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Guo T, Sperber AM, Krieger IV, Duan Y, Chemelewski VR, Sacchettini JC, Herman JK. Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization. J Bacteriol 2024; 206:e0020223. [PMID: 38047707 PMCID: PMC10810218 DOI: 10.1128/jb.00202-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023] Open
Abstract
YisK is an uncharacterized protein in Bacillus subtilis previously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent on mbl and suppressed by mbl mutations. In the present work, we characterize YisK's localization, structure, and enzymatic activity. We show that YisK localizes as puncta that depend on Mbl. YisK belongs to the fumarylacetoacetate hydrolase (FAH) superfamily, and crystal structures revealed close structural similarity to two oxaloacetate (OAA) decarboxylases: human mitochondrial FAHD1 and Corynebacterium glutamicum Cg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA (K m = 134 µM, K cat = 31 min-1). A catalytic dead variant (YisK E148A, E150A) retains wild-type localization and still widens cells following overexpression, indicating these activities are not dependent on YisK catalysis. Conversely, a non-localizing variant (YisK E30A) retains wild-type enzymatic activity in vitro but localizes diffusely and no longer widens cells following overexpression. Together, these results suggest that YisK may be subject to spatial regulation that depends on the cell envelope synthesis machinery. IMPORTANCE The elongasome is a multiprotein complex that guides lengthwise growth in some bacteria. We previously showed that, in B. subtilis, overexpression of an uncharacterized putative enzyme (YisK) perturbed function of the actin-like elongasome protein Mbl. Here, we show that YisK exhibits Mbl-dependent localization. Through biochemical and structural characterization, we demonstrate that, like its mitochondrial homolog FAHD1, YisK can catalyze the decarboxylation of the oxaloacetate to pyruvate and CO2. YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.
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Affiliation(s)
- Tingfeng Guo
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Anthony M. Sperber
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Yi Duan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Veronica R. Chemelewski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Jennifer K. Herman
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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2
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Maher A, Staunton K, Kavanagh K. Analysis of the effect of temperature on protein abundance in Demodex-associated Bacillus oleronius. Pathog Dis 2018; 76:4966982. [PMID: 29648591 DOI: 10.1093/femspd/fty032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/09/2018] [Indexed: 01/10/2023] Open
Abstract
A potential role for bacteria in the induction of rosacea has been suggested. The aim of this work was to characterise the effect of temperature on the production of immunostimulatory proteins by Bacillus oleronius-a bacterium to which rosacea patients show sera reactivity and which was originally isolated from a Demodex mite from a rosacea patient. The affected skin of rosacea patients is at a higher temperature than unaffected skin, and it was postulated that this might alter the protein expression pattern of B. oleronius. B. oleronius growth was reduced at 37°C compared to 30°C but resulted in increased expression of the immune-reactive 62kDa protein (1.65 fold [P < 0.05]). Proteomic analysis revealed increased abundance of a wide range of proteins involved in the stress response (e.g. stress proteins [21.7-fold increase], phosphocarrier protein HPr [438.5-fold increase], 60 kDa chaperonin [12.6-fold increase]). Proteins decreased in abundance after growth at 37°C included ferredoxin (325-fold decrease) and peptidase (244-fold decrease). This work indicates that the increased skin temperature of rosacea patients may alter the growth and protein production pattern of B. oleronius and lead to the greater production of immuo-stimulatory proteins.
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Affiliation(s)
- Amie Maher
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Kara Staunton
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, Ireland
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4
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Modulators of Enterococcus faecalis Cell Envelope Integrity and Antimicrobial Resistance Influence Stable Colonization of the Mammalian Gastrointestinal Tract. Infect Immun 2017; 86:IAI.00381-17. [PMID: 29038125 DOI: 10.1128/iai.00381-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/09/2017] [Indexed: 02/07/2023] Open
Abstract
The Gram-positive bacterium Enterococcus faecalis is both a colonizer of the gastrointestinal tract (GIT) and an agent of serious nosocomial infections. Although it is typically required for pathogenesis, GIT colonization by E. faecalis is poorly understood. E. faecalis tolerates high concentrations of GIT antimicrobials, like cholate and lysozyme, leading us to hypothesize that resistance to intestinal antimicrobials is essential for long-term GIT colonization. Analyses of E. faecalis mutants exhibiting defects in antimicrobial resistance revealed that IreK, a determinant of envelope integrity and antimicrobial resistance, is required for long-term GIT colonization. IreK is a member of the PASTA kinase protein family, bacterial transmembrane signaling proteins implicated in the regulation of cell wall homeostasis. Among several determinants of cholate and lysozyme resistance in E. faecalis, IreK was the only one found to be required for intestinal colonization, emphasizing the importance of this protein to enterococcal adaptation to the GIT. By studying ΔireK suppressor mutants that recovered the ability to colonize the GIT, we identified two conserved enterococcal proteins (OG1RF_11271 and OG1RF_11272) that function antagonistically to IreK and interfere with cell envelope integrity, antimicrobial resistance, and GIT colonization. Our data suggest that IreK, through its kinase activity, inhibits the actions of these proteins. IreK, OG1RF_11271, and OG1RF_11272 are found in all enterococci, suggesting that their effect on GIT colonization is universal across enterococci. Thus, we have defined conserved genes in the enterococcal core genome that influence GIT colonization through their effect on enterococcal envelope integrity and antimicrobial resistance.
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5
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Exploring the Amino Acid Residue Requirements of the RNA Polymerase (RNAP) α Subunit C-Terminal Domain for Productive Interaction between Spx and RNAP of Bacillus subtilis. J Bacteriol 2017; 199:JB.00124-17. [PMID: 28484046 DOI: 10.1128/jb.00124-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/01/2017] [Indexed: 01/21/2023] Open
Abstract
Bacillus subtilis Spx is a global transcriptional regulator that is conserved among Gram-positive bacteria, in which Spx is required for preventing oxidatively induced proteotoxicity. Upon stress induction, Spx engages RNA polymerase (RNAP) through interaction with the C-terminal domain of the rpoA-encoded RNAP α subunit (αCTD). Previous mutational analysis of rpoA revealed that substitutions of Y263 in αCTD severely impaired Spx-activated transcription. Attempts to substitute alanine for αCTD R261, R268, R289, E255, E298, and K294 were unsuccessful, suggesting that these residues are essential. To determine whether these RpoA residues were required for productive Spx-RNAP interaction, we ectopically expressed the putatively lethal rpoA mutant alleles in the rpoAY263C mutant, where "Y263C" indicates the amino acid change that results from mutation of the allele. By complementation analysis, we show that Spx-bound αCTD amino acid residues are not essential for Spx-activated transcription in vivo but that R261A, E298A, and E255A mutants confer a partial defect in NaCl-stress induction of Spx-controlled genes. In addition, strains expressing rpoAE255A are defective in disulfide stress resistance and produce RNAP having a reduced affinity for Spx. The E255 residue corresponds to Escherichia coli αD259, which has been implicated in αCTD-σ70 interaction (σ70 R603, corresponding to R362 of B. subtilis σA). However, the combined rpoAE255A and sigAR362A mutations have an additive negative effect on Spx-dependent expression, suggesting the residues' differing roles in Spx-activated transcription. Our findings suggest that, while αCTD is essential for Spx-activated transcription, Spx is the primary DNA-binding determinant of the Spx-αCTD complex.IMPORTANCE Though extensively studied in Escherichia coli, the role of αCTD in activator-stimulated transcription is largely uncharacterized in Bacillus subtilis Here, we conduct phenotypic analyses of putatively lethal αCTD alanine codon substitution mutants to determine whether these residues function in specific DNA binding at the Spx-αCTD-DNA interface. Our findings suggest that multisubunit RNAP contact to Spx is optimal for activation while Spx fulfills the most stringent requirement of upstream promoter binding. Furthermore, several αCTD residues targeted for mutagenesis in this study are conserved among many bacterial species and thus insights on their function in other regulatory systems may be suggested herein.
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6
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Beckert B, Abdelshahid M, Schäfer H, Steinchen W, Arenz S, Berninghausen O, Beckmann R, Bange G, Turgay K, Wilson DN. Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. EMBO J 2017; 36:2061-2072. [PMID: 28468753 DOI: 10.15252/embj.201696189] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/26/2017] [Accepted: 03/29/2017] [Indexed: 11/09/2022] Open
Abstract
Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In Escherichia coli, dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of E. coli 100S (Ec100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the Bacillus subtilis hibernating 100S (Bs100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the BsHPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as E. coli.
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Affiliation(s)
- Bertrand Beckert
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Maha Abdelshahid
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Heinrich Schäfer
- Naturwissenschaftliche Fakultät, Institut für Mikrobiologie, Leibniz Universität Hannover, Hannover, Germany
| | - Wieland Steinchen
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Kürşad Turgay
- Naturwissenschaftliche Fakultät, Institut für Mikrobiologie, Leibniz Universität Hannover, Hannover, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany .,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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7
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Ranawat P, Rawat S. Stress response physiology of thermophiles. Arch Microbiol 2017; 199:391-414. [DOI: 10.1007/s00203-016-1331-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
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8
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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9
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Yu W, Chen Z, Shen L, Wang Y, Li Q, Yan S, Zhong CJ, He N. Proteomic profiling ofBacillus licheniformisreveals a stress response mechanism in the synthesis of extracellular polymeric flocculants. Biotechnol Bioeng 2015; 113:797-806. [DOI: 10.1002/bit.25838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Wencheng Yu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Zhen Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Liang Shen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Qingbiao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Shan Yan
- Department of Chemistry; State University of New York at Binghamton; Binghamton 13902 New York
| | - Chuan-Jian Zhong
- Department of Chemistry; State University of New York at Binghamton; Binghamton 13902 New York
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
- Department of Chemistry; State University of New York at Binghamton; Binghamton 13902 New York
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10
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Herbst FA, Danielsen HN, Wimmer R, Nielsen PH, Dueholm MS. Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase. Proteomics 2015; 15:3244-52. [PMID: 26122999 DOI: 10.1002/pmic.201400482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/30/2015] [Accepted: 06/26/2015] [Indexed: 01/12/2023]
Abstract
The physiological adaptation to stationary growth by Pseudomonas putida F1, a model organism for the degradation of aromatic compounds, was investigated by proteome-wide label-free quantification.The data unveiled that entrance to the stationary phase did not involve an abrupt switch within the P. putida F1 proteome, but rather an ongoing adaptation that started already during the mid-exponential growth phase. The proteomic adaptations involved a clear increase in amino acid degradation capabilities and a loss of transcriptional as well as translational capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. The results show that it is important to consider significant sample variations when exponentially growing cultures are studied alone or compared across proteomic or transcriptomic literature. All MS data have been deposited in the ProteomeXchange with identifier PXD001219 (http://proteomecentral.proteomexchange.org/dataset/PXD001219).
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Affiliation(s)
- Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Heidi Nolsøe Danielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Reinhard Wimmer
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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11
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Luche S, Eymard-Vernain E, Diemer H, Van Dorsselaer A, Rabilloud T, Lelong C. Zinc oxide induces the stringent response and major reorientations in the central metabolism of Bacillus subtilis. J Proteomics 2015. [PMID: 26211718 DOI: 10.1016/j.jprot.2015.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microorganisms, such as bacteria, are one of the first targets of nanoparticles in the environment. In this study, we tested the effect of two nanoparticles, ZnO and TiO2, with the salt ZnSO4 as the control, on the Gram-positive bacterium Bacillus subtilis by 2D gel electrophoresis-based proteomics. Despite a significant effect on viability (LD50), TiO2 NPs had no detectable effect on the proteomic pattern, while ZnO NPs and ZnSO4 significantly modified B. subtilis metabolism. These results allowed us to conclude that the effects of ZnO observed in this work were mainly attributable to Zn dissolution in the culture media. Proteomic analysis highlighted twelve modulated proteins related to central metabolism: MetE and MccB (cysteine metabolism), OdhA, AspB, IolD, AnsB, PdhB and YtsJ (Krebs cycle) and XylA, YqjI, Drm and Tal (pentose phosphate pathway). Biochemical assays, such as free sulfhydryl, CoA-SH and malate dehydrogenase assays corroborated the observed central metabolism reorientation and showed that Zn stress induced oxidative stress, probably as a consequence of thiol chelation stress by Zn ions. The other patterns affected by ZnO and ZnSO4 were the stringent response and the general stress response. Nine proteins involved in or controlled by the stringent response showed a modified expression profile in the presence of ZnO NPs or ZnSO4: YwaC, SigH, YtxH, YtzB, TufA, RplJ, RpsB, PdhB and Mbl. An increase in the ppGpp concentration confirmed the involvement of the stringent response during a Zn stress. All these metabolic reorientations in response to Zn stress were probably the result of complex regulatory mechanisms including at least the stringent response via YwaC.
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Affiliation(s)
- Sylvie Luche
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Elise Eymard-Vernain
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France
| | - Thierry Rabilloud
- Pro-MD team, UMR CNRS 5249, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Cécile Lelong
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France.
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12
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Ulyanova V, Vershinina V, Ilinskaya O, Harwood CR. Binase-like guanyl-preferring ribonucleases are new members of Bacillus PhoP regulon. Microbiol Res 2014; 170:131-8. [PMID: 25238955 DOI: 10.1016/j.micres.2014.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/24/2014] [Indexed: 11/18/2022]
Abstract
Extracellular low-molecular weight guanyl-preferring ribonucleases (LMW RNases) of Bacillus sp. comprise a group of hydrolytic enzymes that share highly similar structural and catalytic characteristics with barnase, a ribonuclease from Bacillus amyloliquefaciens, and binase, a ribonuclease from Bacillus intermedius. Although the physical-chemical and catalytic properties of Bacillus guanyl-preferring ribonucleases are very similar, there is considerably more variation in the environmental conditions that lead to the induction of the genes encoding these RNases. Based on structural differences of their genes the guanyl-preferring ribonucleases have been sub-divided into binase-like and barnase-like groups. Here we show the ability of the key regulator of phosphate deficiency response, PhoP, to direct the transcription of the binase-like RNases but not barnase-like RNases. These results, together with our demonstration that binase-like RNases are induced in response to phosphate starvation, allow us to categorise this group of ribonucleases as new members of Bacillus PhoP regulon. In contrast, the barnase-like ribonucleases are relatively insensitive to the phosphate concentration and the environmental conditions that are responsible for their induction, and the regulatory elements involved, are currently unknown.
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Affiliation(s)
- Vera Ulyanova
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russian Federation.
| | - Valentina Vershinina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russian Federation.
| | - Olga Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russian Federation.
| | - Colin R Harwood
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom.
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13
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Voigt B, Schroeter R, Jürgen B, Albrecht D, Evers S, Bongaerts J, Maurer KH, Schweder T, Hecker M. The response of Bacillus licheniformis to heat and ethanol stress and the role of the SigB regulon. Proteomics 2014; 13:2140-61. [PMID: 23592518 DOI: 10.1002/pmic.201200297] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 02/22/2013] [Accepted: 03/23/2013] [Indexed: 11/11/2022]
Abstract
The heat and ethanol stress response of Bacillus licheniformis DSM13 was analyzed at the transcriptional and/or translational level. During heat shock, regulons known to be heat-induced in Bacillus subtilis 168 are upregulated in B. licheniformis, such as the HrcA, SigB, CtsR, and CssRS regulon. Upregulation of the SigY regulon and of genes controlled by other extracytoplasmic function (ECF) sigma factors indicates a cell-wall stress triggered by the heat shock. Furthermore, tryptophan synthesis enzymes were upregulated in heat stressed cells as well as regulons involved in usage of alternative carbon and nitrogen sources. Ethanol stress led to an induction of the SigB, HrcA, and CtsR regulons. As indicated by the upregulation of a SigM-dependent protein, ethanol also triggered a cell wall stress. To characterize the SigB regulon of B. licheniformis, we analyzed the heat stress response of a sigB mutant. It is shown that the B. licheniformis SigB regulon comprises additional genes, some of which do not exist in B. subtilis, such as BLi03885, encoding a hypothetical protein, the Na/solute symporter gene BLi02212, the arginase homolog-encoding gene BLi00198 and mcrA, encoding a protein with endonuclease activity.
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Affiliation(s)
- Birgit Voigt
- Institute for Microbiology, University of Greifswald, Greifswald, Germany.
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14
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Antelmann H, Hecker M, Zuber P. Proteomic signatures uncover thiol-specific electrophile resistance mechanisms inBacillus subtilis. Expert Rev Proteomics 2014; 5:77-90. [DOI: 10.1586/14789450.5.1.77] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Van Bokhorst-van de Veen H, Bongers RS, Wels M, Bron PA, Kleerebezem M. Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation. Microb Cell Fact 2013; 12:112. [PMID: 24238744 PMCID: PMC3842655 DOI: 10.1186/1475-2859-12-112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/11/2013] [Indexed: 01/17/2023] Open
Abstract
Background To cope with environmental challenges bacteria possess sophisticated defense mechanisms that involve stress-induced adaptive responses. The canonical stress regulators CtsR and HrcA play a central role in the adaptations to a plethora of stresses in a variety of organisms. Here, we determined the CtsR and HrcA regulons of the lactic acid bacterium Lactobacillus plantarum WCFS1 grown under reference (28°C) and elevated (40°C) temperatures, using ctsR, hrcA, and ctsR-hrcA deletion mutants. Results While the maximum specific growth rates of the mutants and the parental strain were similar at both temperatures (0.33 ± 0.02 h-1 and 0.34 ± 0.03 h-1, respectively), DNA microarray analyses revealed that the CtsR or HrcA deficient strains displayed altered transcription patterns of genes encoding functions involved in transport and binding of sugars and other compounds, primary metabolism, transcription regulation, capsular polysaccharide biosynthesis, as well as fatty acid metabolism. These transcriptional signatures enabled the refinement of the gene repertoire that is directly or indirectly controlled by CtsR and HrcA of L. plantarum. Deletion of both regulators, elicited transcriptional changes of a large variety of additional genes in a temperature-dependent manner, including genes encoding functions involved in cell-envelope remodeling. Moreover, phenotypic assays revealed that both transcription regulators contribute to regulation of resistance to hydrogen peroxide stress. The integration of these results allowed the reconstruction of CtsR and HrcA regulatory networks in L. plantarum, highlighting the significant intertwinement of class I and III stress regulons. Conclusions Taken together, our results enabled the refinement of the CtsR and HrcA regulatory networks in L. plantarum, illustrating the complex nature of adaptive stress responses in this bacterium.
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Ueta M, Wada C, Daifuku T, Sako Y, Bessho Y, Kitamura A, Ohniwa RL, Morikawa K, Yoshida H, Kato T, Miyata T, Namba K, Wada A. Conservation of two distinct types of 100S ribosome in bacteria. Genes Cells 2013; 18:554-74. [PMID: 23663662 DOI: 10.1111/gtc.12057] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 03/19/2013] [Indexed: 11/29/2022]
Abstract
In bacteria, 70S ribosomes (consisting of 30S and 50S subunits) dimerize to form 100S ribosomes, which were first discovered in Escherichia coli. Ribosome modulation factor (RMF) and hibernation promoting factor (HPF) mediate this dimerization in stationary phase. The 100S ribosome is translationally inactive, but it dissociates into two translationally active 70S ribosomes after transfer from starvation to fresh medium. Therefore, the 100S ribosome is called the 'hibernating ribosome'. The gene encoding RMF is found widely throughout the Gammaproteobacteria class, but is not present in any other bacteria. In this study, 100S ribosome formation in six species of Gammaproteobacteria and eight species belonging to other bacterial classes was compared. There were several marked differences between the two groups: (i) Formation of 100S ribosomes was mediated by RMF and short HPF in Gammaproteobacteria species, similar to E. coli, whereas it was mediated only by long HPF in the other bacterial species; (ii) RMF/short HPF-mediated 100S ribosome formation occurred specifically in stationary phase, whereas long HPF-mediated 100S ribosome formation occurred in all growth phases; and (iii) 100S ribosomes formed by long HPF were much more stable than those formed by RMF and short HPF.
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Affiliation(s)
- Masami Ueta
- Yoshida Biological Laboratory, Yamashina, Kyoto 607-8081, Japan
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17
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Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol 2013; 8:848-54. [PMID: 22960854 PMCID: PMC3696893 DOI: 10.1038/nchembio.1063] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/07/2012] [Indexed: 11/08/2022]
Abstract
Annotation of organism-specific metabolic networks is one of the main challenges of systems biology. Importantly, due to inherent uncertainty of computational annotations, predictions of biochemical function need to be treated probabilistically. We present a global probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlations under a single principled framework. The developed method for Global Biochemical reconstruction Using Sampling (GLOBUS) not only provides annotation probabilities for each functional assignment, but also suggests likely alternative functions. GLOBUS is based on statistical Gibbs sampling of probable metabolic annotations and is able to make accurate functional assignments even in cases of remote sequence identity to known enzymes. We apply GLOBUS to genomes of Bacillus subtilis and Staphylococcus aureus, and validate the method predictions by experimentally demonstrating the 6-phosphogluconolactonase activity of ykgB and the role of the sps pathway for rhamnose biosynthesis in B. subtilis.
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van Dijl JM, Hecker M. Bacillus subtilis: from soil bacterium to super-secreting cell factory. Microb Cell Fact 2013; 12:3. [PMID: 23311580 PMCID: PMC3564730 DOI: 10.1186/1475-2859-12-3] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 12/17/2022] Open
Abstract
The biotechnology industry has become a key element in modern societies. Within this industry, the production of recombinant enzymes and biopharmaceutical proteins is of major importance. The global markets for such recombinant proteins are growing rapidly and, accordingly, there is a continuous need for new production platforms that can deliver protein products in greater yields, with higher quality and at lower costs. This calls for the development of next-generation super-secreting cell factories. One of the microbial cell factories that can meet these challenges is the Gram-positive bacterium Bacillus subtilis, an inhabitant of the upper layers of the soil that has the capacity to secrete proteins in the gram per litre range. The engineering of B. subtilis into a next-generation super-secreting cell factory requires combined Systems and Synthetic Biology approaches. In this way, the bacterial protein secretion machinery can be optimized from the single molecule to the network level while, at the same time, taking into account the balanced use of cellular resources. Although highly ambitious, this is an achievable objective due to recent advances in functional genomics and Systems- and Synthetic Biological analyses of B. subtilis cells.
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Affiliation(s)
- Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P,O, box 30001, Groningen, 9700 RB, the Netherlands.
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de Jong IG, Veening JW, Kuipers OP. Single cell analysis of gene expression patterns during carbon starvation in Bacillus subtilis reveals large phenotypic variation. Environ Microbiol 2012; 14:3110-21. [PMID: 23033921 DOI: 10.1111/j.1462-2920.2012.02892.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/30/2012] [Accepted: 09/02/2012] [Indexed: 11/30/2022]
Abstract
How cells dynamically respond to fluctuating environmental conditions depends on the architecture and noise of the underlying genetic circuits. Most work characterizing stress pathways in the model bacterium Bacillus subtilis has been performed on bulk cultures using ensemble assays. However, investigating the single cell response to stress is important since noise might generate significant phenotypic heterogeneity. Here, we study the stress response to carbon source starvation and compare both population and single cell data. Using a top-down approach, we investigate the transcriptional dynamics of various stress-related genes of B. subtilis in response to carbon source starvation and to increased cell density. Our data reveal that most of the tested gene-regulatory networks respond highly heterogeneously to starvation and cells show a large degree of variation in gene expression. The level of highly dynamic diversification within B. subtilis populations under changing environments reflects the necessity to study cells at the single cell level.
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Affiliation(s)
- Imke G de Jong
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
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Rochat T, Nicolas P, Delumeau O, Rabatinová A, Korelusová J, Leduc A, Bessières P, Dervyn E, Krásny L, Noirot P. Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis. Nucleic Acids Res 2012; 40:9571-83. [PMID: 22904090 PMCID: PMC3479203 DOI: 10.1093/nar/gks755] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identified 283 discrete chromosomal sites potentially bound by the Spx–RNA polymerase (Spx–RNAP) complex using chromatin immunoprecipitation of Spx. Three quarters of these sites were located near Sigma(A)-dependent promoters, and upon diamide treatment, the fraction of the Spx–RNAP complex increased in parallel with the number and occupancy of DNA sites. Correlation of Spx–RNAP-binding sites with gene differential expression in wild-type and Δspx strains exposed or not to diamide revealed that 144 transcription units comprising 275 genes were potentially under direct Spx regulation. Spx-controlled promoters exhibited an extended −35 box in which nucleotide composition at the −43/−44 positions strongly correlated with observed activation. In vitro transcription confirmed activation by oxidized Spx of seven newly identified promoters, of which one was also activated by reduced Spx. Our study globally characterized the Spx regulatory network, revealing its role in the basal expression of some genes and its complex interplay with other stress responses.
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21
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Li J, Huang C, Zheng D, Wang Y, Yuan Z. CcpA-Mediated Enhancement of Sugar and Amino Acid Metabolism in Lysinibacillus sphaericus by NMR-Based Metabolomics. J Proteome Res 2012; 11:4654-61. [DOI: 10.1021/pr300469v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Li
- Center for Applied and Environmental
Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic
of China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039,
People’s Republic of China
| | - Chongyang Huang
- Wuhan Center of
Magnetic Resonance,
State Key Laboratory of Magnetic Resonance and Atomic and Molecular
Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People’s
Republic of China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039,
People’s Republic of China
| | - Dasheng Zheng
- Center for Applied and Environmental
Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic
of China
| | - Yulan Wang
- Wuhan Center of
Magnetic Resonance,
State Key Laboratory of Magnetic Resonance and Atomic and Molecular
Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People’s
Republic of China
| | - Zhiming Yuan
- Center for Applied and Environmental
Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic
of China
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22
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Marciniak BC, Trip H, van-der Veek PJ, Kuipers OP. Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins. Microb Cell Fact 2012; 11:66. [PMID: 22624725 PMCID: PMC3514339 DOI: 10.1186/1475-2859-11-66] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/05/2012] [Indexed: 11/14/2022] Open
Abstract
Background Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe) status, its genetic accessibility and its capacity to grow in large fermentations. However, production of heterologous proteins still faces limitations. Results This study aimed at the identification of bottlenecks in secretory protein production by analyzing the response of B. subtilis at the transcriptome level to overproduction of eight secretory proteins of endogenous and heterologous origin and with different subcellular or extracellular destination: secreted proteins (NprE and XynA of B. subtilis, Usp45 of Lactococcus lactis, TEM-1 β-lactamase of Escherichia coli), membrane proteins (LmrA of L. lactis and XylP of Lactobacillus pentosus) and lipoproteins (MntA and YcdH of B. subtilis). Responses specific for proteins with a common localization as well as more general stress responses were observed. The latter include upregulation of genes encoding intracellular stress proteins (groES/EL, CtsR regulated genes). Specific responses include upregulation of the liaIHGFSR operon under Usp45 and TEM-1 β-lactamase overproduction; cssRS, htrA and htrB under all secreted proteins overproduction; sigW and SigW-regulated genes mainly under membrane proteins overproduction; and ykrL (encoding an HtpX homologue) specifically under membrane proteins overproduction. Conclusions The results give better insights into B. subtilis responses to protein overproduction stress and provide potential targets for genetic engineering in order to further improve B. subtilis as a protein production host.
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Affiliation(s)
- Bogumiła C Marciniak
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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23
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Nicholson WL, Moeller R, Horneck G. Transcriptomic responses of germinating Bacillus subtilis spores exposed to 1.5 years of space and simulated martian conditions on the EXPOSE-E experiment PROTECT. ASTROBIOLOGY 2012; 12:469-86. [PMID: 22680693 DOI: 10.1089/ast.2011.0748] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus, it is important to understand their global responses to long-term exposure to space or martian environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low-Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted, fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon), and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated martian conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.
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Affiliation(s)
- Wayne L Nicholson
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Laboratory, Kennedy Space Center, FL 32899, USA.
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24
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Thürmer A, Voigt B, Angelov A, Albrecht D, Hecker M, Liebl W. Proteomic analysis of the extremely thermoacidophilic archaeon Picrophilus torridus at pH and temperature values close to its growth limit. Proteomics 2012; 11:4559-68. [PMID: 22114103 DOI: 10.1002/pmic.201000829] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The thermoacidophilic archaeon Picrophilus torridus belongs to the Thermoplasmatales order and is the most acidophilic organism known to date, growing under extremely acidic conditions around pH 0 (pH(opt) 1) and simultaneously at high temperatures up to 65°C. Some genome features that may be responsible for survival under these harsh conditions have been concluded from the analysis of its 1.55 megabase genome sequence. A proteomic map was generated for P. torridus cells grown to the mid-exponential phase. The soluble fraction of the cells was separated by isoelectric focusing in the pH ranges 4-7 and 3-10, followed by a two dimension (2D) on SDS-PAGE gels. A total of 717 Coomassie collodial-stained protein spots from both pH ranges (pH 4-7 and 3-10) were excised and subjected to LC-MS/MS, leading to the identification of 665 soluble protein spots. Most of the enzymes of the central carbon metabolism were identified on the 2D gels, corroborating biochemically the metabolic pathways predicted from the P. torridus genome sequence. The 2D master gels elaborated in this study represent useful tools for physiological studies of this thermoacidophilic organism. Based on quantitative 2D gel electrophoresis, a proteome study was performed to find pH- or temperature-dependent differences in the proteome composition under changing growth conditions. The proteome expression patterns at two different temperatures (50 and 70°C) and two different pH conditions (pH 0.5 and 1.8) were compared. Several proteins were up-regulated under most stress stimuli tested, pointing to general roles in coping with stress.
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Affiliation(s)
- Andrea Thürmer
- Institute of Microbiology and Genetics, Georg-August-Universität, Göttingen, Germany
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25
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Chernov VM, Chernova OA, Baranova NB, Gorshkov OV, Medvedeva ES, Shaymardanova GF. Mycoplasma adaptation to stress conditions: Proteome shift in Mycoplasma hominis PG37 in response to starvation and low temperatures. Mol Biol 2011. [DOI: 10.1134/s0026893311050037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Zuber P, Chauhan S, Pilaka P, Nakano MM, Gurumoorthy S, Lin AA, Barendt SM, Chi BK, Antelmann H, Mäder U. Phenotype enhancement screen of a regulatory spx mutant unveils a role for the ytpQ gene in the control of iron homeostasis. PLoS One 2011; 6:e25066. [PMID: 21949854 PMCID: PMC3176815 DOI: 10.1371/journal.pone.0025066] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 08/25/2011] [Indexed: 11/22/2022] Open
Abstract
Spx is a global regulator of genes that are induced by disulfide stress in Bacillus subtilis. The regulon that it governs is comprised of over 120 genes based on microarray analysis, although it is not known how many of these are under direct Spx control. Most of the Spx-regulated genes (SRGs) are of unknown function, but many encode products that are conserved in low %GC Gram-positive bacteria. Using a gene-disruption library of B. subtilis genomic mutations, the SRGs were screened for phenotypes related to Spx-controlled activities, such as poor growth in minimal medium and sensitivity to methyglyoxal, but nearly all of the SRG mutations showed little if any phenotype. To uncover SRG function, the mutations were rescreened in an spx mutant background to determine which mutant SRG allele would enhance the spx mutant phenotype. One of the SRGs, ytpQ was the site of a mutation that, when combined with an spx null mutation, elevated the severity of the Spx mutant phenotype, as shown by reduced growth in a minimal medium and by hypersensitivity to methyglyoxal. The ytpQ mutant showed elevated oxidative protein damage when exposed to methylglyoxal, and reduced growth rate in liquid culture. Proteomic and transcriptomic data indicated that the ytpQ mutation caused the derepression of the Fur and PerR regulons of B. subtilis. Our study suggests that the ytpQ gene, encoding a conserved DUF1444 protein, functions directly or indirectly in iron homeostasis. The ytpQ mutant phenotype mimics that of a fur mutation, suggesting a condition of low cellular iron. In vitro transcription analysis indicated that Spx stimulates transcription from the ytpPQR operon within which the ytpQ gene resides. The work uncovers a link between Spx and control of iron homeostasis.
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Affiliation(s)
- Peter Zuber
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, Oregon, United States of America.
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27
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Winter T, Winter J, Polak M, Kusch K, Mäder U, Sietmann R, Ehlbeck J, van Hijum S, Weltmann KD, Hecker M, Kusch H. Characterization of the global impact of low temperature gas plasma on vegetative microorganisms. Proteomics 2011; 11:3518-30. [DOI: 10.1002/pmic.201000637] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 04/29/2011] [Accepted: 06/08/2011] [Indexed: 01/19/2023]
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28
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Schweder T. Bioprocess monitoring by marker gene analysis. Biotechnol J 2011; 6:926-33. [PMID: 21786424 DOI: 10.1002/biot.201100248] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 11/11/2022]
Abstract
The optimization and the scale up of industrial fermentation processes require an efficient and possibly comprehensive analysis of the physiology of the production system throughout the process development. Furthermore, to ensure a good quality control of established bioprocesses, on-line analysis techniques for the determination of marker gene expression are of interest to monitor the productivity and the safety of bioprocesses. A prerequisite for such analyses is the knowledge of genes, the expression of which is critical either for the productivity or for the performance of the bioprocess. This work reviews marker genes that are specific indicators for stress- and nutrient-limitation conditions or for the physiological status of the bacterial production hosts Bacillus subtilis, Bacillus licheniformis and Escherichia coli. The suitability of existing gene expression analysis techniques for bioprocess monitoring is discussed. Analytical approaches that enable a robust and sensitive determination of selected marker mRNAs or proteins are presented.
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Affiliation(s)
- Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany.
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29
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From the genome sequence to the protein inventory of Bacillus subtilis. Proteomics 2011; 11:2971-80. [DOI: 10.1002/pmic.201100090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/07/2011] [Accepted: 04/20/2011] [Indexed: 12/12/2022]
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Schroeter R, Voigt B, Jürgen B, Methling K, Pöther DC, Schäfer H, Albrecht D, Mostertz J, Mäder U, Evers S, Maurer KH, Lalk M, Mascher T, Hecker M, Schweder T. The peroxide stress response of Bacillus licheniformis. Proteomics 2011; 11:2851-66. [DOI: 10.1002/pmic.201000461] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Revised: 03/27/2011] [Accepted: 05/03/2011] [Indexed: 12/31/2022]
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Wu D, He J, Gong Y, Chen D, Zhu X, Qiu N, Sun M, Li M, Yu Z. Proteomic analysis reveals the strategies of Bacillus thuringiensis
YBT-1520 for survival under long-term heat stress. Proteomics 2011; 11:2580-91. [DOI: 10.1002/pmic.201000392] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 03/04/2011] [Accepted: 03/14/2011] [Indexed: 11/05/2022]
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Elsholz AKW, Hempel K, Pöther DC, Becher D, Hecker M, Gerth U. CtsR inactivation during thiol-specific stress in low GC, Gram+ bacteria. Mol Microbiol 2011; 79:772-85. [DOI: 10.1111/j.1365-2958.2010.07489.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Shih TW, Pan TM. Stress responses of thermophilic Geobacillus sp. NTU 03 caused by heat and heat-induced stress. Microbiol Res 2010; 166:346-59. [PMID: 20869219 DOI: 10.1016/j.micres.2010.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 08/02/2010] [Accepted: 08/08/2010] [Indexed: 11/26/2022]
Abstract
A batch culture of Geobacillus sp. NTU 03 was subjected to a rapid temperature shift for investigating the stress response. Several known heat-shock responses for protein, DNA, and cell membrane recurring were observed on two-dimensional (2D) gels. Heat caused protein and cell membrane disruption greatly affected the electron transport chain. Further, heat caused lower dissolved oxygen (DO) solubility resulting in insufficient oxygen to be electron acceptor, and the NADH could not be reoxidized. Hence, we observed seven dehydrogenase that used NADH as electron donor were downregulated on the 2D gels. In contrast, succinate dehydrogenase that used FADH(2) as electron donor was upregulated. However, this induction may simultaneously increase generation of superoxide; therefore the cellular redox state was imbalanced. We observed that superoxide dismutase (2D gel) and zinc ion ABC transporter (mRNA quantification) were upregulated, whereas ferric ion ABC transporter (2D gel and mRNA quantification) was downregulated. Increase in the reactive oxygen or nitrogen species scavenging activities were also observed. For responding the lower DO solubility, a transient activation of nitrate respiration was observed at transcriptional level. Our results support the view that both heat stress and heat-induced stress should be considered together when investigating the stress responses of thermophiles.
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Affiliation(s)
- Tsung-Wei Shih
- Department of Biochemical Science & Technology, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei, Taiwan
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Bobadilla Fazzini RA, Preto MJ, Quintas ACP, Bielecka A, Dos Santos VAPM. Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture. Environ Microbiol 2010; 12:2436-49. [PMID: 20406297 DOI: 10.1111/j.1462-2920.2010.02217.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The high complexity of naturally occurring microbial communities is the major drawback limiting the study of these important biological systems. In this study, a comparison between pure cultures of Pseudomonas reinekei sp. strain MT1 and stable community cultures composed of MT1 plus the addition of Achromobacter xylosoxidans strain MT3 (in a steady-state proportion 9:1) was used as a model system to study bacterial interactions that take place under simultaneous chemical and oxidative stress. Both are members of a real community isolated from a polluted sediment by enrichment in 4-chlorosalicylate (4CS). The analysis of dynamic states was carried out at the proteome, metabolic profile and population dynamic level. Differential protein expression was evaluated under exposure to 4CS and high concentrations of toxic intermediates (4-chlorocatechol and protoanemonin), including proteins from several functional groups and particularly enzymes of aromatic degradation pathways and outer membrane proteins. Remarkably, 4CS addition generated a strong oxidative stress response in pure strain MT1 culture led by alkyl hydroperoxide reductase, while the community showed an enhanced central metabolism response, where A. xylosoxidans MT3 helped to prevent toxic intermediate accumulation. A significant change in the outer membrane composition of P. reinekei MT1 was observed during the chemical stress caused by 4CS and in the presence of A. xylosoxidans MT3, highlighting the expression of the major outer membrane protein OprF, tightly correlated to 4CC concentration profile and its potential detoxification role.
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Nakano MM, Lin A, Zuber CS, Newberry KJ, Brennan RG, Zuber P. Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit. PLoS One 2010; 5:e8664. [PMID: 20084284 PMCID: PMC2801614 DOI: 10.1371/journal.pone.0008664] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 12/19/2009] [Indexed: 12/20/2022] Open
Abstract
Background Spx, an ArsC (arsenate reductase) family member, is a global transcriptional regulator of the microbial stress response and is highly conserved amongst Gram-positive bacteria. Bacillus subtilis Spx protein exerts positive and negative control of transcription through its interaction with the C-terminal domain of the RNA polymerase (RNAP) α subunit (αCTD). Spx activates trxA (thioredoxin) and trxB (thioredoxin reductase) in response to thiol stress, and bears an N-terminal C10XXC13 redox disulfide center that is oxidized in active Spx. Methodology/Principal Findings The structure of mutant SpxC10S showed a change in the conformation of helix α4. Amino acid substitutions R60E and K62E within and adjacent to helix α4 conferred defects in Spx-activated transcription but not Spx-dependent repression. Electrophoretic mobility-shift assays showed αCTD interaction with trxB promoter DNA, but addition of Spx generated a supershifted complex that was disrupted in the presence of reductant (DTT). Interaction of αCTD/Spx complex with promoter DNA required the cis-acting elements -45AGCA-42 and -34AGCG-31 of the trxB promoter. The SpxG52R mutant, defective in αCTD binding, did not interact with the αCTD-trxB complex. SpxR60E not only failed to complex with αCTD-trxB, but also disrupted αCTD-trxB DNA interaction. Conclusions/Significance The results show that Spx and αCTD form a complex that recognizes the promoter DNA of an Spx-controlled gene. A conformational change during oxidation of Spx to the disulfide form likely alters the structure of Spx α helix α4, which contains residues that function in transcriptional activation and αCTD/Spx-promoter interaction. The results suggest that one of these residues, R60 of the α4 region of oxidized Spx, functions in αCTD/Spx-promoter contact but not in αCTD interaction.
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Affiliation(s)
- Michiko M. Nakano
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Ann Lin
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Cole S. Zuber
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Kate J. Newberry
- Department of Biochemistry and Molecular Biology, University of Texas, M. D. Anderson Cancer Center, Texas, United States of America
| | - Richard G. Brennan
- Department of Biochemistry and Molecular Biology, University of Texas, M. D. Anderson Cancer Center, Texas, United States of America
| | - Peter Zuber
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, Beaverton, Oregon, United States of America
- * E-mail:
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Ueta M, Wada C, Wada A. Formation of 100S ribosomes in Staphylococcus aureus by the hibernation promoting factor homolog SaHPF. Genes Cells 2009; 15:43-58. [PMID: 20015224 DOI: 10.1111/j.1365-2443.2009.01364.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In the stationary growth phase of Escherichia coli, the 70S ribosomes are dimerized by the ribosome modulation factor (RMF) and hibernation promoting factor (HPF) proteins to form 100S ribosomes, which lose translational activity. In this study we found 100S ribosomes in the gram-positive bacterium Staphylococcus aureus, which has an HPF homolog (named SaHPF) but no RMF homolog. Unlike in E. coli, 100S ribosomes exist in all growth phases of S. aureus, with the highest levels at the transition from the exponential phase to the stationary phase. To find the key factors involved in 100S formation, we analyzed proteins associated with crude ribosomes using radical-free and highly reducing 2-D PAGE and MALDI TOF/MS. Only the SaHPF levels changed in parallel with the changes in 100S levels. SaHPF bound preferentially to 70S components in 100S ribosomes, with a molar ratio of 1 : 1 relative to the 70S, but some SaHPF was also detected in free 70S ribosomes. High-salt washing of the crude ribosomes released SaHPF and dissociated the 100S ribosomes to their 70S components. When these 70S components were incubated with purified SaHPF in vitro, they re-associated to form 100S. These results suggest that SaHPF is a key protein involved in 100S ribosome formation in S. aureus.
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Affiliation(s)
- Masami Ueta
- Yoshida Biological Laboratory, 11-1, Takehanasotoda-cho, Yamashina-ku, Kyoto 607-8081, Japan
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Red light activates the sigmaB-mediated general stress response of Bacillus subtilis via the energy branch of the upstream signaling cascade. J Bacteriol 2009; 192:755-62. [PMID: 19948797 DOI: 10.1128/jb.00826-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The sigma(B)-dependent general stress response in the common soil bacterium Bacillus subtilis can be elicited by a range of stress factors, such as starvation or an ethanol, salt, or heat shock, via a complex upstream signaling cascade. Additionally, sigma(B) can be activated by blue light via the phototropin homologue YtvA, a component of the environmental branch of the signaling cascade. Here we use a reporter-gene fusion to show that sigma(B) can also be activated by red light via the energy branch of its upstream signaling cascade. Deletion mutagenesis and homologous overproduction experiments indicate that the RsbP protein (composed of an N-terminal Per-ARNT-Sim [PAS] domain and a C-terminal PP2C-type phosphatase domain) is involved in the red light response. This second light input pathway functions complementarily to YtvA; it shows broader spectral sensitivity but requires higher light intensities. These results are confirmed by transcriptome analyses, which show that both light effects result in upregulation of the sigma(B) regulon, with minimal activation of other responses.
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38
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A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol 2009; 192:870-82. [PMID: 19948795 DOI: 10.1128/jb.01106-09] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In its natural habitats, Bacillus subtilis is exposed to changing osmolarity, necessitating adaptive stress responses. Transcriptomic and proteomic approaches can provide a picture of the dynamic changes occurring in salt-stressed B. subtilis cultures because these studies provide an unbiased view of cells coping with high salinity. We applied whole-genome microarray technology and metabolic labeling, combined with state-of-the-art proteomic techniques, to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic upshift. This combined experimental approach provided quantitative data for 3,961 mRNA transcription profiles, 590 expression profiles of proteins detected in the cytosol, and 383 expression profiles of proteins detected in the membrane fraction. Our study uncovered a well-coordinated induction of gene expression subsequent to an osmotic upshift that involves large parts of the SigB, SigW, SigM, and SigX regulons. Additionally osmotic upregulation of a large number of genes that do not belong to these regulons was observed. In total, osmotic upregulation of about 500 B. subtilis genes was detected. Our data provide an unprecedented rich basis for further in-depth investigation of the physiological and genetic responses of B. subtilis to hyperosmotic stress.
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Abstract
The spore-forming bacterium and model prokaryotic genetic system, Bacillus subtilis, is extremely useful in the study of oxidative stress management through proteomic and genome-wide transcriptomic analyses, as well as through detailed structural studies of the regulatory factors that govern the oxidative stress response. The factors that sense oxidants and induce expression of protective activities include the PerR and OhrR proteins, which show acute discrimination for their peroxide stimuli, whereas the general stress control factor, the RNA polymerase sigma(B) subunit and the thiol-based sensor Spx, govern the protective response to oxidants under multiple stress conditions. Some specific and some redundant protective mechanisms are mobilized at different stages of the Bacillus developmental cycle to deal with vulnerable cells in stationary-phase conditions and during spore germination and outgrowth. An important unknown is the nature and influence of the low-molecular-weight thiols that mediate the buffering of the redox environment.
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Affiliation(s)
- Peter Zuber
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, Beaverton, Oregon 97006, USA.
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40
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Atack JM, Kelly DJ. Oxidative stress in Campylobacter jejuni: responses, resistance and regulation. Future Microbiol 2009; 4:677-90. [PMID: 19659424 DOI: 10.2217/fmb.09.44] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Campylobacter jejuni is a major food-borne human pathogen that paradoxically is an oxygen-sensitive microaerophile, yet must resist the oxidative stresses encountered both in the host and in the environment. Recent studies suggest that, perhaps surprisingly, C. jejuni contains a wide range of enzymes involved in oxidative stress defense, and this review focuses on the properties and roles of these proteins. Although the mechanisms of gene regulation are still poorly understood in C. jejuni, several regulators of the oxidative stress response have been identified and their properties are discussed here. We suggest that future studies should be directed towards identifying the role of additional and less well characterized components involved in oxidative stress resistance, as well as providing a more complete picture of the underlying sensing and regulatory mechanisms.
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Affiliation(s)
- John M Atack
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, The University of Sheffield, Sheffield, S3 7HF, UK
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41
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Hecker M, Reder A, Fuchs S, Pagels M, Engelmann S. Physiological proteomics and stress/starvation responses in Bacillus subtilis and Staphylococcus aureus. Res Microbiol 2009; 160:245-58. [PMID: 19403106 DOI: 10.1016/j.resmic.2009.03.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/20/2009] [Accepted: 03/23/2009] [Indexed: 10/20/2022]
Abstract
Gel-based proteomics is a useful approach for visualizing the responses of bacteria to stress and starvation stimuli. In order to face stress/starvation, bacteria have developed very complicated gene expression networks. A proteomic view of stress/starvation responses, however, is only a starting point which should promote follow-up studies aimed at the comprehensive description of single regulons, their signal transduction pathways on the one hand, and their adaptive functions on the other, and finally their integration into complex gene expression networks. This "road map of physiological proteomics" will be demonstrated for the general stress regulon controlled by sigma(B) in Bacillus subtilis and the oxygen starvation response with Rex as a master regulator in Staphylococcus aureus.
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Affiliation(s)
- Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Jahnstrasse 15A, 17487 Greifswald, Germany.
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42
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Lacerda CMR, Reardon KF. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:75-87. [PMID: 19279070 DOI: 10.1093/bfgp/elp005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.
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Affiliation(s)
- Carla M R Lacerda
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
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43
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Wolf C, Hochgräfe F, Kusch H, Albrecht D, Hecker M, Engelmann S. Proteomic analysis of antioxidant strategies of Staphylococcus aureus: diverse responses to different oxidants. Proteomics 2008; 8:3139-53. [PMID: 18604844 DOI: 10.1002/pmic.200701062] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The high resolution 2-D protein gel electrophoresis technique combined with MALDI-TOF MS and a recently developed fluorescence-based thiol modification assay were used to investigate the cellular response of Staphylococcus aureus to oxidative stress. Addition of hydrogen peroxide, diamide, and the superoxide generating agent paraquat to exponentially growing cells revealed complex changes in the protein expression pattern. In particular, proteins involved in detoxification, repair systems, and intermediary metabolism were found to be up-regulated. Interestingly, there is only a small overlap of proteins induced by all these stressors. Exposure to hydrogen peroxide mediated a significant increase of DNA repair enzymes, whereas treatment with diamide affected proteins involved in protein repair and degradation. The activity of proteins under oxidative stress conditions can be modulated by oxidation of thiol groups. In growing cells, protein thiols were found to be mainly present in the reduced state. Diamide mediated a strong increase of reversibly oxidized thiols in a variety of metabolic enzymes. By contrast, hydrogen peroxide resulted in the reversible oxidation especially of proteins with active site cysteines. Moreover, high levels of hydrogen peroxide influenced the pI of three proteins containing cysteines within their active sites (GapA1, AhpC, and HchA) indicating the generation of sulfinic or sulfonic acid by irreversible oxidation of thiols.
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Affiliation(s)
- Carmen Wolf
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
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44
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Hecker M, Antelmann H, Büttner K, Bernhardt J. Gel-based proteomics of Gram-positive bacteria: A powerful tool to address physiological questions. Proteomics 2008; 8:4958-75. [DOI: 10.1002/pmic.200800278] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Palomino MM, Sanchez-Rivas C, Ruzal SM. High salt stress in Bacillus subtilis: involvement of PBP4* as a peptidoglycan hydrolase. Res Microbiol 2008; 160:117-24. [PMID: 19063962 DOI: 10.1016/j.resmic.2008.10.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 10/21/2008] [Accepted: 10/29/2008] [Indexed: 11/19/2022]
Abstract
The study was focused on the role of the penicillin binding protein PBP4* of Bacillus subtilis during growth in high salinity rich media. Using pbpE-lacZ fusion, we found that transcription of the pbpE gene is induced in stationary phase and by increased salinity. This increase was also corroborated at the translation level for PBP4* by western blot. Furthermore, we showed that a strain harboring gene disruption in the structural gene (pbpE) for the PBP4* endopeptidase resulted in a salt-sensitive phenotype and increased sensitivity to cell envelope active antibiotics (vancomycin, penicillin and bacitracin). Since the pbpE gene seems to be part of a two-gene operon with racX, a racX::pRV300 mutant was obtained. This mutant behaved like the wild-type strain with respect to high salt. Electron microscopy showed that high salt and mutation of pbpE resulted in cell wall defects. Whole cells or purified peptidoglycan from WT cultures grown in high salt medium showed increased autolysis and susceptibility to mutanolysin. We demonstrate through zymogram analysis that PBP4* has murein hydrolyze activity. All these results support the hypothesis that peptidoglycan is modified in response to high salt and that PBP4* contributes to this modification.
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Affiliation(s)
- María Mercedes Palomino
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Ciudad Universitaria Pabellón II 4 piso, Buenos Aires, Argentina
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Garénaux A, Guillou S, Ermel G, Wren B, Federighi M, Ritz M. Role of the Cj1371 periplasmic protein and the Cj0355c two-component regulator in the Campylobacter jejuni NCTC 11168 response to oxidative stress caused by paraquat. Res Microbiol 2008; 159:718-26. [PMID: 18775777 DOI: 10.1016/j.resmic.2008.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 08/03/2008] [Indexed: 10/21/2022]
Abstract
Campylobacter jejuni is a microaerophilic pathogen representing one of the major causes of bacterial enteritis in humans. The oxidative stress response after exposure to paraquat, a strong oxidising agent, was analysed by two-dimensional protein electrophoresis and Maldi-ToF mass spectrometry. Oxidative stress and redox-related proteins were overexpressed: FldA flavodoxin and a pyruvate-flavodoxin oxidoreductase encoded by cj1476c. No increase in SodB expression was observed. An additional quantitative RT-PCR analysis showed an increase in katA but not in sodB expression. However, the sodB mutant was very sensitive to paraquat, its basal expression level being essential for oxidative stress resistance. Proteins related to iron homeostasis (Cft and a non-haem iron protein encoded by cj0012c) and general stress response (FusA and MreB) were found overexpressed. Interestingly, a two-component regulator encoded by cj0355c was differentially expressed in the presence of paraquat and could play a role in induction of the C. jejuni oxidative stress response. Virulence factors (CadF, FlaA and a VacJ homolog encoded by cj1371) were also found overexpressed under oxidative stress conditions and a cj1371 mutant showed increased sensitivity to paraquat, suggesting that the Cj1371 periplasmic protein could play a role in C. jejuni oxidative stress resistance.
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Affiliation(s)
- Amélie Garénaux
- UMR-INRA 1014 SECALIM ENVN/ENITIAA, Ecole Nationale Vétérinaire de Nantes, Route de Gachet-La Chantrerie, BP 40706, 44307 Nantes cedex 03, France.
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Lu J, Yang F, Li Y, Zhang X, Xia B, Jin C. Reversible conformational switch revealed by the redox structures of Bacillus subtilis thiol peroxidase. Biochem Biophys Res Commun 2008; 373:414-8. [PMID: 18588855 DOI: 10.1016/j.bbrc.2008.06.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 06/13/2008] [Indexed: 11/18/2022]
Abstract
Bacterial thiol peroxidase (Tpx) is the periplasmic antioxidant enzyme widely distributed in most bacterial species, which catalyzes the reduction of lipid hydroperoxide in vivo. Tpx belongs to the atypical 2-Cys peroxiredoxin (Prx) family and utilizes two active cysteine residues during the redox reaction. Although several crystal structures of Tpx are available, no pair of the redox structures reported thus far. Therefore, the conformational changes coupled to the catalytic reaction remain unclear. Herein, we report the solution structures of Bacillus subtilis Tpx in both the reduced and oxidized forms, the first pair of Tpx structures. The overall structures of both forms are very similar, however, significant differences at the active regions around the C(P) and C(R) residues were observed. In particular, a helix-to-coil transition was observed at the C(R) region between the two forms. Our study reveals a dynamic picture of the conformational switch coupled to the redox reaction, thus provides further insights in understanding the catalytic mechanism of bacterial Tpx.
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Affiliation(s)
- Jie Lu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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48
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Nitric oxide stress induces different responses but mediates comparable protein thiol protection in Bacillus subtilis and Staphylococcus aureus. J Bacteriol 2008; 190:4997-5008. [PMID: 18487332 DOI: 10.1128/jb.01846-07] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nonpathogenic Bacillus subtilis and the pathogen Staphylococcus aureus are gram-positive model organisms that have to cope with the radical nitric oxide (NO) generated by nitrite reductases of denitrifying bacteria and by the inducible NO synthases of immune cells of the host, respectively. The response of both microorganisms to NO was analyzed by using a two-dimensional gel approach. Metabolic labeling of the proteins revealed major changes in the synthesis pattern of cytosolic proteins after the addition of the NO donor MAHMA NONOate. Whereas B. subtilis induced several oxidative stress-responsive regulons controlled by Fur, PerR, OhrR, and Spx, as well as the general stress response controlled by the alternative sigma factor SigB, the more resistant S. aureus showed an increased synthesis rate of proteins involved in anaerobic metabolism. These data were confirmed by nuclear magnetic resonance analyses indicating that NO causes a drastically higher increase in the formation of lactate and butanediol in S. aureus than in B. subtilis. Monitoring the intracellular protein thiol state, we observed no increase in reversible or irreversible protein thiol modifications after NO stress in either organism. Obviously, NO itself does not cause general protein thiol oxidations. In contrast, exposure of cells to NO prior to peroxide stress diminished the irreversible thiol oxidation caused by hydrogen peroxide.
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Marco ML, Wells-Bennik MH. Impact of bacterial genomics on determining quality and safety in the dairy production chain. Int Dairy J 2008. [DOI: 10.1016/j.idairyj.2007.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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50
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Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem 2008; 143:425-33. [PMID: 18174192 DOI: 10.1093/jb/mvm243] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the stationary phase of growth in Escherichia coli, ribosome modulation factor (RMF) and hibernation promoting factor (HPF) dimerize most 70S ribosomes to form 100S ribosomes. The process of 100S formation has been termed 'ribosomal hibernation'. Here, the contributions of HPF to 100S formation and translation were analysed in vitro. HPF bound to, but did not dimerize the 70S ribosome. RMF dimerized and formed immature 90S ribosomes. Binding of both HPF and RMF converted 90S ribosomes to mature 100S ribosomes, which is consistent with the in vivo data. The role of HPF in in vitro translation also was investigated. In an artificial mRNA poly (U)-dependent phenylalanine incorporation assay, HPF bound to ribosomal particles and inhibited translation. In contrast, in a natural MS2 mRNA-dependent leucine incorporation assay, bound HPF was removed and hardly inhibited normal translation. Multiple alignment and phylogenetic analyses indicates that the hibernation system mediated by the HPF homologue, RMF and 100S ribosome formation may be specific to the proteobacteria gamma group. In contrast, most bacteria have at least one HPF homologue, and these homologues can be classified into three types, long HPF, short HPF and YfiA.
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Affiliation(s)
- Masami Ueta
- Department of Physics, Osaka Medical College, Takatsuki, Osaka, Japan
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