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Bian Y, Hu Z, Wang R, Xie S, Sun Y, Liu T, Ma S, Liu B, Tan M, Xu JY. Characterization of substrate distribution and functional implication of lysine acylations in Staphylococcus aureus. J Proteomics 2025; 316:105419. [PMID: 40057026 DOI: 10.1016/j.jprot.2025.105419] [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] [Received: 12/14/2024] [Revised: 03/04/2025] [Accepted: 03/05/2025] [Indexed: 03/14/2025]
Abstract
Staphylococcus aureus (S. aureus) is a major pathogen whose post-translational modifications (PTMs) regulate key biological processes that exert a substantial impact on protein function within this pathogen. In this study, we comprehensively analyzed the overall patterns of three lysine acylation in S. aureus including acetylation, succinylation, and malonylation. Using mass spectrometry, we identified 1249 acetylated, 871 succinylated, and 67 malonylated sites. Bioinformatic analysis furtherly revealed that both lysine acetylation and succinylation exhibited a preferential association with glutamate residues near the modified lysine positions. Pathway enrichment showed that modified substrates were associated with ribosomes and metabolic functions. Additional functional exploration showed that lysine succinylation significantly regulates the enzymatic activity of Glutamyl-tRNA amidotransferase and Carbamoyl phosphate synthase. In conclusion, our study enhanced the comprehension of lysine succinylation in S. aureus and highlights potential targets related to its pathogenicity at the post-translational modification level. SIGNIFICANCE NEW: Lysine acylations play important roles in regulating bacterial survival and pathogenicity in Staphylococcus aureus. However, comprehensive and systematic investigations of the lysine acylomes in S. aureus remain insufficient. In this study, we conducted a comprehensive analysis of three lysine acylation modifications in Staphylococcus aureus subspecies aureus ATCC 25923 using mass spectrometry-based proteomic techniques. The objective was to investigate the potential impact of these modifications on protein function. Our bioinformatics analysis identified a significant correlation between lysine acylations and both ribosomal and metabolic pathways. Through additional experimental validation, we have substantiated that lysine succinylation plays a significant regulatory role in the activities of Glutamyl-tRNA amidinotransferase and Carbamoyl phosphate synthetase, consequently exerting a profound impact on cellular energy metabolism and protein synthesis in S. aureus. Collectively, our study underscores the pivotal role of lysine acylation modifications in S. aureus in modulating enzyme function, thereby offering valuable insights into the biology of S. aureus and informing potential therapeutic strategies.
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Affiliation(s)
- Yunxu Bian
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China
| | - Zunli Hu
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China
| | - Rongzhen Wang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuyu Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yewen Sun
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China
| | - Tianqi Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China
| | - Shaojie Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Minjia Tan
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China; Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jun-Yu Xu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, China; Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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2
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Nonaka D, Kishida M, Hirata Y, Mori A, Kondo A, Mori Y, Noda S, Tanaka T. Modular pathway engineering for enhanced production of para-aminobenzoic acid and 4-amino-phenylalanine in Escherichia coli via glucose/xylose co-utilization. Appl Environ Microbiol 2025; 91:e0246824. [PMID: 40243317 DOI: 10.1128/aem.02468-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 02/28/2025] [Indexed: 04/18/2025] Open
Abstract
The modularization of biosynthetic pathways is a promising approach for enhancing microbial chemical production. We have developed a co-utilization method with glucose and xylose substrates to divide metabolic pathways into distinct production and energy modules to enhance the biosynthesis of para-aminobenzoic acid (pABA) in Escherichia coli. Optimizing initial glucose/xylose concentrations and eliminating carbon leakage resulted in a pABA titer of 8.22 g/L (yield: 0.23 g/g glucose). This strategy was then applied to the biosynthesis of 4APhe, a compound synthesized from chorismate without pyruvate (PYR) release. Utilizing glucose and xylose as co-substrates resulted in the production of 4.90 g/L 4APhe. Although 4APhe production did not benefit from PYR-driven energy generation as pABA production did, high titer was still achieved. This study highlights the effectiveness of modular metabolic pathway division for enhancing the production of key aromatic compounds and provides valuable insight into microbial production of chemicals that require specific biosynthetic donors such as amino groups. IMPORTANCE Microbial biosynthesis of chemicals from renewable resources offers a sustainable alternative to fossil fuel-based production. However, inefficiencies due to substrate diversion into by-products and biomass hinder optimal yields. In this study, we employed a modular metabolic engineering approach, decoupling pathways for chemical production from cell growth. Using glucose and xylose as co-substrates, we achieved the enhancement of p-aminobenzoic acid production in Escherichia coli. Additionally, we demonstrated the versatility of this approach by applying it to the biosynthesis of 4-amino-phenylalanine production. This study highlights the potential of modular metabolic pathway division for increased production of target compounds and provides valuable insight into microbial production of chemicals that require specific biosynthetic donors such as amino groups.
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Affiliation(s)
- Daisuke Nonaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Mayumi Kishida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Ayana Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Shuhei Noda
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
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3
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Yang Y, He H, Liu B, Li Z, Sun J, Zhao Z, Yang Y. Protein lysine acetylation regulates oral microorganisms. Front Cell Infect Microbiol 2025; 15:1594947. [PMID: 40444154 PMCID: PMC12119520 DOI: 10.3389/fcimb.2025.1594947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Accepted: 04/28/2025] [Indexed: 06/02/2025] Open
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, stability, and cellular processes. Lysine acetylation, a widespread PTM, has been extensively characterized for its role in eukaryotic cellular functions, particularly in metabolism, gene expression, and disease progression. However, its involvement in oral microbiota remains inadequately explored. This review examines the emerging significance of lysine acetylation in modulating oral microbial communities. The oral cavity, characterized by its unique anatomical and environmental conditions, serves as a dynamic habitat where microbiota interact with host factors such as diet, immune response, pH, and the level of oxygen. Lysine acetylation enables bacterial adaptation to these fluctuating conditions, influencing microbial metabolism, virulence, and stress responses. For example, acetylation of lactate dehydrogenase in Streptococcus mutans reduces its acidogenicity and aciduricity, which decreases its cariogenic potential. In diverse environmental conditions, including hypoxic or anaerobic environments, acetylation regulates energy utilization pathways and enzyme activities, supporting bacterial survival and adaptation. Additionally, acetylation controls the production of extracellular polysaccharides (EPS), which are essential for biofilm formation and bacterial colonization. The acetylation of virulence factors can modulate the pathogenic potential of oral bacteria, either enhancing or inhibiting their activity depending on the specific context and regulatory mechanisms involved. This review also explores the interactions between acetylation and other PTMs, highlighting their synergistic or antagonistic effects on protein function. A deeper understanding of lysine acetylation mechanisms in oral microbiota could provide valuable insights into microbial adaptation and pathogenesis, revealing potential therapeutic targets for oral diseases.
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Affiliation(s)
- Yuanchao Yang
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
- Hunan Key Laboratory of Oral Health Research, Central South University, Changsha, China
| | - Hailun He
- School of Life Sciences, Central South University, Changsha, China
| | - Bingshi Liu
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
- Hunan Key Laboratory of Oral Health Research, Central South University, Changsha, China
| | - Zhuoyue Li
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
- Hunan Key Laboratory of Oral Health Research, Central South University, Changsha, China
| | - Jiaman Sun
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
- Hunan Key Laboratory of Oral Health Research, Central South University, Changsha, China
| | - Zhili Zhao
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yan Yang
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
- Hunan Key Laboratory of Oral Health Research, Central South University, Changsha, China
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Zhang L, Shi H, Liu Z, Gu J, Deng J. Intracellular acetyl phosphate modulates Escherichia coli pyruvate metabolism. Acta Biochim Biophys Sin (Shanghai) 2025. [PMID: 40370194 DOI: 10.3724/abbs.2025068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2025] Open
Abstract
Lysine acetylation has been shown to be an abundant and vital post-translational modification (PTM) that utilizes acetyl phosphate (AcP) as one of the acetyl group donors in bacteria. The pyruvate dehydrogenase (PDH) complex catalyzes the conversion from pyruvate to acetyl coenzyme A (acetyl-CoA). Thus far, the connection between lysine acetylation and pyruvate metabolism has not been thoroughly investigated. In this study, we show that AcP could acetylate Escherichia coli pyruvate dehydrogenase (AceE) in vitro and in vivo, which could be reversed by protein lysine deacetylase (CobB). In vitro treatment of AceE with AcP also causes increased phosphorylation of the protein, whereas deleting ackA does not affect the phosphorylation of the protein. As a result, in vitro treatment of AceE by AcP leads to decreased enzymatic activity. In contrast, deleting ackA leads to increased acetylation and enzymatic activity of AceE, and deleting pta results in the decreased acetylation and enzymatic activity of AceE. As expected, deleting pta in E. coli causes pyruvate accumulation. Although deleting ackA also causes pyruvate accumulation, decreased expression of the two genes involved in pyruvate metabolism ( ldhA and poxB) is observed in the mutant, indicating that AcP could affect pyruvate metabolism by other routes in addition to modulating the AceE activity. Thus, our results demonstrate that intracellular AcP could modulate pyruvate metabolism in E. coli. For the first time, a linkage between AcP-mediated protein lysine acetylation, pyruvate dehydrogenase activity, and pyruvate metabolism is established.
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Affiliation(s)
- Ling Zhang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongmei Shi
- Institute of Agricultural Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Zixiang Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Gu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiaoyu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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5
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Li X, Fatema N, Gan Q, Fan C. Functional consequences of lysine acetylation of phosphofructokinase isozymes. FEBS J 2025; 292:2545-2558. [PMID: 39940094 PMCID: PMC12103067 DOI: 10.1111/febs.70014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/06/2024] [Accepted: 01/31/2025] [Indexed: 02/14/2025]
Abstract
Phosphofructokinase (Pfk) catalyzes the phosphorylation of fructose 6-phosphate and is a key regulatory point in the glycolysis pathway. Multiple lysine residues in both Pfk isozymes, PfkA and PfkB, have been identified to be acetylated in Escherichia coli by proteomic studies, but no studies have been implemented to further characterize these acetylation events. To investigate the role of Pfk acetylation, the genetic code expansion strategy was used to generate homogeneously acetylated Pfk variants at target lysine sites that have been reported to be acetylated in nature. We found that acetylation of K309 of PfkA and K27 of PfkB decreased PfK enzyme activities significantly. We further investigated the deacetylation and acetylation processes of Pfk isozymes biochemically and genetically. Acetyl phosphate-mediated non-enzymatic acetylation could be the major mechanism of Pfk isozyme acetylation in E. coli, whereas NAD-dependent protein deacylase CobB can remove most of the acetylated lysine residues but not K309 of PfkA and K27 of PfkB, which affect enzyme activities. Because of the important role of Pfk in cellular metabolism, the results of the present study are expected to facilitate studies in the fields of metabolic engineering and research.
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Affiliation(s)
- Xinyu Li
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
| | - Nour Fatema
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
| | - Qinglei Gan
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleARUSA
| | - Chenguang Fan
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleARUSA
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Calles B, Pitarch B, de Lorenzo V. The Structural Permissiveness of Triosephosphate Isomerase (TpiA) of Escherichia coli. Chembiochem 2025; 26:e202400863. [PMID: 39591528 DOI: 10.1002/cbic.202400863] [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: 10/19/2024] [Revised: 11/24/2024] [Accepted: 11/26/2024] [Indexed: 11/28/2024]
Abstract
Triosephosphate isomerase (TpiA) is widely regarded as an example of an optimally evolved enzyme due to its essential role in biological systems, its structural conservation, and its near-perfect kinetic parameters. In this study, we investigated the structural robustness of the archetypal TpiA variant from Escherichia coli using an in vitro 5-amino acid linker scanning method. The resulting library was introduced into a tpiA mutant strain for functional complementation. From this library, 16 TpiA variants that were phenotypically indistinguishable from the wild-type enzyme were selected for further analysis. Although all variants retained enzymatic activities within the wild-type range, several insertions were found in highly structured protein domains where the linker was expected to cause significant structural perturbations. Despite these potentially disruptive additions, the enzymes maintained their activity even when expressed in a dnaK mutant, suggesting that chaperones did not compensate for structural abnormalities in vivo. Additionally, when these mutant TpiA variants were produced using an in vitro transcription/translation system, they exhibited enzymatic activity comparable to, and in some cases exceeding, that of the non-mutated enzyme. AlphaFold2 exposed that insertions reconstructed the local architecture of the nearby amino acid sequences. The evolutionary implications of this remarkable structural resilience are discussed.
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Affiliation(s)
- Belén Calles
- Systems Biology Department, National Center of Biotechnology CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Borja Pitarch
- Systems Biology Department, National Center of Biotechnology CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, National Center of Biotechnology CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
- Correspondence to National Center of Biotechnology CSIC, Calle Darwin 3, Madrid, 28049, Spain
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7
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Roussou S, Pan M, Krömer JO, Lindblad P. Exploring and increased acetate biosynthesis in Synechocystis PCC 6803 through insertion of a heterologous phosphoketolase and overexpressing phosphotransacetylase. Metab Eng 2025; 88:250-260. [PMID: 39863056 DOI: 10.1016/j.ymben.2025.01.008] [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] [Received: 10/18/2024] [Revised: 01/14/2025] [Accepted: 01/21/2025] [Indexed: 01/27/2025]
Abstract
Acetate is a biological anion with many applications in the chemical and food industries. In addition to being a common microbial fermentative end-product, acetate can be produced by photosynthetic cyanobacteria from CO2 using solar energy. Using wild-type cells of the unicellular model cyanobacterium Synechocystis PCC 6803 only low levels of acetate are observed outside the cells. By inserting a heterologous phosphoketolase (PKPa) in the acs locus, encoding acetyl-CoA synthetase responsible for the irreversible conversion of acetate to acetyl-CoA, an increased level of 40 times was observed. Metabolite analyses indicate an enhanced Calvin-Benson-Bassham cycle, based on increased levels of glyceraldehyde 3-phosphate and fructose-1,6-biphosphate, while the decreased levels of 3-phosphoglycerate and pyruvate suggest a quick consumption of the fixed carbon. Acetyl-P and erythrose-4-phosphate showed significantly increased levels, as products of phosphoketolase, while acetyl-CoA remained stable through the experiment. The results of intra- and extra-cellular acetate levels clearly demonstrate an efficient excretion of produced acetate from the cells in the engineered strain. Knock-out of ach and pta showed a reduction in acetate production however, it was not as low as in cells with a single knock-out of ach. Overexpressing acetyl-CoA hydrolase (Ach) and acetate kinase (AckA) did not significantly increase production. In contrast, overexpressing phosphotransacetylase (Pta) in cells containing an inserted PKPa resulted in 80 times more acetate reaching 2.3 g/L after 14 days of cultivation.
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Affiliation(s)
- Stamatina Roussou
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Minmin Pan
- Systems Biotechnology, Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Jens O Krömer
- Systems Biotechnology, Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden.
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Derksen VFAM, Martinsson K, van Mourik AG, Wagenaar CA, Toes REM, Walrabenstein W, Sjöberg D, van Schaardenburg D, Huizinga TWJ, Kastbom A, Svärd A, van der Woude D. Evidence of Site-Specific Mucosal Autoantibody Secretion in Rheumatoid Arthritis. Arthritis Rheumatol 2025; 77:272-282. [PMID: 39420623 PMCID: PMC11865693 DOI: 10.1002/art.43036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 08/03/2024] [Accepted: 09/17/2024] [Indexed: 10/19/2024]
Abstract
OBJECTIVE Anti-citrullinated protein antibodies (ACPA) have been detected in sputum and saliva, indicating that anti-modified protein antibodies (AMPA) can be produced at mucosal sites in patients with rheumatoid arthritis (RA). However, the body's largest mucosal compartment, the gut, has not yet been examined. We therefore investigated the presence of several AMPA (ACPA, anti-carbamylated protein antibodies [anti-CarP], and anti-acetylated protein antibodies [AAPA]) at different mucosal sites, including the intestinal tract. METHODS Paired fecal/ileal wash, saliva, and serum samples of patients with RA and healthy volunteers were collected in two independent cohorts. Data involving feces were replicated in a third cohort. In these secretions, AMPA were analyzed using in-house enzyme-linked immunosorbent assay with unmodified peptides as control. In fecal samples, total IgA and anti-Escherichia coli IgA were measured. RESULTS ACPA, anti-CarP, and AAPA IgA were measurable in saliva of seropositive patients with RA (prevalence 9%-40%). No AMPA could be detected in feces. IgA was present because total IgA and anti-E. coli IgA were detectable in feces of ACPA-positive patients with RA and healthy donors. Results were confirmed in another cohort using colonoscopically collected ileal wash samples. CONCLUSION Our study shows the presence of ACPA, anti-CarP, and AAPA IgA in saliva of ACPA-seropositive patients with RA. However, no AMPA could be detected in feces/ileal wash samples of these patients, although our assays were able to measure other antigen-specific antibodies. These data suggest that mucosal autoantibody secretion may occur in the oral mucosa of patients with RA, whereas no evidence could be found for this process in the lower gastrointestinal tract.
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Affiliation(s)
| | | | | | | | | | | | - Daniel Sjöberg
- Uppsala University, Uppsala, Sweden, and Falun HospitalFalunSweden
| | | | | | | | - Anna Svärd
- Linköping University, Linköping, Sweden, and Uppsala UniversityUppsalaSweden
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Wang Y, Wang G, Zhang L, Cai Q, Lin M, Huang D, Xie Y, Lin W, Lin X. Aeromonas hydrophila CobQ is a new type of NAD +- and Zn 2+-independent protein lysine deacetylase. eLife 2025; 13:RP97511. [PMID: 39998869 PMCID: PMC11856932 DOI: 10.7554/elife.97511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2025] Open
Abstract
Protein NƐ-lysine acetylation (Kac) modifications play crucial roles in diverse physiological and pathological functions in cells. In prokaryotic cells, there are only two types of lysine deacetylases (KDACs) that are Zn2+- or NAD+-dependent. In this study, we reported a protein, AhCobQ, in Aeromonas hydrophila ATCC 7966 that presents NAD+- and Zn2+-independent KDAC activity. Furthermore, its KDAC activity is located in an unidentified domain (from 195 to 245 aa). Interestingly, AhCobQ has no homology with current known KDACs, and no homologous protein was found in eukaryotic cells. A protein substrate analysis showed that AhCobQ has specific protein substrates in common with other known KDACs, indicating that these KDACs can dynamically co-regulate the states of Kac proteins. Microbiological methods employed in this study affirmed AhCobQ's positive regulation of isocitrate dehydrogenase (ICD) enzymatic activity at the K388 site, implicating AhCobQ in the modulation of bacterial enzymatic activities. In summary, our findings present compelling evidence that AhCobQ represents a distinctive type of KDAC with significant roles in bacterial biological functions.
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Affiliation(s)
- Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Agricultural College, Anhui Science and Technology UniversityChuzhouChina
| | - Guibin Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingChina
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Qilan Cai
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Meizhen Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Dongping Huang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Yuyue Xie
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety MonitoringFuzhouChina
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province UniversityFuzhouChina
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry UniversityFuzhouChina
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10
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Lin TH, Wang CY, Wu CC, Lin CT. Impacts of Pta-AckA pathway on CPS biosynthesis and type 3 fimbriae expression in Klebsiella pneumoniae. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2025; 58:48-55. [PMID: 39472242 DOI: 10.1016/j.jmii.2024.10.002] [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: 04/22/2024] [Revised: 09/18/2024] [Accepted: 10/20/2024] [Indexed: 02/08/2025]
Abstract
BACKGROUND Klebsiella pneumoniae is a Gram-negative bacterium that can cause infections, especially in individuals with diabetes. Recently, more hypervirulent strains have emerged, posing a threat even to healthy individuals. Understanding how K. pneumoniae regulates its virulence factors is crucial. Acetyl-phosphate (AcP) is essential for bacterial metabolism and can affect virulence factor expression. However, the role of the Pta-AckA pathway, which regulates AcP levels, in K. pneumoniae pathogenesis remains unclear. METHODS Deletion mutants lacking the pta and ackA, involved in AcP production and hydrolysis, were generated in K. pneumoniae CG43S3. Their effects on AcP levels, the patterns of global acetylated protein, capsular polysaccharide (CPS) amount, serum resistance, type 3 fimbriae expression, biofilm formation, and virulence in G. mellonella larva were assessed. RESULTS Deletion of ackA in K. pneumoniae CG43S3 led to AcP accumulation, while pta deletion abolished AcP synthesis when grown in TB7+1 % glucose. This pathway influenced global protein acetylation, with pta deletion decreasing acetylation and ackA deletion increasing it. Additionally, pta deletion decreased the CPS amount, serum resistance, and type 3 fimbriae expression, while ackA deletion increased these factors. Furthermore, deleting pta and ackA attenuated the infected larva's virulence and death rate. CONCLUSION Our findings highlight the critical role of the Pta-AckA pathway in K. pneumoniae pathogenesis. This pathway regulates AcP levels, global protein acetylation, CPS production, serum resistance, and type 3 fimbriae expression, ultimately impacting virulence. The information provides insights into potential therapeutic targets for combating K. pneumoniae infection.
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Affiliation(s)
- Tien-Huang Lin
- Department of Urology, Taichung Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan; School of Post-Baccalaureate Chinese Medicine, Tzu Chi University, Hualien, Taiwan.
| | - Chen-Yu Wang
- Graduate Institute of Chinese Medicine, School of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Chinese Medicine, China Medical University Hsinchu Hospital, Hsinchu, Taiwan.
| | - Chien-Chen Wu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Ching-Ting Lin
- Graduate Institute of Chinese Medicine, School of Chinese Medicine, China Medical University, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan.
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11
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Fei P, Zhang W, Shang Y, Hu P, Gu Y, Luo Y, Wu H. Carbon-negative bio-production of short-chain carboxylic acids (SCCAs) from syngas via the sequential two-stage bioprocess by Moorella thermoacetica and metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2025; 416:131714. [PMID: 39490540 DOI: 10.1016/j.biortech.2024.131714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 10/14/2024] [Accepted: 10/25/2024] [Indexed: 11/05/2024]
Abstract
Syngas can be efficiently converted to acetate by Moorella thermoacetica under anaerobic conditions, which is environmentally friendly. Coupled with acetate production from syngas, using acetate to synthesize value-added compounds such as short-chain carboxylic acids (SCCAs) becomes a negative-carbon process. Escherichia coli is engineered to utilize acetate as the sole carbon source to produce SCCAs. By knocking out some acetyltransferase genes, introducing exogenous pathway and additional cofactor engineering, the strains can synthesize 3.79 g/L of 3-hydroxypropionic acid (3-HP), 1.83 g/L of (R)-3-hydroxybutyric acid (R-3HB), and 2.31 g/L of butyrate. We used M. thermoacetica to produce acetate from syngas. Subsequently, all engineered E. coli strains were able to produce SCCAs from syngas-derived acetate. The titers of 3-HP, R-3HB, and butyrate are 3.75, 1.68, and 2.04 g/L, with carbon sequestration rates of 51.1, 26.3, and 38.1 %. This coupled bioprocess has great potential for producing a range of other value-added chemicals from syngas.
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Affiliation(s)
- Peng Fei
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Wenrui Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yanzhe Shang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Peng Hu
- Shanghai GTLB Biotech Co., Ltd, 1688 North Guoguan Road, Shanghai 200438, China
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China.
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12
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Sieber A, Parr M, von Ehr J, Dhamotharan K, Kielkowski P, Brewer T, Schäpers A, Krafczyk R, Qi F, Schlundt A, Frishman D, Lassak J. EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences. Nat Commun 2024; 15:10465. [PMID: 39622818 PMCID: PMC11611912 DOI: 10.1038/s41467-024-54556-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 11/13/2024] [Indexed: 12/06/2024] Open
Abstract
Polyproline sequences are deleterious to cells because they stall ribosomes. In bacteria, EF-P plays an important role in overcoming such polyproline sequence-induced ribosome stalling. Additionally, numerous bacteria possess an EF-P paralog called EfpL (also known as YeiP) of unknown function. Here, we functionally and structurally characterize EfpL from Escherichia coli and demonstrate its role in the translational stress response. Through ribosome profiling, we analyze the EfpL arrest motif spectrum and find additional sequences beyond the canonical polyproline motifs that both EF-P and EfpL can resolve. Notably, the two factors can also induce pauses. We further report that EfpL can sense the metabolic state of the cell via lysine acylation. Overall, our work characterizes the role of EfpL in ribosome rescue at proline-containing sequences, and provides evidence that co-occurrence of EF-P and EfpL is an evolutionary driver for higher bacterial growth rates.
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Affiliation(s)
- Alina Sieber
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Julian von Ehr
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
- IMPRS on Cellular Biophysics, Frankfurt, Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Institut für Chemische Epigenetik (ICEM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tess Brewer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Anna Schäpers
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ralph Krafczyk
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Fei Qi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jürgen Lassak
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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13
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Birhanu AG, Riaz T, Støen M, Tønjum T. Differential Abundance of Protein Acylation in Mycobacterium tuberculosis Under Exposure to Nitrosative Stress. Proteomics Clin Appl 2024; 18:e202300212. [PMID: 39082596 DOI: 10.1002/prca.202300212] [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: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 11/15/2024]
Abstract
BACKGROUND Human macrophages generate antimicrobial reactive nitrogen species in response to infection by Mycobacterium tuberculosis (Mtb). Exposure to these redox-reactive compounds induces stress response in Mtb, which can affect posttranslational modifications (PTM). METHODS Here, we present the global analysis of the PTM acylation of Mtb proteins in response to a sublethal dose of nitrosative stress in the form of nitric oxide (NO) using label free quantification. RESULTS A total of 6437 acylation events were identified on 1496 Mtb proteins, and O-acylation accounted for 92.2% of the events identified, while 7.8% were N-acylation events. About 22% of the sites identified were found to be acylated by more than one acyl-group. Furthermore, the abundance of each acyl-group decreased as their molecular weight increased. Quantitative PTM analysis revealed differential abundance of acylation in proteins involved in stress response, iron ion homeostasis, growth, energy metabolism, and antimicrobial resistance (AMR) induced by nitrosative stress over time. CONCLUSIONS The results reveal a potential role of Mtb protein acylation in the bacterial stress responses and AMR. To our knowledge, this is the first report on global O-acylation profile of Mtb in response to NO. This will significantly improve our understanding of the changes in Mtb acylation under nitrosative stress, highly relevant for global health.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbiology, University of Oslo, Nydalen, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Nydalen, Oslo, Norway
| | - Mari Støen
- Department of Microbiology, Oslo University Hospital, Nydalen, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Nydalen, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Nydalen, Oslo, Norway
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14
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Duchovni L, Shmunis G, Lobel L. Posttranslational modifications: an emerging functional layer of diet-host-microbe interactions. mBio 2024; 15:e0238724. [PMID: 39254316 PMCID: PMC11481575 DOI: 10.1128/mbio.02387-24] [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: 09/11/2024] Open
Abstract
The microbiome plays a vital role in human health, with changes in its composition impacting various aspects of the body. Posttranslational modification (PTM) regulates protein activity by attaching chemical groups to amino acids in an enzymatic or non-enzymatic manner. PTMs offer fast and dynamic regulation of protein expression and can be influenced by specific dietary components that induce PTM events in gut microbiomes and their hosts. PTMs on microbiome proteins have been found to contribute to host-microbe interactions. For example, in Escherichia coli, S-sulfhydration of tryptophanase regulates uremic toxin production and chronic kidney disease in mice. On a broader microbial scale, the microbiomes of patients with inflammatory bowel disease exhibit distinct PTM patterns in their metaproteomes. Moreover, pathogens and commensals can alter host PTM profiles through protein secretion and diet-regulated metabolic shifts. The emerging field of metaPTMomics focuses on understanding PTM profiles in the microbiota, their association with lifestyle factors like diet, and their functional effects on host-microbe interactions.
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Affiliation(s)
- Lirit Duchovni
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Genrieta Shmunis
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Lior Lobel
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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15
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Kuhn ML, Rakus JF, Quenet D. Acetylation, ADP-ribosylation and methylation of malate dehydrogenase. Essays Biochem 2024; 68:199-212. [PMID: 38994669 PMCID: PMC11451102 DOI: 10.1042/ebc20230080] [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: 03/18/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024]
Abstract
Metabolism within an organism is regulated by various processes, including post-translational modifications (PTMs). These types of chemical modifications alter the molecular, biochemical, and cellular properties of proteins and allow the organism to respond quickly to different environments, energy states, and stresses. Malate dehydrogenase (MDH) is a metabolic enzyme that is conserved in all domains of life and is extensively modified post-translationally. Due to the central role of MDH, its modification can alter metabolic flux, including the Krebs cycle, glycolysis, and lipid and amino acid metabolism. Despite the importance of both MDH and its extensively post-translationally modified landscape, comprehensive characterization of MDH PTMs, and their effects on MDH structure, function, and metabolic flux remains underexplored. Here, we review three types of MDH PTMs - acetylation, ADP-ribosylation, and methylation - and explore what is known in the literature and how these PTMs potentially affect the 3D structure, enzymatic activity, and interactome of MDH. Finally, we briefly discuss the potential involvement of PTMs in the dynamics of metabolons that include MDH.
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Affiliation(s)
- Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco
State University, San Francisco, CA, U.S.A
| | - John F. Rakus
- School of Sciences, University of Louisiana at Monroe,
Monroe, LA, U.S.A
| | - Delphine Quenet
- Department of Biochemistry, Larner College of Medicine,
University of Vermont, Burlington, VT, U.S.A
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16
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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; 39:334-343. [PMID: 38224336 DOI: 10.1111/omi.12452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [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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17
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Liu T, Zhang M, Fan Y, Zhao L, Huang D, Zhao L, Tan M, Ye BC, Xu JY. Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration. Proteomics 2024; 24:e2300350. [PMID: 38491406 DOI: 10.1002/pmic.202300350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Lysine acylation has been extensively investigated due to its regulatory role in a diverse range of biological functions across prokaryotic and eukaryotic species. In-depth acylomic profiles have the potential to enhance comprehension of the biological implications of organisms. However, the extent of research on global acylation profiles in microorganisms is limited. Here, four lysine acylomes were conducted in Bacillus thuringiensis by using the LC-MS/MS based proteomics combined with antibody-enrichment strategies, and a total of 3438 acetylated sites, 5797 propionylated sites, 1705 succinylated sites, and 925 malonylated sites were identified. The motif analysis of these modified proteins revealed a high conservation of glutamate in acetylation and propionylation, whereas such conservation was not observed in succinylation and malonylation modifications. Besides, conservation analysis showed that homologous acylated proteins in Bacillus subtilis and Escherichia coli were connected with ribosome and aminoacyl-tRNA biosynthesis. Further biological experiments showed that lysine acylation lowered the RNA binding ability of CodY and impaired the in vivo protein activity of MetK. In conclusion, our study expanded the current understanding of the global acylation in Bacillus, and the comparative analysis demonstrated that shared acylation proteins could play important roles in regulating both metabolism and RNA transcription progression.
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Affiliation(s)
- Tianxian Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingya Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yameng Fan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Lei Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Dan Huang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liuchang Zhao
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Henan University, Kaifeng, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jun-Yu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
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18
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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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19
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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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20
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.565030. [PMID: 37961685 PMCID: PMC10635034 DOI: 10.1101/2023.10.31.565030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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21
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. PLoS Genet 2024; 20:e1011287. [PMID: 38768229 PMCID: PMC11142719 DOI: 10.1371/journal.pgen.1011287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/31/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Affiliation(s)
- Samuel A. Adeleye
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
| | - Srujana S. Yadavalli
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
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22
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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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23
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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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24
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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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25
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Fatema N, Li X, Gan Q, Fan C. Characterizing lysine acetylation of glucokinase. Protein Sci 2024; 33:e4845. [PMID: 37996965 PMCID: PMC10731539 DOI: 10.1002/pro.4845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023]
Abstract
Glucokinase (GK) catalyzes the phosphorylation of glucose to form glucose-6-phosphate as the substrate of glycolysis for energy production. Acetylation of lysine residues in Escherichia coli GK has been identified at multiple sites by a series of proteomic studies, but the impact of acetylation on GK functions remains largely unknown. In this study, we applied the genetic code expansion strategy to produce site-specifically acetylated GK variants which naturally exist in cells. Enzyme assays and kinetic analyses showed that lysine acetylation decreases the GK activity, mostly resulting from acetylation of K214 and K216 at the entrance of the active site, which impairs the binding of substrates. We also compared results obtained from the glutamine substitution method and the genetic acetyllysine incorporation approach, showing that glutamine substitution is not always effective for mimicking acetylated lysine. Further genetic studies as well as in vitro acetylation and deacetylation assays were performed to determine acetylation and deacetylation mechanisms, which showed that E. coli GK could be acetylated by acetyl-phosphate without enzymes and deacetylated by CobB deacetylase.
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Affiliation(s)
- Nour Fatema
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
| | - Xinyu Li
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
| | - Qinglei Gan
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
| | - Chenguang Fan
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
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26
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Dale AL, Man L, Cordwell SJ. Global Acetylomics of Campylobacter jejuni Shows Lysine Acetylation Regulates CadF Adhesin Processing and Human Fibronectin Binding. J Proteome Res 2023; 22:3519-3533. [PMID: 37830485 DOI: 10.1021/acs.jproteome.3c00391] [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: 10/14/2023]
Abstract
Lysine acetylation (KAc) is a reversible post-translational modification (PTM) that can alter protein structure and function; however, specific roles for KAc are largely undefined in bacteria. Acetyl-lysine immunoprecipitation and LC-MS/MS identified 5567 acetylated lysines on 1026 proteins from the gastrointestinal pathogen Campylobacter jejuni (∼63% of the predicted proteome). KAc was identified on proteins from all subcellular locations, including the outer membrane (OM) and extracellular proteins. Label-based LC-MS/MS identified proteins and KAc sites during growth in 0.1% sodium deoxycholate (DOC, a component of gut bile salts). 3410 acetylated peptides were quantified, and 784 (from 409 proteins) were differentially abundant in DOC growth. Changes in KAc involved multiple pathways, suggesting a dynamic role for this PTM in bile resistance. As observed elsewhere, we show KAc is primarily nonenzymatically mediated via acetyl-phosphate; however, the deacetylase CobB also contributes to a global elevation of this modification in DOC. We observed several multiply acetylated OM proteins and altered DOC abundance of acetylated peptides in the fibronectin (Fn)-binding adhesin CadF. We show KAc reduces CadF Fn binding and prevalence of lower mass variants. This study provides the first system-wide lysine acetylome of C. jejuni and contributes to our understanding of KAc as an emerging PTM in bacteria.
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Affiliation(s)
- Ashleigh L Dale
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Lok Man
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- Sydney Mass Spectrometry, The University of Sydney, New South Wales 2006, Australia
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27
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Norris V, Kayser C, Muskhelishvili G, Konto-Ghiorghi Y. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiol Rev 2023; 47:fuac049. [PMID: 36549664 DOI: 10.1093/femsre/fuac049] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.
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Affiliation(s)
- Vic Norris
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Clara Kayser
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - Yoan Konto-Ghiorghi
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
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28
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Sun Y, Zhang Y, Zhao T, Luan Y, Wang Y, Yang C, Shen B, Huang X, Li G, Zhao S, Zhao G, Wang Q. Acetylation coordinates the crosstalk between carbon metabolism and ammonium assimilation in Salmonella enterica. EMBO J 2023; 42:e112333. [PMID: 37183585 PMCID: PMC10308350 DOI: 10.15252/embj.2022112333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/21/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Enteric bacteria use up to 15% of their cellular energy for ammonium assimilation via glutamine synthetase (GS)/glutamate synthase (GOGAT) and glutamate dehydrogenase (GDH) in response to varying ammonium availability. However, the sensory mechanisms for effective and appropriate coordination between carbon metabolism and ammonium assimilation have not been fully elucidated. Here, we report that in Salmonella enterica, carbon metabolism coordinates the activities of GS/GDH via functionally reversible protein lysine acetylation. Glucose promotes Pat acetyltransferase-mediated acetylation and activation of adenylylated GS. Simultaneously, glucose induces GDH acetylation to inactivate the enzyme by impeding its catalytic centre, which is reversed upon GDH deacetylation by deacetylase CobB. Molecular dynamics (MD) simulations indicate that adenylylation is required for acetylation-dependent activation of GS. We show that acetylation and deacetylation occur within minutes of "glucose shock" to promptly adapt to ammonium/carbon variation and finely balance glutamine/glutamate synthesis. Finally, in a mouse infection model, reduced S. enterica growth caused by the expression of adenylylation-mimetic GS is rescued by acetylation-mimicking mutations. Thus, glucose-driven acetylation integrates signals from ammonium assimilation and carbon metabolism to fine-tune bacterial growth control.
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Affiliation(s)
- Yunwei Sun
- Department of Gastroenterology of Ruijin Hospital, Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuebin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Tingting Zhao
- Department of Gastroenterology of Ruijin Hospital, Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yi Luan
- Department of Pharmacology, Vascular Biology and Therapeutic ProgramYale University School of MedicineNew HavenCTUSA
| | - Ying Wang
- Department of Gastroenterology of Ruijin Hospital, Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chen Yang
- CAS‐Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Bo Shen
- Department of Gastroenterology of Ruijin Hospital, Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xi Huang
- Department of Gastroenterology of Ruijin Hospital, Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Shimin Zhao
- State Key Lab of Genetic Engineering & Institutes of Biomedical SciencesFudan UniversityShanghaiChina
- Department of Microbiology and Microbial Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Collaborative Innovation Center for Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Guo‐ping Zhao
- CAS‐Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
- State Key Lab of Genetic Engineering & Institutes of Biomedical SciencesFudan UniversityShanghaiChina
- Department of Microbiology and Microbial Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai‐MOST Key Laboratory of Disease and Health GenomicsChinese National Human Genome Center at ShanghaiShanghaiChina
- Department of Microbiology and Li KaShing Institute of Health SciencesThe Chinese University of Hong Kong, Prince of Wales HospitalShatin, New Territories, Hong Kong SARChina
| | - Qijun Wang
- Department of Gastroenterology of Ruijin Hospital, Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Pharmacology, Vascular Biology and Therapeutic ProgramYale University School of MedicineNew HavenCTUSA
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29
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Hirakawa H, Takita A, Sato Y, Hiramoto S, Hashimoto Y, Ohshima N, Minamishima YA, Murakami M, Tomita H. Inactivation of ackA and pta Genes Reduces GlpT Expression and Susceptibility to Fosfomycin in Escherichia coli. Microbiol Spectr 2023; 11:e0506922. [PMID: 37199605 PMCID: PMC10269713 DOI: 10.1128/spectrum.05069-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/29/2023] [Indexed: 05/19/2023] Open
Abstract
Fosfomycin is used to treat a variety of bacterial infections, including urinary tract infections caused by Escherichia coli. In recent years, quinolone-resistant and extended-spectrum β-lactamase (ESBL)-producing bacteria have been increasing. Because fosfomycin is effective against many of these drug-resistant bacteria, the clinical importance of fosfomycin is increasing. Against this background, information on the mechanisms of resistance and the antimicrobial activity of this drug is desired to enhance the usefulness of fosfomycin therapy. In this study, we aimed to explore novel factors affecting the antimicrobial activity of fosfomycin. Here, we found that ackA and pta contribute to fosfomycin activity against E. coli. ackA and pta mutant E. coli had reduced fosfomycin uptake capacity and became less sensitive to this drug. In addition, ackA and pta mutants had decreased expression of glpT that encodes one of the fosfomycin transporters. Expression of glpT is enhanced by a nucleoid-associated protein, Fis. We found that mutations in ackA and pta also caused a decrease in fis expression. Thus, we interpret the decrease in glpT expression in ackA and pta defective strains to be due to a decrease in Fis levels in these mutants. Furthermore, ackA and pta are conserved in multidrug-resistant E. coli isolated from patients with pyelonephritis and enterohemorrhagic E. coli, and deletion of ackA and pta from these strains resulted in decreased susceptibility to fosfomycin. These results suggest that ackA and pta in E. coli contribute to fosfomycin activity and that mutation of these genes may pose a risk of reducing the effect of fosfomycin. IMPORTANCE The spread of drug-resistant bacteria is a major threat in the field of medicine. Although fosfomycin is an old type of antimicrobial agent, it has recently come back into the limelight because of its effectiveness against many drug-resistant bacteria, including quinolone-resistant and ESBL-producing bacteria. Since fosfomycin is taken up into the bacteria by GlpT and UhpT transporters, its antimicrobial activity fluctuates with changes in GlpT and UhpT function and expression. In this study, we found that inactivation of the ackA and pta genes responsible for the acetic acid metabolism system reduced GlpT expression and fosfomycin activity. In other words, this study shows a new genetic mutation that leads to fosfomycin resistance in bacteria. The results of this study will lead to further understanding of the mechanism of fosfomycin resistance and the creation of new ideas to enhance fosfomycin therapy.
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Affiliation(s)
- Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ayako Takita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yumika Sato
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Suguru Hiramoto
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Noriyasu Ohshima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yoji A. Minamishima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Masami Murakami
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
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30
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Fatema N, Fan C. Studying lysine acetylation of citric acid cycle enzymes by genetic code expansion. Mol Microbiol 2023; 119:551-559. [PMID: 36890576 PMCID: PMC10636775 DOI: 10.1111/mmi.15052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Lysine acetylation is one of the most abundant post-translational modifications in nature, affecting many key biological pathways in both prokaryotes and eukaryotes. It has not been long since technological advances led to understanding of the roles of acetylation in biological processes. Most of those studies were based on proteomic analyses, which have identified thousands of acetylation sites in a wide range of proteins. However, the specific role of individual acetylation event remains largely unclear, mostly due to the existence of multiple acetylation and dynamic changes of acetylation levels. To solve these problems, the genetic code expansion technique has been applied in protein acetylation studies, facilitating the incorporation of acetyllysine into a specific lysine position to generate a site-specifically acetylated protein. By this method, the effects of acetylation at a specific lysine residue can be characterized with minimal interferences. Here, we summarized the development of the genetic code expansion technique for lysine acetylation and recent studies on lysine acetylation of citrate acid cycle enzymes in bacteria by this approach, providing a practical application of the genetic code expansion technique in protein acetylation studies.
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Affiliation(s)
- Nour Fatema
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
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31
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Acetylation of Cyclic AMP Receptor Protein by Acetyl Phosphate Modulates Mycobacterial Virulence. Microbiol Spectr 2023; 11:e0400222. [PMID: 36700638 PMCID: PMC9927398 DOI: 10.1128/spectrum.04002-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The success of Mycobacterium tuberculosis (Mtb) as a pathogen is partly attributed to its ability to sense and respond to dynamic host microenvironments. The cyclic AMP (cAMP) receptor protein (CRP) is closely related to the pathogenicity of Mtb and plays an important role in this process. However, the molecular mechanisms guiding the autoregulation and downstream target genes of CRP while Mtb responds to its environment are not fully understood. Here, it is demonstrated that the acetylation of conserved lysine 193 (K193) within the C-terminal DNA-binding domain of CRP reduces its DNA-binding ability and inhibits transcriptional activity. The reversible acetylation status of CRP K193 was shown to significantly affect mycobacterial growth phenotype, alter the stress response, and regulate the expression of biologically relevant genes using a CRP K193 site-specific mutation. Notably, the acetylation level of K193 decreases under CRP-activating conditions, including the presence of cAMP, low pH, high temperature, and oxidative stress, suggesting that microenvironmental signals can directly regulate CRP K193 acetylation. Both cell- and murine-based infection assays confirmed that CRP K193 is critical to the regulation of Mtb virulence. Furthermore, the acetylation of CRP K193 was shown to be dependent on the intracellular metabolic intermediate acetyl phosphate (AcP), and deacetylation was mediated by NAD+-dependent deacetylases. These findings indicate that AcP-mediated acetylation of CRP K193 decreases CRP activity and negatively regulates the pathogenicity of Mtb. We believe that the underlying mechanisms of cross talk between transcription, posttranslational modifications, and metabolites are a common regulatory mechanism for pathogenic bacteria. IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, and the ability of Mtb to survive harsh host conditions has been the subject of intensive research. As a result, we explored the molecular mechanisms guiding downstream target genes of CRP when Mtb responds to its environment. Our study makes a contribution to the literature because we describe the role of acetylated K193 in regulating its binding affinity to target DNA and influencing the virulence of mycobacteria. We discovered that mycobacteria can regulate their pathogenicity through the reversible acetylation of CRP K193 and that this reversible acetylation is mediated by AcP and a NAD+-dependent deacetylase. The regulation of CRPMtb by posttranslational modifications, at the transcriptional level, and by metabolic intermediates contribute to a better understanding of its role in the survival and pathogenicity of mycobacteria.
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Bons J, Rose J, Zhang R, Burton JB, Carrico C, Verdin E, Schilling B. In-depth analysis of the Sirtuin 5-regulated mouse brain malonylome and succinylome using library-free data-independent acquisitions. Proteomics 2023; 23:e2100371. [PMID: 36479818 PMCID: PMC10363399 DOI: 10.1002/pmic.202100371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through the combined effects of multiple PTMs. Lysine residues are targeted for various PTMs, including malonylation and succinylation. However, PTMs offer specific challenges to mass spectrometry-based proteomics during data acquisition and processing. Thus, novel and innovative workflows using data-independent acquisition (DIA) ensure confident PTM identification, precise site localization, and accurate and robust label-free quantification. In this study, we present a powerful approach that combines antibody-based enrichment with comprehensive DIA acquisitions and spectral library-free data processing using directDIA (Spectronaut). Identical DIA data can be used to generate spectral libraries and comprehensively identify and quantify PTMs, reducing the amount of enriched sample and acquisition time needed, while offering a fully automated workflow. We analyzed brains from wild-type and Sirtuin 5 (SIRT5)-knock-out mice, and discovered and quantified 466 malonylated and 2211 succinylated peptides. SIRT5 regulation remodeled the acylomes by targeting 164 malonylated and 578 succinylated sites. Affected pathways included carbohydrate and lipid metabolisms, synaptic vesicle cycle, and neurodegenerative diseases. We found 48 common SIRT5-regulated malonylation and succinylation sites, suggesting potential PTM crosstalk. This innovative and efficient workflow offers deeper insights into the mouse brain lysine malonylome and succinylome.
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Affiliation(s)
- Joanna Bons
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, California, USA
| | - Ran Zhang
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jordan B Burton
- Buck Institute for Research on Aging, Novato, California, USA
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, USA
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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: 9] [Impact Index Per Article: 4.5] [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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Abstract
Antibiotic resistance is increasingly becoming a challenge to public health. The regulation of bacterial metabolism by post-translational modifications (PTMs) has been widely studied. However, the mechanism underlying the regulation of acetylation in bacterial resistance to antibiotics is still unknown. Here, we performed a quantitative analysis of the acetylated proteome of a wild-type (WT) Escherichia coli (E. coli) sensitive strain and ampicillin- (Re-Amp), kanamycin- (Re-Kan), and polymyxin B-resistant (Re-Pol) strains. Based on bioinformatics analysis combined with biochemical validations, we found a common regulatory mechanism between the different resistant strains. Our results showed that protein acetylation negatively regulates bacterial metabolism to regulate antibiotic resistance and positively regulates bacterial motility. Further analyses revealed that key enzymes in various metabolic pathways were differentially acetylated. In particular, pyruvate kinase (PykF), a glycolytic enzyme that regulates bacterial metabolism, and its acetylated form were highly expressed in the three resistant strains and were identified as reversibly acetylated by the deacetylase CobB and the acetyl-transferase PatZ (peptidyl-lysine N-acetyltransferase). Results showed that PykF also could be acetylated by nonenzymatic acetyl phosphatase (AcP) in vitro. Furthermore, the deacetylation of Lys413 in PykF increased PykF enzymatic activity by changing the conformation of its ATP binding site, resulting in an increase in energy production which, in turn, increased the sensitivity of drug-resistant strains to antibiotics. This study provides novel insights for understanding bacterial resistance and lays the foundation for future research on the regulation of acetylation in antibiotic-resistant strains. IMPORTANCE The misuse of antibiotics has resulted in the emergence of many antibiotic-resistant strains which seriously threaten human health. Protein post-translational modifications, especially acetylation, tightly control bacterial metabolism. However, the comprehensive mechanism underlying the regulation of acetylation in bacterial resistance remains unexplored. Here, acetylation was found to positively regulate bacterial motility and negatively regulate energy metabolism, which was common in all antibiotic-resistant strains. Moreover, the acetylation and deacetylation process of PykF was uncovered, and deacetylation of the Lys 413 in PykF was found to contribute to bacterial sensitivity to antibiotics. This study provides a new direction for research on the development of bacterial resistance through post-translational modifications and a theoretical basis for developing antibacterial drugs.
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Chan CCY, Lewis IA. Role of metabolism in uropathogenic Escherichia coli. Trends Microbiol 2022; 30:1174-1204. [PMID: 35941063 DOI: 10.1016/j.tim.2022.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) is responsible for more than 75% of urinary tract infections (UTIs) and has been studied extensively to better understand the molecular underpinnings of infection and pathogenesis. Although the macromolecular adaptations UPEC employs - including the expression of virulence factors, adhesion molecules, and iron-acquisition systems - are well described, the role that metabolism plays in enabling infection is still unclear. However, a growing body of literature shows that metabolic function can have a profound impact on which strains can colonize the urinary tract. The goal of this review is to critically appraise this emerging body of literature to better understand the role that nutritional selection plays in enabling urinary tract colonization and the progression of UTIs.
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Affiliation(s)
- Carly C Y Chan
- Department of Biological Science, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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Liu M, Huo M, Guo L, Fu Y, Xian M, Qi Q, Liu W, Zhao G. Lysine acetylation decreases enzyme activity and protein level of Escherichia coli lactate dehydrogenase. ENGINEERING MICROBIOLOGY 2022; 2:100045. [PMID: 39628700 PMCID: PMC11611030 DOI: 10.1016/j.engmic.2022.100045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 12/06/2024]
Abstract
Lactate is an important bulk chemical with widespread applications and a major byproduct of other chemicals bioprocess in microbial fermentation. Lactate dehydrogenase A (LdhA) catalyzes the synthesis of lactate from pyruvate. Lysine acetylation is an evolutionarily conserved post-translational modification; however, the mechanisms underlying the regulation of LdhA function by lysine acetylation in Escherichia coli remain poorly understood. Herein, we demonstrate acetylation of E. coli LdhA occurs via enzymatic and non-enzymatic mechanisms. Further, we show carbon source type and concentration affect the lysine acetylation status of LdhA via a non-enzymatic mechanism. Lysine acetylation significantly inhibits the enzymatic activity and protein level of LdhA. The results of the present study demonstrate lysine acetylation of E. coli LdhA is irreversible. Understanding of the effects of lysine acetylation on LdhA function may provide a new perspective for regulating lactate production in microbial synthesis.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Meitong Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wei Liu
- Institute of Corrosion Science and Technology, Guangzhou 510530, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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Acetylation of NarL K188 and K192 is involved in regulating Escherichia coli anaerobic nitrate respiration. Appl Microbiol Biotechnol 2022; 106:7209-7221. [PMID: 36178515 DOI: 10.1007/s00253-022-12185-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 11/02/2022]
Abstract
As a facultative anaerobe, Escherichia coli can activate various respiratory chains during anaerobic growth, among which the mode of anaerobic respiration with nitrate allows good energy conservation. NarL is one of the regulatory proteins in the Nar two-component system that regulates anaerobic respiration in E. coli. Previous studies have shown that NarL activates downstream gene regulation through phosphorylation. However, there are few studies on other protein translational modifications that influence the regulatory function of NarL. Herein, we demonstrate that acetylation modification exists on K188 and K192, the two lysine residues involved in contacting to DNA, and the degree of acetylation has significant effects on DNA-binding abilities, thus affecting the anaerobic growth of E. coli. In addition, NarL is mainly regulated by acetyl phosphate, but not by peptidyl-lysine N-acetyltransferase. These results indicate that non-enzymatic acetylation of NarL by AcP is one of the important mechanisms for the nitrate anaerobic respiratory pathway in response to environmental changes, which extends the idea of the mechanism underlying the response of intestinal flora to changes in the intestinal environment. KEY POINTS: • Acetylation was found in NarL, which was mainly mediated by AcP. • Non-enzymatic acetylation at K188 and K192 affects NarL binding ability. • Acetylation of NarL K188 and K192 regulates anaerobic nitrate growth of E. coli.
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Sun P, Ma Q, Zhang L. Comprehensive acetyl-proteomic analysis of Cytospora mali provides insight into its response to the biocontrol agent Bacillus velezensis L-1. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.999510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytospora mali is an important factor for apple valsa canker, and Bacillus veleznesis L-1 is an effective biocontrol agent against apple valsa canker. Quantitative acetyl-proteomics is known to regulate transcriptional activity in different organisms; limited knowledge is available for acetylation modification in C. mali, and its response to biocontrol agents. In this study, using Tandem Mass tag proteomic strategies, we identified 733 modification sites on 416 proteins in C. mali, functions of these proteins were analyzed using GO enrichment and KEGG pathway. Some lysine acetylated proteins are found to be important to the fungal pathogenicity of C. mali, and also the response of fungi to biostress. B. velezensis L-1 suppressed the C. mali QH2 by causing the energy shortage and reduced virulence. Correspondingly, the C. mali QH2 could alleviate the suppression of biostress by upregulation of autophagy, peroxidase, cytochrome P450, ABC transporter and Heat shock protein 70. In summary, our results provided the first lysine acetylome of C. mali and its response to B. velezensis L-1.
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Kalbas D, Meleshin M, Liebscher S, Zessin M, Melesina J, Schiene-Fischer C, Bülbül EF, Bordusa F, Sippl W, Schutkowski M. Small Changes Make the Difference for SIRT2: Two Different Binding Modes for 3-Arylmercapto-Acylated Lysine Derivatives. Biochemistry 2022; 61:1705-1722. [PMID: 35972884 DOI: 10.1021/acs.biochem.2c00211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sirtuins are protein deacylases regulating metabolism and stress responses and implicated in aging-related diseases. Modulators of the human sirtuins 1-7 are sought as chemical tools and potential therapeutics, for example, for treatment of cancer. We were able to show that 3-aryl-mercapto-succinylated- and 3-benzyl-mercapto-succinylated peptide derivatives yield selective Sirt5 inhibitors with low nM Ki values. Here, we synthesized and characterized 3-aryl-mercapto-butyrylated peptide derivatives as effective and selective sirtuin 2 inhibitors with KD values in the low nanomolar range. According to kinetic measurements and microscale thermophoresis/surface plasmon resonance experiments, the respective inhibitors bind with the 3-aryl-mercapto moiety in the selectivity pocket of Sirtuin 2, inducing a rearrangement of the active site. In contrast, 3-aryl-mercapto-nonalyl or palmitoyl derivatives are characterized by a switch in the binding mode blocking both the hydrophobic channel by the fatty acyl chain and the nicotinamide pocket by the 3-aryl-mercapto moiety.
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Affiliation(s)
- Diana Kalbas
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Marat Meleshin
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Sandra Liebscher
- Department of Natural Product Biochemistry, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Matthes Zessin
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Jelena Melesina
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Emre Fatih Bülbül
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Frank Bordusa
- Department of Natural Product Biochemistry, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Wolfgang Sippl
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
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Liu M, Huo M, Liu C, Guo L, Ding Y, Ma Q, Qi Q, Xian M, Zhao G. Lysine acetylation of Escherichia coli lactate dehydrogenase regulates enzyme activity and lactate synthesis. Front Bioeng Biotechnol 2022; 10:966062. [PMID: 36051589 PMCID: PMC9424733 DOI: 10.3389/fbioe.2022.966062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
As an evolutionarily conserved posttranslational modification, protein lysine acetylation plays important roles in many physiological and metabolic processes. However, there are few reports about the applications of lysine acetylation in metabolic regulations. Lactate is a main byproduct in microbial fermentation, and itself also an important bulk chemical with considerable commercial values in many fields. Lactate dehydrogenase (LdhA) is the key enzyme catalyzing lactate synthesis from pyruvate. Here, we reported that Escherichia coli LdhA can be acetylated and the acetylated lysine sites were identified by mass spectrometry. The effects and regulatory mechanisms of acetylated sites on LdhA activity were characterized. Finally, lysine acetylation was successfully used to regulate the lactate synthesis. LdhA (K9R) mutant overexpressed strain improved the lactate titer and glucose conversion efficiency by 1.74 folds than that of wild-type LdhA overexpressed strain. LdhA (K154Q-K248Q) mutant can inhibit lactate accumulation and improve 3HP production. Our study established a paradigm for lysine acetylation in lactate synthesis regulation and suggested that lysine acetylation may be a promising strategy to improve the target production and conversion efficiency in microbial synthesis. The application of lysine acetylation in regulating lactate synthesis also provides a reference for the treatment of lactate-related diseases.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Meitong Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Changshui Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yamei Ding
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Qingjun Ma
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Mo Xian, ; Guang Zhao,
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Mo Xian, ; Guang Zhao,
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Pat- and Pta-mediated protein acetylation is required for horizontally-acquired virulence gene expression in Salmonella Typhimurium. J Microbiol 2022; 60:823-831. [DOI: 10.1007/s12275-022-2095-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
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Xu Z, Wang L, Wang X, Wan M, Tang M, Ding Y. Characterizing the Effect of the Lysine Deacetylation Modification on Enzyme Activity of Pyruvate Kinase I and Pathogenicity of Vibrio alginolyticus. Front Vet Sci 2022; 9:877067. [PMID: 35795782 PMCID: PMC9252168 DOI: 10.3389/fvets.2022.877067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/28/2022] [Indexed: 01/22/2023] Open
Abstract
Pyruvate kinase I (PykF) is one of the key enzymes of glycolysis and plays a crucial role in bacterial metabolism. Several acetylation sites of Vibrio alginolyticus PykF were reported in previous studies and then 11 sites were first verified in this study, however, the specific roles of PykF acetylation remains unclear. Overlap-PCR and homologous recombination were implied to delete V. alginolyticus pykF gene and constructed complementary strains of site-directed mutagenesis for the further research focus on the deacetylation regulation on PykF. The results showed that the pyruvate kinase activity was sharply suppressed in the deacetylation status of K52, K68, and K317 of PykF, as well as the extracellular protease activity was significantly decreased in the deacetylation status of K52 and K68, but not induced with K317. Moreover, the growth rates of V. alginolyticus were not influenced with these three deacetylation sites. The ΔpykF mutant exhibited a 6-fold reduction in virulence to zebrafish. Site-directed mutations of K52R and K68R also showed reduced virulence while mutations of K317R didn't. The in vitro experiments showed that PykF was acetylated by acetyl phosphate (AcP), with the increase of incubation time by AcP, the acetylation level of PykF increased while the enzyme activity of PykF decreased correspondingly. Besides, PykF was deacetylated by CobB deacetylase and in result that the deacetylation was significantly down-regulated while the pyruvate kinase activity of PykF increased. Moreover, deletion of cobB gene had no significant difference in pyruvate kinase activity. These results confirm that CobB can regulate the acetylation level and pyruvate kinase activity of PykF. In summary, the results of this study provide a theoretical basis for further understanding of the deacetylation modification of PykF. It provides a new idea for the prevention and cure of vibriosis.
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Affiliation(s)
- Zhou Xu
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
- Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, China
| | - Linjing Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
- Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, China
| | - Xudong Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
- Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, China
| | - Mingyue Wan
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
- Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, China
| | - Mei Tang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
- Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, China
| | - Yu Ding
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
- Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, China
- *Correspondence: Yu Ding
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Abstract
Numerous cellular processes are regulated in response to the metabolic state of the cell. One such regulatory mechanism involves lysine acetylation, a covalent modification involving the transfer of an acetyl group from central metabolite acetyl-coenzyme A or acetyl phosphate to a lysine residue in a protein.
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Hsieh ML, Kiel N, Jenkins L, Ng WL, Knipling L, Waters C, Hinton D. The Vibrio cholerae master regulator for the activation of biofilm biogenesis genes, VpsR, senses both cyclic di-GMP and phosphate. Nucleic Acids Res 2022; 50:4484-4499. [PMID: 35438787 PMCID: PMC9071405 DOI: 10.1093/nar/gkac253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 01/07/2023] Open
Abstract
Vibrio cholerae biofilm formation/maintenance is controlled by myriad factors; chief among these are the regulator VpsR and cyclic di-guanosine monophosphate (c-di-GMP). VpsR has strong sequence similarity to enhancer binding proteins (EBPs) that activate RNA polymerase containing sigma factor σ54. However, we have previously shown that transcription from promoters within the biofilm biogenesis/maintenance pathways uses VpsR, c-di-GMP and RNA polymerase containing the primary sigma factor (σ70). Previous work suggested that phosphorylation of VpsR at a highly conserved aspartate, which is phosphorylated in other EBPs, might also contribute to activation. Using the biofilm biogenesis promoter PvpsL, we show that in the presence of c-di-GMP, either wild type or the phospho-mimic VpsR D59E activates PvpsL transcription, while the phospho-defective D59A variant does not. Furthermore, when c-di-GMP levels are low, acetyl phosphate (Ac∼P) is required for significant VpsR activity in vivo and in vitro. Although these findings argue that VpsR phosphorylation is needed for activation, we show that VpsR is not phosphorylated or acetylated by Ac∼P and either sodium phosphate or potassium phosphate, which are not phosphate donors, fully substitutes for Ac∼P. We conclude that VpsR is an unusual regulator that senses phosphate directly, rather than through phosphorylation, to aid in the decision to form/maintain biofilm.
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Affiliation(s)
- Meng-Lun Hsieh
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Niklas Kiel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Lisa M Miller Jenkins
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Leslie Knipling
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher M Waters
- Correspondence may also be addressed to Christopher M. Waters. Tel: +1 517 884 5360; Fax: +1 517 355 6463;
| | - Deborah M Hinton
- To whom correspondence should be addressed. Tel: +1 301 496 9885; Fax: +1 301 402 0053;
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Araujo J, Ottinger S, Venkat S, Gan Q, Fan C. Studying Acetylation of Aconitase Isozymes by Genetic Code Expansion. Front Chem 2022; 10:862483. [PMID: 35402385 PMCID: PMC8987015 DOI: 10.3389/fchem.2022.862483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/08/2022] [Indexed: 11/24/2022] Open
Abstract
Aconitase catalyzes the second reaction of the tricarboxylic acid cycle, the reversible conversion of citrate and isocitrate. Escherichia coli has two isoforms of aconitase, AcnA and AcnB. Acetylomic studies have identified acetylation at multiple lysine sites of both E. coli aconitase isozymes, but the impacts of acetylation on aconitases are unknown. In this study, we applied the genetic code expansion approach to produce 14 site-specifically acetylated aconitase variants. Enzyme assays and kinetic analyses showed that acetylation of AcnA K684 decreased the enzyme activity, while acetylation of AcnB K567 increased the enzyme activity. Further in vitro acetylation and deacetylation assays were performed, which indicated that both aconitase isozymes could be acetylated by acetyl-phosphate chemically, and be deacetylated by the CobB deacetylase at most lysine sites. Through this study, we have demonstrated practical applications of genetic code expansion in acetylation studies.
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Affiliation(s)
- Jessica Araujo
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Sara Ottinger
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Sumana Venkat
- Children’s Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
- *Correspondence: Chenguang Fan,
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Abstract
Neisseria gonorrhoeae is an obligate human pathogen that is the cause of the sexually transmitted disease gonorrhoea. Recently, there has been a surge in gonorrhoea cases that has been exacerbated by the rapid rise in gonococcal multidrug resistance to all useful antimicrobials resulting in this organism becoming a significant public health burden. Therefore, there is a clear and present need to understand the organism's biology through its physiology and pathogenesis to help develop new intervention strategies. The gonococcus initially colonises and adheres to host mucosal surfaces utilising a type IV pilus that helps with microcolony formation. Other adhesion strategies include the porin, PorB, and the phase variable outer membrane protein Opa. The gonococcus is able to subvert complement mediated killing and opsonisation by sialylation of its lipooligosaccharide and deploys a series of anti-phagocytic mechanisms. N. gonorrhoeae is a fastidious organism that is able to grow on a limited number of primary carbon sources such as glucose and lactate. The utilization of lactate by the gonococcus has been implicated in a number of pathogenicity mechanisms. The bacterium lives mainly in microaerobic environments and can grow both aerobically and anaerobically with the aid of nitrite. The gonococcus does not produce siderophores for scavenging iron but can utilize some produced by other bacteria, and it is able to successful chelate iron from host haem, transferrin and lactoferrin. The gonococcus is an incredibly versatile human pathogen; in the following chapter, we detail the intricate mechanisms used by the bacterium to invade and survive within the host.
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Affiliation(s)
- Luke R Green
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Joby Cole
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Ernesto Feliz Diaz Parga
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Jonathan G Shaw
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom.
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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: 2.0] [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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Jew KM, Le VTB, Amaral K, Ta A, Nguyen May NM, Law M, Adelstein N, Kuhn ML. Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs. Front Microbiol 2022; 12:805181. [PMID: 35173693 PMCID: PMC8843374 DOI: 10.3389/fmicb.2021.805181] [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: 10/29/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Acetylation is a protein post-translational modification (PTM) that can affect a variety of cellular processes. In bacteria, two PTM Nε-acetylation mechanisms have been identified: non-enzymatic/chemical acetylation via acetyl phosphate or acetyl coenzyme A and enzymatic acetylation via protein acetyltransferases. Prior studies have shown that extensive acetylation of Nε-lysine residues of numerous proteins from a variety of bacteria occurs via non-enzymatic acetylation. In Escherichia coli, new Nε-lysine acetyltransferases (KATs) that enzymatically acetylate other proteins have been identified, thus expanding the repertoire of protein substrates that are potentially regulated by acetylation. Therefore, we designed a study to leverage the wealth of structural data in the Protein Data Bank (PDB) to determine: (1) the 3D location of lysine residues on substrate proteins that are acetylated by E. coli KATs, and (2) investigate whether these residues are conserved on 3D structures of their homologs. Five E. coli KAT substrate proteins that were previously identified as being acetylated by YiaC and had 3D structures in the PDB were selected for further analysis: adenylate kinase (Adk), isocitrate dehydrogenase (Icd), catalase HPII (KatE), methionyl-tRNA formyltransferase (Fmt), and a peroxide stress resistance protein (YaaA). We methodically compared over 350 protein structures of these E. coli enzymes and their homologs; to accurately determine lysine residue conservation requires a strategy that incorporates both flexible structural alignments and visual inspection. Moreover, our results revealed discrepancies in conclusions about lysine residue conservation in homologs when examining linear amino acid sequences compared to 3D structures.
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Affiliation(s)
| | | | | | | | | | | | | | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
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49
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Rose J, Basisty N, Zee T, Wehrfritz C, Bose N, Desprez PY, Kapahi P, Stoller M, Schilling B. Comprehensive proteomic quantification of bladder stone progression in a cystinuric mouse model using data-independent acquisitions. PLoS One 2022; 17:e0250137. [PMID: 35771811 PMCID: PMC9246204 DOI: 10.1371/journal.pone.0250137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/03/2022] [Indexed: 11/21/2022] Open
Abstract
Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.
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Affiliation(s)
- Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Tiffany Zee
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Cameron Wehrfritz
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Neelanjan Bose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | | | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Marshall Stoller
- University of California San Francisco, San Francisco, CA, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, CA, United States of America
- * E-mail:
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Parks AR, Escalante-Semerena JC. Protein N-terminal acylation: An emerging field in bacterial cell physiology. CURRENT TRENDS IN MICROBIOLOGY 2022; 16:1-18. [PMID: 37009250 PMCID: PMC10062008 DOI: 10.31300/ctmb.16.2022.1-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
N-terminal (Nt)-acylation is the irreversible addition of an acyl moiety to the terminal alpha amino group of a peptide chain. This type of modification alters the nature of the N terminus, which can interfere with the function of the modified protein by disrupting protein interactions, function, localization, degradation, hydrophobicity, or charge. Nt acylation is found in all domains of life and is a highly common occurrence in eukaryotic cells. However, in prokaryotes very few cases of Nt acylation have been reported. It was once thought that Nt acylation of proteins, other than ribosomal proteins, was uncommon in prokaryotes, but recent evidence suggests that this modification may be more common than once realized. In this review, we discuss what is known about prokaryotic Nt acetylation and the acetyltransferases that are responsible, as well as recent advancements in this field and currently used methods to study Nt acetylation.
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Affiliation(s)
- Anastacia R. Parks
- Department of Microbiology, University of Georgia, Athens, GA 30606, USA
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