Identification of Streptococcus mitis321A vaccine antigens based on reverse vaccinology

Zhang,Qiao; Lin,Kexiong; Wang,Changzheng; Xu,Zhi; Yang,Li; Ma,Qianli

doi:10.3892/mmr.2018.8799

Identification of Streptococcus mitis321A vaccine antigens based on reverse vaccinology

Authors:
- Qiao Zhang
- Kexiong Lin
- Changzheng Wang
- Zhi Xu
- Li Yang
- Qianli Ma
View Affiliations

Affiliations: Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
Published online on: March 28, 2018 https://doi.org/10.3892/mmr.2018.8799
Pages: 7477-7486
Copyright: © Zhang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Streptococcus mitis (S. mitis) may transform into highly pathogenic bacteria. The aim of the present study was to identify potential antigen targets for designing an effective vaccine against the pathogenic S. mitis321A. The genome of S. mitis321A was sequenced using an Illumina Hiseq2000 instrument. Subsequently, Glimmer 3.02 and Tandem Repeat Finder (TRF) 4.04 were used to predict genes and tandem repeats, respectively, with DNA sequence function analysis using the Basic Local Alignment Search Tool (BLAST) in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups of proteins (COG) databases. Putative gene antigen candidates were screened with BLAST ahead of phylogenetic tree analysis. The DNA sequence assembly size was 2,110,680 bp with 40.12% GC, 6 scaffolds and 9 contig. Consequently, 1,944 genes were predicted, and 119 TRF, 56 microsatellite DNA, 10 minisatellite DNA and 154 transposons were acquired. The predicted genes were associated with various pathways and functions concerning membrane transport and energy metabolism. Multiple putative genes encoding surface proteins, secreted proteins and virulence factors, as well as essential genes were determined. The majority of essential genes belonged to a phylogenetic lineage, while 321AGL000129 and 321AGL000299 were on the same branch. The current study provided useful information regarding the biological function of the S. mitis321A genome and recommends putative antigen candidates for developing a potent vaccine against S. mitis.

View Figures

View References

1	Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, et al: Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. 293:498–506. 2001. View Article : Google Scholar : PubMed/NCBI
2	Alvarez EF, Olarte KE and Ramesh MS: Purpura fulminans secondary to Streptococcus pneumoniae meningitis. Case Rep Infect Dis. 2012:5085032014.
3	Denapaite D, Brückner R, Nuhn M, Reichmann P, Henrich B, Maurer P, Schähle Y, Selbmann P, Zimmermann W and Wambutt R: The genome of Streptococcus mitis B6-what is a commensal? PloS One. 5:e94262010. View Article : Google Scholar : PubMed/NCBI
4	Kilian M, Poulsen K, Blomqvist T, Håvarstein LS, Bek-Thomsen M, Tettelin H and Sørensen UB: Evolution of Streptococcus pneumoniae and its close commensal relatives. PloS One. 3:e26832008. View Article : Google Scholar : PubMed/NCBI
5	Hakenbeck R, Madhour A, Denapaite D and Brückner R: Versatility of choline metabolism and choline-binding proteins in Streptococcus pneumoniae and commensal streptococci. FEMS Microbiol Rev. 33:572–586. 2009. View Article : Google Scholar : PubMed/NCBI
6	Kohno K, Nagafuji K, Tsukamoto H, Horiuchi T, Takase K, Aoki K, Henzan H, Kamezaki K, Takenaka K, Miyamoto T, et al: Infectious complications in patients receiving autologous CD34-selected hematopoietic stem cell transplantation for severe autoimmune diseases. Transpl Infect Dis. 11:318–323. 2009. View Article : Google Scholar : PubMed/NCBI
7	Han XY, Kamana M and Rolston KV: Viridans streptococci isolated by culture from blood of cancer patients: Clinical and microbiologic analysis of 50 cases. J Clin Microbiol. 44:160–165. 2006. View Article : Google Scholar : PubMed/NCBI
8	Mitchell J: Streptococcus mitis: Walking the line between commensalism and pathogenesis. Mol Oral Microbiol. 26:89–98. 2011. View Article : Google Scholar : PubMed/NCBI
9	Shelburne SA, Sahasrabhojane P, Saldana M, Yao H, Su X, Horstmann N, Thompson E and Flores AR: Streptococcus mitis strains causing severe clinical disease in cancer patients. Emerg Infect Dis. 20:762–771. 2014. View Article : Google Scholar : PubMed/NCBI
10	Matsui N, Ito M, Kuramae H, Inukai T, Sakai A and Okugawa M: Infective endocarditis caused by multidrug-resistant Streptococcus mitis in a combined immunocompromised patient: An autopsy case report. J Infect Chemother. 19:321–325. 2013. View Article : Google Scholar : PubMed/NCBI
11	Bochud PY, Eggiman P, Calandra T, Van Melle G, Saghafi L and Francioli P: Bacteremia due to viridans Streptococcus in neutropenic patients with cancer: Clinical spectrum and risk factors. Clin Infect Dis. 18:25–31. 1994. View Article : Google Scholar : PubMed/NCBI
12	Husain E, Whitehead S, Castell A, Thomas EE and Speert DP: Viridans streptococci bacteremia in children with malignancy: Relevance of species identification and penicillin susceptibility. Pediatr Infect Dis J. 24:563–566. 2005. View Article : Google Scholar : PubMed/NCBI
13	Delany I, Rappuoli R and Seib KL: Vaccines, reverse vaccinology, and bacterial pathogenesis. Cold Spring Harb Perspect Med. 3:a0124762013. View Article : Google Scholar : PubMed/NCBI
14	Chen VL, Avci FY and Kasper DL: A maternal vaccine against group B Streptococcus: Past, present, and future. Vaccine. 31 Suppl 4:D13–D19. 2013. View Article : Google Scholar : PubMed/NCBI
15	Talukdar S, Zutshi S, Prashanth KS, Saikia KK and Kumar P: Identification of potential vaccine candidates against Streptococcus pneumoniae by reverse vaccinology approach. Appl Biochem Biotechnol. 172:3026–3041. 2014. View Article : Google Scholar : PubMed/NCBI
16	Xiang Z and He Y: Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics. 14 Suppl 4:S22013. View Article : Google Scholar : PubMed/NCBI
17	Caro-Gomez E, Gazi M, Goez Y and Valbuena G: Discovery of novel cross-protective Rickettsia prowazekii T-cell antigens using a combined reverse vaccinology and in vivo screening approach. Vaccine. 32:4968–4976. 2014. View Article : Google Scholar : PubMed/NCBI
18	Maritz-Olivier C, Van Zyl W and Stutzer C: A systematic, functional genomics, and reverse vaccinology approach to the identification of vaccine candidates in the cattle tick, Rhipicephalus. Ticks Tick Borne Dis. 3:179–187. 2012. View Article : Google Scholar : PubMed/NCBI
19	Melsted P and Pritchard JK: Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics. 12:3332011. View Article : Google Scholar : PubMed/NCBI
20	Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G and Kristiansen K: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272. 2010. View Article : Google Scholar : PubMed/NCBI
21	Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, et al: SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. Gigascience. 1:182012. View Article : Google Scholar : PubMed/NCBI
22	Craig JW, Chang FY, Kim JH, Obiajulu SC and Brady SF: Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl Environ Microbiol. 76:1633–1641. 2010. View Article : Google Scholar : PubMed/NCBI
23	Kanehisa M, Goto S, Kawashima S, Okuno Y and Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:(Database Issue). D277–D780. 2004. View Article : Google Scholar : PubMed/NCBI
24	Tatusov RL, Galperin MY, Natale DA and Koonin EV: The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36. 2000. View Article : Google Scholar : PubMed/NCBI
25	Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, et al: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365–370. 2003. View Article : Google Scholar : PubMed/NCBI
26	Pruitt KD, Tatusova T and Maglott DR: NCBI reference sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33:(Database Issue). D501–D5D4. 2005. View Article : Google Scholar : PubMed/NCBI
27	Consortium GO: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32:(Database Issue). D258–D261. 2004. View Article : Google Scholar : PubMed/NCBI
28	Zdobnov EM and Apweiler R: InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 17:847–848. 2001. View Article : Google Scholar : PubMed/NCBI
29	Sette A and Rappuoli R: Reverse vaccinology: Developing vaccines in the era of genomics. Immunity. 33:530–541. 2010. View Article : Google Scholar : PubMed/NCBI
30	Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, Tettelin H, Brettoni C, Iacobini ET, Rosini R, et al: Identification of a universal Group B Streptococcus vaccine by multiple genome screen. Science. 309:148–150. 2005. View Article : Google Scholar : PubMed/NCBI
31	Chou KC and Shen HB: Cell-PLoc: A package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc. 3:153–162. 2008. View Article : Google Scholar : PubMed/NCBI
32	Lobo I: Basic local alignment search tool (BLAST). Nat Educ. 1:22008.
33	Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al: The Pfam protein families database. Nucleic Acids Res. 32:(Database Issue). D138–D141. 2004. View Article : Google Scholar : PubMed/NCBI
34	Underwood A, Mulder A, Gharbia S and Green J: Virulence Searcher: A tool for searching raw genome sequences from bacterial genomes for putative virulence factors. Clin Microbiol Infect. 11:770–772. 2005. View Article : Google Scholar : PubMed/NCBI
35	Zhang R and Lin Y: DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 37:D455–D458. 2009. View Article : Google Scholar : PubMed/NCBI
36	Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A and Lopez R: Clustal W and Clustal X version 2.0. Bioinformatics. 23:2947–2948. 2007. View Article : Google Scholar : PubMed/NCBI
37	Guindon S, Lethiec F, Duroux P and Gascuel O: PHYML online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33:(Web Server Issue). W557–W559. 2005. View Article : Google Scholar : PubMed/NCBI
38	Balkundi DR, Murray DL, Patterson MJ, Gera R, Scott-Emuakpor A and Kulkarni R: Penicillin-resistant Streptococcus mitis as a cause of septicemia with meningitis in febrile neutropenic children. J Pediatr Hematol Oncol. 19:82–85. 1997. View Article : Google Scholar : PubMed/NCBI
39	Yoshpe-Besancon I, Gripon JC and Ribadeau-Dumas B: Xaa-Pro-dipeptidyl-aminopeptidase from Lactococcus lactis catalyses kinetically controlled synthesis of peptide bonds involving proline. Biotechnol Appl Biochem. 20:131–140. 1994.PubMed/NCBI
40	Kowluru A: Identification and characterization of a novel protein histidine kinase in the islet β cell: Evidence for its regulation by mastoparan, an activator of G-proteins and insulin secretion. Biochem Pharmacol. 63:2091–2100. 2002. View Article : Google Scholar : PubMed/NCBI
41	Torosantucci A, Chiani P, De Bernardis F, Cassone A, Calera JA and Calderone R: Deletion of the two-component histidine kinase gene (CHK1) of Candida albicans contributes to enhanced growth inhibition and killing by human neutrophils in vitro. Infect Immun. 70:985–987. 2002. View Article : Google Scholar : PubMed/NCBI
42	Brenot A, King KY, Janowiak B, Griffith O and Caparon MG: Contribution of glutathione peroxidase to the virulence of Streptococcus pyogenes. Infect Immun. 72:408–413. 2004. View Article : Google Scholar : PubMed/NCBI
43	Fischer W and Haas R: The RecA protein of Helicobacter pylori requires a posttranslational modification for full activity. J Bacteriol. 186:777–784. 2004. View Article : Google Scholar : PubMed/NCBI
44	Kurokawa K, Lee H, Roh KB, Asanuma M, Kim YS, Nakayama H, Shiratsuchi A, Choi Y, Takeuchi O, Kang HJ, et al: The triacylated ATP binding cluster transporter substrate-binding lipoprotein of Staphylococcus aureus functions as a native ligand for Toll-like receptor 2. J Biol Chem. 284:8406–8411. 2009. View Article : Google Scholar : PubMed/NCBI
45	Kolenbrander PE, Andersen RN, Baker RA and Jenkinson HF: The adhesion-associated sca operon in Streptococcus gordonii encodes an inducible high-affinity ABC transporter for Mn²⁺ uptake. J Bacteriol. 180:290–295. 1998.PubMed/NCBI
46	Griffin JE, Gawronski JD, DeJesus MA, Ioerger TR, Akerley BJ and Sassetti CM: High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog. 7:e10022512011. View Article : Google Scholar : PubMed/NCBI
47	Akerley BJ, Rubin EJ, Novick VL, Amaya K, Judson N and Mekalanos JJ: A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc Natl Acad Sci USA. 99:966–971. 2002. View Article : Google Scholar : PubMed/NCBI
48	Sassetti CM, Boyd DH and Rubin EJ: Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci USA. 98:12712–12779. 2001. View Article : Google Scholar : PubMed/NCBI
49	Weigel LM, Clewell DB, Gill SR, Clark NC, McDougal LK, Flannagan SE, Kolonay JF, Shetty J, Killgore GE and Tenover FC: Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science. 302:1569–1571. 2003. View Article : Google Scholar : PubMed/NCBI
50	Ramaswamy S and Musser JM: Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuber Lung Dis. 79:3–29. 1998. View Article : Google Scholar : PubMed/NCBI