1
|
Ghosh S, Mellado Sanchez M, Sue-Ob K, Roy D, Jones A, Blazquez MA, Sadanandom A. Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation. THE PLANT CELL 2024; 36:3131-3144. [PMID: 38923935 PMCID: PMC11371177 DOI: 10.1093/plcell/koae192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation to changing environments. Exploration of the evolutionary emergence of Ubiquitin-like (UBL) systems unveils their origin from prokaryotes, where it is linked to the mechanisms that enable sulfur uptake into biomolecules. We explore the emergence of the SUMO machinery across the plant lineage from single-cell to land plants. We reveal the evolutionary point at which plants acquired the ability to form SUMO chains through the emergence of SUMO E4 ligases, hinting at its role in facilitating multicellularity. Additionally, we explore the possible mechanism for the neofunctionalization of SUMO proteases through the fusion of conserved catalytic domains with divergent sequences. We highlight the pivotal role of SUMO proteases in plant development and adaptation, offering new insights into target specificity mechanisms of SUMO modification during plant evolution. Correlating the emergence of adaptive traits in the plant lineage with established experimental evidence for SUMO in developmental processes, we propose that SUMO modification has evolved to link developmental processes to adaptive functions in land plants.
Collapse
Affiliation(s)
- Srayan Ghosh
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | | | - Kawinnat Sue-Ob
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Dipan Roy
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Andrew Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Miguel A Blazquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, 46022, Spain
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| |
Collapse
|
2
|
Wu W, Huang C. SUMOylation and DeSUMOylation: Prospective therapeutic targets in cancer. Life Sci 2023; 332:122085. [PMID: 37722589 DOI: 10.1016/j.lfs.2023.122085] [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: 08/05/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
The SUMO family is a type of ubiquitin-like protein modification molecule. Its protein modification mechanism is similar to that of ubiquitination: both involve modifier-activating enzyme E1, conjugating enzyme E2 and substrate-specific ligase E3. However, polyubiquitination can lead to the degradation of substrate proteins, while poly-SUMOylation only leads to the degradation of substrate proteins through the proteasome pathway after being recognized by ubiquitin as a signal factor. There are currently five reported subtypes in the SUMO family, namely SUMO1-5. As a reversible dynamic modification, intracellular sentrin/SUMO-specific proteases (SENPs) mainly regulate the reverse reaction pathway of SUMOylation. The SUMOylation modification system affects the localization, activation and turnover of proteins in cells and participates in regulating most nuclear and extranuclear molecular reactions. Abnormal expression of proteins related to the SUMOylation pathway is commonly observed in tumors, indicating that this pathway is closely related to tumor occurrence, metastasis and invasion. This review mainly discusses the composition of members in the protein family related to SUMOylation pathways, mutual connections between SUMOylation and other post-translational modifications on proteins as well as therapeutic drugs developed based on these pathways.
Collapse
Affiliation(s)
- Wenyan Wu
- Kunming University of Science and Technology, Medical School, Kunming 650500, China
| | - Chao Huang
- Kunming University of Science and Technology, Medical School, Kunming 650500, China.
| |
Collapse
|
3
|
Liu J, Wu X, Fang Y, Liu Y, Bello EO, Li Y, Xiong R, Li Y, Fu ZQ, Wang A, Cheng X. A plant RNA virus inhibits NPR1 sumoylation and subverts NPR1-mediated plant immunity. Nat Commun 2023; 14:3580. [PMID: 37328517 PMCID: PMC10275998 DOI: 10.1038/s41467-023-39254-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1) is the master regulator of salicylic acid-mediated basal and systemic acquired resistance in plants. Here, we report that NPR1 plays a pivotal role in restricting compatible infection by turnip mosaic virus, a member of the largest plant RNA virus genus Potyvirus, and that such resistance is counteracted by NUCLEAR INCLUSION B (NIb), the viral RNA-dependent RNA polymerase. We demonstrate that NIb binds to the SUMO-interacting motif 3 (SIM3) of NPR1 to prevent SUMO3 interaction and sumoylation, while sumoylation of NIb by SUMO3 is not essential but can intensify the NIb-NPR1 interaction. We discover that the interaction also impedes the phosphorylation of NPR1 at Ser11/Ser15. Moreover, we show that targeting NPR1 SIM3 is a conserved ability of NIb from diverse potyviruses. These data reveal a molecular "arms race" by which potyviruses deploy NIb to suppress NPR1-mediated resistance through disrupting NPR1 sumoylation.
Collapse
Affiliation(s)
- Jiahui Liu
- College of Plant Protection, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
| | - Xiaoyun Wu
- College of Plant Protection, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
| | - Yue Fang
- College of Plant Protection, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
| | - Ye Liu
- College of Plant Protection, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
| | - Esther Oreofe Bello
- College of Plant Protection, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
| | - Yong Li
- College of Life Science, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China
| | - Ruyi Xiong
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, N5V 4T3, ON, Canada
- A&L Canada Laboratories Lnc., London, N5V 3P5, ON, Canada
| | - Yinzi Li
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, N5V 4T3, ON, Canada
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, N5V 4T3, ON, Canada
| | - Xiaofei Cheng
- College of Plant Protection, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China.
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, 150030, Harbin, Heilongjiang, China.
| |
Collapse
|
4
|
Shimada H, Tanaka K. Rice SUMOs and unification of their names. Genes Genet Syst 2023. [PMID: 37150617 DOI: 10.1266/ggs.22-00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Posttranslational modifications (PTMs) to proteins are regulatory mechanisms that play a critical role in regulating growth and development. The SUMO system is a rapid and dynamic PTM system employed by eukaryotic cells. Plant SUMOs are involved in many physiological processes, such as stress responses, regulation of flowering time and defense reactions to pathogen attack. In Arabidopsis thaliana and rice (Oryza sativa), eight and seven SUMO genes, respectively, were predicted by sequence analysis. Phylogenetic tree analysis of these SUMOs shows that they are divided into two groups. One consists of SUMOs that contain no SUMO acceptor site and are involved in monoSUMOylation of their target proteins. Rice OsSUMO1 and OsSUMO2 are in this group, and are structurally similar to each other and to Arabidopsis AtSUMO1. The other group is composed of SUMOs in which an acceptor site (ΨKXE/D) occurs inside the SUMO molecule, suggesting their involvement in polySUMOylation. Several studies on the rice SUMOs have been performed independently and reported. Individual names of rice SUMOs are confusing, because a unified nomenclature has not been proposed. This review clarifies the attribution of seven rice SUMOs and unifies the individual SUMO names.
Collapse
Affiliation(s)
- Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science
| | - Katsunori Tanaka
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei Gakuin University
| |
Collapse
|
5
|
Dvořák Tomaštíková E, Prochazkova K, Yang F, Jemelkova J, Finke A, Dorn A, Said M, Puchta H, Pecinka A. SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis. THE PLANT CELL 2023; 35:1532-1547. [PMID: 36705512 PMCID: PMC10118267 DOI: 10.1093/plcell/koad020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 05/10/2023]
Abstract
DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
Collapse
Affiliation(s)
| | - Klara Prochazkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Fen Yang
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Jitka Jemelkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Functional Genomics and Proteomics, National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, 12619, Cairo, Egypt
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | | |
Collapse
|
6
|
Hu X, Hao J, Pan L, Xu T, Ren L, Chen Y, Tang M, Liao L, Wang Z. Genome-wide analysis of tandem duplicated genes and their expression under salt stress in seashore paspalum. FRONTIERS IN PLANT SCIENCE 2022; 13:971999. [PMID: 36247543 PMCID: PMC9562133 DOI: 10.3389/fpls.2022.971999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Seashore paspalum (Paspalum vaginatum) is a halophytic, warm-season grass which is closely related to various grain crops. Gene duplication plays an important role in plant evolution, conferring significant plant adaptation at the genomic level. Here, we identified 2,542 tandem duplicated genes (TDGs) in the P. vaginatum genome and estimated the divergence time of pairs of TDGs based on synonymous substitution rates (Ks). Expression of P. vaginatum TDGs resulted in enrichment in many GO terms and KEGG pathways when compared to four other closely-related species. The GO terms included: "ion transmembrane transporter activity," "anion transmembrane transporter activity" and "cation transmembrane transport," and KEGG pathways included "ABC transport." RNA-seq analysis of TDGs showed tissue-specific expression under salt stress, and we speculated that P. vaginatum leaves became adapted to salt stress in the earlier whole-genome duplication (WGD; ~83.3 million years ago; Ma), whereas the entire P. vaginatum plant acquired a large number of TDGs related to salt stress in the second WGD (~23.3 Ma). These results can be used as a reference resource to accelerate salt-resistance research in other grasses and crops.
Collapse
Affiliation(s)
- Xu Hu
- College of Tropical Crops, Hainan University, Haikou, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Jiangshan Hao
- College of Tropical Crops, Hainan University, Haikou, China
- School of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Ling Pan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Tao Xu
- College of Tropical Crops, Hainan University, Haikou, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Longzhou Ren
- College of Tropical Crops, Hainan University, Haikou, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Yu Chen
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Li Liao
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| |
Collapse
|
7
|
Shi B, Hou J, Yang J, Han IJ, Tu D, Ye S, Yu J, Li L. Genome-wide analysis of the CSN genes in land plants and their expression under various abiotic stress and phytohormone conditions in rice. Gene 2022; 850:146905. [PMID: 36181988 DOI: 10.1016/j.gene.2022.146905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/30/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022]
Abstract
The CONSTITUTIVE PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) is a multi-functional protein complex, which is involved in plant growth and abiotic stress response. However, the evolution and function of the CSN genes in land plants are still largely unclear. Here, we have identified 124 CSN genes and constructed phylogenetic trees of these CSN proteins to elucidate their feature and evolution in twelve land plants. Analysis of gene structure, protein property and protein motif composition shows the evolutional conservation and variation of the CSN proteins in land plants. These CSN genes might evolve through whole genome duplication (WGD)/segmental duplication (SD) and tandem duplication (TD). Analysis of promoter cis-elements shows that the CSN genes are implicated in diverse biological processes and different signaling pathways. RT-qPCR indicates that the transcript abundance of the OsCSN genes is up-regulated or down-regulated in response to abiotic stress and treatment with various hormones in rice. These results provide new insights into the CSN gene evolution and its possible function in land plants.
Collapse
Affiliation(s)
- Bozhang Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jin Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Il-Jin Han
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Daoyi Tu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shiqi Ye
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jinfu Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
8
|
Joo H, Lim CW, Lee SC. Pepper SUMO E3 ligase CaDSIZ1 enhances drought tolerance by stabilizing the transcription factor CaDRHB1. THE NEW PHYTOLOGIST 2022; 235:2313-2330. [PMID: 35672943 DOI: 10.1111/nph.18300] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation (SUMOylation) is a reversible post-translational modification associated with protein stability and activity, and modulates hormone signaling and stress responses in plants. Previously, we reported that the pepper dehydration-responsive homeobox domain transcription factor CaDRHB1 acts as a positive modulator of drought response. Here, we show that CaDRHB1 protein stability is enhanced by SUMO E3 ligase Capsicum annuum DRHB1-interacting SAP and Miz domain (SIZ1) (CaDSIZ1)-mediated SUMOylation in response to drought, thereby positively modulating abscisic acid (ABA) signaling and drought responses. Substituting lysine (K) 138 of CaDRHB1 with arginine reduced CaDSIZ1-mediated SUMOylation, indicating that K138 is the principal site for SUMO conjugation. Virus-induced silencing of CaDSIZ1 promoted CaDRHB1 degradation, suggesting that CaDSIZ1 is involved in drought-induced SUMOylation of CaDRHB1. CaDSIZ1 interacted with and facilitated SUMO conjugation of CaDRHB1. CaDRHB1, mainly localized in the nucleus, but also in the cytoplasm in the SUMOylation mimic state, suggesting that SUMOylation of CaDRHB1 promotes its nuclear export, leading to cytoplasmic accumulation. Moreover, CaDSIZ1-silenced pepper plants were less sensitive to ABA and considerably sensitive to drought stress, whereas CaDSIZ1-overexpressing plants displayed ABA-hypersensitive and drought-tolerant phenotypes. Collectively, our data indicate that CaDSIZ1-mediated SUMOylation of CaDRHB1 functions in ABA-mediated drought tolerance.
Collapse
Affiliation(s)
- Hyunhee Joo
- Department of Life Science (BK21 program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974, Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974, Korea
| |
Collapse
|
9
|
Understanding SUMO-mediated adaptive responses in plants to improve crop productivity. Essays Biochem 2022; 66:155-168. [PMID: 35920279 PMCID: PMC9400072 DOI: 10.1042/ebc20210068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 12/30/2022]
Abstract
The response to abiotic and biotic stresses in plants and crops is considered a multifaceted process. Due to their sessile nature, plants have evolved unique mechanisms to ensure that developmental plasticity remains during their life cycle. Among these mechanisms, post-translational modifications (PTMs) are crucial components of adaptive responses in plants and transduce environmental stimuli into cellular signalling through the modulation of proteins. SUMOylation is an emerging PTM that has received recent attention due to its dynamic role in protein modification and has quickly been considered a significant component of adaptive mechanisms in plants during stress with great potential for agricultural improvement programs. In the present review, we outline the concept that small ubiquitin-like modifier (SUMO)-mediated response in plants and crops to abiotic and biotic stresses is a multifaceted process with each component of the SUMO cycle facilitating tolerance to several different environmental stresses. We also highlight the clear increase in SUMO genes in crops when compared with Arabidopsis thaliana. The SUMO system is understudied in crops, given the importance of SUMO for stress responses, and for some SUMO genes, the apparent expansion provides new avenues to discover SUMO-conjugated targets that could regulate beneficial agronomical traits.
Collapse
|
10
|
Hu X, Xiao X, Zhang CL, Wang GL, Zhang YL, Li YY, You CX. Organization and regulation of the apple SUMOylation system under salt and ABA. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 182:22-35. [PMID: 35460932 DOI: 10.1016/j.plaphy.2022.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/13/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Small ubiquitin-related modifier (SUMO)-mediated post-translational protein modification is widely conserved among eukaryotes. SUMOylation refers to the covalent attachment of SUMO to target proteins that alters their function, location, and protein-protein interactions when plants are under abiotic stress. We identified 37 genes in the apple genome that encoded members of the SUMOylation pathway. In addition, RNA-Seq data shows their expression levels between different tissues. We can find that there are mainly expressed genes between each component to ensure that the entire pathway works in the plant. We found that the expression levels of 12 genes were significantly changed under NaCl and ABA treatment through qRT-PCR. MdSIZ1a strongly expression responded to NaCl and ABA treatment. Subsequently, MdSIZ1a was cloned and transformed into apple callus, further verifying the important role of the SUMOylation pathway under stress conditions. The interaction between MdSIZ1a and MdSCEa was verified by yeast two-hybrid, confirming that MdSIZ1a acts as bridge enzyme on MdSCEa and target substrates. Finally, we predicted and analyzed the functional interaction network of E3 ligase to shed light on protein interactions and gene regulatory networks associated with DNA damage repair under abiotic stress in apples.
Collapse
Affiliation(s)
- Xing Hu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xu Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chun-Ling Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Gui-Luan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Ya-Li Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
| |
Collapse
|
11
|
Global Identification and Characterization of C2 Domain-Containing Proteins Associated with Abiotic Stress Response in Rice (Oryza sativa L.). Int J Mol Sci 2022; 23:ijms23042221. [PMID: 35216337 PMCID: PMC8875736 DOI: 10.3390/ijms23042221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/20/2022] Open
Abstract
C2 domain-containing proteins (C2DPs) have been identified in different genomes that contain single or multiple C2 domains in their C- or N-terminal. It possesses higher functional activity in the transmembrane regions. The identification of C2 domains were reported in a previous study, such as multiple C2 domains and transmembrane-region proteins (MCTPs) and N-terminal-TM-C2 domain proteins (NTMC2s) of rice, Arabidopsis thaliana, and cotton, whereas the C2DP gene family in rice has not been comprehensively studied, and the role of the C2DP gene in rice in response to abiotic stress is not yet fully understood. In this study, we identified 82 C2DPs in the rice genome and divided them into seven groups through phylogenetic analysis. The synteny analysis revealed that duplication events were either exhibited within the genome of rice or between the genomes of rice and other species. Through the analysis of cis-acting elements in promoters, expression profiles, and qRT-PCR results, the functions of OsC2DPs were found to be widely distributed in diverse tissues and were extensively involved in phytohormones-related and abiotic stresses response in rice. The prediction of the microRNA (miRNA) targets of OsC2DPs revealed the possibility of regulation by consistent miRNAs. Notably, OsC2DP50/51/52 as a co-tandem duplication exhibited similar expression variations and involved the coincident miRNA-regulation pathway. Moreover, the results of the genotypic variation and haplotype analysis revealed that OsC2DP17, OsC2DP29, and OsC2DP49 were associated with cold stress responses. These findings provided comprehensive insights for characterizations of OsC2DPs in rice as well as for their roles for abiotic stress.
Collapse
|
12
|
Ibrahim EI, Attia KA, Ghazy AI, Itoh K, Almajhdi FN, Al-Doss AA. Molecular Characterization and Functional Localization of a Novel SUMOylation Gene in Oryza sativa. BIOLOGY 2021; 11:biology11010053. [PMID: 35053052 PMCID: PMC8772976 DOI: 10.3390/biology11010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/19/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The small ubiquitin-related modifier genes regulate the function of the cellular proteins, which are associated with cell stress-tolerance. Identification and understanding the functional localization of these genes are very important to mitigate the stresses. In this study, we identified a novel small ubiquitin-related modifier gene and studied its functional localization in the cell. This new finding will be very valuable in increasing our understanding of the mechanism of stress-tolerance. Abstract Small ubiquitin-related modifier (SUMO) regulates the cellular function of diverse proteins through post-translational modifications. The current study defined a new homolog of SUMO genes in the rice genome and named it OsSUMO7. Putative protein analysis of OsSUMO7 detected SUMOylation features, including di-glycine (GG) and consensus motifs (ΨKXE/D) for the SUMOylation site. Phylogenetic analysis demonstrated the high homology of OsSUMO7 with identified rice SUMO genes, which indicates that the OsSUMO7 gene is an evolutionarily conserved SUMO member. RT-PCR analysis revealed that OsSUMO7 was constitutively expressed in all plant organs. Bioinformatic analysis defined the physicochemical properties and structural model prediction of OsSUMO7 proteins. A red fluorescent protein (DsRed), fused with the OsSUMO7 protein, was expressed and localized mainly in the nucleus and formed nuclear subdomain structures. The fusion proteins of SUMO-conjugating enzymes with the OsSUMO7 protein were co-expressed and co-localized in the nucleus and formed nuclear subdomains. This indicated that the OsSUMO7 precursor is processed, activated, and transported to the nucleus through the SUMOylation system of the plant cell.
Collapse
Affiliation(s)
- Eid I. Ibrahim
- Biotechnology Lab., Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.I.G.); (A.A.A.-D.)
- Correspondence: (E.I.I.); (K.A.A.)
| | - Kotb A. Attia
- Center of Excellence in Biotechnology Research, King Saud University, P.O. Box 2455-11451, Riyadh 11451, Saudi Arabia
- Rice Biotechnology Lab., Rice Research Department, Field Crops Research Institute, ARC, Sakha, Kafr, EL-Sheikh 33717, Egypt
- Correspondence: (E.I.I.); (K.A.A.)
| | - Abdelhalim I. Ghazy
- Biotechnology Lab., Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.I.G.); (A.A.A.-D.)
| | - Kimiko Itoh
- Institute of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Fahad N. Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Abdullah A. Al-Doss
- Biotechnology Lab., Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.I.G.); (A.A.A.-D.)
| |
Collapse
|
13
|
Péter C, Nagy F, Viczián A. SUMOylation of different targets fine-tunes phytochrome signaling. THE NEW PHYTOLOGIST 2021; 232:1201-1211. [PMID: 34289130 DOI: 10.1111/nph.17634] [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: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.
Collapse
Affiliation(s)
- Csaba Péter
- Laboratory of Photo and Chronobiology, Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Laboratory of Photo and Chronobiology, Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - András Viczián
- Laboratory of Photo and Chronobiology, Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| |
Collapse
|
14
|
Ingole KD, Kasera M, van den Burg HA, Bhattacharjee S. Antagonism between SUMO1/2 and SUMO3 regulates SUMO conjugate levels and fine-tunes immunity. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6640-6658. [PMID: 34145454 DOI: 10.1093/jxb/erab296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/16/2021] [Indexed: 06/12/2023]
Abstract
The attachment of SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to target proteins regulates a plethora of cellular processes across eukaryotes. In Arabidopsis thaliana, mutants with abnormal SUMO1/2 conjugate levels display a dwarf stature, autoimmunity, and altered stress responses to adverse environmental conditions. Since the SUMO pathway is known to autoregulate its biochemical activity (via allosteric interactions), we assessed whether the emergence of additional SUMO paralogs in Arabidopsis has introduced the capacity of self-regulation by means of isoform diversification in this model plant. By studying the plant defense responses elicited by the bacterial pathogen Pseudomonas syringae pv. tomato, we provide genetic evidence that SUM3, a divergent paralog, acts downstream of the two main SUMO paralogues, SUM1/2. The expression of SUM3 apparently buffers or suppresses the function of SUM1/2 by controlling the timing and amplitude of the immune response. Moreover, SUM1 and SUM2 work additively to suppress both basal and TNL-specific immunity, a specific branch of the immune network. Finally, our data reveal that SUM3 is required for the global increase in SUMO1/2 conjugates upon exposure to biotic and abiotic stresses, namely heat and pathogen exposure. We cannot exclude that this latter effect is independent of the role of SUM3 in immunity.
Collapse
Affiliation(s)
- Kishor D Ingole
- Laboratory of Signal Transduction and Plant Resistance, UNESCO Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad-121 001, Haryana, India
- Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar-751 024, Odisha, India
| | - Mritunjay Kasera
- Laboratory of Signal Transduction and Plant Resistance, UNESCO Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad-121 001, Haryana, India
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Saikat Bhattacharjee
- Laboratory of Signal Transduction and Plant Resistance, UNESCO Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad-121 001, Haryana, India
| |
Collapse
|
15
|
Imbert F, Langford D. Viruses, SUMO, and immunity: the interplay between viruses and the host SUMOylation system. J Neurovirol 2021; 27:531-541. [PMID: 34342851 PMCID: PMC8330205 DOI: 10.1007/s13365-021-00995-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 12/14/2022]
Abstract
The conjugation of small ubiquitin-like modifier (SUMO) proteins to substrates is a well-described post-translational modification that regulates protein activity, subcellular localization, and protein-protein interactions for a variety of downstream cellular activities. Several studies describe SUMOylation as an essential post-translational modification for successful viral infection across a broad range of viruses, including RNA and DNA viruses, both enveloped and un-enveloped. These viruses include but are not limited to herpes viruses, human immunodeficiency virus-1, and coronaviruses. In addition to the SUMOylation of viral proteins during infection, evidence shows that viruses manipulate the SUMO pathway for host protein SUMOylation. SUMOylation of host and viral proteins greatly impacts host innate immunity through viral manipulation of the host SUMOylation machinery to promote viral replication and pathogenesis. Other post-translational modifications like phosphorylation can also modulate SUMO function. For example, phosphorylation of COUP-TF interacting protein 2 (CTIP2) leads to its SUMOylation and subsequent proteasomal degradation. The SUMOylation of CTIP2 and subsequent degradation prevents CTIP2-mediated recruitment of a multi-enzymatic complex to the HIV-1 promoter that usually prevents the transcription of integrated viral DNA. Thus, the "SUMO switch" could have implications for CTIP2-mediated transcriptional repression of HIV-1 in latency and viral persistence. In this review, we describe the consequences of SUMO in innate immunity and then focus on the various ways that viral pathogens have evolved to hijack the conserved SUMO machinery. Increased understanding of the many roles of SUMOylation in viral infections can lead to novel insight into the regulation of viral pathogenesis with the potential to uncover new targets for antiviral therapies.
Collapse
Affiliation(s)
- Fergan Imbert
- Department of Neuroscience, Lewis Katz School of Medicine, Temple University, PA, 19140, Philadelphia, USA
| | - Dianne Langford
- Department of Neuroscience, Lewis Katz School of Medicine, Temple University, PA, 19140, Philadelphia, USA.
| |
Collapse
|
16
|
Gough C, Sadanandom A. Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance. Biomolecules 2021; 11:1122. [PMID: 34439788 PMCID: PMC8392720 DOI: 10.3390/biom11081122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022] Open
Abstract
Plants are constantly threatened by pathogens, so have evolved complex defence signalling networks to overcome pathogen attacks. Post-translational modifications (PTMs) are fundamental to plant immunity, allowing rapid and dynamic responses at the appropriate time. PTM regulation is essential; pathogen effectors often disrupt PTMs in an attempt to evade immune responses. Here, we cover the mechanisms of disease resistance to pathogens, and how growth is balanced with defence, with a focus on the essential roles of PTMs. Alteration of defence-related PTMs has the potential to fine-tune molecular interactions to produce disease-resistant crops, without trade-offs in growth and fitness.
Collapse
Affiliation(s)
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK;
| |
Collapse
|
17
|
Zhao W, Zhang X, Rong J. SUMOylation as a Therapeutic Target for Myocardial Infarction. Front Cardiovasc Med 2021; 8:701583. [PMID: 34395563 PMCID: PMC8355363 DOI: 10.3389/fcvm.2021.701583] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
Myocardial infarction is a prevalent and life-threatening cardiovascular disease. The main goal of existing interventional therapies is to restore coronary reperfusion while few are designed to ameliorate the pathology of heart diseases via targeting the post-translational modifications of those critical proteins. Small ubiquitin-like modifier (SUMO) proteins are recently discovered to form a new type of protein post-translational modifications (PTM), known as SUMOylation. SUMOylation and deSUMOylation are dynamically balanced in the maintenance of various biological processes including cell division, DNA repair, epigenetic transcriptional regulation, and cellular metabolism. Importantly, SUMOylation plays a critical role in the regulation of cardiac functions and the pathology of cardiovascular diseases, especially in heart failure and myocardial infarction. This review summarizes the current understanding on the effects of SUMOylation and SUMOylated proteins in the pathophysiology of myocardial infarction and identifies the potential treatments against myocardial injury via targeting SUMO. Ultimately, this review recommends SUMOylation as a key therapeutic target for treating cardiovascular diseases.
Collapse
Affiliation(s)
- Wei Zhao
- Li Ka Shing Faculty of Medicine, School of Chinese Medicine, University of Hong Kong, Hong Kong, China.,Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiuying Zhang
- Li Ka Shing Faculty of Medicine, School of Chinese Medicine, University of Hong Kong, Hong Kong, China
| | - Jianhui Rong
- Li Ka Shing Faculty of Medicine, School of Chinese Medicine, University of Hong Kong, Hong Kong, China.,Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China
| |
Collapse
|
18
|
Hammoudi V, Beerens B, Jonker MJ, Helderman TA, Vlachakis G, Giesbers M, Kwaaitaal M, van den Burg HA. The protein modifier SUMO is critical for integrity of the Arabidopsis shoot apex at warm ambient temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab262. [PMID: 34106243 DOI: 10.1093/jxb/erab262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Indexed: 06/12/2023]
Abstract
SUMO is a protein modification whose conjugate levels peak during acute heat stress. We find that SUMO is also critical for plant longevity when Arabidopsis experiences a prolonged non-damaging period of only 28 degrees Celsius. Remarkably, this thermo-lethality at 28 degrees was not seen with any other mutant of the SUMO pathway tested. Autoimmunity due to low SUMO1/2 expression levels was not causal for this thermo-lethality. The role of SUMO for thermo-resilience was also distinct from its requirement for thermomorphogenesis - a growth response triggered by the same warm temperature, as only the latter response was dependent on the SUMO ligase SIZ1 as well. Thermo-resilience at 28 degrees Celsius and (acquired) thermotolerance (a response that allows plants to recover and acclimate to brief extreme temperatures) both depend on the HEAT SHOCK TRANSCRIPTION FACTOR A1 (HSFA1). Acquired thermotolerance was, however, normal in the sumo1/2 knockdown mutant. Thus, SUMO-dependent thermo-resilience is potentially controlled in a different way than the protein damage pathway that underpins thermotolerance. Close inspection of shoot apices revealed that the cell patterning and tissue integrity of the shoot apex of the SUMO1/2 knockdown mutant was lost at 28, but not 22 degrees Celsius. We thus describe a novel SUMO-dependent phenotype.
Collapse
Affiliation(s)
- Valentin Hammoudi
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Bas Beerens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology and Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Tieme A Helderman
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Georgios Vlachakis
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Marcel Giesbers
- Wageningen Electron Microscopy Centre, Wageningen University, The Netherlands
| | - Mark Kwaaitaal
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| |
Collapse
|
19
|
Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice. PLANTS 2021; 10:plants10061154. [PMID: 34204124 PMCID: PMC8227427 DOI: 10.3390/plants10061154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022]
Abstract
Starch is a major ingredient in rice, and the amylose content of starch significantly impacts rice quality. OsSS (starch synthase) is a gene family related to the synthesis of amylose and amylopectin, and 10 members have been reported. In the present study, a synteny analysis of a novel family member belonging to the OsSSIV subfamily that contained a starch synthase catalytic domain showed that three segmental duplications and multiple duplications were identified in rice and other species. Expression data showed that the OsSS gene family is involved in diverse expression patterns. The prediction of miRNA targets suggested that OsSS are possibly widely regulated by miRNA functions, with miR156s targeted to OsSSII-3, especially. Haplotype analysis exhibited the relationship between amylose content and diverse genotypes. These results give new insight and a theoretical basis for the improved amylose content and eating quality of rice.
Collapse
|
20
|
Roy D, Sadanandom A. SUMO mediated regulation of transcription factors as a mechanism for transducing environmental cues into cellular signaling in plants. Cell Mol Life Sci 2021; 78:2641-2664. [PMID: 33452901 PMCID: PMC8004507 DOI: 10.1007/s00018-020-03723-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022]
Abstract
Across all species, transcription factors (TFs) are the most frequent targets of SUMOylation. The effect of SUMO conjugation on the functions of transcription factors has been extensively studied in animal systems, with over 200 transcription factors being documented to be modulated by SUMOylation. This has resulted in the establishment of a number of paradigms that seek to explain the mechanisms by which SUMO regulates transcription factor functions. For instance, SUMO has been shown to modulate TF DNA binding activity; regulate both localization as well as the abundance of TFs and also influence the association of TFs with chromatin. With transcription factors being implicated as master regulators of the cellular signalling pathways that maintain phenotypic plasticity in all organisms, in this review, we will discuss how SUMO mediated regulation of transcription factor activity facilitates molecular pathways to mount an appropriate and coherent biological response to environmental cues.
Collapse
Affiliation(s)
- Dipan Roy
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.
| |
Collapse
|
21
|
Bernula P, Pettkó-Szandtner A, Hajdu A, Kozma-Bognár L, Josse EM, Ádám É, Nagy F, Viczián A. SUMOylation of PHYTOCHROME INTERACTING FACTOR 3 promotes photomorphogenesis in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 229:2050-2061. [PMID: 33078389 DOI: 10.1111/nph.17013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/07/2020] [Indexed: 05/22/2023]
Abstract
In Arabidopsis thaliana, phytochrome B (phyB) is the dominant receptor of photomorphogenic development under red light. Phytochrome B interacts with a set of downstream regulatory proteins, including PHYTOCHROME INTERACTING FACTOR 3 (PIF3). The interaction between PIF3 and photoactivated phyB leads to the rapid phosphorylation and degradation of PIF3 and also to the degradation of phyB, events which are required for proper photomorphogenesis. Here we report that PIF3 is SUMOylated at the Lys13 (K13) residue and that we could detect this posttranslational modification in a heterologous experimental system and also in planta. We also found that the SUMO acceptor site mutant PIF3(K13R) binds more strongly to the target promoters than its SUMOylated, wild-type counterpart. Seedlings expressing PIF3(K13R) show an elongated hypocotyl response, elevated photoprotection and higher transcriptional induction of red-light responsive genes compared with plantlets expressing wild-type PIF3. These observations are supported by the lower level of phyB in plants which possess only PIF3(K13R), indicating that SUMOylation of PIF3 also alters photomorphogenesis via the regulation of phyB levels. In conclusion, whereas SUMOylation is generally connected to different stress responses, it also fine-tunes light signalling by reducing the biological activity of PIF3, thus promoting photomorphogenesis.
Collapse
Affiliation(s)
- Péter Bernula
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
| | | | - Anita Hajdu
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
| | - László Kozma-Bognár
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, Szeged, H-6726, Hungary
| | - Eve-Marie Josse
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, H-6720, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
| | - András Viczián
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
| |
Collapse
|
22
|
Srivastava M, Sadanandom A, Srivastava AK. Towards understanding the multifaceted role of SUMOylation in plant growth and development. PHYSIOLOGIA PLANTARUM 2021; 171:77-85. [PMID: 32880960 DOI: 10.1111/ppl.13204] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Post-translational modifications (PTMs) play a critical role in regulating plant growth and development through the modulation of protein functionality and its interaction with its partners. Analysis of the functional implication of PTMs on plant cellular signalling presents grand challenges in understanding their significance. Proteins decorated or modified with another chemical group or polypeptide play a significant role in regulating physiological processes as compared with non-decorated or non-modified proteins. In the past decade, SUMOylation has been emerging as a potent PTM influencing the adaptability of plants to growth, in response to various environmental cues. Deciphering the SUMO-mediated regulation of plant stress responses and its consequences is required to understand the mechanism underneath. Here, we will discuss the recent advances in the role and significance of SUMOylation in plant growth, development and stress response.
Collapse
Affiliation(s)
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | | |
Collapse
|
23
|
An Insight into the Factors Influencing Specificity of the SUMO System in Plants. PLANTS 2020; 9:plants9121788. [PMID: 33348543 PMCID: PMC7767294 DOI: 10.3390/plants9121788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/06/2023]
Abstract
Due to their sessile nature, plants are constantly subjected to various environmental stresses such as drought, salinity, and pathogen infections. Post-translational modifications (PTMs), like SUMOylation, play a vital role in the regulation of plant responses to their environment. The process of SUMOylation typically involves an enzymatic cascade containing the activation, (E1), conjugation (E2), and ligation (E3) of SUMO to a target protein. Additionally, it also requires a class of SUMO proteases that generate mature SUMO from its precursor and cleave it off the target protein, a process termed deSUMOylation. It is now clear that SUMOylation in plants is key to a plethora of adaptive responses. How this is achieved with an extremely limited set of machinery components is still unclear. One possibility is that novel SUMO components are yet to be discovered. However, current knowledge indicates that only a small set of enzymes seem to be responsible for the modification of a large number of SUMO substrates. It is yet unknown where the specificity lies within the SUMO system. Although this seems to be a crucial question in the field of SUMOylation studies, not much is known about the factors that provide specificity. In this review, we highlight the role of the localisation of SUMO components as an important factor that can play a vital role in contributing to the specificity within the process. This will introduce a new facet to our understanding of the mechanisms underlying such a dynamic process.
Collapse
|
24
|
Liu Y, Zhu J, Sun S, Cui F, Han Y, Peng Z, Zhang X, Wan S, Li G. Defining the function of SUMO system in pod development and abiotic stresses in Peanut. BMC PLANT BIOLOGY 2019; 19:593. [PMID: 31884953 PMCID: PMC7194008 DOI: 10.1186/s12870-019-2136-9] [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: 08/22/2019] [Accepted: 11/13/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world's major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB). RESULTS Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses. CONCLUSIONS The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.
Collapse
Affiliation(s)
- Yiyang Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Jiao Zhu
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Sheng Sun
- College of Teacher Education, Heze University, Heze, China
| | - Feng Cui
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yan Han
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Zhenying Peng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xuejie Zhang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Guowei Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| |
Collapse
|
25
|
Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
Collapse
Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
26
|
Structural insights into SUMO E1–E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution. Biochem J 2019; 476:2127-2139. [DOI: 10.1042/bcj20190232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022]
Abstract
Abstract
SUMOylation of proteins involves the concerted action of the E1-activating enzyme, E2-conjugating enzyme and E3-ligases. An essential discrimination step in the SUMOylation pathway corresponds to the initial interaction between E1 ubiquitin-fold domain (UFD) and E2 enzymes. Although E2 orthologs possess high sequence identity, the E2 binding region of the UFD domains has diverged across evolution. Moreover, in reciprocal in vitro conjugation reactions Arabidopsis E1 and E2 SCE1 fail to interact efficiently with cognate human E2 Ubc9 and E1 partners, respectively. To gain more insights into the properties of this interface in evolutionary distant organisms, we solved the crystal structure of SUMO E2 SCE1 and its complex with E1 UFD in Arabidopsis. In addition to a few common structural determinants, the interface between the E1 UFD and E2 in Arabidopsis is distinct compared with human and yeast, in particular by the presence of a longer α-helix in the Arabidopsis UFD domain. Despite the variability of E1 UFD domains in these surfaces, they establish specific interactions with highly conserved surfaces of their cognate E2 enzymes. Functional analysis of the different E2 interface residues between human and Arabidopsis revealed Val37 (Met36 in human), as a determinant that provides specificity in the E1–E2 recognition in plants.
Collapse
|
27
|
Kumar A, Singh A, Kumar P, Sarkar AK. Giberellic Acid-Stimulated Transcript Proteins Evolved through Successive Conjugation of Novel Motifs and Their Subfunctionalization. PLANT PHYSIOLOGY 2019; 180:998-1012. [PMID: 30971449 PMCID: PMC6548256 DOI: 10.1104/pp.19.00305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 03/27/2019] [Indexed: 05/22/2023]
Abstract
Gibberellic Acid Stimulated Transcript (GAST)-like genes encode small polypeptides, some of which have been implicated in diverse biological processes regulating plant growth and development. However, the occurrence of GASTs among plants, their protein structures, and the mechanisms by which they evolved remain elusive. Here, using a customized workflow, we report genes encoding GAST proteins, identify novel motifs and evolutionary patterns contributing to the subfunctionalization of GAST domains, and explore functional conservation across diverse plant groups. We show that GAST-like sequences evolved initially in the vascular plant Selaginella moellendorffii, after the divergence from bryophytes, and later emerged in gymnosperms and angiosperms. GASTs in angiosperms are characterized by four conserved novel motifs; however, relatively fewer conserved motifs exist in pteridophytes and gymnosperms. Phylogenetic analysis revealed that the GAST-Cysteine Rich1 motif evolved early in the S. moellendorffii GAST, which further acquired subfunctionalization through successive conjugation of other motifs and remained conserved across plants, as supported by their collinearity. Functional characterization of two orthologs from the dicot Arabidopsis (Arabidopsis thaliana; Gibberellic Acid-Stimulated Arabidopsis 10) and the monocot rice (Oryza sativa; Gibberellic Acid Stimulated Transcript-Related 9) suggests hormonal regulation, novel roles in seed germination, and functional conservation among diverse plant groups. Computational modeling predicts that these GAST genes are regulated by several factors, including the phytohormones gibberellin and abscisic acid, through conserved cis-motifs present in their promoters, and that they might act as signaling molecules in a complex feedback loop. Thus, our study identifies GASTs and their encoded proteins, uncovers their structure, novel motifs, and evolutionary pattern among plants, and suggests their functional conservation.
Collapse
Affiliation(s)
- Ashutosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pramod Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
28
|
Rosa MT, Abreu IA. Exploring the regulatory levels of SUMOylation to increase crop productivity. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:43-51. [PMID: 31177030 DOI: 10.1016/j.pbi.2019.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
SUMOylation is an essential post-translational modification that affects several cellular processes, from gene replication to stress response. Studies using the SUMO (de)conjugation machinery have provided evidence regarding its potential to improve crop performance and productivity under normal and adverse conditions. However, the pleiotropic effect of SUMOylation can be a disadvantage in both situations, especially when considering unpredictable environmental conditions caused by climate changes. Here, we discuss the pleiotropic effects caused by disrupting the SUMOylation machinery, and new strategies that may help to overcome pleiotropy. We propose exploring the several regulatory levels of SUMOylation recently revealed, including transcriptional, post-transcriptional regulation by alternative splicing, and post-translational modifications. These new findings may provide valuable tools to increase crop productivity.
Collapse
Affiliation(s)
- Margarida Tg Rosa
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.
| |
Collapse
|
29
|
Wang H, Wang M, Xia Z. Overexpression of a maize SUMO conjugating enzyme gene (ZmSCE1e) increases Sumoylation levels and enhances salt and drought tolerance in transgenic tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:113-121. [PMID: 30824044 DOI: 10.1016/j.plantsci.2019.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 05/16/2023]
Abstract
As an essential regulatory process of post-translational modifications, Sumoylation has been shown to play a central role in stress responses in higher plants. However, the mechanisms underlying the involvement of the Sumoylation in stress responses in crops are largely unknown. In this study, a putative SUMO conjugating enzyme ortholog from Zea mays (ZmSCE1e) was isolated. Sequence alignments and phylogenetic analysis showed that ZmSCE1e possesses a central active domain similar to known SCE1 proteins, but is the cereal-specific isoform.The transcript levels of ZmSCE1e were markedly up-regulated by salt or drought stress. Over-expression of ZmSCE1e in tobacco plants increased levels of SUMO conjugates and enhanced their tolerances to salt and drought stresses. ZmSCE1e-transgenic plants showed higher activities of key antioxidant enzymes but lower hydrogen peroxide (H2O2) and malondialdehyde (MDA) accumulations under salt or drought stress. Furthermore, expression of several stress defense genes was significantly elevated as revealed by qPCR in the ZmSCE1e-transgenic lines. Together, these data have demonstrated that ZmSCE1e improved salt and drought tolerance likely by modulating Sumoylation levels, antioxidant capability, and stress defense gene expression in transgenic plants. This study may facilitate our understanding of the biological roles of SCE-mediated Sumoylation under stress conditions in higher plants and accelerate genetic improvement of crop plants tolerant to environmental stresses.
Collapse
Affiliation(s)
- Huanyan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Meiping Wang
- Library of Henan Agricultural University, Zhengzhou 450002, PR China
| | - Zongliang Xia
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, PR China.
| |
Collapse
|
30
|
Gu L, Xia C. Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 2019; 19:9. [PMID: 30621595 PMCID: PMC6325677 DOI: 10.1186/s12862-018-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
Collapse
Affiliation(s)
- Langyu Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
31
|
Augustine RC, Vierstra RD. SUMOylation: re-wiring the plant nucleus during stress and development. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:143-154. [PMID: 30014889 DOI: 10.1016/j.pbi.2018.06.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/11/2018] [Accepted: 06/25/2018] [Indexed: 05/08/2023]
Abstract
Conjugation of small ubiquitin-related modifier (SUMO) to intracellular proteins provides a dynamic regulatory mechanism that enables plants to rapidly defend against environmental challenges. SUMOylation of mostly nuclear proteins is among the fastest stress responses observed but precisely how this post-translational modification provides stress resilience remains unclear. Here, we describe the plant SUMO system and its expanding target catalog, which implicates this modification in DNA repair, chromatin modification/remodeling, transcriptional activation/repression, epigenetics, and RNA metabolism, with a likely outcome being extensive nuclear re-wiring to withstand stress. In parallel, studies have linked SUMO to developmental programs such as gametogenesis and gene silencing. The accumulating data support the notion that SUMOylation substantially influences the transcriptional and epigenetic landscapes to promote stress tolerance and developmental progression.
Collapse
Affiliation(s)
- Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
32
|
Arroyo-Mateos M, Sabarit B, Maio F, Sánchez-Durán MA, Rosas-Díaz T, Prins M, Ruiz-Albert J, Luna AP, van den Burg HA, Bejarano ER. Geminivirus Replication Protein Impairs SUMO Conjugation of Proliferating Cellular Nuclear Antigen at Two Acceptor Sites. J Virol 2018. [PMID: 29950424 DOI: 10.1101/305789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Geminiviruses are DNA viruses that replicate in nuclei of infected plant cells using the plant DNA replication machinery, including PCNA (proliferating cellular nuclear antigen), a cofactor that orchestrates genome duplication and maintenance by recruiting crucial players to replication forks. These viruses encode a multifunctional protein, Rep, which is essential for viral replication, induces the accumulation of the host replication machinery, and interacts with several host proteins, including PCNA and the SUMO E2 conjugation enzyme (SCE1). Posttranslational modification of PCNA by ubiquitin or SUMO plays an essential role in the switching of PCNA between interacting partners during DNA metabolism processes (e.g., replication, recombination, and repair, etc.). In yeast, PCNA sumoylation has been associated with DNA repair involving homologous recombination (HR). Previously, we reported that ectopic Rep expression results in very specific changes in the sumoylation pattern of plant cells. In this work, we show, using a reconstituted sumoylation system in Escherichia coli, that tomato PCNA is sumoylated at two residues, K254 and K164, and that coexpression of the geminivirus protein Rep suppresses sumoylation at these lysines. Finally, we confirm that PCNA is sumoylated in planta and that Rep also interferes with PCNA sumoylation in plant cells.IMPORTANCE SUMO adducts have a key role in regulating the activity of animal and yeast PCNA on DNA repair and replication. Our work demonstrates for the first time that sumoylation of plant PCNA occurs in plant cells and that a plant virus interferes with this modification. This work marks the importance of sumoylation in allowing viral infection and replication in plants. Moreover, it constitutes a prime example of how viral proteins interfere with posttranslational modifications of selected host factors to create a proper environment for infection.
Collapse
Affiliation(s)
- Manuel Arroyo-Mateos
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Blanca Sabarit
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Francesca Maio
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Miguel A Sánchez-Durán
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Tabata Rosas-Díaz
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Marcel Prins
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
- Keygene NV, Wageningen, The Netherlands
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Ana P Luna
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Deptartmento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| |
Collapse
|
33
|
Benlloch R, Lois LM. Sumoylation in plants: mechanistic insights and its role in drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4539-4554. [PMID: 29931319 DOI: 10.1093/jxb/ery233] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/11/2018] [Indexed: 05/20/2023]
Abstract
Post-translational modification by SUMO is an essential process that has a major role in the regulation of plant development and stress responses. Such diverse biological functions are accompanied by functional diversification among the SUMO conjugation machinery components and regulatory mechanisms that has just started to be identified in plants. In this review, we focus on the current knowledge of the SUMO conjugation system in plants in terms of components, substrate specificity, cognate interactions, enzyme activity, and subcellular localization. In addition, we analyze existing data on the role of SUMOylation in plant drought tolerance in model plants and crop species, paying attention to the genetic approaches used to stimulate or inhibit endogenous SUMO conjugation. The role in drought tolerance of potential SUMO targets identified in proteomic analyses is also discussed. Overall, the complexity of SUMOylation and the multiple genetic and environmental factors that are integrated to confer drought tolerance highlight the need for significant efforts to understand the interplay between SUMO and drought.
Collapse
Affiliation(s)
- Reyes Benlloch
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| |
Collapse
|
34
|
Geminivirus Replication Protein Impairs SUMO Conjugation of Proliferating Cellular Nuclear Antigen at Two Acceptor Sites. J Virol 2018; 92:JVI.00611-18. [PMID: 29950424 DOI: 10.1128/jvi.00611-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/22/2018] [Indexed: 02/08/2023] Open
Abstract
Geminiviruses are DNA viruses that replicate in nuclei of infected plant cells using the plant DNA replication machinery, including PCNA (proliferating cellular nuclear antigen), a cofactor that orchestrates genome duplication and maintenance by recruiting crucial players to replication forks. These viruses encode a multifunctional protein, Rep, which is essential for viral replication, induces the accumulation of the host replication machinery, and interacts with several host proteins, including PCNA and the SUMO E2 conjugation enzyme (SCE1). Posttranslational modification of PCNA by ubiquitin or SUMO plays an essential role in the switching of PCNA between interacting partners during DNA metabolism processes (e.g., replication, recombination, and repair, etc.). In yeast, PCNA sumoylation has been associated with DNA repair involving homologous recombination (HR). Previously, we reported that ectopic Rep expression results in very specific changes in the sumoylation pattern of plant cells. In this work, we show, using a reconstituted sumoylation system in Escherichia coli, that tomato PCNA is sumoylated at two residues, K254 and K164, and that coexpression of the geminivirus protein Rep suppresses sumoylation at these lysines. Finally, we confirm that PCNA is sumoylated in planta and that Rep also interferes with PCNA sumoylation in plant cells.IMPORTANCE SUMO adducts have a key role in regulating the activity of animal and yeast PCNA on DNA repair and replication. Our work demonstrates for the first time that sumoylation of plant PCNA occurs in plant cells and that a plant virus interferes with this modification. This work marks the importance of sumoylation in allowing viral infection and replication in plants. Moreover, it constitutes a prime example of how viral proteins interfere with posttranslational modifications of selected host factors to create a proper environment for infection.
Collapse
|
35
|
Hua Z, Doroodian P, Vu W. Contrasting duplication patterns reflect functional diversities of ubiquitin and ubiquitin-like protein modifiers in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:296-311. [PMID: 29738099 DOI: 10.1111/tpj.13951] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 03/29/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Ubiquitin (Ub) and Ub-like proteins, collectively forming the ubiquiton family, regulate nearly all aspects of cellular processes via post-translational modifications. Studies devoted to specific members suggested a large expansion of this family in plants; however, a lack of systematic analysis hinders the comparison of individual members at both evolutionary history and functional divergence levels, which may provide new insight into biological functions. In this work, we first retrieved a total of 5856 members of 17 known ubiquiton subfamilies in 50 plant genomes by searching both prior annotations and missing loci in each genome. We then applied this list to analyze the duplication history of major ubiquiton subfamilies in plants. We show that autophagy-related protein 8 (ATG8), membrane-anchored Ub-fold (MUB), small Ub-like modifier (SUMO) and Ub loci encode 88% of the plant ubiquiton family. Although whole genome duplications (WGDs) significantly expanded the family, we discovered contrasting duplication patterns both in species and in subfamilies. Within the family, the ATG8 and MUB members were primarily duplicated through WGDs, whereas a significant number of Ub and SUMO loci were generated through retroposition and tandem duplications, respectively. Although Ub coding regions are highly conserved in plants, promoter activity analysis demonstrated lineage-specific expression patterns of polyUb genes in Oryza sativa (rice) and Arabidopsis, confirming their retroposition origin. Based on the theory of dosage balance constraints, our study suggests that ubiquiton members duplicated through WGDs play crucial roles in plants, and that the regulatory pathways involving ATG8 and MUB are more conserved than those controlled by Ub and SUMO.
Collapse
Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, 45701, USA
| | - Paymon Doroodian
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - William Vu
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| |
Collapse
|
36
|
Verma V, Croley F, Sadanandom A. Fifty shades of SUMO: its role in immunity and at the fulcrum of the growth-defence balance. MOLECULAR PLANT PATHOLOGY 2018; 19:1537-1544. [PMID: 29024335 PMCID: PMC6637990 DOI: 10.1111/mpp.12625] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 05/10/2023]
Abstract
The sessile nature of plants requires them to cope with an ever-changing environment. Effective adaptive responses require sophisticated cellular mechanisms at the post-transcriptional and post-translational levels. Post-translational modification by small ubiquitin-like modifier (SUMO) proteins is emerging as a key player in these adaptive responses. SUMO conjugation can rapidly change the overall fate of target proteins by altering their stability or interaction with partner proteins or DNA. SUMOylation entails an enzyme cascade that leads to the activation, conjugation and ligation of SUMO to lysine residues of target proteins. In addition to their SUMO processing activities, SUMO proteases also possess de-conjugative activity capable of cleaving SUMO from target proteins, providing reversibility and buffering to the pathway. These proteases play critical roles in the maintenance of the SUMO machinery in equilibrium. We hypothesize that SUMO proteases provide the all-important substrate specificity within the SUMO system. Furthermore, we provide an overview of the role of SUMO in plant innate immunity. SUMOylation also overlaps with multiple growth-promoting and defence-related hormone signalling pathways, and hence is pivotal for the maintenance of the growth-defence balance. This review aims to highlight the intricate molecular mechanisms utilized by SUMO to regulate plant defence and to stabilize the growth-defence equilibrium.
Collapse
Affiliation(s)
- Vivek Verma
- Department of BiosciencesDurham UniversityDurham DH1 3LEUK
| | - Fenella Croley
- Department of BiosciencesDurham UniversityDurham DH1 3LEUK
| | - Ari Sadanandom
- Department of BiosciencesDurham UniversityDurham DH1 3LEUK
| |
Collapse
|
37
|
Rytz TC, Miller MJ, McLoughlin F, Augustine RC, Marshall RS, Juan YT, Charng YY, Scalf M, Smith LM, Vierstra RD. SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 during Heat Stress. THE PLANT CELL 2018; 30:1077-1099. [PMID: 29588388 PMCID: PMC6002191 DOI: 10.1105/tpc.17.00993] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/15/2018] [Accepted: 03/26/2018] [Indexed: 05/20/2023]
Abstract
The posttranslational addition of small ubiquitin-like modifier (SUMO) is an essential protein modification in plants that provides protection against numerous environmental challenges. Ligation is accomplished by a small set of SUMO ligases, with the SAP-MIZ domain-containing SIZ1 and METHYL METHANESULFONATE-SENSITIVE21 (MMS21) ligases having critical roles in stress protection and DNA endoreduplication/repair, respectively. To help identify their corresponding targets in Arabidopsis thaliana, we used siz1 and mms21 mutants for proteomic analyses of SUMOylated proteins enriched via an engineered SUMO1 isoform suitable for mass spectrometric studies. Through multiple data sets from seedlings grown at normal temperatures or exposed to heat stress, we identified over 1000 SUMO targets, most of which are nuclear localized. Whereas no targets could be assigned to MMS21, suggesting that it modifies only a few low abundance proteins, numerous targets could be assigned to SIZ1, including major transcription factors, coactivators/repressors, and chromatin modifiers connected to abiotic and biotic stress defense, some of which associate into multisubunit regulatory complexes. SIZ1 itself is also a target, but studies with mutants protected from SUMOylation failed to uncover a regulatory role. The catalog of SIZ1 substrates indicates that SUMOylation by this ligase provides stress protection by modifying a large array of key nuclear regulators.
Collapse
Affiliation(s)
- Thérèse C Rytz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Marcus J Miller
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Yu-Ting Juan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
38
|
DiSUMO-LIKE Interacts with RNA-Binding Proteins and Affects Cell-Cycle Progression during Maize Embryogenesis. Curr Biol 2018; 28:1548-1560.e5. [DOI: 10.1016/j.cub.2018.03.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 03/01/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022]
|
39
|
SUMO chain formation relies on the amino-terminal region of SUMO-conjugating enzyme and has dedicated substrates in plants. Biochem J 2018; 475:61-74. [PMID: 29133528 PMCID: PMC5748838 DOI: 10.1042/bcj20170472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/06/2017] [Accepted: 11/10/2017] [Indexed: 11/17/2022]
Abstract
The small ubiquitin-related modifier (SUMO) conjugation apparatus usually attaches single SUMO moieties to its substrates, but SUMO chains have also been identified. To better define the biochemical requirements and characteristics of SUMO chain formation, mutations in surface-exposed Lys residues of Arabidopsis SUMO-conjugating enzyme (SCE) were tested for in vitro activity. Lys-to-Arg changes in the amino-terminal region of SCE allowed SUMO acceptance from SUMO-activating enzyme and supported substrate mono-sumoylation, but these mutations had significant effects on SUMO chain assembly. We found no indication that SUMO modification of SCE promotes chain formation. A substrate was identified that is modified by SUMO chain addition, showing that SCE can distinguish substrates for either mono-sumoylation or SUMO chain attachment. It is also shown that SCE with active site Cys mutated to Ser can accept SUMO to form an oxyester, but cannot transfer this SUMO moiety onto substrates, explaining a previously known dominant negative effect of this mutation.
Collapse
|
40
|
Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
Collapse
Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| |
Collapse
|
41
|
Zhao T, Schranz ME. Network approaches for plant phylogenomic synteny analysis. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:129-134. [PMID: 28327435 DOI: 10.1016/j.pbi.2017.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/17/2017] [Accepted: 03/01/2017] [Indexed: 05/07/2023]
Abstract
Network analysis approaches have been widely applied across disciplines. In biology, network analysis is now frequently adopted to organize protein-protein interactions, organize pathways and/or to interpret gene co-expression patterns. However, comparative genomic analyses still largely rely on pairwise comparisons and linear visualizations between genomes. In this article, we discuss the challenges and prospects for establishing a generalized plant phylogenomic synteny network approach needed to interpret the wealth of new and emerging genomic data. We illustrate our approach with an example synteny network of B-class floral MADS-box genes. A broad synteny network approach holds great promise for understanding the evolutionary history of genes and genomes across broad phylogenetic groups and divergence times.
Collapse
Affiliation(s)
- Tao Zhao
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands.
| |
Collapse
|
42
|
Hammoudi V, Vlachakis G, de Jonge R, Breit TM, van den Burg HA. Genetic characterization of T-DNA insertions in the genome of the Arabidopsis thaliana sumo1/2 knock-down line. PLANT SIGNALING & BEHAVIOR 2017; 12:e1293216. [PMID: 28267405 PMCID: PMC5399896 DOI: 10.1080/15592324.2017.1293216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 06/06/2023]
Abstract
Sumoylation is an essential post-translational modification in Arabidopsis thaliana, which entails the conjugation of the SUMO protein onto lysine residues in target proteins. In Arabidopsis, 2 closely related genes, SUMO1 and SUMO2, act redundantly and are in combination essential for plant development, i.e. the combined loss of SUMO1 and SUMO2 results in embryo-lethality. To circumvent this lethality, SUMO2 was previously knocked down in a sumo1 knockout background by expressing an artificial microRNA that targets SUMO2 (amiR-SUMO2). This sumo1/2KD line with low SUMO2 levels represents a valuable genetics tool to investigate SUMO function in planta. Here, we re-sequenced the whole-genome of this sumo1/2KD line and identified 2 amiR-SUMO2 insertions in this line, which were confirmed by PCR-genotyping. Identification of these 2 insertions enables genetics with this tool.
Collapse
Affiliation(s)
- Valentin Hammoudi
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Georgios Vlachakis
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Ronnie de Jonge
- VIB Department of Plant Systems Biology, Ghent University, Belgium
| | - Timo M. Breit
- RNA Biology & Applied Bioinformatics, University of Amsterdam, the Netherlands
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
43
|
Mazur MJ, Spears BJ, Djajasaputra A, van der Gragt M, Vlachakis G, Beerens B, Gassmann W, van den Burg HA. Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci. FRONTIERS IN PLANT SCIENCE 2017; 8:2043. [PMID: 29250092 PMCID: PMC5714883 DOI: 10.3389/fpls.2017.02043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 05/20/2023]
Abstract
In Arabidopsis more than 400 proteins have been identified as SUMO targets, both in vivo and in vitro. Among others, transcription factors (TFs) are common targets for SUMO conjugation. Here we aimed to exhaustively screen for TFs that interact with the SUMO machinery using an arrayed yeast two-hybrid library containing more than 1,100 TFs. We identified 76 interactors that foremost interact with the SUMO conjugation enzyme SCE1 and/or the SUMO E3 ligase SIZ1. These interactors belong to various TF families, which control a wide range of processes in plant development and stress signaling. Amongst these interactors, the TCP family was overrepresented with several TCPs interacting with different proteins of the SUMO conjugation cycle. For a subset of these TCPs we confirmed that the catalytic site of SCE1 is essential for this interaction. In agreement, TCP1, TCP3, TCP8, TCP14, and TCP15 were readily SUMO modified in an E. coli sumoylation assay. Strikingly, these TCP-SCE1 interactions were found to redistribute these TCPs into nuclear foci/speckles, suggesting that these TCP foci represent sites for SUMO (conjugation) activity.
Collapse
Affiliation(s)
- Magdalena J. Mazur
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Benjamin J. Spears
- Division of Plant Sciences, C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
| | - André Djajasaputra
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Michelle van der Gragt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Georgios Vlachakis
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Bas Beerens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Walter Gassmann
- Division of Plant Sciences, C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Harrold A. van den Burg
| |
Collapse
|
44
|
Augustine RC, York SL, Rytz TC, Vierstra RD. Defining the SUMO System in Maize: SUMOylation Is Up-Regulated during Endosperm Development and Rapidly Induced by Stress. PLANT PHYSIOLOGY 2016; 171:2191-210. [PMID: 27208252 PMCID: PMC4936565 DOI: 10.1104/pp.16.00353] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/12/2016] [Indexed: 05/03/2023]
Abstract
In response to abiotic and biotic challenges, plants rapidly attach small ubiquitin-related modifier (SUMO) to a large collection of nuclear proteins, with studies in Arabidopsis (Arabidopsis thaliana) linking SUMOylation to stress tolerance via its modification of factors involved in chromatin and RNA dynamics. Despite this importance, little is known about SUMOylation in crop species. Here, we describe the plant SUMO system at the phylogenetic, biochemical, and transcriptional levels with a focus on maize (Zea mays). In addition to canonical SUMOs, land plants encode a loosely constrained noncanonical isoform and a variant containing a long extension upstream of the signature β-grasp fold, with cereals also expressing a novel diSUMO polypeptide bearing two SUMO β-grasp domains in tandem. Maize and other cereals also synthesize a unique SUMO-conjugating enzyme variant with more restricted expression patterns that is enzymatically active despite a distinct electrostatic surface. Maize SUMOylation primarily impacts nuclear substrates, is strongly induced by high temperatures, and displays a memory that suppresses subsequent conjugation. Both in-depth transcript and conjugate profiles in various maize organs point to tissue/cell-specific functions for SUMOylation, with potentially significant roles during embryo and endosperm maturation. Collectively, these studies define the organization of the maize SUMO system and imply important functions during seed development and stress defense.
Collapse
Affiliation(s)
- Robert C Augustine
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706; andDepartment of Biology, Washington University, St. Louis, Missouri 63130
| | - Samuel L York
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706; andDepartment of Biology, Washington University, St. Louis, Missouri 63130
| | - Thérèse C Rytz
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706; andDepartment of Biology, Washington University, St. Louis, Missouri 63130
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706; andDepartment of Biology, Washington University, St. Louis, Missouri 63130
| |
Collapse
|