Browse > Article
http://dx.doi.org/10.4014/jmb.1510.10081

Comparative Analysis of the Complete Genome of Lactobacillus plantarum GB-LP2 and Potential Candidate Genes for Host Immune System Enhancement  

Kwak, Woori (C&K Genomics)
Kim, Kwondo (C&K Genomics)
Lee, Chul (Interdisciplinary Program in Bioinformatics, Seoul National University)
Lee, Chanho (Genebiotech Co. Ltd.)
Kang, Jungsun (Genebiotech Co. Ltd.)
Cho, Kyungjin (Genebiotech Co. Ltd.)
Yoon, Sook Hee (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Kang, Dae-Kyung (Department of Animal Resources Science, Dankook University)
Kim, Heebal (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Heo, Jaeyoung (C&K Genomics)
Cho, Seoae (C&K Genomics)
Publication Information
Journal of Microbiology and Biotechnology / v.26, no.4, 2016 , pp. 684-692 More about this Journal
Abstract
Acute respiratory virus infectious diseases are a growing health problem, particularly among children and the elderly. Much effort has been made to develop probiotics that prevent influenza virus infections by enhancing innate immunity in the respiratory tract until vaccines are available. Lactobacillus plantarum GB-LP2, isolated from a traditional Korean fermented vegetable, has exhibited preventive effects on influenza virus infection in mice. To identify the molecular basis of this strain, we conducted a whole-genome assembly study. The single circular DNA chromosome of 3,284,304 bp was completely assembled and 3,250 protein-encoding genes were predicted. Evolutionarily accelerated genes related to the phenotypic trait of anti-infective activities for influenza virus were identified. These genes encode three integral membrane proteins, a teichoic acid export ATP-binding protein and a glucosamine - fructose-6-phosphate aminotransferase involved in host innate immunity, the nonspecific DNA-binding protein Dps, which protects bacteria from oxidative damage, and the response regulator of the three-component quorum-sensing regulatory system, which is related to the capacity of adhesion to the surface of the respiratory tract and competition with pathogens. This is the first study to identify the genetic backgrounds of the antiviral activity in L. plantarum strains. These findings provide insight into the anti-infective activities of L. plantarum and the development of preventive probiotics.
Keywords
Lacatobacillus plantarum GB-LP2; comparative genomics; host immune enhancement; anti-viral effect;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.   DOI
2 Barreteau H, Kovaè A, Boniface A, Sova M, Gobec S, Blanot D. 2008. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol. Rev. 32: 168-207.   DOI
3 Boge T, Rémigy M, Vaudaine S, Tanguy J, Bourdet-Sicard R, van der Werf S. 2009. A probiotic fermented dairy drink improves antibody response to influenza vaccination in the elderly in two randomised controlled trials. Vaccine 27: 5677-5684.   DOI
4 Bosch A, Biesbroek G, Trzcinski K, Sanders E, Bogaert D. 2013. Viral and bacterial interactions in the upper respiratory tract. PLoS Pathog. 9: e1003057.   DOI
5 Bron PA, van Baarlen P, Kleerebezem M. 2012. Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa. Nat. Rev. Microbiol. 10: 66-78.   DOI
6 Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. 2009. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120.   DOI
7 Chiancone E, Ceci P. 2010. The multifaceted capacity of Dps proteins to combat bacterial stress conditions: detoxification of iron and hydrogen peroxide and DNA binding. Biochim. Biophys. Acta 1800: 798-805.   DOI
8 Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.   DOI
9 Choi S-W, Youn H-N, Hong W, Park J-K, Yuk S-S, Kwon J-H, et al. 2015. Intranasal administration model for evaluating protection against influenza virus in mice. J. Bacteriol. Virol. 45: 44-50.   DOI
10 Ferguson NM, Cummings DA, Fraser C, Cajka JC, Cooley PC, Burke DS. 2006. Strategies for mitigating an influenza pandemic. Nature 442: 448-452.   DOI
11 Ferguson NM, Fraser C, Donnelly CA, Ghani AC, Anderson RM. 2004. Public health risk from the avian H5N1 influenza epidemic. Science 304: 968.   DOI
12 Harata G, He F, Hiruta N, Kawase M, Kubota A, Hiramatsu M, Yausi H. 2011. Intranasally administered TMC0356 protects mice from H1N1 influenza virus infection by stimulating respiratory immune responses. World J. Microbiol. Biotechnol. 2: 411-416.   DOI
13 Joseph C, Togawa Y, Shindo N. 2013. Bacterial and viral infections associated with influenza. Influenza Other Respir. Viruses 7: 105-113.   DOI
14 Kechaou N, Chain F, Gratadoux J-J, Blugeon S, Bertho N, Chevalier C, et al. 2013. Identification of one novel candidate probiotic Lactobacillus plantarum strain active against influenza virus infection in mice by a large-scale screening. Appl. Environ. Microbiol. 79: 1491-1499.   DOI
15 Leyer GJ, Li S, Mubasher ME, Reifer C, Ouwehand AC. 2009. Probiotic effects on cold and influenza-like symptom incidence and duration in children. Pediatrics 124: e172-e179.   DOI
16 Kim KM, Sung S, Caetano-Anollés G, Han JY, Kim H. 2008. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 36: e110-e110.   DOI
17 Löytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635.   DOI
18 Lebeer S, Vanderleyden J, De Keersmaecker SC. 2008. Genes and molecules of lactobacilli supporting probiotic action. Microbiol. Mol. Biol. Rev. 72: 728-764.   DOI
19 Liévin-Le Moal V, Servin AL. 2014. Anti-infective activities of Lactobacillus strains in the human intestinal microbiota: from probiotics to gastrointestinal anti-infectious biotherapeutic agents. Clin. Microbiol. Rev. 27: 167-199.   DOI
20 Liu Z-H, Kang L, Wang J-P. 2014. Basic and clinical research on the regulation of the intestinal barrier by Lactobacillus and its active protein components: a review with experience of one center. Mol. Biol. Rep. 41: 8037-8046.   DOI
21 Liu Z, Ma Y, Moyer MP, Zhang P, Shi C, Qin H. 2012. Involvement of the mannose receptor and p38 mitogen-activated protein kinase signaling pathway of the microdomain of the integral membrane protein after enteropathogenic Escherichia coli infection. Infect. Immun. 80: 1343-1350.   DOI
22 Maldonado-Barragán A, Ruiz-Barba JL, Jiménez-Díaz R. 2009. Knockout of three-component regulatory systems reveals that the apparently constitutive plantaricin-production phenotype shown by Lactobacillus plantarum on solid medium is regulated via quorum sensing. Int. J. Food Microbiol. 130: 35-42.   DOI
23 Sander B, Nizam A, Garrison LP, Postma MJ, Halloran ME, Longini IM Jr. 2009. Economic evaluation of influenza pandemic mitigation strategies in the United States using a stochastic microsimulation transmission model. Value Health 12: 226-233.   DOI
24 Park M-K, Ngo V, Kwon Y-M, Lee Y-T, Yoo S, Cho YH, et al. 2013. Lactobacillus plantarum DK119 as a probiotic confers protection against influenza virus by modulating innate immunity. PLoS One 8: e75368.   DOI
25 Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Nat. Acad. Sci. USA 106: 19126-19131.   DOI
26 Rizzardini G, Eskesen D, Calder PC, Capetti A, Jespersen L, Clerici M. 2012. Evaluation of the immune benefits of two probiotic strains Bifidobacterium animalis ssp. lactis, BB-12® and Lactobacillus paracasei ssp. paracasei, L. casei 431® in an influenza vaccination model: a randomised, double-blind, placebo-controlled study. Br. J. Nutr. 107: 876-884.   DOI
27 Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, et al. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459: 1122-1125.   DOI
28 Sturme MH, Francke C, Siezen RJ, de Vos WM, Kleerebezem M. 2007. Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1. Microbiology 153: 3939-3947.   DOI
29 Suo C, Yin Y, Wang X, Lou X, Song D, Wang X, Gu Q. 2012. Effects of Lactobacillus plantarum ZJ316 on pig growth and pork quality. BMC Vet. Res. 8: 89.   DOI
30 Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577.   DOI
31 Youn H-N, Lee D-H, Lee Y-N, Park J-K, Yuk S-S, Yang SY, et al. 2012. Intranasal administration of live Lactobacillus species facilitates protection against influenza virus infection in mice. Antiviral Res. 93: 138-143.   DOI
32 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evolut. 30: 2725-2729.   DOI
33 Wu S, Zhu Z, Fu L, Niu B, Li W. 2011. Web MGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12: 444.   DOI
34 Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.   DOI
35 Zelaya H, Tada A, Vizoso-Pinto MG, Salva S, Kanmani P, Agüero G, et al. 2015. Nasal priming with immunobiotic Lactobacillus rhamnosus modulates inflammation–coagulation interactions and reduces influenza virus-associated pulmonary damage. Inflamm. Res. 64: 589-602.   DOI