1
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Han J, Wang L, Tang X, Liu R, Shi L, Zhu J, Zhao M. Glsirt1-mediated deacetylation of GlCAT regulates intracellular ROS levels, affecting ganoderic acid biosynthesis in Ganoderma lucidum. Free Radic Biol Med 2024; 216:1-11. [PMID: 38458391 DOI: 10.1016/j.freeradbiomed.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. However, in Basidiomycetes, the extent of lysine acetylation of nonhistone proteins remains largely unknown. Recently, we identified the deacetylase Glsirt1 as a key regulator of the biosynthesis of ganoderic acid (GA), a key secondary metabolite of Ganoderma lucidum. To gain insight into the characteristics, extent, and biological function of Glsirt1-mediated lysine acetylation in G. lucidum, we aimed to identify additional Glsirt1 substrates via comparison of acetylomes between wild-type (WT) and Glsirt1-silenced mutants. A large amount of Glsirt1-dependent lysine acetylation occurs in G. lucidum according to the results of this omics analysis, involving energy metabolism, protein synthesis, the stress response and other pathways. Our results suggest that GlCAT is a direct target of Glsirt1 and that the deacetylation of GlCAT by Glsirt1 reduces catalase activity, thereby leading to the accumulation of intracellular reactive oxygen species (ROS) and positively regulating the biosynthesis of GA. Our findings provide evidence for the involvement of nonhistone lysine acetylation in the biological processes of G. lucidum and help elucidate the involvement of important ROS signaling molecules in regulating physiological and biochemical processes in this organism. In conclusion, this proteomic analysis reveals a striking breadth of cellular processes affected by lysine acetylation and provides new nodes of intervention in the biosynthesis of secondary metabolites in G. lucidum.
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Affiliation(s)
- Jing Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Lingshuai Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Xin Tang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Rui Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
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2
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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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3
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Tejada-Arranz A, Lulla A, Bouilloux-Lafont M, Turlin E, Pei XY, Douché T, Matondo M, Williams AH, Raynal B, Luisi BF, De Reuse H. Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease. Nat Commun 2023; 14:8072. [PMID: 38057323 PMCID: PMC10700544 DOI: 10.1038/s41467-023-43825-8] [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: 10/20/2021] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM structures of RNase J and determined that it assembles into dimers and tetramers in vitro. We found that RNase J extracted from H. pylori is acetylated on multiple lysine residues. Alanine substitution of several of these residues impacts on H. pylori morphology, and thus on RNase J function in vivo. Mutations of Lysine 649 modulates RNase J oligomerization in vitro, which in turn influences ribonuclease activity in vitro. Our structural analyses of RNase J reveal loops that gate access to the active site and rationalizes how acetylation state of K649 can influence activity. We propose acetylation as a regulatory level controlling the activity of RNase J and its potential cooperation with other enzymes of RNA metabolism in H. pylori.
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Affiliation(s)
- Alejandro Tejada-Arranz
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, Institut Pasteur, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
- Biozentrum, University of Basel, Basel, Switzerland
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Maxime Bouilloux-Lafont
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, Institut Pasteur, Paris, France
| | - Evelyne Turlin
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, Institut Pasteur, Paris, France
| | - Xue-Yuan Pei
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Thibaut Douché
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie, C2RT, USR CNRS 2000, Institut Pasteur, Paris, France
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie, C2RT, USR CNRS 2000, Institut Pasteur, Paris, France
| | - Allison H Williams
- University of California San Francisco, Cellular Molecular Pharmacology, San Francisco, CA, USA
| | - Bertrand Raynal
- Département de Biologie structurale et chimie, Plateforme de biophysique moléculaire, Institut Pasteur, Paris, France
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Hilde De Reuse
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, Institut Pasteur, Paris, France.
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4
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Fellner M, Walsh A, Dela Ahator S, Aftab N, Sutherland B, Tan EW, Bakker AT, Martin NI, van der Stelt M, Lentz CS. Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response. ACS Infect Dis 2023; 9:2119-2132. [PMID: 37824340 PMCID: PMC10644348 DOI: 10.1021/acsinfecdis.3c00246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 10/14/2023]
Abstract
The development of new treatment options for bacterial infections requires access to new targets for antibiotics and antivirulence strategies. Chemoproteomic approaches are powerful tools for profiling and identifying novel druggable target candidates, but their functions often remain uncharacterized. Previously, we used activity-based protein profiling in the opportunistic pathogen Staphylococcus aureus to identify active serine hydrolases termed fluorophosphonate-binding hydrolases (Fph). Here, we provide the first characterization of S. aureus FphH, a conserved, putative carboxylesterase (referred to as yvaK in Bacillus subtilis) at the molecular and cellular level. First, phenotypic characterization of fphH-deficient transposon mutants revealed phenotypes during growth under nutrient deprivation, biofilm formation, and intracellular survival. Biochemical and structural investigations revealed that FphH acts as an esterase and lipase based on a fold well suited to act on a small to long hydrophobic unbranched lipid group within its substrate and can be inhibited by active site-targeting oxadiazoles. Prompted by a previous observation that fphH expression was upregulated in response to fusidic acid, we found that FphH can deacetylate this ribosome-targeting antibiotic, but the lack of FphH function did not infer major changes in antibiotic susceptibility. In conclusion, our results indicate a functional role of this hydrolase in S. aureus stress responses, and hypothetical functions connecting FphH with components of the ribosome rescue system that are conserved in the same gene cluster across Bacillales are discussed. Our atomic characterization of FphH will facilitate the development of specific FphH inhibitors and probes to elucidate its physiological role and validity as a drug target.
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Affiliation(s)
- Matthias Fellner
- Biochemistry
Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Annabel Walsh
- Biochemistry
Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Stephen Dela Ahator
- Research
Group for Host-Microbe Interactions, Department of Medical Biology
and Centre for New Antibacterial Strategies (CANS) UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Nadia Aftab
- Research
Group for Host-Microbe Interactions, Department of Medical Biology
and Centre for New Antibacterial Strategies (CANS) UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ben Sutherland
- Department
of Chemistry, Division of Sciences, University
of Otago, Dunedin 9054, New Zealand
| | - Eng W. Tan
- Department
of Chemistry, Division of Sciences, University
of Otago, Dunedin 9054, New Zealand
| | - Alexander T. Bakker
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333
BE Leiden, The Netherlands
| | - Mario van der Stelt
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Christian S. Lentz
- Research
Group for Host-Microbe Interactions, Department of Medical Biology
and Centre for New Antibacterial Strategies (CANS) UiT, The Arctic University of Norway, 9037 Tromsø, Norway
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5
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Jiang HW, Chen H, Zheng YX, Wang XN, Meng Q, Xie J, Zhang J, Zhang C, Xu ZW, Chen ZQ, Wang L, Kong WS, Zhou K, Ma ML, Zhang HN, Guo SJ, Xue JB, Hou JL, Liu ZY, Niu WX, Wang FJ, Wang T, Li W, Wang RN, Dang YJ, Czajkowsky DM, Pei J, Dong JJ, Tao SC. Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1869-1887. [PMID: 37059927 PMCID: PMC10103678 DOI: 10.1007/s11427-023-2316-2] [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: 01/20/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/16/2023]
Abstract
Protein-biomolecule interactions play pivotal roles in almost all biological processes. For a biomolecule of interest, the identification of the interacting protein(s) is essential. For this need, although many assays are available, highly robust and reliable methods are always desired. By combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin (SA)-biotin system, we developed the Specific Pupylation as IDEntity Reporter (SPIDER) method for identifying protein-biomolecule interactions. Using SPIDER, we validated the interactions between the known binding proteins of protein, DNA, RNA, and small molecule. We successfully applied SPIDER to construct the global protein interactome for m6A and mRNA, identified a variety of uncharacterized m6A binding proteins, and validated SRSF7 as a potential m6A reader. We globally identified the binding proteins for lenalidomide and CobB. Moreover, we identified SARS-CoV-2-specific receptors on the cell membrane. Overall, SPIDER is powerful and highly accessible for the study of protein-biomolecule interactions.
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Affiliation(s)
- He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingfeng Meng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jiong Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200240, China
| | - ChangSheng Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhao-Wei Xu
- Key Laboratory of Gastrointestinal Cancer, Fujian Medical University, Ministry of Education, Fuzhou, 350122, China
| | - Zi-Qing Chen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08540, USA
| | - Lei Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei-Sha Kong
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kuan Zhou
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming-Liang Ma
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing-Li Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhe-Yi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wen-Xue Niu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fang-Jun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tao Wang
- Institute of Systems Biology, Shenzhen Bay Laboratory, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Rui-Na Wang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200240, China
| | - Yong-Jun Dang
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, Chongqing, 400016, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - JianFeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Jia-Jia Dong
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200240, China.
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China.
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6
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Noell SE, Brennan E, Washburn Q, Davis EW, Hellweger FL, Giovannoni SJ. Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility. Environ Microbiol 2023. [PMID: 36826469 DOI: 10.1111/1462-2920.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14 C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth Brennan
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Oregon, USA
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7
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Duan H, Zhang X, Figeys D. An emerging field: Post-translational modification in microbiome. Proteomics 2023; 23:e2100389. [PMID: 36239139 DOI: 10.1002/pmic.202100389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Post-translational modifications (PTMs) play an essential role in most biological processes. PTMs on human proteins have been extensively studied. Studies on bacterial PTMs are emerging, which demonstrate that bacterial PTMs are different from human PTMs in their types, mechanisms and functions. Few PTM studies have been done on the microbiome. Here, we reviewed several studied PTMs in bacteria including phosphorylation, acetylation, succinylation, glycosylation, and proteases. We discussed the enzymes responsible for each PTM and their functions. We also summarized the current methods used to study microbiome PTMs and the observations demonstrating the roles of PTM in the microbe-microbe interactions within the microbiome and their interactions with the environment or host. Although new methods and tools for PTM studies are still needed, the existing technologies have made great progress enabling a deeper understanding of the functional regulation of the microbiome. Large-scale application of these microbiome-wide PTM studies will provide a better understanding of the microbiome and its roles in the development of human diseases.
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Affiliation(s)
- Haonan Duan
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xu Zhang
- Center for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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8
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Dong H, Zhang J, Zhang H, Han Y, Lu C, Chen C, Tan X, Wang S, Bai X, Zhai G, Tian S, Zhang T, Cheng Z, Li E, Xu L, Zhang K. YiaC and CobB regulate lysine lactylation in Escherichia coli. Nat Commun 2022; 13:6628. [PMID: 36333310 PMCID: PMC9636275 DOI: 10.1038/s41467-022-34399-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Lysine lactylation (Kla) has recently been reported to participate in regulating transcription in human cells. However, the characterization, regulatory mechanism and functional consequence of Kla in prokaryotes remain unclear. Here, we report that YiaC functions as a lysine lactylase and that CobB serves as a lysine delactylase in the regulation of metabolism. We demonstrate that YiaC catalyzes the addition of Kla, while CobB erases this PTM both in vitro and intracellularly. Moreover, we show that YdiF can catalyze the formation of a lactyl-coenzyme A, which donates lactyl group for Kla. Quantitative proteomic analysis further reveals 446 endogenous Kla sites targeted by CobB and 79 candidates targeted by YiaC in Escherichia coli (E. coli). Furthermore, we present that Kla can influence the functions of metabolic enzymes. Interestingly, we demonstrate that CobB can specifically modulate the activity of PykF by regulating K382la, promoting glycolysis and bacterial growth. Our study identifies the regulatory enzymes and functional network of Kla and reveals a Kla-mediated molecular mechanism catalyzed by CobB for glycolysis regulation in E. coli.
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Affiliation(s)
- Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, 515041, Shantou, Guangdong, China
| | - Jianji Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Hui Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Yue Han
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Congcong Lu
- College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Chen Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xiaoxia Tan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Siyu Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Tao Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Zhongyi Cheng
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou, 310018, Zhejiang, China
| | - Enmin Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, 515041, Shantou, Guangdong, China
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 515041, Shantou, Guangdong, China
| | - Liyan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, 515041, Shantou, Guangdong, China.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin Medical University, 300070, Tianjin, China.
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, Medical University General Hospital, Tianjin Medical University, 300070, Tianjin, China.
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9
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Song L, Zhan H, Wang Y, Lin Z, Li B, Shen L, Jiao Y, Li Y, Wang F, Yang J. Cross-Talk of Protein Expression and Lysine Acetylation in Response to TMV Infection in Nicotiana benthamiana. ACS OMEGA 2022; 7:32496-32511. [PMID: 36120045 PMCID: PMC9475610 DOI: 10.1021/acsomega.2c03917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Lysine acetylation (Kac), a reversible PTM, plays an essential role in various biological processes, including those involving metabolic pathways, pathogen resistance, and transcription, in both prokaryotes and eukaryotes. TMV, the major factor that causes the poor quality of Solanaceae crops worldwide, directly alters many metabolic processes in tobacco. However, the extent and function of Kac during TMV infection have not been determined. The validation test to detect Kac level and viral expression after TMV infection and Nicotinamide (NAM) treatment clarified that acetylation was involved in TMV infection. Furthermore, we comprehensively analyzed the changes in the proteome and acetylome of TMV-infected tobacco (Nicotiana benthamiana) seedlings via LC-MS/MS in conjunction with highly sensitive immune-affinity purification. In total, 2082 lysine-acetylated sites on 1319 proteins differentially expressed in response to TMV infection were identified. Extensive bioinformatic studies disclosed changes in acetylation of proteins engaged in cellular metabolism and biological processes. The vital influence of Kac in fatty acid degradation and alpha-linolenic acid metabolism was also revealed in TMV-infected seedlings. This study first revealed Kac information in N. benthamiana under TMV infection and expanded upon the existing landscape of acetylation in pathogen infection.
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Affiliation(s)
- Liyun Song
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Huaixu Zhan
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Graduate
School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yujie Wang
- Luoyang
Branch of Henan Tobacco Company, Luoyang 471000, China
| | - Zhonglong Lin
- Yunnan
Tobacco Company of the China National Tobacco Corporation, Kunming 650011, China
| | - Bin Li
- Sichuan
Tobacco Company, Chengdu 610017, China
| | - Lili Shen
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yubing Jiao
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ying Li
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fenglong Wang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jinguang Yang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
the Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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10
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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11
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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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12
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Kurita D, Himeno H. Bacterial Ribosome Rescue Systems. Microorganisms 2022; 10:372. [PMID: 35208827 PMCID: PMC8874680 DOI: 10.3390/microorganisms10020372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 12/10/2022] Open
Abstract
To maintain proteostasis, the cell employs multiple ribosome rescue systems to relieve the stalled ribosome on problematic mRNA. One example of problematic mRNA is non-stop mRNA that lacks an in-frame stop codon produced by endonucleolytic cleavage or transcription error. In Escherichia coli, there are at least three ribosome rescue systems that deal with the ribosome stalled on non-stop mRNA. According to one estimation, 2-4% of translation is the target of ribosome rescue systems even under normal growth conditions. In the present review, we discuss the recent findings of ribosome rescue systems in bacteria.
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Affiliation(s)
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Hirosaki University, 3, Bunkyo-cho, Hirosaki 036-8561, Japan;
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13
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Condon C, Pellegrini O, Gilet L, Durand S, Braun F. Walking from E. coli to B. subtilis, one ribonuclease at a time. C R Biol 2021; 344:357-371. [DOI: 10.5802/crbiol.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022]
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14
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Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation. mBio 2021; 12:e0033421. [PMID: 34253058 PMCID: PMC8406268 DOI: 10.1128/mbio.00334-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacterial and eukaryotic hibernation factors prevent translation by physically blocking the decoding center of ribosomes, a phenomenon called ribosome hibernation that often occurs in response to nutrient deprivation. The human pathogen Staphylococcus aureus lacking the sole hibernation factor HPF undergoes massive ribosome degradation via an unknown pathway. Using genetic and biochemical approaches, we find that inactivating the 3′-to-5′ exonuclease RNase R suppresses ribosome degradation in the Δhpf mutant. In vitro cell-free degradation assays confirm that 30S and 70S ribosomes isolated from the Δhpf mutant are extremely susceptible to RNase R, in stark contrast to nucleolytic resistance of the HPF-bound 70S and 100S complexes isolated from the wild type. In the absence of HPF, specific S. aureus 16S rRNA helices are sensitive to nucleolytic cleavage. These RNase hot spots are distinct from that found in the Escherichia coli ribosomes. S. aureus RNase R is associated with ribosomes, but unlike the E. coli counterpart, it is not regulated by general stressors and acetylation. The results not only highlight key differences between the evolutionarily conserved RNase R homologs but also provide direct evidence that HPF preserves ribosome integrity beyond its role in translational avoidance, thereby poising the hibernating ribosomes for rapid resumption of translation.
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15
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Protein acetyltransferases mediate bacterial adaptation to a diverse environment. J Bacteriol 2021; 203:e0023121. [PMID: 34251868 DOI: 10.1128/jb.00231-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein lysine acetylation is a conserved post-translational modification that modulates several cellular processes. Protein acetylation and its physiological implications are well understood in eukaryotes; however, its role is emerging in bacteria. Lysine acetylation in bacteria is fine-tuned by the concerted action of lysine acetyltransferases (KATs), protein deacetylases (KDACs), metabolic intermediates- acetyl-coenzyme A (Ac-CoA) and acetyl phosphate (AcP). AcP mediated nonenzymatic acetylation is predominant in bacteria due to its high acetyl transfer potential whereas, enzymatic acetylation by bacterial KATs (bKAT) are considered less abundant. SePat, the first bKAT discovered in Salmonella enterica, regulates the activity of the central metabolic enzyme- acetyl-CoA synthetase, through its acetylation. Recent studies have highlighted the role of bKATs in stress responses like pH tolerance, nutrient stress, persister cell formation, antibiotic resistance and pathogenesis. Bacterial genomes encode many putative bKATs of unknown biological function and significance. Detailed characterization of putative and partially characterized bKATs is important to decipher the acetylation mediated regulation in bacteria. Proper synthesis of information about the diverse roles of bKATs is missing to date, which can lead to the discovery of new antimicrobial targets in future. In this review, we provide an overview of the diverse physiological roles of known bKATs, and their mode of regulation in different bacteria. We also highlight existing gaps in the literature and present questions that may help understand the regulatory mechanisms mediated by bKATs in adaptation to a diverse habitat.
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16
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Yuan B, Liu T, Cheng Y, Gao S, Li L, Cai L, Yang J, Chen J, Zhong K. Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection. Front Microbiol 2021; 12:672559. [PMID: 34084157 PMCID: PMC8166574 DOI: 10.3389/fmicb.2021.672559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.
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Affiliation(s)
- Bowen Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China.,Yantai Academy of Agricultural Science, Yantai, China
| | - Linzhi Li
- Yantai Academy of Agricultural Science, Yantai, China
| | - Linna Cai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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17
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Abstract
Ribonucleases (RNases) are essential for almost every aspect of RNA metabolism. However, despite their important metabolic roles, RNases can also be destructive enzymes. As a consequence, cells must carefully regulate the amount, the activity, and the localization of RNases to avoid the inappropriate degradation of essential RNA molecules. In addition, bacterial cells often must adjust RNase levels as environmental situations demand, also requiring careful regulation of these critical enzymes. As the need for strict control of RNases has become more evident, multiple mechanisms for this regulation have been identified and studied, and these are described in this review. The major conclusion that emerges is that no common regulatory mechanism applies to all RNases, or even to a family of RNases; rather, a wide variety of processes have evolved that act on these enzymes, and in some cases, multiple regulatory mechanisms can even act on a single RNase. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA;
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18
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021; 59:341-359. [PMID: 33779951 DOI: 10.1007/s12275-021-0650-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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19
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Hu J, Xia X, Zhao Q, Li S. Lysine acetylation of NKG2D ligand Rae-1 stabilizes the protein and sensitizes tumor cells to NKG2D immune surveillance. Cancer Lett 2021; 502:143-153. [PMID: 33279621 PMCID: PMC10142196 DOI: 10.1016/j.canlet.2020.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 02/08/2023]
Abstract
Shedding, loss of expression, or internalization of natural killer group 2, member D (NKG2D) ligands from the tumor cell surface leads to immune evasion, which is associated with poor prognosis in patients with cancer. In many cancers, matrix metalloproteinases cause the proteolytic shedding of NKG2D ligands. However, it remained unclear how to protect NKG2D ligands from shedding. Here, we showed that the shedding of the mouse NKG2D ligand Rae-1 can be prevented by two critical acetyltransferases, GCN5 and PCAF, which acetylate the lysine residues of Rae-1 to avoid shedding both in vitro and in vivo. In contrast, mutations at lysines 80 and 87 of Rae-1 abrogated this acetylation and thereby desensitized tumor cells to NKG2D-dependent immune surveillance. Notably, the protein levels of GCN5 correlated with the expression levels of the human NKG2D ligand ULPB1 in a human tumor tissue microarray and, more importantly, with prolonged overall survival in many cancers. Our results suggest that the acetylation of Rae-1 protein at lysines 80 and 87 by GCN5 and PCAF protects Rae-1 from shedding so as to activate NKG2D-dependent immune surveillance. This discovery may shed light on new targets for NKG2D immunotherapy in cancer treatment.
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Affiliation(s)
- Jiemiao Hu
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 853, Houston, TX, 77030, USA
| | - Xueqing Xia
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 853, Houston, TX, 77030, USA
| | - Qingnan Zhao
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 853, Houston, TX, 77030, USA
| | - Shulin Li
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 853, Houston, TX, 77030, USA.
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20
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021:10.1007/s12275-021-0650-3. [PMID: 33565052 DOI: 10.1007/s12275-021-0650-3] [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: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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21
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Ceyssens PJ, De Smet J, Wagemans J, Akulenko N, Klimuk E, Hedge S, Voet M, Hendrix H, Paeshuyse J, Landuyt B, Xu H, Blanchard J, Severinov K, Lavigne R. The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit. Viruses 2020; 12:v12090976. [PMID: 32887488 PMCID: PMC7552054 DOI: 10.3390/v12090976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/20/2022] Open
Abstract
In this study, we describe the biological function of the phage-encoded protein RNA polymerase alpha subunit cleavage protein (Rac), a predicted Gcn5-related acetyltransferase encoded by phiKMV-like viruses. These phages encode a single-subunit RNA polymerase for transcription of their late (structure- and lysis-associated) genes, whereas the bacterial RNA polymerase is used at the earlier stages of infection. Rac mediates the inactivation of bacterial transcription by introducing a specific cleavage in the α subunit of the bacterial RNA polymerase. This cleavage occurs within the flexible linker sequence and disconnects the C-terminal domain, required for transcription initiation from most highly active cellular promoters. To achieve this, Rac likely taps into a novel post-translational modification (PTM) mechanism within the host Pseudomonas aeruginosa. From an evolutionary perspective, this novel phage-encoded regulation mechanism confirms the importance of PTMs in the prokaryotic metabolism and represents a new way by which phages can hijack the bacterial host metabolism.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen De Smet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Evgeny Klimuk
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Subray Hedge
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Marleen Voet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Hanne Hendrix
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jan Paeshuyse
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Bart Landuyt
- Department of Biology, KU Leuven, 3000 Leuven, Belgium;
| | - Hua Xu
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - John Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
- Correspondence: ; Tel.: +32-16-379-524
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22
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Novak J, Fabrik I, Jurnecka D, Holubova J, Stanek O, Sebo P. Bordetella pertussis Acetylome is Shaped by Lysine Deacetylase Bkd1. J Proteome Res 2020; 19:3680-3696. [PMID: 32674575 DOI: 10.1021/acs.jproteome.0c00178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of proteins enable swift physiological adaptation of cells to altered growth conditions and stress. Aside from protein phosphorylation, acetylation on ε-amino groups of lysine residues (N-ε-lysine acetylation) represents another important post-translational modification of proteins. For many bacterial pathogens, including the whooping cough agent Bordetella pertussis, the role and extent of protein acetylation remain to be defined. We expressed in Escherichia coli the BP0960 and BP3063 genes encoding two putative deacetylases of B. pertussis and show that BP0960 encodes a lysine deacetylase enzyme, named Bkd1, that regulates acetylation of a range of B. pertussis proteins. Comparison of the proteome and acetylome of a Δbkd1 mutant with the proteome and acetylome of wild-type B. pertussis (PRIDE ID. PXD016384) revealed that acetylation on lysine residues may modulate activities or stabilities of proteins involved in bacterial metabolism and histone-like proteins. However, increased acetylation of the BvgA response regulator protein of the B. pertussis master virulence-regulating BvgAS two-component system affected neither the total levels of produced BvgA nor its phosphorylation status. Indeed, the Δbkd1 mutant was not impaired in the production of key virulence factors and its survival within human macrophages in vitro was not affected. The Δbkd1 mutant exhibited an increased growth rate under carbon source-limiting conditions and its virulence in the in vivo mouse lung infection model was somewhat affected. These results indicate that the lysine deacetylase Bkd1 and N-ε-lysine acetylation primarily modulate the general metabolism rather than the virulence of B. pertussis.
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Affiliation(s)
- Jakub Novak
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic.,Faculty of Science, Charles University, Prague 11636, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove 50005, Czech Republic
| | - David Jurnecka
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic.,Faculty of Science, Charles University, Prague 11636, Czech Republic
| | - Jana Holubova
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Ondrej Stanek
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
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23
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Chen H, Previero A, Deutscher MP. A novel mechanism of ribonuclease regulation: GcvB and Hfq stabilize the mRNA that encodes RNase BN/Z during exponential phase. J Biol Chem 2019; 294:19997-20008. [PMID: 31744883 DOI: 10.1074/jbc.ra119.011367] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/13/2019] [Indexed: 11/06/2022] Open
Abstract
RNase BN, the Escherichia coli RNase Z family member, plays a limited role in tRNA metabolism, in contrast to most other organisms. However, RNase BN does act on 6S RNA, the global transcription regulator, degrading it in exponential-phase cells and maintaining it at low levels during this phase of growth. RNase BN levels decrease in stationary-phase cells, leading to elevation of 6S RNA and subsequent regulation of RNA polymerase. These findings were the first indication that RNase BN itself is growth phase-regulated. Here, we analyze the mechanism of this regulation of RNase BN. We find that RNase BN decreases in stationary phase because its mRNA becomes unstable, due primarily to its degradation by RNase E. However, in exponential-phase cells rbn mRNA is stabilized due to binding by the sRNA, GcvB, and the protein, Hfq, which reduce cleavage by RNase E. Because the amount of GcvB decreases in stationary phase, rbn mRNA is less protected and becomes increasingly unstable resulting in reduction in the amount of RNase BN. The small RNA-dependent, positive regulation of RNase BN in exponential-phase cells is the first example of this novel mechanism for RNase regulation.
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Affiliation(s)
- Hua Chen
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
| | - Angelica Previero
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
| | - Murray P Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
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24
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Defining the impact of exoribonucleases in the shift between exponential and stationary phases. Sci Rep 2019; 9:16271. [PMID: 31700028 PMCID: PMC6838162 DOI: 10.1038/s41598-019-52453-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 10/12/2019] [Indexed: 01/26/2023] Open
Abstract
The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.
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25
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Xu Z, Zhang H, Zhang X, Jiang H, Liu C, Wu F, Qian L, Hao B, Czajkowsky DM, Guo S, Xu Z, Bi L, Wang S, Li H, Tan M, Yan W, Feng L, Hou J, Tao S. Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP. EMBO J 2019; 38:e100948. [PMID: 31418899 PMCID: PMC6745502 DOI: 10.15252/embj.2018100948] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis of acetyl-CoA. Interestingly, we also found that one of the key enzymes directly involved in c-di-GMP production, DgcZ, is a substrate of CobB. Deacetylation of DgcZ by CobB enhances its activity and thus the production of c-di-GMP. Our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.
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Affiliation(s)
- Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Hainan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xingrun Zhang
- MOE Key Laboratory of Protein SciencesCenter for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Department of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina
| | - Hewei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Chengxi Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Fanlin Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Lili Qian
- The Chemical Proteomics Center and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Bingbing Hao
- The Chemical Proteomics Center and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | | | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Zhijing Xu
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Lijun Bi
- National Key Laboratory of BiomacromoleculesKey Laboratory of Non‐Coding RNA and Key Laboratory of Protein and Peptide PharmaceuticalsInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- School of Stomatology and MedicineFoshan UniversityFoshanChina
| | - Shihua Wang
- School of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Haitao Li
- MOE Key Laboratory of Protein SciencesCenter for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
- Department of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Lei Feng
- Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jingli Hou
- Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Sheng‐ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related GenesShanghaiChina
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26
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Christensen DG, Xie X, Basisty N, Byrnes J, McSweeney S, Schilling B, Wolfe AJ. Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions. Front Microbiol 2019; 10:1604. [PMID: 31354686 PMCID: PMC6640162 DOI: 10.3389/fmicb.2019.01604] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.
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Affiliation(s)
- David G. Christensen
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States
| | - James Byrnes
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | - Sean McSweeney
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | | | - Alan J. Wolfe
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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27
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Dong H, Zhai G, Chen C, Bai X, Tian S, Hu D, Fan E, Zhang K. Protein lysine de-2-hydroxyisobutyrylation by CobB in prokaryotes. SCIENCE ADVANCES 2019; 5:eaaw6703. [PMID: 31328167 PMCID: PMC6636992 DOI: 10.1126/sciadv.aaw6703] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/13/2019] [Indexed: 05/06/2023]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to be an evolutionarily conserved histone mark. Here, we report that CobB serves as a lysine de-2-hydroxyisobutyrylation enzyme that regulates glycolysis and cell growth in prokaryotes. We identified the specific binding of CobB to Khib using a novel self-assembled multivalent photocrosslinking peptide probe and demonstrated that CobB can catalyze lysine de-2-hydroxyisobutyrylation both in vivo and in vitro. R58 of CobB is a critical site for its de-2-hydroxyisobutyrylase activity. Using a quantitative proteomics approach, we identified 99 endogenous substrates that are targeted by CobB for de-2-hydroxyisobutyrylation. We further demonstrated that CobB can regulate the catalytic activities of enolase (ENO) by removing K343hib and K326ac of ENO simultaneously, which account for changes of bacterial growth. In brief, our study dissects a Khib-mediated molecular mechanism that is catalyzed by CobB for the regulation of the activity of metabolic enzymes as well as the cell growth of bacteria.
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Affiliation(s)
- Hanyang Dong
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Cong Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Deqing Hu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Freiburg, Germany
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Corresponding author.
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28
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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29
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Wellner K, Mörl M. Post-Transcriptional Regulation of tRNA Pools To Govern the Central Dogma: A Perspective. Biochemistry 2019; 58:299-304. [PMID: 30192518 DOI: 10.1021/acs.biochem.8b00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their initial discovery, tRNAs have risen from sole adapter molecules during protein synthesis to pivotal modulators of gene expression. Through their many interactions with tRNA-associated protein factors, they play a central role in maintaining cell homeostasis, especially regarding the fine-tuning in response to a rapidly changing cellular environment. Here, we provide a perspective on current tRNA topics with a spotlight on the regulation of post-transcriptional shaping of tRNA molecules. First, we give an update on aberrant structural features that a yet functional fraction of mitochondrial tRNAs can exhibit. Then, we outline several aspects of the regulatory contribution of ribonucleases with a focus on tRNA processing versus tRNA elimination. We close with a comment on the possible consequences for the intracellular examination of nascent tRNA precursors regarding respective processing factors that have been shown to associate with the tRNA transcription machinery in alternative moonlighting functions.
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Affiliation(s)
- Karolin Wellner
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
| | - Mario Mörl
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
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30
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Chen G, Cao M, Yu J, Guo X, Shi S. Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou's general PseAAC. J Theor Biol 2019; 461:92-101. [DOI: 10.1016/j.jtbi.2018.10.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
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31
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Xu D, He H, Jiang X, Hua R, Chen H, Yang L, Cheng J, Duan J, Li Q. SIRT2 plays a novel role on progesterone, estradiol and testosterone synthesis via PPARs/LXRα pathways in bovine ovarian granular cells. J Steroid Biochem Mol Biol 2019; 185:27-38. [PMID: 30009951 DOI: 10.1016/j.jsbmb.2018.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/27/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022]
Abstract
SIRT2 has been shown to possess NAD+-dependent deacetylase and desuccinylase enzymatic activities, it also regulates metabolism homeostasis in mammals. Previous data has suggested that resveratrol, a potential activator of Sirtuins, played a stimulation role in steroidogenesis. Unfortunately, to date, the physiological roles of SIRT2 in ovarian granular cells (GCs) are largely unknown. Here, we studied the function and molecular mechanisms of SIRT2 on steroid hormone synthesis in GCs from Qinchuan cattle. Immunohistochemistry and western blotting showed that SIRT2 was expressed not only in GCs and cumulus cells, but also in oocytes and theca cells. We found that the secretion of progesterone was induced, whereas that of estrogen and testosterone secretion was suppressed by treatment with the SIRT2 inhibitor (Thiomyristoyl or SirReal2) or siRNA. Additionally, the PPARs/LXRα signaling pathways were suppressed by SIRT2 siRNA or inhibitors. The mRNA expression of CYP17, aromatase and StAR was suppressed, but the abundance of CYP11A1 mRNA was induced by SIRT2 inhibition. Furthermore, the PPARα agonist or PPARγ antagonist could mimic the effects of SIRT2 inhibition on hormones levels and gene expression associated with steroid hormone biosynthesis. In turn, those effects were abolished by the LXRα agonist (LXR-623). Together, these data support the hypothesis that SIRT2 regulates steroid hormone synthesis via the PPARs/LXRα pathways in GCs.
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Affiliation(s)
- Dejun Xu
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China. -
| | - Huanshan He
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Xiaohan Jiang
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Rongmao Hua
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Huali Chen
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Li Yang
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Jianyong Cheng
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Jiaxin Duan
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
| | - Qingwang Li
- Northwest A&F University, College of Animal Science and Technology, Yangling, Shaanxi, 712100, China.
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32
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Liu GT, Jiang JF, Liu XN, Jiang JZ, Sun L, Duan W, Li RM, Wang Y, Lecourieux D, Liu CH, Li SH, Wang LJ. New insights into the heat responses of grape leaves via combined phosphoproteomic and acetylproteomic analyses. HORTICULTURE RESEARCH 2019; 6:100. [PMID: 31666961 PMCID: PMC6804945 DOI: 10.1038/s41438-019-0183-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Heat stress is a serious and widespread threat to the quality and yield of many crop species, including grape (Vitis vinifera L.), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature regimes. The phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphosites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35 °C, 40 °C, and 45 °C in comparison with the proteome profiles of plants grown at 25 °C. The greatest number of changes was observed at the relatively high temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the response to high temperatures. This finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving acetylation. Nineteen proteins were identified with changes associated with both phosphorylation and acetylation, which is consistent with crosstalk between these posttranslational modification types.
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Affiliation(s)
- Guo-Tian Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jian-Fu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Xin-Na Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jin-Zhu Jiang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
| | - Rui-Min Li
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - David Lecourieux
- Universite´ de Bordeaux, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
- INRA, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
| | - Chong-Huai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Li-Jun Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
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Dressaire C, Pobre V, Laguerre S, Girbal L, Arraiano CM, Cocaign-Bousquet M. PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. BMC Genomics 2018; 19:848. [PMID: 30486791 PMCID: PMC6264599 DOI: 10.1186/s12864-018-5259-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/16/2018] [Indexed: 12/02/2022] Open
Abstract
Background Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions This work had identified PNPase as a central player associated with mRNA degradation in stationary phase. Electronic supplementary material The online version of this article (10.1186/s12864-018-5259-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémentine Dressaire
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - Cecilia Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Jiang J, Gai Z, Wang Y, Fan K, Sun L, Wang H, Ding Z. Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition. BMC Genomics 2018; 19:840. [PMID: 30477445 PMCID: PMC6258439 DOI: 10.1186/s12864-018-5250-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 11/14/2018] [Indexed: 02/02/2023] Open
Abstract
Background Nε-Acetylation of lysine residues, a frequently occurring post-translational modification, plays important functions in regulating physiology and metabolism. However, the information of global overview of protein acetylome under nitrogen-starvation/resupply in tea (Camellia sinensis) leaves was limited. And the full function of lysine acetylated proteins of tea plants in nitrogen absorption and assimilation remains unclear. Results Here, we performed the global review of lysine acetylome in tea leaves under nitrogen (N)-starvation/resupply, using peptide prefractionation, immunoaffinity enrichment, and coupling with high sensitive LC-MS/MS combined with affinity purification analysis. Altogether, 2229 lysine acetylation sites on 1286 proteins were identified, of which 16 conserved motifs in E*KacK, Kac*K, Kac*R, Kac*HK, Kac*N, Kac*S, Kac*T, Kac*D, were extracted from 2180 acetylated peptides. Approximately, 36.76% of the acetylated lysines were located in the regions of ordered secondary structures. The most of the identified lysine acetylation proteins were located in the chloroplast (39%) and cytoplasm (29%). The largest group of acetylated proteins consisted of many enzymes, such as ATP synthase, ribosomal proteins and malate dehydrogenase [NADP], which were related to metabolism (38%) in the biological process. These acetylated proteins were mainly enriched in three primary protein complexes of photosynthesis: photosystem I, photosystem II and the cytochrome b6/f complex. And some acetylated proteins related to glycolysis and secondary metabolite biosynthesis were increased/decreased under N-resupply. Moreover, the PPI (protein-protein interaction) analysis revealed that the diverse interactions of identified acetylated proteins mainly involved in photosynthesis and ribosome. Conclusion The results suggested that lysine acetylated proteins might play regulating roles in metabolic process in tea leaves. The critical regulatory roles mainly involved in diverse aspects of metabolic processes, especially in photosynthesis, glycolysis and secondary metabolism. A lot of proteins related to the photosynthesis and glycolysis were found to be acetylated, including LHCA1, LHCA3, LHCB6, psaE, psaD, psaN, GAPDH, PEPC, ENL and petC. And some proteins related to flavonoids were also found to be acetylated, including PAL, DFR, naringenin 3-dioxygenase and CHI. The provided data may serve as important resources for exploring the physiological, biochemical, and genetic role of lysine acetylation in tea plants. Data are available via ProteomeXchange with identifier PXD008931. Electronic supplementary material The online version of this article (10.1186/s12864-018-5250-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jutang Jiang
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Zhongshuai Gai
- College of Life Science, Yantai University, Yantai, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Hui Wang
- Rizhao Tea Research Institute of Shandong, Rizhao, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China.
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Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ. Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli. mBio 2018; 9:e01905-18. [PMID: 30352934 PMCID: PMC6199490 DOI: 10.1128/mbio.01905-18] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Posttranslational modifications, such as Nε-lysine acetylation, regulate protein function. Nε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an Nε-lysine residue of a protein. The enzymatic mechanism uses Nε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Nε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria.IMPORTANCENε-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Nε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new Nε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.
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Affiliation(s)
- David G Christensen
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Jesse G Meyer
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jackson T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | | | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | | | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
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Umehara T, Kosono S, Söll D, Tamura K. Lysine Acetylation Regulates Alanyl-tRNA Synthetase Activity in Escherichia coli. Genes (Basel) 2018; 9:genes9100473. [PMID: 30274179 PMCID: PMC6209979 DOI: 10.3390/genes9100473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 11/19/2022] Open
Abstract
Protein lysine acetylation is a widely conserved posttranslational modification in all three domains of life. Lysine acetylation frequently occurs in aminoacyl-tRNA synthetases (aaRSs) from many organisms. In this study, we determined the impact of the naturally occurring acetylation at lysine-73 (K73) in Escherichia coli class II alanyl-tRNA synthetase (AlaRS) on its alanylation activity. We prepared an AlaRS K73Ac variant in which Nε-acetyl-l-lysine was incorporated at position 73 using an expanded genetic code system in E. coli. The AlaRS K73Ac variant showed low activity compared to the AlaRS wild type (WT). Nicotinamide treatment or CobB-deletion in an E. coli led to elevated acetylation levels of AlaRS K73Ac and strongly reduced alanylation activities. We assumed that alanylation by AlaRS is affected by K73 acetylation, and the modification is sensitive to CobB deacetylase in vivo. We also showed that E. coli expresses two CobB isoforms (CobB-L and CobB-S) in vivo. CobB-S displayed the deacetylase activity of the AlaRS K73Ac variant in vitro. Our results imply a potential regulatory role for lysine acetylation in controlling the activity of aaRSs and protein synthesis.
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Affiliation(s)
- Takuya Umehara
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan.
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.
- Center for Sustainable Resource Science, RIKEN, Saitama 351-0198, Japan.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan.
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Pobre V, Arraiano CM. Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-Seq. Methods Enzymol 2018; 612:1-24. [PMID: 30502937 DOI: 10.1016/bs.mie.2018.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Differential RNA-Seq is a next-generation technology method to determine the significant transcriptomic differences between two and more samples. With this method it is possible to analyze the total RNA content of different samples making it the best global analysis method currently available to study the roles of exoribonucleases in the cell. These enzymes are responsible for the RNA processing and degradation in the cells and therefore affect the total RNA pool in ways not yet fully understood. In Escherichia coli there are three main degradative exoribonucleases RNase II, RNase R, and PNPase that degrade the RNA from the 3' to the 5'-end. These enzymes have several roles in the cell and even though they are degradative enzymes RNase II and PNPase can also protect some RNAs from degradation and PNPase can also act as an RNA polymerase under some conditions. The multiplicity of roles of these exoribonucleases leads to a very high number of transcripts that are affected by their absence in the cell. With the differential RNA-Seq it is possible to obtain a much deeper understanding of how these enzymes work and regulate the bacterial gene expression. In this chapter we have described a differential RNA-Seq data analysis protocol applied to the study of exoribonucleases. We also included the protocol for experimental validation of the RNA-Seq data using qPCR and motility assays. Although the methods described in this chapter were applied to the study of the exoribonucleases, they can also be used for other differential RNA-Seq studies.
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Affiliation(s)
- Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Mohanty BK, Kushner SR. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria. Microbiol Spectr 2018; 6:10.1128/microbiolspec.RWR-0011-2017. [PMID: 29676246 PMCID: PMC5912700 DOI: 10.1128/microbiolspec.rwr-0011-2017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Indexed: 02/08/2023] Open
Abstract
Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this review, we discuss the various enzymes that control transcription, translation, and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5' and 3' termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript are matured to individual 16S, 23S, and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and nontranslated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions, Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase, as well as proteins that regulate the catalytic activity of particular RNases. Under certain stress conditions, an additional group of specialized endonucleases facilitate the cell's ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I, participate in multiple RNA processing and decay pathways.
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Affiliation(s)
| | - Sidney R Kushner
- Department of Genetics
- Department of Microbiology, University of Georgia, Athens, GA 30602
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Xu JY, Xu Z, Liu X, Tan M, Ye BC. Protein Acetylation and Butyrylation Regulate the Phenotype and Metabolic Shifts of the Endospore-forming Clostridium acetobutylicum. Mol Cell Proteomics 2018. [PMID: 29523768 DOI: 10.1074/mcp.ra117.000372] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Clostridium acetobutylicum is a strict anaerobic, endospore-forming bacterium, which is used for the production of the high energy biofuel butanol in metabolic engineering. The life cycle of C. acetobutylicum can be divided into two phases, with acetic and butyric acids being produced in the exponential phase (acidogenesis) and butanol formed in the stationary phase (solventogenesis). During the transitional phase from acidogenesis to solventogenesis and latter stationary phase, concentration peaks of the metabolic intermediates butyryl phosphate and acetyl phosphate are observed. As an acyl group donor, acyl-phosphate chemically acylates protein substrates. However, the regulatory mechanism of lysine acetylation and butyrylation involved in the phenotype and solventogenesis of C. acetobutylicum remains unknown. In our study, we conducted quantitative analysis of protein acetylome and butyrylome to explore the dynamic change of lysine acetylation and butyrylation in the exponential phase, transitional phase, and stationary phase of C. acetobutylicum Total 458 lysine acetylation sites and 1078 lysine butyrylation sites were identified in 254 and 373 substrates, respectively. Bioinformatics analysis uncovered the similarities and differences between the two acylation modifications in C. acetobutylicum Mutation analysis of butyrate kinase and the central transcriptional factor Spo0A was performed to characterize the unique role of lysine butyrylation in the metabolic pathway and sporulation process of C. acetobutylicum Moreover, quantitative proteomic assays were performed to reveal the relationship between protein features (e.g. gene expression level and lysine acylation level) and metabolites in the three growth stages. This study expanded our knowledge of lysine acetylation and butyrylation in Clostridia and constituted a resource for functional studies on lysine acylation in bacteria.
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Affiliation(s)
- Jun-Yu Xu
- From the ‡Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.,¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhen Xu
- From the ‡Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.,¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - XinXin Liu
- ¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Minjia Tan
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Bang-Ce Ye
- From the ‡Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China; .,¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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Sang Y, Ren J, Qin R, Liu S, Cui Z, Cheng S, Liu X, Lu J, Tao J, Yao YF. Acetylation Regulating Protein Stability and DNA-Binding Ability of HilD, thus Modulating Salmonella Typhimurium Virulence. J Infect Dis 2017; 216:1018-1026. [PMID: 28329249 DOI: 10.1093/infdis/jix102] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 02/21/2017] [Indexed: 02/04/2023] Open
Abstract
HilD, a dominant regulator of Salmonella pathogenicity island 1, can be acetylated by protein acetyltransferase (Pat) in Salmonella Typhimurium, and the acetylation is beneficial to its stability. However, the underlying mechanism of HilD stability regulated by acetylation is not clear. We show here that lysine 297 (K297) located in the helix-turn-helix motif, can be acetylated by Pat. Acetylation of K297 increases HilD stability, but reduces its DNA-binding affinity. In turn, the deacetylated K297 enhances the DNA-binding ability but decreases HilD stability. Under the Salmonella pathogenicity island 1-inducing condition, the acetylation level of K297 is down-regulated. The acetylated K297 (mimicked by glutamine substitution) causes attenuated invasion in HeLa cells, as well as impaired virulence in mouse model, compared with the deacetylated K297 (mimicked by arginine substitution), suggesting that deacetylation of K297 is essential for Salmonella virulence. These findings demonstrate that the acetylation of K297 can regulate both protein stability and DNA-binding ability. This regulation mediated by acetylation not only degrades redundant HilD to keep a moderate protein level to facilitate S. Typhimurium growth but also maintains an appropriate DNA-binding activity of HilD to ensure bacterial pathogenicity.
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Affiliation(s)
- Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences
| | - Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences
| | - Ran Qin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University
| | - Shuting Liu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University
| | - Sen Cheng
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
| | - Jing Tao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences.,Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine
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Abstract
Nε-Lysine acetylation is now recognized as an abundant posttranslational modification (PTM) that influences many essential biological pathways. Advancements in mass spectrometry-based proteomics have led to the discovery that bacteria contain hundreds of acetylated proteins, contrary to the prior notion of acetylation events being rare in bacteria. Although the mechanisms that regulate protein acetylation are still not fully defined, it is understood that this modification is finely tuned via both enzymatic and nonenzymatic mechanisms. The opposing actions of Gcn5-related N-acetyltransferases (GNATs) and deacetylases, including sirtuins, provide the enzymatic control of lysine acetylation. A nonenzymatic mechanism of acetylation has also been demonstrated and proven to be prominent in bacteria, as well as in mitochondria. The functional consequences of the vast majority of the identified acetylation sites remain unknown. From studies in mammalian systems, acetylation of critical lysine residues was shown to impact protein function by altering its structure, subcellular localization, and interactions. It is becoming apparent that the same diversity of functions can be found in bacteria. Here, we review current knowledge of the mechanisms and the functional consequences of acetylation in bacteria. Additionally, we discuss the methods available for detecting acetylation sites, including quantitative mass spectrometry-based methods, which promise to promote this field of research. We conclude with possible future directions and broader implications of the study of protein acetylation in bacteria.
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Ren J, Sang Y, Lu J, Yao YF. Protein Acetylation and Its Role in Bacterial Virulence. Trends Microbiol 2017; 25:768-779. [PMID: 28462789 DOI: 10.1016/j.tim.2017.04.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.
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Affiliation(s)
- Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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Wei W, Liu T, Li X, Wang R, Zhao W, Zhao G, Zhao S, Zhou Z. Lysine acetylation regulates the function of the global anaerobic transcription factor FnrL in Rhodobacter sphaeroides. Mol Microbiol 2017; 104:278-293. [PMID: 28118511 DOI: 10.1111/mmi.13627] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 01/04/2023]
Abstract
The metabolism of the purple non-sulfur bacterium Rhodobacter sphaeroides is versatile and it can grow under various conditions. Here, we report evidence that the anaerobic photosynthetic metabolism of R. sphaeroides is regulated by protein lysine acetylation. Using a proteomic approach, 59 acetylated peptides were detected. Among them is the global anaerobic transcription factor FnrL, which regulates the biosynthetic pathway of tetrapyrroles and synthesis of the photosynthetic apparatus. Lysine 223 of FnrL was identified as acetylated. We show that all three lysines in the DNA binding domain (K223, K213 and K175) of FnrL can be acetylated by acetyl-phosphate in vitro. A bacterial deacetylase homolog, RsCobB can deacetylate FnrL in vitro. The transcription of genes downstream of FnrL decreased when the DNA binding domain of FnrL was acetylated, as revealed by chromatin immunoprecipitation and acetylation-mimicking mutagenesis. An increasing number of acetylated lysines resulted in a further decrease in DNA binding ability. These results demonstrate that the lysine acetylation can fine tune the function of the oxygen-sensitive FnrL; thus, it might regulate anaerobic photosynthetic metabolism of R. sphaeroides.
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Affiliation(s)
- Wei Wei
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, 650091, China
| | - Xinfeng Li
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ruofan Wang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shimin Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Cohen O, Oberhardt M, Yizhak K, Ruppin E. Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy. PLoS One 2016; 11:e0168444. [PMID: 27997585 PMCID: PMC5173180 DOI: 10.1371/journal.pone.0168444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 12/01/2016] [Indexed: 11/23/2022] Open
Abstract
Genetic robustness is a hallmark of cells, occurring through many mechanisms and at many levels. Essential genes lack the common robustness mechanism of genetic redundancy (i.e., existing alongside other genes with the same function), and thus appear at first glance to leave cells highly vulnerable to genetic or environmental perturbations. Here we explore a hypothesis that cells might protect against essential gene loss through mechanisms that occur at various cellular levels aside from the level of the gene. Using Escherichia coli and Saccharomyces cerevisiae as models, we find that essential genes are enriched over non-essential genes for properties we call "coding efficiency" and "coding robustness", denoting respectively a gene's efficiency of translation and robustness to non-synonymous mutations. The coding efficiency levels of essential genes are highly positively correlated with their evolutionary conservation levels, suggesting that this feature plays a key role in protecting conserved, evolutionarily important genes. We then extend our hypothesis into the realm of metabolic networks, showing that essential metabolic reactions are encoded by more "robust" genes than non-essential reactions, and that essential metabolites are produced by more reactions than non-essential metabolites. Taken together, these results testify that robustness at the gene-loss level and at the mutation level (and more generally, at two cellular levels that are usually treated separately) are not decoupled, but rather, that cellular vulnerability exposed due to complete gene loss is compensated by increased mutational robustness. Why some genes are backed up primarily against loss and others against mutations still remains an open question.
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Affiliation(s)
- Osher Cohen
- School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew Oberhardt
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States of America
| | - Keren Yizhak
- School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eytan Ruppin
- School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States of America
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Fan B, Li YL, Li L, Peng XJ, Bu C, Wu XQ, Borriss R. Malonylome analysis of rhizobacterium Bacillus amyloliquefaciens FZB42 reveals involvement of lysine malonylation in polyketide synthesis and plant-bacteria interactions. J Proteomics 2016; 154:1-12. [PMID: 27939684 DOI: 10.1016/j.jprot.2016.11.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/24/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
Using the combination of affinity enrichment and high-resolution LC-MS/MS analysis, we performed a large-scale lysine malonylation analysis in the model representative of Gram-positive plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens FZB42. Altogether, 809 malonyllysine sites in 382 proteins were identified. The bioinformatic analysis revealed that lysine malonylation occurs on the proteins involved in a variety of biological functions including central carbon metabolism, fatty acid biosynthesis and metabolism, NAD(P) binding and translation machinery. A group of proteins known to be implicated in rhizobacterium-plant interaction were also malonylated; especially, the enzymes responsible for antibiotic production including polyketide synthases (PKSs) and nonribosomal peptide synthases (NRPSs) were highly malonylated. Furthermore, our analysis showed malonylation occurred on proteins structure with higher surface accessibility and appeared to be conserved in many bacteria but not in archaea. The results provide us valuable insights into the potential roles of lysine malonylation in governing bacterial metabolism and cellular processes. BIOLOGICAL SIGNIFICANCE Although in mammalian cells some important findings have been discovered that protein malonylation is related to basic metabolism and chronic disease, few studies have been performed on prokaryotic malonylome. In this study, we determined the malonylation profiles of Bacillus amyloliquefaciens FZB42, a model organism of Gram-positive plant growth-promoting rhizobacteria. FZB42 is known for the extensive investigations on its strong ability of producing antimicrobial polyketides and its potent activities of stimulating plant growth. Our analysis shows that malonylation is highly related to the polyketide synthases and the proteins involved bacterial interactions with plants. The results not only provide one of the first malonylomes for exploring the biochemical nature of bacterial proteins, but also shed light on the better understanding of bacterial antibiotic biosynthesis and plant-microbe interaction.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
| | - Yu-Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
| | - Lei Li
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
| | - Xiao-Jun Peng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China.
| | - Chen Bu
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China.
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China.
| | - Rainer Borriss
- Fachgebiet Phytomedizin, Albrecht Daniel Thaer Institut für Agrar- und Gartenbauwissenschaften, Lebenswissenschaftliche Fakultät, Humboldt Universität zu Berlin, 14195 Berlin, Germany.
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48
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Phosphinothricin Acetyltransferases Identified Using In Vivo, In Vitro, and Bioinformatic Analyses. Appl Environ Microbiol 2016; 82:7041-7051. [PMID: 27694229 DOI: 10.1128/aem.02604-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/17/2016] [Indexed: 11/20/2022] Open
Abstract
Acetylation of small molecules is widespread in nature, and in some cases, cells use this process to detoxify harmful chemicals. Streptomyces species utilize a Gcn5 N-acetyltransferase (GNAT), known as Bar, to acetylate and detoxify a self-produced toxin, phosphinothricin (PPT), a glutamate analogue. Bar homologues, such as MddA from Salmonella enterica, acetylate methionine analogues such as methionine sulfoximine (MSX) and methionine sulfone (MSO), but not PPT, even though Bar homologues are annotated as PPT acetyltransferases. S. enterica was used as a heterologous host to determine whether or not putative PPT acetyltransferases from various sources could acetylate PPT, MSX, and MSO. In vitro and in vivo analyses identified substrates acetylated by putative PPT acetyltransferases from Deinococcus radiodurans (DR_1057 and DR_1182) and Geobacillus kaustophilus (GK0593 and GK2920). In vivo, synthesis of DR_1182, GK0593, and GK2920 blocked the inhibitory effects of PPT, MSX, and MSO. In contrast, DR_1057 did not detoxify any of the above substrates. Results of in vitro studies were consistent with the in vivo results. In addition, phylogenetic analyses were used to predict the functionality of annotated PPT acetyltransferases in Burkholderia xenovorans, Bacillus subtilis, Staphylococcus aureus, Acinetobacter baylyi, and Escherichia coli IMPORTANCE: The work reported here provides an example of the use of a heterologous system for the identification of enzyme function. Many members of this superfamily of proteins do not have a known function, or it has been annotated solely on the basis of sequence homology to previously characterized enzymes. The critical role of Gcn5 N-acetyltransferases (GNATs) in the modulation of central metabolic processes, and in controlling metabolic stress, necessitates approaches that can reveal their physiological role. The combination of in vivo, in vitro, and bioinformatics approaches reported here identified GNATs that can acetylate and detoxify phosphinothricin.
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Sun M, Xu J, Wu Z, Zhai L, Liu C, Cheng Z, Xu G, Tao S, Ye BC, Zhao Y, Tan M. Characterization of Protein Lysine Propionylation in Escherichia coli: Global Profiling, Dynamic Change, and Enzymatic Regulation. J Proteome Res 2016; 15:4696-4708. [DOI: 10.1021/acs.jproteome.6b00798] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mingwei Sun
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Junyu Xu
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- Lab
of Biosystems and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Zhixiang Wu
- Pediatric
Surgery Department, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, P. R. China
| | - Linhui Zhai
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chengxi Liu
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, P. R. China
| | - Guofeng Xu
- Pediatric
Surgery Department, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, P. R. China
| | - Shengce Tao
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Bang-Ce Ye
- Lab
of Biosystems and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yingming Zhao
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- Ben
May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, United States
| | - Minjia Tan
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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50
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Song L, Wang G, Malhotra A, Deutscher MP, Liang W. Reversible acetylation on Lys501 regulates the activity of RNase II. Nucleic Acids Res 2016; 44:1979-88. [PMID: 26847092 PMCID: PMC4797298 DOI: 10.1093/nar/gkw053] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/17/2022] Open
Abstract
RNase II, a 3' to 5' processive exoribonuclease, is the major hydrolytic enzyme in Escherichia coli accounting for ∼90% of the total activity. Despite its importance, little is actually known about regulation of this enzyme. We show here that one residue, Lys501, is acetylated in RNase II. This modification, reversibly controlled by the acetyltransferase Pka, and the deacetylase CobB, affects binding of the substrate and thus decreases the catalytic activity of RNase II. As a consequence, the steady-state level of target RNAs of RNase II may be altered in the cells. We also find that under conditions of slowed growth, the acetylation level of RNase II is elevated and the activity of RNase II decreases, emphasizing the importance of this regulatory process. These findings indicate that acetylation can regulate the activity of a bacterial ribonuclease.
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Affiliation(s)
- Limin Song
- The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Guangyuan Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Arun Malhotra
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Wenxing Liang
- The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
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