1
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Kutscha R, Tomin T, Birner-Gruenberger R, Bekiaris PS, Klamt S, Pflügl S. Efficiency of acetate-based isopropanol synthesis in Escherichia coli W is controlled by ATP demand. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:110. [PMID: 39103876 DOI: 10.1186/s13068-024-02534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Due to increasing ecological concerns, microbial production of biochemicals from sustainable carbon sources like acetate is rapidly gaining importance. However, to successfully establish large-scale production scenarios, a solid understanding of metabolic driving forces is required to inform bioprocess design. To generate such knowledge, we constructed isopropanol-producing Escherichia coli W strains. RESULTS Based on strain screening and metabolic considerations, a 2-stage process was designed, incorporating a growth phase followed by a nitrogen-starvation phase. This process design yielded the highest isopropanol titers on acetate to date (13.3 g L-1). Additionally, we performed shotgun and acetylated proteomics, and identified several stress conditions in the bioreactor scenarios, such as acid stress and impaired sulfur uptake. Metabolic modeling allowed for an in-depth characterization of intracellular flux distributions, uncovering cellular demand for ATP and acetyl-CoA as limiting factors for routing carbon toward the isopropanol pathway. Moreover, we asserted the importance of a balance between fluxes of the NADPH-providing isocitrate dehydrogenase (ICDH) and the product pathway. CONCLUSIONS Using the newly gained system-level understanding for isopropanol production from acetate, we assessed possible engineering approaches and propose process designs to maximize production. Collectively, our work contributes to the establishment and optimization of acetate-based bioproduction systems.
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Affiliation(s)
- Regina Kutscha
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, Vienna, Austria
| | - Ruth Birner-Gruenberger
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, Vienna, Austria
| | - Pavlos Stephanos Bekiaris
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
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2
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024; 23:2733-2749. [PMID: 38442041 PMCID: PMC11296938 DOI: 10.1021/acs.jproteome.3c00912] [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] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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3
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Qin C, Graf LG, Striska K, Janetzky M, Geist N, Specht R, Schulze S, Palm GJ, Girbardt B, Dörre B, Berndt L, Kemnitz S, Doerr M, Bornscheuer UT, Delcea M, Lammers M. Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule. Nat Commun 2024; 15:6002. [PMID: 39019872 PMCID: PMC11255334 DOI: 10.1038/s41467-024-49952-0] [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: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Abstract
The AMP-forming acetyl-CoA synthetase is regulated by lysine acetylation both in bacteria and eukaryotes. However, the underlying mechanism is poorly understood. The Bacillus subtilis acetyltransferase AcuA and the AMP-forming acetyl-CoA synthetase AcsA form an AcuA•AcsA complex, dissociating upon lysine acetylation of AcsA by AcuA. Crystal structures of AcsA from Chloroflexota bacterium in the apo form and in complex with acetyl-adenosine-5'-monophosphate (acetyl-AMP) support the flexible C-terminal domain adopting different conformations. AlphaFold2 predictions suggest binding of AcuA stabilizes AcsA in an undescribed conformation. We show the AcuA•AcsA complex dissociates upon acetyl-coenzyme A (acetyl-CoA) dependent acetylation of AcsA by AcuA. We discover an intrinsic phosphotransacetylase activity enabling AcuA•AcsA generating acetyl-CoA from acetyl-phosphate (AcP) and coenzyme A (CoA) used by AcuA to acetylate and inactivate AcsA. Here, we provide mechanistic insights into the regulation of AMP-forming acetyl-CoA synthetases by lysine acetylation and discover an intrinsic phosphotransacetylase allowing modulation of its activity based on AcP and CoA levels.
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Affiliation(s)
- Chuan Qin
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Leonie G Graf
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Kilian Striska
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Markus Janetzky
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Norman Geist
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Robin Specht
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Britta Girbardt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Babett Dörre
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Stefan Kemnitz
- Department for High Performance Computing, University Computing Center, University of Greifswald, 17489, Greifswald, Germany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany.
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4
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Rizo J, Encarnación-Guevara S. Bacterial protein acetylation: mechanisms, functions, and methods for study. Front Cell Infect Microbiol 2024; 14:1408947. [PMID: 39027134 PMCID: PMC11254643 DOI: 10.3389/fcimb.2024.1408947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Lysine acetylation is an evolutionarily conserved protein modification that changes protein functions and plays an essential role in many cellular processes, such as central metabolism, transcriptional regulation, chemotaxis, and pathogen virulence. It can alter DNA binding, enzymatic activity, protein-protein interactions, protein stability, or protein localization. In prokaryotes, lysine acetylation occurs non-enzymatically and by the action of lysine acetyltransferases (KAT). In enzymatic acetylation, KAT transfers the acetyl group from acetyl-CoA (AcCoA) to the lysine side chain. In contrast, acetyl phosphate (AcP) is the acetyl donor of chemical acetylation. Regardless of the acetylation type, the removal of acetyl groups from acetyl lysines occurs only enzymatically by lysine deacetylases (KDAC). KATs are grouped into three main superfamilies based on their catalytic domain sequences and biochemical characteristics of catalysis. Specifically, members of the GNAT are found in eukaryotes and prokaryotes and have a core structural domain architecture. These enzymes can acetylate small molecules, metabolites, peptides, and proteins. This review presents current knowledge of acetylation mechanisms and functional implications in bacterial metabolism, pathogenicity, stress response, translation, and the emerging topic of protein acetylation in the gut microbiome. Additionally, the methods used to elucidate the biological significance of acetylation in bacteria, such as relative quantification and stoichiometry quantification, and the genetic code expansion tool (CGE), are reviewed.
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Affiliation(s)
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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5
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Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
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Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
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6
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Li Q, Lin J, Ma H, Yuan L, Liu X, Xiong J, Miao W, Yang M, Ge F. Identification and Functional Analysis of Lysine 2-Hydroxyisobutyrylation in Cyanobacteria. J Proteome Res 2024; 23:1689-1701. [PMID: 38565891 DOI: 10.1021/acs.jproteome.3c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cyanobacteria are the oldest prokaryotic photoautotrophic microorganisms and have evolved complicated post-translational modification (PTM) machinery to respond to environmental stress. Lysine 2-hydroxyisobutyrylation (Khib) is a newly identified PTM that is reported to play important roles in diverse biological processes, however, its distribution and function in cyanobacteria have not been reported. Here, we performed the first systematic studies of Khib in a model cyanobacterium Synechococcus sp. strain PCC 7002 (Syn7002) using peptide prefractionation, pan-Khib antibody enrichment, and high-accuracy mass spectrometry (MS) analysis. A total of 1875 high-confidence Khib sites on 618 proteins were identified, and a large proportion of Khib sites are present on proteins in the cellular metabolism, protein synthesis, and photosynthesis pathways. Using site-directed mutagenesis and functional studies, we showed that Khib of glutaredoxin (Grx) affects the efficiency of the PS II reaction center and H2O2 resistance in Syn7002. Together, this study provides novel insights into the functions of Khib in cyanobacteria and suggests that reversible Khib may influence the stress response and photosynthesis in both cyanobacteria and plants.
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Affiliation(s)
- Qiaoya Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Lin
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Ma
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Jie Xiong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Miao
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [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: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
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Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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8
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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9
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Lin Y, Ma Q, Yan J, Gong T, Huang J, Chen J, Li J, Qiu Y, Wang X, Lei Z, Zeng J, Wang L, Zhou X, Li Y. Inhibition of Streptococcus mutans growth and biofilm formation through protein acetylation. Mol Oral Microbiol 2024. [PMID: 38224336 DOI: 10.1111/omi.12452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/25/2023] [Accepted: 12/25/2023] [Indexed: 01/16/2024]
Abstract
Numerous cellular processes are regulated in response to the metabolic state of the cell, and one such regulatory mechanism involves lysine acetylation. Lysine acetylation has been proven to play an important role in the virulence of Streptococcus mutans, a major cariogenic bacterial species. S. mutans' glucosyltransferases (Gtfs) are responsible for synthesizing extracellular polysaccharides (EPS) and contributing to biofilm formation. One of the most common nonsteroidal anti-inflammatory drugs is acetylsalicylic acid (ASA), which can acetylate proteins through a nonenzymatic transacetylation reaction. Herein, we investigated the inhibitory effects of ASA on S. mutans. ASA treatment was observed to impede the growth of S. mutans, leading to a reduction in the production of water-insoluble EPS and the formation of biofilm. Moreover, ASA decreased the enzyme activity of Gtfs while increasing the protein acetylation level. The in vivo anticaries efficacy of ASA has further been proved using the rat caries model. In conclusion, ASA as an acetylation agent attenuated the cariogenic virulence of S. mutans, suggesting the potential value of protein acetylation on antimicrobial and anti-biofilm applications to S. mutans.
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Affiliation(s)
- Yongwang Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Qizhao Ma
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jun Huang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiamin Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jing Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yang Qiu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zixue Lei
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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10
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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. Influence of N ε-Lysine Acetylation on the Formation of Protein Aggregates and Antibiotic Persistence in E. coli. Molecules 2024; 29:383. [PMID: 38257296 PMCID: PMC10819833 DOI: 10.3390/molecules29020383] [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: 12/21/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous studies indicate that reversible Nε-lysine acetylation in bacteria may play a key role in the regulation of metabolic processes, transcription and translation, biofilm formation, virulence, and drug resistance. Using appropriate mutant strains deficient in non-enzymatic acetylation and enzymatic acetylation or deacetylation pathways, we investigated the influence of protein acetylation on cell viability, protein aggregation, and persister formation in Escherichia coli. Lysine acetylation was found to increase protein aggregation and cell viability under the late stationary phase. Moreover, increased lysine acetylation stimulated the formation of persisters. These results suggest that acetylation-dependent aggregation may improve the survival of bacteria under adverse conditions (such as the late stationary phase) and during antibiotic treatment. Further experiments revealed that acetylation-favorable conditions may increase persister formation in Klebsiella pneumoniae clinical isolate. However, the exact mechanisms underlying the relationship between acetylation and persistence in this pathogen remain to be elucidated.
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Affiliation(s)
| | | | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (K.S.-S.); (D.K.-W.)
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11
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Peng T, Das T, Ding K, Hang HC. Functional analysis of protein post-translational modifications using genetic codon expansion. Protein Sci 2023; 32:e4618. [PMID: 36883310 PMCID: PMC10031814 DOI: 10.1002/pro.4618] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins not only exponentially increase the diversity of proteoforms, but also contribute to dynamically modulating the localization, stability, activity, and interaction of proteins. Understanding the biological consequences and functions of specific PTMs has been challenging for many reasons, including the dynamic nature of many PTMs and the technical limitations to access homogenously modified proteins. The genetic code expansion technology has emerged to provide unique approaches for studying PTMs. Through site-specific incorporation of unnatural amino acids (UAAs) bearing PTMs or their mimics into proteins, genetic code expansion allows the generation of homogenous proteins with site-specific modifications and atomic resolution both in vitro and in vivo. With this technology, various PTMs and mimics have been precisely introduced into proteins. In this review, we summarize the UAAs and approaches that have been recently developed to site-specifically install PTMs and their mimics into proteins for functional studies of PTMs.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
- Institute of Chemical Biology, Shenzhen Bay LaboratoryShenzhenChina
| | - Tandrila Das
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
| | - Ke Ding
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Howard C. Hang
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
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12
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Schastnaya E, Doubleday PF, Maurer L, Sauer U. Non-enzymatic acetylation inhibits glycolytic enzymes in Escherichia coli. Cell Rep 2023; 42:111950. [PMID: 36640332 DOI: 10.1016/j.celrep.2022.111950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
Advanced mass spectrometry methods have detected thousands of post-translational phosphorylation and acetylation sites in bacteria, but their functional role and the enzymes catalyzing these modifications remain largely unknown. In addition to enzymatic acetylation, lysine residues can also be chemically acetylated by the metabolite acetyl phosphate. In Escherichia coli, acetylation at over 3,000 sites has been linked to acetyl phosphate, but the functionality of this widespread non-enzymatic acetylation is even less clear than the enzyme-catalyzed one. Here, we investigate the role of acetyl-phosphate-mediated acetylation in E. coli central metabolism. Out of 19 enzymes investigated, only GapA and GpmA are acetylated at high stoichiometry, which inhibits their activity by interfering with substrate binding, effectively reducing glycolysis when flux to or from acetate is high. Extrapolating our results to the whole proteome, maximally 10% of the reported non-enzymatically acetylated proteins are expected to reach a stoichiometry that could inhibit their activity.
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Affiliation(s)
- Evgeniya Schastnaya
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Life Science Zurich PhD Program on Systems Biology, 8093 Zurich, Switzerland
| | | | - Luca Maurer
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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13
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M A B Alsarraf H, Lam Ung K, Johansen MD, Dimon J, Olieric V, Kremer L, Blaise M. Biochemical, structural, and functional studies reveal that MAB_4324c from Mycobacterium abscessus is an active tandem repeat N-acetyltransferase. FEBS Lett 2022; 596:1516-1532. [PMID: 35470425 DOI: 10.1002/1873-3468.14360] [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: 02/10/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022]
Abstract
Mycobacterium abscessus is a pathogenic non-tuberculous mycobacterium that possesses an intrinsic drug-resistance profile. Several N-acetyltransferases mediate drug resistance and/or participate in M. abscessus virulence. Mining the M. abscessus genome has revealed genes encoding additional N-acetyltransferases whose functions remain uncharacterized, among them MAB_4324c. Here, we showed that the purified MAB_4324c protein is a N-acetyltransferase able to acetylate small polyamine substrates. The crystal structure of MAB_4324c was solved at high resolution in complex with its cofactor, revealing the presence of two GCN5-related N-acetyltransferase domains and a cryptic binding site for NADPH. Genetic studies demonstrate that MAB_4324c is not essential for in vitro growth of M. abscessus, however overexpression of the protein enhanced the uptake and survival of M. abscessus in THP-1 macrophages.
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Affiliation(s)
- Husam M A B Alsarraf
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kien Lam Ung
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,Department of molecular biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Matt D Johansen
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Juliette Dimon
- IRIM, Université de Montpellier, CNRS, Montpellier, France
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen-PSI, Switzerland
| | - Laurent Kremer
- IRIM, Université de Montpellier, CNRS, Montpellier, France.,INSERM, IRIM, Montpellier, France
| | - Mickaël Blaise
- IRIM, Université de Montpellier, CNRS, Montpellier, France
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14
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Marín-Hernández Á, Rodríguez-Zavala JS, Jasso-Chávez R, Saavedra E, Moreno-Sánchez R. Protein acetylation effects on enzyme activity and metabolic pathway fluxes. J Cell Biochem 2021; 123:701-718. [PMID: 34931340 DOI: 10.1002/jcb.30197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/11/2022]
Abstract
Acetylation of proteins seems a widespread process found in the three domains of life. Several studies have shown that besides histones, acetylation of lysine residues also occurs in non-nuclear proteins. Hence, it has been suggested that this covalent modification is a mechanism that might regulate diverse metabolic pathways by modulating enzyme activity, stability, and/or subcellular localization or interaction with other proteins. However, protein acetylation levels seem to have low correlation with modification of enzyme activity and pathway fluxes. In addition, the results obtained with mutant enzymes that presumably mimic acetylation have frequently been over-interpreted. Moreover, there is a generalized lack of rigorous enzyme kinetic analysis in parallel to acetylation level determinations. The purpose of this review is to analyze the current findings on the impact of acetylation on metabolic enzymes and its repercussion on metabolic pathways function/regulation.
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Affiliation(s)
| | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
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