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Liu H, Guan F, Liu T, Yang L, Fan L, Liu X, Luo H, Wu N, Yao B, Tian J, Huang H. MECE: a method for enhancing the catalytic efficiency of glycoside hydrolase based on deep neural networks and molecular evolution. Sci Bull (Beijing) 2023; 68:2793-2805. [PMID: 37867059 DOI: 10.1016/j.scib.2023.09.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/14/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023]
Abstract
The demand for high efficiency glycoside hydrolases (GHs) is on the rise due to their various industrial applications. However, improving the catalytic efficiency of an enzyme remains a challenge. This investigation showcases the capability of a deep neural network and method for enhancing the catalytic efficiency (MECE) platform to predict mutations that improve catalytic activity in GHs. The MECE platform includes DeepGH, a deep learning model that is able to identify GH families and functional residues. This model was developed utilizing 119 GH family protein sequences obtained from the Carbohydrate-Active enZYmes (CAZy) database. After undergoing ten-fold cross-validation, the DeepGH models exhibited a predictive accuracy of 96.73%. The utilization of gradient-weighted class activation mapping (Grad-CAM) was used to aid us in comprehending the classification features, which in turn facilitated the creation of enzyme mutants. As a result, the MECE platform was validated with the development of CHIS1754-MUT7, a mutant that boasts seven amino acid substitutions. The kcat/Km of CHIS1754-MUT7 was found to be 23.53 times greater than that of the wild type CHIS1754. Due to its high computational efficiency and low experimental cost, this method offers significant advantages and presents a novel approach for the intelligent design of enzyme catalytic efficiency. As a result, it holds great promise for a wide range of applications.
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Affiliation(s)
- Hanqing Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Tuoyu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixin Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lingxi Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiying Luo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Yao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jian Tian
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Huoqing Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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2
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Wieczorek P, Jarmołowski A, Szweykowska-Kulińska Z, Kozak M, Taube M. Solution structure and behaviour of the Arabidopsis thaliana HYL1 protein. Biochim Biophys Acta Gen Subj 2023; 1867:130376. [PMID: 37150226 DOI: 10.1016/j.bbagen.2023.130376] [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: 01/30/2023] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
In plants, microRNA biogenesis involves the complex assembly of molecular processes that are mostly governed by three proteins: RNase III protein DCL1 and two RNA binding proteins, SERRATE and HYL1. HYL1 protein is a double stranded RNA binding protein that is needed for the precise excision of miRNA/miRNA* duplex from the stem-loop containing primary miRNA gene transcripts. Moreover, HYL1 protein partners with HSP90 and CARP9 proteins to load the miRNA molecules onto the AGO1 endonuclease. HYL1 protein as a crucial player in the biogenesis pathway is regulated by its phosphorylation status to fine tune the levels of miRNA in various physiological conditions. HYL1 protein consists of two dsRNA binding domains (dsRBD) that are involved in RNA binding and dimerization and a C-terminal disordered tail of unknown function. Although the spatial structures of the individual dsRBDs have been determined there is a lack of information about the behaviour and structure of the full length protein. Using small the angle X-ray scattering (SAXS) technique we investigated the structure and dynamic of the HYL1 protein from Arabidopsis thaliana in solution. We show that the C-terminal domain is disordered and dynamic in solution and that HYL1 protein dimerization is dependent on the concentration. HYL1 protein lacking a C-terminal tail and a nuclear localisation signal (NLS) fragment is almost exclusively monomeric and similarly to full-length protein has a dynamic nature in solution. Our results point for the first time to the role of the C-terminal fragment in stabilisation of HYL1 dimer formation.
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Affiliation(s)
- Przemysław Wieczorek
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Michał Taube
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland.
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Xu W, Dou Y, Geng H, Fu J, Dan Z, Liang T, Cheng M, Zhao W, Zeng Y, Hu Z, Huang W. OsGRP3 Enhances Drought Resistance by Altering Phenylpropanoid Biosynthesis Pathway in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms23137045. [PMID: 35806050 PMCID: PMC9266740 DOI: 10.3390/ijms23137045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/07/2023] Open
Abstract
As a sessile organism, rice often faces various kinds of abiotic stresses, such as drought stress. Drought stress seriously harms plant growth and damages crop yield every year. Therefore, it is urgent to elucidate the mechanisms of drought resistance in rice. In this study, we identified a glycine-rich RNA-binding protein, OsGRP3, in rice. Evolutionary analysis showed that it was closely related to OsGR-RBP4, which was involved in various abiotic stresses. The expression of OsGRP3 was shown to be induced by several abiotic stress treatments and phytohormone treatments. Then, the drought tolerance tests of transgenic plants confirmed that OsGRP3 enhanced drought resistance in rice. Meanwhile, the yeast two-hybrid assay, bimolecular luminescence complementation assay and bimolecular fluorescence complementation assay demonstrated that OsGRP3 bound with itself may affect the RNA chaperone function. Subsequently, the RNA-seq analysis, physiological experiments and histochemical staining showed that OsGRP3 influenced the phenylpropanoid biosynthesis pathway and further modulated lignin accumulation. Herein, our findings suggested that OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid biosynthesis pathway and further increasing lignin accumulation.
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Affiliation(s)
- Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangfan Dou
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han Geng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jinmei Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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4
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Roy S, Boral S, Maiti S, Kushwaha T, Basak AJ, Lee W, Basak A, Gholap SL, Inampudi KK, De S. Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition. FEBS J 2021; 289:2847-2864. [PMID: 34837346 DOI: 10.1111/febs.16301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/30/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2022]
Abstract
Human RNA-binding motif 3 protein (RBM3) is a cold-shock protein which functions in various aspects of global protein synthesis, cell proliferation and apoptosis by interacting with the components of basal translational machinery. RBM3 plays important roles in tumour progression and cancer metastasis, and also has been shown to be involved in neuroprotection and endoplasmic reticulum stress response. Here, we have solved the solution NMR structure of the N-terminal 84 residue RNA recognition motif (RRM) of RBM3. The remaining residues are rich in RGG and YGG motifs and are disordered. The RRM domain adopts a βαββαβ topology, which is found in many RNA-binding proteins. NMR-monitored titration experiments and molecular dynamic simulations show that the beta-sheet and two loops form the RNA-binding interface. Hydrogen bond, pi-pi and pi-cation are the key interactions between the RNA and the RRM domain. NMR, size exclusion chromatography and chemical cross-linking experiments show that RBM3 forms oligomers in solution, which is favoured by decrease in temperature, thus, potentially linking it to its function as a cold-shock protein. Temperature-dependent NMR studies revealed that oligomerization of the RRM domain occurs via nonspecific interactions. Overall, this study provides the detailed structural analysis of RRM domain of RBM3, its interaction with RNA and the molecular basis of its temperature-dependent oligomerization.
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Affiliation(s)
- Sayantani Roy
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Soumendu Boral
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Snigdha Maiti
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Aditya J Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, CO, USA
| | - Amit Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, India.,Department of Chemistry, Indian Institute of Technology Kharagpur, India
| | - Shivajirao L Gholap
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, India
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5
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Perea W, Greenbaum NL. Label-free horizontal EMSA for analysis of protein-RNA interactions. Anal Biochem 2020; 599:113736. [PMID: 32304696 DOI: 10.1016/j.ab.2020.113736] [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] [Received: 01/17/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 11/25/2022]
Abstract
We describe a method to analyze the affinity and specificity of interactions between proteins and RNA using horizontal PAGE under non-denaturing conditions. The method permits tracking of migration of anionic and cationic biomolecules and complexes toward anode and cathode, respectively, therefore enabling quantification of bound and free biomolecules of different charges and affinity of their intermolecular interactions. The gel is stained with a fluorescent intercalating dye (SYBR®Gold or ethidium bromide) for visualization of nucleic acids followed by Coomassie® Brilliant Blue R-250 for visualizations of proteins; the dissociation constant is determined separately from the intensity of unshifted and shifted bands visualized by each dye. The method permits calculation of bound and unbound anionic nucleic acid and cationic protein components in the same gel, regardless of charge, under identical conditions, and avoids the need for radioisotope or fluorescent labeling of either component.
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Affiliation(s)
- William Perea
- Department of Chemistry, Hunter College of the City University of New York, 695 Park Ave, New York, NY, 10065, USA
| | - Nancy L Greenbaum
- Department of Chemistry, Hunter College of the City University of New York, 695 Park Ave, New York, NY, 10065, USA; Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA.
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6
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Huang X, Yu R, Li W, Geng L, Jing X, Zhu C, Liu H. Identification and characterisation of a glycine-rich RNA-binding protein as an endogenous suppressor of RNA silencing from Nicotiana glutinosa. PLANTA 2019; 249:1811-1822. [PMID: 30840177 DOI: 10.1007/s00425-019-03122-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 05/08/2023]
Abstract
MAIN CONCLUSION This study shows that NgRBP suppresses both local and systemic RNA silencing induced by sense- or double-stranded RNA, and the RNA binding activity is essential for its function. To counteract host defence, many plant viruses encode viral suppressors of RNA silencing targeting various stages of RNA silencing. There is increasing evidence that the plants also encode endogenous suppressors of RNA silencing (ESR) to regulate this pathway. In this study, using Agrobacterium infiltration assays, we characterized NgRBP, a glycine-rich RNA-binding protein from Nicotiana glutinosa, as an ESR. Our results indicated that NgRBP suppressed both local and systemic RNA silencing induced by sense- or double-stranded RNA. We also demonstrated that NgRBP could promote Potato Virus X (PVX) infection in N. benthamiana. NgRBP knockdown by virus-induced gene silencing enhanced PVX and Cucumber mosaic virus resistance in N. glutinosa. RNA immunoprecipitation and electrophoretic mobility shift assays showed that NgRBP bound to GFP mRNA, dsRNA rather than siRNA. These findings provide the evidence that NgRBP acts as an ESR and the RNA affinity of NgRBP plays the key role in its ESR activity. NgRBP responds to multiple signals such as ABA, MeJA, SA, and Tobacco mosaic virus infection. Therefore, it could participate in the regulation of gene expression under specific conditions.
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Affiliation(s)
- Xu Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Ru Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Wenjing Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Liwei Geng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiuli Jing
- Institute of Immunology, Taishan Medical University, Tai'an, Shandong, China
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hongmei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.
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7
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Meyer K, Köster T, Nolte C, Weinholdt C, Lewinski M, Grosse I, Staiger D. Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. Genome Biol 2017; 18:204. [PMID: 29084609 PMCID: PMC5663106 DOI: 10.1186/s13059-017-1332-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Background Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) genome-wide to determine the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. Results iCLIP identifies 858 transcripts with significantly enriched crosslink sites in plants expressing AtGRP7-GFP that are absent in plants expressing an RNA-binding-dead AtGRP7 variant or GFP alone. To independently validate the targets, we performed RNA immunoprecipitation (RIP)-sequencing of AtGRP7-GFP plants subjected to formaldehyde fixation. Of the iCLIP targets, 452 were also identified by RIP-seq and represent a set of high-confidence binders. AtGRP7 can bind to all transcript regions, with a preference for 3′ untranslated regions. In the vicinity of crosslink sites, U/C-rich motifs are overrepresented. Cross-referencing the targets against transcriptome changes in AtGRP7 loss-of-function mutants or AtGRP7-overexpressing plants reveals a predominantly negative effect of AtGRP7 on its targets. In particular, elevated AtGRP7 levels lead to damping of circadian oscillations of transcripts, including DORMANCY/AUXIN ASSOCIATED FAMILY PROTEIN2 and CCR-LIKE. Furthermore, several targets show changes in alternative splicing or polyadenylation in response to altered AtGRP7 levels. Conclusions We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1332-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christine Nolte
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Claus Weinholdt
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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8
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Covarrubias AA, Cuevas-Velazquez CL, Romero-Pérez PS, Rendón-Luna DF, Chater CCC. Structural disorder in plant proteins: where plasticity meets sessility. Cell Mol Life Sci 2017; 74:3119-3147. [PMID: 28643166 PMCID: PMC11107788 DOI: 10.1007/s00018-017-2557-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023]
Abstract
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.
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Affiliation(s)
- Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico.
| | - Cesar L Cuevas-Velazquez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Paulette S Romero-Pérez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - David F Rendón-Luna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Caspar C C Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
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9
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Shi X, Castandet B, Germain A, Hanson MR, Bentolila S. ORRM5, an RNA recognition motif-containing protein, has a unique effect on mitochondrial RNA editing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2833-2847. [PMID: 28549172 PMCID: PMC5853588 DOI: 10.1093/jxb/erx139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/30/2017] [Indexed: 05/02/2023]
Abstract
Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors. Here we report the identification of organelle RRM protein 5 (ORRM5) as a mitochondrial editing factor with a unique mode of action. Unlike other ORRM editing factors, the absence of ORRM5 in orrm5 mutant plants results in an increase of the editing extent in 14% of the mitochondrial sites surveyed. The orrm5 mutant also exhibits a reduced splicing efficiency of the first nad5 intron and slower growth and delayed flowering time. ORRM5 contains an RNA recognition motif (RRM) and a glycine-rich domain at the C terminus. The RRM provides the editing activity of ORRM5 and is able to complement the splicing but not the morphological defects.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Correspondence:
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10
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Singh S, Virdi AS, Jaswal R, Chawla M, Kapoor S, Mohapatra SB, Manoj N, Pareek A, Kumar S, Singh P. A temperature-responsive gene in sorghum encodes a glycine-rich protein that interacts with calmodulin. Biochimie 2017; 137:115-123. [PMID: 28322928 DOI: 10.1016/j.biochi.2017.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/22/2017] [Accepted: 03/15/2017] [Indexed: 11/26/2022]
Abstract
Imposition of different biotic and abiotic stress conditions results in an increase in intracellular levels of Ca2+ which is sensed by various sensor proteins. Calmodulin (CaM) is one of the best studied transducers of Ca2+ signals. CaM undergoes conformational changes upon binding to Ca2+ and interacts with different types of proteins, thereby, regulating their activities. The present study reports the cloning and characterization of a sorghum cDNA encoding a protein (SbGRBP) that shows homology to glycine-rich RNA-binding proteins. The expression of SbGRBP in the sorghum seedlings is modulated by heat stress. The SbGRBP protein is localized in the nucleus as well as in cytosol, and shows interaction with CaM that requires the presence of Ca2+. SbGRBP depicts binding to single- and also double-stranded DNA. Fluorescence spectroscopic analyses suggest that interaction of SbGRBP with nucleic acids may be modulated after binding with CaM. To our knowledge, this is the first study to provide evidence for interaction of a stress regulated glycine-rich RNA-binding protein with CaM.
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Affiliation(s)
- Supreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Amardeep Singh Virdi
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Rajdeep Jaswal
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Palampur, 176061 Himachal Pradesh, India
| | - Mrinalini Chawla
- Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Samar B Mohapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sanjay Kumar
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Palampur, 176061 Himachal Pradesh, India.
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
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11
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Ectopic Expression of Plant RNA Chaperone Offering Multiple Stress Tolerance in E. coli. Mol Biotechnol 2017; 59:66-72. [DOI: 10.1007/s12033-017-9992-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Shi X, Germain A, Hanson MR, Bentolila S. RNA Recognition Motif-Containing Protein ORRM4 Broadly Affects Mitochondrial RNA Editing and Impacts Plant Development and Flowering. PLANT PHYSIOLOGY 2016; 170:294-309. [PMID: 26578708 PMCID: PMC4704580 DOI: 10.1104/pp.15.01280] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
Abstract
Plant RNA editosomes modify cytidines (C) to uridines (U) at specific sites in plastid and mitochondrial transcripts. Members of the RNA-editing factor interacting protein (RIP) family and Organelle RNA Recognition Motif-containing (ORRM) family are essential components of the Arabidopsis (Arabidopsis thaliana) editosome. ORRM2 and ORRM3 have been recently identified as minor mitochondrial editing factors whose silencing reduces editing efficiency at ∼6% of the mitochondrial C targets. Here we report the identification of ORRM4 (for organelle RRM protein 4) as a novel, major mitochondrial editing factor that controls ∼44% of the mitochondrial editing sites. C-to-U conversion is reduced, but not eliminated completely, at the affected sites. The orrm4 mutant exhibits slower growth and delayed flowering time. ORRM4 affects editing in a site-specific way, though orrm4 mutation affects editing of the entire transcript of certain genes. ORRM4 contains an RRM domain at the N terminus and a Gly-rich domain at the C terminus. The RRM domain provides the editing activity of ORRM4, whereas the Gly-rich domain is required for its interaction with ORRM3 and with itself. The presence of ORRM4 in the editosome is further supported by its interaction with RIP1 in a bimolecular fluorescence complementation assay. The identification of ORRM4 as a major mitochondrial editing factor further expands our knowledge of the composition of the RNA editosome and reveals that adequate mitochondrial editing is necessary for normal plant development.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
| | - Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 (X.S., A.G., M.R.H., S.B.)
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13
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Lewinski M, Hallmann A, Staiger D. Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. Mol Genet Genomics 2015; 291:763-73. [DOI: 10.1007/s00438-015-1144-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/06/2015] [Indexed: 11/28/2022]
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14
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Tripet B, Mason KE, Eilers BJ, Burns J, Powell P, Fischer AM, Copié V. Structural and biochemical analysis of the Hordeum vulgare L. HvGR-RBP1 protein, a glycine-rich RNA-binding protein involved in the regulation of barley plant development and stress response. Biochemistry 2014; 53:7945-60. [PMID: 25495582 PMCID: PMC4278681 DOI: 10.1021/bi5007223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 11/25/2014] [Indexed: 12/26/2022]
Abstract
The timing of whole-plant senescence influences important agricultural traits such as yield and grain protein content. Post-transcriptional regulation by plant RNA-binding proteins is essential for proper control of gene expression, development, and stress responses. Here, we report the three-dimensional solution NMR structure and nucleic acid-binding properties of the barley glycine-rich RNA-binding protein HvGR-RBP1, whose transcript has been identified as being >45-fold up-regulated in early-as compared to late-senescing near-isogenic barley germplasm. NMR analysis reveals that HvGR-RBP1 is a multidomain protein comprising a well-folded N-terminal RNA Recognition Motif (RRM) and a structurally disordered C-terminal glycine-rich domain. Chemical shift differences observed in 2D (1)H-(15)N correlation (HSQC) NMR spectra of full-length HvGR-RBP1 and N-HvGR-RBP1 (RRM domain only) suggest that the two domains can interact both in-trans and intramolecularly, similar to what is observed in the tobacco NtGR-RBP1 protein. Further, we show that the RRM domain of HvGR-RBP1 binds single-stranded DNA nucleotide fragments containing the consensus nucleotide sequence 5'-TTCTGX-3' with low micromolar affinity in vitro. We also demonstrate that the C-terminal glycine-rich (HvGR) domain of Hv-GR-RBP1 can interact nonspecifically with ssRNA in vitro. Structural similarities with other plant glycine-rich RNA-binding proteins suggest that HvGR-RBP1 may be multifunctional. Based on gene expression analysis following cold stress in barley and E. coli growth studies following cold shock treatment, we conclude that HvGR-RBP1 functions in a manner similar to cold-shock proteins and harbors RNA chaperone activity. HvGR-RBP1 is therefore not only involved in the regulation of barley development including senescence, but also functions in plant responses to environmental stress.
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MESH Headings
- Cold-Shock Response/physiology
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Hordeum/genetics
- Hordeum/metabolism
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
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Affiliation(s)
- Brian
P. Tripet
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Katelyn E. Mason
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Brian J. Eilers
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Jennifer Burns
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Paul Powell
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Andreas M. Fischer
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Valérie Copié
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
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15
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Leder V, Lummer M, Tegeler K, Humpert F, Lewinski M, Schüttpelz M, Staiger D. Mutational definition of binding requirements of an hnRNP-like protein in Arabidopsis using fluorescence correlation spectroscopy. Biochem Biophys Res Commun 2014; 453:69-74. [PMID: 25251471 DOI: 10.1016/j.bbrc.2014.09.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/15/2014] [Indexed: 12/23/2022]
Abstract
Arabidopsis thaliana glycine-rich RNA binding protein 7 (AtGRP7) is part of a negative feedback loop through which it regulates alternative splicing and steady-state abundance of its pre-mRNA. Here we use fluorescence correlation spectroscopy to investigate the requirements for AtGRP7 binding to its intron using fluorescently-labelled synthetic oligonucleotides. By systematically introducing point mutations we identify three nucleotides that lead to an increased Kd value when mutated and thus are critical for AtGRP7 binding. Simultaneous mutation of all three residues abrogates binding. The paralogue AtGRP8 binds to an overlapping motif but with a different sequence preference, in line with overlapping but not identical functions of this protein pair. Truncation of the glycine-rich domain reduces the binding affinity of AtGRP7, showing for the first time that the glycine-rich stretch of a plant hnRNP-like protein contributes to binding. Mutation of the conserved R(49) that is crucial for AtGRP7 function in pathogen defence and splicing abolishes binding.
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Affiliation(s)
- Verena Leder
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany; Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Martina Lummer
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany
| | - Kathrin Tegeler
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany; Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Fabian Humpert
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Martin Lewinski
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany.
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