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Coorssen JR, Padula MP. Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience. Proteomes 2024; 12:14. [PMID: 38651373 PMCID: PMC11036260 DOI: 10.3390/proteomes12020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.
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Affiliation(s)
- Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE), St. Catharines, ON L2N 4X2, Canada
| | - Matthew P. Padula
- School of Life Sciences and Proteomics, Lipidomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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2
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Wagner GE, Stanjek TFP, Albrecht D, Lipp M, Dunachie SJ, Föderl-Höbenreich E, Riedel K, Kohler A, Steinmetz I, Kohler C. Deciphering the human antibody response against Burkholderia pseudomallei during melioidosis using a comprehensive immunoproteome approach. Front Immunol 2023; 14:1294113. [PMID: 38146371 PMCID: PMC10749318 DOI: 10.3389/fimmu.2023.1294113] [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: 09/14/2023] [Accepted: 11/22/2023] [Indexed: 12/27/2023] Open
Abstract
Introduction The environmental bacterium Burkholderia pseudomallei causes the often fatal and massively underreported infectious disease melioidosis. Antigens inducing protective immunity in experimental models have recently been identified and serodiagnostic tools have been improved. However, further elucidation of the antigenic repertoire of B. pseudomallei during human infection for diagnostic and vaccine purposes is required. The adaptation of B. pseudomallei to very different habitats is reflected by a huge genome and a selective transcriptional response to a variety of conditions. We, therefore, hypothesized that exposure of B. pseudomallei to culture conditions mimicking habitats encountered in the human host might unravel novel antigens that are recognized by melioidosis patients. Methods and results In this study, B. pseudomallei was exposed to various stress and growth conditions, including anaerobiosis, acid stress, oxidative stress, iron starvation and osmotic stress. Immunogenic proteins were identified by probing two-dimensional Western blots of B. pseudomallei intracellular and extracellular protein extracts with sera from melioidosis patients and controls and subsequent MALDI-TOF MS. Among B. pseudomallei specific immunogenic signals, 90 % (55/61) of extracellular immunogenic proteins were identified by acid, osmotic or oxidative stress. A total of 84 % (44/52) of intracellular antigens originated from the stationary growth phase, acidic, oxidative and anaerobic conditions. The majority of the extracellular and intracellular protein antigens were identified in only one of the various stress conditions. Sixty-three immunoreactive proteins and an additional 38 candidates from a literature screening were heterologously expressed and subjected to dot blot analysis using melioidosis sera and controls. Our experiments confirmed melioidosis-specific signals in 58 of our immunoproteome candidates. These include 15 antigens with average signal ratios (melioidosis:controls) greater than 10 and another 26 with average ratios greater than 5, including new promising serodiagnostic candidates with a very high signal-to-noise ratio. Conclusion Our study shows that a comprehensive B. pseudomallei immunoproteomics approach, using conditions which are likely to be encountered during infection, can identify novel antibody targets previously unrecognized in human melioidosis.
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Affiliation(s)
- Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Michaela Lipp
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Susanna J. Dunachie
- Nuffield Department of Medicine (NDM) Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Esther Föderl-Höbenreich
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Diagnostic & Research Institute of Pathology, Medical University Graz, Graz, Austria
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Anne Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine, Greifswald, Germany
| | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine, Greifswald, Germany
| | - Christian Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine, Greifswald, Germany
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3
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Pimentel-Filho NDJ, Fuchs S, Baracat-Pereira MC, Mantovani HC, Riedel K, Vanetti MCD. Protein expression profiling of Staphylococcus aureus in response to the bacteriocin bovicin HC5. Appl Microbiol Biotechnol 2021; 105:7857-7869. [PMID: 34554273 DOI: 10.1007/s00253-021-11594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Alternative strategies to antibiotic treatment are required to inhibit pathogens, including Staphylococcus aureus. Bacteriocins, such as the lantibiotic bovicin HC5, have shown potential to control pathogens. This study aims to evaluate the stress response of S. aureus to bovicin HC5 using a proteomic approach. Sublethal concentrations of the bacteriocin repressed the synthesis of 62 cytoplasmic proteins, whereas 42 proteins were induced in S. aureus COL. Specifically, synthesis of several proteins involved in amino acid biosynthesis, mainly products of ilv-leu operon, and DNA metabolism, such as DNA polymerase I, decreased following bovicin treatment while proteins involved in catabolism, mainly tricarboxylic acid cycle metabolism, and chaperones were over-expressed. The levels of CodY and CcpA, important regulators involved in the stationary phase adaptation and catabolite repression, respectively, also increased in the presence of the bacteriocin. These results indicate that stress caused by the sublethal concentration of bovicin HC5 in the cell membrane results in growth reduction, reduced protein synthesis, and, at the same time, enhanced the levels of chaperones and enzymes involved in energy-efficient catabolism in an attempt to restore energy and cell homeostasis. These results bring relevant information to amplify the knowledge concerning the bacterial physiological changes in response to the stress caused by the cell exposition to bovicin HC5. New potential targets for controlling this pathogen can also be determined from the new protein expression pattern presented. KEY POINTS: • Bovicin HC5 changed the synthesis of cytoplasmic proteins of S. aureus. • Bovicin HC5 interfered in the synthesis of proteins of amino acids biosynthesis. • Synthesis of chaperones enhanced in the presence of sublethal dosage of bovicin HC5.
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Affiliation(s)
- Natan de Jesus Pimentel-Filho
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-000, Brazil.,Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17489, Greifswald, Germany.,Centro de Ciências da Natureza, Universidade Federal de São Carlos, Rod. Lauri Simões de Barros, km 12 - SP 189, Buri, SP, 18290-000, Brazil
| | - Stephan Fuchs
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17489, Greifswald, Germany
| | - Maria Cristina Baracat-Pereira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-000, Brazil
| | - Hilário Cuquetto Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-000, Brazil
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17489, Greifswald, Germany
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4
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Kohler C, Proctor RA, Bayer AS, Yeaman MR, Lalk M, Engelmann S, Mishra NN. Proteomic and Membrane Lipid Correlates of Reduced Host Defense Peptide. Antibiotics (Basel) 2019; 8:antibiotics8040169. [PMID: 31569354 PMCID: PMC6963496 DOI: 10.3390/antibiotics8040169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/31/2022] Open
Abstract
We previously described a transposon mutant in Staphylococcus aureus strain SH1000 that exhibited reduced susceptibility to cationic thrombin-induced platelet microbicidal proteins (tPMPs). The transposon insertion site was mapped to the gene snoD, the staphylococcal nuo orthologue. Hence, further studies have been performed to understand how this mutation impacts susceptibility to tPMP, by comparing proteomics profiling and membrane lipid analyses of the parent vs. mutant strains. Surprisingly, the mutant showed differential regulation of only a single protein when cultivated aerobically (FadB), and only a small number of proteins under anaerobic growth conditions (AdhE, DapE, Ddh, Ald1, IlvA1, AgrA, Rot, SA2366, and SA2367). Corresponding to FadB impact on lipid remodeling, membrane fatty acid analyses showed that the snoD mutant contained more short chain anteiso-, but fewer short chain iso-branched chain fatty acids under both aerobic and anaerobic conditions vs. the parental strain. Based upon these proteomic and membrane compositional data, a hypothetical “network” model was developed to explain the impact of the snoD mutation upon tPMP susceptibility.
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Affiliation(s)
- Christian Kohler
- Universität Greifswald, Institut für Mikrobiologie und Molekularbiologie,17487 Greifswald, Germany.
| | - Richard A Proctor
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
| | - Arnold S Bayer
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center Torrance, CA 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Michael R Yeaman
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center Torrance, CA 90502, USA.
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
- Division of Molecular Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.
| | - Michael Lalk
- University Greifswald, Institute of Biochemistry, 17487 Greifswald, Germany.
| | - Susanne Engelmann
- Universität Greifswald, Institut für Mikrobiologie und Molekularbiologie,17487 Greifswald, Germany.
- Institute for Microbiology, Technical University Braunschweig, Institute for Microbiology, 38106 Braunschweig, Germany.
- Helmholtz Center for Infectious Research, Microbial Proteomics, 38124 Braunschweig, Germany.
| | - Nagendra N Mishra
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center Torrance, CA 90502, USA.
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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5
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Handtke S, Albrecht D, Otto A, Becher D, Hecker M, Voigt B. The Proteomic Response of Bacillus pumilus Cells to Glucose Starvation. Proteomics 2019; 18. [PMID: 29193752 DOI: 10.1002/pmic.201700109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 10/23/2017] [Indexed: 01/07/2023]
Abstract
Since starvation for carbon sources is a common condition for bacteria in nature and it can also occur in industrial fermentation processes due to mixing zones, knowledge about the response of cells to carbon starvation is beneficial. The preferred carbon source for bacilli is glucose. The response of Bacillus pumilus cells to glucose starvation using metabolic labeling and quantitative proteomics was analyzed. Glucose starvation led to an extensive reprogramming of the protein expression pattern in B. pumilus. The amounts of proteins of the central carbon metabolic pathways (glycolysis and TCC) remained stable in starving cells. Proteins for gluconeogenesis were found in higher amounts during starvation. Furthermore, many proteins involved in acquisition and usage of alternative carbon sources were present in elevated amounts in starving cells. Enzymes for fatty acid degradation and proteases and peptidases were also found in higher abundance when cells entered stationary phase. Among the proteins found in lower amounts were many enzymes involved in amino acid and nucleotide synthesis and several NRPS and PKS proteins.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany
| | - Andreas Otto
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology,, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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6
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Burby PE, Simmons ZW, Simmons LA. DdcA antagonizes a bacterial DNA damage checkpoint. Mol Microbiol 2019; 111:237-253. [PMID: 30315724 PMCID: PMC6351180 DOI: 10.1111/mmi.14151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
Abstract
Bacteria coordinate DNA replication and cell division, ensuring a complete set of genetic material is passed onto the next generation. When bacteria encounter DNA damage, a cell cycle checkpoint is activated by expressing a cell division inhibitor. The prevailing model is that activation of the DNA damage response and protease-mediated degradation of the inhibitor is sufficient to regulate the checkpoint process. Our recent genome-wide screens identified the gene ddcA as critical for surviving exposure to DNA damage. Similar to the checkpoint recovery proteases, the DNA damage sensitivity resulting from ddcA deletion depends on the checkpoint enforcement protein YneA. Using several genetic approaches, we show that DdcA function is distinct from the checkpoint recovery process. Deletion of ddcA resulted in sensitivity to yneA overexpression independent of YneA protein levels and stability, further supporting the conclusion that DdcA regulates YneA independent of proteolysis. Using a functional GFP-YneA fusion we found that DdcA prevents YneA-dependent cell elongation independent of YneA localization. Together, our results suggest that DdcA acts by helping to set a threshold of YneA required to establish the cell cycle checkpoint, uncovering a new regulatory step controlling activation of the DNA damage checkpoint in Bacillus subtilis.
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Affiliation(s)
- Peter E. Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Zackary W. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
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7
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Alimohammadi F, Sharifian Gh M, Attanayake NH, Thenuwara AC, Gogotsi Y, Anasori B, Strongin DR. Antimicrobial Properties of 2D MnO 2 and MoS 2 Nanomaterials Vertically Aligned on Graphene Materials and Ti 3C 2 MXene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7192-7200. [PMID: 29782792 DOI: 10.1021/acs.langmuir.8b00262] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Two-dimensional (2D) nanomaterials have attracted considerable attention in biomedical and environmental applications due to their antimicrobial activity. In the interest of investigating the primary antimicrobial mode-of-action of 2D nanomaterials, we studied the antimicrobial properties of MnO2 and MoS2, toward Gram-positive and Gram-negative bacteria. Bacillus subtilis and Escherichia coli bacteria were treated individually with 100 μg/mL of randomly oriented and vertically aligned nanomaterials for ∼3 h in the dark. The vertically aligned 2D MnO2 and MoS2 were grown on 2D sheets of graphene oxide, reduced graphene oxide, and Ti3C2 MXene. Measurements to determine the viability of bacteria in the presence of the 2D nanomaterials performed by using two complementary techniques, flow cytometry, and fluorescence imaging showed that, while MnO2 and MoS2 nanosheets show different antibacterial activities, in both cases, Gram-positive bacteria show a higher loss in membrane integrity. Scanning electron microscopy images suggest that the 2D nanomaterials, which have a detrimental effect on bacteria viability, compromise the cell wall, leading to significant morphological changes. We propose that the peptidoglycan mesh (PM) in the bacterial wall is likely the primary target of the 2D nanomaterials. Vertically aligned 2D MnO2 nanosheets showed the highest antimicrobial activity, suggesting that the edges of the nanosheets were likely compromising the cell walls upon contact.
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Affiliation(s)
- Farbod Alimohammadi
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Mohammad Sharifian Gh
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Nuwan H Attanayake
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Akila C Thenuwara
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Yury Gogotsi
- Department of Materials Science and Engineering, and A. J. Drexel Nanomaterials Institute , Drexel University , Philadelphia , Pennsylvania 19104 , United States
| | - Babak Anasori
- Department of Materials Science and Engineering, and A. J. Drexel Nanomaterials Institute , Drexel University , Philadelphia , Pennsylvania 19104 , United States
| | - Daniel R Strongin
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
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8
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Abstract
Absolute protein quantification for the analysis of proteome dynamics is more and more required by the scientific community. Therefore a number of methods have recently been reported that aim at determining concentrations of single proteins in complex samples, all of them having their advantages and limitations. However, for all of these methods an accurate and protein unspecific determination of the total protein amount in a given sample is urgently needed. Here a ninhydrin-based assay established to reach this goal is described. Moreover, an optimized protocol for protein digestion is an inevitable prerequisite for all mass spectrometry-based approaches aiming at absolute protein quantification. In this chapter, various aspects are described which have to be considered during validation of a suitable digestion method and a detailed protocol is presented that can be applied to the digestion of soluble proteins originated from microbes.In order to provide an absolute protein quantification workflow applicable for small scale and large scale approaches, a step-by-step guide is provided for the so-called AQUA-strategy (AQUA = absolute quantification), including selection of suited standard peptides, the development of optimized MS methods and the determination of absolute protein concentration using stable isotope dilution and selected reaction monitoring (SID-SRM). Subsequently, a workflow is introduced that combines targeted mass spectrometry and two-dimensional polyacrylamide gel electrophoresis for the large-scale determination of absolute protein amounts.
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Affiliation(s)
- Sandra Maaß
- Department of Microbial Proteomics, Institute for Microbiology, University Greifswald, Greifswald, Germany.
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9
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Hentschker C, Dewald C, Otto A, Büttner K, Hecker M, Becher D. Global quantification of phosphoproteins combining metabolic labeling and gel-based proteomics in B. pumilus. Electrophoresis 2017; 39:334-343. [DOI: 10.1002/elps.201700220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 09/11/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Christian Hentschker
- Department of Microbial Proteomics; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Carolin Dewald
- Chair of Materials Science; Otto Schott Institute of Materials Research; Friedrich-Schiller-University Jena; Jena Germany
| | - Andreas Otto
- Department of Microbial Proteomics; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Knut Büttner
- Department of Microbial Physiology and Molecular Biology; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Michael Hecker
- Department of Microbial Physiology and Molecular Biology; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Dörte Becher
- Department of Microbial Proteomics; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
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10
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Handtke S, Albrecht D, Zühlke D, Otto A, Becher D, Schweder T, Riedel K, Hecker M, Voigt B. Bacillus pumilus KatX2 confers enhanced hydrogen peroxide resistance to a Bacillus subtilis PkatA::katX2 mutant strain. Microb Cell Fact 2017; 16:72. [PMID: 28446175 PMCID: PMC5406934 DOI: 10.1186/s12934-017-0684-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/19/2017] [Indexed: 11/27/2022] Open
Abstract
Background Bacillus pumilus cells exhibit a significantly higher resistance to hydrogen peroxide compared to closely related Bacilli like Bacillus subtilis. Results In this study we analyzed features of the catalase KatX2 of B. pumilus as one of the most important parts of the cellular response to hydrogen peroxide. KatX2, the vegetative catalase expressed in B. pumilus, was compared to the vegetative catalase KatA of B. subtilis. Data of our study demonstrate that B. pumilus can degrade toxic concentrations of hydrogen peroxide faster than B. subtilis. By replacing B. subtiliskatA gene by katX2 we could significantly enhance its resistance to H2O2 and its potential to eliminate this toxic compound. Mutant cells showed a 1.5- to 2-fold higher survival to toxic concentrations of hydrogen peroxide compared to wild type cells. Furthermore, we found reversible but also irreversible oxidations of the KatX2 protein which, in contrast to KatA, contains several cysteine residues. Conclusions Our study indicates that the catalase KatX2 plays a major role in the increased resistance of B. pumilus to oxidative stress caused by hydrogen peroxide. Resistance to hydrogen peroxide of other Bacilli can be enhanced by exchanging the native catalase in the cells with katX2. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0684-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Daniela Zühlke
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Andreas Otto
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Kathrin Riedel
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany. .,Institute of Marine Biotechnology, 17489, Greifswald, Germany. .,Research Institute for Leather and Plastic Sheeting, Meißner-Ring 1-5, 09599, Freiberg, Germany.
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11
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Rasool K, Helal M, Ali A, Ren CE, Gogotsi Y, Mahmoud KA. Antibacterial Activity of Ti₃C₂Tx MXene. ACS NANO 2016; 10:3674-84. [PMID: 26909865 DOI: 10.1021/acsnano.6b00181] [Citation(s) in RCA: 524] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MXenes are a family of atomically thin, two-dimensional (2D) transition metal carbides and carbonitrides with many attractive properties. Two-dimensional Ti3C2Tx (MXene) has been recently explored for applications in water desalination/purification membranes. A major success indicator for any water treatment membrane is the resistance to biofouling. To validate this and to understand better the health and environmental impacts of the new 2D carbides, we investigated the antibacterial properties of single- and few-layer Ti3C2Tx MXene flakes in colloidal solution. The antibacterial properties of Ti3C2Tx were tested against Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis) by using bacterial growth curves based on optical densities (OD) and colonies growth on agar nutritive plates. Ti3C2Tx shows a higher antibacterial efficiency toward both Gram-negative E. coli and Gram-positive B. subtilis compared with graphene oxide (GO), which has been widely reported as an antibacterial agent. Concentration dependent antibacterial activity was observed and more than 98% bacterial cell viability loss was found at 200 μg/mL Ti3C2Tx for both bacterial cells within 4 h of exposure, as confirmed by colony forming unit (CFU) and regrowth curve. Antibacterial mechanism investigation by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) coupled with lactate dehydrogenase (LDH) release assay indicated the damage to the cell membrane, which resulted in release of cytoplasmic materials from the bacterial cells. Reactive oxygen species (ROS) dependent and independent stress induction by Ti3C2Tx was investigated in two separate abiotic assays. MXenes are expected to be resistant to biofouling and offer bactericidal properties.
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Affiliation(s)
- Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University (HBKU) , P.O. Box 5825, Doha, Qatar
| | - Mohamed Helal
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University (HBKU) , P.O. Box 5825, Doha, Qatar
| | - Adnan Ali
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University (HBKU) , P.O. Box 5825, Doha, Qatar
| | - Chang E Ren
- Department of Materials Science and Engineering and A.J. Drexel Nanomaterials Institute, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Yury Gogotsi
- Department of Materials Science and Engineering and A.J. Drexel Nanomaterials Institute, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Khaled A Mahmoud
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University (HBKU) , P.O. Box 5825, Doha, Qatar
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12
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster. J Proteomics 2015; 125:1-16. [DOI: 10.1016/j.jprot.2015.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 01/05/2023]
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13
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Voigt B, Albrecht D, Sievers S, Becher D, Bongaerts J, Evers S, Schweder T, Maurer KH, Hecker M. High-resolution proteome maps of Bacillus licheniformis
cells growing in minimal medium. Proteomics 2015; 15:2629-33. [DOI: 10.1002/pmic.201400504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/09/2015] [Accepted: 04/09/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Birgit Voigt
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dirk Albrecht
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Susanne Sievers
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dörte Becher
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology; Aachen University of Applied Sciences; Jülich Germany
| | | | - Thomas Schweder
- Institute of Pharmacy; Ernst-Moritz-Arndt-University; Greifswald Germany
| | | | - Michael Hecker
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
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14
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CodY regulates expression of the Bacillus subtilis extracellular proteases Vpr and Mpr. J Bacteriol 2015; 197:1423-32. [PMID: 25666135 DOI: 10.1128/jb.02588-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED CodY is a global transcriptional regulator in low-G+C Gram-positive bacteria that is responsive to GTP and branched-chain amino acids. By interacting with its two cofactors, it is able to sense the nutritional and energetic status of the cell and respond by regulating expression of adaptive genetic programs. In Bacillus subtilis, more than 200 genes, including those for peptide transporters, intracellular proteolytic enzymes, and amino acid degradative pathways, are controlled by CodY. In this study, we demonstrated that expression of two extracellular proteases, Vpr and Mpr, is negatively controlled by CodY. By gel mobility shift and DNase I footprinting assays, we showed that CodY binds to the regulatory regions of both genes, in the vicinity of their transcription start points. The mpr gene is also characterized by the presence of a second, higher-affinity CodY-binding site located at the beginning of its coding sequence. Using strains carrying vpr- or mpr-lacZ transcriptional fusions in which CodY-binding sites were mutated, we demonstrated that repression of both protease genes is due to the direct effect by CodY and that the mpr internal site is required for regulation. The vpr promoter is a rare example of a sigma H-dependent promoter that is regulated by CodY. In a codY null mutant, Vpr became one of the more abundant proteins of the B. subtilis exoproteome. IMPORTANCE CodY is a global transcriptional regulator of metabolism and virulence in low-G+C Gram-positive bacteria. In B. subtilis, more than 200 genes, including those for peptide transporters, intracellular proteolytic enzymes, and amino acid degradative pathways, are controlled by CodY. However, no role for B. subtilis CodY in regulating expression of extracellular proteases has been established to date. In this work, we demonstrate that by binding to the regulatory regions of the corresponding genes, B. subtilis CodY negatively controls expression of Vpr and Mpr, two extracellular proteases. Thus, in B. subtilis, CodY can now be seen to regulate the entire protein utilization pathway.
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15
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Yuan S, Jiang W, Chen L, Guo Y, Liu Z. A novel serine hydroxymethyltransferase from marine bacterium Alcanivorax sp. and its application on enzymatic synthesis of L-serine. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M. Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach. J Biotechnol 2014; 192 Pt A:204-14. [PMID: 25281541 DOI: 10.1016/j.jbiotec.2014.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 12/18/2022]
Abstract
Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Sonja Volland
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Karen Methling
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Jenny Nehls
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Heinrich-Mußmannstr. 1, 52428 Jülich, Germany.
| | | | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
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17
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Kohlmann Y, Pohlmann A, Schwartz E, Zühlke D, Otto A, Albrecht D, Grimmler C, Ehrenreich A, Voigt B, Becher D, Hecker M, Friedrich B, Cramm R. Coping with Anoxia: A Comprehensive Proteomic and Transcriptomic Survey of Denitrification. J Proteome Res 2014; 13:4325-38. [DOI: 10.1021/pr500491r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yvonne Kohlmann
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Anne Pohlmann
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Edward Schwartz
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Daniela Zühlke
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Andreas Otto
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Dirk Albrecht
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Christina Grimmler
- Forschungsstelle für Nahrungsmittelqualität der Universität Bayreuth, 95326 Kulmbach, Germany
| | - Armin Ehrenreich
- Lehrstuhl
für Mikrobiologie, Technische Universität München, Emil-Ramann-Straße
4, 85354 Freising, Germany
| | - Birgit Voigt
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Dörte Becher
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Michael Hecker
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Bärbel Friedrich
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Rainer Cramm
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
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18
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Maaβ S, Wachlin G, Bernhardt J, Eymann C, Fromion V, Riedel K, Becher D, Hecker M. Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteomics 2014; 13:2260-76. [PMID: 24878497 PMCID: PMC4159648 DOI: 10.1074/mcp.m113.035741] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/02/2014] [Indexed: 11/06/2022] Open
Abstract
Systems biology based on high quality absolute quantification data, which are mandatory for the simulation of biological processes, successively becomes important for life sciences. We provide protein concentrations on the level of molecules per cell for more than 700 cytosolic proteins of the Gram-positive model bacterium Bacillus subtilis during adaptation to changing growth conditions. As glucose starvation and heat stress are typical challenges in B. subtilis' natural environment and induce both, specific and general stress and starvation proteins, these conditions were selected as models for starvation and stress responses. Analyzing samples from numerous time points along the bacterial growth curve yielded reliable and physiologically relevant data suitable for modeling of cellular regulation under altered growth conditions. The analysis of the adaptational processes based on protein molecules per cell revealed stress-specific modulation of general adaptive responses in terms of protein amount and proteome composition. Furthermore, analysis of protein repartition during glucose starvation showed that biomass seems to be redistributed from proteins involved in amino acid biosynthesis to enzymes of the central carbon metabolism. In contrast, during heat stress most resources of the cell, namely those from amino acid synthetic pathways, are used to increase the amount of chaperones and proteases. Analysis of dynamical aspects of protein synthesis during heat stress adaptation revealed, that these proteins make up almost 30% of the protein mass accumulated during early phases of this stress.
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Affiliation(s)
- Sandra Maaβ
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Gerhild Wachlin
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Christine Eymann
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Vincent Fromion
- §INRA, Mathématique Informatique et Génome UR1077, 78350 Jouy-en-Josas, France
| | - Katharina Riedel
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany;
| | - Michael Hecker
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
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19
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Zhang J, Ferré-D'Amaré AR. Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Mol Cell 2014; 55:148-55. [PMID: 24954903 DOI: 10.1016/j.molcel.2014.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 01/01/2023]
Abstract
T-boxes are gene-regulatory mRNA elements with which Gram-positive bacteria sense amino acid availability. T-boxes have two functional domains. Stem I recognizes the overall shape and anticodon of tRNA, while a 3' domain evaluates its aminoacylation status, overcoming an otherwise stable transcriptional terminator if the bound tRNA is uncharged. Although T-boxes are believed to evaluate tRNA charge status without using any proteins, this has not been demonstrated experimentally because of the instability of aminoacyl-tRNA. Using a simple method to prepare homogeneous aminoacyl-tRNA, we show that the Bacillus subtilis glyQS T-box functions independently of any tRNA-binding protein. Comparison of aminoacyl-tRNA analogs demonstrates that the T-box detects the molecular volume of tRNA 3'-substituents. Calorimetry and fluorescence lifetime analysis of labeled RNAs shows that the tRNA acceptor end coaxially stacks on a helix in the T-box 3' domain. This intimate intermolecular association, selective for uncharged tRNA, stabilizes the antiterminator conformation of the T-box.
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Affiliation(s)
- Jinwei Zhang
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
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20
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Endo A, Kurusu Y. Identification ofin VivoSubstrates of the Chaperonin GroEL fromBacillus subtilis. Biosci Biotechnol Biochem 2014; 71:1073-7. [PMID: 17420574 DOI: 10.1271/bbb.60640] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We investigated GroEL substrates from Bacillus subtilis 168 using the single-ring mutant of B. subtilis GroEL. We identified 28 candidates for GroEL substrates, of which Spo0B, Ald, Eno, SpoIIP, and FbaA were involved in spore formation, and Rnc, Tuf, Eno, Tsf, and FbaA were essential for B. subtilis growth. As observed at the protein level, the amount of SpoIIP interaction with GroEL increased at 3 h after initiation of sporulation.
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Affiliation(s)
- Ayako Endo
- Laboratory of Molecular Microbiology, College of Agriculture, Ibaraki University, Inashiki, Ibaraki, Japan
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21
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Wisniewska M, Happonen L, Kahn F, Varjosalo M, Malmström L, Rosenberger G, Karlsson C, Cazzamali G, Pozdnyakova I, Frick IM, Björck L, Streicher W, Malmström J, Wikström M. Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes. J Biol Chem 2014; 289:18175-88. [PMID: 24825900 DOI: 10.1074/jbc.m114.565978] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pyogenes is a significant bacterial pathogen in the human population. The importance of virulence factors for the survival and colonization of S. pyogenes is well established, and many of these factors are exposed to the extracellular environment, enabling bacterial interactions with the host. In the present study, we quantitatively analyzed and compared S. pyogenes proteins in the growth medium of a strain that is virulent to mice with a non-virulent strain. Particularly, one of these proteins was present at significantly higher levels in stationary growth medium from the virulent strain. We determined the three-dimensional structure of the protein that showed a unique tetrameric organization composed of four helix-loop-helix motifs. Affinity pull-down mass spectrometry analysis in human plasma demonstrated that the protein interacts with histidine-rich glycoprotein (HRG), and the name sHIP (streptococcal histidine-rich glycoprotein-interacting protein) is therefore proposed. HRG has antibacterial activity, and when challenged by HRG, sHIP was found to rescue S. pyogenes bacteria. This and the finding that patients with invasive S. pyogenes infection respond with antibody production against sHIP suggest a role for the protein in S. pyogenes pathogenesis.
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Affiliation(s)
- Magdalena Wisniewska
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lotta Happonen
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Fredrik Kahn
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Markku Varjosalo
- the Institute of Biotechnology, Viikinkaari 1, University of Helsinki, FI-00014 Helsinki, Finland, and
| | - Lars Malmström
- the Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Christofer Karlsson
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Giuseppe Cazzamali
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Irina Pozdnyakova
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Inga-Maria Frick
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Lars Björck
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Werner Streicher
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Johan Malmström
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Mats Wikström
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark,
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22
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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23
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Osmekhina E, Shvetsova A, Ruottinen M, Neubauer P. Quantitative and sensitive RNA based detection of Bacillus spores. Front Microbiol 2014; 5:92. [PMID: 24653718 PMCID: PMC3949131 DOI: 10.3389/fmicb.2014.00092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 02/19/2014] [Indexed: 11/13/2022] Open
Abstract
The fast and reliable detection of bacterial spores is of great importance and still remains a challenge. Here we describe a direct RNA-based diagnostic method for the specific detection of viable bacterial spores which does not depends on an enzymatic amplification step and therefore is directly appropriate for quantification. The procedure includes the following steps: (i) heat activation of spores, (ii) germination and enrichment cultivation, (iii) cell lysis, and (iv) analysis of 16S rRNA in crude cell lysates using a sandwich hybridization assay. The sensitivity of the method is dependent on the cultivation time and the detection limit; it is possible to detect 10 spores per ml when the RNA analysis is performed after 6 h of enrichment cultivation. At spore concentrations above 10(6) spores per ml the cultivation time can be shortened to 30 min. Total analysis times are in the range of 2-8 h depending on the spore concentration in samples. The developed procedure is optimized at the example of Bacillus subtilis spores but should be applicable to other organisms. The new method can easily be modified for other target RNAs and is suitable for specific detection of spores from known groups of organisms.
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Affiliation(s)
- Ekaterina Osmekhina
- Department of Process and Environmental Engineering and Biocenter Oulu, University of Oulu Oulu, Finland
| | - Antonina Shvetsova
- Department of Biochemistry and Biocenter Oulu, University of Oulu Oulu, Finland
| | - Maria Ruottinen
- Department of Process and Environmental Engineering and Biocenter Oulu, University of Oulu Oulu, Finland
| | - Peter Neubauer
- Department of Process and Environmental Engineering and Biocenter Oulu, University of Oulu Oulu, Finland ; Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin Berlin, Germany
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24
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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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25
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Wu Z, Sahin O, Wang F, Zhang Q. Proteomic identification of immunodominant membrane-related antigens in Campylobacter jejuni associated with sheep abortion. J Proteomics 2014; 99:111-22. [PMID: 24487037 DOI: 10.1016/j.jprot.2014.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/24/2013] [Accepted: 01/14/2014] [Indexed: 11/25/2022]
Abstract
UNLABELLED Campylobacter jejuni clone SA is the predominant agent inducing sheep abortion and a zoonotic agent causing gastroenteritis in humans in the United States. In an attempt to identify antigens of clone SA that may be useful for vaccine development, immunoproteomic analyses were conducted to characterize the membrane proteome of C. jejuni clone SA. 2-DE of C. jejuni membrane-related proteins was followed by immunoblotting analyses using convalescent sera that were derived from ewes naturally infected by C. jejuni clone SA. Totally 140 immunoreactive spots were identified, 50 of which were shared by all tested convalescent sheep sera. Conserved and immunodominant spots were identified by mass spectrometry. Among the 26 identified immunogenic proteins, there were 8 cytoplasmic proteins, 2 cytoplasmic membrane proteins, 11 periplasmic proteins, 3 outer membrane proteins, and 2 extracellular proteins. Notably, many of the immunodominant antigens were periplasmic proteins including HtrA, ZnuA, CjaA, LivK, CgpA, and others, some of which were previously shown to induce protective immunity. Interestingly, 11 immunoreactive proteins including 9 periplasmic proteins are known N-linked glycosylated proteins. These findings reveal immunogens that may potentially elicit protective immune responses and provide a foundation for developing vaccines against C. jejuni induced sheep abortion. BIOLOGICAL SIGNIFICANCE Campylobacter jejuni clone SA is the predominant agent inducing sheep abortion and incurs a significant economic loss to sheep producers. This emergent strain is also a zoonotic agent, causing gastroenteritis in humans. However, the immunogens of C. jejuni induced abortion are largely unknown. Considering the significance of C. jejuni clone SA in causing sheep abortion and foodborne illnesses, protective vaccines are needed to control its transmission and spread. Additionally, immunological markers are required for detection and identification of this highly pathogenic clone. To address these needs, we applied an immunoproteomic approach to identify the membrane-associated antigens of this highly virulent C. jejuni clone associated with sheep abortions in the U.S. The findings reveal immunogens that may potentially elicit protective immune responses and provide a foundation for developing vaccines against C. jejuni induced sheep abortion.
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Affiliation(s)
- Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Orhan Sahin
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Fei Wang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
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26
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Handtke S, Schroeter R, Jürgen B, Methling K, Schlüter R, Albrecht D, van Hijum SAFT, Bongaerts J, Maurer KH, Lalk M, Schweder T, Hecker M, Voigt B. Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress. PLoS One 2014; 9:e85625. [PMID: 24465625 PMCID: PMC3896406 DOI: 10.1371/journal.pone.0085625] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/05/2013] [Indexed: 12/16/2022] Open
Abstract
Bacillus pumilus is characterized by a higher oxidative stress resistance than other comparable industrially relevant Bacilli such as B. subtilis or B. licheniformis. In this study the response of B. pumilus to oxidative stress was investigated during a treatment with high concentrations of hydrogen peroxide at the proteome, transcriptome and metabolome level. Genes/proteins belonging to regulons, which are known to have important functions in the oxidative stress response of other organisms, were found to be upregulated, such as the Fur, Spx, SOS or CtsR regulon. Strikingly, parts of the fundamental PerR regulon responding to peroxide stress in B. subtilis are not encoded in the B. pumilus genome. Thus, B. pumilus misses the catalase KatA, the DNA-protection protein MrgA or the alkyl hydroperoxide reductase AhpCF. Data of this study suggests that the catalase KatX2 takes over the function of the missing KatA in the oxidative stress response of B. pumilus. The genome-wide expression analysis revealed an induction of bacillithiol (Cys-GlcN-malate, BSH) relevant genes. An analysis of the intracellular metabolites detected high intracellular levels of this protective metabolite, which indicates the importance of bacillithiol in the peroxide stress resistance of B. pumilus.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Rebecca Schroeter
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Britta Jürgen
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Sacha A. F. T. van Hijum
- Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; and Division Processing and Safety, NIZO Food Research B.V., Ede, The Netherlands
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Jülich, Germany
| | | | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
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27
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Kim D, Yu BJ, Kim JA, Lee YJ, Choi SG, Kang S, Pan JG. The acetylproteome of Gram-positive model bacterium Bacillus subtilis. Proteomics 2013; 13:1726-36. [PMID: 23468065 DOI: 10.1002/pmic.201200001] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 02/08/2013] [Accepted: 02/18/2013] [Indexed: 12/31/2022]
Abstract
N(ε) -lysine acetylation, a reversible and highly regulated PTM, has been shown to occur in the model Gram-negative bacteria Escherichia coli and Salmonella enterica. Here, we extend this acetylproteome analysis to Bacillus subtilis, a model Gram-positive bacterium. Through anti-acetyllysine antibody-based immunoseparation of acetylpeptides followed by nano-HPLC/MS/MS analysis, we identified 332 unique lysine-acetylated sites on 185 proteins. These proteins are mainly involved in cellular housekeeping functions such as central metabolism and protein synthesis. Fifity-nine of the lysine-acetylated proteins showed homology with lysine-acetylated proteins previously identified in E. coli, suggesting that acetylated proteins are more conserved. Notably, acetylation was found at or near the active sites predicted by Prosite signature, including SdhA, RocA, Kbl, YwjH, and YfmT, indicating that lysine acetylation may affect their activities. In 2-amino-3-ketobutyrate CoA ligase Kbl, a class II aminotransferase, a lysine residue involved in pyridoxal phosphate attachment was found to be acetylated. This data set provides evidence for the generality of lysine acetylation in eubacteria and opens opportunities to explore the consequences of acetylation modification on the molecular physiology of B. subtilis.
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Affiliation(s)
- Dooil Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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28
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Wiegand S, Voigt B, Albrecht D, Bongaerts J, Evers S, Hecker M, Daniel R, Liesegang H. Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production. Microb Cell Fact 2013; 12:120. [PMID: 24313996 PMCID: PMC3878961 DOI: 10.1186/1475-2859-12-120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 12/01/2013] [Indexed: 11/10/2022] Open
Abstract
Background Industrial fermentations can generally be described as dynamic biotransformation processes in which microorganisms convert energy rich substrates into a desired product. The knowledge of active physiological pathways, reflected by corresponding gene activities, allows the identification of beneficial or disadvantageous performances of the microbial host. Whole transcriptome RNA-Seq is a powerful tool to accomplish in-depth quantification of these gene activities, since the low background noise and the absence of an upper limit of quantification allow the detection of transcripts with high dynamic ranges. Such data enable the identification of potential bottlenecks and futile energetic cycles, which in turn can lead to targets for rational approaches to productivity improvement. Here we present an overview of the dynamics of gene activity during an industrial-oriented fermentation process with Bacillus licheniformis, an important industrial enzyme producer. Thereby, valuable insights which help to understand the complex interactions during such processes are provided. Results Whole transcriptome RNA-Seq has been performed to study the gene expression at five selected growth stages of an industrial-oriented protease production process employing a germination deficient derivative of B. licheniformis DSM13. Since a significant amount of genes in Bacillus strains are regulated posttranscriptionally, the generated data have been confirmed by 2D gel-based proteomics. Regulatory events affecting the coordinated activity of hundreds of genes have been analyzed. The data enabled the identification of genes involved in the adaptations to changing environmental conditions during the fermentation process. A special focus of the analyses was on genes contributing to central carbon metabolism, amino acid transport and metabolism, starvation and stress responses and protein secretion. Genes contributing to lantibiotics production and Tat-dependent protein secretion have been pointed out as potential optimization targets. Conclusions The presented data give unprecedented insights into the complex adaptations of bacterial production strains to the changing physiological demands during an industrial-oriented fermentation. These are, to our knowledge, the first publicly available data that document quantifiable transcriptional responses of the commonly employed production strain B. licheniformis to changing conditions over the course of a typical fermentation process in such extensive depth.
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Affiliation(s)
| | | | | | | | | | | | | | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Norddeutsches Zentrum für Mikrobielle Genomforschung, Georg-August-Universität Göttingen, Grisebachstr, 8, D-37077 Göttingen, Germany.
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29
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Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges. PLoS One 2013; 8:e80956. [PMID: 24348917 PMCID: PMC3858371 DOI: 10.1371/journal.pone.0080956] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Gram-positive endospore-forming bacterium Bacillus licheniformis can be found widely in nature and it is exploited in industrial processes for the manufacturing of antibiotics, specialty chemicals, and enzymes. Both in its varied natural habitats and in industrial settings, B. licheniformis cells will be exposed to increases in the external osmolarity, conditions that trigger water efflux, impair turgor, cause the cessation of growth, and negatively affect the productivity of cell factories in biotechnological processes. We have taken here both systems-wide and targeted physiological approaches to unravel the core of the osmostress responses of B. licheniformis. Cells were suddenly subjected to an osmotic upshift of considerable magnitude (with 1 M NaCl), and their transcriptional profile was then recorded in a time-resolved fashion on a genome-wide scale. A bioinformatics cluster analysis was used to group the osmotically up-regulated genes into categories that are functionally associated with the synthesis and import of osmostress-relieving compounds (compatible solutes), the SigB-controlled general stress response, and genes whose functional annotation suggests that salt stress triggers secondary oxidative stress responses in B. licheniformis. The data set focusing on the transcriptional profile of B. licheniformis was enriched by proteomics aimed at identifying those proteins that were accumulated by the cells through increased biosynthesis in response to osmotic stress. Furthermore, these global approaches were augmented by a set of experiments that addressed the synthesis of the compatible solutes proline and glycine betaine and assessed the growth-enhancing effects of various osmoprotectants. Combined, our data provide a blueprint of the cellular adjustment processes of B. licheniformis to both sudden and sustained osmotic stress.
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30
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Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM. Proteomic analysis ofBacillus subtilisstrains engineered for improved production of heterologous proteins. Proteomics 2013; 13:3298-308. [DOI: 10.1002/pmic.201300183] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/25/2013] [Accepted: 08/21/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Susanne Pohl
- Centre for Bacterial Cell Biology; Baddiley-Clark Building; Newcastle University; Newcastle upon Tyne UK
| | - Gaurav Bhavsar
- Cobra Biologics; Stephenson Building; Keele Science Park; Keele Staffordshire UK
| | - Joanne Hulme
- Cobra Biologics; Stephenson Building; Keele Science Park; Keele Staffordshire UK
| | - Alexandra E. Bloor
- Cobra Biologics; Stephenson Building; Keele Science Park; Keele Staffordshire UK
| | - Goksel Misirli
- Centre for Bacterial Cell Biology; Baddiley-Clark Building; Newcastle University; Newcastle upon Tyne UK
- Computing Science; Claremont Tower; Newcastle University; Newcastle upon Tyne UK
| | - Matthew W. Leckenby
- Cobra Biologics; Stephenson Building; Keele Science Park; Keele Staffordshire UK
| | - David S. Radford
- Cobra Biologics; Stephenson Building; Keele Science Park; Keele Staffordshire UK
| | - Wendy Smith
- Centre for Bacterial Cell Biology; Baddiley-Clark Building; Newcastle University; Newcastle upon Tyne UK
- Computing Science; Claremont Tower; Newcastle University; Newcastle upon Tyne UK
| | - Anil Wipat
- Centre for Bacterial Cell Biology; Baddiley-Clark Building; Newcastle University; Newcastle upon Tyne UK
- Computing Science; Claremont Tower; Newcastle University; Newcastle upon Tyne UK
| | - E. Diane Williamson
- Biomedical Sciences; Defence Science and Technology Laboratory, Porton Down; Salisbury Wiltshire UK
| | - Colin R. Harwood
- Centre for Bacterial Cell Biology; Baddiley-Clark Building; Newcastle University; Newcastle upon Tyne UK
| | - Rocky M. Cranenburgh
- Cobra Biologics; Stephenson Building; Keele Science Park; Keele Staffordshire UK
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31
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Fuchs S, Zühlke D, Pané-Farré J, Kusch H, Wolf C, Reiß S, Binh LTN, Albrecht D, Riedel K, Hecker M, Engelmann S. Aureolib - a proteome signature library: towards an understanding of staphylococcus aureus pathophysiology. PLoS One 2013; 8:e70669. [PMID: 23967085 PMCID: PMC3742771 DOI: 10.1371/journal.pone.0070669] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 06/21/2013] [Indexed: 11/19/2022] Open
Abstract
Gel-based proteomics is a powerful approach to study the physiology of Staphylococcus aureus under various growth restricting conditions. We analyzed 679 protein spots from a reference 2-dimensional gel of cytosolic proteins of S. aureus COL by mass spectrometry resulting in 521 different proteins. 4,692 time dependent protein synthesis profiles were generated by exposing S. aureus to nine infection-related stress and starvation stimuli (H2O2, diamide, paraquat, NO, fermentation, nitrate respiration, heat shock, puromycin, mupirocin). These expression profiles are stored in an online resource called Aureolib (http://www.aureolib.de). Moreover, information on target genes of 75 regulators and regulatory elements were included in the database. Cross-comparisons of this extensive data collection of protein synthesis profiles using the tools implemented in Aureolib lead to the identification of stress and starvation specific marker proteins. Altogether, 226 protein synthesis profiles showed induction ratios of 2.5-fold or higher under at least one of the tested conditions with 157 protein synthesis profiles specifically induced in response to a single stimulus. The respective proteins might serve as marker proteins for the corresponding stimulus. By contrast, proteins whose synthesis was increased or repressed in response to more than four stimuli are rather exceptional. The only protein that was induced by six stimuli is the universal stress protein SACOL1759. Most strikingly, cluster analyses of synthesis profiles of proteins differentially synthesized under at least one condition revealed only in rare cases a grouping that correlated with known regulon structures. The most prominent examples are the GapR, Rex, and CtsR regulon. In contrast, protein synthesis profiles of proteins belonging to the CodY and σ(B) regulon are widely distributed. In summary, Aureolib is by far the most comprehensive protein expression database for S. aureus and provides an essential tool to decipher more complex adaptation processes in S. aureus during host pathogen interaction.
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Affiliation(s)
- Stephan Fuchs
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Daniela Zühlke
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Jan Pané-Farré
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Harald Kusch
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Carmen Wolf
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Swantje Reiß
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Le Thi Nguyen Binh
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Dirk Albrecht
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Susanne Engelmann
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
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32
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Moche M, Albrecht D, Maaß S, Hecker M, Westermeier R, Büttner K. The new horizon in 2D electrophoresis: New technology to increase resolution and sensitivity. Electrophoresis 2013; 34:1510-8. [DOI: 10.1002/elps.201200618] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/18/2013] [Accepted: 02/14/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Martin Moche
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Dirk Albrecht
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Sandra Maaß
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | - Michael Hecker
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
| | | | - Knut Büttner
- Institute for Microbiology; Ernst-Moritz-Arndt University; Greifswald; Germany
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33
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Feng J, Michalik S, Varming AN, Andersen JH, Albrecht D, Jelsbak L, Krieger S, Ohlsen K, Hecker M, Gerth U, Ingmer H, Frees D. Trapping and Proteomic Identification of Cellular Substrates of the ClpP Protease in Staphylococcus aureus. J Proteome Res 2013; 12:547-58. [DOI: 10.1021/pr300394r] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingyuan Feng
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Stephan Michalik
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Anders N. Varming
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Julie H. Andersen
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Dirk Albrecht
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Lotte Jelsbak
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Stefanie Krieger
- Institute for Molecular
Infectionsbiology, Würzburg University, Würzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular
Infectionsbiology, Würzburg University, Würzburg, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Ulf Gerth
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Hanne Ingmer
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Dorte Frees
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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34
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Paul D. Osmotic stress adaptations in rhizobacteria. J Basic Microbiol 2012; 53:101-10. [PMID: 22581676 DOI: 10.1002/jobm.201100288] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 11/24/2011] [Indexed: 01/01/2023]
Abstract
Rhizobacteria have been reported to be beneficial to the plants in many different ways. Increasing salinity in the coastal agricultural zones has been shown to be a threat to the plant and microbial life in the area. Exposure of microorganisms to high-osmolality environments triggers rapid fluxes of cell water along the osmotic gradient out of the cell, thus causing a reduction in turgor and dehydration of the cytoplasm. The microorganisms have developed various adaptations to counteract the outflow of water. The first response to osmotic up shifts and the resulting efflux of cellular water is uptake of K⁺ and cells start to accumulate compatible solutes. Yet another mechanism is by altering the cell envelope composition resulting in changes in proteins, periplasmic glucans, and capsular, exo and lipopolysaccharides. Bacteria also initiate a program of gene expression in response to osmotic stress by high NaCl concentrations, which are manifested as a set of proteins produced in increased amounts in response to the stress. Genomics, transcriptomics and proteomics approaches have revealed the key components in molecular basis of bacteria salt adaptation. Understanding the mechanisms of osmo-adaptation in rhizobacteria would also be relevant from an ecological and an applicative point of view.
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Affiliation(s)
- Diby Paul
- Department of Environmental Engineering, Konkuk University, Hwayang Dong, Gwanjin Gu, Seoul, Rep. Korea.
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35
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Poehlein A, Schmidt S, Kaster AK, Goenrich M, Vollmers J, Thürmer A, Bertsch J, Schuchmann K, Voigt B, Hecker M, Daniel R, Thauer RK, Gottschalk G, Müller V. An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis. PLoS One 2012; 7:e33439. [PMID: 22479398 PMCID: PMC3315566 DOI: 10.1371/journal.pone.0033439] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/09/2012] [Indexed: 11/18/2022] Open
Abstract
Synthesis of acetate from carbon dioxide and molecular hydrogen is considered to be the first carbon assimilation pathway on earth. It combines carbon dioxide fixation into acetyl-CoA with the production of ATP via an energized cell membrane. How the pathway is coupled with the net synthesis of ATP has been an enigma. The anaerobic, acetogenic bacterium Acetobacterium woodii uses an ancient version of this pathway without cytochromes and quinones. It generates a sodium ion potential across the cell membrane by the sodium-motive ferredoxin:NAD oxidoreductase (Rnf). The genome sequence of A. woodii solves the enigma: it uncovers Rnf as the only ion-motive enzyme coupled to the pathway and unravels a metabolism designed to produce reduced ferredoxin and overcome energetic barriers by virtue of electron-bifurcating, soluble enzymes.
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Affiliation(s)
- Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Göttingen, Germany
| | - Silke Schmidt
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | | | - Meike Goenrich
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - John Vollmers
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Göttingen, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Göttingen, Germany
| | - Johannes Bertsch
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Kai Schuchmann
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Birgit Voigt
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Göttingen, Germany
| | - Rudolf K. Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gerhard Gottschalk
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Göttingen, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
- * E-mail:
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36
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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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Thi Nguyen HB, Schumann W. The sporulation control gene spo0M of Bacillus subtilis is a target of the FtsH metalloprotease. Res Microbiol 2012; 163:114-8. [DOI: 10.1016/j.resmic.2011.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 10/10/2011] [Indexed: 11/26/2022]
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Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium. J Bacteriol 2012; 194:1552-61. [PMID: 22228732 DOI: 10.1128/jb.06429-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This dynamic proteome study describes the physiology of growth and survival of Deinococcus geothermalis, in conditions simulating paper machine waters being aerobic, warm, and low in carbon and manganese. The industrial environment of this species differs from its natural habitats, geothermal springs and deep ocean subsurfaces, by being highly exposed to oxygen. Quantitative proteome analysis using two-dimensional gel electrophoresis and bioinformatic tools showed expression change for 165 proteins, from which 47 were assigned to a function. We propose that D. geothermalis grew and survived in aerobic conditions by channeling central carbon metabolism to pathways where mainly NADPH rather than NADH was retrieved from the carbon source. A major part of the carbon substrate was converted into succinate, which was not a fermentation product but likely served combating reactive oxygen species (ROS). Transition from growth to nongrowth resulted in downregulation of the oxidative phosphorylation observed as reduced expression of V-type ATPase responsible for ATP synthesis in D. geothermalis. The battle against oxidative stress was seen as upregulation of superoxide dismutase (Mn dependent) and catalase, as well as several protein repair enzymes, including FeS cluster assembly proteins of the iron-sulfur cluster assembly protein system, peptidylprolyl isomerase, and chaperones. Addition of soluble Mn reinitiated respiration and proliferation with concomitant acidification, indicating that aerobic metabolism was restricted by access to manganese. We conclude that D. geothermalis prefers to combat ROS using manganese-dependent enzymes, but when manganese is not available central carbon metabolism is used to produce ROS neutralizing metabolites at the expense of high utilization of carbon substrate.
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Rosen R, Ron EZ. Proteomics of a plant pathogen: Agrobacterium tumefaciens. Proteomics 2011; 11:3134-42. [DOI: 10.1002/pmic.201100019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/13/2011] [Accepted: 03/14/2011] [Indexed: 12/31/2022]
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40
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Pohl S, Tu WY, Aldridge PD, Gillespie C, Hahne H, Mäder U, Read TD, Harwood CR. Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis
to oxidative stress. Proteomics 2011; 11:3036-55. [DOI: 10.1002/pmic.201100085] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/28/2011] [Accepted: 04/05/2011] [Indexed: 11/12/2022]
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41
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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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42
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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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43
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Mao L, Jiang S, Wang B, Chen L, Yao Q, Chen K. Protein profile of Bacillus subtilis spore. Curr Microbiol 2011; 63:198-205. [PMID: 21667307 DOI: 10.1007/s00284-011-9967-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022]
Abstract
Natural wild-type strains of Bacillus subtilis spore is regarded as a non-pathogenic for both human and animal, and has been classified as a novel food which is currently being used as probiotics added in the consumption. To identify B. subtilis spore proteins, we have accomplished a preliminary proteomic analysis of B. subtilis spore, with a combination of two-dimensional electrophoretic separations and matrix-assisted laser desorption ionization tandem time of flight mass spectrometry (MALDI-TOF-MS). In this article, we presented a reference map of 158 B. subtilis spore proteins with an isoelectric point (pI) between 4 and 7. Followed by mass spectrometry (MS) analysis, we identified 71 B. subtilis spore proteins with high level of confidence. Database searches, combined with hydropathy analysis and GO analysis revealed that most of the B. subtilis spore proteins were hydrophilic proteins related to catalytic function. These results should accelerate efforts to understand the resistance of spore to harsh conditions.
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Affiliation(s)
- Langyong Mao
- Institute of Life Sciences, Jiangsu University, #301 Xuefu Road, Zhenjiang, Jiangsu, People's Republic of China
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44
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Wolf C, Kusch H, Monecke S, Albrecht D, Holtfreter S, von Eiff C, Petzl W, Rainard P, Bröker BM, Engelmann S. Genomic and proteomic characterization of Staphylococcus aureus mastitis isolates of bovine origin. Proteomics 2011; 11:2491-502. [PMID: 21595036 DOI: 10.1002/pmic.201000698] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 12/26/2022]
Abstract
Staphylococcus aureus colonizes and infects humans as well as animals. In the present study, 17 S. aureus strains isolated from cows suffering from mastitis were characterized. The well-established multilocus sequence typing (MLST) technique and a diagnostic microarray covering 185 S. aureus virulence and resistance genes were used for genetic and epidemiological analyses. Virulence gene expression studies were performed by analyzing the extracellular protein pattern of each isolate on 2-D gels. By this way, a pronounced heterogeneity of the extracellular proteome between the bovine isolates has been observed which was attributed to genome plasticity and variation of gene expression. Merely 12 proteins were expressed in at least 80% of the isolates, i.e. Atl, Aur, GlpQ, Hla, LtaS, Nuc, PdhB, SAB0846, SAB2176, SAB0566, SspA, and SspB forming the core exoproteome. Fifteen extracellular proteins were highly variably expressed and only present in less than 20% of the isolates. This includes the serine proteases SplB, C, and F, and the superantigens SEC-bov, SEL and TSST-1. Compared to human isolates we identified at least six proteins with significantly different expression frequencies. While SAB0846 was expressed more frequently in bovine isolates, LytM, EbpS, Spa, Geh, and LukL1 were seen less frequently in these isolates.
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Affiliation(s)
- Carmen Wolf
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
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Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics 2011; 11:1915-35. [PMID: 21472852 DOI: 10.1002/pmic.201000151] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 01/24/2011] [Accepted: 01/31/2011] [Indexed: 11/07/2022]
Abstract
Comparing proteomics and metabolomics allows insights into Staphylococcus aureus physiological growth. We update genome and proteome information and deliver strain-specific metabolic models for three S. aureus strains (COL, N315, and Newman). We find a number of differences in metabolism and enzymes. Growth experiments (glucose or combined with oxygen limitation) were conducted to measure external metabolites. Fluxes of the central metabolism were calculated from these data with low error. In exponential phase, glycolysis is active and amino acids are used for growth. In later phases, dehydroquinate synthetase is suppressed and acetate metabolism starts. There are strain-specific differences for these phases. A time series of 2-D gel protein expression data on COL strain delivered a second data set (glucose limitation) on which fluxes were calculated. The comparison with the metabolite-predicted fluxes shows, in general, good correlation. Outliers point to different regulated enzymes for S. aureus COL under these limitations. In exponential growth, there is lower activity for some enzymes in upper glycolysis and pentose phosphate pathway and stronger activity for some in lower glycolysis. In transition phase, aspartate kinase is expressed to meet amino acid requirements and in later phases there is high expression of glyceraldehyde-3-phosphate dehydrogenase and lysine synthetase. Central metabolite fluxes and protein expression of their enzymes correlate in S. aureus.
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Affiliation(s)
- Chunguang Liang
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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Dmitriev AV, Chaussee MS. The Streptococcus pyogenes proteome: maps, virulence factors and vaccine candidates. Future Microbiol 2011; 5:1539-51. [PMID: 21073313 DOI: 10.2217/fmb.10.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Streptococcus pyogenes is an important cause of human morbidity and mortality worldwide. A wealth of genomic information related to this pathogen has facilitated exploration of the proteome, particularly in response to environmental conditions thought to mimic various aspects of pathogenesis. Proteomic approaches are also used to identify immunoreactive proteins for vaccine development and to identify proteins that may induce autoimmunity. These studies have revealed new mechanisms involved in regulating the S. pyogenes proteome, which has opened up new avenues in the study of S. pyogenes pathogenesis. This article describes the methods used, and progress being made towards characterizing the S. pyogenes proteome, including studies seeking to identify potential vaccine candidates.
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Affiliation(s)
- Alexander V Dmitriev
- Department of Molecular Microbiology, Institute of Experimental Medicine. acad. Pavlov str., 12, Saint-Petersburg, 197376, Russia
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47
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Wilmes B, Kock H, Glagla S, Albrecht D, Voigt B, Markert S, Gardebrecht A, Bode R, Danchin A, Feller G, Hecker M, Schweder T. Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Appl Environ Microbiol 2011; 77:1276-83. [PMID: 21183643 PMCID: PMC3067249 DOI: 10.1128/aem.01750-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments.
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Affiliation(s)
- Boris Wilmes
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Holger Kock
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Susanne Glagla
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Dirk Albrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Birgit Voigt
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Stephanie Markert
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antje Gardebrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Rüdiger Bode
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antoine Danchin
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Georges Feller
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Michael Hecker
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Thomas Schweder
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
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Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. MOLECULAR BIOSYSTEMS 2011; 7:1241-53. [DOI: 10.1039/c0mb00315h] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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CtsR, the Gram-positive master regulator of protein quality control, feels the heat. EMBO J 2010; 29:3621-9. [PMID: 20852588 DOI: 10.1038/emboj.2010.228] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 08/20/2010] [Indexed: 11/08/2022] Open
Abstract
Protein quality networks are required for the maintenance of proper protein homeostasis and essential for viability and growth of all living organisms. Hence, regulation and coordination of these networks are critical for survival during stress as well as for virulence of pathogenic species. In low GC, Gram-positive bacteria central protein quality networks are under the control of the global repressor CtsR. Here, we provide evidence that CtsR activity during heat stress is mediated by intrinsic heat sensing through a glycine-rich loop, probably in all Gram-positive species. Moreover, a function for the recently identified arginine kinase McsB is confirmed, however, not for initial inactivation and dissociation of CtsR from the DNA, but for heat-dependent auto-activation of McsB as an adaptor for ClpCP-mediated degradation of CtsR.
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50
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Pasztor L, Ziebandt AK, Nega M, Schlag M, Haase S, Franz-Wachtel M, Madlung J, Nordheim A, Heinrichs DE, Götz F. Staphylococcal major autolysin (Atl) is involved in excretion of cytoplasmic proteins. J Biol Chem 2010; 285:36794-803. [PMID: 20847047 DOI: 10.1074/jbc.m110.167312] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Many microorganisms excrete typical cytoplasmic proteins into the culture supernatant. As none of the classical secretion systems appears to be involved, this type of secretion was referred to as "nonclassical protein secretion." Here, we demonstrate that in Staphylococcus aureus the major autolysin plays a crucial role in release of cytoplasmic proteins. Comparative secretome analysis revealed that in the wild type S. aureus strain, 22 typical cytoplasmic proteins were excreted into the culture supernatant, although in the atl mutant they were significantly decreased. The presence or absence of prophages had little influence on the secretome pattern. In the atl mutant, secondary peptidoglycan hydrolases were increased in the secretome; the corresponding genes were transcriptionally up-regulated suggesting a compensatory mechanism for the atl mutation. Using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a cytoplasmic indicator enzyme, we showed that all clinical isolates tested excreted this protein. In the wall teichoic acid-deficient tagO mutant with its increased autolysis activity, GAPDH was excreted in even higher amounts than in the WT, confirming the importance of autolysis in excretion of cytoplasmic proteins. To answer the question of how discriminatory the excretion of cytoplasmic proteins is, we performed a two-dimensional PAGE of cytoplasmic proteins isolated from WT. Surprisingly, the most abundant proteins in the cytoplasm were not found in the secretome of the WT, suggesting that there exists a selection mechanism in the excretion of cytoplasmic proteins. As the major autolysin binds at the septum site, we assume that the proteins are preferentially released at and during septum formation.
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Affiliation(s)
- Linda Pasztor
- Department of Microbial Genetics, University of Tübingen, D-72076 Tübingen, Germany
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