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Glycogen-Degrading Activities of Catalytic Domains of α-Amylase and α-Amylase-Pullulanase Enzymes Conserved in Gardnerella spp. from the Vaginal Microbiome. J Bacteriol 2023; 205:e0039322. [PMID: 36744900 PMCID: PMC9945562 DOI: 10.1128/jb.00393-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gardnerella spp. are associated with bacterial vaginosis in which normally dominant lactobacilli are replaced with facultative and anaerobic bacteria, including Gardnerella spp. Co-occurrence of multiple species of Gardnerella is common in the vagina, and competition for nutrients such as glycogen likely contributes to the differential abundances of Gardnerella spp. Glycogen must be digested into smaller components for uptake, a process that depends on the combined action of glycogen-degrading enzymes. In this study, the ability of culture supernatants of 15 isolates of Gardnerella spp. to produce glucose, maltose, maltotriose, and maltotetraose from glycogen was demonstrated. Carbohydrate-active enzymes (CAZymes) were identified bioinformatically in Gardnerella proteomes using dbCAN2. Identified proteins included a single-domain α-amylase (EC 3.2.1.1) (encoded by all 15 isolates) and an α-amylase-pullulanase (EC 3.2.1.41) containing amylase, carbohydrate binding modules, and pullulanase domains (14/15 isolates). To verify the sequence-based functional predictions, the amylase and pullulanase domains of the α-amylase-pullulanase and the single-domain α-amylase were each produced in Escherichia coli. The α-amylase domain from the α-amylase-pullulanase released maltose, maltotriose, and maltotetraose from glycogen, and the pullulanase domain released maltotriose from pullulan and maltose from glycogen, demonstrating that the Gardnerella α-amylase-pullulanase is capable of hydrolyzing α-1,4 and α-1,6 glycosidic bonds. Similarly, the single-domain α-amylase protein also produced maltose, maltotriose, and maltotetraose from glycogen. Our findings show that Gardnerella spp. produce extracellular amylase enzymes as "public goods" that can digest glycogen into maltose, maltotriose, and maltotetraose that can be used by the vaginal microbiota. IMPORTANCE Increased abundance of Gardnerella spp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms, and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community, but little is known about the contribution of bacterial enzymes to the metabolism of glycogen, a major food source available to vaginal bacteria. The significance of our research is characterizing the activity of enzymes conserved in Gardnerella species that contribute to the ability of these bacteria to utilize glycogen.
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Evolutionary Relationships and Divergence of Filamin Gene Family Involved in Development and Stress in Cotton ( Gossypium hirsutum L.). Genes (Basel) 2022; 13:genes13122313. [PMID: 36553581 PMCID: PMC9777546 DOI: 10.3390/genes13122313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
Filamin protein is characterized by an N-terminal actin-binding domain that is followed by 24 Ig (immunoglobulin)-like repeats, which act as hubs for interactions with a variety of proteins. In humans, this family has been found to be involved in cancer cell invasion and metastasis and can be involved in a variety of growth signal transduction processes, but it is less studied in plants. Therefore, in this study, 54 Filamin gene family members from 23 plant species were investigated and divided into two subfamilies: FLMN and GEX2. Subcellular localization showed that most of the Filamin gene family members were located in the cell membrane. A total of 47 Filamin gene pairs were identified, most of which were whole-genome copies. Through the analyses of cis-acting elements, expression patterns and quantitative fluorescence, it was found that GH_ A02G0519 and GH_ D02G0539 are mainly expressed in the reproductive organs of upland cotton, and their interacting proteins are also related to the fertilization process, whereas GH_A02G0216 and GH_D02G0235 were related to stress. Thus, it is speculated that two genes of the GEX2 subfamily (GH_A02G0519 and GH_D02G0539) may be involved in the reproductive development of cotton and may affect the fertilization process of cotton. This study provides a theoretical basis for the further study of the cotton Filamin gene family.
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Cathro P, McCarthy P, Hoffmann P, Kidd S, Zilm P. Enterococcus faecalis V583 cell membrane protein expression to alkaline stress. FEMS Microbiol Lett 2022; 369:6679558. [PMID: 36044998 PMCID: PMC9491840 DOI: 10.1093/femsle/fnac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
Enterococcus faecalis is able to adapt to alkaline conditions and is commonly recovered from teeth in which endodontic treatment has failed. The role that E. faecalis membrane proteins play in survival strategies to extreme alkaline conditions is unclear. We grew E. faecalis V583 in a chemostat at pH 8 and 11 at one-tenth the organism’s relative maximum growth rate. Following membrane shaving, isotope-coding protein labels were added at the peptide level to samples and then combined. The relative proportion of membrane proteins were identified using LC-ESI mass spectrometry and MaxQuant analysis. Ratios of membrane proteins were log2 transformed, with proteins deviating by more than 1 SD of the mean considered to be up- or down-regulated. A total of six proteins were up-regulated in pH 11 including: EF0669 (polysaccharide biosynthesis family); EF1927 (glycerol uptake facilitator), and EF0114 (glycosyl hydrolase). A total of five proteins were down-regulated including: EF0108 (C4-dicarboxylate transporter); EF1838 (PTS system IIC component); EF0456 (PTS system IID component); and EF0022 (PTS mannose-specific IID component). In extreme alkaline conditions, the membrane proteins of E. faecalis seem to be involved in a shift of carbohydrate metabolism from the PTS system to glycerol, which supports the formation of a protective capsule protecting the cell.
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Affiliation(s)
- Peter Cathro
- Oral Microbiology Laboratory, School of Dentistry, The University of Adelaide, Adelaide, South Australia
| | - Peter McCarthy
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre, The University of Adelaide, Adelaide, South Australia, Australia5005
| | - Stephen Kidd
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Peter Zilm
- Oral Microbiology Laboratory, School of Dentistry, The University of Adelaide, Adelaide, South Australia
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Lin K, Zhao N, Cai Y, Lin Y, Han S, Zheng S. Genome-Scale Mining of Novel Anchor Proteins of Corynebacterium glutamicum. Front Microbiol 2022; 12:677702. [PMID: 35185806 PMCID: PMC8854784 DOI: 10.3389/fmicb.2021.677702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022] Open
Abstract
The display of recombinant proteins on the surfaces of bacteria is a research topic with many possible biotechnology applications—among which, the choice of host cell and anchoring motif is the key for efficient display. Corynebacterium glutamicum is a promising host for surface display due to its natural advantages, while single screening methods and fewer anchor proteins restrict its application. In this study, the subcellular localization (SCL) predictor LocateP and tied-mixture hidden Markov models were used to analyze all five known endogenous anchor proteins of C. glutamicum and test the accuracy of the predictions. Using these two tools, the SCLs of all proteins encoded by the genome of C. glutamicum 13032 were predicted, and 14 potential anchor proteins were screened. Compared with the positive controls NCgl1221 and NCgl1337, three anchoring proteins—NCgl1307, NCgl2775, and NCgl0717—performed better. This study also discussed the applicability of the anchor protein screening method used in this experiment to other bacteria.
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Affiliation(s)
- Kerui Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Nannan Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Youhua Cai
- Star Lake Bioscience Co. Inc., Zhaoqing Guangdong, Zhaoqing, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Shuangyan Han,
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Suiping Zheng,
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The Membrane Proteome of Spores and Vegetative Cells of the Food-Borne Pathogen Bacillus cereus. Int J Mol Sci 2021; 22:ijms222212475. [PMID: 34830357 PMCID: PMC8624511 DOI: 10.3390/ijms222212475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Membrane proteins are fascinating since they play an important role in diverse cellular functions and constitute many drug targets. Membrane proteins are challenging to analyze. The spore, the most resistant form of known life, harbors a compressed inner membrane. This membrane acts not only as a barrier for undesired molecules but also as a scaffold for proteins involved in signal transduction and the transport of metabolites during spore germination and subsequent vegetative growth. In this study, we adapted a membrane enrichment method to study the membrane proteome of spores and cells of the food-borne pathogen Bacillus cereus using quantitative proteomics. Using bioinformatics filtering we identify and quantify 498 vegetative cell membrane proteins and 244 spore inner membrane proteins. Comparison of vegetative and spore membrane proteins showed there were 54 spore membrane-specific and 308 cell membrane-specific proteins. Functional characterization of these proteins showed that the cell membrane proteome has a far larger number of transporters, receptors and proteins related to cell division and motility. This was also reflected in the much higher expression level of many of these proteins in the cellular membrane for those proteins that were in common with the spore inner membrane. The spore inner membrane had specific expression of several germinant receptors and spore-specific proteins, but also seemed to show a preference towards the use of simple carbohydrates like glucose and fructose owing to only expressing transporters for these. These results show the differences in membrane proteome composition and show us the specific proteins necessary in the inner membrane of a dormant spore of this toxigenic spore-forming bacterium to survive adverse conditions.
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Three Distinct Proteases Are Responsible for Overall Cell Surface Proteolysis in Streptococcus thermophilus. Appl Environ Microbiol 2021; 87:e0129221. [PMID: 34550764 DOI: 10.1128/aem.01292-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The lactic acid bacterium Streptococcus thermophilus was believed to display only two distinct proteases at the cell surface, namely, the cell envelope protease PrtS and the housekeeping protease HtrA. Using peptidomics, we demonstrate here the existence of an additional active cell surface protease, which shares significant homology with the SepM protease of Streptococcus mutans. Although all three proteases-PrtS, HtrA, and SepM-are involved in the turnover of surface proteins, they demonstrate distinct substrate specificities. In particular, SepM cleaves proteins involved in cell wall metabolism and cell elongation, and its inactivation has consequences for cell morphology. When all three proteases are inactivated, the residual cell-surface proteolysis of S. thermophilus is approximately 5% of that of the wild-type strain. IMPORTANCE Streptococcus thermophilus is a lactic acid bacterium used widely as a starter in the dairy industry. Due to its "generally recognized as safe" status and its weak cell surface proteolytic activity, it is also considered a potential bacterial vector for heterologous protein production. Our identification of a new cell surface protease made it possible to construct a mutant strain with a 95% reduction in surface proteolysis, which could be useful in numerous biotechnological applications.
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Exploring the Bile Stress Response of Lactobacillus mucosae LM1 through Exoproteome Analysis. Molecules 2021; 26:molecules26185695. [PMID: 34577166 PMCID: PMC8467624 DOI: 10.3390/molecules26185695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 11/27/2022] Open
Abstract
Lactobacillus sp. have long been studied for their great potential in probiotic applications. Recently, proteomics analysis has become a useful tool for studies on potential lactobacilli probiotics. Specifically, proteomics has helped determine and describe the physiological changes that lactic acid bacteria undergo in specific conditions, especially in the host gut. In particular, the extracellular proteome, or exoproteome, of lactobacilli contains proteins specific to host– or environment–microbe interactions. Using gel-free, label-free ultra-high performance liquid chromatography tandem mass spectrometry, we explored the exoproteome of the probiotic candidate Lactobacillus mucosae LM1 subjected to bile treatment, to determine the proteins it may use against bile stress in the gut. Bile stress increased the size of the LM1 exoproteome, secreting ribosomal proteins (50S ribosomal protein L27 and L16) and metabolic proteins (lactate dehydrogenase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate dehydrogenases, among others) that might have moonlighting functions in the LM1 bile stress response. Interestingly, membrane-associated proteins (transporters, peptidase, ligase and cell division protein ftsH) were among the key proteins whose secretion were induced by the LM1 bile stress response. These specific proteins from LM1 exoproteome will be useful in observing the proposed bile response mechanisms via in vitro experiments. Our data also reveal the possible beneficial effects of LM1 to the host gut.
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Approaching In Vivo Models of Pneumococcus-Host Interaction: Insights into Surface Proteins, Capsule Production, and Extracellular Vesicles. Pathogens 2021; 10:pathogens10091098. [PMID: 34578131 PMCID: PMC8471892 DOI: 10.3390/pathogens10091098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Infections caused by the Gram-positive bacterium Streptococcus pneumoniae have become a major health problem worldwide because of their high morbidity and mortality rates, especially in developing countries. This microorganism colonizes the human upper respiratory tract and becomes pathogenic under certain circumstances, which are not well known. In the interaction with the host, bacterial surface structures and proteins play major roles. To gain knowledge into gradual changes and adaptive mechanisms that this pathogen undergoes from when it enters the host, we mimicked several in vivo situations representing interaction with epithelial and macrophage cells, as well as a condition of presence in blood. Then, we analyzed, in four pneumococcal strains, two major surface structures, the capsule and extracellular vesicles produced by the pneumococci, as well as surface proteins by proteomics, using the “shaving” approach, followed by LC-MS/MS. We found important differences in both surface ultrastructures and proteins among the culture conditions and strains used. Thus, this work provides insights into physiological adaptations of the pneumococcus when it interacts with the host, which may be useful for the design of strategies to combat infections caused by this pathogen.
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Within-Host Adaptation of Staphylococcus aureus in a Bovine Mastitis Infection Is Associated with Increased Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168840. [PMID: 34445550 PMCID: PMC8396210 DOI: 10.3390/ijms22168840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Within-host adaptation is a typical feature of chronic, persistent Staphylococcus aureus infections. Research projects addressing adaptive changes due to bacterial in-host evolution increase our understanding of the pathogen’s strategies to survive and persist for a long time in various hosts such as human and bovine. In this study, we investigated the adaptive processes of S. aureus during chronic, persistent bovine mastitis using a previously isolated isogenic strain pair from a dairy cow with chronic, subclinical mastitis, in which the last variant (host-adapted, Sigma factor SigB-deficient) quickly replaced the initial, dominant variant. The strain pair was cultivated under specific in vitro infection-relevant growth-limiting conditions (iron-depleted RPMI under oxygen limitation). We used a combinatory approach of surfaceomics, molecular spectroscopic fingerprinting and in vitro phenotypic assays. Cellular cytotoxicity assays using red blood cells and bovine mammary epithelial cells (MAC-T) revealed changes towards a more cytotoxic phenotype in the host-adapted isolate with an increased alpha-hemolysin (α-toxin) secretion, suggesting an improved capacity to penetrate and disseminate the udder tissue. Our results foster the hypothesis that within-host evolved SigB-deficiency favours extracellular persistence in S. aureus infections. Here, we provide new insights into one possible adaptive strategy employed by S. aureus during chronic, bovine mastitis, and we emphasise the need to analyse genotype–phenotype associations under different infection-relevant growth conditions.
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10
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Goff JL, Wang Y, Boyanov MI, Yu Q, Kemner KM, Fein JB, Yee N. Tellurite Adsorption onto Bacterial Surfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10378-10386. [PMID: 34279081 DOI: 10.1021/acs.est.1c01001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Tellurium (Te) is an emerging contaminant and its chemical transformation in the environment is strongly influenced by microbial processes. In this study, we investigated the adsorption of tellurite [Te(IV), TeO32-] onto the common soil bacterium Bacillus subtilis. Thiol-blocking experiments were carried out to investigate the role of cell surface sulfhydryl sites in tellurite binding, and extended X-ray absorption fine structure (EXAFS) spectroscopy was performed to determine the chemical speciation of the adsorbed tellurite. The results indicate that tellurite reacts with sulfhydryl functional groups in the extracellular polymeric substances (EPS) produced by B. subtilis. Upon binding to sulfhydryl sites in the EPS, the Te changes from Te-O bonds to Te-S coordination. Further analysis of the surface-associated molecules shows that the EPS of B. subtilis contain proteins. Removal of the proteinaceous EPS dramatically decreases tellurite adsorption and the sulfhydryl surface site concentration. These findings indicate that sulfhydryl binding in EPS plays a key role in tellurite adsorption on bacterial surfaces.
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Affiliation(s)
- Jennifer L Goff
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Yuwei Wang
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Maxim I Boyanov
- Bulgarian Academy of Sciences, Institute of Chemical Engineering, Sofia 1113, Bulgaria
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Qiang Yu
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jeremy B Fein
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nathan Yee
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey 08901, United States
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11
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Comparative Exoproteome Analysis of Streptococcus suis Human Isolates. Microorganisms 2021; 9:microorganisms9061287. [PMID: 34204746 PMCID: PMC8231589 DOI: 10.3390/microorganisms9061287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 11/23/2022] Open
Abstract
The swine pathogen Streptococcus suis is a Gram-positive bacterium which causes infections in pigs, with an impact in animal health and in the livestock industry, and it is also an important zoonotic agent. During the infection process, surface and secreted proteins are essential in the interaction between microorganisms and their hosts. Here, we report a comparative proteomic analysis of the proteins released to the extracellular milieu in six human clinical isolates belonging to the highly prevalent and virulent serotype 2. The total secreted content was precipitated and analyzed by GeLC-MS/MS. In the six strains, 144 proteins assigned to each of the categories of extracellular or surface proteins were identified, as well as 680 predicted cytoplasmic proteins, many of which are putative moonlighting proteins. Of the nine predicted signal peptide-I secreted proteins, seven had relevant antigenic potential when they were analyzed through bioinformatic analysis. This is the first work comparing the exoproteome fraction of several human isolates of this important pathogen.
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12
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Fuchs S, Kucklick M, Lehmann E, Beckmann A, Wilkens M, Kolte B, Mustafayeva A, Ludwig T, Diwo M, Wissing J, Jänsch L, Ahrens CH, Ignatova Z, Engelmann S. Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach. PLoS Genet 2021; 17:e1009585. [PMID: 34061833 PMCID: PMC8195425 DOI: 10.1371/journal.pgen.1009585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 06/11/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023] Open
Abstract
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.
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Affiliation(s)
- Stephan Fuchs
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
| | - Martin Kucklick
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Erik Lehmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Alexander Beckmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maya Wilkens
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Baban Kolte
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Ayten Mustafayeva
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Tobias Ludwig
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maurice Diwo
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Josef Wissing
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Lothar Jänsch
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoya Ignatova
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Susanne Engelmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
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Tran BM, Prabha H, Iyer A, O'Byrne C, Abee T, Poolman B. Measurement of Protein Mobility in Listeria monocytogenes Reveals a Unique Tolerance to Osmotic Stress and Temperature Dependence of Diffusion. Front Microbiol 2021; 12:640149. [PMID: 33679676 PMCID: PMC7925416 DOI: 10.3389/fmicb.2021.640149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/21/2021] [Indexed: 11/18/2022] Open
Abstract
Protein mobility in the cytoplasm is essential for cellular functions, and slow diffusion may limit the rates of biochemical reactions in the living cell. Here, we determined the apparent lateral diffusion coefficient (DL) of GFP in Listeria monocytogenes as a function of osmotic stress, temperature, and media composition. We find that DL is much less affected by hyperosmotic stress in L. monocytogenes than under similar conditions in Lactococcus lactis and Escherichia coli. We find a temperature optimum for protein diffusion in L. monocytogenes at 30°C, which deviates from predicted trends from the generalized Stokes-Einstein equation under dilute conditions and suggests that the structure of the cytoplasm and macromolecular crowding vary as a function of temperature. The turgor pressure of L. monocytogenes is comparable to other Gram-positive bacteria like Bacillus subtilis and L. lactis but higher in a knockout strain lacking the stress-inducible sigma factor SigB. We discuss these findings in the context of how L. monocytogenes survives during environmental transmission and interaction with the human host.
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Affiliation(s)
- Buu Minh Tran
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
| | - Haritha Prabha
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
| | - Aditya Iyer
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
| | - Conor O'Byrne
- School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University Research, Wageningen, Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
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Bagon BB, Valeriano VDV, Oh JK, Pajarillo EAB, Lee JY, Kang DK. Exoproteome Perspective on the Bile Stress Response of Lactobacillus johnsonii. Proteomes 2021; 9:proteomes9010010. [PMID: 33578796 PMCID: PMC7931105 DOI: 10.3390/proteomes9010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
Probiotics must not only exert a health-promoting effect but also be capable of adapting to the harsh environment of the gastrointestinal (GI) tract. Probiotics in the GI tract must survive the cell wall-disrupting effect of bile acids. We investigated the exoproteome of Lactobacillus johnsonii PF01 and C1-10 under bile stress. A comparative analysis revealed the similarities between the two L. johnsonii exoproteomes, as well as their different responses to bile. The large number of metabolic proteins in L. johnsonii revealed its metabolic adaptation to meet protein synthesis requirements under bile stress. In addition, cell wall modifications occurred in response to bile. Furthermore, some extracellular proteins of L. johnsonii may have moonlighting function in the presence of bile. Enolase, L-lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, 50s ribosomal protein L7/L12, and cellobiose-specific phosphotransferase system (PTS) sugar transporter were significantly upregulated under bile stress, suggesting a leading role in the collective bile stress response of L. johnsonii from its exoproteome perspective.
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Affiliation(s)
- Bernadette B. Bagon
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Valerie Diane V. Valeriano
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Ju Kyoung Oh
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Edward Alain B. Pajarillo
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Ji Yoon Lee
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea;
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
- Correspondence:
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15
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Multi-omics Approach Reveals How Yeast Extract Peptides Shape Streptococcus thermophilus Metabolism. Appl Environ Microbiol 2020; 86:AEM.01446-20. [PMID: 32769193 DOI: 10.1128/aem.01446-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Peptides present in growth media are essential for nitrogen nutrition and optimal growth of lactic acid bacteria. In addition, according to their amino acid composition, they can also directly or indirectly play regulatory roles and influence global metabolism. This is especially relevant during the propagation phase to produce high cell counts of active lactic acid bacteria used as starters in the dairy industry. In the present work, we aimed at investigating how the respective compositions of two different yeast extracts, with a specific focus on peptide content, influenced Streptococcus thermophilus metabolism during growth under pH-controlled conditions. In addition to free amino acid quantification, we used a multi-omics approach (peptidomics, proteomics, and transcriptomics) to identify peptides initially present in the two culture media and to follow S. thermophilus gene expression and bacterial protein production during growth. The free amino acid and peptide compositions of the two yeast extracts differed qualitatively and quantitatively. Nevertheless, the two yeast extracts sustained similar levels of growth of S. thermophilus and led to equivalent final biomasses. However, transcriptomics and proteomics showed differential gene expression and protein production in several S. thermophilus metabolic pathways, especially amino acid, citrate, urease, purine, and pyrimidine metabolisms. The probable role of the regulator CodY is discussed in this context. Moreover, we observed significant differences in the production of regulators and of a quorum sensing regulatory system. The possible roles of yeast extract peptides on the modulation of the quorum sensing system expression are evaluated.IMPORTANCE Improving the performance and industrial robustness of bacteria used in fermentations and food industry remains a challenge. We showed here that two Streptococcus thermophilus fermentations, performed with the same strain in media that differ only by their yeast extract compositions and, more especially, their peptide contents, led to similar growth kinetics and final biomasses, but several genes and proteins were differentially expressed/produced. In other words, subtle variations in peptide composition of the growth medium can finely tune the metabolism status of the starter. Our work, therefore, suggests that acting on growth medium components and especially on their peptide content, we could modulate bacterial metabolism and produce bacteria differently programmed for further purposes. This might have applications for preparing active starter cultures.
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Millan-Oropeza A, Henry C, Lejeune C, David M, Virolle MJ. Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. Sci Rep 2020; 10:8492. [PMID: 32444655 PMCID: PMC7244524 DOI: 10.1038/s41598-020-65087-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Most currently used antibiotics originate from Streptomycetes and phosphate limitation is an important trigger of their biosynthesis. Understanding the molecular processes underpinning such regulation is of crucial importance to exploit the great metabolic diversity of these bacteria and get a better understanding of the role of these molecules in the physiology of the producing bacteria. To contribute to this field, a comparative proteomic analysis of two closely related model strains, Streptomyces lividans and Streptomyces coelicolor was carried out. These strains possess identical biosynthetic pathways directing the synthesis of three well-characterized antibiotics (CDA, RED and ACT) but only S. coelicolor expresses them at a high level. Previous studies established that the antibiotic producer, S. coelicolor, is characterized by an oxidative metabolism and a reduced triacylglycerol content compared to the none producer, S. lividans, characterized by a glycolytic metabolism. Our proteomic data support these findings and reveal that these drastically different metabolic features could, at least in part, due to the weaker abundance of proteins of the two component system PhoR/PhoP in S. coelicolor compared to S. lividans. In condition of phosphate limitation, PhoR/PhoP is known to control positively and negatively, respectively, phosphate and nitrogen assimilation and our study revealed that it might also control the expression of some genes of central carbon metabolism. The tuning down of the regulatory role of PhoR/PhoP in S. coelicolor is thus expected to be correlated with low and high phosphate and nitrogen availability, respectively and with changes in central carbon metabolic features. These changes are likely to be responsible for the observed differences between S. coelicolor and S. lividans concerning energetic metabolism, triacylglycerol biosynthesis and antibiotic production. Furthermore, a novel view of the contribution of the bio-active molecules produced in this context, to the regulation of the energetic metabolism of the producing bacteria, is proposed and discussed.
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Affiliation(s)
- Aaron Millan-Oropeza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Lejeune
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Michelle David
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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17
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Tkáčová Z, Pulzová LB, Mochnáčová E, Jiménez-Munguía I, Bhide K, Mertinková P, Majerová P, Kulkarni A, Kováč A, Bhide M. Identification of the proteins of Borrelia garinii interacting with human brain microvascular endothelial cells. Ticks Tick Borne Dis 2020; 11:101451. [PMID: 32360026 DOI: 10.1016/j.ttbdis.2020.101451] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 11/25/2022]
Abstract
Lyme borreliosis is one of the major tick-borne diseases in Europe. Events of the translocation of Borrelia across the blood-brain barrier (BBB) involve multiple interactions between borrelial surface proteins and receptors on the brain microvascular endothelial cells (hBMECs). In this study, we aimed to identify proteins of Borrelia that plausibly interact with hBMECs. The surface proteome of live Borrelia (a neuroinvasive strain of B. garinii) was crosslinked with biotin prior to its incubation with hBMECs. The interacting proteins were recovered by affinity purification, followed by SWATH-MS. Twenty-four interacting candidates were grouped into outer membrane proteins (n = 12) and inner membrane proteins (n = 12) based on the subcellular location as per the predictions of LocateP. Other algorithms like TMHMM 2.0 and LipoP, ontology search and literature review were subsequently applied to each of the identified protein candidates to shortlist the most probable interactors. Six proteins namely, LysM domain protein, BESBP-5, Antigen S1, CRASP-1 (Bg071), Erp23 protein and Mlp family Lipoprotein were selected to produce their recombinant forms and experimentally validate their interaction with hBMECs. All the recombinant proteins interacted with hBMECs, in ELISA and immunocytochemistry. We present here a high-throughput approach of generating a dataset of plausible borrelial ligands followed by a systematic bioinformatic pipeline to categorize the proteins for experimental validation.
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Affiliation(s)
- Zuzana Tkáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia
| | - Lucia Borszéková Pulzová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia
| | - Evelína Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia
| | - Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia
| | - Patrícia Mertinková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia
| | - Petra Majerová
- Institute of Neuroimmunology of Slovak Academy of Sciences, 84510, Bratislava, Slovakia
| | - Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia; Institute of Neuroimmunology of Slovak Academy of Sciences, 84510, Bratislava, Slovakia
| | - Andrej Kováč
- Institute of Neuroimmunology of Slovak Academy of Sciences, 84510, Bratislava, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Komenskeho 73, 04001, Kosice, Slovakia; Institute of Neuroimmunology of Slovak Academy of Sciences, 84510, Bratislava, Slovakia.
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18
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Interactions between Lactobacillus plantarum NCU116 and its environments based on extracellular proteins and polysaccharides prediction by comparative analysis. Genomics 2020; 112:3579-3587. [PMID: 32320822 DOI: 10.1016/j.ygeno.2020.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 01/27/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022]
Abstract
Lactic acid bacteria (LAB) play a significant role in food industry and artisan fermented-food. Most of the applicable LABs were commonly obtained from natural fermented food or human gut. And Lactobacillus plantarum NCU116 was screened from a LAB-dominated traditional Chinese sauerkraut (TCS). In order to comprehend the interaction between NCU116 and its environments, comparative genomics were performed to identify genes involved in extracellular protein biosynthesis and secretion. Four secretory pathways were identified, including Sec and FPE pathways, holins and efflux ABC transporter system. Then 348 potential secretory proteins were identified, including 11 alpha-amylases responsible for degradation of macromolecules, and 8 mucus binding proteins which attribute to adherence to intestine epithelium. Besides, EPS clusters of NCU116 (EPS116) were identified and analyzed by comparing to other strains, which suggested a novel genotype of EPS clusters. These findings could be critical to extend the application of NCU116 in food and pharmaceuticals industries.
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19
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Proteomic and Bioinformatic Analysis of Streptococcus suis Human Isolates: Combined Prediction of Potential Vaccine Candidates. Vaccines (Basel) 2020; 8:vaccines8020188. [PMID: 32325736 PMCID: PMC7348792 DOI: 10.3390/vaccines8020188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 12/15/2022] Open
Abstract
Streptococcus suis is a Gram-positive bacterium responsible for major infections in pigs and economic losses in the livestock industry, but also an emerging zoonotic pathogen causing serious diseases in humans. No vaccine is available so far against this microorganism. Conserved surface proteins are among the most promising candidates for new and effective vaccines. Until now, research on this pathogen has focused on swine isolates, but there is a lack of studies to identify and characterize surface proteins from human clinical isolates. In this work, we performed a comparative proteomic analysis of six clinical isolates from human patients, all belonging to the major serotype 2, by “shaving” the live bacterial cells with trypsin, followed by LC-MS/MS analysis. We identified 131 predicted surface proteins and carried out a label-free semi-quantitative analysis of protein abundances within the six strains. Then, we combined our proteomics results with bioinformatic tools to help improving the selection of novel antigens that can enter the pipeline of vaccine candidate testing. Our work is then a complement to the reverse vaccinology concept.
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20
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Wolden R, Pain M, Karlsson R, Karlsson A, Aarag Fredheim EG, Cavanagh JP. Identification of surface proteins in a clinical Staphylococcus haemolyticus isolate by bacterial surface shaving. BMC Microbiol 2020; 20:80. [PMID: 32264835 PMCID: PMC7137321 DOI: 10.1186/s12866-020-01778-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Background The skin commensal Staphylococcus haemolyticus is an emerging nosocomial pathogen. Despite its clinical relevance, published information about S. haemolyticus virulence factors is scarce. In this study, the adhesive and biofilm forming properties of ten clinical and ten commensal S. haemolyticus strains were examined using standard adhesion and biofilm assays. One of the clinical strains was used to identify expressed surface proteins using bacterial surface shaving. Protein abundance was examined by a comparative analysis between bacterial protein expression after human keratinocyte (HaCaT) colonization and growth in cell culture media supplemented with serum. Relative protein quantification was performed by labeling peptides with tandem mass tags (TMT) prior to Mass Spectrometry analysis. Surface proteins can be used as novel targets for antimicrobial treatment and in diagnostics. Results Adherence to fibronectin, collagen and plastic was low in all tested strains, but with significantly higher adhesion to fibronectin (p = 0.041) and collagen (p = 0.001) in the commensal strains. There was a trend towards higher degree of biofilm formation in the clinical strains (p = 0.059). By using surface shaving, 325 proteins were detected, of which 65 were classified as surface proteins. Analyses showed that the abundance of nineteen (5.8%) proteins were significantly changed following HaCaT colonization. The bacterial Toll/interleukin-1 like (TIRs) domain containing protein (p = 0.04), the transglycosylase SceD (p = 0.01), and the bifunctional autolysin Atl (p = 0.04) showed a 1.4, 1.6- and 1.5-fold increased abundance. The staphylococcal secretory antigen (SsaA) (p = 0.04) was significantly downregulated (− 1.5 fold change) following HaCaT colonization. Among the 65 surface proteins the elastin binding protein (Ebps), LPXAG and LPXSG domain containing proteins and five LPXTG domain containing proteins were identified; three Sdr-like proteins, the extracellular matrix binding protein Embp and a SasH-like protein. Conclusions This study has provided novel knowledge about expression of S. haemolyticus surface proteins after direct contact with eukaryotic cells and in media supplemented with serum. We have identified surface proteins and immune evasive proteins previously only functionally described in other staphylococcal species. The identification of expressed proteins after host-microbe interaction offers a tool for the discovery and design of novel targets for antimicrobial treatment.
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Affiliation(s)
- Runa Wolden
- Pediatric Research group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Pain
- Pediatric Research group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roger Karlsson
- Nanoxis Consulting AB, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-413 46, Gothenburg, Region Västra Götaland, Sweden
| | | | - Elizabeth G Aarag Fredheim
- Microbial Pharmacology and Population Biology, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jorunn Pauline Cavanagh
- Pediatric Research group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway. .,Department of Pediatrics, The University Hospital of North Norway, Tromsø, Norway.
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21
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Satyam R, Bhardwaj T, Jha NK, Jha SK, Nand P. Toward a chimeric vaccine against multiple isolates of Mycobacteroides - An integrative approach. Life Sci 2020; 250:117541. [PMID: 32169520 DOI: 10.1016/j.lfs.2020.117541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/07/2020] [Accepted: 03/08/2020] [Indexed: 01/31/2023]
Abstract
AIM Nontuberculous mycobacterial (NTM) infection such as endophthalmitis, dacryocystitis, and canaliculitis are pervasive across the globe and are currently managed by antibiotics. However, the recent cases of Mycobacteroides developing drug resistance reported along with the improper practice of medicine intrigued us to explore its genomic and proteomic canvas at a global scale and develop a chimeric vaccine against Mycobacteroides. MAIN METHODS We carried out a vivid genomic study on five recently sequenced strains of Mycobacteroides and explored their Pan-core genome/proteome in three different phases. The promiscuous antigenic proteins were identified via a subtractive proteomics approach that qualified for virulence causation, resistance and essentiality factors for this notorious bacterium. An integrated pipeline was developed for the identification of B-Cell, MHC (Major histocompatibility complex) class I and II epitopes. KEY FINDINGS Phase I identified the shreds of evidence of reductive evolution and propensity of the Pan-genome of Mycobacteroides getting closed soon. Phase II and Phase III produced 8 vaccine constructs. Our final vaccine construct, V6 qualified for all tests such as absence for allergenicity, presence of antigenicity, etc. V6 contains β-defensin as an adjuvant, linkers, Lysosomal-associated membrane protein 1 (LAMP1) signal peptide, and PADRE (Pan HLA-DR epitopes) amino acid sequence. Besides, V6 also interacts with a maximum number of MHC molecules and the TLR4/MD2 (Toll-like receptor 4/Myeloid differentiation factor 2) complex confirmed by docking and molecular dynamics simulation studies. SIGNIFICANCE The knowledge harnessed from the current study can help improve the current treatment regimens or in an event of an outbreak and propel further related studies.
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Affiliation(s)
- Rohit Satyam
- Department of Biotechnology, Noida Institute of Engineering and Technology (NIET), Greater Noida, India
| | - Tulika Bhardwaj
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India.
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Parma Nand
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
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22
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Li L, Bannantine JP, Campo JJ, Randall A, Grohn YT, Schilling MA, Katani R, Radzio-Basu J, Easterling L, Kapur V. Identification of Sero-Diagnostic Antigens for the Early Diagnosis of Johne's Disease using MAP Protein Microarrays. Sci Rep 2019; 9:17573. [PMID: 31772281 PMCID: PMC6879513 DOI: 10.1038/s41598-019-53973-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/07/2019] [Indexed: 01/20/2023] Open
Abstract
Considerable effort has been directed toward controlling Johne’s disease (JD), a chronic granulomatous intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) in cattle and other ruminants. However, progress in controlling the spread of MAP infection has been impeded by the lack of reliable diagnostic tests that can identify animals early in the infection process and help break the transmission chain. To identify reliable antigens for early diagnosis of MAP infection, we constructed a MAP protein array with 868 purified recombinant MAP proteins, and screened a total of 180 well-characterized serum samples from cows assigned to 4 groups based on previous serological and fecal test results: negative low exposure (NL, n = 30); negative high exposure (NH, n = 30); fecal-positive, ELISA-negative (F + E−, n = 60); and both fecal- and ELISA-positive (F + E+, n = 60). The analyses identified a total of 49 candidate antigens in the NH, F + E−, and F + E+ with reactivity compared with the NL group (p < 0.01), a majority of which have not been previously identified. While some of the antigens were identified as reactive in only one of the groups, others showed reactivity in multiple groups, including NH (n = 28), F + E− (n = 26), and F + E+ (n = 17) groups. Using combinations of top reactive antigens in each group, the results reveal sensitivities of 60.0%, 73.3%, and 81.7% in the NH, F + E−, and F + E+, respectively at 90% specificity, suggesting that early detection of infection in animals may be possible and enable better opportunities to reduce within herd transmission that may be otherwise missed by traditional serological assays that are biased towards more heavily infected animals. Together, the results suggest that several of the novel candidate antigens identified in this study, particularly those that were reactive in the NH and F + E− groups, have potential utility for the early sero-diagnosis of MAP infection.
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Affiliation(s)
- Lingling Li
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - John P Bannantine
- National Animal Disease Center, USDA-ARS, Ames, IA, United States of America
| | - Joseph J Campo
- Antigen Discovery, Inc., Irvine, CA, United States of America
| | - Arlo Randall
- Antigen Discovery, Inc., Irvine, CA, United States of America
| | - Yrjo T Grohn
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States of America
| | - Megan A Schilling
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America
| | - Robab Katani
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America.,Applied Biological and Biosafety Research Laboratory, The Pennsylvania State University, University Park, PA, United States of America
| | - Jessica Radzio-Basu
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Applied Biological and Biosafety Research Laboratory, The Pennsylvania State University, University Park, PA, United States of America
| | - Laurel Easterling
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America. .,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America. .,Applied Biological and Biosafety Research Laboratory, The Pennsylvania State University, University Park, PA, United States of America.
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23
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Avello M, Davis KP, Grossman AD. Identification, characterization and benefits of an exclusion system in an integrative and conjugative element of Bacillus subtilis. Mol Microbiol 2019; 112:1066-1082. [PMID: 31361051 PMCID: PMC6827876 DOI: 10.1111/mmi.14359] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 01/09/2023]
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer from cell to cell by conjugation (like plasmids) and integrate into the chromosomes of bacterial hosts (like lysogenic phages or transposons). ICEs are prevalent in bacterial chromosomes and play a major role in bacterial evolution by promoting horizontal gene transfer. Exclusion prevents the redundant transfer of conjugative elements into host cells that already contain a copy of the element. Exclusion has been characterized mostly for conjugative elements of Gram-negative bacteria. Here, we report the identification and characterization of an exclusion mechanism in ICEBs1 from the Gram-positive bacterium Bacillus subtilis. We found that cells containing ICEBs1 inhibit the activity of the ICEBs1-encoded conjugation machinery in other cells. This inhibition (exclusion) was specific to the cognate conjugation machinery and the ICEBs1 gene yddJ was both necessary and sufficient to mediate exclusion by recipient cells. Through a mutagenesis and enrichment screen, we identified exclusion-resistant mutations in the ICEBs1 gene conG. Using genes from a heterologous but related ICE, we found that the exclusion specificity was determined by ConG and YddJ. Finally, we found that under conditions that support conjugation, exclusion provides a selective advantage to the element and its host cells.
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Affiliation(s)
| | | | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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24
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Plavec TV, Štrukelj B, Berlec A. Screening for New Surface Anchoring Domains for Lactococcus lactis. Front Microbiol 2019; 10:1879. [PMID: 31456787 PMCID: PMC6700490 DOI: 10.3389/fmicb.2019.01879] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/30/2019] [Indexed: 12/14/2022] Open
Abstract
The display of recombinant proteins on bacterial surfaces is a developing research area with a wide range of potential biotechnological applications. The lactic acid bacterium Lactococcus lactis is an attractive host for such surface display, and a promising vector for in vivo delivery of bioactive proteins. Surface-displayed recombinant proteins are usually anchored to the bacterial cell wall through anchoring domains. Here, we investigated alternatives to the commonly applied lactococcal lysine motif (LysM)-containing surface anchoring domain, the C-terminus of AcmA (cAcmA). We screened 15 anchoring domains of lactococcal or phage origins that belong to the Pfam categories LPXTG, LysM, CW_1, Cpl-7, WxL, SH3, and ChW, which can provide non-covalent or covalent binding to the cell wall. LPXTG, LysM, the duplicated CW_1 and SH3 domains promoted significant surface display of two model proteins, B domain and DARPin I07, although the display achieved was lower than that for the reference anchoring domain, cAcmA. On the other hand, the ChW-containing anchoring domain of the lactococcal phage AM12 endolysin (cAM12) demonstrated surface display comparable to that of cAcmA. The anchoring ability of cAM12 was confirmed by enabling non-covalent heterologous anchoring of the B domain on wild-type bacteria, as well as anchoring of CXCL8-binding evasin-3, which provided potential therapeutic applicability; both were displayed to an extent comparable to that of cAcmA. We have thereby demonstrated the effective use of different protein anchoring domains in L. lactis, with ChW-containing cAM12 the most promising alternative to the established approaches for surface display on L. lactis.
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Affiliation(s)
- Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Štrukelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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25
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Han GS, Yu ZG. ML-rRBF-ECOC: A Multi-Label Learning Classifier for Predicting Protein Subcellular Localization with Both Single and Multiple Sites. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190103143945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The subcellular localization of a protein is closely related with its functions
and interactions. More and more evidences show that proteins may simultaneously exist at, or move
between, two or more different subcellular localizations. Therefore, predicting protein subcellular localization
is an important but challenging problem.
Observation:
Most of the existing methods for predicting protein subcellular localization assume that a
protein locates at a single site. Although a few methods have been proposed to deal with proteins with
multiple sites, correlations between subcellular localization are not efficiently taken into account. In
this paper, we propose an integrated method for predicting protein subcellular localizations with both
single site and multiple sites.
Methods:
Firstly, we extend the Multi-Label Radial Basis Function (ML-RBF) method to the regularized
version, and augment the first layer of ML-RBF to take local correlations between subcellular localization
into account. Secondly, we embed the modified ML-RBF into a multi-label Error-Correcting
Output Codes (ECOC) method in order to further consider the subcellular localization dependency. We
name our method ML-rRBF-ECOC. Finally, the performance of ML-rRBF-ECOC is evaluated on
three benchmark datasets.
Results:
The results demonstrate that ML-rRBF-ECOC has highly competitive performance to the related
multi-label learning method and some state-of-the-art methods for predicting protein subcellular
localizations with multiple sites. Considering dependency between subcellular localizations can contribute
to the improvement of prediction performance.
Conclusion:
This also indicates that correlations between different subcellular localizations really exist.
Our method at least plays a complementary role to existing methods for predicting protein subcellular
localizations with multiple sites.
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Affiliation(s)
- Guo-Sheng Han
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan 411105, China
| | - Zu-Guo Yu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan 411105, China
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26
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Henry C, Haller L, Blein-Nicolas M, Zivy M, Canette A, Verbrugghe M, Mézange C, Boulay M, Gardan R, Samson S, Martin V, André-Leroux G, Monnet V. Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Front Microbiol 2019; 10:1329. [PMID: 31275266 PMCID: PMC6593474 DOI: 10.3389/fmicb.2019.01329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/28/2019] [Indexed: 12/17/2022] Open
Abstract
Protein phosphorylation especially on serine/threonine/tyrosine residues are frequent in many bacteria. This post-translational modification has been associated with pathogenicity and virulence in various species. However, only few data have been produced so far on generally recognized as safe bacteria used in food fermentations. A family of kinases known as Hanks-type kinases is suspected to be responsible for, at least, a part of these phosphorylations in eukaryotes as in bacteria. The objective of our work was to establish the first phosphoproteome of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy fermentations in order to identified the proteins and pathways tagged by Ser/Thr/Tyr phosphorylations. In addition, we have evaluated the role in this process of the only Hanks-type kinase encoded in the S. thermophilus genome. We have constructed a mutant defective for the Hanks type kinase in S. thermophilus and established the proteomes and phosphoproteomes of the wild type and the mutant strains. To do that, we have enriched our samples in phosphopeptides with titane beads and used dimethyl tags to compare phosphopeptide abundances. Peptides and phosphopeptides were analyzed on a last generation LC-MS/MS system. We have identified and quantified 891 proteins representing half of the theoretical proteome. Among these proteins, 106 contained phosphorylated peptides. Various functional groups of proteins (amino acid, carbon and nucleotide metabolism, translation, cell cycle, stress response, …) were found phosphorylated. The phosphoproteome was only weakly reduced in the Hanks-type kinase mutant indicating that this enzyme is only one of the players in the phosphorylation process. The proteins that are modified by the Hanks-type kinase mainly belong to the divisome.
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Affiliation(s)
- Céline Henry
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Lucia Haller
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Micalis Institute, ComBac, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mélisande Blein-Nicolas
- PAPPSO, GQE - Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michel Zivy
- PAPPSO, GQE - Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexis Canette
- Micalis Institute, MIMA2, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Morgane Verbrugghe
- Micalis Institute, ComBac, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Christine Mézange
- Micalis Institute, ComBac, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mylène Boulay
- Micalis Institute, ComBac, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rozenn Gardan
- Micalis Institute, ComBac, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Samantha Samson
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Véronique Monnet
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Micalis Institute, ComBac, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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27
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Graf AC, Leonard A, Schäuble M, Rieckmann LM, Hoyer J, Maass S, Lalk M, Becher D, Pané-Farré J, Riedel K. Virulence Factors Produced by Staphylococcus aureus Biofilms Have a Moonlighting Function Contributing to Biofilm Integrity. Mol Cell Proteomics 2019; 18:1036-1053. [PMID: 30850421 PMCID: PMC6553939 DOI: 10.1074/mcp.ra118.001120] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus is the causative agent of various biofilm-associated infections in humans causing major healthcare problems worldwide. This type of infection is inherently difficult to treat because of a reduced metabolic activity of biofilm-embedded cells and the protective nature of a surrounding extracellular matrix (ECM). However, little is known about S. aureus biofilm physiology and the proteinaceous composition of the ECM. Thus, we cultivated S. aureus biofilms in a flow system and comprehensively profiled intracellular and extracellular (ECM and flow-through (FT)) biofilm proteomes, as well as the extracellular metabolome compared with planktonic cultures. Our analyses revealed the expression of many pathogenicity factors within S. aureus biofilms as indicated by a high abundance of capsule biosynthesis proteins along with various secreted virulence factors, including hemolysins, leukotoxins, and lipases as a part of the ECM. The activity of ECM virulence factors was confirmed in a hemolysis assay and a Galleria mellonella pathogenicity model. In addition, we uncovered a so far unacknowledged moonlighting function of secreted virulence factors and ribosomal proteins trapped in the ECM: namely their contribution to biofilm integrity. Mechanistically, it was revealed that this stabilizing effect is mediated by the strong positive charge of alkaline virulence factors and ribosomal proteins in an acidic ECM environment, which is caused by the release of fermentation products like formate, lactate, and acetate because of oxygen limitation in biofilms. The strong positive charge of these proteins most likely mediates electrostatic interactions with anionic cell surface components, eDNA, and anionic metabolites. In consequence, this leads to strong cell aggregation and biofilm stabilization. Collectively, our study identified a new molecular mechanism during S. aureus biofilm formation and thus significantly widens the understanding of biofilm-associated S. aureus infections - an essential prerequisite for the development of novel antimicrobial therapies.
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Affiliation(s)
- Alexander C Graf
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Anne Leonard
- §Institute of Biochemistry, Department of Cellular Biochemistry and Metabolomics
| | - Manuel Schäuble
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Lisa M Rieckmann
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Juliane Hoyer
- ¶Institute of Microbiology, Department of Microbial Proteomics; University of Greifswald, Germany
| | - Sandra Maass
- ¶Institute of Microbiology, Department of Microbial Proteomics; University of Greifswald, Germany
| | - Michael Lalk
- §Institute of Biochemistry, Department of Cellular Biochemistry and Metabolomics
| | - Dörte Becher
- ¶Institute of Microbiology, Department of Microbial Proteomics; University of Greifswald, Germany
| | - Jan Pané-Farré
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology
| | - Katharina Riedel
- From the ‡Institute of Microbiology, Department of Microbial Physiology and Molecular Biology;
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28
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Cartmell A, Muñoz-Muñoz J, Briggs JA, Ndeh DA, Lowe EC, Baslé A, Terrapon N, Stott K, Heunis T, Gray J, Yu L, Dupree P, Fernandes PZ, Shah S, Williams SJ, Labourel A, Trost M, Henrissat B, Gilbert HJ. A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation. Nat Microbiol 2018; 3:1314-1326. [PMID: 30349080 PMCID: PMC6217937 DOI: 10.1038/s41564-018-0258-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 08/30/2018] [Indexed: 12/24/2022]
Abstract
Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a β1,3-galactan backbone and β1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally relevant AGPs are degraded in the HGM are poorly understood. Here we explore how the HGM organism Bacteroides thetaiotaomicron metabolizes AGPs. We propose a sequential degradative model in which exo-acting glycoside hydrolase (GH) family 43 β1,3-galactanases release the side chains. These oligosaccharide side chains are depolymerized by the synergistic action of exo-acting enzymes in which catalytic interactions are dependent on whether degradation is initiated by a lyase or GH. We identified two GHs that establish two previously undiscovered GH families. The crystal structures of the exo-β1,3-galactanases identified a key specificity determinant and departure from the canonical catalytic apparatus of GH43 enzymes. Growth studies of Bacteroidetes spp. on complex AGP revealed 3 keystone organisms that facilitated utilization of the glycan by 17 recipient bacteria, which included B. thetaiotaomicron. A surface endo-β1,3-galactanase, when engineered into B. thetaiotaomicron, enabled the bacterium to utilize complex AGPs and act as a keystone organism.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jose Muñoz-Muñoz
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Jonathon A Briggs
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tiaan Heunis
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Li Yu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pearl Z Fernandes
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Sayali Shah
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Aurore Labourel
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthias Trost
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
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29
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Analysis of Staphylococcus aureus proteins secreted inside infected human epithelial cells. Int J Med Microbiol 2018; 308:664-674. [DOI: 10.1016/j.ijmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 05/24/2018] [Accepted: 06/16/2018] [Indexed: 11/22/2022] Open
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30
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Andreou A, Giastas P, Christoforides E, Eliopoulos EE. Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. Genes (Basel) 2018; 9:E386. [PMID: 30065210 PMCID: PMC6115787 DOI: 10.3390/genes9080386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O- or N-acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain. Genomes of Bacillus anthracis and its relative Bacillus cereus contain multiple genes of putative or known PDAs. A comparison of the functional domains of the recently determined PDAs from B. anthracis and B. cereus and multiple amino acid and nucleotide sequence alignments and phylogenetic analysis performed on these closely related species showed that there were distinct differences in binding site formation, despite the high conservation on the protein sequence, the folding level and the active site assembly. This may indicate that, subject to biochemical verification, the binding site-forming sequence fragments are under functionally driven evolutionary pressure to accommodate and recognize distinct polysaccharide residues according to cell location, use, or environment. Finally, we discuss the suggestion of the paralogous nature of at least two genes of B. anthracis, ba0330 and ba0331, via specific differences in gene sequence, protein structure, selection pressure and available localization patterns. This study may contribute to understanding the mechanisms under which sequences evolve in their structures and how evolutionary processes enable structural variations.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece.
| | - Elias Christoforides
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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31
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Jiménez-Munguía I, Pulzova L, Kanova E, Tomeckova Z, Majerova P, Bhide K, Comor L, Sirochmanova I, Kovac A, Bhide M. Proteomic and bioinformatic pipeline to screen the ligands of S. pneumoniae interacting with human brain microvascular endothelial cells. Sci Rep 2018; 8:5231. [PMID: 29588455 PMCID: PMC5869694 DOI: 10.1038/s41598-018-23485-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/14/2018] [Indexed: 01/17/2023] Open
Abstract
The mechanisms by which Streptococcus pneumoniae penetrates the blood-brain barrier (BBB), reach the CNS and causes meningitis are not fully understood. Adhesion of bacterial cells on the brain microvascular endothelial cells (BMECs), mediated through protein-protein interactions, is one of the crucial steps in translocation of bacteria across BBB. In this work, we proposed a systematic workflow for identification of cell wall associated ligands of pneumococcus that might adhere to the human BMECs. The proteome of S. pneumoniae was biotinylated and incubated with BMECs. Interacting proteins were recovered by affinity purification and identified by data independent acquisition (DIA). A total of 44 proteins were identified from which 22 were found to be surface-exposed. Based on the subcellular location, ontology, protein interactive analysis and literature review, five ligands (adhesion lipoprotein, endo-β-N-acetylglucosaminidase, PhtA and two hypothetical proteins, Spr0777 and Spr1730) were selected to validate experimentally (ELISA and immunocytochemistry) the ligand-BMECs interaction. In this study, we proposed a high-throughput approach to generate a dataset of plausible bacterial ligands followed by systematic bioinformatics pipeline to categorize the protein candidates for experimental validation. The approach proposed here could contribute in the fast and reliable screening of ligands that interact with host cells.
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Affiliation(s)
- Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Lucia Pulzova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Evelina Kanova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Zuzana Tomeckova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Petra Majerova
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Katarina Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Ivana Sirochmanova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic.
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovak Republic.
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32
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Tsolis KC, Tsare EP, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anné J, Karamanou S, Klapa MI, Economou A. Comprehensive subcellular topologies of polypeptides in Streptomyces. Microb Cell Fact 2018; 17:43. [PMID: 29544487 PMCID: PMC5853079 DOI: 10.1186/s12934-018-0892-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. Results Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known. Conclusions SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism. Electronic supplementary material The online version of this article (10.1186/s12934-018-0892-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos C Tsolis
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Evridiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.,Department of General Biology, School of Medicine, University of Patras, Patras, Greece
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology-FoRTH, P.O. Box 1385, Iraklio, Crete, Greece
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Katerina Kanaki
- Institute of Molecular Biology and Biotechnology-FoRTH, P.O. Box 1385, Iraklio, Crete, Greece
| | - Reshmi Ramakrishnan
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Maria I Klapa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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33
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Nielsen H. Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms. Curr Top Microbiol Immunol 2017; 404:129-158. [PMID: 26728066 DOI: 10.1007/82_2015_5006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
When predicting the subcellular localization of proteins from their amino acid sequences, there are basically three approaches: signal-based, global property-based, and homology-based. Each of these has its advantages and drawbacks, and it is important when comparing methods to know which approach was used. Various statistical and machine learning algorithms are used with all three approaches, and various measures and standards are employed when reporting the performances of the developed methods. This chapter presents a number of available methods for prediction of sorting signals and subcellular localization, but rather than providing a checklist of which predictors to use, it aims to function as a guide for critical assessment of prediction methods.
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Affiliation(s)
- Henrik Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet building 208, 2800, Lyngby, Denmark.
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34
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Millan-Oropeza A, Henry C, Blein-Nicolas M, Aubert-Frambourg A, Moussa F, Bleton J, Virolle MJ. Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J Proteome Res 2017; 16:2597-2613. [DOI: 10.1021/acs.jproteome.7b00163] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aaron Millan-Oropeza
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Céline Henry
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mélisande Blein-Nicolas
- Génétique
Quantitative et Évolution (GQE) - Le Moulon, INRA, Univ Paris-Sud,
CNRS, AgroParisTech, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Anne Aubert-Frambourg
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fathi Moussa
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Jean Bleton
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Marie-Jöelle Virolle
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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35
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Vu CH, Kolata J, Stentzel S, Beyer A, Gesell Salazar M, Steil L, Pané-Farré J, Rühmling V, Engelmann S, Götz F, van Dijl JM, Hecker M, Mäder U, Schmidt F, Völker U, Bröker BM. Adaptive immune response to lipoproteins of Staphylococcus aureus in healthy subjects. Proteomics 2016; 16:2667-2677. [PMID: 27324828 PMCID: PMC5096053 DOI: 10.1002/pmic.201600151] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/31/2016] [Accepted: 06/16/2016] [Indexed: 01/03/2023]
Abstract
Staphylococcus aureus is a frequent commensal but also a dangerous pathogen, causing many forms of infection ranging from mild to life‐threatening conditions. Among its virulence factors are lipoproteins, which are anchored in the bacterial cell membrane. Lipoproteins perform various functions in colonization, immune evasion, and immunomodulation. These proteins are potent activators of innate immune receptors termed Toll‐like receptors 2 and 6. This study addressed the specific B‐cell and T‐cell responses directed to lipoproteins in human S. aureus carriers and non‐carriers. 2D immune proteomics and ELISA approaches revealed that titers of antibodies (IgG) binding to S. aureus lipoproteins were very low. Proliferation assays and cytokine profiling data showed only subtle responses of T cells; some lipoproteins did not elicit proliferation. Hence, the robust activation of the innate immune system by S. aureus lipoproteins does not translate into a strong adaptive immune response. Reasons for this may include inaccessibility of lipoproteins for B cells as well as ineffective processing and presentation of the antigens to T cells.
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Affiliation(s)
- Chi Hai Vu
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Julia Kolata
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany.,Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sebastian Stentzel
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Anica Beyer
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Vanessa Rühmling
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanne Engelmann
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Helmholtz Center for Infection Research, Microbial Proteomics, Braunschweig, Germany.,Institute for Microbiology, University of Braunschweig, Braunschweig, Germany
| | - Friedrich Götz
- Department of Microbial Genetics, University of Tübingen, Tübingen, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Michael Hecker
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank Schmidt
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Barbara M Bröker
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany.
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36
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Guillot A, Boulay M, Chambellon É, Gitton C, Monnet V, Juillard V. Mass Spectrometry Analysis of the Extracellular Peptidome of Lactococcus lactis: Lines of Evidence for the Coexistence of Extracellular Protein Hydrolysis and Intracellular Peptide Excretion. J Proteome Res 2016; 15:3214-24. [DOI: 10.1021/acs.jproteome.6b00424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alain Guillot
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Mylène Boulay
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Émilie Chambellon
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Christophe Gitton
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Véronique Monnet
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Vincent Juillard
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
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Zühlke D, Dörries K, Bernhardt J, Maaß S, Muntel J, Liebscher V, Pané-Farré J, Riedel K, Lalk M, Völker U, Engelmann S, Becher D, Fuchs S, Hecker M. Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis. Sci Rep 2016; 6:28172. [PMID: 27344979 PMCID: PMC4921807 DOI: 10.1038/srep28172] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/31/2016] [Indexed: 01/19/2023] Open
Abstract
Absolute protein quantification was applied to follow the dynamics of the cytoplasmic proteome of Staphylococcus aureus in response to long-term oxygen starvation. For 1,168 proteins, the majority of all expressed proteins, molecule numbers per cell have been determined to monitor the cellular investments in single branches of bacterial life for the first time. In the presence of glucose the anaerobic protein pattern is characterized by increased amounts of glycolytic and fermentative enzymes such as Eno, GapA1, Ldh1, and PflB. Interestingly, the ferritin-like protein FtnA belongs to the most abundant proteins during anaerobic growth. Depletion of glucose finally leads to an accumulation of different enzymes such as ArcB1, ArcB2, and ArcC2 involved in arginine deiminase pathway. Concentrations of 29 exo- and 78 endometabolites were comparatively assessed and have been integrated to the metabolic networks. Here we provide an almost complete picture on the response to oxygen starvation, from signal transduction pathways to gene expression pattern, from metabolic reorganization after oxygen depletion to beginning cell death and lysis after glucose exhaustion. This experimental approach can be considered as a proof of principle how to combine cell physiology with quantitative proteomics for a new dimension in understanding simple life processes as an entity.
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Affiliation(s)
- Daniela Zühlke
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Kirsten Dörries
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Sandra Maaß
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Jan Muntel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Volkmar Liebscher
- Department of Mathematics and Informatics, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Strasse 47, D-17487 Greifswald, Germany
| | - Jan Pané-Farré
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15 a, D-17487 Greifswald, Germany
| | - Susanne Engelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Institute of Microbiology, Technical University Braunschweig, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.,Helmholtz Institute for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Burgstrasse 37, D-38855 Wernigerode, Germany
| | - Michael Hecker
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
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38
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Cathro P, McCarthy P, Hoffmann P, Zilm P. Isolation and identification of Enterococcus faecalis membrane proteins using membrane shaving, 1D SDS/PAGE, and mass spectrometry. FEBS Open Bio 2016; 6:586-93. [PMID: 27419061 PMCID: PMC4887974 DOI: 10.1002/2211-5463.12075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/22/2016] [Accepted: 04/11/2016] [Indexed: 11/24/2022] Open
Abstract
Enterococcus faecalis is a significant nosocomial pathogen, which is able to survive in diverse environments and resist killing with antimicrobial therapies. The expression of cell membrane proteins play an important role in how bacteria respond to environmental stress. As such, the capacity to identify and study membrane protein expression is critical to our understanding of how specific proteins influence bacterial survival. Here, we describe a combined approach to identify membrane proteins of E. faecalis ATCC V583 using membranes fractionated by either 1D SDS/PAGE or membrane shaving, coupled with LC‐ESI mass spectrometry. We identified 222 membrane‐associated proteins, which represent approximately 24% of the predicted membrane‐associated proteome: 170 were isolated using 1D SDS/PAGE and 68 with membrane shaving, with 36 proteins being common to both the techniques. Of the proteins identified by membrane shaving, 97% were membrane‐associated with the majority being integral membrane proteins (89%). Most of the proteins identified with known physiology are involved with transportation across the membrane. The combined 1D SDS/PAGE and membrane shaving approach has produced the greatest number of membrane proteins identified from E. faecalis to date. These protocols will aid future researchers investigating changes in the membrane proteome of E. faecalis by improving our understanding of how E. faecalis adapts and responds to its environment.
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Affiliation(s)
- Peter Cathro
- Oral Microbiology Laboratory School of Dentistry The University of Adelaide South Australia Australia
| | - Peter McCarthy
- Neurovascular Research Laboratory Centre for Cancer Biology University of South Australia Adelaide South Australia Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre The University of Adelaide South Australia Australia
| | - Peter Zilm
- Oral Microbiology Laboratory School of Dentistry The University of Adelaide South Australia Australia
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39
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Tiong HK, Hartson SD, Muriana PM. Comparison of Surface Proteomes of Adherence Variants of Listeria Monocytogenes Using LC-MS/MS for Identification of Potential Surface Adhesins. Pathogens 2016; 5:E40. [PMID: 27196934 PMCID: PMC4931391 DOI: 10.3390/pathogens5020040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/19/2016] [Accepted: 05/11/2016] [Indexed: 12/19/2022] Open
Abstract
The ability of Listeria monocytogenes to adhere and form biofilms leads to persistence in food processing plants and food-associated listeriosis. The role of specific surface proteins as adhesins to attach Listeria cells to various contact surfaces has not been well characterized to date. In prior research comparing different methods for surface protein extraction, the Ghost urea method revealed cleaner protein content as verified by the least cytoplasmic protein detected in surface extracts using LC-MS/MS. The same technique was utilized to extract and detect surface proteins among two surface-adherent phenotypic strains of L. monocytogenes (i.e., strongly and weakly adherent). Of 640 total proteins detected among planktonic and sessile cells, 21 protein members were exclusively detected in the sessile cells. Relative LC-MS/MS detection and quantification of surface-extracted proteins from the planktonic weakly adherent (CW35) and strongly adherent strains (99-38) were examined by protein mass normalization of proteins. We found that L. monocytogenes 99-38 exhibited a total of 22 surface proteins that were over-expressed: 11 proteins were detected in surface extracts of both sessile and planktonic 99-38 that were ≥5-fold over-expressed while another 11 proteins were detected only in planktonic 99-38 cells that were ≥10-fold over-expressed. Our results suggest that these protein members are worthy of further investigation for their involvement as surface adhesins.
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Affiliation(s)
- Hung King Tiong
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA.
- Robert M. Kerr Food & Agricultural Products Centre, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Peter M Muriana
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA.
- Robert M. Kerr Food & Agricultural Products Centre, Oklahoma State University, Stillwater, OK 74078, USA.
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40
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Gagic D, Ciric M, Wen WX, Ng F, Rakonjac J. Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. Front Microbiol 2016; 7:429. [PMID: 27092113 PMCID: PMC4823517 DOI: 10.3389/fmicb.2016.00429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/17/2016] [Indexed: 01/12/2023] Open
Abstract
Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to “bait” of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.
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Affiliation(s)
- Dragana Gagic
- Institute of Fundamental Sciences, Massey UniversityPalmerston North, New Zealand; Animal Science, Grasslands Research Centre, AgResearch Ltd, Palmerston NorthNew Zealand
| | - Milica Ciric
- Institute of Fundamental Sciences, Massey UniversityPalmerston North, New Zealand; Animal Science, Grasslands Research Centre, AgResearch Ltd, Palmerston NorthNew Zealand
| | - Wesley X Wen
- Institute of Fundamental Sciences, Massey University Palmerston North, New Zealand
| | - Filomena Ng
- Animal Science, Grasslands Research Centre, AgResearch Ltd, Palmerston North New Zealand
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University Palmerston North, New Zealand
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41
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Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal SA, Kim J, Degivry MC, Quéré G, Garault P, van Hylckama Vlieg JET, Garrett WS, Doré J, Veiga P. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME JOURNAL 2016; 10:2235-45. [PMID: 26953599 PMCID: PMC4989305 DOI: 10.1038/ismej.2016.13] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/18/2016] [Accepted: 01/08/2016] [Indexed: 01/01/2023]
Abstract
Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host's autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases.
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Affiliation(s)
- Chenhong Zhang
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Muriel Derrien
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | | | - Sonia A Ballal
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Kim
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Gaëlle Quéré
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Peggy Garault
- Life Science, Danone Nutricia Research, Palaiseau, France
| | | | | | - Joël Doré
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Patrick Veiga
- Life Science, Danone Nutricia Research, Palaiseau, France.,Harvard T. H. Chan School of Public Health, Boston, MA, USA
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42
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Wei X, Wang S, Zhao X, Wang X, Li H, Lin W, Lu J, Zhurina D, Li B, Riedel CU, Sun Y, Yuan J. Proteomic Profiling of Bifidobacterium bifidum S17 Cultivated Under In Vitro Conditions. Front Microbiol 2016; 7:97. [PMID: 26903976 PMCID: PMC4751264 DOI: 10.3389/fmicb.2016.00097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/18/2016] [Indexed: 01/04/2023] Open
Abstract
Bifidobacteria are frequently used in probiotic food and dairy products. Bifidobacterium bifidum S17 is a promising probiotic candidate strain that displays strong adhesion to intestinal epithelial cells and elicits potent anti-inflammatory capacity both in vitro and in murine models of colitis. The recently sequenced genome of B. bifidum S17 has a size of about 2.2 Mb and encodes 1,782 predicted protein-coding genes. In the present study, a comprehensive proteomic profiling was carried out to identify and characterize proteins expressed by B. bifidum S17. A total of 1148 proteins entries were identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), representing 64.4% of the predicted proteome. 719 proteins could be assigned to functional categories according to cluster of orthologous groups of proteins (COGs). The COG distribution of the detected proteins highly correlates with that of the complete predicted proteome suggesting a good coverage and representation of the genomic content of B. bifidum S17 by the proteome. COGs that were highly present in the proteome of B. bifidum S17 were Translation, Amino Acid Transport and Metabolism, and Carbohydrate Transport and Metabolism. Complete sets of enzymes for both the bifidus shunt and the Embden-Meyerh of pathway were identified. Further bioinformatic analysis yielded 28 proteins with a predicted extracellular localization including 14 proteins with an LPxTG-motif for cell wall anchoring and two proteins (elongation factor Tu and enolase) with a potential moonlighting function in adhesion. Amongst the predicted extracellular proteins were five of six pilin proteins encoded in the B. bifidum S17 genome as well as several other proteins with a potential role in interaction with host structures. The presented results are the first compilation of a proteomic reference profile for a B. bifidum strain and will facilitate analysis of the molecular mechanisms of physiology, host-interactions and beneficial effects of a potential probiotic strain.
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Affiliation(s)
- Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Simiao Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Weishi Lin
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Lu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Daria Zhurina
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Boxing Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Yansong Sun
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
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43
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Zheng L, Abhyankar W, Ouwerling N, Dekker HL, van Veen H, van der Wel NN, Roseboom W, de Koning LJ, Brul S, de Koster CG. Bacillus subtilis Spore Inner Membrane Proteome. J Proteome Res 2016; 15:585-94. [PMID: 26731423 DOI: 10.1021/acs.jproteome.5b00976] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The endospore is the dormant form of Bacillus subtilis and many other Firmicutes. By sporulation, these spore formers can survive very harsh physical and chemical conditions. Yet, they need to go through germination to return to their growing form. The spore inner membrane (IM) has been shown to play an essential role in triggering the initiation of germination. In this study, we isolated the IM of bacterial spores, in parallel with the isolation of the membrane of vegetative cells. With the use of GeLC-MS/MS, over 900 proteins were identified from the B. subtilis spore IM preparations. By bioinformatics-based membrane protein predictions, ca. one-third could be predicted to be membrane-localized. A large number of unique proteins as well as proteins common to the two membrane proteomes were identified. In addition to previously known IM proteins, a number of IM proteins were newly identified, at least some of which are likely to provide new insights into IM physiology, unveiling proteins putatively involved in spore germination machinery and hence putative germination inhibition targets.
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Affiliation(s)
| | | | | | | | - Henk van Veen
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comparative proteome analysis of Actinoplanes sp. SE50/110 grown with maltose or glucose shows minor differences for acarbose biosynthesis proteins but major differences for saccharide transporters. J Proteomics 2016; 131:140-148. [DOI: 10.1016/j.jprot.2015.10.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/13/2015] [Accepted: 10/20/2015] [Indexed: 01/08/2023]
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Solis N, Cordwell SJ. Cell Shaving and False-Positive Control Strategies Coupled to Novel Statistical Tools to Profile Gram-Positive Bacterial Surface Proteomes. Methods Mol Biol 2016; 1440:47-55. [PMID: 27311663 DOI: 10.1007/978-1-4939-3676-2_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A powerful start to the discovery and design of novel vaccines, and for better understanding of host-pathogen interactions, is to profile bacterial surfaces using the proteolytic digestion of surface-exposed proteins under mild conditions. This "cell shaving" approach has the benefit of both identifying surface proteins and their surface-exposed epitopes, which are those most likely to interact with host cells and/or the immune system, providing a comprehensive overview of bacterial cell topography. An essential requirement for successful cell shaving is to account for (or minimize) cellular lysis that can occur during the shaving procedure and thus generate data that is biased towards non-surface (e.g., cytoplasmic) proteins. This is further complicated by the presence of "moonlighting" proteins, which are proteins predicted to be intracellular but with validated surface or extracellular functions. Here, we describe an optimized cell shaving protocol for Gram-positive bacteria that uses proteolytic digestion and a "false-positive" control to reduce the number of intracellular contaminants in these datasets. Released surface-exposed peptides are analyzed by liquid chromatography (LC) coupled to high-resolution tandem mass spectrometry (MS/MS). Additionally, the probabilities of proteins being surface exposed can be further calculated by applying novel statistical tools.
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Affiliation(s)
- Nestor Solis
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia
- Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Stuart J Cordwell
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia.
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, The Hub Building D17, Sydney, NSW, 2006, Australia.
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FSL. PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. Nucleic Acids Res 2015; 44:D663-8. [PMID: 26602691 PMCID: PMC4702898 DOI: 10.1093/nar/gkv1271] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/03/2015] [Indexed: 01/01/2023] Open
Abstract
Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and has practical applications such as identification of potential vaccine components or diagnostic/drug targets. PSORTdb (http://db.psort.org) comprises manually curated SCLs for proteins which have been experimentally verified (ePSORTdb), as well as pre-computed SCL predictions for deduced proteomes from bacterial and archaeal complete genomes available from NCBI (cPSORTdb). We now report PSORTdb 3.0. It features improvements increasing user-friendliness, and further expands both ePSORTdb and cPSORTdb with a focus on improving protein SCL data in cases where it is most difficult—proteins associated with non-classical Gram-positive/Gram-negative/Gram-variable cell envelopes. ePSORTdb data curation was expanded, including adding in additional cell envelope localizations, and incorporating markers for cPSORTdb to automatically computationally identify if new genomes to be analysed fall into certain atypical cell envelope categories (i.e. Deinococcus-Thermus, Thermotogae, Corynebacteriales/Corynebacterineae, including Mycobacteria). The number of predicted proteins in cPSORTdb has increased from 3 700 000 when PSORTdb 2.0 was released to over 13 000 000 currently. PSORTdb 3.0 will be of wider use to researchers studying a greater diversity of monoderm or diderm microbes, including medically, agriculturally and industrially important species that have non-classical outer membranes or other cell envelope features.
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Affiliation(s)
- Michael A Peabody
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Matthew R Laird
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Caitlyn Vlasschaert
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Raymond Lo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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Reverón I, de las Rivas B, Matesanz R, Muñoz R, López de Felipe F. Molecular adaptation of Lactobacillus plantarum WCFS1 to gallic acid revealed by genome-scale transcriptomic signature and physiological analysis. Microb Cell Fact 2015; 14:160. [PMID: 26453568 PMCID: PMC4600210 DOI: 10.1186/s12934-015-0345-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Gallic acid (GA) is a model hydroxybenzoic acid that occurs esterified in the lignocellulosic biomass of higher plants. GA displays relevant biological activities including anticancer properties. Owing to its antimicrobial and cellulase-inhibiting activities, GA also imposes constraints to the fermentability of lignocellulosic hydrolysates. In depth-knowledge of the mechanisms used by tolerant microorganisms to adapt to hydroxybenzoic acids would be a step forward to improve the bioavailability of GA or select/engineer production hosts with improved metabolic traits for the bioconversion of pretreated lignocellulosic biomass. Results Whole genome transcriptional profiling using DNA microarrays was used to characterize the molecular response of Lactobacillus plantarum WCFS1 to GA. Expression levels of 14 and 40 genes were differentially regulated at 1.5 and 15 mM GA, respectively. The transcriptomic analysis identified a marked induction of genes with confirmed or related roles to gastrointestinal survival, the repression of genes coding for certain ABC-type transporters and modulation of genes involved in the control of intracellular ammonia levels, among other responses. Most notably, a core set of genes dedicated to produce GA from polyphenols (tanBLp), decarboxylate GA to pyrogallol (lpdB, lpdC and lpdD) and transport functions (lp_2943) was highly overexpressed at both GA concentrations. Correspondingly, resting cells of strain WCFS1 induced by GA, but not their non-induced controls, produced pyrogallol. Gene expression and organization of genes involved in GA metabolism suggested a chemiosmotic mechanism of energy generation. Resting cells of L. plantarum induced by GA generated a membrane potential and a pH gradient across the membrane immediately upon addition of GA. Altogether, transcriptome profiling correlated with physiological observations indicating that a proton motive force could be generated during GA metabolism as a result of electrogenic GA uptake coupled with proton consumption by the intracellular gallate decarboxylase. Conclusions The combination of transcriptome and physiological analyses revealed versatile molecular mechanisms involved in the adaptation of L. plantarum to GA. These data provide a platform to improve the survival of Lactobacillus in the gut. Our data may also guide the selection/engineering of microorganisms that better tolerate phenolic inhibitors present in pretreated lignocellulosic feedstocks. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
| | - Blanca de las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
| | - Ruth Matesanz
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain.
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
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Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens. J Immunol Res 2015; 2015:156241. [PMID: 26526043 PMCID: PMC4615220 DOI: 10.1155/2015/156241] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/02/2015] [Indexed: 01/08/2023] Open
Abstract
Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.
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Sinnige JC, de Been M, Zhou M, Bonten MJM, Willems RJL, Top J. Growth condition-dependent cell surface proteome analysis of Enterococcus faecium. Proteomics 2015; 15:3806-14. [PMID: 26316380 DOI: 10.1002/pmic.201500138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/16/2015] [Accepted: 08/24/2015] [Indexed: 01/25/2023]
Abstract
The last 30 years Enterococcus faecium has become an important nosocomial pathogen in hospitals worldwide. The aim of this study was to obtain insight in the cell surface proteome of E. faecium when grown in laboratory and clinically relevant conditions. Enterococcus faecium E1162, a clinical blood stream isolate, was grown until mid-log phase in brain heart infusion medium (BHI) with, or without 0.02% bile salts, Tryptic Soy Broth with 1% glucose (TSBg) and urine, and its cell surface was "shaved" using immobilized trypsin. Peptides were identified using MS/MS. Mapping against the translated E1162 whole genome sequence identified 67 proteins that were differentially detected in different conditions. In urine, 14 proteins were significantly more and nine proteins less abundant relative to the other conditions. Growth in BHI-bile and TSBg, revealed four and six proteins, respectively, which were uniquely present in these conditions while two proteins were uniquely present in both conditions. Thus, proteolytic shaving of E. faecium cells identified differentially surface exposed proteins in different growth conditions. These proteins are of special interest as they provide more insight in the adaptive mechanisms and may serve as targets for the development of novel therapeutics against this multi-resistant emerging pathogen. All MS data have been deposited in the ProteomeXchange with identifier PXD002497 (http://proteomecentral.proteomexchange.org/dataset/PXD002497).
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Affiliation(s)
- Jan C Sinnige
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark de Been
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Biodiversity Centre, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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50
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Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D. Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions. J Proteome Res 2015; 14:3804-22. [DOI: 10.1021/acs.jproteome.5b00148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Moche
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Kristina Plate
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Katharina Riedel
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße
15, 17487 Greifswald, Germany
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