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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; 23:2680-2699. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [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: 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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2
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Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
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Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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3
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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4
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Wang ZQ, Yang Y, Zhang JY, Zeng X, Zhang CC. Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120. Commun Biol 2023; 6:643. [PMID: 37322092 PMCID: PMC10272220 DOI: 10.1038/s42003-023-05012-9] [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: 02/03/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Transcriptional and translational regulations are important mechanisms for cell adaptation to environmental conditions. In addition to house-keeping tRNAs, the genome of the filamentous cyanobacterium Anabaena sp. strain PCC 7120 (Anabaena) has a long tRNA operon (trn operon) consisting of 26 genes present on a megaplasmid. The trn operon is repressed under standard culture conditions, but is activated under translational stress in the presence of antibiotics targeting translation. Using the toxic amino acid analog β-N-methylamino-L-alanine (BMAA) as a tool, we isolated and characterized several BMAA-resistance mutants from Anabaena, and identified one gene of unknown function, all0854, named as trcR, encoding a transcription factor belonging to the ribbon-helix-helix (RHH) family. We provide evidence that TrcR represses the expression of the trn operon and is thus the missing link between the trn operon and translational stress response. TrcR represses the expression of several other genes involved in translational control, and is required for maintaining translational fidelity. TrcR, as well as its binding sites, are highly conserved in cyanobacteria, and its functions represent an important mechanism for the coupling of the transcriptional and translational regulations in cyanobacteria.
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Affiliation(s)
- Zi-Qian Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- Institute AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, People's Republic of China.
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5
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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6
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Wang M, Zhu Q, Yao N, Liang W, Ma X, Li J, Li X, Wang L, Liang W. The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress. Int J Mol Sci 2023; 24:ijms24098446. [PMID: 37176152 PMCID: PMC10179182 DOI: 10.3390/ijms24098446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/06/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023] Open
Abstract
Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO2 fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.
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Affiliation(s)
- Meng Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Qiang Zhu
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Ning Yao
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Wangli Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaoxia Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jingjing Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaoxu Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
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7
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Dhakal D, Kokkaliari S, Rubin GM, Paul VJ, Ding Y, Luesch H. Biosynthesis of Lyngbyastatins 1 and 3, Cytotoxic Depsipeptides from an Okeania sp. Marine Cyanobacterium. JOURNAL OF NATURAL PRODUCTS 2023; 86:85-93. [PMID: 36546857 PMCID: PMC10197921 DOI: 10.1021/acs.jnatprod.2c00782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Lyngbyastatins (Lbns) 1 (1) and 3 (2) belong to a group of cyclic depsipeptides that inhibit cancer cell proliferation. These compounds have been isolated from different marine cyanobacterial collections, while further development of these compounds relies on their lengthy total synthesis. Biosynthetic studies of these compounds can provide viable strategies to access these compounds and develop new analogs. In this study, we report the identification and characterization of one Lbn biosynthetic gene cluster (BGC) from the marine cyanobacterium Okeania sp. VPG18-21. We initially identified 1 and 2 in the organic extract by mass spectrometry and performed the targeted isolation of these compounds, which feature a (2S,3R)-3-amino-2-methylpentanoic acid (MAP) and a (2S,3R)-3-amino-2-methylhexanoic acid (Amha) moiety, respectively. Parallel metagenomic sequencing of VPG18-21 led to the identification of a putative Lbn BGC that encodes six megaenzymes (LbnA-F), including one polyketide synthase (PKS, LbnE), four nonribosomal peptide synthetases (NRPSs, LbnB-D and -F), and one PKS-NRPS hybrid (LbnA). Bioinformatic analysis of these enzymes suggested that the BGC produces 1 and 2. Furthermore, our biochemical studies of three recombinant adenylation domains uncovered their substrate specificities, supporting the identity of the BGC. Finally, we identified near-complete Lbn-like BGCs in the genomes of two other marine cyanobacteria.
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Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Sofia Kokkaliari
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Garret M. Rubin
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Valerie J. Paul
- Smithsonian Marine Station at Ft. Pierce, 701 Seaway Drive, Ft. Pierce, Florida 34949, United States
| | - Yousong Ding
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
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8
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The increasing role of structural proteomics in cyanobacteria. Essays Biochem 2022; 67:269-282. [PMID: 36503929 PMCID: PMC10070481 DOI: 10.1042/ebc20220095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Abstract
Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.
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9
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Tang H, Zhan Z, Zhang Y, Huang X. Propionylation of lysine, a new mechanism of short-chain fatty acids affecting bacterial virulence. Am J Transl Res 2022; 14:5773-5784. [PMID: 36105019 PMCID: PMC9452321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Propionic acid (PA) is a major component of short-chain fatty acids produced by Bacteroidetes spp. Lysine propionylation is a novel type of protein regulatory posttranslational modification that is widespread in prokaryotes and eukaryotes, as well as in cellular processes, it affects DNA binding affinity, protein stability, and enzyme activity. In this review of published literature, we provide evidence that the level of propionyl modification is influenced by the concentration of PA and the PA metabolic intermediate (propionyl-CoA) and discuss the possibility of PA affecting enteropathogenic bacterial virulence. The understanding of propionyl modification is helpful to better understand the mechanism of PA-producing Bacteroidetes affecting the virulence of pathogenic intestinal bacteria. It may provide novel choices for the prevention and treatment of pathogenic intestinal bacteria.
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Affiliation(s)
- Hao Tang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Ziyang Zhan
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Ying Zhang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
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10
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Li A, Deng Y, Tan Y, Chen M. A Transfer Learning-Based Approach for Lysine Propionylation Prediction. Front Physiol 2021; 12:658633. [PMID: 33967828 PMCID: PMC8096918 DOI: 10.3389/fphys.2021.658633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Lysine propionylation is a newly discovered posttranslational modification (PTM) and plays a key role in the cellular process. Although proteomics techniques was capable of detecting propionylation, large-scale detection was still challenging. To bridge this gap, we presented a transfer learning-based method for computationally predicting propionylation sites. The recurrent neural network-based deep learning model was trained firstly by the malonylation and then fine-tuned by the propionylation. The trained model served as feature extractor where protein sequences as input were translated into numerical vectors. The support vector machine was used as the final classifier. The proposed method reached a matthews correlation coefficient (MCC) of 0.6615 on the 10-fold crossvalidation and 0.3174 on the independent test, outperforming state-of-the-art methods. The enrichment analysis indicated that the propionylation was associated with these GO terms (GO:0016620, GO:0051287, GO:0003735, GO:0006096, and GO:0005737) and with metabolism. We developed a user-friendly online tool for predicting propoinylation sites which is available at http://47.113.117.61/.
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Affiliation(s)
- Ang Li
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Yingwei Deng
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Yan Tan
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
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11
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Ding Q, Zhang Z, Li Y, Liu H, Hao Q, Yang Y, Ringø E, Olsen RE, Clarke JL, Ran C, Zhou Z. Propionate induces intestinal oxidative stress via Sod2 propionylation in zebrafish. iScience 2021; 24:102515. [PMID: 34142031 PMCID: PMC8188496 DOI: 10.1016/j.isci.2021.102515] [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] [Received: 01/15/2021] [Revised: 03/17/2021] [Accepted: 05/03/2021] [Indexed: 12/21/2022] Open
Abstract
Propionate and propionyl-CoA accumulation have been associated with the development of mitochondrial dysfunction. In this study, we show that propionate induces intestinal damage in zebrafish when fed a high-fat diet (HFD). The intestinal damage was associated with oxidative stress owing to compromised superoxide dismutase 2 (Sod2) activity. Global lysine propionylation analysis of the intestinal samples showed that Sod2 was propionylated at lysine 132 (K132), and further biochemical assays demonstrated that K132 propionylation suppressed Sod2 activity. In addition, sirtuin 3 (Sirt3) played an important role in regulating Sod2 activity via modulating de-propionylation. Finally, we revealed that intestinal oxidative stress resulting from Sod2 propionylation contributed to compositional change of gut microbiota. Collectively, our results in this study show that there is a link between Sod2 propionylation and oxidative stress in zebrafish intestines and highlight the potential mechanism of intestinal problems associated with high propionate levels. Propionate supplementation in high-fat diet induces intestinal damage Propionate induces oxidative stress via Sod2 propionylation at 132 lysine site Increased Sod2 propionylation is associated with reduced expression of Sirt3 Intestinal oxidative stress alters gut microbiota composition
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Affiliation(s)
- Qianwen Ding
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Li
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongliang Liu
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang Hao
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Einar Ringø
- Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Rolf Erik Olsen
- Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | | | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhou
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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12
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Liu X, Yang M, Liu Y, Ge F, Zhao J. Structural and Functional Insights into a Lysine Deacylase in the Cyanobacterium Synechococcus sp. PCC 7002. PLANT PHYSIOLOGY 2020; 184:762-776. [PMID: 32719110 PMCID: PMC7536712 DOI: 10.1104/pp.20.00583] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Lys deacylases are essential regulators of cell biology in many contexts. Here, we have identified CddA (cyanobacterial deacetylase/depropionylase), a Lys deacylase enzyme expressed in the cyanobacterium Synechococcus sp. PCC 7002 that has both deacetylase and depropionylase activity. Loss of the gene cddA led to slower growth and impaired linear and cyclic photosynthetic electron transfer. We determined the crystal structure of this depropionylase/deacetylase at 2.1 Å resolution and established that it has a unique and characteristically folded α/β structure. We detected an acyl binding site within CddA via site-directed mutagenesis and demonstrated that this site is essential for the deproprionylase activity of this enzyme. Through a proteomic approach, we identified a total of 598 Lys residues across 382 proteins that were capable of undergoing propionylation. These propionylated proteins were highly enriched for photosynthetic and metabolic functionality. We additionally demonstrated that CddA was capable of catalyzing in vivo and in vitro Lys depropionylation and deacetylation of Fru-1,6-bisphosphatase, thereby regulating its enzymatic activity. Our identification of a Lys deacylase provides insight into the mechanisms globally regulating photosynthesis and carbon metabolism in cyanobacteria and potentially in other photosynthetic organisms as well.
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Affiliation(s)
- 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 100049, 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
| | - Yingfang Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, 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
- 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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