwhile, RB-GRPs participated in different abiotic stresses (Abscisic acid, salt and Polyethylene glycol) responses and tissues at different developmental stages between two cotton species were showed by gene expression analysis. This research would provide insight into the evolution and function of the RB-GRPs in Gossypium species.
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Affiliation(s)
- Wencui Yang
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Min Yu
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changsong Zou
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Cairui Lu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Daoqian Yu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pengfei Jiang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hong Zhang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China
- * E-mail: (GS); (ZZ)
| | - Zhuqing Zhou
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (GS); (ZZ)
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Huang X, Yu R, Li W, Geng L, Jing X, Zhu C, Liu H. Identification and characterisation of a glycine-rich RNA-binding protein as an endogenous suppressor of RNA silencing from Nicotiana glutinosa. PLANTA 2019; 249:1811-1822. [PMID: 30840177 DOI: 10.1007/s00425-019-03122-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 05/08/2023]
Abstract
MAIN CONCLUSION This study shows that NgRBP suppresses both local and systemic RNA silencing induced by sense- or double-stranded RNA, and the RNA binding activity is essential for its function. To counteract host defence, many plant viruses encode viral suppressors of RNA silencing targeting various stages of RNA silencing. There is increasing evidence that the plants also encode endogenous suppressors of RNA silencing (ESR) to regulate this pathway. In this study, using Agrobacterium infiltration assays, we characterized NgRBP, a glycine-rich RNA-binding protein from Nicotiana glutinosa, as an ESR. Our results indicated that NgRBP suppressed both local and systemic RNA silencing induced by sense- or double-stranded RNA. We also demonstrated that NgRBP could promote Potato Virus X (PVX) infection in N. benthamiana. NgRBP knockdown by virus-induced gene silencing enhanced PVX and Cucumber mosaic virus resistance in N. glutinosa. RNA immunoprecipitation and electrophoretic mobility shift assays showed that NgRBP bound to GFP mRNA, dsRNA rather than siRNA. These findings provide the evidence that NgRBP acts as an ESR and the RNA affinity of NgRBP plays the key role in its ESR activity. NgRBP responds to multiple signals such as ABA, MeJA, SA, and Tobacco mosaic virus infection. Therefore, it could participate in the regulation of gene expression under specific conditions.
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Affiliation(s)
- Xu Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Ru Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Wenjing Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Liwei Geng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiuli Jing
- Institute of Immunology, Taishan Medical University, Tai'an, Shandong, China
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hongmei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.
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Yeap WC, Namasivayam P, Ooi TEK, Appleton DR, Kulaveerasingam H, Ho CL. EgRBP42 from oil palm enhances adaptation to stress in Arabidopsis through regulation of nucleocytoplasmic transport of stress-responsive mRNAs. PLANT, CELL & ENVIRONMENT 2019; 42:1657-1673. [PMID: 30549047 DOI: 10.1111/pce.13503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Abiotic stress reduces plant growth and crop productivity. However, the mechanism underlying posttranscriptional regulations of stress response remains elusive. Herein, we report the posttranscriptional mechanism of nucleocytoplasmic RNA transport of stress-responsive transcripts mediated by EgRBP42, a heterogeneous nuclear ribonucleoprotein-like RNA-binding protein from oil palm, which could be necessary for rapid protein translation to confer abiotic stress tolerance in plants. Transgenic Arabidopsis overexpressing EgRBP42 showed early flowering through alteration of gene expression of flowering regulators and exhibited tolerance towards heat, cold, drought, flood, and salinity stresses with enhanced poststress recovery response by increasing the expression of its target stress-responsive genes. EgRBP42 harbours nucleocytoplasmic shuttling activity mediated by the nuclear localization signal and the M9-like domain of EgRBP42 and interacts directly with regulators in the nucleus, membrane, and the cytoplasm. EgRBP42 regulates the nucleocytoplasmic RNA transport of target stress-responsive transcripts through direct binding to their AG-rich motifs. Additionally, EgRBP42 transcript and protein induction by environmental stimuli are regulated at the transcriptional and posttranscriptional levels. Taken together, the posttranscriptional regulation of RNA transport mediated by EgRBP42 may change the stress-responsive protein profiles under abiotic stress conditions leading to a better adaptation of plants to environmental changes.
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Affiliation(s)
- Wan-Chin Yeap
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Tony Eng Keong Ooi
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - David Ross Appleton
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Plantation Berhad, Research and Development, Sime Darby Research Sdn Bhd, R&D Centre-Upstream, Kuala Langat, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Malaysia
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Lenka SK, Singh AK, Muthusamy SK, Smita S, Chinnusamy V, Bansal KC. Heterologous expression of rice RNA-binding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:482-491. [PMID: 30940336 DOI: 10.1071/fp18241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Imparting cold stress tolerance to crops is a major challenge in subtropical agriculture. New genes conferring cold tolerance needs to be identified and characterised for sustainable crop production in low-temperature stress affected areas. Here we report functional characterisation of OsRBGD3, classified previously as a class D glycine-rich RNA recognition motif (RRM) containing proteins from a drought-tolerant Indica rice cultivar N22. The gene was isolated by screening yeast one-hybrid library using the minimal promoter region of the OsMYB38 that is necessary for cold stress-responsive expression. OsRBGD3 exhibited cold, drought and salt stress inductive expression in a drought tolerant N22 rice cultivar as compared with susceptible variety IR64. OsRBGD3 was found to be localised to both nuclear and cytoplasmic subcellular destinations. Constitutive overexpression of the OsRBGD3 in transgenic Arabidopsis conferred tolerance to cold stress. ABA sensitivity was also observed in transgenic lines suggesting the regulatory role of this gene in the ABA signalling pathway. OsRBGD3 overexpression also attributed to significant root development and early flowering in transgenics. Hence, OsRBGD3 could be an important target for developing cold tolerant early flowering rice and other crops' genotypes for increasing production in low temperature affected areas.
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Affiliation(s)
- Sangram K Lenka
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India
| | - Amit K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Senthilkumar K Muthusamy
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India
| | - Shuchi Smita
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and Department of Immunology, School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Viswanathan Chinnusamy
- ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi, 110012, India
| | - Kailash C Bansal
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India; and Corresponding author.
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Proteome of rice roots treated with exogenous proline. 3 Biotech 2019; 9:101. [PMID: 30800612 DOI: 10.1007/s13205-019-1615-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/04/2019] [Indexed: 01/09/2023] Open
Abstract
Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expressed proteins were identified by mass spectrometry. Proline-treated rice roots showed up-regulation and down-regulation of nine and eight proteins, respectively, when compared to those in the control. Among the differentially expressed proteins, the down-regulation of glutathione reductase and peroxidase could be involved in the regulation of cellular hydrogen peroxide and reactive oxygen species levels that modulate the root cell wall structure. Differentially expressed proteins identified as pathogenesis-related proteins might be related to stress adaptive mechanisms in response to exogenous proline treatment. In addition, differentially expressed protein identified as the fructose-bisphosphate aldolases and cytochrome c oxidase might be associated with energy metabolism, which is needed during root developmental process. This is the first attempt to study the changes in rice root proteome treated with proline. The acquired information could open new avenues for further functional studies on the involvement of proline in modulating root development and its relation to stress adaptation of plants.
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Li LQ, Lyu CC, Li JH, Tong Z, Lu YF, Wang XY, Ni S, Yang SM, Zeng FC, Lu LM. Physiological Analysis and Proteome Quantification of Alligator Weed Stems in Response to Potassium Deficiency Stress. Int J Mol Sci 2019; 20:ijms20010221. [PMID: 30626112 PMCID: PMC6337362 DOI: 10.3390/ijms20010221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023] Open
Abstract
The macronutrient potassium is essential to plant growth, development and stress response. Alligator weed (Alternanthera philoxeroides) has a high tolerance to potassium deficiency (LK) stress. The stem is the primary organ responsible for transporting molecules from the underground root system to the aboveground parts of the plant. However, proteomic changes in response to LK stress are largely unknown in alligator weed stems. In this study, we investigated the physiological and proteomic changes in alligator weed stems under LK stress. First, the chlorophyll and soluble protein content and SOD and POD activity were significantly altered after 15 days of LK treatment. The quantitative proteomic analysis suggested that a total of 296 proteins were differentially abundant proteins (DAPs). The functional annotation analysis revealed that LK stress elicited complex proteomic alterations that were involved in oxidative phosphorylation, plant-pathogen interactions, glycolysis/gluconeogenesis, sugar metabolism, and transport in stems. The subcellular locations analysis suggested 104 proteins showed chloroplastic localization, 81 proteins showed cytoplasmic localization and 40 showed nuclear localization. The protein–protein interaction analysis revealed that 56 proteins were involved in the interaction network, including 9 proteins involved in the ribosome network and 9 in the oxidative phosphorylation network. Additionally, the expressed changes of 5 DAPs were similar between the proteomic quantification analysis and the PRM-MS analysis, and the expression levels of eight genes that encode DAPs were further verified using an RT-qPCR analysis. These results provide valuable information on the adaptive mechanisms in alligator weed stems under LK stress and facilitate the development of efficient strategies for genetically engineering potassium-tolerant crops.
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Affiliation(s)
- Li-Qin Li
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Cheng-Cheng Lyu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Jia-Hao Li
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Zhu Tong
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Yi-Fei Lu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Xi-Yao Wang
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Su Ni
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Shi-Min Yang
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Fu-Chun Zeng
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Li-Ming Lu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
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Legeay M, Aubourg S, Renou JP, Duval B. Large scale study of anti-sense regulation by differential network analysis. BMC SYSTEMS BIOLOGY 2018; 12:95. [PMID: 30458828 PMCID: PMC6245689 DOI: 10.1186/s12918-018-0613-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Systems biology aims to analyse regulation mechanisms into the cell. By mapping interactions observed in different situations, differential network analysis has shown its power to reveal specific cellular responses or specific dysfunctional regulations. In this work, we propose to explore on a large scale the role of natural anti-sense transcription on gene regulation mechanisms, and we focus our study on apple (Malus domestica) in the context of fruit ripening in cold storage. Results We present a differential functional analysis of the sense and anti-sense transcriptomic data that reveals functional terms linked to the ripening process. To develop our differential network analysis, we introduce our inference method of an Extended Core Network; this method is inspired by C3NET, but extends the notion of significant interactions. By comparing two extended core networks, one inferred with sense data and the other one inferred with sense and anti-sense data, our differential analysis is first performed on a local view and reveals AS-impacted genes, genes that have important interactions impacted by anti-sense transcription. The motifs surrounding AS-impacted genes gather transcripts with functions mostly consistent with the biological context of the data used and the method allows us to identify new actors involved in ripening and cold acclimation pathways and to decipher their interactions. Then from a more global view, we compute minimal sub-networks that connect the AS-impacted genes using Steiner trees. Those Steiner trees allow us to study the rewiring of the AS-impacted genes in the network with anti-sense actors. Conclusion Anti-sense transcription is usually ignored in transcriptomic studies. The large-scale differential analysis of apple data that we propose reveals that anti-sense regulation may have an important impact in several cellular stress response mechanisms. Our data mining process enables to highlight specific interactions that deserve further experimental investigations. Electronic supplementary material The online version of this article (10.1186/s12918-018-0613-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc Legeay
- LERIA, Université d'Angers, 2 bd Lavoisier, Angers, 49045, France.,IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Sébastien Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Jean-Pierre Renou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Béatrice Duval
- LERIA, Université d'Angers, 2 bd Lavoisier, Angers, 49045, France.
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Genome-wide identification and expression analysis of glycine-rich RNA-binding protein family in sweet potato wild relative Ipomoea trifida. Gene 2018; 686:177-186. [PMID: 30453066 DOI: 10.1016/j.gene.2018.11.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 10/08/2018] [Accepted: 11/15/2018] [Indexed: 01/31/2023]
Abstract
Glycine-rich RNA-binding proteins (GRPs) contain RNA recognition motif (RRM) and glycine-rich domains at the N- or C-terminus, respectively, and they participate in varied physiological and biochemical processes, as well as environmental stresses. Sweet potato from the genus Ipomoea is one of the most important crops. However, the role of the GRP gene family in Ipomoea plant species has not been reported yet. At the same time, the genome of sweet potato remains to be elucidated, but the genome of I. trifida which is most probably the progenitor of the sweet potato was released recently. In this regard, we carried out genome-wide analysis of GRP family members in I. trifida. Here, we identified nine GRP genes in I. trifida and investigated their motif distribution, promoters and gene structure. Subsequently, we performed phylogenetic analysis with the GRP genes from I. trifida, Arabidopsis thaliana, Zea mays L. and Oryza sativa to investigate their phylogenetic relationship. Moreover, we studied the expression patterns of ItGRPs in the roots, stems, young and mature leaves and flowers and found that ItGRP genes were tissue-specific. Meanwhile, the expression profiles under four abiotic stress conditions, including heat, cold, salt and drought stress treatments, revealed that some genes were markedly up-regulated or down-regulated. Taken together, our findings will provide reference to studies on the function of GRP genes in the development and stress response of I. trifida.
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Guzicka M, Pawlowski TA, Staszak A, Rozkowski R, Chmura DJ. Molecular and structural changes in vegetative buds of Norway spruce during dormancy in natural weather conditions. TREE PHYSIOLOGY 2018; 38:721-734. [PMID: 29300984 DOI: 10.1093/treephys/tpx156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/20/2017] [Indexed: 05/08/2023]
Abstract
The dormancy and the growth of trees in temperate climates are synchronized with seasons. Preparation for dormancy and its proper progression are key for survival and development in the next season. Using a unique approach that combined microscopy and proteomic methods, we investigated changes in Norway spruce (Picea abies (L.) H. Karst.) embryonic shoots during four distinct stages of dormancy in natural weather conditions. We identified 13 proteins that varied among dormancy stages, and were linked to regulation of protein level; functioning of chloroplasts and other plastids; DNA and RNA regulation; and oxidative stress. We also found a group of five proteins, related to cold hardiness, that did not differ in expression among stages of dormancy, but had the highest abundancy level. Ultrastructure of organelles is tightly linked to their metabolic activity, and hence may indicate dormancy status. The observed ultrastructure during endodormancy was stable, whereas during ecodormancy, the structural changes were dynamic and related mainly to nucleus, plastids and mitochondria. At the ultrastructural level, the lack of starch and the presence of callose in plasmodesmata in all regions of embryonic shoot were indicators of full endodormancy. At the initiation of ecodormancy, we noted an increase in metabolic activity of organelles, tissue-specific starch hyperaccumulation and degradation. However, in proteomic analysis, we did not find variation in expression of proteins related to starch degradation or to symplastic isolation of cells. The combination of ultrastructural and proteomic methods gave a more complete picture of vegetative bud dormancy than either of them applied separately. We found some changes at the structural level, but not their analogues in the proteome. Our study suggests a very important role of plastids' organization and metabolism, and their protection in the course of dormancy and during the shift from endo- to ecodormancy and the acquisition of growth competence.
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Affiliation(s)
- Marzenna Guzicka
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Tomasz A Pawlowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Aleksandra Staszak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Roman Rozkowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Daniel J Chmura
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
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Wang B, Wang G, Shen F, Zhu S. A Glycine-Rich RNA-Binding Protein, CsGR-RBP3, Is Involved in Defense Responses Against Cold Stress in Harvested Cucumber ( Cucumis sativus L.) Fruit. FRONTIERS IN PLANT SCIENCE 2018; 9:540. [PMID: 29740470 PMCID: PMC5925850 DOI: 10.3389/fpls.2018.00540] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
Plant glycine-rich RNA-binding proteins (GR-RBPs) have been shown to play important roles in response to abiotic stresses in actively proliferating organs such as young plants, root tips, and flowers, but their roles in chilling responses of harvested fruit remains largely unknown. Here, we investigated the role of CsGR-RBP3 in the chilling response of cucumber fruit. Pre-storage cold acclimation at 10°C (PsCA) for 3 days significantly enhanced chilling tolerance of cucumber fruit compared with the control fruit that were stored at 5°C. In the control fruit, only one of the six cucumber CsGR-RBP genes, CsGR-RBP2, was enhanced whereas the other five, i.e., CsGR-RBP3, CsGR-RBP4, CsGR-RBP5, CsGR-RBP-blt801, and CsGR-RBP-RZ1A were not. However, in the fruit exposed to PsCA before storage at 5°C, CsGR-RBP2 transcript levels were not obviously different from those in the controls, whereas the other five were highly upregulated, with CsGR-RBP3 the most significantly induced. Treatment with endogenous ABA and NO biosynthesis inhibitors, tungstate and L-nitro-arginine methyl ester, respectively, prior to PsCA treatment, clearly downregulated CsGR-RBP3 expression and significantly aggravated chilling injury. These results suggest a strong connection between CsGR-RBP3 expression and chilling tolerance in cucumber fruit. Transient expression in tobacco suggests CsGR-RBP3 was located in the mitochondria, implying a role for CsGR-RBP3 in maintaining mitochondria-related functions under low temperature. Arabidopsis lines overexpressing CsGR-RBP3 displayed faster growth at 23°C, lower electrolyte leakage and higher Fv/Fm ratio at 0°C, and higher survival rate at -20°C, than wild-type plants. Under cold stress conditions, Arabidopsis plants overexpressing CsGR-RBP3 displayed lower reactive oxygen species levels, and higher catalase and superoxide dismutase expression and activities, compared with the wild-type plants. In addition, overexpression of CsGR-RBP3 significantly upregulated nine Arabidopsis genes involved in defense responses to various stresses, including chilling. These results strongly suggest CsGR-RBP3 plays a positive role in defense against chilling stress.
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Affiliation(s)
| | | | | | - Shijiang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
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Deng H, Cheema J, Zhang H, Woolfenden H, Norris M, Liu Z, Liu Q, Yang X, Yang M, Deng X, Cao X, Ding Y. Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants. MOLECULAR PLANT 2018; 11:607-622. [PMID: 29409859 PMCID: PMC5886760 DOI: 10.1016/j.molp.2018.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/11/2018] [Accepted: 01/25/2018] [Indexed: 05/07/2023]
Abstract
RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, we have successfully generated in vivo Structure-seq libraries in rice. We found that the structural flexibility of mRNAs might associate with the dynamics of biological function. Higher N6-methyladenosine (m6A) modification tends to have less RNA structure in 3' UTR, whereas GC content does not significantly affect in vivo mRNA structure to maintain efficient biological processes such as translation. Comparative analysis of RNA structurome between rice and Arabidopsis revealed that higher GC content does not lead to stronger structure and less RNA structural flexibility. Moreover, we found a weak correlation between sequence and structure conservation of the orthologs between rice and Arabidopsis. The conservation and divergence of both sequence and in vivo RNA structure corresponds to diverse and specific biological processes. Our results indicate that RNA secondary structure might offer a separate layer of selection to the sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently in various biological processes to maintain robustness in development and adaptational flexibility during angiosperm evolution.
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Affiliation(s)
- Hongjing Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hang Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hugh Woolfenden
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Norris
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhenshan Liu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qi Liu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Minglei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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Liu H, Gao Y, Song X, Ma Q, Zhang J, Pei D. A novel rejuvenation approach to induce endohormones and improve rhizogenesis in mature Juglans tree. PLANT METHODS 2018; 14:13. [PMID: 29449873 PMCID: PMC5806478 DOI: 10.1186/s13007-018-0280-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 02/03/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Juglans is a difficult-to-root tree. In the present study, we successfully rejuvenated stock plants by grafting and then burying them horizontally. RESULTS Rooting rates of rejuvenated shoots were 98.1% 20 days after cutting. We recorded spatial and temporal variation in endogenous indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellin A3 (GA3) and zeatin-riboside (ZR) under root induction. The four types of endohormones were mainly confined to the phloem sieve and companion cells (S&Cs) at the base of either rejuvenated or mature soft shoots. IAA and ABA levels were higher in rejuvenated shoots than in mature shoots, whereas the opposite was true for GA3 and ZR. During rooting induction, GA3 was the first hormone to be observed outside phloem S&Cs, followed by IAA, ABA and ZR. In rejuvenating soft shoots, IAA accumulated in the cross-sectional areas of the cambium and phloem, where root primordia were evident. CONCLUSIONS The improvement in the rooting ability that was evident after rejuvenation most likely results a transformation of the plant to a juvenile form, from elevated IAA levels in phloem S&Cs and from a promotion of all four endohormones outside phloem S&Cs, in particular, from an accumulation of IAA in the cross-sectional areas of the cambium and phloem.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Ying Gao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, 300384 China
| | - Xiaobo Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Junpei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
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Czolpinska M, Rurek M. Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. FRONTIERS IN PLANT SCIENCE 2018; 9:302. [PMID: 29568308 PMCID: PMC5852109 DOI: 10.3389/fpls.2018.00302] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 05/21/2023]
Abstract
Seed plants are sessile organisms that have developed a plethora of strategies for sensing, avoiding, and responding to stress. Several proteins, including the glycine-rich protein (GRP) superfamily, are involved in cellular stress responses and signaling. GRPs are characterized by high glycine content and the presence of conserved segments including glycine-containing structural motifs composed of repetitive amino acid residues. The general structure of this superfamily facilitates division of GRPs into five main subclasses. Although the participation of GRPs in plant stress response has been indicated in numerous model and non-model plant species, relatively little is known about the key physiological processes and molecular mechanisms in which those proteins are engaged. Class I, II, and IV members are known to be involved in hormone signaling, stress acclimation, and floral development, and are crucial for regulation of plant cells growth. GRPs of class IV [RNA-binding proteins (RBPs)] are involved in alternative splicing or regulation of transcription and stomatal movement, seed, pollen, and stamen development; their accumulation is regulated by the circadian clock. Owing to the fact that the overexpression of GRPs can confer tolerance to stress (e.g., some are involved in cold acclimation and may improve growth at low temperatures), these proteins could play a promising role in agriculture through plant genetic engineering. Consequently, isolation, cloning, characterization, and functional validation of novel GRPs expressed in response to the diverse stress conditions are expected to be growing areas of research in the coming years. According to our knowledge, this is the first comprehensive review on participation of plant GRPs in the response to diverse stress stimuli.
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Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana. RNA TECHNOLOGIES 2018. [PMCID: PMC7122672 DOI: 10.1007/978-3-319-92967-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Proteins that specifically interact with mRNAs orchestrate mRNA processing steps all the way from transcription to decay. Thus, these RNA-binding proteins represent an important control mechanism to double check which proportion of nascent pre-mRNAs is ultimately available for translation into distinct proteins. Here, we discuss recent progress to obtain a systems-level understanding of in vivo RNA–protein interactions in the reference plant Arabidopsis thaliana using protein-centric and RNA-centric methods as well as combined protein binding site and structure probing.
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Szuba A, Lorenc-Plucińska G. Field proteomics of Populus alba grown in a heavily modified environment - An example of a tannery waste landfill. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:1557-1571. [PMID: 28712470 DOI: 10.1016/j.scitotenv.2017.06.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
Tannery waste is highly toxic and dangerous to living organisms because of the high heavy metal content, especially chromium [Cr(III)]. This study analysed the proteomic response of the Populus alba L. clone 'Villafranca' grown for 4years on a tannery waste landfill. In this extremely hostile environment, the plants struggled with continuous stress, which inhibited growth by 54%, with a 67% decrease in tree height and diameter at breast height compared to those of the forest reference plot, respectively. The leaves and roots of the tannery landfill-grown plants produced strong proteomic stress signals for protection against reactive oxygen species (ROS) and repair to ROS-damaged proteins and DNA as well as signals for protection of the photosynthetic apparatus. The content of HSP80 was also high. However, primary metabolic pathways were generally unaffected, and signals of increased protein protection, but not turnover, were found, indicating mechanisms of adaptation to long-term stress conditions present at the landfill. A proteomic tool, two-dimensional electrophoresis coupled with tandem mass spectrometry, was successfully applied in this environmental in situ study of distant plots (280km apart).
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Affiliation(s)
- Agnieszka Szuba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland.
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Melencion SMB, Chi YH, Pham TT, Paeng SK, Wi SD, Lee C, Ryu SW, Koo SS, Lee SY. RNA Chaperone Function of a Universal Stress Protein in Arabidopsis Confers Enhanced Cold Stress Tolerance in Plants. Int J Mol Sci 2017; 18:ijms18122546. [PMID: 29186920 PMCID: PMC5751149 DOI: 10.3390/ijms18122546] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 02/07/2023] Open
Abstract
The physiological function of Arabidopsis thaliana universal stress protein (AtUSP) in plant has remained unclear. Thus, we report here the functional role of the Arabidopsis universal stress protein, AtUSP (At3g53990). To determine how AtUSP affects physiological responses towards cold stress, AtUSP overexpression (AtUSP OE) and T-DNA insertion knock-out (atusp, SALK_146059) mutant lines were used. The results indicated that AtUSP OE enhanced plant tolerance to cold stress, whereas atusp did not. AtUSP is localized in the nucleus and cytoplasm, and cold stress significantly affects RNA metabolism such as by misfolding and secondary structure changes of RNA. Therefore, we investigated the relationship of AtUSP with RNA metabolism. We found that AtUSP can bind nucleic acids, including single- and double-stranded DNA and luciferase mRNA. AtUSP also displayed strong nucleic acid-melting activity. We expressed AtUSP in RL211 Escherichia coli, which contains a hairpin-loop RNA structure upstream of chloramphenicol acetyltransferase (CAT), and observed that AtUSP exhibited anti-termination activity that enabled CAT gene expression. AtUSP expression in the cold-sensitive Escherichia coli (E. coli) mutant BX04 complemented the cold sensitivity of the mutant cells. As these properties are typical characteristics of RNA chaperones, we conclude that AtUSP functions as a RNA chaperone under cold-shock conditions. Thus, the enhanced tolerance of AtUSP OE lines to cold stress is mediated by the RNA chaperone function of AtUSP.
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Affiliation(s)
- Sarah Mae Boyles Melencion
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Yong Hun Chi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Thuy Thi Pham
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Changyu Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seoung Woo Ryu
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sung Sun Koo
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
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iTRAQ-based quantitative proteomic analysis in vernalization-treated faba bean (Vicia faba L.). PLoS One 2017; 12:e0187436. [PMID: 29121109 PMCID: PMC5679601 DOI: 10.1371/journal.pone.0187436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Vernalization is classically defined as the induction of flowering process by exposure of the plants to a prolonged cold condition. Normally, it is considered as a precondition of flowering. Vicia faba, commonly known as faba bean, belongs to family Fabaceae. It is one of the plant species that has been cultivated in the earliest human settlements. In this study, an iTRAQ-LC-MS/MS-based quantitative proteomic analysis has been conducted to compare the vernalized faba bean seedlings and its corresponding control. In total, 91 proteins from various functional categories were observed to be differentially accumulated in vernalized faba bean seedlings. Subsequent gene ontology analysis indicated that several biological processes or metabolic pathways including photosynthesis and phytic acid metabolism were differentially respond to vernalization in comparison to the control sample. Further investigation revealed that a family of proteins nominated as glycine-rich RNA-binding factor was accumulated in vernalized seedlings, indicating an extra layer of regulation by alternative splicing on transcript abundance in response to vernalization. These findings raise a possibility that these candidate proteins could be important to represent the responsive network under vernalization process. Therefore, we propose that the regulation of vernalization in faba bean not only occurs at the transcriptional level as previously reported, but also at the post-transcriptional level.
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Covarrubias AA, Cuevas-Velazquez CL, Romero-Pérez PS, Rendón-Luna DF, Chater CCC. Structural disorder in plant proteins: where plasticity meets sessility. Cell Mol Life Sci 2017; 74:3119-3147. [PMID: 28643166 PMCID: PMC11107788 DOI: 10.1007/s00018-017-2557-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023]
Abstract
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.
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Affiliation(s)
- Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico.
| | - Cesar L Cuevas-Velazquez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Paulette S Romero-Pérez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - David F Rendón-Luna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Caspar C C Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
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