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Young JW, Zhao Z, Wason IS, Duong van Hoa F. A Dual Detergent Strategy to Capture a Bacterial Outer Membrane Proteome in Peptidiscs for Characterization by Mass Spectrometry and Binding Assays. J Proteome Res 2022; 22:1537-1545. [PMID: 36516475 DOI: 10.1021/acs.jproteome.2c00560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outer membrane of Gram-negative bacteria plays a critical role in protecting the cell against external stressors, including antibiotics, and therefore is a prime target for antimicrobial discovery. To facilitate the discovery efforts, a precise knowledge of the outer membrane proteome, and possible variations during pathogenesis, is important. Characterization of the bacterial outer membrane remain challenging, however, and low throughput, due to the high hydrophobicity and relatively low abundance of this cell compartment. Here we adapt our peptidisc-based method to selectively isolate the outer membrane proteome before analysis by mass spectrometry. Using a dual detergent membrane solubilization approach, followed by protein purification in peptidiscs, we capture over 70 outer membrane proteins, including 26 integral β-barrels and 26 lipoproteins. Many of these proteins are present at high peptide intensities, indicative of a high abundance in the library sample. We further show that the isolated outer membrane proteome can be employed in downstream ligand-binding assays. This peptidisc library made of outer membrane proteins may therefore be useful to systematically survey other bacterial outer membrane proteomes, but also as a nanoparticle format able to support the discovery of next-generation antimicrobials. Data are available via ProteomeXchange identifier PXD036749.
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Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Piel LMW, Durfee CJ, White SN. Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species. BMC Bioinformatics 2021; 22:296. [PMID: 34078271 PMCID: PMC8170629 DOI: 10.1186/s12859-021-04181-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/10/2021] [Indexed: 12/29/2022] Open
Abstract
Background Coxiella burnetii is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surface isolated proteins confer protection but can produce a reactogenic immune responses. Thereby a protective vaccine that does not cause aberrant immune reactions is required. The critical role of T-cell immunity in control of C. burnetii has been made clear, since either CD8+ or CD4+ T cells can empower clearance. The purpose of this study was to identify C. burnetii proteins bearing epitopes that interact with major histocompatibility complexes (MHC) from multiple host species (human, mouse, and cattle). Results Of the annotated 1815 proteins from the Nine Mile Phase I (RSA 493) assembly, 402 proteins were removed from analysis due to a lack of inter-isolate conservation. An additional 391 proteins were eliminated from assessment to avoid potential autoimmune responses due to the presence of host homology. We analyzed the remaining 1022 proteins for their ability to produce peptides that bind MHCI or MHCII. MHCI and MHCII predicted epitopes were filtered and compared between species yielding 777 MHCI epitopes and 453 MHCII epitopes. These epitopes were further examined for presentation by both MHCI and MHCII, and for proteins that contained multiple epitopes. There were 31 epitopes that overlapped positionally between MHCI and MHCII across host species. Of these, there were 9 epitopes represented within proteins containing ≥ 5 total epitopes, where an additional 24 proteins were also epitope dense. In all, 55 proteins were found to contain high scoring T-cell epitopes. Besides the well-studied protein Com1, most identified proteins were novel when compared to previously studied vaccine candidates. Conclusion These data represent the first proteome-wide evaluation of C. burnetii peptide epitopes. Furthermore, the inclusion of human, mouse, and bovine data capture a range of hosts for this zoonotic pathogen plus an important model organism. This work provides new vaccine targets for future vaccination efforts and enhances opportunities for selecting multiple T-cell epitope types to include within a vaccine. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04181-w.
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Affiliation(s)
| | - Codie J Durfee
- USDA-ARS Animal Disease Research Unit, Pullman, WA, 99164, USA
| | - Stephen N White
- USDA-ARS Animal Disease Research Unit, Pullman, WA, 99164, USA. .,Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, 99164, USA. .,Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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Sharma V, Mobeen F, Prakash T. In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB). 3 Biotech 2020; 10:376. [PMID: 32802718 PMCID: PMC7406594 DOI: 10.1007/s13205-020-02371-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 07/28/2020] [Indexed: 12/01/2022] Open
Abstract
The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.
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Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, 175005 Himachal Pradesh India
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, 175005 Himachal Pradesh India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, 175005 Himachal Pradesh India
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Jia FF, Zhang LJ, Pang XH, Gu XX, Abdelazez A, Liang Y, Sun SR, Meng XC. Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells. Genomics 2017; 109:432-437. [PMID: 28676278 DOI: 10.1016/j.ygeno.2017.06.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/07/2017] [Accepted: 06/28/2017] [Indexed: 02/06/2023]
Abstract
Lactobacillus plantarum KLDS1.0391 is a probiotic strain isolated from the traditional fermented dairy products and identified to produce bacteriocin against Gram-positive and Gram-negative bacteria. Previous studies showed that the strain has a high resistance to gastrointestinal stress and has a high adhesion ability to the intestinal epithelial cells (Caco-2). We reported the entire genome sequence of this strain, which contains a circular 2,886,607-bp chromosome and three circular plasmids. Genes, which are related to the biosynthesis of bacteriocins, the stress resistance to gastrointestinal tract environment and adhesive performance, were identified. Whole genome sequence of Lactobacillus plantarum KLDS1.0391 will be helpful for its applications in food industry.
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Affiliation(s)
- Fang-Fang Jia
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Lu-Ji Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xue-Hui Pang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xin-Xi Gu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China; College of Food Science and Technology, Agricultural University of Hebei, Baoding 071000, China
| | - Amro Abdelazez
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Department of Dairy Microbiology, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt
| | - Yu Liang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Si-Rui Sun
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xiang-Chen Meng
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, China.
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Zhu D, Sun Y, Huo GC, Yang L, Liu F, Li A, Meng XC. Complete genome sequence of Bifidobacterium animalis subsp. lactis KLDS 2.0603, a probiotic strain with digestive tract resistance and adhesion to the intestinal epithelial cells. J Biotechnol 2016; 220:49-50. [DOI: 10.1016/j.jbiotec.2016.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/13/2016] [Indexed: 01/08/2023]
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In Silico Sub-unit Hexavalent Peptide Vaccine Against an Staphylococcus aureus Biofilm-Related Infection. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9489-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Rees MA, Kleifeld O, Crellin PK, Ho B, Stinear TP, Smith AI, Coppel RL. Proteomic Characterization of a Natural Host–Pathogen Interaction: Repertoire of in Vivo Expressed Bacterial and Host Surface-Associated Proteins. J Proteome Res 2014; 14:120-32. [DOI: 10.1021/pr5010086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Timothy P. Stinear
- Department
of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
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Valeriano VD, Parungao-Balolong MM, Kang DK. In vitro evaluation of the mucin-adhesion ability and probiotic potential of Lactobacillus mucosae LM1. J Appl Microbiol 2014; 117:485-97. [PMID: 24807045 DOI: 10.1111/jam.12539] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/23/2014] [Accepted: 03/28/2014] [Indexed: 11/28/2022]
Abstract
AIMS In this report, we characterized the probiotic potential of Lactobacillus mucosae LM1, focusing on its in vitro mucin-adhesion abilities. METHODS AND RESULTS Screening assays were used to evaluate LM1. Previous studies on Lact. mucosae species have been performed, but few have examined the ability of this species to adhere to and colonize the intestinal mucosa. Thus, adhesion, aggregation and pathogen inhibition assays of LM1 along with microbial adhesion to solvents (MATS) assay were carried out in comparison with another putative probiotic, Lactobacillus johnsonii PF01, and the commercial strain, Lactobacillus rhamnosus GG. Based on MATS assay, the cell surfaces of the lactobacilli strains were found to be hydrophobic and highly electron-donating, but the average hydropathy (GRAVY) index of predicted surface-exposed proteins in the LM1 genome indicated that most were hydrophilic. LM1 showed the highest adhesion, aggregation and hydrophobicity among the strains tested and significantly inhibited the adhesion of Escherichia coli K88 and Salmonella enterica serovar Typhimurium KCCM 40253. Correlations among adhesion, aggregation and hydrophobicity, as well as between coaggregation and displacement of E. coli, were observed. CONCLUSIONS Increased adhesion may not always correlate with increased pathogen inhibition due to various strain-specific mechanisms. Nevertheless, LM1 has promising probiotic properties that can be explored further using a genomics approach. SIGNIFICANCE AND IMPACT OF THE STUDY Our data on adhesion of LM1 strain showed a significant correlation between adhesion, hydrophobicity of cell surface and autoaggregation. This study gives basic knowledge for the elucidation of the adhesion mechanism of Lactobacillus sp. and prediction of its adherence in specific host models.
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Affiliation(s)
- V D Valeriano
- Department of Animal Resources Science, Dankook University, Cheonan, Korea
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