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Li Q, Lin J, Ma H, Yuan L, Liu X, Xiong J, Miao W, Yang M, Ge F. Identification and Functional Analysis of Lysine 2-Hydroxyisobutyrylation in Cyanobacteria. J Proteome Res 2024; 23:1689-1701. [PMID: 38565891 DOI: 10.1021/acs.jproteome.3c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cyanobacteria are the oldest prokaryotic photoautotrophic microorganisms and have evolved complicated post-translational modification (PTM) machinery to respond to environmental stress. Lysine 2-hydroxyisobutyrylation (Khib) is a newly identified PTM that is reported to play important roles in diverse biological processes, however, its distribution and function in cyanobacteria have not been reported. Here, we performed the first systematic studies of Khib in a model cyanobacterium Synechococcus sp. strain PCC 7002 (Syn7002) using peptide prefractionation, pan-Khib antibody enrichment, and high-accuracy mass spectrometry (MS) analysis. A total of 1875 high-confidence Khib sites on 618 proteins were identified, and a large proportion of Khib sites are present on proteins in the cellular metabolism, protein synthesis, and photosynthesis pathways. Using site-directed mutagenesis and functional studies, we showed that Khib of glutaredoxin (Grx) affects the efficiency of the PS II reaction center and H2O2 resistance in Syn7002. Together, this study provides novel insights into the functions of Khib in cyanobacteria and suggests that reversible Khib may influence the stress response and photosynthesis in both cyanobacteria and plants.
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Affiliation(s)
- Qiaoya Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Lin
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Ma
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Jie Xiong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Miao
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Srivastava R, Singh N, Kanda T, Yadav S, Yadav S, Atri N. Cyanobacterial Proteomics: Diversity and Dynamics. J Proteome Res 2024. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.
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Affiliation(s)
| | - Nidhi Singh
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Tripti Kanda
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Yadav
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
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Liu Y, Feng W, Wang Y, Wu B. Crosstalk between protein post-translational modifications and phase separation. Cell Commun Signal 2024; 22:110. [PMID: 38347544 PMCID: PMC10860296 DOI: 10.1186/s12964-023-01380-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024] Open
Abstract
The phenomenon of phase separation is quite common in cells, and it is involved in multiple processes of life activities. However, the current research on the correlation between protein modifications and phase separation and the interference with the tendency of phase separation has some limitations. Here we focus on several post-translational modifications of proteins, including protein phosphorylation modification at multiple sites, methylation modification, acetylation modification, ubiquitination modification, SUMOylation modification, etc., which regulate the formation of phase separation and the stability of phase separation structure through multivalent interactions. This regulatory role is closely related to the development of neurodegenerative diseases, tumors, viral infections, and other diseases, and also plays essential functions in environmental stress, DNA damage repair, transcriptional regulation, signal transduction, and cell homeostasis of living organisms, which provides an idea to explore the interaction between novel protein post-translational modifications and phase separation. Video Abstract.
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Affiliation(s)
- Yang Liu
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenjuan Feng
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yunshan Wang
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Basic Medical Research Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Bin Wu
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
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Jia K, Yang M, Liu X, Zhang Q, Cao G, Ge F, Zhao J. Deciphering the structure, function, and mechanism of lysine acetyltransferase cGNAT2 in cyanobacteria. PLANT PHYSIOLOGY 2024; 194:634-661. [PMID: 37770070 DOI: 10.1093/plphys/kiad509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023]
Abstract
Lysine acetylation is a conserved regulatory posttranslational protein modification that is performed by lysine acetyltransferases (KATs). By catalyzing the transfer of acetyl groups to substrate proteins, KATs play critical regulatory roles in all domains of life; however, no KATs have yet been identified in cyanobacteria. Here, we tested all predicted KATs in the cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) and demonstrated that A1596, which we named cyanobacterial Gcn5-related N-acetyltransferase (cGNAT2), can catalyze lysine acetylation in vivo and in vitro. Eight amino acid residues were identified as the key residues in the putative active site of cGNAT2, as indicated by structural simulation and site-directed mutagenesis. The loss of cGNAT2 altered both growth and photosynthetic electron transport in Syn7002. In addition, quantitative analysis of the lysine acetylome identified 548 endogenous substrates of cGNAT2 in Syn7002. We further demonstrated that cGNAT2 can acetylate NAD(P)H dehydrogenase J (NdhJ) in vivo and in vitro, with the inability to acetylate K89 residues, thus decreasing NdhJ activity and affecting both growth and electron transport in Syn7002. In summary, this study identified a KAT in cyanobacteria and revealed that cGNAT2 regulates growth and photosynthesis in Syn7002 through an acetylation-mediated mechanism.
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Affiliation(s)
- Kun Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Qi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoxiang Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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cKMT1 is a new lysine methyltransferase that methylates the ferredoxin-NADP(+) oxidoreductase (FNR) and regulates energy transfer in cyanobacteria. Mol Cell Proteomics 2023; 22:100521. [PMID: 36858286 PMCID: PMC10090440 DOI: 10.1016/j.mcpro.2023.100521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Lysine methylation is a conserved and dynamic regulatory post-translational modification performed by lysine methyltransferases (KMTs). KMTs catalyze the transfer of mono-, di-, or tri-methyl groups to substrate proteins and play a critical regulatory role in all domains of life. To date, only one KMT has been identified in cyanobacteria. Here, we tested all of the predicted KMTs in the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis), and we biochemically characterized sll1526 that we termed cKMT1 (cyanobacterial lysine methyltransferase 1), and determined that it can catalyze lysine methylation both in vivo and in vitro. Loss of cKMT1 alters photosynthetic electron transfer in Synechocystis. We analyzed cKMT1-regulated methylation sites in Synechocystis using a timsTOF Pro instrument. We identified 305 class I lysine methylation sites within 232 proteins, and of these, 80 methylation sites in 58 proteins were hypomethylated in ΔcKMT1 cells. We further demonstrated that cKMT1 could methylate ferredoxin-NADP(+) oxidoreductase (FNR) and its potential sites of action on FNR were identified. Amino acid residues H118 and Y219 were identified as key residues in the putative active site of cKMT1 as indicated by structure simulation, site-directed mutagenesis, and KMT activity measurement. Using mutations that mimic the unmethylated forms of FNR, we demonstrated that the inability to methylate K139 residues results in a decrease in the redox activity of FNR and affects energy transfer in Synechocystis. Together, our study identified a new KMT in Synechocystis and elucidated a methylation-mediated molecular mechanism catalyzed by cKMT1 for the regulation of energy transfer in cyanobacteria.
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Xu C, Wang B, Yang L, Zhongming Hu L, Yi L, Wang Y, Chen S, Emili A, Wan C. Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:715-727. [PMID: 33636367 PMCID: PMC9880817 DOI: 10.1016/j.gpb.2020.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 04/04/2020] [Accepted: 06/12/2020] [Indexed: 01/31/2023]
Abstract
Synechocystis sp. PCC 6803 (hereafter: Synechocystis) is a model organism for studying photosynthesis, energy metabolism, and environmental stress. Although known as the first fully sequenced phototrophic organism, Synechocystis still has almost half of its proteome without functional annotations. In this study, by using co-fractionation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS), we define 291 multi-protein complexes, encompassing 24,092 protein-protein interactions (PPIs) among 2062 distinct gene products. This information not only reveals the roles of photosynthesis in metabolism, cell motility, DNA repair, cell division, and other physiological processes, but also shows how protein functions vary from bacteria to higher plants due to changes in interaction partners. It also allows us to uncover the functions of hypothetical proteins, such as Sll0445, Sll0446, and Sll0447 involved in photosynthesis and cell motility, and Sll1334 involved in regulation of fatty acid biogenesis. Here we present the most extensive PPI data for Synechocystis so far, which provide critical insights into fundamental molecular mechanisms in cyanobacteria.
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Affiliation(s)
- Chen Xu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Bing Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Lin Yang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Lucas Zhongming Hu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 2E8, Canada
| | - Lanxing Yi
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Yaxuan Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Shenglan Chen
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 2E8, Canada,Departments of Biochemistry and Biology, Boston University, Boston, MA 02215, USA
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China,Corresponding author.
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7
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Pathania R, Srivastava A, Srivastava S, Shukla P. Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions. BIORESOURCE TECHNOLOGY 2022; 343:126007. [PMID: 34634665 DOI: 10.1016/j.biortech.2021.126007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria are oxygenic photoautotrophs whose metabolism contains key biochemical pathways to fix atmospheric CO2 and synthesize various metabolites. The development of bioengineering tools has enabled the manipulation of cyanobacterial chassis to produce various valuable bioproducts photosynthetically. However, effective utilization of cyanobacteria as photosynthetic cell factories needs a detailed understanding of their metabolism and its interaction with other cellular processes. Implementing systems and synthetic biology tools has generated a wealth of information on various metabolic pathways. However, to design effective engineering strategies for further improvement in growth, photosynthetic efficiency, and enhanced production of target biochemicals, in-depth knowledge of their carbon/nitrogen metabolism, pathway fluxe distribution, genetic regulation and integrative analyses are necessary. In this review, we discuss the recent advances in the development of genome-scale metabolic models (GSMMs), omics analyses (metabolomics, transcriptomics, proteomics, fluxomics), and integrative modeling approaches to showcase the current understanding of cyanobacterial metabolism.
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Affiliation(s)
- Ruchi Pathania
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi 110067, India; DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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8
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Arif Y, Singh P, Siddiqui H, Bajguz A, Hayat S. Salinity induced physiological and biochemical changes in plants: An omic approach towards salt stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:64-77. [PMID: 32906023 DOI: 10.1016/j.plaphy.2020.08.042] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/28/2020] [Accepted: 08/23/2020] [Indexed: 05/18/2023]
Abstract
Salinity is one of the major threats to sustainable agriculture that globally decreases plant production by impairing various physiological, biochemical, and molecular function. In particular, salinity hampers germination, growth, photosynthesis, transpiration, and stomatal conductance. Salinity decreases leaf water potential and turgor pressure and generates osmotic stress. Salinity enhances reactive oxygen species (ROS) content in the plant cell as a result of ion toxicity and disturbs ion homeostasis. Thus, it imbalances nutrient uptake, disintegrates membrane, and various ultrastructure. Consequently, salinity leads to osmotic and ionic stress. Plants respond to salinity by modulating various morpho-physiological, anatomical, and biochemical traits by regulating ion homeostasis and compartmentalization, antioxidant machinery, and biosynthesis of osmoprotectants and phytohormones, i. e, auxins, abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellins, salicylic acid, jasmonic acid, and polyamines. Thus, this further modulates plant osmoticum, decreases ion toxicity, and scavenges ROS. Plants upregulate various genes and proteins that participate in salinity tolerance. They also promote the production of various phytohormones and metabolites that mitigate the toxic effect of salinity. Based on recent papers, the deleterious effect of salinity on plant physiology is discussed. Furthermore, it evaluates the physiological and biochemical responses of the plant to salinity along with phytohormone response. This review paper also highlights omics (genomics, transcriptomics, proteomics, and metabolomics) approach to understand salt stress tolerance.
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Affiliation(s)
- Yamshi Arif
- Aligarh Muslim University, Faculty of Life Sciences, Department of Botany, Plant Physiology Section, Aligarh, 202002, India
| | - Priyanka Singh
- Aligarh Muslim University, Faculty of Life Sciences, Department of Botany, Plant Physiology Section, Aligarh, 202002, India
| | - Husna Siddiqui
- Aligarh Muslim University, Faculty of Life Sciences, Department of Botany, Plant Physiology Section, Aligarh, 202002, India
| | - Andrzej Bajguz
- University of Bialystok, Faculty of Biology, Department of Biology and Plant Ecology, Konstantego Ciolkowskiego 1J, 15-245, Bialystok, Poland.
| | - Shamsul Hayat
- Aligarh Muslim University, Faculty of Life Sciences, Department of Botany, Plant Physiology Section, Aligarh, 202002, India
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Lin X, Yang M, Liu X, Cheng Z, Ge F. Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:289-304. [PMID: 33130100 PMCID: PMC7801250 DOI: 10.1016/j.gpb.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 03/03/2019] [Accepted: 04/19/2019] [Indexed: 12/25/2022]
Abstract
Protein lysine methylation is a prevalent post-translational modification (PTM) and plays critical roles in all domains of life. However, its extent and function in photosynthetic organisms are still largely unknown. Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation. Here we integrated propionylation of monomethylated proteins, enrichment of the modified peptides, and mass spectrometry (MS) analysis to identify monomethylated proteins in Synechocystis sp. PCC 6803 (Synechocystis). Overall, we identified 376 monomethylation sites in 270 proteins, with numerous monomethylated proteins participating in photosynthesis and carbon metabolism. We subsequently demonstrated that CpcM, a previously identified asparagine methyltransferase in Synechocystis, could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480. The loss of CpcM led to decreases in the maximum quantum yield in primary photosystem II (PSII) and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis. We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria. The large number of monomethylated proteins and the identification of CpcM as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.
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Affiliation(s)
- Xiaohuang Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Gomes Gradíssimo D, Pereira Xavier L, Valadares Santos A. Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy. Molecules 2020; 25:E4331. [PMID: 32971731 PMCID: PMC7571216 DOI: 10.3390/molecules25184331] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Conventional petrochemical plastics have become a serious environmental problem. Its unbridled use, especially in non-durable goods, has generated an accumulation of waste that is difficult to measure, threatening aquatic and terrestrial ecosystems. The replacement of these plastics with cleaner alternatives, such as polyhydroxyalkanoates (PHA), can only be achieved by cost reductions in the production of microbial bioplastics, in order to compete with the very low costs of fossil fuel plastics. The biggest costs are carbon sources and nutrients, which can be appeased with the use of photosynthetic organisms, such as cyanobacteria, that have a minimum requirement for nutrients, and also using agro-industrial waste, such as the livestock industry, which in turn benefits from the by-products of PHA biotechnological production, for example pigments and nutrients. Circular economy can help solve the current problems in the search for a sustainable production of bioplastic: reducing production costs, reusing waste, mitigating CO2, promoting bioremediation and making better use of cyanobacteria metabolites in different industries.
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Affiliation(s)
- Diana Gomes Gradíssimo
- Post Graduation Program in Biotechnology, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
| | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
| | - Agenor Valadares Santos
- Post Graduation Program in Biotechnology, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
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11
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Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis. Molecules 2020; 25:molecules25163582. [PMID: 32781706 PMCID: PMC7466104 DOI: 10.3390/molecules25163582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The photosynthetic apparatus and metabolic enzymes of cyanobacteria are subject to various controls, such as transcriptional regulation and post-translational modifications, to ensure that the entire cellular system functions optimally. In particular, phosphorylation plays key roles in many cellular controls such as enzyme activity, signal transduction, and photosynthetic apparatus restructuring. Therefore, elucidating the governing functions of phosphorylation is crucial to understanding the regulatory mechanisms underlying metabolism and photosynthesis. In this study, we determined protein content and phosphorylation levels to reveal the regulation of intracellular metabolism and photosynthesis in Synechocystis sp. PCC 6803; for this, we obtained quantitative data of proteins and their phosphorylated forms involved in photosynthesis and metabolism under various growth conditions (photoautotrophic, mixotrophic, heterotrophic, dark, and nitrogen-deprived conditions) using targeted proteomic and phosphoproteomic analyses with nano-liquid chromatography-triple quadrupole mass spectrometry. The results indicated that in addition to the regulation of protein expression, the regulation of phosphorylation levels of cyanobacterial photosynthetic apparatus and metabolic enzymes was pivotal for adapting to changing environmental conditions. Furthermore, reduced protein levels of CpcC and altered phosphorylation levels of CpcB, ApcA, OCP, and PsbV contributed to the cellular response of the photosynthesis apparatus to nitrogen deficiency.
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12
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Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria. Int J Mol Sci 2019; 20:ijms20194792. [PMID: 31561603 PMCID: PMC6801645 DOI: 10.3390/ijms20194792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.
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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Battchikova N, Muth-Pawlak D, Aro EM. Proteomics of cyanobacteria: current horizons. Curr Opin Biotechnol 2018; 54:65-71. [DOI: 10.1016/j.copbio.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 12/01/2022]
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Ma Y, Yang M, Lin X, Liu X, Huang H, Ge F. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria. J Proteome Res 2017; 16:2030-2043. [DOI: 10.1021/acs.jproteome.7b00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yanyan Ma
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Huang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Zhang J, Yang MK, Zeng H, Ge F. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Mol Cell Proteomics 2016; 15:3529-3539. [PMID: 27630248 DOI: 10.1074/mcp.m116.060046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.
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Affiliation(s)
- Jia Zhang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ming-Kun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Honghui Zeng
- §Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; .,§Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
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Jungblut P, Thiede B, Schlüter H. Towards deciphering proteomes via the proteoform, protein speciation, moonlighting and protein code concepts. J Proteomics 2016; 134:1-4. [DOI: 10.1016/j.jprot.2016.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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