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Lu Z, Huang W, Zhu L, Liang G, Huang Y, Wu J, Chen R, Li X, Liu X. Cytological Observation and RNA-Seq Analyses Reveal miR9564 and Its Target Associated with Pollen Sterility in Autotetraploid Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:1461. [PMID: 38891270 PMCID: PMC11175005 DOI: 10.3390/plants13111461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Understanding the regulation of autotetraploid sterility is essential for harnessing the strong advantages in genomic buffer capacity, biodiversity, and heterosis of autotetraploid rice. miRNAs play crucial roles in fertility regulation, yet information about their reproductive roles and target genes in tetraploid rice remains limited. Here, we used three tetraploid lines, H1 (fertile), HF (fertile), and LF (sterile), to investigate cytological features and identify factors associated with autotetraploid sterility. LF showed abnormal meiosis, resulting in low pollen fertility and viability, ultimately leading to scarce fertilization and a low-seed setting compared to H1 and HF. RNA-seq revealed 30 miRNA-candidate target pairs related to autotetraploid pollen sterility. These pairs showed opposite expression patterns, with differential expression between fertile lines (H1 and HF) and the sterile line (LF). qRT-PCR confirmed that miR9564, miR528, and miR27874 were highly expressed in the anthers of H1 and HF but not in LF, while opposite results were obtained in their targets (ARPS, M2T, and OsRPC53). Haplotype and expression pattern analyses revealed that ARPS was specifically expressed in lines with the same haplotype of MIR9564 (the precursor of miR9564) as LF. Furthermore, the Dual-GFP assay verified that miR9564 inhibited the fluorescence signal of ARPS-GFP. The over-expression of ARPS significantly decreased the seed setting rate (59.10%) and pollen fertility (50.44%) of neo-tetraploid rice, suggesting that ARPS plays important roles in autotetraploid pollen sterility. This study provides insights into the cytological characteristic and miRNA expression profiles of tetraploid lines with different fertility, shedding light on the role of miRNAs in polyploid rice.
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Affiliation(s)
- Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Weicong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lianjun Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Guobin Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Rou Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiang Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Srivastava M, Verma V, Srivastava AK. The converging path of protein SUMOylation in phytohormone signalling: highlights and new frontiers. PLANT CELL REPORTS 2021; 40:2047-2061. [PMID: 34129078 DOI: 10.1007/s00299-021-02732-2] [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: 03/30/2021] [Accepted: 06/05/2021] [Indexed: 06/12/2023]
Abstract
The intersection of phytohormone signalling pathways with SUMOylation, a key post-translational modification, offers an additional layer of control to the phytohormone signalling for sophisticated regulation of plant development. Plants live in a constantly changing environment that are often challenging for the growth and development of plants. Phytohormones play a critical role in modulating molecular-level changes for enabling plants to resist climatic aberrations. The orchestration of such effective molecular responses entails rapid regulation of phytohormone signalling at transcriptional, translational and post-translational levels. Post-translational modifications have emerged as a key player in modulating hormonal pathways. The current review lays emphasis on the role of SUMOylation, a key post-translational modification, in manipulating individual hormone signalling pathways for better plant adaptability. Here, we discuss the recent advancement in the field and highlights how SUMO targets key signalling intermediates including transcription factors to provide a quick response to different biotic or abiotic stresses, sometimes even prior to changes in hormone levels. The understanding of the convergence of SUMOylation and hormonal pathways will offer an additional layer of control to the phytohormone signalling for an intricate and sophisticated regulation of plant development and can be utilised as a tool to generate climate-resilient crops.
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Affiliation(s)
| | - Vivek Verma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India.
| | - Anjil Kumar Srivastava
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), S.A.S. Nagar, Mohali, Punjab, 140306, India.
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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.
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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
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SUMO enables substrate selectivity by mitogen-activated protein kinases to regulate immunity in plants. Proc Natl Acad Sci U S A 2021; 118:2021351118. [PMID: 33649235 PMCID: PMC7958252 DOI: 10.1073/pnas.2021351118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The versatility of mitogen-activated protein kinases (MAPKs) in translating exogenous and endogenous stimuli into appropriate cellular responses depends on its substrate specificity. In animals, several mechanisms have been proposed about how MAPKs maintain specificity to regulate distinct functional pathways. However, little is known of mechanisms that enable substrate selectivity in plant MAPKs. Small ubiquitin-like modifier (SUMO), a posttranslational modification system, plays an important role in plant development and defense by rapid reprogramming of cellular events. In this study we identified a functional SUMO interaction motif (SIM) in Arabidopsis MPK3 and MPK6 that reveals a mechanism for selective interaction of MPK3/6 with SUMO-conjugated WRKY33, during defense. We show that WRKY33 is rapidly SUMOylated in response to Botrytis cinerea infection and flg22 elicitor treatment. SUMOylation mediates WRKY33 phosphorylation by MPKs and consequent transcription factor activity. Disruption of either WRKY33 SUMO or MPK3/6 SIM sites attenuates their interaction and inactivates WRKY33-mediated defense. However, MPK3/6 SIM mutants show normal interaction with a non-SUMOylated form of another transcription factor, SPEECHLESS, unraveling a role for SUMOylation in differential substrate selectivity by MPKs. We reveal that the SUMO proteases, SUMO PROTEASE RELATED TO FERTILITY1 (SPF1) and SPF2 control WRKY33 SUMOylation and demonstrate a role for these SUMO proteases in defense. Our data reveal a mechanism by which MPK3/6 prioritize molecular pathways by differentially selecting substrates using the SUMO-SIM module during defense responses.
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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.
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Affiliation(s)
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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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.
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Qu GP, Li H, Lin XL, Kong X, Hu ZL, Jin YH, Liu Y, Song HL, Kim DH, Lin R, Li J, Jin JB. Reversible SUMOylation of FHY1 Regulates Phytochrome A Signaling in Arabidopsis. MOLECULAR PLANT 2020; 13:879-893. [PMID: 32298785 DOI: 10.1016/j.molp.2020.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/15/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
In response to far-red light (FR), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) transports the photoactivated phytochrome A (phyA), the primary FR photoreceptor, into the nucleus, where it initiates FR signaling in plants. Light promotes the 26S proteasome-mediated degradation of FHY1, which desensitizes FR signaling, but the underlying regulatory mechanism remains largely unknown. Here, we show that reversible SUMOylation of FHY1 tightly regulates this process. Lysine K32 (K32) and K103 are major SUMOylation sites of FHY1. We found that FR exposure promotes the SUMOylation of FHY1, which accelerates its degradation. Furthermore, we discovered that ARABIDOPSIS SUMO PROTEASE 1 (ASP1) interacts with FHY1 in the nucleus under FR and facilitates its deSUMOylation. FHY1 was strongly SUMOylated and its protein level was decreased in the asp1-1 loss-of-function mutant compared with that in the wild type under FR. Consistently, asp1-1 seedlings exhibited a decreased sensitivity to FR, suggesting that ASP1 plays an important role in the maintenance of proper FHY1 levels under FR. Genetic analysis further revealed that ASP1 regulates FR signaling through an FHY1- and phyA-dependent pathway. Interestingly, We found that continuous FR inhibits ASP1 accumulation, perhaps contributing to the desensitization of FR signaling. Taken together, these results indicate that FR-induced SUMOylation and ASP1-dependent deSUMOylation of FHY1 represent a key regulatory mechanism that fine-tunes FR signaling.
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Affiliation(s)
- Gao-Ping Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiao-Li Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiangxiong Kong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zi-Liang Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yin Hua Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hang-Lin Song
- Yanbian Academy of Agriculture Sciences, Yanji 133001, China
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon 57922, South Korea
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Srivastava M, Srivastava AK, Orosa-Puente B, Campanaro A, Zhang C, Sadanandom A. SUMO Conjugation to BZR1 Enables Brassinosteroid Signaling to Integrate Environmental Cues to Shape Plant Growth. Curr Biol 2020; 30:1410-1423.e3. [PMID: 32109396 PMCID: PMC7181186 DOI: 10.1016/j.cub.2020.01.089] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/07/2020] [Accepted: 01/30/2020] [Indexed: 01/21/2023]
Abstract
Brassinosteroids (BRs) play crucial roles in plant development, but little is known of mechanisms that integrate environmental cues into BR signaling. Conjugation to the small ubiquitin-like modifier (SUMO) is emerging as an important mechanism to transduce environmental cues into cellular signaling. In this study, we show that SUMOylation of BZR1, a key transcription factor of BR signaling, provides a conduit for environmental influence to modulate growth during stress. SUMOylation stabilizes BZR1 in the nucleus by inhibiting its interaction with BIN2 kinase. During salt stress, Arabidopsis plants arrest growth through deSUMOylation of BZR1 in the cytoplasm by promoting the accumulation of the BZR1 targeting SUMO protease, ULP1a. ULP1a mutants are salt tolerant and insensitive to the BR inhibitor, brassinazole. BR treatment stimulates ULP1a degradation, allowing SUMOylated BZR1 to accumulate and promote growth. This study uncovers a mechanism for integrating environmental cues into BR signaling to shape growth. BZR1 SUMOylation allows brassinosteroids to shape plant growth to its environment SUMOylation stabilizes BZR1 by inhibiting BIN2 interaction, promoting plant growth Salinity stimulates BZR1 deSUMOylation via ULP1a SUMO protease to suppress growth BRs destabilize ULP1a, allowing SUMOylated BZR1 to accumulate and promote growth
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Affiliation(s)
- Moumita Srivastava
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Anjil K Srivastava
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | | | - Alberto Campanaro
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Cunjin Zhang
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK.
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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.
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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
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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.
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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.
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Morrell R, Sadanandom A. Dealing With Stress: A Review of Plant SUMO Proteases. FRONTIERS IN PLANT SCIENCE 2019; 10:1122. [PMID: 31620153 PMCID: PMC6759571 DOI: 10.3389/fpls.2019.01122] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/14/2019] [Indexed: 05/18/2023]
Abstract
The SUMO system is a rapid dynamic post-translational mechanism employed by eukaryotic cells to respond to stress. Plant cells experience hyperSUMOylation of substrates in response to stresses such as heat, ethanol, and drought. Many SUMOylated proteins are located in the nucleus, SUMOylation altering many nuclear processes. The SUMO proteases play two key functions in the SUMO cycle by generating free SUMO; they have an important role in regulating the SUMO cycle, and by cleaving SUMO off SUMOylated proteins, they provide specificity to which proteins become SUMOylated. This review summarizes the broad literature of plant SUMO proteases describing their catalytic activity, domains and structure, evolution, localization, and response to stress and highlighting potential new areas of research in the future.
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Rosa MTG, Almeida DM, Pires IS, da Rosa Farias D, Martins AG, da Maia LC, de Oliveira AC, Saibo NJM, Oliveira MM, Abreu IA. Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases. BMC PLANT BIOLOGY 2018; 18:349. [PMID: 30541427 PMCID: PMC6291987 DOI: 10.1186/s12870-018-1547-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND SUMOylation is an essential eukaryotic post-translation modification that, in plants, regulates numerous cellular processes, ranging from seed development to stress response. Using rice as a model crop plant, we searched for potential regulatory points that may influence the activity of the rice SUMOylation machinery genes. RESULTS We analyzed the presence of putative cis-acting regulatory elements (CREs) within the promoter regions of the rice SUMOylation machinery genes and found CREs related to different cellular processes, including hormone signaling. We confirmed that the transcript levels of genes involved in target-SUMOylation, containing ABA- and GA-related CREs, are responsive to treatments with these hormones. Transcriptional analysis in Nipponbare (spp. japonica) and LC-93-4 (spp. indica), showed that the transcript levels of all studied genes are maintained in the two subspecies, under normal growth. OsSUMO3 is an exceptional case since it is expressed at low levels or is not detectable at all in LC-93-4 roots and shoots, respectively. We revealed post-transcriptional regulation by alternative splicing (AS) for all genes studied, except for SUMO coding genes, OsSIZ2, OsOTS3, and OsELS2. Some AS forms have the potential to alter protein domains and catalytic centers. We also performed the molecular and phenotypic characterization of T-DNA insertion lines of some of the genes under study. Knockouts of OsFUG1 and OsELS1 showed increased SUMOylation levels and non-overlapping phenotypes. The fug1 line showed a dwarf phenotype, and significant defects in fertility, seed weight, and panicle architecture, while the els1 line showed early flowering and decreased plant height. We suggest that OsELS1 is an ortholog of AtEsd4, which was also supported by our phylogenetic analysis. CONCLUSIONS Overall, we provide a comprehensive analysis of the rice SUMOylation machinery and discuss possible effects of the regulation of these genes at the transcriptional and post-transcriptional level. We also contribute to the characterization of two rice SUMO proteases, OsELS1 and OsFUG1.
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Affiliation(s)
- Margarida T. G. Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - Diego M. Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
- IBET, Av. da República, 2780-157 Oeiras, Portugal
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA), Université de Montpellier (UM), Montpellier, France
| | - Inês S. Pires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
- Frontiers Media SA, Avenue du Tribunal-Fédéral 34, CH-1015 Lausanne, Switzerland
| | - Daniel da Rosa Farias
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Alice G. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - Luciano Carlos da Maia
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - António Costa de Oliveira
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
| | - Isabel A. Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157 Oeiras, Portugal
- IBET, Av. da República, 2780-157 Oeiras, Portugal
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13
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Garapati HS, Mishra K. Comparative genomics of nuclear envelope proteins. BMC Genomics 2018; 19:823. [PMID: 30445911 PMCID: PMC6240307 DOI: 10.1186/s12864-018-5218-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as a hub for a number of important nuclear events including transcription, repair, and regulated gene expression. The proteins associated with the nuclear envelope mediate the NE functions and maintain its structural integrity, which is crucial for survival. In spite of the importance of this structure, knowledge of the protein composition of the nuclear envelope and their function, are limited to very few organisms belonging to Opisthokonta and Archaeplastida supergroups. The NE composition is largely unknown in organisms outside these two supergroups. RESULTS In this study, we have taken a comparative sequence analysis approach to identify the NE proteome that is present across all five eukaryotic supergroups. We identified 22 proteins involved in various nuclear functions to be part of the core NE proteome. The presence of these proteins across eukaryotes, suggests that they are traceable to the Last Eukaryotic Common Ancestor (LECA). Additionally, we also identified the NE proteins that have evolved in a lineage specific manner and those that have been preserved only in a subset of organisms. CONCLUSIONS Our study identifies the conserved features of the nuclear envelope across eukaryotes and provides insights into the potential composition and the functionalities that were constituents of the LECA NE.
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Affiliation(s)
- Hita Sony Garapati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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14
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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.
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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.
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15
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Liebers M, Chevalier F, Blanvillain R, Pfannschmidt T. PAP genes are tissue- and cell-specific markers of chloroplast development. PLANTA 2018; 248:629-646. [PMID: 29855700 DOI: 10.1007/s00425-018-2924-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/21/2018] [Indexed: 05/03/2023]
Abstract
Expression of PAP genes is strongly coordinated and represents a highly selective cell-specific marker associated with the development of chloroplasts in photosynthetically active organs of Arabidopsis seedlings and adult plants. Transcription in plastids of plants depends on the activity of phage-type single-subunit nuclear-encoded RNA polymerases (NEP) and a prokaryotic multi-subunit plastid-encoded RNA polymerase (PEP). PEP is comprised of the core subunits α, β, β' and β″ encoded by rpoA, rpoB/C1/C2 genes located on the plastome. This core enzyme needs to interact with nuclear-encoded sigma factors for proper promoter recognition. In chloroplasts, the core enzyme is surrounded by additional 12 nuclear-encoded subunits, all of eukaryotic origin. These PEP-associated proteins (PAPs) were found to be essential for chloroplast biogenesis as Arabidopsis inactivation mutants for each of them revealed albino or pale-green phenotypes. In silico analysis of transcriptomic data suggests that PAP genes represent a tightly controlled regulon, whereas wetlab data are sparse and correspond to the expression of individual genes mostly studied at the seedling stage. Using RT-PCR, transient, and stable expression assays of PAP promoter-GUS-constructs, we do provide, in this study, a comprehensive expression catalogue for PAP genes throughout the life cycle of Arabidopsis. We demonstrate a selective impact of light on PAP gene expression and uncover a high tissue specificity that is coupled to developmental progression especially during the transition from skotomorphogenesis to photomorphogenesis. Our data imply that PAP gene expression precedes the formation of chloroplasts rendering PAP genes a tissue- and cell-specific marker of chloroplast biogenesis.
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Affiliation(s)
- Monique Liebers
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
| | - Fabien Chevalier
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
| | - Robert Blanvillain
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France.
| | - Thomas Pfannschmidt
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France.
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16
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Garrido E, Srivastava AK, Sadanandom A. Exploiting protein modification systems to boost crop productivity: SUMO proteases in focus. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4625-4632. [PMID: 29897480 PMCID: PMC6117578 DOI: 10.1093/jxb/ery222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent years, post-translational modification (PTM) of proteins has emerged as a key process that integrates plant growth and response to a changing environment. During the processes of domestication and breeding, plants were selected for various yield and adaptational characteristics. The post-translational modifier small ubiquitin-like modifier (SUMO) protein is known to have a role in the regulation of a number of these characteristics. Using bioinformatics, we mined the genomes of cereal and Brassica crops and their non-crop relatives Arabidopsis thaliana and Brachypodium distachyon for ubiquitin-like protease (ULP) SUMO protease sequences. We discovered that the SUMO system in cereal crops is disproportionately elaborate in comparison with that in B. distachyon. We use these data to propose deSUMOylation as a mechanism for specificity in the SUMO system.
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Affiliation(s)
- Emma Garrido
- Department of Biosciences, Durham University, Stockton Road, Durham, UK
| | | | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham, UK
- Correspondence:
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17
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Castro PH, Santos MÂ, Freitas S, Cana-Quijada P, Lourenço T, Rodrigues MAA, Fonseca F, Ruiz-Albert J, Azevedo JE, Tavares RM, Castillo AG, Bejarano ER, Azevedo H. Arabidopsis thaliana SPF1 and SPF2 are nuclear-located ULP2-like SUMO proteases that act downstream of SIZ1 in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4633-4649. [PMID: 30053161 PMCID: PMC6117582 DOI: 10.1093/jxb/ery265] [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] [Indexed: 05/18/2023]
Abstract
Post-translational modifiers such as the small ubiquitin-like modifier (SUMO) peptide act as fast and reversible protein regulators. Functional characterization of the sumoylation machinery has determined the key regulatory role that SUMO plays in plant development. Unlike components of the SUMO conjugation pathway, SUMO proteases (ULPs) are encoded by a relatively large gene family and are potential sources of specificity within the pathway. This study reports a thorough comparative genomics and phylogenetic characterization of plant ULPs, revealing the presence of one ULP1-like and three ULP2-like SUMO protease subgroups within plant genomes. As representatives of an under-studied subgroup, Arabidopsis SPF1 and SPF2 were subjected to functional characterization. Loss-of-function mutants implicated both proteins with vegetative growth, flowering time, and seed size and yield. Mutants constitutively accumulated SUMO conjugates, and yeast complementation assays associated these proteins with the function of ScUlp2 but not ScUlp1. Fluorescence imaging placed both proteins in the plant cell nucleoplasm. Transcriptomics analysis indicated strong regulatory involvement in secondary metabolism, cell wall remodelling, and nitrate assimilation. Furthermore, developmental defects of the spf1-1 spf2-2 (spf1/2) double-mutant opposed those of the major E3 ligase siz1 mutant and, most significantly, developmental and transcriptomic characterization of the siz1 spf1/2 triple-mutant placed SIZ1 as epistatic to SPF1 and SPF2.
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Affiliation(s)
- Pedro Humberto Castro
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
- CIBIO, InBIO—Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Miguel Ângelo Santos
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Sara Freitas
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
- CIBIO, InBIO—Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Pepe Cana-Quijada
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Tiago Lourenço
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Mafalda A A Rodrigues
- PRPlants Lab, GPlantS Unit, Instituto de Tecnologia Química e Biológica—Universidade Nova de Lisboa, Estação Agronómica Nacional, Oeiras, Portugal
| | - Fátima Fonseca
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Javier Ruiz-Albert
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Rui Manuel Tavares
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Araceli G Castillo
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Eduardo R Bejarano
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Herlander Azevedo
- CIBIO, InBIO—Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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18
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Castro PH, Bachmair A, Bejarano ER, Coupland G, Lois LM, Sadanandom A, van den Burg HA, Vierstra RD, Azevedo H. Revised nomenclature and functional overview of the ULP gene family of plant deSUMOylating proteases. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4505-4509. [PMID: 30124991 PMCID: PMC6117577 DOI: 10.1093/jxb/ery301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Pedro Humberto Castro
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairão, Portugal
- Correspondence: ,
| | - Andreas Bachmair
- Dept of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Eduardo R Bejarano
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Ari Sadanandom
- Durham Centre for Crop Improvement Technology, Department of BioSciences, Durham University, Durham, United Kingdom
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Richard D Vierstra
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Herlander Azevedo
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Correspondence: ,
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19
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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.
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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
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20
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Mishra N, Srivastava AP, Esmaeili N, Hu W, Shen G. Overexpression of the rice gene OsSIZ1 in Arabidopsis improves drought-, heat-, and salt-tolerance simultaneously. PLoS One 2018; 13:e0201716. [PMID: 30092010 PMCID: PMC6084956 DOI: 10.1371/journal.pone.0201716] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/21/2018] [Indexed: 12/26/2022] Open
Abstract
Sumoylation is one of the post translational modifications, which affects cellular processes in plants through conjugation of small ubiquitin like modifier (SUMO) to target substrate proteins. Response to various abiotic environmental stresses is one of the major cellular functions regulated by SUMO conjugation. SIZ1 is a SUMO E3 ligase, facilitating a vital step in the sumoylation pathway. In this report, it is demonstrated that over-expression of the rice gene OsSIZ1 in Arabidopsis leads to increased tolerance to multiple abiotic stresses. For example, OsSIZ1-overexpressing plants exhibited enhanced tolerance to salt, drought, and heat stresses, and generated greater seed yields under a variety of stress conditions. Furthermore, OsSIZ1-overexpressing plants were able to exclude sodium ions more efficiently when grown in saline soils and accumulate higher potassium ions as compared to wild-type plants. Further analysis revealed that OsSIZ1-overexpressing plants expressed higher transcript levels of P5CS, a gene involved in the biosynthesis of proline, under both salt and drought stress conditions. Therefore, proline here is acting as an osmoprotectant to alleviate damages caused by drought and salt stresses. These results demonstrate that the rice gene OsSIZ1 has a great potential to be used for improving crop's tolerance to several abiotic stresses.
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Affiliation(s)
- Neelam Mishra
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Department of Botany, St. Joseph’s College, Bangalore, India
| | - Anurag P. Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Nardana Esmaeili
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Wenjun Hu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
| | - Guoxin Shen
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
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21
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Zhan E, Zhou H, Li S, Liu L, Tan T, Lin H. OTS1-dependent deSUMOylation increases tolerance to high copper levels in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:310-322. [PMID: 29205850 DOI: 10.1111/jipb.12618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/30/2017] [Indexed: 06/07/2023]
Abstract
The conjugation of SUMO (small ubiquitin-like modifier) to protein substrates is a reversible process (SUMOylation/deSUMOylation) that regulates plant development and stress responses. The essential metal copper (Cu) is required for normal plant growth, but excess amounts are toxic. The SUMO E3 ligase, SIZ1, and SIZ1-mediated SUMOylation function in plant tolerance to excess Cu. It is unknown whether deSUMOylation also contributes to Cu tolerance in plants. Here, we report that OTS1, a protease that cleaves SUMO from its substrate proteins, participates in Cu tolerance in Arabidopsis thaliana (Arabidopsis). OTS1 loss-of-function mutants (ots1-2 and ots1-3) displayed increased sensitivity to excess Cu. Redox homeostasis and the balance between SUMOylation and deSUMOylation were disrupted in the ots1-3 mutant under excess Cu conditions. The ots1-3 mutant accumulated higher levels of Cu in both shoots and roots compared to wild type. Specific Cu-related metal transporter genes were upregulated due to the loss-of-function of OTS1, which might explain the high Cu levels in ots1-3. These results suggest that the SUMOylation/deSUMOylation machinery is activated in response to excess Cu, and modulates Cu homeostasis and tolerance by regulating both Cu uptake and detoxification. Together, our findings provide insight into the biological function and regulatory role of SUMOylation/deSUMOylation in plant tolerance to Cu.
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Affiliation(s)
- Erbao Zhan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Huapeng Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Sha Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Lei Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tinghong Tan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
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22
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Liu L, Jiang Y, Zhang X, Wang X, Wang Y, Han Y, Coupland G, Jin JB, Searle I, Fu YF, Chen F. Two SUMO Proteases SUMO PROTEASE RELATED TO FERTILITY1 and 2 Are Required for Fertility in Arabidopsis. PLANT PHYSIOLOGY 2017; 175:1703-1719. [PMID: 29066667 PMCID: PMC5717720 DOI: 10.1104/pp.17.00021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 10/22/2017] [Indexed: 05/21/2023]
Abstract
In plants, the posttranslational modification small ubiquitin-like modifier (SUMO) is involved in regulating several important developmental and cellular processes, including flowering time control and responses to biotic and abiotic stresses. Here, we report two proteases, SUMO PROTEASE RELATED TO FERTILITY1 (SPF1) and SPF2, that regulate male and female gamete and embryo development and remove SUMO from proteins in vitro and in vivo. spf1 mutants exhibit abnormal floral structures and embryo development, while spf2 mutants exhibit largely a wild-type phenotype. However, spf1 spf2 double mutants exhibit severe abnormalities in microgametogenesis, megagametogenesis, and embryo development, suggesting that the two genes are functionally redundant. Mutation of SPF1 and SPF2 genes also results in misexpression of generative- and embryo-specific genes. In vitro, SPF1 and SPF2 process SUMO1 precursors into a mature form, and as expected in vivo, spf1 and spf2 mutants accumulate SUMO conjugates. Using a yeast two-hybrid screen, we identified EMBRYO SAC DEVELOPMENT ARREST9 (EDA9) as an SPF1-interacting protein. In vivo, we demonstrate that EDA9 is sumolyated and that, in spf1 mutants, EDA9-SUMO conjugates increase in abundance, demonstrating that EDA9 is a substrate of SPF1. Together, our results demonstrate that SPF1 and SPF2 are two SUMO proteases important for plant development in Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
- Linpo Liu
- MOA Key Laboratory of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
- College of Biological Sciences, State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, 100094 Beijing, People's Republic of China
| | - Ying Jiang
- MOA Key Laboratory of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
- College of Biological Sciences, State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, 100094 Beijing, People's Republic of China
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, 100097 Beijing, People's Republic of China
| | - Xiaomei Zhang
- MOA Key Laboratory of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
| | - Xu Wang
- MOA Key Laboratory of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
| | - Yanbing Wang
- College of Life Sciences, Peking University, 100871 Beijing, People's Republic of China
| | - Yuzhen Han
- College of Biological Sciences, State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, 100094 Beijing, People's Republic of China
| | - George Coupland
- Max Planck Institute for Plant Breeding, D-50829 Cologne, Germany
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, People's Republic of China
| | - Iain Searle
- School of Biological Sciences, University of Adelaide-Shanghai Jiao Tong University Joint Centre for Agriculture and Health, University of Adelaide, Adelaide 5005, Australia
| | - Yong-Fu Fu
- MOA Key Laboratory of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
| | - Fulu Chen
- MOA Key Laboratory of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
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23
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Kim JY, Song JT, Seo HS. Post-translational modifications of Arabidopsis E3 SUMO ligase AtSIZ1 are controlled by environmental conditions. FEBS Open Bio 2017; 7:1622-1634. [PMID: 28979848 PMCID: PMC5623694 DOI: 10.1002/2211-5463.12309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/27/2017] [Accepted: 08/29/2017] [Indexed: 01/04/2023] Open
Abstract
Sumoylation regulates numerous cellular functions in plants as well as in other eukaryotic systems. However, the regulatory mechanisms controlling E3 small ubiquitin‐related modifier (SUMO) ligase are not well understood. Here, post‐translational modification of the Arabidopsis E3 SUMO ligase AtSIZ1 was shown to be specifically controlled by abiotic stresses. AtSIZ1 ubiquitination was induced by exposure to heat stress in transgenic plants overexpressing the E3 ubiquitin ligase COP1. In addition, AtSIZ1 ubiquitination was strongly enhanced in transgenic plants overexpressing SUMO isopeptidase ESD4 under heat stress. By contrast, drought stress induced sumoylation rather than ubiquitination of AtSIZ1 and sumoylated forms of AtSIZ1 accumulated in esd4 and cop1–4 mutants. Moreover, siz1 mutants were found to be tolerant to heat and drought stresses. Taken together, these results indicate that ubiquitination and sumoylation of AtSIZ1 in response to abiotic stresses depend on the activities of COP1 and ESD4 and that the activity and stability of AtSIZ1 can be specifically controlled by different abiotic stresses.
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Affiliation(s)
- Joo Yong Kim
- Department of Plant ScienceResearch Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding InstituteSeoul National UniversityKorea
| | - Jong Tae Song
- School of Applied BiosciencesKyungpook National UniversityDaeguKorea
| | - Hak Soo Seo
- Department of Plant ScienceResearch Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding InstituteSeoul National UniversityKorea.,Bio-MAX InstituteSeoul National UniversityKorea
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Datta M, Kaushik S, Jyoti A, Mathur N, Kothari SL, Jain A. SIZ1-mediated SUMOylation during phosphate homeostasis in plants: Looking beyond the tip of the iceberg. Semin Cell Dev Biol 2017; 74:123-132. [PMID: 28903074 DOI: 10.1016/j.semcdb.2017.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 11/27/2022]
Abstract
Availability of phosphate (Pi) is often limited in rhizospheres in different agroclimatic zones and adversely affects growth and development of plants. To circumvent this impasse, there is an urgent need and global consensus to develop Pi use efficient crops. To achieve this goal, it is essential to identify the molecular entities that exert regulatory influences on the sensing and signaling cascade governing Pi homeostasis. SIZ1 encodes a small ubiquitin-like modifier (SUMO E3) ligase, and plays a pivotal role in the post-translational SUMOylation of proteins. In this review, we discuss the reverse genetics approach conventionally used for providing circumstantial evidence towards the regulatory influences of SIZ1 on several morphophysiological and molecular traits that govern Pi homeostasis in taxonomically diverse Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice) model species. However, the efforts have been rather modest in identifying SUMO protein targets that play key roles in the maintenance of Pi homeostasis in these model plants contrary to the plethora of them now known in lower organisms and animals. Therefore, to predict the SIZ1-mediated SUMOylome involved in Pi homeostasis, the state-of-the-art high-throughput technologies often used for animals thus provide an attractive paradigm towards achieving the long-term goal of developing Pi use efficient crops.
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Affiliation(s)
- Manali Datta
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Anupam Jyoti
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Nidhi Mathur
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Shanker L Kothari
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India
| | - Ajay Jain
- Amity Centre for Nanobiotechnology and Plant Nutrition, Amity University Rajasthan, Jaipur, India.
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25
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Regulation of Plant Cellular and Organismal Development by SUMO. SUMO REGULATION OF CELLULAR PROCESSES 2017; 963:227-247. [DOI: 10.1007/978-3-319-50044-7_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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26
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Liu L, Yan X, Kong X, Zhao Y, Gong Z, Jin JB, Guo Y. Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway. PLANT PHYSIOLOGY 2017; 173:655-667. [PMID: 27852949 PMCID: PMC5210737 DOI: 10.1104/pp.16.01365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/14/2016] [Indexed: 05/21/2023]
Abstract
The expression of genes with aberrant structure is prevented at both the transcriptional and posttranscriptional regulation levels. Aberrant gene silencing at the posttranscriptional level is well studied; however, it is not well understood how aberrant genes are silenced at the transcriptional level. In this study, through genetic screening a transgenic report line that harbors an aberrant gene (35S-LUC, lacking 3'-untranslated region [3'-UTR]) and lacks luciferase (LUC) activity, we identify that the small ubiquitin-like modifier (SUMO) protease OTS1 gene is required for maintaining the silence of the reporter 35S-LUC and an endogenous mutator-like element MULE-F19G14 at the transcriptional level, which requires DNA-dependent RNA polymerase (Pol) V and DDR complex, but not Pol IV. The increased transcripts in ots1 mutants are terminated by the 3'-UTRs of downstream genes. In addition to ots1 mutations, mutations in several known or putative SUMO proteases and two SUMO E3 ligases, SIZ1 and MMS21, have similar effects on this silencing regulation. Taken together, our results reveal that the enzymes involved in the SUMOylation process restrain aberrant gene transcription by using a downstream gene 3'-UTR, and this regulation requires a functional Pol V-dependent pathway in Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Xiaojing Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Xiangxiong Kong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Yiqiang Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Jing Bo Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (L.L., X.Y., Y.Z., Z.G., Y.G.); and
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China (X.K., J.B.J.)
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27
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Liebers M, Grübler B, Chevalier F, Lerbs-Mache S, Merendino L, Blanvillain R, Pfannschmidt T. Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development. FRONTIERS IN PLANT SCIENCE 2017; 8:23. [PMID: 28154576 PMCID: PMC5243808 DOI: 10.3389/fpls.2017.00023] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/05/2017] [Indexed: 05/10/2023]
Abstract
Plastids display a high morphological and functional diversity. Starting from an undifferentiated small proplastid, these plant cell organelles can develop into four major forms: etioplasts in the dark, chloroplasts in green tissues, chromoplasts in colored flowers and fruits and amyloplasts in roots. The various forms are interconvertible into each other depending on tissue context and respective environmental condition. Research of the last two decades uncovered that each plastid type contains its own specific proteome that can be highly different from that of the other types. Composition of these proteomes largely defines the enzymatic functionality of the respective plastid. The vast majority of plastid proteins is encoded in the nucleus and must be imported from the cytosol. However, a subset of proteins of the photosynthetic and gene expression machineries are encoded on the plastid genome and are transcribed by a complex transcriptional apparatus consisting of phage-type nuclear-encoded RNA polymerases and a bacterial-type plastid-encoded RNA polymerase. Both types recognize specific sets of promoters and transcribe partly over-lapping as well as specific sets of genes. Here we summarize the current knowledge about the sequential activity of these plastid RNA polymerases and their relative activities in different types of plastids. Based on published plastid gene expression profiles we hypothesize that each conversion from one plastid type into another is either accompanied or even preceded by significant changes in plastid transcription suggesting that these changes represent important determinants of plastid morphology and protein composition and, hence, the plastid type.
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Kong X, Luo X, Qu GP, Liu P, Jin JB. Arabidopsis SUMO protease ASP1 positively regulates flowering time partially through regulating FLC stability . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:15-29. [PMID: 27925396 DOI: 10.1111/jipb.12509] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
The initiation of flowering is tightly regulated by the endogenous and environment signals, which is crucial for the reproductive success of flowering plants. It is well known that autonomous and vernalization pathways repress transcription of FLOWERING LOCUS C (FLC), a focal floral repressor, but how its protein stability is regulated remains largely unknown. Here, we found that mutations in a novel Arabidopsis SUMO protease 1 (ASP1) resulted in a strong late-flowering phenotype under long-days, but to a lesser extent under short-days. ASP1 localizes in the nucleus and exhibited a SUMO protease activity in vitro and in vivo. The conserved Cys-577 in ASP1 is critical for its enzymatic activity, as well as its physiological function in the regulation of flowering time. Genetic and gene expression analyses demonstrated that ASP1 promotes transcription of positive regulators of flowering, such as FT, SOC1 and FD, and may function in both CO-dependent photoperiod pathway and FLC-dependent pathways. Although the transcription level of FLC was not affected in the loss-of-function asp1 mutant, the protein stability of FLC was increased in the asp1 mutant. Taken together, this study identified a novel bona fide SUMO protease, ASP1, which positively regulates transition to flowering at least partly by repressing FLC protein stability.
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Affiliation(s)
- Xiangxiong Kong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Luo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Gao-Ping Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
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29
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Castro PH, Couto D, Freitas S, Verde N, Macho AP, Huguet S, Botella MA, Ruiz-Albert J, Tavares RM, Bejarano ER, Azevedo H. SUMO proteases ULP1c and ULP1d are required for development and osmotic stress responses in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2016; 92:143-59. [PMID: 27325215 DOI: 10.1007/s11103-016-0500-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/30/2016] [Indexed: 05/12/2023]
Abstract
Sumoylation is an essential post-translational regulator of plant development and the response to environmental stimuli. SUMO conjugation occurs via an E1-E2-E3 cascade, and can be removed by SUMO proteases (ULPs). ULPs are numerous and likely to function as sources of specificity within the pathway, yet most ULPs remain functionally unresolved. In this report we used loss-of-function reverse genetics and transcriptomics to functionally characterize Arabidopsis thaliana ULP1c and ULP1d SUMO proteases. GUS reporter assays implicated ULP1c/d in various developmental stages, and subsequent defects in growth and germination were uncovered using loss-of-function mutants. Microarray analysis evidenced not only a deregulation of genes involved in development, but also in genes controlled by various drought-associated transcriptional regulators. We demonstrated that ulp1c ulp1d displayed diminished in vitro root growth under low water potential and higher stomatal aperture, yet leaf transpirational water loss and whole drought tolerance were not significantly altered. Generation of a triple siz1 ulp1c ulp1d mutant suggests that ULP1c/d and the SUMO E3 ligase SIZ1 may display separate functions in development yet operate epistatically in response to water deficit. We provide experimental evidence that Arabidopsis ULP1c and ULP1d proteases act redundantly as positive regulators of growth, and operate mainly as isopeptidases downstream of SIZ1 in the control of water deficit responses.
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Affiliation(s)
- Pedro Humberto Castro
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071, Malaga, Spain
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Daniel Couto
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK
| | - Sara Freitas
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Nuno Verde
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Alberto P Macho
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071, Malaga, Spain
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 201602, Shanghai, China
| | - Stéphanie Huguet
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, 2 rue G. Crémieux, CP 5708, 91057, Evry Cedex, France
| | - Miguel Angel Botella
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Molecular y Bioquímica, Universidad de Málaga, Campus Teatinos, 29071, Malaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071, Malaga, Spain
| | - Rui Manuel Tavares
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Eduardo Rodríguez Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071, Malaga, Spain
| | - Herlânder Azevedo
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
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Zhang RF, Guo Y, Li YY, Zhou LJ, Hao YJ, You CX. Functional identification of MdSIZ1 as a SUMO E3 ligase in apple. JOURNAL OF PLANT PHYSIOLOGY 2016; 198:69-80. [PMID: 27152458 DOI: 10.1016/j.jplph.2016.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
SUMOylation, the conjugation of target proteins with SUMO (small ubiquitin-related modifier), is a type of post-translational modification in eukaryotes and involves the sequential action of activation (E1), conjugation (E2) and ligation (E3) enzymes. In Arabidopsis, the AtSIZ1 protein is a SUMO E3 ligase that promotes the conjugation of SUMO proteins to target substrates. Here, we isolated and identified a SUMO E3 ligase, MdSIZ1, in apple, which was similar to AtSIZ1. SUMOylation analysis showed that MdSIZ1 had SUMO E3 ligase activity in vitro and in vivo. SUMO conjugation was increased by high temperatures, low temperatures, and abscisic acid (ABA). The ectopic expression of MdSIZ1 in Arabidopsis siz1-2 mutant plants partially complemented the morphological mutant phenotype and enhanced the levels of SUMO conjugation. Taken together, these results suggest that MdSIZ1-mediated SUMO conjugation of target proteins is an important process that regulates the adaptation of apple plants to various environmental stresses.
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Affiliation(s)
- Rui-Fen Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Shandong Agricultural University, Tai-An, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Ying Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Shandong Agricultural University, Tai-An, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Shandong Agricultural University, Tai-An, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Li-Jie Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Shandong Agricultural University, Tai-An, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Shandong Agricultural University, Tai-An, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China.
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Shandong Agricultural University, Tai-An, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China.
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Srivastava AK, Zhang C, Sadanandom A. Rice OVERLY TOLERANT TO SALT 1 (OTS1) SUMO protease is a positive regulator of seed germination and root development. PLANT SIGNALING & BEHAVIOR 2016; 11:e1173301. [PMID: 27119209 PMCID: PMC4973764 DOI: 10.1080/15592324.2016.1173301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 05/22/2023]
Abstract
Salinity is one of the major environmental stresses affecting rice production worldwide. Improving rice salt tolerance is a critical step for sustainable food production. Posttranslational modifications of proteins greatly expand proteome diversity, increase functionality and allow quick responses to environmental stresses, all at low cost to the cell. SUMO mediated modification of substrate proteins is a highly dynamic process governed by the balance of activities of SUMO E3 ligases and deconjugating SUMO proteases. In recent years, SUMO (Small Ubiquitin like Modifier) conjugation of proteins has emerged as an influential regulator of stress signaling in the model plant Arabidopsis. However SUMOylation remain largely under studied in crop plants. We recently identified the SUMO protease gene family in rice and demonstrated a role for OsOTS1 SUMO proteases in salt stress. Interestingly, rice plants silencing OsOTS1 also show significantly reduced germination rate. Knockdown of OsOTS1 gene expression affects root growth by primarily reducing cell size rather than cell division.
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Affiliation(s)
| | - Cunjin Zhang
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - Ari Sadanandom
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
- Contect Ari Sadanandom , School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
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32
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Yates G, Srivastava AK, Sadanandom A. SUMO proteases: uncovering the roles of deSUMOylation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2541-8. [PMID: 27012284 DOI: 10.1093/jxb/erw092] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plants have evolved to cope with changing environmental conditions. One way plants achieve this is through post-translational modification of target proteins by ubiquitination and SUMOylation. These post-translational modifiers (PMs) can alter stability, protein-protein interactions, and the overall fate of the protein. Both of these systems have remarkable similarities in terms of the process leading to attachment of the PM to its substrate : having to undertake activation, conjugation, and finally ligation to the target. In the ubiquitin system, there are a vast number of ubiquitin ligase enzymes (E3s) that provide specificity for the attachment of ubiquitin. With the SUMO system, only a small number of SUMO E3 ligases have so far been identified in the fully sequenced plant genomes. In Arabidopsis thaliana, there are only two SUMO E3s, compared to over 1400 ubiquitin E3s, a trend also observed in crop species such as Oryza sativa and Zea mays Recent research indicates that removing SUMO from its substrate by the enzymatically active SUMO proteases is a vital part of this system. A class of SUMO proteases called ubiquitin-like proteases (ULPs) are widespread in all eukaryotes; within plants, both monocot and dicot kingdoms have conserved and divergent ULPs and ULP-like proteases. This paper examines the roles ULPs have in stress responses and highlights the 'fine-tuning' of SUMO attachment/removal in balancing growth versus stress.
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Affiliation(s)
- Gary Yates
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Anjil Kumar Srivastava
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Ari Sadanandom
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
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Elrouby N. Analysis of Small Ubiquitin-Like Modifier (SUMO) Targets Reflects the Essential Nature of Protein SUMOylation and Provides Insight to Elucidate the Role of SUMO in Plant Development. PLANT PHYSIOLOGY 2015; 169:1006-17. [PMID: 26320229 PMCID: PMC4587472 DOI: 10.1104/pp.15.01014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/28/2015] [Indexed: 05/09/2023]
Abstract
Posttranslational modification of proteins by small ubiquitin-like modifier (SUMO) has received much attention, reflected by a flood of recent studies implicating SUMO in a wide range of cellular and molecular activities, many of which are conserved throughout eukaryotes. Whereas most of these studies were performed in vitro or in single cells, plants provide an excellent system to study the role of SUMO at the developmental level. Consistent with its essential roles during plant development, mutations of the basic SUMOylation machinery in Arabidopsis (Arabidopsis thaliana) cause embryo stage arrest or major developmental defects due to perturbation of the dynamics of target SUMOylation. Efforts to identify SUMO protein targets in Arabidopsis have been modest; however, recent success in identifying thousands of human SUMO targets using unique experimental designs can potentially help identify plant SUMO targets more efficiently. Here, known Arabidopsis SUMO targets are reevaluated, and potential approaches to dissect the roles of SUMO in plant development are discussed.
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Affiliation(s)
- Nabil Elrouby
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
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34
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Parry G. The plant nuclear envelope and regulation of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1673-85. [PMID: 25680795 DOI: 10.1093/jxb/erv023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The nuclear envelope (NE) separates the key mechanisms of transcription and translation, and as such is a critical control point in all eukaryotic cells. In plants, the proteins of the NE influence a number of processes including the control of nucleo-cytoplasmic transport of RNA and protein, chromatin localization to the nuclear periphery, and direct chromatin binding by members of the nuclear pore complex (NPC). In this review I attempt to bring these roles under the umbrella of their effect on gene expression, even though the complex nature of this cellular environment means there is considerable overlap of effects. Although the volume of research in plant cells has greatly improved over recent years, it is clear that our understanding of how the components of the NE either directly or indirectly influence gene expression is still in its infancy.
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Affiliation(s)
- Geraint Parry
- University of Liverpool, Institute of Integrative Biology, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK
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35
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Villajuana-Bonequi M, Elrouby N, Nordström K, Griebel T, Bachmair A, Coupland G. Elevated salicylic acid levels conferred by increased expression of ISOCHORISMATE SYNTHASE 1 contribute to hyperaccumulation of SUMO1 conjugates in the Arabidopsis mutant early in short days 4. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:206-19. [PMID: 24816345 DOI: 10.1111/tpj.12549] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/25/2014] [Accepted: 04/30/2014] [Indexed: 05/05/2023]
Abstract
Post-translational modification of proteins by attachment of small ubiquitin-like modifier (SUMO) is essential for plant growth and development. Mutations in the SUMO protease early in short days 4 (ESD4) cause hyperaccumulation of conjugates formed between SUMO and its substrates, and phenotypically are associated with extreme early flowering and impaired growth. We performed a suppressor mutagenesis screen of esd4 and identified a series of mutants called suppressor of esd4 (sed), which delay flowering, enhance growth and reduce hyperaccumulation of SUMO conjugates. Genetic mapping and genome sequencing indicated that one of these mutations (sed111) is in the gene salicylic acid induction-deficient 2 (SID2), which encodes ISOCHORISMATE SYNTHASE I, an enzyme required for biosynthesis of salicylic acid (SA). Analyses showed that compared with wild-type plants, esd4 contains higher levels of SID2 mRNA and about threefold more SA, whereas sed111 contains lower SA levels. Other sed mutants also contain lower SA levels but are not mutant for SID2, although most reduce SID2 mRNA levels. Therefore, higher SA levels contribute to the small size, early flowering and elevated SUMO conjugate levels of esd4. Our results support previous data indicating that SUMO homeostasis influences SA biosynthesis in wild-type plants, and also demonstrate that elevated levels of SA strongly increase the abundance of SUMO conjugates.
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Affiliation(s)
- Mitzi Villajuana-Bonequi
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829, Cologne, Germany
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36
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Castaño-Miquel L, Seguí J, Manrique S, Teixeira I, Carretero-Paulet L, Atencio F, Lois LM. Diversification of SUMO-activating enzyme in Arabidopsis: implications in SUMO conjugation. MOLECULAR PLANT 2013; 6:1646-60. [PMID: 23482370 DOI: 10.1093/mp/sst049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sumoylation is an essential posttranslational modification that participates in many biological processes including stress responses. However, little is known about the mechanisms that control Small Ubiquitin-like MOdifier (SUMO) conjugation in vivo. We have evaluated the regulatory role of the heterodimeric E1 activating enzyme, which catalyzes the first step in SUMO conjugation. We have established that the E1 large SAE2 and small SAE1 subunits are encoded by one and three genes, respectively, in the Arabidopsis genome. The three paralogs genes SAE1a, SAE1b1, and SAE1b2 are the result of two independent duplication events. Since SAE1b1 and SAE1b2 correspond to two identical copies, only two E1 small subunit isoforms are present in vivo: SAE1a and SAE1b. The E1 heterodimer nuclear localization is modulated by the C-terminal tail of the SAE2 subunit. In vitro, SUMO conjugation rate is dependent on the SAE1 isoform contained in the E1 holoenzyme and our results suggest that downstream steps to SUMO-E1 thioester bond formation are affected. In vivo, SAE1a isoform deletion in T-DNA insertion mutant plants conferred sumoylation defects upon abiotic stress, consistent with a sumoylation defective phenotype. Our results support previous data pointing to a regulatory role of the E1 activating enzyme during SUMO conjugation and provide a novel mechanism to control sumoylation in vivo by diversification of the E1 small subunit.
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Affiliation(s)
- Laura Castaño-Miquel
- Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
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37
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Raorane ML, Mutte SK, Varadarajan AR, Pabuayon IM, Kohli A. Protein SUMOylation and plant abiotic stress signaling: in silico case study of rice RLKs, heat-shock and Ca(2+)-binding proteins. PLANT CELL REPORTS 2013; 32:1053-65. [PMID: 23666184 DOI: 10.1007/s00299-013-1452-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 05/25/2023]
Abstract
Plants respond to stress conditions through early stress-response factors (ESRF), which serve the function of stress sensing and/or signal transduction. These mainly comprise qualitative and/or quantitative flux in the redox molecules, calcium ions (Ca(2+)), phosphatidic acid, hexose sugars and phytohormones. The role of resident proteins such as phytohormone receptors and G-proteins as first messengers under stress is well established. Yet, within the modern omics context, most of the stress response at the protein level is injudiciously attributed to substantial up- or down-regulation of expression measured at the RNA or protein level. Proteins such as kinases and transcription factors (TFs) that exhibit cascade effects are primary candidates for studies in plant stress tolerance. However, resident-protein post-translational modification (PTM), specifically in response to particular conditions such as stress, is a candidate for immediate and potent 'quick reaction force' (QRF) kind of effects. Stress-mediated SUMOylation of TFs and other proteins have been observed. SUMOylation can change the rate of activity, function or location of the modified protein. Early SUMOylation of resident proteins can act in the stress signal transduction or in adaptive response. Here, we consider brief background information on ESRFs to establish the crosstalk between these factors that impinge on PTMs. We then illustrate connections of protein SUMOylation to phytohormones and TFs. Finally, we present results of an in silico analysis of rice Receptor-Like Kinases, heat-shock and calcium-binding proteins to identify members of these gene families, whose basal expression under drought but potential SUMOylation presents them as QRF candidates for roles in stress signaling/response.
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Affiliation(s)
- Manish L Raorane
- Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777 Metro Manila, Philippines
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Li Z, Hu Q, Zhou M, Vandenbrink J, Li D, Menchyk N, Reighard S, Norris A, Liu H, Sun D, Luo H. Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:432-45. [PMID: 23231430 DOI: 10.1111/pbi.12030] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/01/2012] [Accepted: 11/06/2012] [Indexed: 05/20/2023]
Abstract
Sumoylation is a posttranslational regulatory process in higher eukaryotes modifying substrate proteins through conjugation of small ubiquitin-related modifiers (SUMOs). Sumoylation modulates protein stability, subcellular localization and activity; thus, it regulates most cellular functions including response to environmental stress in plants. To study the feasibility of manipulating SUMO E3 ligase, one of the important components in the sumoylation pathway in transgenic (TG) crop plants for improving overall plant performance under adverse environmental conditions, we have analysed TG creeping bentgrass (Agrostis stolonifera L.) plants constitutively expressing OsSIZ1, a rice SUMO E3 ligase. Overexpression of OsSIZ1 led to increased photosynthesis and overall plant growth. When subjected to water deficiency and heat stress, OsSIZ1 plants exhibited drastically enhanced performance associated with more robust root growth, higher water retention and cell membrane integrity than wild-type (WT) controls. OsSIZ1 plants also displayed significantly better growth than WT controls under phosphate-starvation conditions, which was associated with a higher uptake of phosphate (Pi) and other minerals, such as potassium and zinc. Further analysis revealed that overexpression of OsSIZ1 enhanced stress-induced SUMO conjugation to substrate in TG plants, which was associated with modified expression of stress-related genes. This strongly supports a role sumoylation plays in regulating multiple molecular pathways involved in plant stress response, establishing a direct link between sumoylation and plant response to environmental adversities. Our results demonstrate the great potential of genetic manipulation of sumoylation process in TG crop species for improved resistance to broad abiotic stresses.
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Affiliation(s)
- Zhigang Li
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
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New insights into the role of the small ubiquitin-like modifier (SUMO) in plants. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 300:161-209. [PMID: 23273862 DOI: 10.1016/b978-0-12-405210-9.00005-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small ubiquitin-like modifier (SUMO) is a small (∼12kDa) protein that occurs in all eukaryotes and participates in the reversible posttranslational modification of target cellular proteins. The three-dimensional structure of SUMO and ubiquitin (Ub) are superimposable although there is very little similarity in their primary amino acid sequences. In all organisms, conjugation and deconjugation of Ub and SUMO proceed by the same reactions while using pathway-specific enzymes. SUMO conjugation in plants is a part of the controls governing important biological processes such as growth, development, flowering, environmental (abiotic) stress responses, and response to pathogen infection. Most of the evidence for this comes from genetic analyses. Recent efforts to dissect the function of sumoylation have focused on uncovering targets of SUMO conjugation by using either a yeast two-hybrid screen employing components of the SUMO cycle as bait or by using affinity purification of SUMO-conjugated proteins followed by identification of these proteins by mass spectrometry. This chapter reviews the current knowledge regarding sumoylation in plants, with special focus on the model plant Arabidopsis thaliana.
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40
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Miller MJ, Scalf M, Rytz TC, Hubler SL, Smith LM, Vierstra RD. Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis. Mol Cell Proteomics 2012. [PMID: 23197790 DOI: 10.1074/mcp.m112.025056] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The stress-induced attachment of small ubiquitin-like modifier (SUMO) to a diverse collection of nuclear proteins regulating chromatin architecture, transcription, and RNA biology has been implicated in protecting plants and animals against numerous environmental challenges. In order to better understand stress-induced SUMOylation, we combined stringent purification of SUMO conjugates with isobaric tag for relative and absolute quantification mass spectrometry and an advanced method to adjust for sample-to-sample variation so as to study quantitatively the SUMOylation dynamics of intact Arabidopsis seedlings subjected to stress. Inspection of 172 SUMO substrates during and after heat shock (37 °C) revealed that stress mostly increases the abundance of existing conjugates, as opposed to modifying new targets. Some of the most robustly up-regulated targets participate in RNA processing and turnover and RNA-directed DNA modification, thus implicating SUMO as a regulator of the transcriptome during stress. Many of these targets were also strongly SUMOylated during ethanol and oxidative stress, suggesting that their modification is crucial for general stress tolerance. Collectively, our quantitative data emphasize the importance of SUMO to RNA-related processes protecting plants from adverse environments.
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Affiliation(s)
- Marcus J Miller
- Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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41
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Castro PH, Tavares RM, Bejarano ER, Azevedo H. SUMO, a heavyweight player in plant abiotic stress responses. Cell Mol Life Sci 2012; 69:3269-83. [PMID: 22903295 PMCID: PMC11114757 DOI: 10.1007/s00018-012-1094-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 11/27/2022]
Abstract
Protein post-translational modifications diversify the proteome and install new regulatory levels that are crucial for the maintenance of cellular homeostasis. Over the last decade, the ubiquitin-like modifying peptide small ubiquitin-like modifier (SUMO) has been shown to regulate various nuclear processes, including transcriptional control. In plants, the sumoylation pathway has been significantly implicated in the response to environmental stimuli, including heat, cold, drought, and salt stresses, modulation of abscisic acid and other hormones, and nutrient homeostasis. This review focuses on the emerging importance of SUMO in the abiotic stress response, summarizing the molecular implications of sumoylation and emphasizing how high-throughput approaches aimed at identifying the full set of SUMO targets will greatly enhance our understanding of the SUMO-abiotic stress association.
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Affiliation(s)
- Pedro Humberto Castro
- CBFP/Biology Department, Center for Biodiversity, Functional and Integrative Genomics (BioFIG), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Departamento de Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga–Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Rui Manuel Tavares
- CBFP/Biology Department, Center for Biodiversity, Functional and Integrative Genomics (BioFIG), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eduardo R. Bejarano
- Departamento de Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga–Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Herlânder Azevedo
- CBFP/Biology Department, Center for Biodiversity, Functional and Integrative Genomics (BioFIG), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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42
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Castro PH, Tavares RM, Bejarano ER, Azevedo H. SUMO, a heavyweight player in plant abiotic stress responses. Cell Mol Life Sci 2012. [PMID: 22903295 DOI: 10.1007/s00018-00012-01094–1012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Protein post-translational modifications diversify the proteome and install new regulatory levels that are crucial for the maintenance of cellular homeostasis. Over the last decade, the ubiquitin-like modifying peptide small ubiquitin-like modifier (SUMO) has been shown to regulate various nuclear processes, including transcriptional control. In plants, the sumoylation pathway has been significantly implicated in the response to environmental stimuli, including heat, cold, drought, and salt stresses, modulation of abscisic acid and other hormones, and nutrient homeostasis. This review focuses on the emerging importance of SUMO in the abiotic stress response, summarizing the molecular implications of sumoylation and emphasizing how high-throughput approaches aimed at identifying the full set of SUMO targets will greatly enhance our understanding of the SUMO-abiotic stress association.
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Affiliation(s)
- Pedro Humberto Castro
- CBFP/Biology Department, Center for Biodiversity, Functional and Integrative Genomics, University of Minho, Campus de Gualtar, Braga, Portugal
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43
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Novatchkova M, Tomanov K, Hofmann K, Stuible HP, Bachmair A. Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. THE NEW PHYTOLOGIST 2012; 195:23-31. [PMID: 22799003 PMCID: PMC3399776 DOI: 10.1111/j.1469-8137.2012.04135.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The conjugation of the small ubiquitin-related modifier, SUMO, to substrate proteins is a reversible and dynamic process, and an important response of plants to environmental challenges. Nevertheless, reliable data have so far been restricted largely to the model plant Arabidopsis thaliana. The increasing availability of genome information for other plant species offers the possibility to identify a core set of indispensable components, and to discover species-specific features of the sumoylation pathway. We analyzed the enzymes responsible for the conjugation of SUMO to substrates for their conservation between dicots and monocots. We thus assembled gene sets that relate the Arabidopsis SUMO conjugation system to that of the dicot species tomato, grapevine and poplar, and to four plant species from the monocot class: rice, Brachypodium distachyon, Sorghum bicolor and maize. We found that a core set of genes with clear assignment in Arabidopsis had highly conserved homologs in all tested plants. However, we also observed a variation in the copy number of homologous genes, and sequence variations that suggested monocot-specific variants. Generally, SUMO ligases and proteases showed the most pronounced differences. Finally, we identified potential SUMO chain-binding ubiquitin ligases, pointing to an in vivo function of SUMO chains as degradation signals in plants.
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Affiliation(s)
- Maria Novatchkova
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Konstantin Tomanov
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Hans-Peter Stuible
- Physical Engineering Department, University of Applied Sciences of Gelsenkirchen, August-Schmidt-Ring 10, D-45665 Recklinghausen, Germany
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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Tsiatsiani L, Gevaert K, Van Breusegem F. Natural substrates of plant proteases: how can protease degradomics extend our knowledge? PHYSIOLOGIA PLANTARUM 2012; 145:28-40. [PMID: 22008056 DOI: 10.1111/j.1399-3054.2011.01534.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite the key role of proteolysis in various intensively studied biological processes, such as plant immunity, seed development and abiotic stress responses, our knowledge on the identity of natural protease substrates in plants remains scarce. In the genome of the model plant Arabidopsis thaliana, for instance, approximately 700 genes code for proteases. However, only a few natural substrates have been identified, mainly because of the previous lack of sensitive proteomics technologies enabling the identification of low abundant proteins, together with a delay in the implementation of these technologies in the field of plant research. Here, we review the current knowledge on the identity of natural plant protease substrates and describe recently established degradomics technologies that should allow proteome-wide studies of plant proteases in the near future.
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Affiliation(s)
- Liana Tsiatsiani
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
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45
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van den Berg BHJ, Tholey A. Mass spectrometry-based proteomics strategies for protease cleavage site identification. Proteomics 2012; 12:516-29. [PMID: 22246699 DOI: 10.1002/pmic.201100379] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/14/2011] [Accepted: 09/17/2011] [Indexed: 01/22/2023]
Abstract
Protease-catalyzed hydrolysis of peptide bonds is one of the most pivotal post-translational modifications fulfilling manifold functions in the regulation of cellular processes. Therefore, dysregulation of proteolytic reactions plays a central role in many pathophysiological events. For this reason, understanding the molecular mechanisms in proteolytic reactions, in particular the knowledge of proteases involved in complex processes, expression levels and activity of protease and knowledge of the targeted substrates are an indispensable prerequisite for targeted drug development. The present review focuses on mass spectrometry-based proteomic methods for the analysis of protease cleavage sites, including the identification of the hydrolyzed bonds as well as of the surrounding sequence. Peptide- and protein-centric approaches and bioinformatic tools for experimental data interpretation will be presented and the major advantages and drawbacks of the different approaches will be addressed. The recent applications of these approaches for the analysis of biological function of different protease classes and potential future directions will be discussed.
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Affiliation(s)
- Bart H J van den Berg
- AG Systematische Proteomforschung, Institut für Experimentelle Medizin, Christian-Albrechts-Universität, Kiel, Germany.
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Park HJ, Kim WY, Park HC, Lee SY, Bohnert HJ, Yun DJ. SUMO and SUMOylation in plants. Mol Cells 2011; 32:305-16. [PMID: 21912873 PMCID: PMC3887640 DOI: 10.1007/s10059-011-0122-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022] Open
Abstract
The traditional focus on the central dogma of molecular biology, from gene through RNA to protein, has now been replaced by the recognition of an additional mechanism. The new regulatory mechanism, post-translational modifications to proteins, can actively alter protein function or activity introducing additional levels of functional complexity by altering cellular and sub-cellular location, protein interactions and the outcome of biochemical reaction chains. Modifications by ubiquitin (Ub) and ubiquitin-like modifiers systems are conserved in all eukaryotic organisms. One of them, small ubiquitin-like modifier (SUMO) is present in plants. The SUMO mechanism includes several isoforms of proteins that are involved in reactions of sumoylation and de-sumoylation. Sumoylation affects several important processes in plants. Outstanding among those are responses to environmental stresses. These may be abiotic stresses, such as phosphate deficiency, heat, low temperature, and drought, or biotic stressses, as well including defense reactions to pathogen infection. Also, the regulations of flowering time, cell growth and development, and nitrogen assimilation have recently been added to this list. Identification of SUMO targets is material to characterize the function of sumoylation or desumoylation. Affinity purification and mass spectrometric identification have been done lately in plants. Further SUMO noncovalent binding appears to have function in other model organisms and SUMO interacting proteins in plants will be of interest to plant biologists who dissect the dynamic function of SUMO. This review will discuss results of recent insights into the role of sumoylation in plants.
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Affiliation(s)
- Hee Jin Park
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyeong Cheol Park
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Hans J. Bohnert
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dae-Jin Yun
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
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