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Liu Y, Liu X, Dong X, Yin Z, Xie Z, Luo Y. Systematic Analysis of Lysine Acetylation Reveals Diverse Functions in Azorhizobium caulinodans Strain ORS571. Microbiol Spectr 2023; 11:e0353922. [PMID: 36475778 PMCID: PMC9927263 DOI: 10.1128/spectrum.03539-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
Protein acetylation can quickly modify the physiology of bacteria to respond to changes in environmental or nutritional conditions, but little information on these modifications is available in rhizobia. In this study, we report the lysine acetylome of Azorhizobium caulinodans strain ORS571, a model rhizobium isolated from stem nodules of the tropical legume Sesbania rostrata that is capable of fixing nitrogen in the free-living state and during symbiosis. Antibody enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were used to characterize the acetylome. There are 2,302 acetylation sites from 982 proteins, accounting for 20.8% of the total proteins. Analysis of the acetylated motifs showed the preferences for the amino acid residues around acetylated lysines. The response regulator CheY1, previously characterized to be involved in chemotaxis in strain ORS571, was identified as an acetylated protein, and a mutation of the acetylated site of CheY1 significantly impaired the strain's motility. In addition, a Zn+-dependent deacetylase (AZC_0414) was characterized, and the construction of a deletion mutant strain showed that it played a role in chemotaxis. Our study provides the first global analysis of lysine acetylation in ORS571, suggesting that acetylation plays a role in various physiological processes. In addition, we demonstrate its involvement in the chemotaxis process. The acetylome of ORS571 provides insights to investigate the regulation mechanism of rhizobial physiology. IMPORTANCE Acetylation is an important modification that regulates protein function and has been found to regulate physiological processes in various bacteria. The physiology of rhizobium A. caulinodans ORS571 is regulated by multiple mechanisms both when free living and in symbiosis with the host; however, the regulatory role of acetylation is not yet known. Here, we took an acetylome-wide approach to identify acetylated proteins in A. caulinodans ORS571 and performed clustering analyses. Acetylation of chemotaxis proteins was preliminarily investigated, and the upstream acetylation-regulating enzyme involved in chemotaxis was characterized. These findings provide new insights to explore the physiological mechanisms of rhizobia.
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Affiliation(s)
- Yanan Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiaoyan Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Yongming Luo
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [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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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: 1.0] [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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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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Abstract
Nε-lysine acetylation is an important, dynamic regulatory posttranslational modification (PTM) that is common in bacteria. Protein acetylomes have been characterized for more than 30 different species, and it is known that acetylation plays important regulatory roles in many essential biological processes. The levels of acetylation are enzymatically controlled by the opposing actions of lysine acetyltransferases and deacetylases. In bacteria, a second mechanism of acetylation exists and occurs via an enzyme-independent manner using the secondary metabolite acetyl-phosphate. Nonenzymatic acetylation accounts for global low levels of acetylation. Recently, studies concerning the role of protein acetylation in bacterial virulence have begun. Acetylated virulence factors have been identified and further characterized. The roles of the enzymes that acetylate and deacetylate proteins in the establishment of infection and biofilm formation have also been investigated. In this review, we discuss the acetylomes of human bacterial pathogens. We highlight examples of known acetylated virulence proteins and examine how they affect survival in the host. Finally, we discuss how acetylation might influence host-pathogen interactions and look at the contribution of acetylation to antimicrobial resistance.
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Afanzar O, Di Paolo D, Eisenstein M, Levi K, Plochowietz A, Kapanidis AN, Berry RM, Eisenbach M. The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility. EMBO J 2021; 40:e104683. [PMID: 33620739 PMCID: PMC7957414 DOI: 10.15252/embj.2020104683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 12/17/2020] [Accepted: 01/19/2021] [Indexed: 11/20/2022] Open
Abstract
Regulatory switches are wide spread in many biological systems. Uniquely among them, the switch of the bacterial flagellar motor is not an on/off switch but rather controls the motor’s direction of rotation in response to binding of the signaling protein CheY. Despite its extensive study, the molecular mechanism underlying this switch has remained largely unclear. Here, we resolved the functions of each of the three CheY‐binding sites at the switch in E. coli, as well as their different dependencies on phosphorylation and acetylation of CheY. Based on this, we propose that CheY motor switching activity is potentiated upon binding to the first site. Binding of potentiated CheY to the second site produces unstable switching and at the same time enables CheY binding to the third site, an event that stabilizes the switched state. Thereby, this mechanism exemplifies a unique combination of tight motor regulation with inherent switching flexibility.
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Affiliation(s)
- Oshri Afanzar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Diana Di Paolo
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Miriam Eisenstein
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Kohava Levi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Richard Michael Berry
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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Lei L, Zeng J, Wang L, Gong T, Zheng X, Qiu W, Zhang R, Yun L, Yang Y, Li Y. Quantitative acetylome analysis reveals involvement of glucosyltransferase acetylation in Streptococcus mutans biofilm formation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 13:86-97. [PMID: 33185947 DOI: 10.1111/1758-2229.12907] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/11/2020] [Indexed: 02/05/2023]
Abstract
Streptococcus mutans (S. mutans) effectively utilizes dietary sucrose for the exopolysaccharide productions, which are mostly synthesized by the effects of glucosyltransferases (Gtfs). In the present study, the acetylome of S. mutans was identified and quantitative acetylome analysis of the bacterial biofilm growth (SMB) was compared with that of planktonic growth (SMP). The dynamic changes of protein acetylation were quantified using the integrated approach involving TMT labeling and Kac affinity enrichment followed by high-resolution mass spectrometry-based quantitative proteomics. In total, 973 acetylation sites in 445 proteins were identified, among which 617 acetylation sites in 302 proteins were quantitated. The overall analysis indicated that 22.7% of proteins were acetylated. Among the quantified proteins in SMB, the acetylation degree of lysine in 56 sites increased, while that of lysine decreased in 52 sites. In the acetylome of S. mutans, six significantly enriched motifs were identified and obtained including Kac****K, KacF, Kac****R, KacY, KacH, F*Kac. In addition, KEGG pathway-based enrichment analysis indicated significant enrichments in glycolysis/gluconeogenesis, and RNA degradation. Particularly, most downregulated acetylated lysine proteins were glucosyltransferase-SI, glucosyltransferase-I, and glucosyltransferase-S in S. mutans biofilm, which probably reveals a switch-off mechanism for the regulation of glucosyltransferases function during the biofilm development.
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Affiliation(s)
- Lei Lei
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lingyun Wang
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tao Gong
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wei Qiu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ru Zhang
- Department of Endodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Libing Yun
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Science, Sichuan University, Chengdu, China
| | - Yingming Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Christensen DG, Xie X, Basisty N, Byrnes J, McSweeney S, Schilling B, Wolfe AJ. Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions. Front Microbiol 2019; 10:1604. [PMID: 31354686 PMCID: PMC6640162 DOI: 10.3389/fmicb.2019.01604] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.
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Affiliation(s)
- David G. Christensen
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States
| | - James Byrnes
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | - Sean McSweeney
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | | | - Alan J. Wolfe
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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Singh KK, Bhardwaj N, Sankhe GD, Udaykumar N, Singh R, Malhotra V, Saini DK. Acetylation of Response Regulator Proteins, TcrX and MtrA in M. tuberculosis Tunes their Phosphotransfer Ability and Modulates Two-Component Signaling Crosstalk. J Mol Biol 2019; 431:777-793. [DOI: 10.1016/j.jmb.2019.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 01/31/2023]
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10
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Ford KM, Antani JD, Nagarajan A, Johnson MM, Lele PP. Switching and Torque Generation in Swarming E. coli. Front Microbiol 2018; 9:2197. [PMID: 30279682 PMCID: PMC6153309 DOI: 10.3389/fmicb.2018.02197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli swarm on semi-solid surfaces with the aid of flagella. It has been hypothesized that swarmer cells overcome the increased viscous drag near surfaces by developing higher flagellar thrust and by promoting surface wetness with the aid of a flagellar switch. The switch enables reversals between clockwise (CW) and counterclockwise (CCW) directions of rotation of the flagellar motor. Here, we measured the behavior of flagellar motors in swarmer cells. Results indicated that although the torque was similar to that in planktonic cells, the tendency to rotate CCW was higher in swarmer cells. This suggested that swarmers likely have a smaller pool of phosphorylated CheY. Results further indicated that the upregulation of the flagellin gene was not critical for flagellar thrust or swarming. Consistent with earlier reports, moisture added to the swarm surface restored swarming in a CCW-only mutant, but not in a FliG mutant that rotated motors CW-only (FliGCW). Fluorescence assays revealed that FliGCW cells grown on agar surfaces carried fewer flagella than planktonic FliGCW cells. The surface-dependent reduction in flagella correlated with a reduction in the number of putative flagellar preassemblies. These results hint toward a possibility that the conformational dynamics of switch proteins play a role in the proper assembly of flagellar complexes and flagellar export, thereby aiding bacterial swarming.
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Affiliation(s)
- Katie M Ford
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Aravindh Nagarajan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Madeline M Johnson
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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Gaviard C, Jouenne T, Hardouin J. Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications. Expert Rev Proteomics 2018; 15:757-772. [DOI: 10.1080/14789450.2018.1516550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
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12
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Li Y, Krishnan K, Duncan MJ. Post-translational regulation of a Porphyromonas gingivalis regulator. J Oral Microbiol 2018; 10:1487743. [PMID: 29988788 PMCID: PMC6032018 DOI: 10.1080/20002297.2018.1487743] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/29/2018] [Indexed: 02/05/2023] Open
Abstract
Background: Bacteria use two-component signal transduction systems (among others) to perceive and respond to environmental changes. Within the genus Porphyromonas, we observed degeneration of these systems, as exemplified by the loss of RprX, the sensor kinase partner of the RprY. Objective: The purpose of this study was to investigate modulation of RprY function by acetylation. Design: The transcriptional activity of the rprY-pat genes were measured by RT-PCR and 5ʹ-RACE. The acetylation of RprY were detected by western blotting. Electromobility shift and in vitro ChIP assays were used to measure the DNA binding activity of RprY. The expression of RprY target genes was measured by qRT-PCR. Effects of acetylation on phosphorylation of RprY were measured by Phos-tag gels. Results: The rprY gene is cotranscribed with pat. RprY is acetylated in vivo, and autoacetylated in vitro in a reaction that is enhanced by Pat; the CobB sirtuin deacetylates RprY. Acetylation reduced the DNA binding of RprY. Induced oxidative stress decreased production of RprY in vivo, increased its acetylation and increased expression of nqrA. Conclusions: We propose that to compensate for the loss of RprX, P. gingivalis has evolved a novel mechanism to inactivate RprY through acetylation.
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Affiliation(s)
- Yuqing Li
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Karthik Krishnan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Office of Dean of Research and Graduate Studies, Shiv Nadar University, Gautam Buddha Nagar, India
| | - Margaret J Duncan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
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13
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Castro NSS, Laia CAT, Maiti BK, Cerqueira NMFSA, Moura I, Carepo MSP. Small phospho-donors phosphorylate MorR without inducing protein conformational changes. Biophys Chem 2018; 240:25-33. [PMID: 29883882 DOI: 10.1016/j.bpc.2018.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/10/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Phosphorylation is an essential mechanism of protein control and plays an important role in biology. The two-component system (TCS) is a bacterial regulation mechanism mediated by a response regulator (RR) protein and a kinase protein, which synchronize the regulatory circuit according to the environment. Phosphorylation is a key element in TCS function as it controls RR activity. In the present study, we characterize the behavior of MorR, an RR associated with Mo homeostasis, upon acetylphosphate and phosphoramidate treatment in vitro. Our results show that MorR was phosphorylated by both phospho-donors. Fluorescence experiments showed that MorR tryptophan emission is quenched by phosphoramidate. Furthermore, theoretical and computational results demonstrate that phosphorylation by phosphoramidate is more favorable than that by acetylphosphate. In conclusion, phosphorylated MorR is a monomeric protein and phosphorylation does not appear to induce observable conformational changes in the protein structure.
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Affiliation(s)
- Nathália S S Castro
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - César A T Laia
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Biplab K Maiti
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Nuno M F S A Cerqueira
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Isabel Moura
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Marta S P Carepo
- LAQV-REQUIMTE, Departamento de Química, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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14
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Gaviard C, Broutin I, Cosette P, Dé E, Jouenne T, Hardouin J. Lysine Succinylation and Acetylation in Pseudomonas aeruginosa. J Proteome Res 2018; 17:2449-2459. [DOI: 10.1021/acs.jproteome.8b00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Isabelle Broutin
- LCRB, UMR 8015, CNRS, University Paris Descartes, Sorbonne Paris City, 75270 Paris Cedex 06, France
| | - Pascal Cosette
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
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15
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Türkowsky D, Esken J, Goris T, Schubert T, Diekert G, Jehmlich N, von Bergen M. A Retentive Memory of Tetrachloroethene Respiration in Sulfurospirillum halorespirans - involved Proteins and a possible link to Acetylation of a Two-Component Regulatory System. J Proteomics 2018; 181:36-46. [PMID: 29617628 DOI: 10.1016/j.jprot.2018.03.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/08/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
Abstract
Organohalide respiration (OHR), comprising the reductive dehalogenation of halogenated organic compounds, is subject to a unique memory effect and long-term transcriptional downregulation of the involved genes in Sulfurospirillum multivorans. Gene expression ceases slowly over approximately 100 generations in the absence of tetrachloroethene (PCE). However, the molecular mechanisms of this regulation process are not understood. We show here that Sulfurospirillum halorespirans undergoes the same type of regulation when cultivated without chlorinated ethenes for a long period of time. In addition, we compared the proteomes of S. halorespirans cells cultivated in the presence of PCE with those of cells long- and short-term cultivated with nitrate as the sole electron acceptor. Important OHR-related proteins previously unidentified in S. multivorans include a histidine kinase, a putative quinol dehydrogenase membrane protein, and a PCE-induced porin. Since for some regulatory proteins a posttranslational regulation of activity by lysine acetylations is known, we also analyzed the acetylome of S. halorespirans, revealing that 32% of the proteome was acetylated in at least one condition. The data indicate that the response regulator and the histidine kinase of a two-component system most probably involved in induction of PCE respiration are highly acetylated during short-term cultivation with nitrate in the absence of PCE. SIGNIFICANCE The so far unique long-term downregulation of organohalide respiration is now identified in a second species suggesting a broader distribution of this regulatory phenomenon. An improved protein extraction method allowed the identification of proteins most probably involved in transcriptional regulation of OHR in Sulfurospirillum spp. Our data indicate that acetylations of regulatory proteins are involved in this extreme, sustained standby-mode of metabolic enzymes in the absence of a substrate. This first published acetylome of Epsilonproteobacteria might help to study other ecologically or medically important species of this clade.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jens Esken
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße, 34, Germany.
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16
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Xu JY, Xu Z, Liu X, Tan M, Ye BC. Protein Acetylation and Butyrylation Regulate the Phenotype and Metabolic Shifts of the Endospore-forming Clostridium acetobutylicum. Mol Cell Proteomics 2018. [PMID: 29523768 DOI: 10.1074/mcp.ra117.000372] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Clostridium acetobutylicum is a strict anaerobic, endospore-forming bacterium, which is used for the production of the high energy biofuel butanol in metabolic engineering. The life cycle of C. acetobutylicum can be divided into two phases, with acetic and butyric acids being produced in the exponential phase (acidogenesis) and butanol formed in the stationary phase (solventogenesis). During the transitional phase from acidogenesis to solventogenesis and latter stationary phase, concentration peaks of the metabolic intermediates butyryl phosphate and acetyl phosphate are observed. As an acyl group donor, acyl-phosphate chemically acylates protein substrates. However, the regulatory mechanism of lysine acetylation and butyrylation involved in the phenotype and solventogenesis of C. acetobutylicum remains unknown. In our study, we conducted quantitative analysis of protein acetylome and butyrylome to explore the dynamic change of lysine acetylation and butyrylation in the exponential phase, transitional phase, and stationary phase of C. acetobutylicum Total 458 lysine acetylation sites and 1078 lysine butyrylation sites were identified in 254 and 373 substrates, respectively. Bioinformatics analysis uncovered the similarities and differences between the two acylation modifications in C. acetobutylicum Mutation analysis of butyrate kinase and the central transcriptional factor Spo0A was performed to characterize the unique role of lysine butyrylation in the metabolic pathway and sporulation process of C. acetobutylicum Moreover, quantitative proteomic assays were performed to reveal the relationship between protein features (e.g. gene expression level and lysine acylation level) and metabolites in the three growth stages. This study expanded our knowledge of lysine acetylation and butyrylation in Clostridia and constituted a resource for functional studies on lysine acylation in bacteria.
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Affiliation(s)
- Jun-Yu Xu
- From the ‡Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.,¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhen Xu
- From the ‡Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.,¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - XinXin Liu
- ¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Minjia Tan
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Bang-Ce Ye
- From the ‡Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China; .,¶Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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17
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Abstract
Motility is a central feature of many microorganisms and provides an efficient strategy to respond to environmental changes. Bacteria and archaea have developed fundamentally different rotary motors enabling their motility, termed flagellum and archaellum, respectively. Bacterial motility along chemical gradients, called chemotaxis, critically relies on the response regulator CheY, which, when phosphorylated, inverses the rotational direction of the flagellum via a switch complex at the base of the motor. The structural difference between archaellum and flagellum and the presence of functional CheY in archaea raises the question of how the CheY protein changed to allow communication with the archaeal motility machinery. Here we show that archaeal CheY shares the overall structure and mechanism of magnesium-dependent phosphorylation with its bacterial counterpart. However, bacterial and archaeal CheY differ in the electrostatic potential of the helix α4. The helix α4 is important in bacteria for interaction with the flagellar switch complex, a structure that is absent in archaea. We demonstrated that phosphorylation-dependent activation, and conserved residues in the archaeal CheY helix α4, are important for interaction with the archaeal-specific adaptor protein CheF. This forms a bridge between the chemotaxis system and the archaeal motility machinery. Conclusively, archaeal CheY proteins conserved the central mechanistic features between bacteria and archaea, but differ in the helix α4 to allow binding to an archaellum-specific interaction partner.
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18
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Gallego-Jara J, Écija Conesa A, de Diego Puente T, Lozano Terol G, Cánovas Díaz M. Characterization of CobB kinetics and inhibition by nicotinamide. PLoS One 2017; 12:e0189689. [PMID: 29253849 PMCID: PMC5734772 DOI: 10.1371/journal.pone.0189689] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022] Open
Abstract
Lysine acetylation has emerged as a global protein regulation system in all domains of life. Sirtuins, or Sir2-like enzymes, are a family of histone deacetylases characterized by their employing NAD+ as a co-substrate. Sirtuins can deacetylate several acetylated proteins, but a consensus substrate recognition sequence has not yet been established. Product inhibition of many eukaryotic sirtuins by nicotinamide and its analogues has been studied in vitro due to their potential role as anticancer agents. In this work, the kinetics of CobB, the main Escherichia coli deacetylase, have been characterized. To our knowledge, this is the first kinetic characterization of a sirtuin employing a fully acetylated and natively folded protein as a substrate. CobB deacetylated several acetyl-CoA synthetase acetylated lysines with a single kinetic rate. In addition, in vitro nicotinamide inhibition of CobB has been characterized, and the intracellular nicotinamide concentrations have been determined under different growth conditions. The results suggest that nicotinamide can act as a CobB regulator in vivo. A nicotinamidase deletion strain was thus phenotypically characterized, and it behaved similarly to the ΔcobB strain. The results of this work demonstrate the potential regulatory role of the nicotinamide metabolite in vivo.
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Affiliation(s)
- 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”, Murcia, Spain
- * E-mail:
| | - Ana Écija Conesa
- 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”, 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”, Murcia, Spain
| | - 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”, Murcia, Spain
| | - 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”, Murcia, Spain
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19
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Zhang M, Xu JY, Hu H, Ye BC, Tan M. Systematic Proteomic Analysis of Protein Methylation in Prokaryotes and Eukaryotes Revealed Distinct Substrate Specificity. Proteomics 2017; 18. [PMID: 29150981 DOI: 10.1002/pmic.201700300] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/25/2017] [Indexed: 11/07/2022]
Abstract
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, is largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles. In this study, we deeply explored the methylated sites in three species Escherichia coli, Saccharomyces cerevisiae, and HeLa cells by employing MS-based proteomic approach coupled with heavy methyl SILAC method. We identify a total of 234 methylated sites on 187 proteins with high localization confidence, including 94 unreported methylated sites on nine different amino acid residues. KEGG and gene ontology analysis show the pathways enriched with methylated proteins are mainly involved in central metabolism for E. coli and S. cerevisiae, but related to spliceosome for HeLa cells. The analysis of methylation preference on different amino acids is conducted in three species. Protein N-terminal methylation is dominant in E. coli while methylated lysines and arginines are widely identified in S. cerevisiae and HeLa cells, respectively. To study whether some atypical protein methylation has biological relevance in the pathological process in mammalian cells, we focus on histone methylation in diet-induced obese (DIO) mouse. Two glutamate methylation sites showed statistical significance in DIO mice compared with chow-fed mice, suggesting their potential roles in diabetes and obesity. Together, these findings expanded the methylome database from microbes to mammals, which will benefit our further appreciation for the protein methylation as well as its possible functions on disease.
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Affiliation(s)
- Min Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Yu Xu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao Hu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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20
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Zhou Q, Zhou YN, Jin DJ, Tse-Dinh YC. Deacetylation of topoisomerase I is an important physiological function of E. coli CobB. Nucleic Acids Res 2017; 45:5349-5358. [PMID: 28398568 PMCID: PMC5605244 DOI: 10.1093/nar/gkx250] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 04/03/2017] [Indexed: 01/08/2023] Open
Abstract
Escherichia coli topoisomerase I (TopA), a regulator of global and local DNA supercoiling, is modified by Nε-Lysine acetylation. The NAD+-dependent protein deacetylase CobB can reverse both enzymatic and non-enzymatic lysine acetylation modification in E. coli. Here, we show that the absence of CobB in a ΔcobB mutant reduces intracellular TopA catalytic activity and increases negative DNA supercoiling. TopA expression level is elevated as topA transcription responds to the increased negative supercoiling. The slow growth phenotype of the ΔcobB mutant can be partially compensated by further increase of intracellular TopA level via overexpression of recombinant TopA. The relaxation activity of purified TopA is decreased by in vitro non-enzymatic acetyl phosphate mediated lysine acetylation, and the presence of purified CobB protects TopA from inactivation by such non-enzymatic acetylation. The specific activity of TopA expressed from His-tagged fusion construct in the chromosome is inversely proportional to the degree of in vivo lysine acetylation during growth transition and growth arrest. These findings demonstrate that E. coli TopA catalytic activity can be modulated by lysine acetylation–deacetylation, and prevention of TopA inactivation from excess lysine acetylation and consequent increase in negative DNA supercoiling is an important physiological function of the CobB protein deacetylase.
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Affiliation(s)
- Qingxuan Zhou
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yan Ning Zhou
- Transcription Control Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ding Jun Jin
- Transcription Control Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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21
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Venkat S, Gregory C, Sturges J, Gan Q, Fan C. Studying the Lysine Acetylation of Malate Dehydrogenase. J Mol Biol 2017; 429:1396-1405. [PMID: 28366830 PMCID: PMC5479488 DOI: 10.1016/j.jmb.2017.03.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022]
Abstract
Protein acetylation plays important roles in many biological processes. Malate dehydrogenase (MDH), a key enzyme in the tricarboxylic acid cycle, has been identified to be acetylated in bacteria by proteomic studies, but no further characterization has been reported. One challenge for studying protein acetylation is to get purely acetylated proteins at specific positions. Here, we applied the genetic code expansion strategy to site-specifically incorporate Nε-acetyllysine into MDH. The acetylation of lysine residues in MDH could enhance its enzyme activity. The Escherichia coli deacetylase CobB could deacetylate acetylated MDH, while the E. coli acetyltransferase YfiQ cannot acetylate MDH efficiently. Our results also demonstrated that acetyl-CoA or acetyl-phosphate could acetylate MDH chemically in vitro. Furthermore, the acetylation level of MDH was shown to be affected by carbon sources in the growth medium.
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Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Caroline Gregory
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jourdan Sturges
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
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22
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Ren J, Sang Y, Lu J, Yao YF. Protein Acetylation and Its Role in Bacterial Virulence. Trends Microbiol 2017; 25:768-779. [PMID: 28462789 DOI: 10.1016/j.tim.2017.04.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.
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Affiliation(s)
- Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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23
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Wei W, Liu T, Li X, Wang R, Zhao W, Zhao G, Zhao S, Zhou Z. Lysine acetylation regulates the function of the global anaerobic transcription factor FnrL in Rhodobacter sphaeroides. Mol Microbiol 2017; 104:278-293. [PMID: 28118511 DOI: 10.1111/mmi.13627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 01/04/2023]
Abstract
The metabolism of the purple non-sulfur bacterium Rhodobacter sphaeroides is versatile and it can grow under various conditions. Here, we report evidence that the anaerobic photosynthetic metabolism of R. sphaeroides is regulated by protein lysine acetylation. Using a proteomic approach, 59 acetylated peptides were detected. Among them is the global anaerobic transcription factor FnrL, which regulates the biosynthetic pathway of tetrapyrroles and synthesis of the photosynthetic apparatus. Lysine 223 of FnrL was identified as acetylated. We show that all three lysines in the DNA binding domain (K223, K213 and K175) of FnrL can be acetylated by acetyl-phosphate in vitro. A bacterial deacetylase homolog, RsCobB can deacetylate FnrL in vitro. The transcription of genes downstream of FnrL decreased when the DNA binding domain of FnrL was acetylated, as revealed by chromatin immunoprecipitation and acetylation-mimicking mutagenesis. An increasing number of acetylated lysines resulted in a further decrease in DNA binding ability. These results demonstrate that the lysine acetylation can fine tune the function of the oxygen-sensitive FnrL; thus, it might regulate anaerobic photosynthetic metabolism of R. sphaeroides.
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Affiliation(s)
- Wei Wei
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, 650091, China
| | - Xinfeng Li
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ruofan Wang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shimin Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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24
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Amin R, Franz-Wachtel M, Tiffert Y, Heberer M, Meky M, Ahmed Y, Matthews A, Krysenko S, Jakobi M, Hinder M, Moore J, Okoniewski N, Maček B, Wohlleben W, Bera A. Post-translational Serine/Threonine Phosphorylation and Lysine Acetylation: A Novel Regulatory Aspect of the Global Nitrogen Response Regulator GlnR in S. coelicolor M145. Front Mol Biosci 2016; 3:38. [PMID: 27556027 PMCID: PMC4977719 DOI: 10.3389/fmolb.2016.00038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/25/2016] [Indexed: 01/03/2023] Open
Abstract
Soil-dwelling Streptomyces bacteria such as S.coelicolor have to constantly adapt to the nitrogen (N) availability in their habitat. Thus, strict transcriptional and post-translational control of the N-assimilation is fundamental for survival of this species. GlnR is a global response regulator that controls transcription of the genes related to the N-assimilation in S. coelicolor and other members of the Actinomycetales. GlnR represents an atypical orphan response regulator that is not activated by the phosphorylation of the conserved aspartate residue (Asp 50). We have applied transcriptional analysis, LC-MS/MS analysis and electrophoretic mobility shift assays (EMSAs) to understand the regulation of GlnR in S. coelicolor M145. The expression of glnR and GlnR-target genes was revisited under four different N-defined conditions and a complex N-rich condition. Although, the expression of selected GlnR-target genes was strongly responsive to changing N-concentrations, the glnR expression itself was independent of the N-availability. Using LC-MS/MSanalysis we demonstrated that GlnR was post-translationally modified. The post-translational modifications of GlnR comprise phosphorylation of the serine/threonine residues and acetylation of lysine residues. In the complex N-rich medium GlnR was phosphorylated on six serine/threonine residues and acetylated on one lysine residue. Under defined N-excess conditions only two phosphorylated residues were detected whereas under defined N-limiting conditions no phosphorylation was observed. GlnR phosphorylation is thus clearly correlated with N-rich conditions. Furthermore, GlnR was acetylated on four lysine residues independently of the N-concentration in the defined media and on only one lysine residue in the complex N-rich medium. Using EMSAs we demonstrated that phosphorylation inhibited the binding of GlnR to its targets genes, whereas acetylation had little influence on the formation of GlnR-DNA complex. This study clearly demonstrated that GlnR DNA-binding affinity is modulated by post-translational modifications in response to changing N-conditions in order to elicit a proper transcriptional response to the latter.
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Affiliation(s)
- Rafat Amin
- Department of Pathology, Dow International Medical College, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences Karachi, Pakistan
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, Interdepartmental Institute for Cell Biology (IFIZ), University of Tübingen Tübingen, Germany
| | - Yvonne Tiffert
- B.R.A.I.N. Biotechnology Research and Information Network AG Zwingenberg, Germany
| | - Martin Heberer
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Mohamed Meky
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Yousra Ahmed
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of TübingenTübingen, Germany; Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University CampusSaarbrücken, Germany
| | - Arne Matthews
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Sergii Krysenko
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Marco Jakobi
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Markus Hinder
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Jane Moore
- John Innes Center, Norwich Research Park Norwich, UK
| | - Nicole Okoniewski
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, Interdepartmental Institute for Cell Biology (IFIZ), University of Tübingen Tübingen, Germany
| | - Wolfgang Wohlleben
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Agnieszka Bera
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
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25
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Song L, Wang G, Malhotra A, Deutscher MP, Liang W. Reversible acetylation on Lys501 regulates the activity of RNase II. Nucleic Acids Res 2016; 44:1979-88. [PMID: 26847092 PMCID: PMC4797298 DOI: 10.1093/nar/gkw053] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/17/2022] Open
Abstract
RNase II, a 3' to 5' processive exoribonuclease, is the major hydrolytic enzyme in Escherichia coli accounting for ∼90% of the total activity. Despite its importance, little is actually known about regulation of this enzyme. We show here that one residue, Lys501, is acetylated in RNase II. This modification, reversibly controlled by the acetyltransferase Pka, and the deacetylase CobB, affects binding of the substrate and thus decreases the catalytic activity of RNase II. As a consequence, the steady-state level of target RNAs of RNase II may be altered in the cells. We also find that under conditions of slowed growth, the acetylation level of RNase II is elevated and the activity of RNase II decreases, emphasizing the importance of this regulatory process. These findings indicate that acetylation can regulate the activity of a bacterial ribonuclease.
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Affiliation(s)
- Limin Song
- The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Guangyuan Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Arun Malhotra
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Wenxing Liang
- The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
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Ouidir T, Jouenne T, Hardouin J. Post-translational modifications in Pseudomonas aeruginosa revolutionized by proteomic analysis. Biochimie 2016; 125:66-74. [PMID: 26952777 DOI: 10.1016/j.biochi.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe infections in vulnerable individuals. It is known that post-translational modifications (PTMs) play a key role in bacterial physiology. Their characterization is still challenging and the recent advances in proteomics allow large-scale and high-throughput analyses of PTMs. Here, we provide an overview of proteomic data about the modified proteins in P. aeruginosa. We emphasize the significant contribution of proteomics in knowledge enhancement of PTMs (phosphorylation, N-acetylation and glycosylation) and we discuss their importance in P. aeruginosa physiology.
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Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France.
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Bacterial protein acetylation: new discoveries unanswered questions. Curr Genet 2015; 62:335-41. [PMID: 26660885 DOI: 10.1007/s00294-015-0552-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022]
Abstract
Nε-acetylation is emerging as an abundant post-translational modification of bacterial proteins. Two mechanisms have been identified: one is enzymatic, dependent on an acetyltransferase and acetyl-coenzyme A; the other is non-enzymatic and depends on the reactivity of acetyl phosphate. Some, but not most, of those acetylations are reversed by deacetylases. This review will briefly describe the current status of the field and raise questions that need answering.
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Schilling B, Christensen D, Davis R, Sahu AK, Hu LI, Walker-Peddakotla A, Sorensen DJ, Zemaitaitis B, Gibson BW, Wolfe AJ. Protein acetylation dynamics in response to carbon overflow in Escherichia coli. Mol Microbiol 2015; 98:847-63. [PMID: 26264774 DOI: 10.1111/mmi.13161] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2015] [Indexed: 12/11/2022]
Abstract
In Escherichia coli, acetylation of proteins at lysines depends largely on a non-enzymatic acetyl phosphate-dependent mechanism. To assess the functional significance of this post-translational modification, we first grew wild-type cells in buffered tryptone broth with glucose and monitored acetylation over time by immunochemistry. Most acetylation occurred in stationary phase and paralleled glucose consumption and acetate excretion, which began upon entry into stationary phase. Transcription of rprA, a stationary phase regulator, exhibited similar behavior. To identify sites and substrates with significant acetylation changes, we used label-free, quantitative proteomics to monitor changes in protein acetylation. During growth, both the number of identified sites and the extent of acetylation increased with considerable variation among lysines from the same protein. As glucose-regulated lysine acetylation was predominant in central metabolic pathways and overlapped with acetyl phosphate-regulated acetylation sites, we deleted the major carbon regulator CRP and observed a dramatic loss of acetylation that could be restored by deleting the enzyme that degrades acetyl phosphate. We propose that acetyl phosphate-dependent acetylation is a response to carbon flux that could regulate central metabolism.
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Affiliation(s)
| | - David Christensen
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Robert Davis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | | | - Linda I Hu
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Arti Walker-Peddakotla
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | | | - Bozena Zemaitaitis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94143, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
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Hentchel KL, Escalante-Semerena JC. Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress. Microbiol Mol Biol Rev 2015; 79:321-46. [PMID: 26179745 PMCID: PMC4503791 DOI: 10.1128/mmbr.00020-15] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. Although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic acids (e.g., short-, medium-, and long-chain mono- and dicarboxylic aliphatics and aromatics) to modify a large suite of targets. Acetylation of biomolecules has been studied for decades within the context of histone-dependent regulation of gene expression and antibiotic resistance. It was not until the early 2000s that the connection between metabolism, physiology, and protein acetylation was reported. This was the first instance of a metabolic enzyme (acetyl coenzyme A [acetyl-CoA] synthetase) whose activity was controlled by acetylation via a regulatory system responsive to physiological cues. The above-mentioned system was comprised of an acyltransferase and a partner deacylase. Given the reversibility of the acylation process, this system is also referred to as reversible lysine acylation (RLA). A wealth of information has been obtained since the discovery of RLA in prokaryotes, and we are just beginning to visualize the extent of the impact that this regulatory system has on cell function.
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Affiliation(s)
- Kristy L Hentchel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Abstract
For a generation of microbiologists who study pathogenesis in the context of the human microbiome, understanding the diversity of bacterial metabolism is essential. In this chapter, I briefly describe how and why I became, and remain, interested in metabolism. I then will describe and compare some of the strategies used by bacteria to consume sugars as one example of metabolic diversity. I will end with a plea to embrace metabolism in the endeavor to understand pathogenesis.
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Affiliation(s)
- Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois
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Bernal V, Castaño-Cerezo S, Gallego-Jara J, Écija-Conesa A, de Diego T, Iborra JL, Cánovas M. Regulation of bacterial physiology by lysine acetylation of proteins. N Biotechnol 2014; 31:586-95. [DOI: 10.1016/j.nbt.2014.03.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/28/2014] [Accepted: 03/02/2014] [Indexed: 01/10/2023]
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Unexpected extensive lysine acetylation in the trump-card antibiotic producer Streptomyces roseosporus revealed by proteome-wide profiling. J Proteomics 2014; 106:260-9. [DOI: 10.1016/j.jprot.2014.04.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/14/2014] [Accepted: 04/09/2014] [Indexed: 01/10/2023]
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Kuhn ML, Zemaitaitis B, Hu LI, Sahu A, Sorensen D, Minasov G, Lima BP, Scholle M, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ. Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One 2014; 9:e94816. [PMID: 24756028 PMCID: PMC3995681 DOI: 10.1371/journal.pone.0094816] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
The emerging view of Nε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that Nε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial Nε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bozena Zemaitaitis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Linda I. Hu
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Alexandria Sahu
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Dylan Sorensen
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bruno P. Lima
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Michael Scholle
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Milan Mrksich
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, Novato, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
- * E-mail:
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Josenhans C, Jung K, Rao CV, Wolfe AJ. A tale of two machines: a review of the BLAST meeting, Tucson, AZ, 20-24 January 2013. Mol Microbiol 2013; 91:6-25. [PMID: 24125587 DOI: 10.1111/mmi.12427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2013] [Indexed: 01/06/2023]
Abstract
Since its inception, Bacterial Locomotion and Signal Transduction (BLAST) meetings have been the place to exchange and share the latest developments in the field of bacterial signal transduction and motility. At the 12th BLAST meeting, held last January in Tucson, AZ, researchers from all over the world met to report and discuss progress in diverse aspects of the field. The majority of these advances, however, came at the level of atomic level structures and their associated mechanisms. This was especially true of the biological machines that sense and respond to environmental changes.
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Affiliation(s)
- Christine Josenhans
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
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Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2013; 97:265-86. [PMID: 23994099 DOI: 10.1016/j.jprot.2013.08.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/08/2013] [Accepted: 08/10/2013] [Indexed: 12/12/2022]
Abstract
The post-translational modification (PTM) of proteins plays a critical role in the regulation of a broad range of cellular processes in eukaryotes. Yet their role in governing similar systems in the conventionally presumed 'simpler' forms of life has been largely neglected and, until recently, was thought to occur only rarely, with some modifications assumed to be limited to higher organisms alone. Recent developments in mass spectrometry-based proteomics have provided an unparalleled power to enrich, identify and quantify peptides with PTMs. Additional modifications to biological molecules such as lipids and carbohydrates that are essential for bacterial pathophysiology have only recently been detected on proteins. Here we review bacterial protein PTMs, focusing on phosphorylation, acetylation, proteolytic degradation, methylation and lipidation and the roles they play in bacterial adaptation - thus highlighting the importance of proteomic techniques in a field that is only just in its infancy. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Joel A Cain
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Nestor Solis
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006, Australia.
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Okanishi H, Kim K, Masui R, Kuramitsu S. Acetylome with structural mapping reveals the significance of lysine acetylation in Thermus thermophilus. J Proteome Res 2013; 12:3952-68. [PMID: 23901841 DOI: 10.1021/pr400245k] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lysine acetylation in proteins has recently been globally identified in bacteria and eukaryotes. Even though acetylproteins are known to be involved in various cellular processes, its physiological significance has not yet been resolved. Using a proteomics approach in combination with immunoprecipitation, we identified 197 lysine acetylation sites and 4 N-terminal acetylation sites from 128 proteins in Thermus thermophilus HB8, an extremely thermophilic eubacterium. Our analyses revealed that identified acetylproteins are well conserved across all three domains of life and are mainly involved in central metabolism and translation. To characterize the functional significance further, we successfully mapped 172 acetylation sites on their 59 authentic and 54 homologous protein structures. Although the percentage of acetylation on ordered structures was higher than that of the disordered structure, no tendency of acetylation in T. thermophilus was detected in secondary structures. However, the acetylated lysine was situated near the negatively charged glutamic acid residues. In tertiary structure analyses, 58 sites of 103 acetylations mapped on 59 authentic structures of T. thermophilus were located within a considerable distance that can disrupt electrostatic interactions and hydrogen bonding networks on protein surfaces, demonstrating the physiological significance of the acetylation that can directly alter the protein structure. In addition, we found 16 acetylation sites related to Schiff base formation, ligand binding, and protein-RNA and protein-protein interactions that involve the potential function of the proteins. The structural mapping of acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins.
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Affiliation(s)
- Hiroki Okanishi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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Li R, Chen P, Gu J, Deng JY. Acetylation reduces the ability of CheY to undergo autophosphorylation. FEMS Microbiol Lett 2013; 347:70-6. [PMID: 23905870 DOI: 10.1111/1574-6968.12224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/17/2013] [Accepted: 07/17/2013] [Indexed: 11/28/2022] Open
Abstract
CheY, the response regulator of the chemotaxis system in Escherichia coli, can be regulated by two covalent modifications - phosphorylation and acetylation. Both covalent modifications are involved in chemotaxis, but the mechanism and role of the acetylation are still obscure. While acetylation was shown to repress the binding of CheY to its target proteins, the effect of acetylation on the ability of CheY to undergo autophosphorylate with AcP is not fully investigated. To obtain more information on the function of this acetylation, we successfully expressed and purified CheY protein with a 6 × His-tag on the C-terminus. Subsequently, acetylated CheY (AcCheY) was obtained with AcCoA as the acetyl donor, and the acetylation level of AcCheY was confirmed by Western blotting and then mass spectrometry. Using tryptophan fluorescence intensity measurements as a monitor of phosphorylation, we showed that acetylation reduces the ability of CheY to undergo autophosphorylation.
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Affiliation(s)
- Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Acetylation of the response regulator RcsB controls transcription from a small RNA promoter. J Bacteriol 2013; 195:4174-86. [PMID: 23852870 DOI: 10.1128/jb.00383-13] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nε-lysine acetylation was recently discovered on many bacterial proteins that function in diverse cellular processes. Thus, many questions remain unanswered. For example, what mechanisms regulate lysine acetylation? Does acetylation affect physiology? To help answer these questions, we studied the Escherichia coli response regulator and transcription factor RcsB, which is reported to be acetylated in vitro. To characterize RcsB acetylation, we monitored transcription from the rprA promoter, which requires RcsB. The conventional view is that RcsB is activated by phosphorylation through either the Rcs phosphorelay or acetyl phosphate. We affirmed that rprA transcription requires phosphorylated RcsB and showed that acetyl-phosphate (AcP) is a phosphoryl group donor to RcsB. However, a mutant that accumulates AcP (ackA) exhibited a reduction in rprA transcription instead of the predicted increase. rprA transcription also diminished in the cobB mutant, which lacks the only known E. coli protein deacetylase. This suggests the existence of an inhibitory mechanism that involves lysine acetylation, a supposition supported by the observation that RcsB isolated from the ackA or cobB mutant was hyperacetylated. Finally, we used a genetic approach to identify an AckA- and CobB-sensitive lysine (Lys-154) that controls RcsB activity. We propose that acetylation inhibits RcsB activity and that some of this inhibition acts through the acetylation of Lys-154.
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Zhang QF, Zhang Q, Gu J, Gong P, Wang XD, Wang X, Tu S, Bi LJ, Bi L, Yu ZN, Yu Z, Zhang ZP, Zhang Z, Cui ZQ, Cui Z, Wei HP, Wei H, Tao SC, Tao S, Zhang XE, Zhang X, Deng JY. Reversibly acetylated lysine residues play important roles in the enzymatic activity of Escherichia coli N-hydroxyarylamine O-acetyltransferase. FEBS J 2013; 280:1966-79. [PMID: 23452042 DOI: 10.1111/febs.12216] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 02/17/2013] [Accepted: 02/25/2013] [Indexed: 11/30/2022]
Abstract
CobB is a bacterial NAD(+)-dependent protein deacetylase. Although progress has been made in functional studies of this protein in recent years, its substrates and biological functions are still largely unclear. Using proteome microarray technology, potential substrates of Escherichia coli CobB were screened and nine proteins were identified, including N-hydroxyarylamine O-acetyltransferase (NhoA). In vitro acetylation/deacetylation of NhoA was verified by western blotting and mass spectrometry, and two acetylated lysine residues were identified. Site-specific mutagenesis experiments showed that mutation of each acetylated lysine decreased the acetylation level of NhoA in vitro. Further analysis showed that variant NhoA proteins carrying substitutions at the two acetylated lysine residues are involved in both the O-acetyltransferase and N-acetyltransferase activity of NhoA. Structural analyses were also performed to explore the effects of the acetylated lysine residues on the activity of NhoA. These results suggest that reversible acetylation may play a role in the activity of Escherichia coli NhoA.
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Affiliation(s)
- Qun-Fang Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Hung CC, Garner CD, Slauch JM, Dwyer ZW, Lawhon SD, Frye JG, McClelland M, Ahmer BMM, Altier C. The intestinal fatty acid propionate inhibits Salmonella invasion through the post-translational control of HilD. Mol Microbiol 2013; 87:1045-60. [PMID: 23289537 DOI: 10.1111/mmi.12149] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2012] [Indexed: 11/26/2022]
Abstract
To cause disease, Salmonella must invade the intestinal epithelium employing genes encoded within Salmonella Pathogenicity Island 1 (SPI1). We show here that propionate, a fatty acid abundant in the intestine of animals, repressed SPI1 at physiologically relevant concentration and pH, reducing expression of SPI1 transcriptional regulators and consequently decreasing expression and secretion of effector proteins, leading to reduced bacterial penetration of cultured epithelial cells. Essential to repression was hilD, which occupies the apex of the regulatory cascade within SPI1, as loss of only this gene among those of the regulon prevented repression of SPI1 transcription by propionate. Regulation through hilD, however, was achieved through the control of neither transcription nor translation. Instead, growth of Salmonella in propionate significantly reduced the stability of HilD. Extending protein half-life using a Lon protease mutant demonstrated that protein stability itself did not dictate the effects of propionate and suggested modification of HilD with subsequent degradation as the means of action. Furthermore, repression was significantly lessened in a mutant unable to produce propionyl-CoA, while further metabolism of propionyl-CoA appeared not to be required. These results suggest a mechanism of control of Salmonella virulence in which HilD is post-translationally modified using the high-energy intermediate propionyl-CoA.
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Affiliation(s)
- Chien-Che Hung
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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41
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Xie L, Li W, Xie J. Prokaryotic Nε-lysine acetylomes and implications for new antibiotics. J Cell Biochem 2012; 113:3601-9. [DOI: 10.1002/jcb.24245] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Soufi B, Soares NC, Ravikumar V, Macek B. Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation. Curr Opin Microbiol 2012; 15:357-63. [PMID: 22633124 DOI: 10.1016/j.mib.2012.05.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 12/23/2022]
Abstract
Recent advances in gel-free, mass spectrometry-based proteomics have firmly established existence of serine phosphorylation, threonine phosphorylation, tyrosine phosphorylation and lysine acetylation on many bacterial proteins. Intriguingly, numerous proteins have been shown to be modified by both modifications, leading to the emerging concept of cross-talk between posttranslational modifications in bacteria. This concept is further supported by biological follow-up studies that are starting to reveal bacterial proteins and processes regulated by multiple modifications. In this review, we provide an overview of the large-scale studies involving protein phosphorylation and acetylation in bacteria and discuss some of the current examples of cross-talk between these and other bacterial modifications.
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Liang W, Malhotra A, Deutscher MP. Acetylation regulates the stability of a bacterial protein: growth stage-dependent modification of RNase R. Mol Cell 2011; 44:160-6. [PMID: 21981926 PMCID: PMC3191462 DOI: 10.1016/j.molcel.2011.06.037] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/19/2011] [Accepted: 06/29/2011] [Indexed: 11/17/2022]
Abstract
RNase R, an Escherichia coli exoribonuclease important for degradation of structured RNAs, increases 3- to 10-fold under certain stress conditions, due to an increased half-life for this usually unstable protein. Components of the trans-translation machinery, tmRNA, and its associated protein, SmpB, are essential for RNase R instability. However, it is not understood why exponential phase RNase R is unstable or how it becomes stabilized in stationary phase. Here, we show that these phenomena are regulated by acetylation catalyzed by YfiQ protein. One residue, Lys544, is acetylated in exponential phase RNase R, but not in the stationary phase protein, resulting in tighter binding of tmRNA-SmpB to the C-terminal region of exponential phase RNase R and subsequent proteolytic degradation. Removal of the positive charge at Lys544 or a negative charge in the C-terminal region likely disrupts their interaction, facilitating tmRNA-SmpB binding. These findings indicate that acetylation can regulate the stability of a bacterial protein.
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Affiliation(s)
- Wenxing Liang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA
| | - Arun Malhotra
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA
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Brown MT, Delalez NJ, Armitage JP. Protein dynamics and mechanisms controlling the rotational behaviour of the bacterial flagellar motor. Curr Opin Microbiol 2011; 14:734-40. [PMID: 21955888 DOI: 10.1016/j.mib.2011.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/01/2011] [Accepted: 09/08/2011] [Indexed: 10/17/2022]
Abstract
The proteins that make up the bacterial flagellar rotary motor have recently been shown to be more dynamic than previously thought, with some key proteins exchanging with pools of proteins in the membrane/cytoplasm. It has also become clear that in addition to simply switching in response to chemosensory signals, the rotation of the bacterial flagellar motor can be slowed or stopped, using a clutch or a brake, by signals from metabolism and growth state.
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Affiliation(s)
- Mostyn T Brown
- Oxford Centre for Integrative Systems Biology and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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45
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Jones JD, O'Connor CD. Protein acetylation in prokaryotes. Proteomics 2011; 11:3012-22. [PMID: 21674803 DOI: 10.1002/pmic.201000812] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/14/2011] [Accepted: 03/28/2011] [Indexed: 11/11/2022]
Abstract
Protein acetylation plays a critical regulatory role in eukaryotes but until recently its significance and function in bacteria and the archaea were obscure. It is now clear, however, that prokaryotes have the capacity to acetylate both the α-amino groups of N-terminal residues and the ε-amino groups of lysine side chains. In this review, we bring together information indicating that such acetylation is widespread and that it is likely to regulate fundamental cellular processes. We particularly focus on lysine acetylation, which recent studies show can occur in proteins involved in transcription, translation, pathways associated with central metabolism and stress responses. Intriguingly, specific acetylated lysine residues map to critical regions in the three-dimensional structures of key proteins, e.g. to active sites or to surfaces that dock with other major cellular components. Like phosphorylation, acetylation appears to be an ancient reversible modification that can be present at multiple sites in proteins, thereby potentially producing epigenetic combinatorial complexity. It may be particularly important in regulating central metabolism in prokaryotes due to the requirement for acetyl-CoA and NAD(+) for protein acetyltransferases and Sir2-type deacetylases, respectively.
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46
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Kobir A, Shi L, Boskovic A, Grangeasse C, Franjevic D, Mijakovic I. Protein phosphorylation in bacterial signal transduction. Biochim Biophys Acta Gen Subj 2011; 1810:989-94. [PMID: 21266190 DOI: 10.1016/j.bbagen.2011.01.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/15/2010] [Accepted: 01/18/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND Protein phosphorylation has emerged as one of the major post translational modifications in bacteria, involved in regulating a myriad of physiological processes. In a complex and dynamic system such as the bacterial cell, connectivity of its components accounts for a number of emergent properties. This article is part of a Special Issue entitled: Systems Biology of Microorganisms. SCOPE OF REVIEW This review focuses on the implications of bacterial protein phosphorylation in cell signaling and regulation and highlights the connections and cross talk between various signaling pathways: bacterial two-component systems and serine/threonine kinases, but also the interference between phosphorylation and other post-translational modifications (methylation and acetylation). MAJOR CONCLUSIONS Recent technical developments in high accuracy mass spectrometry have profoundly transformed proteomics, and today exhaustive site-specific phosphoproteomes are available for a number of bacterial species. Nevertheless, prediction of phosphorylation sites remains the main guide for many researchers, so we discuss the characteristics, limits and advantages of available phosphorylation predictors. GENERAL SIGNIFICANCE The advent of quantitative phosphoproteomics has brought the field on the doorstep of systems biology, but a number of challenges remain before the bacterial phosphorylation networks can be efficiently modeled and their physiological role understood. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.
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Affiliation(s)
- Ahasanul Kobir
- Micalis, AgroParisTech-INRA UMR 1319, Jouy en Josas, France
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47
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Control of protein function by reversible Nɛ-lysine acetylation in bacteria. Curr Opin Microbiol 2011; 14:200-4. [PMID: 21239213 DOI: 10.1016/j.mib.2010.12.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 11/20/2022]
Abstract
Recently published work indicates that reversible N(ɛ)-lysine (N(ɛ)-Lys) acetylation of proteins in bacteria may be as diverse, and as important for cellular function, as it has been reported in eukaryotes for the last five decades. In addition to biochemical and genetic approaches, proteomic studies have identified N(ɛ)-Lys acetylation of proteins and enzymes involved in diverse cellular activities such as transcription, translation, stress response, detoxification, and especially carbohydrate and energy metabolism. These findings provide a platform for elucidating the molecular mechanisms behind modulation of enzyme activity by N(ɛ)-Lys acetylation, as well as for understanding how the prokaryotic cell maintains homeostasis in a changing environment.
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48
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Thao S, Chen CS, Zhu H, Escalante-Semerena JC. Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS One 2010; 5:e15123. [PMID: 21217812 PMCID: PMC3013089 DOI: 10.1371/journal.pone.0015123] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 10/21/2010] [Indexed: 01/04/2023] Open
Abstract
Evidence suggesting that eukaryotes and archaea use reversible N(ε)-lysine (N(ε)-Lys) acetylation to modulate gene expression has been reported, but evidence for bacterial use of N(ε)-Lys acetylation for this purpose is lacking. Here, we report data in support of the notion that bacteria can control gene expression by modulating the acetylation state of transcription factors (TFs). We screened the E. coli proteome for substrates of the bacterial Gcn5-like protein acetyltransferase (Pat). Pat acetylated four TFs, including the RcsB global regulatory protein, which controls cell division, and capsule and flagellum biosynthesis in many bacteria. Pat acetylated residue Lys180 of RcsB, and the NAD(+)-dependent Sir2 (sirtuin)-like protein deacetylase (CobB) deacetylated acetylated RcsB (RcsB(Ac)), demonstrating that N(ε)-Lys acetylation of RcsB is reversible. Analysis of RcsB(Ac) and variant RcsB proteins carrying substitutions at Lys180 provided biochemical and physiological evidence implicating Lys180 as a critical residue for RcsB DNA-binding activity. These findings further the likelihood that reversible N(ε)-Lys acetylation of transcription factors is a mode of regulation of gene expression used by all cells.
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Affiliation(s)
- Sandy Thao
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Chien-Sheng Chen
- Department of Pharmacology and Molecular Sciences and High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences and High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Kim GW, Yang XJ. Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem Sci 2010; 36:211-20. [PMID: 21075636 DOI: 10.1016/j.tibs.2010.10.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/06/2010] [Accepted: 10/13/2010] [Indexed: 12/14/2022]
Abstract
Recent proteomic studies reveal that 5-10% of mammalian and bacterial proteins undergo lysine acetylation, a post-translational modification that adds an acetyl group to the ɛ-amino group of lysine residues. Many of these proteins are not canonical targets, such as histones and transcription factors, suggesting that this modification plays a much wider role than previously appreciated. These studies also suggest that lysine acetylomes are at least comparable with (if not larger than) phosphoproteomes. Although many of the newly identified acetylation events still require validation, they constitute an important framework for further research and the development of new drugs useful in treating a variety of pathologies. Herein, we summarize these proteomic studies and highlight recent reports linking lysine acetylation to heterochromatin assembly, sister chromatid cohesion, cytoskeleton dynamics, autophagy, receptor signaling, RNA processing and metabolic control.
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Affiliation(s)
- Go-Woon Kim
- The Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3A 1A3, Canada
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Abstract
Protein acetylation has historically been considered a predominantly eukaryotic phenomenon. Recent evidence, however, supports the hypothesis that acetylation broadly impacts bacterial physiology. To explore more rapidly the impact of protein acetylation in bacteria, microbiologists can benefit from the strong foundation established by investigators of protein acetylation in eukaryotes. To help advance this learning process, we will summarize the current understanding of protein acetylation in eukaryotes, discuss the emerging link between acetylation and metabolism and highlight the best-studied examples of protein acetylation in bacteria.
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Affiliation(s)
- Linda I Hu
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, 2160 S. First Avenue, Building 105, Maywood, IL 60153, USA
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