1
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Grasso S, Dabene V, Hendriks MMW, Zwartjens P, Pellaux R, Held M, Panke S, van Dijl JM, Meyer A, van Rij T. Signal Peptide Efficiency: From High-Throughput Data to Prediction and Explanation. ACS Synth Biol 2023; 12:390-404. [PMID: 36649479 PMCID: PMC9942255 DOI: 10.1021/acssynbio.2c00328] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The passage of proteins across biological membranes via the general secretory (Sec) pathway is a universally conserved process with critical functions in cell physiology and important industrial applications. Proteins are directed into the Sec pathway by a signal peptide at their N-terminus. Estimating the impact of physicochemical signal peptide features on protein secretion levels has not been achieved so far, partially due to the extreme sequence variability of signal peptides. To elucidate relevant features of the signal peptide sequence that influence secretion efficiency, an evaluation of ∼12,000 different designed signal peptides was performed using a novel miniaturized high-throughput assay. The results were used to train a machine learning model, and a post-hoc explanation of the model is provided. By describing each signal peptide with a selection of 156 physicochemical features, it is now possible to both quantify feature importance and predict the protein secretion levels directed by each signal peptide. Our analyses allow the detection and explanation of the relevant signal peptide features influencing the efficiency of protein secretion, generating a versatile tool for the de novo design and in silico evaluation of signal peptides.
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Affiliation(s)
- Stefano Grasso
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands,DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands
| | - Valentina Dabene
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland,FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | | | - Priscilla Zwartjens
- DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands
| | - René Pellaux
- FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | - Martin Held
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland
| | - Sven Panke
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands,. Phone: +31503615187
| | - Andreas Meyer
- FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | - Tjeerd van Rij
- DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands,. Phone: +31628441843
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2
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Chafsey I, Ostrowski R, Guilbaud M, Teixeira P, Herry JM, Caccia N, Chambon C, Hébraud M, Azeredo J, Bellon-Fontaine MN, Popowska M, Desvaux M. Deep impact of the inactivation of the SecA2-only protein export pathway on the proteosurfaceome of Listeria monocytogenes. J Proteomics 2022; 250:104388. [PMID: 34601155 DOI: 10.1016/j.jprot.2021.104388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 01/23/2023]
Abstract
Listeria monocytogenes presents a dimorphism associated to the SecA2 activity with cells having a normal rod shape or a dysmorphic elongated filamentous form. Besides variation of the cell and colony morphotype, this cell differentiation has profound ecophysiological and physiopathological implications with collateral effects on virulence and pathogenicity, biotope colonisation, bacterial adhesion and biofilm formation. This suggests the SecA2-only protein export could influence the listerial cell surface, which was investigated first by characterising its properties in L. monocytogenes wt and ΔsecA2. The degree of hydrophilicity and Lewis acid-base properties appeared significantly affected upon SecA2 inactivation. As modification of electrostatic properties would owe to modification in the composition of cell-surface proteins, the proteosurfaceome was further investigated by shotgun label-free proteomic analysis with a comparative relative quantitative approach. Following secretomic analysis, the protein secretion routes of the identified proteins were mapped considering the cognate transport and post-translocational maturation systems, as well as protein categories and subcellular localisation. Differential protein abundance profiles coupled to network analysis revealed the SecA2 dependence of 48 proteins, including some related to cell envelope biogenesis, translation and protein export, which could account for modifications of adhesion and surface properties of L. monocytogenes upon SecA2 inactivation. This investigation unravelled the profound influence of SecA2 activity on the cell surface properties and proteosurfaceome of L. monocytogenes, which provides advanced insights about its ecophysiopathology. SIGNIFICANCE: L. monocytogenes is a foodborne zoonotic pathogen and etiological agent of human listeriosis. This species presents a cellular dimorphism associated to the SecA2 activity that has profound physiopathological and ecophysiological implications with collateral effects on bacterial virulence and colonisation. To explore the influence of the SecA2-only protein export on the listerial cell, the surface properties of L. monocytogenes expressing or depleted of SecA2 was characterised by microelectrophoresis, microbial affinity to solvents and contact angles analyses. As modifications of hydrophilicity and Lewis acid-base electrostatic properties would owe to modification in the composition of cell-surface proteins, the proteinaceous subset of the surfaceome, i.e. the proteosurfaceome, was investigated further by shotgun label-free proteomic analysis. This subproteome appeared quite impacted upon SecA2 inactivation with the identification of proteins accounting for modifications in the cell surface properties. The profound influence of SecA2 activity on the cell surface of L. monocytogenes was unravelled, which provides advanced insights about its ecophysiopathology.
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Affiliation(s)
- Ingrid Chafsey
- INRAE, Université Clermont Auvergne, UMR454 MEDiS, 63000 Clermont-Ferrand, France
| | - Rafal Ostrowski
- University of Warsaw, Faculty of Biology, Department of Bacterial Physiology, Applied Microbiology, Institute of Microbiology, Warsaw, Poland
| | - Morgan Guilbaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91300 Massy, France
| | - Pilar Teixeira
- University of Minho, Centre of Biological Engineering, Campus de Gualtar, Braga 4710-057, Portugal
| | - Jean-Marie Herry
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91300 Massy, France
| | - Nelly Caccia
- INRAE, Université Clermont Auvergne, UMR454 MEDiS, 63000 Clermont-Ferrand, France
| | - Christophe Chambon
- INRAE, Plateforme d'Exploration du Métabolisme, 63122 Saint-Genès Champanelle, France
| | - Michel Hébraud
- INRAE, Université Clermont Auvergne, UMR454 MEDiS, 63000 Clermont-Ferrand, France; INRAE, Plateforme d'Exploration du Métabolisme, 63122 Saint-Genès Champanelle, France
| | - Joana Azeredo
- University of Minho, Centre of Biological Engineering, Campus de Gualtar, Braga 4710-057, Portugal
| | | | - Magdalena Popowska
- University of Warsaw, Faculty of Biology, Department of Bacterial Physiology, Applied Microbiology, Institute of Microbiology, Warsaw, Poland.
| | - Mickaël Desvaux
- INRAE, Université Clermont Auvergne, UMR454 MEDiS, 63000 Clermont-Ferrand, France.
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3
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Anchoring of heterologous proteins in multiple Lactobacillus species using anchors derived from Lactobacillus plantarum. Sci Rep 2020; 10:9640. [PMID: 32541679 PMCID: PMC7295990 DOI: 10.1038/s41598-020-66531-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Members of the genus Lactobacillus have a long history in food applications and are considered as promising and safe hosts for delivery of medically interesting proteins. We have assessed multiple surface anchors derived from Lactobacillus plantarum for protein surface display in multiple Lactobacillus species, using a Mycobacterium tuberculosis hybrid antigen as test protein. The anchors tested were a lipoprotein anchor and two cell wall anchors, one non-covalent (LysM domain) and one covalent (sortase-based anchoring using the LPXTG motif). Thus, three different expression vectors for surface-anchoring were tested in eight Lactobacillus species. When using the LPXTG and LysM cell wall anchors, surface display, as assessed by flow cytometry and fluorescence microscopy, was observed in all species except Lactobacillus acidophilus. Use of the cell membrane anchor revealed more variation in the apparent degree of surface-exposure among the various lactobacilli. Overproduction of the secreted and anchored antigen impaired bacterial growth rate to extents that varied among the lactobacilli and were dependent on the type of anchor. Overall, these results show that surface anchors derived from L. plantarum are promising candidates for efficient anchoring of medically interesting proteins in other food grade Lactobacillus species.
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4
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Zhang K, Su L, Wu J. Recent Advances in Recombinant Protein Production byBacillus subtilis. Annu Rev Food Sci Technol 2020; 11:295-318. [DOI: 10.1146/annurev-food-032519-051750] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacillus subtilis has become a widely used microbial cell factory for the production of recombinant proteins, especially those associated with foods and food processing. Recent advances in genetic manipulation and proteomic analysis have been used to greatly improve protein production in B. subtilis. This review begins with a discussion of genome-editing technologies and application of the CRISPR–Cas9 system to B. subtilis. A summary of the characteristics of crucial legacy strains is followed by suggestions regarding the choice of origin strain for genetic manipulation. Finally, the review analyzes the genes and operons of B. subtilis that are important for the production of secretory proteins and provides suggestions and examples of how they can be altered to improve protein production. This review is intended to promote the engineering of this valuable microbial cell factory for better recombinant protein production.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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5
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Gingimaps: Protein Localization in the Oral Pathogen Porphyromonas gingivalis. Microbiol Mol Biol Rev 2020; 84:84/1/e00032-19. [PMID: 31896547 DOI: 10.1128/mmbr.00032-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Porphyromonas gingivalis is an oral pathogen involved in the widespread disease periodontitis. In recent years, however, this bacterium has been implicated in the etiology of another common disorder, the autoimmune disease rheumatoid arthritis. Periodontitis and rheumatoid arthritis were known to correlate for decades, but only recently a possible molecular connection underlying this association has been unveiled. P. gingivalis possesses an enzyme that citrullinates certain host proteins and, potentially, elicits autoimmune antibodies against such citrullinated proteins. These autoantibodies are highly specific for rheumatoid arthritis and have been purported both as a symptom and a potential cause of the disease. The citrullinating enzyme and other major virulence factors of P. gingivalis, including some that were implicated in the etiology of rheumatoid arthritis, are targeted to the host tissue as secreted or outer-membrane-bound proteins. These targeting events play pivotal roles in the interactions between the pathogen and its human host. Accordingly, the overall protein sorting and secretion events in P. gingivalis are of prime relevance for understanding its full disease-causing potential and for developing preventive and therapeutic approaches. The aim of this review is therefore to offer a comprehensive overview of the subcellular and extracellular localization of all proteins in three reference strains and four clinical isolates of P. gingivalis, as well as the mechanisms employed to reach these destinations.
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6
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Asher A, Ganesan I, Klasek L, Theg SM. Isolation of Physiologically Active Thylakoids and Their Use in Energy-Dependent Protein Transport Assays. J Vis Exp 2018:58393. [PMID: 30320750 PMCID: PMC6235370 DOI: 10.3791/58393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chloroplasts are the organelles in green plants responsible for carrying out numerous essential metabolic pathways, most notably photosynthesis. Within the chloroplasts, the thylakoid membrane system houses all the photosynthetic pigments, reaction center complexes, and most of the electron carriers, and is responsible for light-dependent ATP synthesis. Over 90% of chloroplast proteins are encoded in the nucleus, translated in the cytosol, and subsequently imported into the chloroplast. Further protein transport into or across the thylakoid membrane utilizes one of four translocation pathways. Here, we describe a high-yield method for isolation of transport-competent thylakoids from peas (Pisum sativum), along with transport assays through the three energy-dependent cpTat, cpSec1, and cpSRP-mediated pathways. These methods enable experiments relating to thylakoid protein localization, transport energetics, and the mechanisms of protein translocation across biological membranes.
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Affiliation(s)
- Anthony Asher
- Department of Plant Biology, University of California - Davis
| | - Iniyan Ganesan
- Department of Plant Biology, University of California - Davis
| | - Laura Klasek
- Department of Plant Biology, University of California - Davis
| | - Steven M Theg
- Department of Plant Biology, University of California - Davis;
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7
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Kumari N, Götz F, Nguyen MT. Aspartate tightens the anchoring of staphylococcal lipoproteins to the cytoplasmic membrane. Microbiologyopen 2017; 6. [PMID: 28901671 PMCID: PMC5727369 DOI: 10.1002/mbo3.525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/22/2017] [Accepted: 07/03/2017] [Indexed: 12/16/2022] Open
Abstract
In gram-negative bacteria, the ABC transporter LolCDE complex translocates outer membrane-specific lipoproteins (Lpp) from the inner membrane to the outer membrane. Lpp possessing aspartate (Asp) at position +2 are not translocated because it functions as a LolCDE avoidance signal. In gram-positive bacteria, lacking an outer membrane and the Lol system, Lpp are only anchored at the outer leaflet of the cytoplasmic membrane. However, the release of Lpp particularly in pathogenic or commensal species is crucial for immune modulation. Here, we provide evidence that in Staphylococcus aureus Asp at position +2 plays a role in withholding Lpp to the cytoplasmic membrane. Screening of published exoproteomic data of S. aureus revealed that Lpp mainly with Gly or Ser at position +2 were found in exoproteome, but there was no Lpp with Asp+2. The occurrence of Lpp with Asp+2 is infrequent in gram-positive bacteria. In S. aureus USA300 only seven of the 67 Lpp possess Asp+2; among them five Lpp represented Lpl lipoproteins involved in host cell invasion. Our study demonstrated that replacing the Asp+2 present in Lpl8 with a Ser enhances its release into the supernatant. However, there is no different release of Asp+2 and Ser+2 in mprF mutant that lacks the positive charge of lysyl-phosphatidylglycerol (Lys-PG). Moreover, substitution of Ser+2 by Asp in SitC (MntC) did not lead to a decreased release indicating that in staphylococci positions +3 and +4 might also be important for a tighter anchoring of Lpp. Here, we show that Asp in position +2 and adjacent amino acids contribute in tightening the anchoring of Lpp by interaction of the negative charged Asp with the positive charged Lys-PG.
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Affiliation(s)
- Nimerta Kumari
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbial Genetics, University of Tübingen, Tübingen, Germany.,Institute of Microbiology, University of Sindh, Jamshoro, Pakistan
| | - Friedrich Götz
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbial Genetics, University of Tübingen, Tübingen, Germany
| | - Minh-Thu Nguyen
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbial Genetics, University of Tübingen, Tübingen, Germany.,School of Biological and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
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8
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Vallecillo AJ, Parada C, Morales P, Espitia C. Rhodococcus erythropolis as a host for expression, secretion and glycosylation of Mycobacterium tuberculosis proteins. Microb Cell Fact 2017; 16:12. [PMID: 28103877 PMCID: PMC5248525 DOI: 10.1186/s12934-017-0628-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/10/2017] [Indexed: 11/17/2022] Open
Abstract
Background Glycosylation is one of the most abundant posttranslational polypeptide chain modification in nature. Although carbohydrate modification of protein antigens from many microbial pathogens constitutes important components of B cell epitopes, the role in T cell immunity is not completely understood. There is growing evidence about the importance of these modifications in host bacteria interactions in tuberculosis. It is known, that the sugars present in some Mycobacterium tuberculosis glycoproteins play an important role in both humoral and cellular immune response against the pathogen. Since this modification is lost in the recombinant proteins expressed in Escherichia coli, it is fundamental to search for host bacteria with the capacity to modify the foreign proteins. Amongst the bacteria that are likely to have this possibility are some members of Rhodococcus genus which are Gram-positive bacteria, with high GC-content and genetically very close related to M. tuberculosis. Results In this work, apa, pstS1 and lprG genes that coding for M. tuberculosis glycoproteins were cloned and expressed in Rhodococcus erythropolis. All recombinant proteins were mannosylated as demonstrated by their interaction with mannose binding lectin Concanavalin A. In addition, as native proteins recombinants Apa and PstS1 were secreted to the culture medium in contrast with LprG that was retained in the cell wall. Conclusions Together these results, point out R. erythropolis, as a new host for expression of M. tuberculosis glycoproteins.
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Affiliation(s)
- Antonio J Vallecillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico, D.F., Mexico.,Escuela de Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad de Cuenca, C.P. 010220, Cuenca, Azu., Ecuador
| | - Cristina Parada
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico, D.F., Mexico
| | - Pedro Morales
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico, D.F., Mexico
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico, D.F., Mexico.
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9
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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10
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Fernandes S, São-José C. More than a hole: the holin lethal function may be required to fully sensitize bacteria to the lytic action of canonical endolysins. Mol Microbiol 2016; 102:92-106. [DOI: 10.1111/mmi.13448] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Sofia Fernandes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa, Av. Prof. Gama Pinto; Lisboa 1649-003 Portugal
| | - Carlos São-José
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa, Av. Prof. Gama Pinto; Lisboa 1649-003 Portugal
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11
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Hu X, Yan H, Liu K, Hu J, Qi C, Yang J, Liu Y, Zhao J, Liu J. Identification and characterization of a novel stress-responsive outer membrane protein Lip40 from Actinobacillus pleuropneumoniae. BMC Biotechnol 2015; 15:106. [PMID: 26608465 PMCID: PMC4660844 DOI: 10.1186/s12896-015-0199-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/29/2015] [Indexed: 01/30/2023] Open
Abstract
Background Actinobacillus pleuropneumoniae, a Gram-negative bacterium, is the causative agent of porcine pleuropneumonia, a highly contagious and often fatal disease. Because current vaccines confer limited protection against A. pleuropneumoniae infection, the development of more effective vaccines is urgently required. The identification of immunogenic and protective antigens, such as an outer-membrane lipoprotein, will advance this purpose. Results Sixty putative lipoproteins were predicted from the genomic sequence of A. pleuropneumoniae using multiple algorithms. Here, we focused on the characteristics of the putative lipoprotein Lip40 from A. pleuropneumoniae strain SLW01 (serovar 1). Lip40 shares sequence similarity with many bacterial lipoproteins, and the structural prediction of Lip40 suggests that it is similar to A. pleuropneumoniae TbpB. The N-terminus of Lip40 contains an interesting tandemly repeated sequence, Q(E/D/P)QPK. Real-time RT–PCR indicated that the expression of lip40 was significantly upregulated at 42 °C, at 16 °C, and under anaerobic conditions. Recombinant Lip40 (rLip40) produced in Escherichia coli BL21(DE3) was specifically recognized by porcine convalescent serum directed against A. pleuropneumoniae. Lip40 was confirmed to localize at the bacterial outer membrane, and its expression was significantly stimulated when A. pleuropneumoniae was cultured under various stress conditions. Lip40 also protected 75 % of mice from fatal virulent A. pleuropneumoniae infection. Conclusions The immunogenic outer-membrane protein Lip40 is stress responsive, protects mice against infection, and might be a virulence determinant. Further investigation of Lip40 should expedite vaccine development and provide insight into the pathogenesis of A. pleuropneumoniae. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuehe Hu
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Hao Yan
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Ke Liu
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Jiansheng Hu
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Chao Qi
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Jihong Yang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Yanli Liu
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Jin Zhao
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Jinlin Liu
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
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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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Molecular engineering of secretory machinery components for high-level secretion of proteins in Bacillus species. ACTA ACUST UNITED AC 2014; 41:1599-607. [DOI: 10.1007/s10295-014-1506-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 08/27/2014] [Indexed: 12/19/2022]
Abstract
Abstract
Secretory expression of valuable enzymes by Bacillus subtilis and its related species has attracted intensive work over the past three decades. Although many proteins have been expressed and secreted, the titers of some recombinant enzymes are still low to meet the needs of practical applications. Signal peptides that located at the N-terminal of nascent peptide chains play crucial roles in the secretion process. In this mini-review, we summarize recent progress in secretory expression of recombinant proteins in Bacillus species. In particular, we highlighted and discussed the advances in molecular engineering of secretory machinery components, construction of signal sequence libraries and identification of functional signal peptides with high-throughput screening strategy. The prospects of future research are also proposed.
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14
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Johnson CM, Grossman AD. Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis. Mol Microbiol 2014; 93:1284-301. [PMID: 25069588 DOI: 10.1111/mmi.12736] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2014] [Indexed: 01/28/2023]
Abstract
Conjugation, a major type of horizontal gene transfer in bacteria, involves transfer of DNA from a donor to a recipient using donor-encoded conjugation machinery. Using a high-throughput screen (Tn-seq), we identified genes in recipients that contribute to acquisition of the integrative and conjugative element ICEBs1 by Bacillus subtilis. We found that null mutations in some genes caused an increase, and others a decrease in conjugation efficiency. Some mutations affected conjugation only when present in recipients. Other mutations affected conjugation when present in donors or recipients. Most of the genes identified are known or predicted to affect the cell envelope. Several encode enzymes involved in phospholipid biosynthesis and one encodes a homologue of penicillin-binding proteins. Two of the genes identified also affected conjugation of Tn916, indicating that their roles in conjugation may be general. We did not identify any genes in recipients that were essential for ICEBs1 conjugation, indicating that if there are such genes, then these are either essential for cell growth or redundant. Our results indicate that acquisition of ICEBs1, and perhaps other conjugative elements, is robust and not easily avoided by mutation and that several membrane-related functions affect the efficiency of conjugation.
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Affiliation(s)
- Christopher M Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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15
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16
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Mining the bacterial unknown proteome: identification and characterization of a novel family of highly conserved protective antigens in Staphylococcus aureus. Biochem J 2014; 455:273-84. [PMID: 23895222 DOI: 10.1042/bj20130540] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the human pathogen Staphylococcus aureus, there exists an enormous diversity of proteins containing DUFs (domains of unknown function). In the present study, we characterized the family of conserved staphylococcal antigens (Csa) classified as DUF576 and taxonomically restricted to Staphylococci. The 18 Csa paralogues in S. aureus Newman are highly similar at the sequence level, yet were found to be expressed in multiple cellular locations. Extracellular Csa1A was shown to be post-translationally processed and released. Molecular interaction studies revealed that Csa1A interacts with other Csa paralogues, suggesting that these proteins are involved in the same cellular process. The structures of Csa1A and Csa1B were determined by X-ray crystallography, unveiling a peculiar structure with limited structural similarity to other known proteins. Our results provide the first detailed biological characterization of this family and confirm the uniqueness of this family also at the structural level. We also provide evidence that Csa family members elicit protective immunity in in vivo animal models of staphylococcal infections, indicating a possible important role for these proteins in S. aureus biology and pathogenesis. These findings identify the Csa family as new potential vaccine candidates, and underline the importance of mining the bacterial unknown proteome to identify new targets for preventive vaccines.
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Pribyl T, Moche M, Dreisbach A, Bijlsma JJE, Saleh M, Abdullah MR, Hecker M, van Dijl JM, Becher D, Hammerschmidt S. Influence of impaired lipoprotein biogenesis on surface and exoproteome of Streptococcus pneumoniae. J Proteome Res 2014; 13:650-67. [PMID: 24387739 DOI: 10.1021/pr400768v] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Surface proteins are important for the fitness and virulence of the Gram-positive pathogen Streptococcus pneumoniae. They are crucial for interaction of the pathogen with its human host during infection. Therefore, the analysis of the pneumococcal surface proteome is an important task that requires powerful tools. In this study, two different methods, an optimized biotinylation approach and shaving with trypsin beads, were applied to study the pneumococcal surface proteome and to identify surface-exposed protein domains, respectively. The identification of nearly 95% of the predicted lipoproteins and 75% of the predicted sortase substrates reflects the high coverage of the two classical surface protein classes accomplished in this study. Furthermore, the biotinylation approach was applied to study the impact of an impaired lipoprotein maturation pathway on the cell envelope proteome and exoproteome. Loss of the lipoprotein diacylglyceryl transferase Lgt leads to striking changes in the lipoprotein distribution. Many lipoproteins disappear from the surface proteome and accumulate in the exoproteome. Further insights into lipoprotein processing in pneumococci are provided by immunoblot analyses of bacterial lysates and corresponding supernatant fractions. Taken together, the first comprehensive overview of the pneumococcal surface and exoproteome is presented, and a model for lipoprotein processing in S. pneumoniae is proposed.
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Affiliation(s)
- Thomas Pribyl
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald , Friedrich-Ludwig-Jahn-Str. 15a, Greifswald D-17487, Germany
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18
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Brülle JK, Tschumi A, Sander P. Lipoproteins of slow-growing Mycobacteria carry three fatty acids and are N-acylated by apolipoprotein N-acyltransferase BCG_2070c. BMC Microbiol 2013; 13:223. [PMID: 24093492 PMCID: PMC3850990 DOI: 10.1186/1471-2180-13-223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 09/30/2013] [Indexed: 12/20/2022] Open
Abstract
Background Lipoproteins are virulence factors of Mycobacterium tuberculosis. Bacterial lipoproteins are modified by the consecutive action of preprolipoprotein diacylglyceryl transferase (Lgt), prolipoprotein signal peptidase (LspA) and apolipoprotein N- acyltransferase (Lnt) leading to the formation of mature triacylated lipoproteins. Lnt homologues are found in Gram-negative and high GC-rich Gram-positive, but not in low GC-rich Gram-positive bacteria, although N-acylation is observed. In fast-growing Mycobacterium smegmatis, the molecular structure of the lipid modification of lipoproteins was resolved recently as a diacylglyceryl residue carrying ester-bound palmitic acid and ester-bound tuberculostearic acid and an additional amide-bound palmitic acid. Results We exploit the vaccine strain Mycobacterium bovis BCG as model organism to investigate lipoprotein modifications in slow-growing mycobacteria. Using Escherichia coli Lnt as a query in BLASTp search, we identified BCG_2070c and BCG_2279c as putative lnt genes in M. bovis BCG. Lipoproteins LprF, LpqH, LpqL and LppX were expressed in M. bovis BCG and BCG_2070c lnt knock-out mutant and lipid modifications were analyzed at molecular level by matrix-assisted laser desorption ionization time-of-flight/time-of-flight analysis. Lipoprotein N-acylation was observed in wildtype but not in BCG_2070c mutants. Lipoprotein N- acylation with palmitoyl and tuberculostearyl residues was observed. Conclusions Lipoproteins are triacylated in slow-growing mycobacteria. BCG_2070c encodes a functional Lnt in M. bovis BCG. We identified mycobacteria-specific tuberculostearic acid as further substrate for N-acylation in slow-growing mycobacteria.
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Affiliation(s)
- Juliane K Brülle
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30/32, CH-8006, Zurich, Switzerland.
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19
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Johnson B, Selle K, O'Flaherty S, Goh YJ, Klaenhammer T. Identification of extracellular surface-layer associated proteins in Lactobacillus acidophilus NCFM. MICROBIOLOGY-SGM 2013; 159:2269-2282. [PMID: 24002751 PMCID: PMC3836491 DOI: 10.1099/mic.0.070755-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial surface (S-) layers are crystalline arrays of self-assembling, proteinaceous subunits called S-layer proteins (Slps), with molecular masses ranging from 40 to 200 kDa. The S-layer-forming bacterium Lactobacillus acidophilus NCFM expresses three major Slps: SlpA (46 kDa), SlpB (47 kDa) and SlpX (51 kDa). SlpA has a demonstrated role in adhesion to Caco-2 intestinal epithelial cells in vitro, and has been shown to modulate dendritic cell (DC) and T-cell functionalities with murine DCs. In this study, a modification of a standard lithium chloride S-layer extraction revealed 37 proteins were solubilized from the S-layer wash fraction. Of these, 30 have predicted cleavage sites for secretion, 24 are predicted to be extracellular, six are lipid-anchored, three have N-terminal hydrophobic membrane spanning regions and four are intracellular, potentially moonlighting proteins. Some of these proteins, designated S-layer associated proteins (SLAPs), may be loosely associated with or embedded within the bacterial S-layer complex. Lba-1029, a putative SLAP gene, was deleted from the chromosome of L. acidophilus. Phenotypic characterization of the deletion mutant demonstrated that the SLAP LBA1029 contributes to a pro-inflammatory TNF-α response from murine DCs. This study identified extracellular proteins and putative SLAPs of L. acidophilus NCFM using LC-MS/MS. SLAPs appear to impart important surface display features and immunological properties to microbes that are coated by S-layers.
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Affiliation(s)
- Brant Johnson
- Department of Microbiology, North Carolina State University, Raleigh, NC, USA
| | - Kurt Selle
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Todd Klaenhammer
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.,Department of Microbiology, North Carolina State University, Raleigh, NC, USA
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Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, van Dijl JM. Extracytoplasmic proteases determining the cleavage and release of secreted proteins, lipoproteins, and membrane proteins in Bacillus subtilis. J Proteome Res 2013; 12:4101-10. [PMID: 23937099 DOI: 10.1021/pr400433h] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gram-positive bacteria are known to export many proteins to the cell wall and growth medium, and accordingly, many studies have addressed the respective protein export mechanisms. In contrast, very little is known about the subsequent fate of these proteins. The present studies were therefore aimed at determining the fate of native exported proteins in the model organism Bacillus subtilis. Specifically, we employed a gel electrophoresis-based liquid chromatography-mass spectrometry approach to distinguish the roles of the membrane-associated quality control proteases HtrA and HtrB from those of eight other proteases that are present in the cell wall and/or growth medium of B. subtilis. Notably, HtrA and HtrB were previously shown to counteract potentially detrimental "protein export stresses" upon overproduction of membrane or secreted proteins. Our results show that many secreted proteins, lipoproteins, and membrane proteins of B. subtilis are potential substrates of extracytoplasmic proteases. Moreover, potentially important roles of HtrA and HtrB in the folding of native secreted proteins into a protease-resistant conformation, the liberation of lipoproteins from the membrane-cell wall interface, and the degradation of membrane proteins are uncovered. Altogether, our observations show that HtrA and HtrB are crucial for maintaining the integrity of the B. subtilis cell even under nonstress conditions.
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Affiliation(s)
- Laxmi Krishnappa
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, The Netherlands
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21
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van Dijl JM, Hecker M. Bacillus subtilis: from soil bacterium to super-secreting cell factory. Microb Cell Fact 2013; 12:3. [PMID: 23311580 PMCID: PMC3564730 DOI: 10.1186/1475-2859-12-3] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 12/17/2022] Open
Abstract
The biotechnology industry has become a key element in modern societies. Within this industry, the production of recombinant enzymes and biopharmaceutical proteins is of major importance. The global markets for such recombinant proteins are growing rapidly and, accordingly, there is a continuous need for new production platforms that can deliver protein products in greater yields, with higher quality and at lower costs. This calls for the development of next-generation super-secreting cell factories. One of the microbial cell factories that can meet these challenges is the Gram-positive bacterium Bacillus subtilis, an inhabitant of the upper layers of the soil that has the capacity to secrete proteins in the gram per litre range. The engineering of B. subtilis into a next-generation super-secreting cell factory requires combined Systems and Synthetic Biology approaches. In this way, the bacterial protein secretion machinery can be optimized from the single molecule to the network level while, at the same time, taking into account the balanced use of cellular resources. Although highly ambitious, this is an achievable objective due to recent advances in functional genomics and Systems- and Synthetic Biological analyses of B. subtilis cells.
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Affiliation(s)
- Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P,O, box 30001, Groningen, 9700 RB, the Netherlands.
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22
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Renier S, Chambon C, Viala D, Chagnot C, Hébraud M, Desvaux M. Exoproteomic analysis of the SecA2-dependent secretion in Listeria monocytogenes EGD-e. J Proteomics 2013; 80:183-95. [PMID: 23291529 DOI: 10.1016/j.jprot.2012.11.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 11/12/2012] [Accepted: 11/29/2012] [Indexed: 12/21/2022]
Abstract
As part of the Sec translocase, the accessory ATPase SecA2 is present in some pathogenic Gram-positive bacteria. In Listeria monocytogenes, deletion of secA2 results in filamentous cells that form rough colonies and have lower virulence. However, only a few proteins have been identified that are secreted by this pathway. This investigation aims to provide the first exoproteomic analysis of the SecA2-dependent secretion in L. monocytogenes EGD-e. By using media and temperatures relevant to bacterial physiology, we demonstrated that the rough colony and elongated bacterial cell morphotypes are highly dependent on growth conditions. Subsequently, comparative exoproteomic analyses of the ΔsecA2 versus wt strains were performed in chemically defined medium at 20°C and 37°C. Analyzing the proteomic data following the secretomics-based method, part of the proteins appeared routed towards the Sec pathway and exhibited an N-terminal signal peptide. For another significant part, they were primarily cytoplasmic proteins, thus lacking signal peptide and with no predictable secretion pathway. In total, 13 proteins were newly identified as secreted via SecA2, which were essentially associated with cell-wall metabolism, adhesion and/or biofilm formation. From this comparative exoproteomic analysis, new insights into the L. monocytogenes physiology are discussed in relation to its saprophytic and pathogenic lifestyle.
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Affiliation(s)
- Sandra Renier
- INRA, UR454 Microbiologie, F-63122 Saint-Genès Champanelle, France
| | - Christophe Chambon
- INRA, Plate-forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France
| | - Didier Viala
- INRA, Plate-forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France
| | - Caroline Chagnot
- INRA, UR454 Microbiologie, F-63122 Saint-Genès Champanelle, France
| | - Michel Hébraud
- INRA, UR454 Microbiologie, F-63122 Saint-Genès Champanelle, France; INRA, Plate-forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France
| | - Mickaël Desvaux
- INRA, UR454 Microbiologie, F-63122 Saint-Genès Champanelle, France.
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23
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Membrane proteases in the bacterial protein secretion and quality control pathway. Microbiol Mol Biol Rev 2012; 76:311-30. [PMID: 22688815 DOI: 10.1128/mmbr.05019-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteolytic cleavage of proteins that are permanently or transiently associated with the cytoplasmic membrane is crucially important for a wide range of essential processes in bacteria. This applies in particular to the secretion of proteins and to membrane protein quality control. Major progress has been made in elucidating the structure-function relationships of many of the responsible membrane proteases, including signal peptidases, signal peptide hydrolases, FtsH, the rhomboid protease GlpG, and the site 1 protease DegS. These enzymes employ very different mechanisms to cleave substrates at the cytoplasmic and extracytoplasmic membrane surfaces or within the plane of the membrane. This review highlights the different ways that bacterial membrane proteases degrade their substrates, with special emphasis on catalytic mechanisms and substrate delivery to the respective active sites.
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Mohiman N, Argentini M, Batt SM, Cornu D, Masi M, Eggeling L, Besra G, Bayan N. The ppm operon is essential for acylation and glycosylation of lipoproteins in Corynebacterium glutamicum. PLoS One 2012; 7:e46225. [PMID: 23029442 PMCID: PMC3460810 DOI: 10.1371/journal.pone.0046225] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/29/2012] [Indexed: 11/18/2022] Open
Abstract
Background Due to their contribution to bacterial virulence, lipoproteins and members of the lipoprotein biogenesis pathway represent potent drug targets. Following translocation across the inner membrane, lipoprotein precursors are acylated by lipoprotein diacylglycerol transferase (Lgt), cleaved off their signal peptides by lipoprotein signal peptidase (Lsp) and, in Gram-negative bacteria, further triacylated by lipoprotein N-acyl transferase (Lnt). The existence of an active apolipoprotein N-acyltransferase (Ms-Ppm2) involved in the N-acylation of LppX was recently reported in M. smegmatis. Ms-Ppm2 is part of the ppm operon in which Ppm1, a polyprenol-monophosphomannose synthase, has been shown to be essential in lipoglycans synthesis but whose function in lipoprotein biosynthesis is completely unknown. Results In order to clarify the role of the ppm operon in lipoprotein biosynthesis, we investigated the post-translational modifications of two model lipoproteins (AmyE and LppX) in C. glutamicum Δppm1 and Δppm2 mutants. Our results show that both proteins are anchored into the membrane and that their N-termini are N-acylated by Cg-Ppm2. The acylated N-terminal peptide of LppX was also found to be modified by hexose moieties. This O-glycosylation is localized in the N-terminal peptide of LppX and disappeared in the Δppm1 mutant. While compromised in the absence of Cg-Ppm2, LppX O-glycosylation could be restored when Cg-Ppm1, Cg-Ppm2 or the homologous Mt-Ppm1 of M. tuberculosis was overexpressed. Conclusion Together, these results show for the first time that Cg-Ppm1 (Ppm synthase) and Cg-Ppm2 (Lnt) operate in a common biosynthetic pathway in which lipoprotein N-acylation and glycosylation are tightly coupled.
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Affiliation(s)
- Niloofar Mohiman
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Centre National de la Recherche Scientifique UMR 8619, Orsay, France
| | - Manuela Argentini
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles, Gif sur Yvette, France
| | - Sarah M. Batt
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - David Cornu
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles, Gif sur Yvette, France
| | - Muriel Masi
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Centre National de la Recherche Scientifique UMR 8619, Orsay, France
| | | | - Gurdyal Besra
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicolas Bayan
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Centre National de la Recherche Scientifique UMR 8619, Orsay, France
- * E-mail:
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25
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Renier S, Micheau P, Talon R, Hébraud M, Desvaux M. Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PLoS One 2012; 7:e42982. [PMID: 22912771 PMCID: PMC3415414 DOI: 10.1371/journal.pone.0042982] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/13/2012] [Indexed: 11/20/2022] Open
Abstract
Genome-scale prediction of subcellular localization (SCL) is not only useful for inferring protein function but also for supporting proteomic data. In line with the secretome concept, a rational and original analytical strategy mimicking the secretion steps that determine ultimate SCL was developed for Gram-positive (monoderm) bacteria. Based on the biology of protein secretion, a flowchart and decision trees were designed considering (i) membrane targeting, (ii) protein secretion systems, (iii) membrane retention, and (iv) cell-wall retention by domains or post-translocational modifications, as well as (v) incorporation to cell-surface supramolecular structures. Using Listeria monocytogenes as a case study, results were compared with known data set from SCL predictors and experimental proteomics. While in good agreement with experimental extracytoplasmic fractions, the secretomics-based method outperforms other genomic analyses, which were simply not intended to be as inclusive. Compared to all other localization predictors, this method does not only supply a static snapshot of protein SCL but also offers the full picture of the secretion process dynamics: (i) the protein routing is detailed, (ii) the number of distinct SCL and protein categories is comprehensive, (iii) the description of protein type and topology is provided, (iv) the SCL is unambiguously differentiated from the protein category, and (v) the multiple SCL and protein category are fully considered. In that sense, the secretomics-based method is much more than a SCL predictor. Besides a major step forward in genomics and proteomics of protein secretion, the secretomics-based method appears as a strategy of choice to generate in silico hypotheses for experimental testing.
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Affiliation(s)
- Sandra Renier
- INRA, UR454 Microbiology, Saint-Genès Champanelle, France
| | - Pierre Micheau
- INRA, UR454 Microbiology, Saint-Genès Champanelle, France
| | - Régine Talon
- INRA, UR454 Microbiology, Saint-Genès Champanelle, France
| | - Michel Hébraud
- INRA, UR454 Microbiology, Saint-Genès Champanelle, France
| | - Mickaël Desvaux
- INRA, UR454 Microbiology, Saint-Genès Champanelle, France
- * E-mail:
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26
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Olaya-Abril A, Gómez-Gascón L, Jiménez-Munguía I, Obando I, Rodríguez-Ortega MJ. Another turn of the screw in shaving Gram-positive bacteria: Optimization of proteomics surface protein identification in Streptococcus pneumoniae. J Proteomics 2012; 75:3733-46. [DOI: 10.1016/j.jprot.2012.04.037] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/13/2012] [Accepted: 04/26/2012] [Indexed: 11/30/2022]
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Vangone A, Oliva R, Cavallo L. CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. BMC Bioinformatics 2012; 13 Suppl 4:S19. [PMID: 22536965 PMCID: PMC3434444 DOI: 10.1186/1471-2105-13-s4-s19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background The development of accurate protein-protein docking programs is making this kind of simulations an effective tool to predict the 3D structure and the surface of interaction between the molecular partners in macromolecular complexes. However, correctly scoring multiple docking solutions is still an open problem. As a consequence, the accurate and tedious screening of many docking models is usually required in the analysis step. Methods All the programs under CONS-COCOMAPS have been written in python, taking advantage of python libraries such as SciPy and Matplotlib. CONS-COCOMAPS is freely available as a web tool at the URL: http://www.molnac.unisa.it/BioTools/conscocomaps/. Results Here we presented CONS-COCOMAPS, a novel tool to easily measure and visualize the consensus in multiple docking solutions. CONS-COCOMAPS uses the conservation of inter-residue contacts as an estimate of the similarity between different docking solutions. To visualize the conservation, CONS-COCOMAPS uses intermolecular contact maps. Conclusions The application of CONS-COCOMAPS to test-cases taken from recent CAPRI rounds has shown that it is very efficient in highlighting even a very weak consensus that often is biologically meaningful.
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Affiliation(s)
- Anna Vangone
- Department of Applied Sciences, University Parthenope of Naples, Centro Direzionale Isola C4, Naples, 80143, Italy
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28
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Abstract
Staphylococcus aureus is an important human pathogen whose virulence relies on the secretion of many different proteins. In general, the secretion of most proteins in S. aureus, as well as other bacteria, is dependent on the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein to the general secretory pathway. The arylomycins are a class of natural product antibiotics that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. While wild-type S. aureus (NCTC 8325) is naturally resistant to the arylomycins, sensitivity is conferred via a point mutation in its SPase. Here, we use a synthetic arylomycin along with a sensitized strain of S. aureus and multidimensional protein identification technology (MudPIT) mass spectrometry to identify 46 proteins whose extracellular accumulation requires SPase activity. Forty-four possess identifiable Sec-type signal peptides and thus are likely canonically secreted proteins, while four also appear to possess cell wall retention signals. We also identified the soluble C-terminal domains of two transmembrane proteins, lipoteichoic acid synthase, LtaS, and O-acyteltransferase, OatA, both of which appear to have noncanonical, internal SPase cleavage sites. Lastly, we identified three proteins, HtrA, PrsA, and SAOUHSC_01761, whose secretion is induced by arylomycin treatment. In addition to elucidating fundamental aspects of the physiology and pathology of S. aureus, the data suggest that an arylomycin-based therapeutic would reduce virulence while simultaneously eradicating an infection.
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Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, Herzberg C, Commichau FM, Lewis RJ, Stülke J. RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J Bacteriol 2011; 193:5431-41. [PMID: 21803996 PMCID: PMC3187381 DOI: 10.1128/jb.05500-11] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 07/21/2011] [Indexed: 12/12/2022] Open
Abstract
The control of mRNA stability is an important component of regulation in bacteria. Processing and degradation of mRNAs are initiated by an endonucleolytic attack, and the cleavage products are processively degraded by exoribonucleases. In many bacteria, these RNases, as well as RNA helicases and other proteins, are organized in a protein complex called the RNA degradosome. In Escherichia coli, the RNA degradosome is assembled around the essential endoribonuclease E. In Bacillus subtilis, the recently discovered essential endoribonuclease RNase Y is involved in the initiation of RNA degradation. Moreover, RNase Y interacts with other RNases, the RNA helicase CshA, and the glycolytic enzymes enolase and phosphofructokinase in a degradosome-like complex. In this work, we have studied the domain organization of RNase Y and the contribution of the domains to protein-protein interactions. We provide evidence for the physical interaction between RNase Y and the degradosome partners in vivo. We present experimental and bioinformatic data which indicate that the RNase Y contains significant regions of intrinsic disorder and discuss the possible functional implications of this finding. The localization of RNase Y in the membrane is essential both for the viability of B. subtilis and for all interactions that involve RNase Y. The results presented in this study provide novel evidence for the idea that RNase Y is the functional equivalent of RNase E, even though the two enzymes do not share any sequence similarity.
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Affiliation(s)
- Martin Lehnik-Habrink
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Joseph Newman
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Fabian M. Rothe
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Alexandra S. Solovyova
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Cecilia Rodrigues
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Christina Herzberg
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Fabian M. Commichau
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Richard J. Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
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de Souza GA, Leversen NA, Målen H, Wiker HG. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway. J Proteomics 2011; 75:502-10. [PMID: 21920479 DOI: 10.1016/j.jprot.2011.08.016] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/16/2011] [Accepted: 08/18/2011] [Indexed: 11/29/2022]
Abstract
Correct protein compartmentalization is a key step for molecular function and cell viability, and this is especially true for membrane and externalized proteins of bacteria. Recent proteomic reports of Bacillus subtilis have shown that many proteins with Sec-like signal peptides and absence of a transmembrane helix domain are still observed in membrane-enriched fractions, but further evidence about signal peptide cleavage or soluble protein contamination is still needed. Here we report a proteomic screening of identified peptides in culture filtrate, membrane fraction and whole cell lysate of Mycobacterium tuberculosis. We were able to detect peptide sequencing evidence that shows that the predicted signal peptide was kept uncleaved for several types of proteins such as mammalian cell entry (Mce) proteins and PE or PE-PGRS proteins. Label-free quantitation of all proteins identified in each fraction showed that the majority of these proteins with uncleaved signal peptides are, indeed, enriched in the Triton X-114 lipid phase. Some of these proteins are likely to be located in the inner membrane while others may be outer membrane proteins.
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Affiliation(s)
- Gustavo A de Souza
- Section for Microbiology and Immunology, the Gade Institute, University of Bergen, N-5021 Bergen, Norway
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Ogura M. ZnuABC and ZosA zinc transporters are differently involved in competence development in Bacillus subtilis. ACTA ACUST UNITED AC 2011; 150:615-25. [DOI: 10.1093/jb/mvr098] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Solis N, Cordwell SJ. Current methodologies for proteomics of bacterial surface-exposed and cell envelope proteins. Proteomics 2011; 11:3169-89. [DOI: 10.1002/pmic.201000808] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/16/2011] [Accepted: 04/05/2011] [Indexed: 12/18/2022]
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33
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Dreisbach A, van Dijl JM, Buist G. The cell surface proteome of Staphylococcus aureus. Proteomics 2011; 11:3154-68. [PMID: 21630461 DOI: 10.1002/pmic.201000823] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 02/27/2011] [Accepted: 03/07/2011] [Indexed: 01/15/2023]
Abstract
The Gram-positive bacterium Staphylococcus aureus is a wide spread opportunistic pathogen that can cause a range of life-threatening diseases. To obtain a better understanding of the global mechanisms for pathogenesis and to identify novel targets for therapeutic interventions, the S. aureus proteome has been recently 'dissected' in several studies. Proteins that are exposed on the cell surface - collectively referred to as the 'surfacome' - have received particular attention, because they can directly interact with extracellular molecules, including drugs and antibodies. Accordingly, these proteins represent interesting candidate targets for active or passive immunization against S. aureus. Here, we review the proteomics strategies used, and we compare the results that were so far obtained. Since the surfacome is part of the cell wall proteome, we first present an overview of general properties of the S. aureus cell envelope, cell wall-associated proteins and mechanisms for protein attachment to the cell wall. Then we zoom in on the surfacome, and discuss the pro's and con's of the specific strategies that have been applied for surfacome profiling. The insights thus obtained may serve as leads for future studies on the S. aureus surfacome and possible applications.
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Affiliation(s)
- Annette Dreisbach
- Department of Medical Microbiology, University Medical Centre Groningen and University of Groningen, Groningen, The Netherlands
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Berrêdo-Pinho M, Kalume DE, Correa PR, Gomes LHF, Pereira MP, da Silva RF, Castello-Branco LRR, Degrave WM, Mendonça-Lima L. Proteomic profile of culture filtrate from the Brazilian vaccine strain Mycobacterium bovis BCG Moreau compared to M. bovis BCG Pasteur. BMC Microbiol 2011; 11:80. [PMID: 21507239 PMCID: PMC3094199 DOI: 10.1186/1471-2180-11-80] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 04/20/2011] [Indexed: 01/07/2023] Open
Abstract
Background Bacille Calmette-Guerin (BCG) is currently the only available vaccine against tuberculosis (TB) and comprises a heterogeneous family of sub-strains with genotypic and phenotypic differences. The World Health Organization (WHO) affirms that the characterization of BCG sub-strains, both on genomic and proteomic levels, is crucial for a better comprehension of the vaccine. In addition, these studies can contribute in the development of a more efficient vaccine against TB. Here, we combine two-dimensional electrophoresis (2DE) and mass spectrometry to analyse the proteomic profile of culture filtrate proteins (CFPs) from M. bovis BCG Moreau, the Brazilian vaccine strain, comparing it to that of BCG Pasteur. CFPs are considered of great importance given their dominant immunogenicity and role in pathogenesis, being available for interaction with host cells since early infection. Results The 2DE proteomic map of M. bovis BCG Moreau CFPs in the pH range 3 - 8 allowed the identification of 158 spots corresponding to 101 different proteins, identified by MS/MS. Comparison to BCG Pasteur highlights the great similarity between these BCG strains. However, quantitative analysis shows a higher expression of immunogenic proteins such as Rv1860 (BCG1896, Apa), Rv1926c (BCG1965c, Mpb63) and Rv1886c (BCG1923c, Ag85B) in BCG Moreau when compared to BCG Pasteur, while some heat shock proteins, such as Rv0440 (BCG0479, GroEL2) and Rv0350 (BCG0389, DnaK), show the opposite pattern. Conclusions Here we report the detailed 2DE profile of CFPs from M. bovis BCG Moreau and its comparison to BCG Pasteur, identifying differences that may provide relevant information on vaccine efficacy. These findings contribute to the detailed characterization of the Brazilian vaccine strain against TB, revealing aspects that may lead to a better understanding of the factors leading to BCG's variable protective efficacy against TB.
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Affiliation(s)
- Marcia Berrêdo-Pinho
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, FIOCRUZ, Avenida Brasil, 4365, Manguinhos, CEP 21040 -900 Rio de Janeiro, RJ, Brazil
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35
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Adamczyk-Poplawska M, Markowicz S, Jagusztyn-Krynicka EK. Proteomics for development of vaccine. J Proteomics 2011; 74:2596-616. [PMID: 21310271 DOI: 10.1016/j.jprot.2011.01.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/26/2011] [Accepted: 01/31/2011] [Indexed: 12/20/2022]
Abstract
The success of genome projects has provided us with a vast amount of information on genes of many pathogenic species and has raised hopes for rapid progress in combating infectious diseases, both by construction of new effective vaccines and by creating a new generation of therapeutic drugs. Proteomics, a strategy complementary to the genomic-based approach, when combined with immunomics (looking for immunogenic proteins) and vaccinomics (characterization of host response to immunization), delivers valuable information on pathogen-host cell interaction. It also speeds the identification and detailed characterization of new antigens, which are potential candidates for vaccine development. This review begins with an overview of the global status of vaccinology based on WHO data. The main part of this review describes the impact of proteomic strategies on advancements in constructing effective antibacterial, antiviral and anticancer vaccines. Diverse aspects of disease mechanisms and disease preventions have been investigated by proteomics.
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Affiliation(s)
- Monika Adamczyk-Poplawska
- Department of Virology, Institute of Microbiology, Biology Faculty, Warsaw University, Warsaw, Poland
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Abstract
Bacterial protein secretion is a highly orchestrated process that is essential for infection and virulence. Despite extensive efforts to predict or experimentally detect proteins that are secreted, the characterization of the bacterial secretome has remained challenging. A central event in protein secretion is the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein for secretion via the general secretory pathway, and the arylomycins are a class of natural products that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. Here, using an arylomycin derivative, along with two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identify 11 proteins whose secretion from stationary-phase Staphylococcus epidermidis is dependent on SPase activity, 9 of which are predicted to be translated with canonical N-terminal signal peptides. In addition, we find that the presence of extracellular domains of lipoteichoic acid synthase (LtaS) and the β-lactam response sensor BlaR1 in the medium is dependent on SPase activity, suggesting that they are cleaved at noncanonical sites within the protein. In all, the data define the proteins whose stationary-phase secretion depends on SPase and also suggest that the arylomycins should be valuable chemical biology tools for the study of protein secretion in a wide variety of different bacteria.
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Desvaux M, Dumas E, Chafsey I, Chambon C, Hébraud M. Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics. J Proteome Res 2010; 9:5076-92. [PMID: 20839850 DOI: 10.1021/pr1003642] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Defined as proteins actively transported via secretion systems, secreted proteins can have radically different subcellular destinations in monoderm (Gram-positive) bacteria. From degradative enzymes in saprophytes to virulence factors in pathogens, secreted proteins are the main tools used by bacteria to interact with their surroundings. The etiological agent of listeriosis, Listeria monocytogenes, is a Gram-positive facultative intracellular foodborne pathogen, whose ecological niche is the soil and as such should be primarily considered as a ubiquitous saprophyte. Recent advances on protein secretion systems in this species prompted us to investigate the exoproteome. First, an original and rational bioinformatic strategy was developed to mimic the protein exportation steps leading to the extracellular localization of secreted proteins; 79 exoproteins were predicted as secreted via Sec, 1 exoprotein via Tat, 4 bacteriocins via ABC exporters, 3 exoproteins via holins, and 3 exoproteins via the WXG100 system. This bioinformatic analysis allowed for defining a databank of the mature protein set in L. monocytogenes, which was used for generating the theoretical exoproteome and for subsequent protein identification by proteomics. 2-DE proteomic analyses were performed over a wide pI range to experimentally cover the largest protein spectrum possible. A total of 120 spots could be resolved and identified, which corresponded to 50 distinct proteins. These exoproteins were essentially virulence factors, degradative enzymes, and proteins of unknown functions, which exportation would essentially rely on the Sec pathway or nonclassical secretion. This investigation resulted in the first comprehensive appraisal of the exoproteome of L. monocytogenes EGD-e based on theoretical and experimental secretomic analyses, which further provided indications on listerial physiology in relation with its habitat and lifestyle. The novel and rational strategy described here is generic and has been purposely designed for the prediction of proteins localized extracellularly in monoderm bacteria.
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Affiliation(s)
- Mickaël Desvaux
- INRA, UR454 Microbiology, Food Quality and Safety Team, Saint-Genès Champanelle, France.
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38
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Ravipaty S, Reilly JP. Comprehensive characterization of methicillin-resistant Staphylococcus aureus subsp. aureus COL secretome by two-dimensional liquid chromatography and mass spectrometry. Mol Cell Proteomics 2010; 9:1898-919. [PMID: 20418541 DOI: 10.1074/mcp.m900494-mcp200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Two-dimensional LC combined with whole protein and peptide mass spectrometry is used to characterize proteins secreted by methicillin-resistant Staphylococcus aureus COL. Protein identifications were accomplished via off-line protein fractionation followed by digestion and subsequent peptide analysis by reverse phase LC-ESI-LTQ-FT-MS/MS. Peptide MS/MS analysis identified 127 proteins comprising 59 secreted proteins, seven cell wall-anchored proteins, four lipoproteins, four membrane proteins, and 53 cytoplasmic proteins. The identified secreted proteins included various virulence factors of known functions (cytotoxins, enterotoxins, proteases, lipolytic enzymes, peptidoglycan hydrolases, etc.). Accurate whole protein mass measurement (+/-1.5 Da) of the secreted proteins combined with peptide analysis enabled identification of signal peptide cleavage sites and various post-translational modifications. In addition, new observations were possible using the present approach. Although signal peptide cleavage is highly specific, signal peptide processing can occur at more than one site. Surprisingly, cleaved signal peptides and their fragments can be observed in the extracellular medium. The prediction accuracies of several signal peptide prediction programs were also evaluated.
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Affiliation(s)
- Shobha Ravipaty
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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39
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Hempel K, Pané-Farré J, Otto A, Sievers S, Hecker M, Becher D. Quantitative Cell Surface Proteome Profiling for SigB-Dependent Protein Expression in the Human Pathogen Staphylococcus aureus via Biotinylation Approach. J Proteome Res 2010; 9:1579-90. [DOI: 10.1021/pr901143a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kristina Hempel
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Andreas Otto
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
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40
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Pohl S, Harwood CR. Heterologous Protein Secretion by Bacillus Species. ADVANCES IN APPLIED MICROBIOLOGY 2010; 73:1-25. [DOI: 10.1016/s0065-2164(10)73001-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Becher D, Hempel K, Sievers S, Zühlke D, Pané-Farré J, Otto A, Fuchs S, Albrecht D, Bernhardt J, Engelmann S, Völker U, van Dijl JM, Hecker M. A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome. PLoS One 2009; 4:e8176. [PMID: 19997597 PMCID: PMC2781549 DOI: 10.1371/journal.pone.0008176] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 11/09/2009] [Indexed: 11/28/2022] Open
Abstract
The genome sequence is the “blue-print of life,” but proteomics provides the link to the actual physiology of living cells. Because of their low complexity bacteria are excellent model systems to identify the entire protein assembly of a living organism. Here we show that the majority of proteins expressed in growing and non-growing cells of the human pathogen Staphylococcus aureus can be identified and even quantified by a metabolic labeling proteomic approach. S. aureus has been selected as model for this proteomic study, because it poses a major risk to our health care system by combining high pathogenicity with an increasing frequency of multiple antibiotic resistance, thus requiring the development of new anti-staphylococcal therapy strategies. Since such strategies will likely have to target extracellular and surface-exposed virulence factors as well as staphylococcal survival and adaptation capabilities, we decided to combine four subproteomic fractions: cytosolic proteins, membrane-bound proteins, cell surface-associated and extracellular proteins, to comprehensively cover the entire proteome of S. aureus. This quantitative proteomics approach integrating data ranging from gene expression to subcellular localization in growing and non-growing cells is a proof of principle for whole-cell physiological proteomics that can now be extended to address physiological questions in infection-relevant settings. Importantly, with more than 1700 identified proteins (and 1450 quantified proteins) corresponding to a coverage of about three-quarters of the expressed proteins, our model study represents the most comprehensive quantification of a bacterial proteome reported to date. It thus paves the way towards a new level in understanding of cell physiology and pathophysiology of S. aureus and related pathogenic bacteria, opening new avenues for infection-related research on this crucial pathogen.
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Affiliation(s)
- Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Kristina Hempel
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Andreas Otto
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Stephan Fuchs
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
- * E-mail:
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Bendz M, Möller MC, Arrigoni G, Wåhlander Å, Stella R, Cappadona S, Levander F, Hederstedt L, James P. Quantification of Membrane Proteins Using Nonspecific Protease Digestions. J Proteome Res 2009; 8:5666-73. [DOI: 10.1021/pr900741t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Maria Bendz
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Mirja Carlsson Möller
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Giorgio Arrigoni
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Åsa Wåhlander
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Roberto Stella
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Salvatore Cappadona
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Fredrik Levander
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Lars Hederstedt
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
| | - Peter James
- Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden, Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden, Department of Cell & Organism Biology, Lund University, Sweden, Department of Biological Chemistry, University of Padova, Italy, and Department of Bioengineering, IIT Unit, Politecnico di Milano, Italy
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Dumas E, Desvaux M, Chambon C, Hébraud M. Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis. Proteomics 2009; 9:3136-55. [DOI: 10.1002/pmic.200800765] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. J Proteome Res 2009; 7:5082-93. [PMID: 19367716 DOI: 10.1021/pr800162c] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods based on regular expression patterns, in various data sets containing experimentally characterized lipoproteins, secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins. The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides. PRED-LIPO is freely available at http://bioinformatics.biol.uoa.gr/PRED-LIPO/, and we anticipate that it will be a valuable tool for the experimentalists studying secreted proteins and lipoproteins from Gram-positive bacteria.
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Affiliation(s)
- Pantelis G Bagos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece.
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45
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Hahne H, Wolff S, Hecker M, Becher D. From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 2009; 8:4123-36. [PMID: 18763711 DOI: 10.1002/pmic.200800258] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The analysis of integral membrane proteins (IMPs) with mass spectrometry-centered technologies has undergone great progress during the past few years, allowing for the analysis of several hundreds of IMPs. In this study, we investigated three promising shotgun approaches for the identification of IMPs of the model organism Bacillus subtilis. One comprises a classical membrane preparation procedure with carbonate and high-ionic-strength buffers, followed by SDS-PAGE and LC-MS/MS analysis. The two others are based on enzymatic trimming of the crude membrane fraction either with trypsin or proteinase K and subsequent gel-free analysis. As a result, we observed the highest degree of complementarity between the gel-based and the proteinase K approach, since the first exclusively addresses soluble loops and domains of IMPs and gave rise to 8709 unique peptides, whereas the latter contributed 1180 unique peptide identifications from otherwise inaccessible transmembrane helices (TMHs). All three methods contribute significant numbers (381, 284, and 276, respectively) to the total of 527 IMP identifications from the membrane fraction of exponentially growing B. subtilis cells, thus representing approximately 69% of all transcribed IMPs.
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Affiliation(s)
- Hannes Hahne
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
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46
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Abstract
About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.
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Affiliation(s)
- Ansgar Poetsch
- Lehrstuhl für Biochemie der Pflanzen, Ruhr Universität Bochum, Bochum, Germany.
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47
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Barinov A, Loux V, Hammani A, Nicolas P, Langella P, Ehrlich D, Maguin E, van de Guchte M. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria. Proteomics 2009; 9:61-73. [DOI: 10.1002/pmic.200800195] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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48
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Sartain MJ, Belisle JT. N-Terminal clustering of the O-glycosylation sites in the Mycobacterium tuberculosis lipoprotein SodC. Glycobiology 2009; 19:38-51. [PMID: 18842962 PMCID: PMC2733778 DOI: 10.1093/glycob/cwn102] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/26/2008] [Accepted: 09/28/2008] [Indexed: 12/16/2022] Open
Abstract
SodC is one of two superoxide dismutases produced by Mycobacterium tuberculosis. This protein was previously shown to contribute to virulence and to act as a B-cell antigen. SodC is also a putative lipoprotein, and like other Sec-translocated mycobacterial proteins it was suggested to be modified with glycosyl units. To definitively define the glycosylation of SodC, we applied an approach that combined site-directed mutagenesis, lectin binding, and mass spectrometry. This resulted in identification of six O-glycosylated residues within a 13-amino-acid region near the N-terminus. Each residue was modified with one to three hexose units, and the most dominant SodC glycoform was modified with nine hexose units. In addition to O-glycosylation of threonine residues, this study provides the first evidence of serine O-glycosylation in mycobacteria. When combined with bioinformatic analyses, the clustering of O-glycosylation appeared to occur in a region of SodC with a disordered structure and not in regions important to the enzymatic activity of SodC. The use of recombinant amino acid substitutions to alter glycosylation sites provided further evidence that glycosylation influences proteolytic processing and ultimately positioning of cell wall proteins.
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Affiliation(s)
- Mark J Sartain
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523, USA
| | - John T Belisle
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523, USA
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Immunity to the bacteriocin sublancin 168 Is determined by the SunI (YolF) protein of Bacillus subtilis. Antimicrob Agents Chemother 2008; 53:651-61. [PMID: 19047653 DOI: 10.1128/aac.01189-08] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis strain 168 produces the extremely stable lantibiotic sublancin 168, which has a broad spectrum of bactericidal activity. Both sublancin 168 production and producer immunity are determined by the SPbeta prophage. While the sunA and sunT genes for sublancin 168 production have been known for several years, the genetic basis for sublancin 168 producer immunity has remained elusive. Therefore, the present studies were aimed at identifying an SPbeta gene(s) for sublancin 168 immunity. By systematic deletion analysis, we were able to pinpoint one gene, named yolF, as the sublancin 168 producer immunity gene. Growth inhibition assays performed using plates and liquid cultures revealed that YolF is both required and sufficient for sublancin 168 immunity even when heterologously produced in the sublancin-sensitive bacterium Staphylococcus aureus. Accordingly, we propose to rename yolF to sunI (for sublancin immunity). Subcellular localization studies indicate that the SunI protein is anchored to the membrane with a single N-terminal membrane-spanning domain that has an N(out)-C(in) topology. Thus, the bulk of the protein faces the cytoplasm of B. subtilis. This topology has not yet been reported for known bacteriocin producer immunity proteins, which implies that SunI belongs to a novel class of bacteriocin antagonists.
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Effect of Bacillus mucilaginosus on weathering of phosphorite and a preliminary analysis of bacterial proteins. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11631-008-0209-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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