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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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Bano Z, Westhoff P. A K homology (KH) domain protein identified by a forward genetic screen affects bundle sheath anatomy in Arabidopsis thaliana. PLANT DIRECT 2024; 8:e577. [PMID: 38576996 PMCID: PMC10990680 DOI: 10.1002/pld3.577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 04/06/2024]
Abstract
Because of their photosynthetic capacity, leaves function as solar panels providing the basis for the growth of the entire plant. Although the molecular mechanisms of leaf development have been well studied in model dicot and monocot species, a lot of information is still needed about the interplay of the genes that regulate cell division and differentiation and thereby affect the photosynthetic performance of the leaf. We were specifically interested in understanding the differentiation of mesophyll and bundle sheath cells in Arabidopsis thaliana and aimed to identify genes that are involved in determining bundle sheath anatomy. To this end, we established a forward genetic screen by using ethyl methanesulfonate (EMS) for mutagenizing a reporter line expressing a chloroplast-targeted green fluorescent protein (sGFP) under the control of a bundle sheath-specific promoter. Based on the GFP fluorescence phenotype, numerous mutants were produced, and by pursuing a mapping-by-sequencing approach, the genomic segments containing mutated candidate genes were identified. One of the lines with an enhanced GFP fluorescence phenotype (named ELEVATED BUNDLE SHEATH CELLS SIGNAL 1 [ebss1]) was selected for further study, and the responsible gene was verified by CRISPR/Cas9-based mutagenesis of candidate genes located in the mapped genomic segment. The verified gene, At2g25970, encodes a K homology (KH) domain-containing protein.
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Affiliation(s)
- Zahida Bano
- Institute of Plant Molecular and Developmental BiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental BiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
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Nanni A, Titus-McQuillan J, Bankole KS, Pardo-Palacios F, Signor S, Vlaho S, Moskalenko O, Morse A, Rogers RL, Conesa A, McIntyre LM. Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD. Nucleic Acids Res 2024; 52:e28. [PMID: 38340337 PMCID: PMC10954468 DOI: 10.1093/nar/gkae056] [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: 07/21/2023] [Revised: 11/29/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Advances in affordable transcriptome sequencing combined with better exon and gene prediction has motivated many to compare transcription across the tree of life. We develop a mathematical framework to calculate complexity and compare transcript models. Structural features, i.e. intron retention (IR), donor/acceptor site variation, alternative exon cassettes, alternative 5'/3' UTRs, are compared and the distance between transcript models is calculated with nucleotide level precision. All metrics are implemented in a PyPi package, TranD and output can be used to summarize splicing patterns for a transcriptome (1GTF) and between transcriptomes (2GTF). TranD output enables quantitative comparisons between: annotations augmented by empirical RNA-seq data and the original transcript models; transcript model prediction tools for longread RNA-seq (e.g. FLAIR versus Isoseq3); alternate annotations for a species (e.g. RefSeq vs Ensembl); and between closely related species. In C. elegans, Z. mays, D. melanogaster, D. simulans and H. sapiens, alternative exons were observed more frequently in combination with an alternative donor/acceptor than alone. Transcript models in RefSeq and Ensembl are linked and both have unique transcript models with empirical support. D. melanogaster and D. simulans, share many transcript models and long-read RNAseq data suggests that both species are under-annotated. We recommend combined references.
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Affiliation(s)
- Adalena Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - James Titus-McQuillan
- University of North Carolina at Charlotte Department of Bioinformatics and Genomics Charlotte, NC, USA
| | - Kinfeosioluwa S Bankole
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | | | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Srna Vlaho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Oleksandr Moskalenko
- University of Florida Research Computing, University of Florida, Gainesville, FL 32611, USA
| | - Alison M Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rebekah L Rogers
- University of North Carolina at Charlotte Department of Bioinformatics and Genomics Charlotte, NC, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology. Spanish National Research Council, Paterna, Spain
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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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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Ren D, Liu H, Sun X, Zhang F, Jiang L, Wang Y, Jiang N, Yan P, Cui J, Yang J, Li Z, Lu P, Luo X. Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:66-85. [PMID: 37970747 DOI: 10.1111/jipb.13583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/29/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.
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Affiliation(s)
- Ding Ren
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xuejun Sun
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ling Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
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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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Sumitha MK, Kalimuthu M, Aarthy M, Paramasivan R, Kumar A, Gupta B. In silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA-binding proteins in Aedes aegypti. Parasitol Res 2023; 122:2847-2857. [PMID: 37735272 DOI: 10.1007/s00436-023-07969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023]
Abstract
RNA-binding proteins (RBPs) are the proteins that bind RNAs and regulate their functioning. RBPs in mosquitoes are gaining attention due to their ability to bind flaviviruses and regulate their replication and transmission. Despite their relevance, RBPs in mosquitoes are not explored much. In this study, we screened the whole genome of Aedes aegypti, the primary vector of several pathogenic viruses, and identified the proteins containing RNA recognition motif (RRM), the most abundant protein domain in eukaryotes. Using several in silico strategies, a total of 135 RRM-containing RBPs were identified in Ae. aegypti. The proteins were characterized based on their available annotations and the sequence similarity with Drosophila melanogaster. Ae. aegypti RRM-containing RBPs included serine/arginine-rich (SR) proteins, polyadenylate-binding proteins (PABP), heteronuclear ribonucleoproteins (hnRNP), small nuclear ribonucleoproteins (snRNP), splicing factors, eukaryotic initiation factors, transformers, and nucleolysins. Phylogenetic analysis revealed that the proteins and the domain organization are conserved among Ae. aegypti, Bombyx mori, and Drosophila melanogaster. However, the gene length and the intron-exon organization varied across the insect species. Expression analysis of the genes encoding RBPs using publicly available RNA sequencing data for different developmental time points of the mosquito life cycle starting from the ovary and eggs up to the adults revealed stage-specific expression with several genes preferentially expressed in early embryonic stages and blood-fed female ovaries. This is the first database for the Ae. aegypti RBPs that can serve as the reference base for future investigations. Stage-specific genes can be further explored to determine their role in mosquito growth and development with a focus on developing novel mosquito control strategies.
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Affiliation(s)
- Melveettil Kishor Sumitha
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Mariapillai Kalimuthu
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Rajaiah Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India.
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Hoffmann G, López-González S, Mahboubi A, Hanson J, Hafrén A. Cauliflower mosaic virus protein P6 is a multivalent node for RNA granule proteins and interferes with stress granule responses during plant infection. THE PLANT CELL 2023; 35:3363-3382. [PMID: 37040611 PMCID: PMC10473198 DOI: 10.1093/plcell/koad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/06/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.
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Affiliation(s)
- Gesa Hoffmann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Silvia López-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Amir Mahboubi
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
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9
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Zhang Y, Xu Y, Skaggs TH, Ferreira JFS, Chen X, Sandhu D. Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants. THE PLANT CELL 2023; 35:2750-2772. [PMID: 37144845 PMCID: PMC10396368 DOI: 10.1093/plcell/koad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs in plants have been predominantly limited to proteins interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded a highly comprehensive RNA-binding proteome (RBPome), uncovering 2,517 RBPs from Arabidopsis (Arabidopsis thaliana) leaf and root samples with a highly diverse array of RNA-binding domains. We identified traditional RBPs that participate in various aspects of RNA metabolism and a plethora of nonclassical proteins moonlighting as RBPs. We uncovered constitutive and tissue-specific RBPs essential for normal development and, more importantly, revealed RBPs crucial for salinity stress responses from a RBP-RNA dynamics perspective. Remarkably, 40% of the RBPs are non-poly(A) RBPs that were not previously annotated as RBPs, signifying the advantage of PPE in unbiasedly retrieving RBPs. We propose that intrinsically disordered regions contribute to their nonclassical binding and provide evidence that enzymatic domains from metabolic enzymes have additional roles in RNA binding. Taken together, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues and pave the way for investigating RBP functions under different physiological and stress conditions at the posttranscriptional level.
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Affiliation(s)
- Yong Zhang
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Todd H Skaggs
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
| | | | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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10
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Wang T, Wang X, Wang H, Yu C, Xiao C, Zhao Y, Han H, Zhao S, Shao Q, Zhu J, Zhao Y, Wang P, Ma C. Arabidopsis SRPKII family proteins regulate flowering via phosphorylation of SR proteins and effects on gene expression and alternative splicing. THE NEW PHYTOLOGIST 2023; 238:1889-1907. [PMID: 36942955 DOI: 10.1111/nph.18895] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/07/2023] [Indexed: 05/04/2023]
Abstract
Alternative splicing of pre-mRNAs is crucial for plant growth and development. Serine/arginine-rich (SR) proteins are a conserved family of RNA-binding proteins that are critical for both constitutive and alternative splicing. However, how phosphorylation of SR proteins regulates gene transcription and alternative splicing during plant development is poorly understood. We found that the Arabidopsis thaliana L. SR protein-specific kinase II family proteins (SRPKIIs) play an important role in plant development, including flowering. SRPKIIs regulate the phosphorylation status of a subset of specific SR proteins, including SR45 and SC35, which subsequently mediates their subcellular localization. A phospho-dead SR45 mutant inhibits the assembly of the apoptosis-and splicing-associated protein complex and thereby upregulates the expression of FLOWERING LOCUS C (FLC) via epigenetic modification. The splicing efficiency of FLC introns was significantly increased in the shoot apex of the srpkii mutant. Transcriptomic analysis revealed that SRPKIIs regulate the alternative splicing of c. 400 genes, which largely overlap with those regulated by SR45 and SC35-SCL family proteins. In summary, we found that Arabidopsis SRPKIIs specifically affect the phosphorylation status of a subset SR proteins and regulate the expression and alternative splicing of FLC to control flowering time.
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Affiliation(s)
- Tongtong Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Xiaofeng Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Haiyan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Chao Yu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Chengyun Xiao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Yiwu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Huanan Han
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Shuangshuang Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Qun Shao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Pingping Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
| | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan, Shandong, 250014, China
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11
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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [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: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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12
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Fabian M, Gao M, Zhang XN, Shi J, Vrydagh L, Kim SH, Patel P, Hu AR, Lu H. The flowering time regulator FLK controls pathogen defense in Arabidopsis thaliana. PLANT PHYSIOLOGY 2023; 191:2461-2474. [PMID: 36662556 PMCID: PMC10069895 DOI: 10.1093/plphys/kiad021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 05/22/2023]
Abstract
Plant disease resistance is a complex process that is maintained in an intricate balance with development. Increasing evidence indicates the importance of posttranscriptional regulation of plant defense by RNA binding proteins. In a genetic screen for suppressors of Arabidopsis (Arabidopsis thaliana) accelerated cell death 6-1 (acd6-1), a small constitutive defense mutant whose defense level is grossly in a reverse proportion to plant size, we identified an allele of the canonical flowering regulatory gene FLOWERING LOCUS K HOMOLOGY DOMAIN (FLK) encoding a putative protein with triple K homology (KH) repeats. The KH repeat is an ancient RNA binding motif found in proteins from diverse organisms. The relevance of KH-domain proteins in pathogen resistance is largely unexplored. In addition to late flowering, the flk mutants exhibited decreased resistance to the bacterial pathogen Pseudomonas syringae and increased resistance to the necrotrophic fungal pathogen Botrytis cinerea. We further found that the flk mutations compromised basal defense and defense signaling mediated by salicylic acid (SA). Mutant analysis revealed complex genetic interactions between FLK and several major SA pathway genes. RNA-seq data showed that FLK regulates expression abundance of some major defense- and development-related genes as well as alternative splicing of a number of genes. Among the genes affected by FLK is ACD6, whose transcripts had increased intron retentions influenced by the flk mutations. Thus, this study provides mechanistic support for flk suppression of acd6-1 and establishes that FLK is a multifunctional gene involved in regulating pathogen defense and development of plants.
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Affiliation(s)
- Matthew Fabian
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Min Gao
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
- Biochemistry Program, Department of Biology, St Bonaventure University, St Bonaventure, New York 14778, USA
| | - Xiao-Ning Zhang
- Biochemistry Program, Department of Biology, St Bonaventure University, St Bonaventure, New York 14778, USA
| | - Jiangli Shi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
- Department of Biology Education, Korea National University of Education, Chungbuk 28644, Korea
| | - Leah Vrydagh
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Sung-Ha Kim
- Department of Biology Education, Korea National University of Education, Chungbuk 28644, Korea
| | - Priyank Patel
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Anna R Hu
- Biochemistry Program, Department of Biology, St Bonaventure University, St Bonaventure, New York 14778, USA
| | - Hua Lu
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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13
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Wang L, Xu F, Yu F. Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation. PLANT, CELL & ENVIRONMENT 2023; 46:718-732. [PMID: 36609800 DOI: 10.1111/pce.14537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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14
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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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15
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Ai G, Li T, Zhu H, Dong X, Fu X, Xia C, Pan W, Jing M, Shen D, Xia A, Tyler BM, Dou D. BPL3 binds the long non-coding RNA nalncFL7 to suppress FORKED-LIKE7 and modulate HAI1-mediated MPK3/6 dephosphorylation in plant immunity. THE PLANT CELL 2023; 35:598-616. [PMID: 36269178 PMCID: PMC9806616 DOI: 10.1093/plcell/koac311] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
RNA-binding proteins (RBPs) participate in a diverse set of biological processes in plants, but their functions and underlying mechanisms in plant-pathogen interactions are largely unknown. We previously showed that Arabidopsis thaliana BPA1-LIKE PROTEIN3 (BPL3) belongs to a conserved plant RBP family and negatively regulates reactive oxygen species (ROS) accumulation and cell death under biotic stress. In this study, we demonstrate that BPL3 suppresses FORKED-LIKE7 (FL7) transcript accumulation and raises levels of the cis-natural antisense long non-coding RNA (lncRNA) of FL7 (nalncFL7). FL7 positively regulated plant immunity to Phytophthora capsici while nalncFL7 negatively regulated resistance. We also showed that BPL3 directly binds to and stabilizes nalncFL7. Moreover, nalncFL7 suppressed accumulation of FL7 transcripts. Furthermore, FL7 interacted with HIGHLY ABA-INDUCED PP2C1 (HAI1), a type 2C protein phosphatase, and inhibited HAI1 phosphatase activity. By suppressing HAI1 activity, FL7 increased the phosphorylation levels of MITOGEN-ACTIVATED PROTEIN KINASE 3 (MPK3) and MPK6, thus enhancing immunity responses. BPL3 and FL7 are conserved in all plant species tested, but the BPL3-nalncFL7-FL7 cascade was specific to the Brassicaceae. Thus, we identified a conserved BPL3-nalncFL7-FL7 cascade that coordinates plant immunity.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohua Dong
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowei Fu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuyan Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiye Pan
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Brett M Tyler
- Center for Quantitative Life Sciences and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Daolong Dou
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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16
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Shi W, Yang J, Chen D, Yin C, Zhang H, Xu X, Pan X, Wang R, Fei L, Li M, Qi L, Bhadauria V, Liu J, Peng YL. The rice blast fungus SR protein 1 regulates alternative splicing with unique mechanisms. PLoS Pathog 2022; 18:e1011036. [PMID: 36480554 PMCID: PMC9767378 DOI: 10.1371/journal.ppat.1011036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/20/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are well known as splicing factors in humans, model animals and plants. However, they are largely unknown in regulating pre-mRNA splicing of filamentous fungi. Here we report that the SR protein MoSrp1 enhances and suppresses alternative splicing in a model fungal plant pathogen Magnaporthe oryzae. Deletion of MoSRP1 caused multiple defects, including reduced virulence and thousands of aberrant alternative splicing events in mycelia, most of which were suppressed or enhanced intron splicing. A GUAG consensus bound by MoSrp1 was identified in more than 94% of the intron or/and proximate exons having the aberrant splicing. The dual functions of regulating alternative splicing of MoSrp1 were exemplified in enhancing and suppressing the consensus-mediated efficient splicing of the introns in MoATF1 and MoMTP1, respectively, which both were important for mycelial growth, conidiation, and virulence. Interestingly, MoSrp1 had a conserved sumoylation site that was essential to nuclear localization and enhancing GUAG binding. Further, we showed that MoSrp1 interacted with a splicing factor and two components of the exon-joining complex via its N-terminal RNA recognition domain, which was required to regulate mycelial growth, development and virulence. In contrast, the C-terminus was important only for virulence and stress responses but not for mycelial growth and development. In addition, only orthologues from Pezizomycotina species could completely rescue defects of the deletion mutants. This study reveals that the fungal conserved SR protein Srp1 regulates alternative splicing in a unique manner.
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Affiliation(s)
- Wei Shi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jun Yang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Deng Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Changfa Yin
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Huixia Zhang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaozhou Xu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiao Pan
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ruijin Wang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Liwang Fei
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Mengfei Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Linlu Qi
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Vijai Bhadauria
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junfeng Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- * E-mail:
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17
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Liu T, Zhang X, Zhang H, Cheng Z, Liu J, Zhou C, Luo S, Luo W, Li S, Xing X, Chang Y, Shi C, Ren Y, Zhu S, Lei C, Guo X, Wang J, Zhao Z, Wang H, Zhai H, Lin Q, Wan J. Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA. THE PLANT CELL 2022; 34:3301-3318. [PMID: 35670739 PMCID: PMC9421477 DOI: 10.1093/plcell/koac169] [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: 08/16/2021] [Accepted: 05/11/2022] [Indexed: 06/09/2023]
Abstract
Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.
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Affiliation(s)
| | | | | | | | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weifeng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinxin Xing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanqi Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cuilan Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huqu Zhai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- Author for correspondence: (J.W.), (Q.L.)
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Li X, Yang Y, Zeng N, Qu G, Fu D, Zhu B, Luo Y, Ostersetzer-Biran O, Zhu H. Glycine-rich RNA-binding cofactor RZ1AL is associated with tomato ripening and development. HORTICULTURE RESEARCH 2022; 9:uhac134. [PMID: 35937858 PMCID: PMC9350831 DOI: 10.1093/hr/uhac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Tomato ripening is a complex and dynamic process coordinated by many regulatory elements, including plant hormones, transcription factors, and numerous ripening-related RNAs and proteins. Although recent studies have shown that some RNA-binding proteins are involved in the regulation of the ripening process, understanding of how RNA-binding proteins affect fruit ripening is still limited. Here, we report the analysis of a glycine-rich RNA-binding protein, RZ1A-Like (RZ1AL), which plays an important role in tomato ripening, especially fruit coloring. To analyze the functions of RZ1AL in fruit development and ripening, we generated knockout cr-rz1al mutant lines via the CRISPR/Cas9 gene-editing system. Knockout of RZ1AL reduced fruit lycopene content and weight in the cr-rz1al mutant plants. RZ1AL encodes a nucleus-localized protein that is associated with Cajal-related bodies. RNA-seq data demonstrated that the expression levels of genes that encode several key enzymes associated with carotenoid biosynthesis and metabolism were notably downregulated in cr-rz1al fruits. Proteomic analysis revealed that the levels of various ribosomal subunit proteins were reduced. This could affect the translation of ripening-related proteins such as ZDS. Collectively, our findings demonstrate that RZ1AL may participate in the regulation of carotenoid biosynthesis and metabolism and affect tomato development and fruit ripening.
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Affiliation(s)
- Xindi Li
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77840, USA
| | - Yongfang Yang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ni Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Guiqin Qu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem 9190401, Israel
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19
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Kufel J, Diachenko N, Golisz A. Alternative splicing as a key player in the fine-tuning of the immunity response in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2022; 23:1226-1238. [PMID: 35567423 PMCID: PMC9276941 DOI: 10.1111/mpp.13228] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/01/2023]
Abstract
Plants, like animals, are constantly exposed to abiotic and biotic stresses, which often inhibit plant growth and development, and cause tissue damage, disease, and even plant death. Efficient and timely response to stress requires appropriate co- and posttranscriptional reprogramming of gene expression. Alternative pre-mRNA splicing provides an important layer of this regulation by controlling the level of factors involved in stress response and generating additional protein isoforms with specific features. Recent high-throughput studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection. Despite extensive work, the exact mechanisms underlying these relationships are still unclear, but the contribution of alternative protein isoforms to the defence response and the role of regulatory factors, including components of the splicing machinery, have been established. Modulation of gene expression in response to stress includes alternative splicing, chromatin remodelling, histone modifications, and nucleosome occupancy. How these processes affect plant immunity is mostly unknown, but these facets open new regulatory possibilities. Here we provide an overview of the current state of knowledge and recent findings regarding the growing importance of alternative splicing in plant response to biotic stress.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Nataliia Diachenko
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Anna Golisz
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
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20
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Zhang Y, Fan S, Hua C, Teo ZWN, Kiang JX, Shen L, Yu H. Phase separation of HRLP regulates flowering time in Arabidopsis. SCIENCE ADVANCES 2022; 8:eabn5488. [PMID: 35731874 PMCID: PMC9217094 DOI: 10.1126/sciadv.abn5488] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
RNA binding proteins mediate posttranscriptional RNA metabolism and play regulatory roles in many developmental processes in eukaryotes. Despite their known effects on the floral transition from vegetative to reproductive growth in plants, the underlying mechanisms remain largely obscure. Here, we show that a hitherto unknown RNA binding protein, hnRNP R-LIKE PROTEIN (HRLP), inhibits cotranscriptional splicing of a key floral repressor gene FLOWERING LOCUS C (FLC). This, in turn, facilitates R-loop formation near FLC intron I to repress its transcription, thereby promoting the floral transition in Arabidopsis thaliana. HRLP, together with the splicing factor ARGININE/SERINE-RICH 45, forms phase-separated nuclear condensates with liquid-like properties, which is essential for HRLP function in regulating FLC splicing, R-loop formation, and RNA Polymerase II recruitment. Our findings reveal that inhibition of cotranscriptional splicing of FLC by nuclear HRLP condensates constitutes the molecular basis for down-regulation of FLC transcript levels to ensure the reproductive success of Arabidopsis.
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Affiliation(s)
- Yu Zhang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Sheng Fan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Changmei Hua
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Zhi Wei Norman Teo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Jian Xuan Kiang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Corresponding author. (L.S.); (H.Y.)
| | - Hao Yu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Corresponding author. (L.S.); (H.Y.)
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21
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Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23010511. [PMID: 35008936 PMCID: PMC8745409 DOI: 10.3390/ijms23010511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
K-homologous (KH) family is a type of nucleic acid-binding protein containing the KH domain and has been found to affect splicing and transcriptional regulation. However, KH family genes haven’t been investigated in plant species systematically. In this study, we identified 30 genes that belonged to the KH family based on HMM of the KH domain in Arabidopsis thaliana. Phylogenetic tree analysis showed that the KH family is grouped into three subgroups. Synteny analysis showed that AtKH9 and AtKH29 have the conserved synteny relationship between A. thaliana and the other five species. The AtKH9 and AtKH29 were located in the cytoplasm and nucleus. The seed germination rates of the mutants atkh9 and atkh29 were higher than wild-type after abscisic acid (ABA) and salicylic acid (SA) treatments. In addition, the expression of ABA-related genes, such as ABRE-binding factor 2 (ABF2), ABRE-binding factor 4 (ABF4), and delta 1-pyrroline-5-carboxylate synthase (P5CS), and an SA-related gene pathogenesis-related proteins b (PR1b) were downregulated after ABA and SA treatments, respectively. These results suggested that atkh9 and atkh29 mutants inhibit the effect of ABA and SA on seed germination. In conclusion, our results provide valuable information for further exploration of the function of KH family genes and propose directions and ideas for the identification and characterization of KH family genes in other plants.
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22
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Chen Y, Weng X, Zhou X, Gu J, Hu Q, Luo Q, Wen M, Li C, Wang ZY. Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153574. [PMID: 34890846 DOI: 10.1016/j.jplph.2021.153574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.
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Affiliation(s)
- Yanhang Chen
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Xun Weng
- College of Life Sciences, South China Agricultural University, Guangdong, 510642, China
| | - Xiaoxia Zhou
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Jinbao Gu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qing Hu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qingwen Luo
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Mingfu Wen
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Cong Li
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
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23
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Zhao N, Su XM, Liu ZW, Zhou JX, Su YN, Cai XW, Chen L, Wu Z, He XJ. The RNA recognition motif-containing protein UBA2c prevents early flowering by promoting transcription of the flowering repressor FLM in Arabidopsis. THE NEW PHYTOLOGIST 2022; 233:751-765. [PMID: 34724229 DOI: 10.1111/nph.17836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
FLOWERING LOCUS M (FLM) is a well-known MADS-box transcription factor that is required for preventing early flowering under low temperatures in Arabidopsis thaliana. Alternative splicing of FLM is involved in the regulation of temperature-responsive flowering. However, how the basic transcript level of FLM is regulated is largely unknown. Here, we conducted forward genetic screening and identified a previously uncharacterized flowering repressor gene, UBA2c. Genetic analyses indicated that UBA2c represses flowering at least by promoting FLM transcription. We further demonstrated that UBA2c directly binds to FLM chromatin and facilitates FLM transcription by inhibiting histone H3K27 trimethylation, a histone marker related to transcriptional repression. UBA2c encodes a protein containing two putative RNA recognition motifs (RRMs) and one prion-like domain (PrLD). We found that UBA2c forms speckles in the nucleus and that both the RRMs and PrLD are required not only for forming the nuclear speckles but also for the biological function of UBA2c. These results identify a previously unknown flowering repressor and provide insights into the regulation of flowering time.
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Affiliation(s)
- Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
| | - Xiao-Min Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ling Chen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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24
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Sajeev N, Baral A, America AHP, Willems LAJ, Merret R, Bentsink L. The mRNA-binding proteome of a critical phase transition during Arabidopsis seed germination. THE NEW PHYTOLOGIST 2022; 233:251-264. [PMID: 34643285 PMCID: PMC9298696 DOI: 10.1111/nph.17800] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/01/2021] [Indexed: 05/22/2023]
Abstract
Arabidopsis thaliana seed germination is marked by extensive translational control at two critical phase transitions. The first transition refers to the start of hydration, the hydration translational shift. The second shift, the germination translational shift (GTS) is the phase between testa rupture and radicle protrusion at which the seed makes the all or nothing decision to germinate. The mechanism behind the translational regulation at these phase transitions is unknown. RNA binding proteins (RBPs) are versatile players in the post-transcriptional control of messenger RNAs (mRNAs) and as such candidates for regulating translation during seed germination. Here, we report the mRNA binding protein repertoire of seeds during the GTS. Thirty seed specific RBPs and 22 dynamic RBPs were identified during the GTS, like the putative RBP Vacuolar ATPase subunit A and RBP HSP101. Several stress granule markers were identified in this study, which suggests that seeds are prepared to quickly adapt the translation of specific mRNAs in response to changes in environmental conditions during the GTS. Taken together this study provides a detailed insight into the world of RBPs during seed germination and their possible regulatory role during this developmentally regulated process.
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Affiliation(s)
- Nikita Sajeev
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
| | - Anirban Baral
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
| | | | - Leo A. J. Willems
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
| | - Rémy Merret
- Laboratoire Génome et Développement des PlantesCNRS‐LGDP UMR 5096Perpignan66860France
| | - Leónie Bentsink
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
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25
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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: 6] [Impact Index Per Article: 3.0] [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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26
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Radkova M, Revalska M, Zhiponova M, Iantcheva A. Evaluation of the role of Medicago truncatula Zn finger CCHC type protein after heterologous expression in Arabidopsis thaliana. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.2006786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Mariana Radkova
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Miglena Revalska
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Anelia Iantcheva
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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27
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The Role of Pumilio RNA Binding Protein in Plants. Biomolecules 2021; 11:biom11121851. [PMID: 34944494 PMCID: PMC8699478 DOI: 10.3390/biom11121851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Eukaryotic organisms have a posttranscriptional/translational regulation system for the control of translational efficiency. RNA binding proteins (RBPs) have been known to control target genes. One type of protein, Pumilio (Pum)/Puf family RNA binding proteins, show a specific binding of 3′ untranslational region (3′ UTR) of target mRNA and function as a post-transcriptional/translational regulator in eukaryotic cells. Plant Pum protein is involved in development and biotic/abiotic stresses. Interestingly, Arabidopsis Pum can control target genes in a sequence-specific manner and rRNA processing in a sequence-nonspecific manner. As shown in in silico Pum gene expression analysis, Arabidopsis and rice Pum genes are responsive to biotic/abiotic stresses. Plant Pum can commonly contribute to host gene regulation at the post-transcriptional/translational step, as can mammalian Pum. However, the function of plant Pum proteins is not yet fully known. In this review, we briefly summarize the function of plant Pum in defense, development, and environmental responses via recent research and bioinformatics data.
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28
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Zhao S, Hamada M. Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization. BMC Bioinformatics 2021; 22:554. [PMID: 34781902 PMCID: PMC8594109 DOI: 10.1186/s12859-021-04430-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein-RNA interactions play key roles in many processes regulating gene expression. To understand the underlying binding preference, ultraviolet cross-linking and immunoprecipitation (CLIP)-based methods have been used to identify the binding sites for hundreds of RNA-binding proteins (RBPs) in vivo. Using these large-scale experimental data to infer RNA binding preference and predict missing binding sites has become a great challenge. Some existing deep-learning models have demonstrated high prediction accuracy for individual RBPs. However, it remains difficult to avoid significant bias due to the experimental protocol. The DeepRiPe method was recently developed to solve this problem via introducing multi-task or multi-label learning into this field. However, this method has not reached an ideal level of prediction power due to the weak neural network architecture. RESULTS Compared to the DeepRiPe approach, our Multi-resBind method demonstrated substantial improvements using the same large-scale PAR-CLIP dataset with respect to an increase in the area under the receiver operating characteristic curve and average precision. We conducted extensive experiments to evaluate the impact of various types of input data on the final prediction accuracy. The same approach was used to evaluate the effect of loss functions. Finally, a modified integrated gradient was employed to generate attribution maps. The patterns disentangled from relative contributions according to context offer biological insights into the underlying mechanism of protein-RNA interactions. CONCLUSIONS Here, we propose Multi-resBind as a new multi-label deep-learning approach to infer protein-RNA binding preferences and predict novel interactions. The results clearly demonstrate that Multi-resBind is a promising tool to predict unknown binding sites in vivo and gain biology insights into why the neural network makes a given prediction.
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Affiliation(s)
- Shitao Zhao
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. .,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. .,Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.
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29
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Boher P, Soler M, Fernández-Piñán S, Torrent X, Müller SY, Kelly KA, Serra O, Figueras M. Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress. BMC PLANT BIOLOGY 2021; 21:409. [PMID: 34493224 PMCID: PMC8424952 DOI: 10.1186/s12870-021-03141-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. RESULTS To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue. CONCLUSIONS The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.
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Affiliation(s)
- Pau Boher
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Marçal Soler
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sandra Fernández-Piñán
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Xènia Torrent
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sebastian Y. Müller
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Olga Serra
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Mercè Figueras
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
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Juurakko CL, Bredow M, Nakayama T, Imai H, Kawamura Y, diCenzo GC, Uemura M, Walker VK. The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance. G3-GENES GENOMES GENETICS 2021; 11:6321953. [PMID: 34544140 PMCID: PMC8661430 DOI: 10.1093/g3journal/jkab198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
In order to survive subzero temperatures, some plants undergo cold acclimation (CA) where low, nonfreezing temperatures, and/or shortened day lengths allow cold-hardening and survival during subsequent freeze events. Central to this response is the plasma membrane (PM), where low temperature is perceived and cellular homeostasis must be preserved by maintaining membrane integrity. Here, we present the first PM proteome of cold-acclimated Brachypodium distachyon, a model species for the study of monocot crops. A time-course experiment investigated CA-induced changes in the proteome following two-phase partitioning PM enrichment and label-free quantification by nano-liquid chromatography-mass spectrophotometry. Two days of CA were sufficient for membrane protection as well as an initial increase in sugar levels and coincided with a significant change in the abundance of 154 proteins. Prolonged CA resulted in further increases in soluble sugars and abundance changes in more than 680 proteins, suggesting both a necessary early response to low-temperature treatment, as well as a sustained CA response elicited over several days. A meta-analysis revealed that the identified PM proteins have known roles in low-temperature tolerance, metabolism, transport, and pathogen defense as well as drought, osmotic stress, and salt resistance suggesting crosstalk between stress responses, such that CA may prime plants for other abiotic and biotic stresses. The PM proteins identified here present keys to an understanding of cold tolerance in monocot crops and the hope of addressing economic losses associated with modern climate-mediated increases in frost events.
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Affiliation(s)
- Collin L Juurakko
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Melissa Bredow
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Takato Nakayama
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Yukio Kawamura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Matsuo Uemura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.,Department of Biomedical and Molecular Sciences, School of Environmental Studies, Queen's University, Kingston, ON K7L 3N6, Canada
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31
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Zhou H, Wekesa JS, Luan Y, Meng J. PRPI-SC: an ensemble deep learning model for predicting plant lncRNA-protein interactions. BMC Bioinformatics 2021; 22:415. [PMID: 34429059 PMCID: PMC8385908 DOI: 10.1186/s12859-021-04328-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Plant long non-coding RNAs (lncRNAs) play vital roles in many biological processes mainly through interactions with RNA-binding protein (RBP). To understand the function of lncRNAs, a fundamental method is to identify which types of proteins interact with the lncRNAs. However, the models or rules of interactions are a major challenge when calculating and estimating the types of RBP. RESULTS In this study, we propose an ensemble deep learning model to predict plant lncRNA-protein interactions using stacked denoising autoencoder and convolutional neural network based on sequence and structural information, named PRPI-SC. PRPI-SC predicts interactions between lncRNAs and proteins based on the k-mer features of RNAs and proteins. Experiments proved good results on Arabidopsis thaliana and Zea mays datasets (ATH948 and ZEA22133). The accuracy rates of ATH948 and ZEA22133 datasets were 88.9% and 82.6%, respectively. PRPI-SC also performed well on some public RNA protein interaction datasets. CONCLUSIONS PRPI-SC accurately predicts the interaction between plant lncRNA and protein, which plays a guiding role in studying the function and expression of plant lncRNA. At the same time, PRPI-SC has a strong generalization ability and good prediction effect for non-plant data.
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Affiliation(s)
- Haoran Zhou
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024 Liaoning China
| | - Jael Sanyanda Wekesa
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024 Liaoning China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024 Liaoning China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024 Liaoning China
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32
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Maruri-López I, Figueroa NE, Hernández-Sánchez IE, Chodasiewicz M. Plant Stress Granules: Trends and Beyond. FRONTIERS IN PLANT SCIENCE 2021; 12:722643. [PMID: 34434210 PMCID: PMC8381727 DOI: 10.3389/fpls.2021.722643] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/01/2021] [Indexed: 05/20/2023]
Abstract
Stress granules (SGs) are dynamic membrane-less condensates transiently assembled through liquid-liquid phase separation (LLPS) in response to stress. SGs display a biphasic architecture constituted of core and shell phases. The core is a conserved SG fraction fundamental for its assembly and consists primarily of proteins with intrinsically disordered regions and RNA-binding domains, along with translational-related proteins. The shell fraction contains specific SG components that differ among species, cell type, and developmental stage and might include metabolic enzymes, receptors, transcription factors, untranslated mRNAs, and small molecules. SGs assembly positively correlates with stalled translation associated with stress responses playing a pivotal role during the adaptive cellular response, post-stress recovery, signaling, and metabolic rewire. After stress, SG disassembly releases mRNA and proteins to the cytoplasm to reactivate translation and reassume cell growth and development. However, under severe stress conditions or aberrant cellular behavior, SG dynamics are severely disturbed, affecting cellular homeostasis and leading to cell death in the most critical cases. The majority of research on SGs has focused on yeast and mammals as model organism. Nevertheless, the study of plant SGs has attracted attention in the last few years. Genetics studies and adapted techniques from other non-plant models, such as affinity capture coupled with multi-omics analyses, have enriched our understanding of SG composition in plants. Despite these efforts, the investigation of plant SGs is still an emerging field in plant biology research. In this review, we compile and discuss the accumulated progress of plant SGs regarding their composition, organization, dynamics, regulation, and their relation to other cytoplasmic foci. Lastly, we will explore the possible connections among the most exciting findings of SGs from mammalian, yeast, and plants, which might help provide a complete view of the biology of plant SGs in the future.
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Affiliation(s)
| | | | | | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Alvarado-Marchena L, Marquez-Molins J, Martinez-Perez M, Aparicio F, Pallás V. Mapping of Functional Subdomains in the atALKBH9B m 6A-Demethylase Required for Its Binding to the Viral RNA and to the Coat Protein of Alfalfa Mosaic Virus. FRONTIERS IN PLANT SCIENCE 2021; 12:701683. [PMID: 34290728 PMCID: PMC8287571 DOI: 10.3389/fpls.2021.701683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/09/2021] [Indexed: 06/01/2023]
Abstract
N 6-methyladenosine (m6A) modification is a dynamically regulated RNA modification that impacts many cellular processes and pathways. This epitranscriptomic methylation relies on the participation of RNA methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. We previously demonstrated that the Arabidopsis thaliana protein atALKBH9B showed m6A-demethylase activity and interacted with the coat protein (CP) of alfalfa mosaic virus (AMV), causing a profound impact on the viral infection cycle. To dissect the functional activity of atALKBH9B in AMV infection, we performed a protein-mapping analysis to identify the putative domains required for regulating this process. In this context, the mutational analysis of the protein revealed that the residues between 427 and 467 positions are critical for in vitro binding to the AMV RNA. The atALKBH9B amino acid sequence showed intrinsically disordered regions (IDRs) located at the N-terminal part delimiting the internal AlkB-like domain and at the C-terminal part. We identified an RNA binding domain containing an RGxxxRGG motif that overlaps with the C-terminal IDR. Moreover, bimolecular fluorescent experiments allowed us to determine that residues located between 387 and 427 are critical for the interaction with the AMV CP, which should be critical for modulating the viral infection process. Finally, we observed that atALKBH9B deletions of either N-terminal 20 residues or the C-terminal's last 40 amino acids impede their accumulation in siRNA bodies. The involvement of the regions responsible for RNA and viral CP binding and those required for its localization in stress granules in the viral cycle is discussed.
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34
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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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35
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Ma W, Liu Z, Beier S, Houben A, Carpentier S. Identification of rye B chromosome-associated peptides by mass spectrometry. THE NEW PHYTOLOGIST 2021; 230:2179-2185. [PMID: 33503271 DOI: 10.1111/nph.17238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
B chromosomes (Bs) are supernumerary dispensable components of the standard genome (A chromosomes, As) that have been found in many eukaryotes. So far, it is unkown whether the B-derived transcripts translate to proteins or if the host proteome is changed due to the presence of Bs. Comparative mass spectrometry was performed using the protein samples isolated from shoots of rye plants with and without Bs. We aimed to identify B-associated peptides and analyzed the effects of Bs on the total proteome. Our comparative proteome analysis demonstrates that the presence of rye Bs affects the total proteome including different biological function processes. We found 319 of 16 776 quantified features in at least three out of five +B plants but not in 0B plants; 31 of 319 features were identified as B-associated peptide features. According to our data mining, one B-specific protein fragment showed similarity to a glycine-rich RNA binding protein which differed from its A-paralogue by two amino acid insertions. Our result represents a milestone in B chromosome research, because this is the first report to demonstrate the existence of Bs changing the proteome of the host.
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Affiliation(s)
- Wei Ma
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - ZhaoJun Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences Life, Science Center Weihenstephan, Crop Physiology, Technical University Munich, Alte Akademie 12, Freising, 85354, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Sebastien Carpentier
- Department of Biosystems, KU Leuven, Willem Decroylaan 42, 2455-3001 Leuven, Belgium
- SYBIOMA, KULeuven, Herestraat 49, Leuven, 3000, Belgium
- Genetic Resources, Bioversity International, Willem Decroylaan 42, 2455-3001 Leuven, Belgium
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36
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Castro-Bustos S, Maruri-López I, Ortega-Amaro MA, Serrano M, Ovando-Vázquez C, Jiménez-Bremont JF. An interactome analysis reveals that Arabidopsis thaliana GRDP2 interacts with proteins involved in post-transcriptional processes. Cell Stress Chaperones 2021; 27:165-176. [PMID: 35174430 PMCID: PMC8943079 DOI: 10.1007/s12192-022-01261-5] [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: 12/09/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022] Open
Abstract
The Arabidopsis thaliana glycine-rich domain protein 2 (AtGRDP2) gene encodes a protein of unknown function that is involved in plant growth and salt stress tolerance. The AtGRDP2 protein (787 aa, At4g37900) is constituted by three domains: a DUF1399 located at the N-terminus, a potential RNA Recognition Motif (RRM) in the central region, and a short glycine-rich domain at the C-terminus. Herein, we analyzed the subcellular localization of AtGRDP2 protein as a GFP translational fusion and found it was localized in the cytosol and the nucleus of tobacco leaf cells. Truncated versions of AtGRDP2 showed that the DUF1399 or the RRM domains were sufficient for nuclear localization. In addition, we performed a yeast two-hybrid split-ubiquitin assay (Y2H) to identify potential interactors for AtGRDP2 protein. The Y2H assay identified proteins associated with RNA binding functions such as PABN3 (At5g65260), EF-1α (At1g07920), and CL15 (At3g25920). Heterodimeric associations in planta between AtGRDP2 and its interactors were carried out by Bimolecular Fluorescence Complementation (BiFC) assays. The data revealed heterodimeric interactions between AtGRDP2 and PABN3 in the nucleus and AtGRDP2 with EF-1α in the cytosol, while AtGRDP2-CL15 associations occurred only in the chloroplasts. Finally, functional characterization of the protein-protein interaction regions revealed that both DUF1399 and RRM domains were key for heterodimerization with its interactors. The AtGRDP2 interaction with these proteins in different compartments suggests that this glycine-rich domain protein is involved in post-transcriptional processes.
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Affiliation(s)
- Saraí Castro-Bustos
- Laboratorio de Biotecnología Molecular de Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C, San Luis Potosí, SLP, Mexico
| | - Israel Maruri-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - María Azucena Ortega-Amaro
- Laboratorio de Biotecnología Molecular de Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C, San Luis Potosí, SLP, Mexico
- Coordinación Académica Región Altiplano Oeste, Universidad Autónoma de San Luis Potosí, Salinas de Hidalgo, SLP, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Cesaré Ovando-Vázquez
- CONACyT-Centro Nacional de Supercómputo, Instituto Potosino de Investigación Científica y Tecnológica, A.C, San Luis Potosí, SLP, Mexico
| | - Juan Francisco Jiménez-Bremont
- Laboratorio de Biotecnología Molecular de Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C, San Luis Potosí, SLP, Mexico.
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OsCRP1, a Ribonucleoprotein Gene, Regulates Chloroplast mRNA Stability That Confers Drought and Cold Tolerance. Int J Mol Sci 2021; 22:ijms22041673. [PMID: 33562320 PMCID: PMC7915912 DOI: 10.3390/ijms22041673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded and highly abundant proteins that are proposed to function in chloroplast RNA metabolism. However, the molecular mechanisms underlying the regulation of chloroplast RNAs involved in stress tolerance are poorly understood. Here, we demonstrate that CHLOROPLAST RNA-BINDING PROTEIN 1 (OsCRP1), a rice (Oryza sativa) cpRNP gene, is essential for stabilization of RNAs from the NAD(P)H dehydrogenase (NDH) complex, which in turn enhances drought and cold stress tolerance. An RNA-immunoprecipitation assay revealed that OsCRP1 is associated with a set of chloroplast RNAs. Transcript profiling indicated that the mRNA levels of genes from the NDH complex significantly increased in the OsCRP1 overexpressing compared to non-transgenic plants, whereas the pattern in OsCRP1 RNAi plants were opposite. Importantly, the OsCRP1 overexpressing plants showed a higher cyclic electron transport (CET) activity, which is essential for elevated levels of ATP for photosynthesis. Additionally, overexpression of OsCRP1 resulted in significantly enhanced drought and cold stress tolerance with higher ATP levels compared to wild type. Thus, our findings suggest that overexpression of OsCRP1 stabilizes a set of mRNAs from genes of the NDH complex involved in increasing CET activity and production of ATP, which consequently confers enhanced drought and cold tolerance.
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38
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Yadav M, Singh RS, Hogan D, Vidhyasagar V, Yang S, Chung IYW, Kusalik A, Dmitriev OY, Cygler M, Wu Y. The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase. J Biol Chem 2021; 296:100085. [PMID: 33199368 PMCID: PMC7949032 DOI: 10.1074/jbc.ra120.015824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins. Recently, we found that the DEAD-box helicase DDX43 contains a KH domain in its N-terminus; however, its function remains unknown. Here, we purified recombinant DDX43 KH domain protein and found that it prefers binding ssDNA and ssRNA. Electrophoretic mobility shift assay and NMR revealed that the KH domain favors pyrimidines over purines. Mutational analysis showed that the GXXG loop in the KH domain is involved in pyrimidine binding. Moreover, we found that an alanine residue adjacent to the GXXG loop is critical for binding. Systematic evolution of ligands by exponential enrichment, chromatin immunoprecipitation-seq, and cross-linking immunoprecipitation-seq showed that the KH domain binds C-/T-rich DNA and U-rich RNA. Bioinformatics analysis suggested that the KH domain prefers to bind promoters. Using 15N-heteronuclear single quantum coherence NMR, the optimal binding sequence was identified as TTGT. Finally, we found that the full-length DDX43 helicase prefers DNA or RNA substrates with TTGT or UUGU single-stranded tails and that the KH domain is critically important for sequence specificity and unwinding processivity. Collectively, our results demonstrated that the KH domain facilitates the substrate specificity and processivity of the DDX43 helicase.
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Affiliation(s)
- Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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Wang H, Liu S, Dai X, Yang Y, Luo Y, Gao Y, Liu X, Wei W, Wang H, Xu X, Reddy ASN, Jaiswal P, Li W, Liu B, Gu L. PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:655565. [PMID: 34122478 PMCID: PMC8195342 DOI: 10.3389/fpls.2021.655565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 05/16/2023]
Abstract
Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yongkang Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunjun Luo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Bo Liu,
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Lianfeng Gu,
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Dai GY, Chen DK, Sun YP, Liang WY, Liu Y, Huang LQ, Li YK, He JF, Yao N. The Arabidopsis KH-domain protein FLOWERING LOCUS Y delays flowering by upregulating FLOWERING LOCUS C family members. PLANT CELL REPORTS 2020; 39:1705-1717. [PMID: 32948902 DOI: 10.1007/s00299-020-02598-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
We identified FLY as a previously uncharacterized RNA-binding-family protein that controls flowering time by positively regulating the expression of FLC clade members. The ability of flowering plants to adjust the timing of the floral transition based on endogenous and environmental signals contributes to their adaptive success. In Arabidopsis thaliana, the MADS-domain protein FLOWERING LOCUS C (FLC) and the FLC clade members FLOWERING LOCUS M/MADS AFFECTING FLOWERING1 (FLM/MAF1), MAF2, MAF3, MAF4, and MAF5 form nuclear complexes that repress flowering under noninductive conditions. However, how FLM/MAF genes are regulated requires further study. Using a genetic strategy, we showed that the previously uncharacterized K-homology (KH) domain protein FLOWERING LOCUS Y (FLY) modulates flowering time. The fly-1 knockout mutant and FLY artificial microRNA knockdown line flowered earlier than the wild type under long- and short-day conditions. The knockout fly-1 allele, a SALK T-DNA insertion mutant, contains an ~ 110-kb genomic deletion induced by T-DNA integration. FLC clade members were downregulated in the fly-1 mutants and FLY artificial microRNA knockdown line, whereas the level of the FLC antisense transcript COOLAIR was similar to that of the wild type. Our results identify FLY as a regulator that affects flowering time through upregulation of FLC clade members.
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Affiliation(s)
- Guang-Yi Dai
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ding-Kang Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yun-Peng Sun
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wei-Yi Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li-Qun Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong-Kang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Fan He
- School of Agriculture, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Nan Yao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Cheng X, Cao J, Gao C, Gao W, Yan S, Yao H, Xu K, Liu X, Xu D, Pan X, Lu J, Chang C, Zhang H, Ma C. Identification of the wheat C3H gene family and expression analysis of candidates associated with seed dormancy and germination. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:524-537. [PMID: 33053501 DOI: 10.1016/j.plaphy.2020.09.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/28/2020] [Indexed: 05/01/2023]
Abstract
C3H zinc finger transcription factors play important roles in managing various biotic/abiotic stresses in Aarabidopsis, rice, and maize. The functions of these factors in wheat, however, remain largely unclear. We identified 88 TaC3H genes that were divided into four subfamilies in this analysis. Gene structure and conserved domain analyses indicate that most members of the same subfamily have similar structures. A total of 76 paralogous and 48 orthologous pairs were identified and Ka/Ks values were used to analyze replication relationships amongst wheat, rice, and Arabidopsis. Gene ontology (GO) annotation analysis showed that most TaC3H genes possessed molecular functions, while transcriptome results showed that the 88 TaC3H genes responded to water imbibition. Microarray data for 53 TaC3H genes were obtained and heat maps were generated; these results indicate that these genes are expressed in 13 wheat tissues. Subcellular localization prediction analysis indicates that most TaC3H genes are located in the nucleus. Promoter analysis indicates that most TaC3H genes contained cis-elements including ABRE, GARE-motif, and MBS, indicating that these can respond to various biotic/abiotic stresses. Transcriptome data and quantitative real-time PCR analysis of wheat cultivars with contrasting seed dormancy phenotypes show that five genes TaC3H4/-18/-37/-51/-72 were very likely involved in seed dormancy and germination. Exogenous ABA treatment further indicated that these five genes were responsive to ABA, suggesting that there may be a crosstalk between these genes and ABA signaling pathway in controlling seed dormancy and germination. These results provide a theoretical basis for subsequent studies on TaC3H gene function and also contribute to studies on the C3H gene in other species.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Chang Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Wei Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Shengnan Yan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Hui Yao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Kangle Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xue Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Dongmei Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xu Pan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
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Song H, Kim H, Hwang BH, Yi H, Hur Y. Natural variation in glycine-rich region of Brassica oleracea cold shock domain protein 5 (BoCSDP5) is associated with low temperature tolerance. Genes Genomics 2020; 42:1407-1417. [PMID: 33094377 DOI: 10.1007/s13258-020-01010-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Low temperature (LT) or cold stress is a major environmental stress that seriously affects plant growth and development, limiting crop productivity. Cold shock domain proteins (CSDPs), which are present in most living organism, are involved in RNA metabolisms influencing abiotic stress tolerance. OBJECTIVE The aims of this study are to identify target gene for LT-tolerance, like CSDPs, characterize genetics, and develop molecular marker distinguishing LT-tolerance in cabbage (Brassica oleracea var. capitata). METHODS Semi-quantitative RT-PCR or qRT-PCR was used in gene expression study. LT-tolerance was determined by electrolyte leakage and PCR with allelic specific primers. RESULTS Allelic variation was found in BoCSDP5 coding sequence (CDs) between LT-tolerant (BN106 and BN553) and -susceptible inbred lines (BN107 and BN554). LT-tolerant inbred lines contained variant type of BoCSDP5 (named as BoCSDP5v) which encodes extra CCHC zinc finger domain at C-terminus. Association of LT-tolerance with BoCSDP5v was confirmed by electrolyte leakage and segregation using genetic population derived from BN553 and BN554 cross. Allelic variation in BoCSDP5 gene does not influence the rate of gene expression, but produces different proteins with different number of CCHC zinc finger domains. LT-tolerance marker designed on the basis of polymorphism between BoCSDP5 and BoCSDP5v was confirmed with samples used in previous B. oleracea CIRCADIAN CLOCK ASSOCIATED 1 (BoCCA1) marker validation. CONCLUSIONS LT-tolerant allele (BoCSDP5v) is dominant and independent of CBF pathway, and sufficient to generate molecular markers to identify LT-tolerant cabbage when it is used in combination with another marker, like BoCCA1-derived one. Production and analysis of overexpressing plants of BoCSDP1, BoCSDP3, BoCSDP5 and BoCSDP5v will be required for elucidating the function of CCHC zinc finger domains in LT-tolerance.
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Affiliation(s)
- Hayoung Song
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - HyeRan Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Byung-Ho Hwang
- Biotechnology and Breeding Institute of Asia Seed Co., Icheon-si, Gyeonggi-do, 17414, Republic of Korea
| | - Hankuil Yi
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Yoonkang Hur
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Wu J, Liu H, Lu S, Hua J, Zou B. Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice. Genome 2020; 64:515-524. [PMID: 33049157 DOI: 10.1139/gen-2020-0007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chloroplast ribonucleoproteins (cpRNPs) are implicated in splicing, editing, and stability control of chloroplast RNAs as well as in regulating development and stress tolerance. To facilitate a comprehensive understanding of their functions, we carried out a genome-wide identification, curation, and phylogenetic analysis of cpRNP genes in Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Ten cpRNP genes were identified in each of Arabidopsis and rice genomes based on the presence of two RRM (RNA-recognition motif) domains and an N-terminal chloroplast targeting signal peptide in the predicted proteins. These proteins are localized to chloroplasts. Gene expression analysis revealed that cpRNP genes have differential tissue expression patterns and some cpRNP genes are induced by abiotic stresses such as cold, heat, and drought. Taken together, our study provides a comprehensive annotation of the cpRNP gene family and their expression patterns in Arabidopsis and rice which will facilitate further studies on their roles in plant growth and stress responses.
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Affiliation(s)
- Jiawen Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Huimin Liu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan Lu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Hua
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baohong Zou
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Zhu Y, Wu W, Shao W, Chen J, Shi X, Ma X, Xu YZ, Huang W, Huang J. SPLICING FACTOR1 Is Important in Chloroplast Development under Cold Stress. PLANT PHYSIOLOGY 2020; 184:973-987. [PMID: 32732348 PMCID: PMC7536683 DOI: 10.1104/pp.20.00706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/20/2020] [Indexed: 05/20/2023]
Abstract
RNA SPLICING FACTOR1 (SF1) is responsible for recognizing the branch point site (BPS) sequence in introns and is critical for pre-mRNA splicing. In Arabidopsis (Arabidopsis thaliana), splicing factor1 (AtSF1) has been shown to retain the conserved function, but it is unexpected that null atsf1 mutants are viable. Here, we identified an allele of atsf1, named suppressor of thf1-4 (sot4), from suppressor screening for leaf variegation of thylakoid formation1 The sot4 mutant resulting from the G-to-R mutation at the highly conserved 198th amino acid residue within the functionally unknown domain exhibits leaf virescence associated with less accumulation of mature plastid ribosomal RNA, particularly under cold stress. Interestingly, the same point mutation in yeast Saccharomyces cerevisiae MUD synthetic-lethal 5p (SF1/Msl5p) also causes hypersensitivity to coldness and a low splicing activity for the introns with suboptimal BPS sequences. Transcriptomic profiling and reverse-transcription quantitative PCR analyses showed that expression of many genes were up- or downregulated in atsf1 via insufficient intron splicing. Our search for a BPS consensus from the retained introns in atsf1 transcriptomes, combined with RNA electrophoresis mobility shift assays, revealed that AtSF1 directly binds to the BPS consensus containing 5'-CU(U/A)AU-3'. Taken together, our data provide insight into a role for AtSF1 in regulating intron splicing efficiency, which helps plants acclimate to coldness.
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Affiliation(s)
- Yajuan Zhu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjuan Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Jingli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoning Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoyu Ma
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yong-Zhen Xu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weihua Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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Marondedze C. The increasing diversity and complexity of the RNA-binding protein repertoire in plants. Proc Biol Sci 2020; 287:20201397. [PMID: 32962543 PMCID: PMC7542812 DOI: 10.1098/rspb.2020.1397] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Post-transcriptional regulation has far-reaching implications on the fate of RNAs. It is gaining increasing momentum as a critical component in adjusting global cellular transcript levels during development and in response to environmental stresses. In this process, RNA-binding proteins (RBPs) are indispensable chaperones that naturally bind RNA via one or multiple globular RNA-binding domains (RBDs) changing the function or fate of the bound RNAs. Despite the technical challenges faced in plants in large-scale studies, several hundreds of these RBPs have been discovered and elucidated globally over the past few years. Recent discoveries have more than doubled the number of proteins implicated in RNA interaction, including identification of RBPs lacking classical RBDs. This review will discuss these new emerging classes of RBPs, focusing on the current state of the RBP repertoire in Arabidopsis thaliana, including the diverse functional roles derived from quantitative studies implicating RBPs in abiotic stress responses. Notably, this review highlights that 836 RBPs are enriched as Arabidopsis RBPs while 1865 can be classified as candidate RBPs. The review will also outline outstanding areas within this field that require addressing to advance our understanding and potential biotechnological applications of RBPs.
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Affiliation(s)
- C. Marondedze
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Biochemistry, Midlands State University, P. Bag 9055, Gweru, Zimbabwe
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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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47
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González G, Aguilera F, D'Afonseca V. Transcriptome profiling of raspberry ( Rubus idaeus Var. Amira) in response to infection by tomato ringspot virus (ToRSV). Heliyon 2020; 6:e04518. [PMID: 32817888 PMCID: PMC7424221 DOI: 10.1016/j.heliyon.2020.e04518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/28/2019] [Accepted: 07/17/2020] [Indexed: 11/01/2022] Open
Abstract
Raspberry (Rubus sp.) is a berries fruit with an ongoing agricultural and commercial interest due to its high contents of flavonoids and nutrients beneficial for human health. The growing demand for raspberries is facing great challenges associated mainly with the dispersal of diseases, which produces a decrease in productivity and fruit quality. A broad range of genomic resources is available for other Rosaceae species; however, genomic resources for species of the Rubus genus are still limited. Here, we characterize the transcriptome of the Rubus idaeus (Var. Amira) in order to 1) provide clues in the transcriptional changes of R. idaeus against tomato ringspot virus (ToRSV); and 2) generate genomic resources for this economically important species. We generate more than 200 million sequencing reads from two mRNA samples of raspberry, infected and not infected by ToRSV, using Illumina technology. After de novo assembly, we obtained 68,853 predicted protein-coding sequences of which 71.3% and 61.3% were annotated using Gene Ontology and Pfam databases, respectively. Moreover, we find 2,340 genes with differential expression between raspberries infected and not infected by ToRSV. Analysis of these genes shows functional enrichments of the oxidation-reduction process, cell wall biogenesis, terpene synthase activity, and lyase activity. These genes could be involved in the raspberry immune response through the interaction of different metabolic pathways; however, this statement needs further investigations. Up-regulation of genes encoding terpene synthases, multicopper oxidases, laccases, and beta-glucosidases might suggest that these enzymes appear to be the predominant transcriptome immune response of R. idaeus against ToRSV. Furthermore, we identify thousands of molecular markers (i.e., SSRs and SNPs), increasing considerably the genomic resources currently available for raspberries. This study is the first report on investigating the transcriptional changes of R. idaeus against ToRSV.
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Affiliation(s)
- Gloria González
- Center of Biotechnology for Natural Resources (CenBIO), Faculty of Agricultural Sciences and Forestry, Universidad Católica del Maule, Talca, Chile
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Vívian D'Afonseca
- Vice Rectory of Research and Post-Graduation (VRIP), Universidad Católica del Maule, Talca, Chile
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Lu X, Cheng Y, Gao M, Li M, Xu X. Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). Front Genet 2020; 11:774. [PMID: 32849790 PMCID: PMC7396569 DOI: 10.3389/fgene.2020.00774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 11/15/2022] Open
Abstract
Plant Glycine-rich proteins (GRP), a superfamily with a glycine-rich domain, play an important role in various stresses such as high or low temperature stress and drought stress. GRP genes have been studied in many plants, but seldom in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a total of 64 GRP genes were identified in Chinese cabbage by homology comparative analysis. The physical and chemical characteristics predicted by ProtParam tool revealed that 62.5% of BrGRPs were alkaline, 53.1% were stable, and 79.7% were hydrophilic. Conserved domain analysis by MEME and TBtools showed that 64 BrGRPs contained 20 of the same conserved motifs, based on which BrGRPs were classified into five main classes and four subclasses in class IV to clarify their evolutionary relationship. Our results demonstrated that The BrGRP genes were located on ten chromosomes and in three different subgenomes of Chinese cabbage, and 43 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the transcriptome data, 64 BrGRP genes showed abnormal expression under high temperature stress, 52 under low temperature stress, 39 under drought stress, and 23 responses to soft rot. A large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE were found in their promoter regions by PlantCare, which corresponded with differential expressions. Two BrGRP genes-w546 (Bra030284) and w1409 (Bra014000), both belonging to the subfamily Subclass IVa RBP-GRP (RNA binding protein-glycine rich protein), were up-regulated under 150 mmol⋅L-1 NaCl stress in Chinese cabbage. However, the overexpressed w546 gene could significantly inhibit seed germination, while w1409 significantly accelerated seed germination under 100 mmol⋅L-1 NaCl or 300 mmol⋅L-1 mannitol stresses. In short, most BrGRP genes showed abnormal expression under adversity stress, and some were involved in multiple stress responses, suggesting a potential capacity to resist multiple biotic and abiotic stresses, which is worthy of further study. Our study provides a systematic investigation of the molecular characteristics and expression patterns of BrGRP genes and promotes for further work on improving stress resistance of Chinese cabbage.
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Affiliation(s)
| | | | | | | | - Xiaoyong Xu
- College of Horticulture, Shanxi Agricultural University; and Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
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Thomas QA, Ard R, Liu J, Li B, Wang J, Pelechano V, Marquardt S. Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis. Nat Commun 2020; 11:2589. [PMID: 32444691 PMCID: PMC7244574 DOI: 10.1038/s41467-020-16390-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/29/2020] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.
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Affiliation(s)
- Quentin Angelo Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ryan Ard
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jinghan Liu
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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Yan Z, Shi H, Liu Y, Jing M, Han Y. KHZ1 and KHZ2, novel members of the autonomous pathway, repress the splicing efficiency of FLC pre-mRNA in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1375-1386. [PMID: 31701139 PMCID: PMC7031081 DOI: 10.1093/jxb/erz499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 05/03/2023]
Abstract
As one of the most important events during the life cycle of flowering plants, the floral transition is of crucial importance for plant propagation and requires the precise coordination of multiple endogenous and external signals. There have been at least four flowering pathways (i.e. photoperiod, vernalization, gibberellin, and autonomous) identified in Arabidopsis. We previously reported that two Arabidopsis RNA-binding proteins, KHZ1 and KHZ2, redundantly promote flowering. However, the underlying mechanism was unclear. Here, we found that the double mutant khz1 khz2 flowered late under both long-day and short-day conditions, but responded to vernalization and gibberellin treatments. The late-flowering phenotype was almost completely rescued by mutating FLOWERING LOCUS C (FLC) and fully rescued by overexpressing FLOWERING LOCUS T (FT). Additional experiments demonstrated that the KHZs could form homodimers or interact to form heterodimers, localized to nuclear dots, and repressed the splicing efficiency of FLC pre-mRNA. Together, these data indicate that the KHZs could promote flowering via the autonomous pathway by repressing the splicing efficiency of FLC pre-mRNA.
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Affiliation(s)
- Zongyun Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Correspondence:
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