[논문]Comparative Genomic Analysis of Lactobacillus plantarum GB-LP1 Isolated from Traditional Korean Fermented Food

Yu, Jihyun; Ahn, Sojin; Kim, Kwondo; Caetano-Anolles, Kelsey; Lee, Chanho; Kang, Jungsun; Cho, Kyungjin; Yoon, Sook Hee; Kang, Dae-Kyung; Kim, Heebal

doi:10.4014/jmb.1704.04005

Comparative Genomic Analysis of Lactobacillus plantarum GB-LP1 Isolated from Traditional Korean Fermented Food 원문보기

Journal of microbiology and biotechnology, v.27 no.8, 2017년, pp.1419 - 1427

Yu, Jihyun (Department of Agricultural Biotechnology and Research Institute of Population Genomics, Seoul National University) , Ahn, Sojin (Interdisciplinary Program in Bioinformatics, Seoul National University) , Kim, Kwondo (Interdisciplinary Program in Bioinformatics, Seoul National University) , Caetano-Anolles, Kelsey (Department of Agricultural Biotechnology and Research Institute of Population Genomics, 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 of Population Genomics, Seoul National University) , Kang, Dae-Kyung (Department of Animal Resources Science, Dankook University) , Kim, Heebal (Department of Agricultural Biotechnology and Research Institute of Population Genomics, Seoul National University)

Abstract ▼ AI-Helper

As probiotics play an important role in maintaining a healthy gut flora environment through antitoxin activity and inhibition of pathogen colonization, they have been of interest to the medical research community for quite some time now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in fermented food, are of particular interest given their easy accessibility. We performed whole-genome sequencing and genomic analysis on a GB-LP1 strain of L. plantarum isolated from Korean traditional fermented food; this strain is well known for its functions in immune response, suppression of pathogen growth, and antitoxin effects. The complete genome sequence of GB-LP1 is a single chromosome of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution, which may have antibiotic and antitoxin functions. The aim of the present study was to predict strain specific-genomic characteristics and assess the potential of this new strain as lactic acid bacteria at the genomic level using in silico analysis. These results provide insight into the L. plantarum species as well as confirm the possibility of its utility as a candidate probiotic.

주제어

AI 본문요약
AI-Helper

* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.

가설 설정

plantarum GB-LP1 showed substitution of proline to leucine for protein TldD, which belongs to the TldE/TldD proteolytic complex. We hypothesize that the substitution of proline results in structural modification of post-translational proteins and their interaction with other proteins.

제안 방법

Analysis of comparative nucleotide substitution was conducted on the orthologous gene set in order to identify the specific gene-related effects of the GB-LP1 strain of L. plantarum. One hypothetical gene and two enzymerelated genes were determined as significant evolutionarily accelerated genes through dNdS analysis based on the branch site (Table 2).
The total CRISPR region was 130 bp long and the start position was 2,669,898 bp. As a result of GI analysis, nine putative GIs were identified using three methods: IslandPick, SIGI-HMM, and IslandPath-DIMOB. Among these methods, the GI detected using IslandPick was related with integrase/recombinase and putative type II restriction enzyme methylase subunit via SEED annotation.
In this study, we de novo constructed the complete genome sequence of L. plantarum GB-LP1, a novel strain isolated from Korea traditional fermented food. Genetic relatedness between GB-LP1 and known complete sequences of L.

이론/모형

Regarding each ortholog gene, the dN (rate of non-synonymous substitution) and dS (rate of synonymous substitution) values were calculated using codeml of PAML4 with the maximum-likelihood method [28]. Evolutionarily accelerated genes were estimated using the branch-site model. We ascertained genomic islands related to horizontal transfer using the multiple prediction methods within the IslandViewer3 package.
After removing poorly aligned sites using the GBlocks program [25], we reconstructed a phylogenetic tree based on orthologous sequences concatenated into one sequence. Phylogenetic analysis was conducted within MEGA6 [26] using the neighbor-joining method. Additionally, one-to-one comparison of sequences was performed against the closest-related strains, JDM1 and DOMLa, in order to identify the unmatched DNA regions of GB-LP1, and was detected using ACT [27].
Additionally, one-to-one comparison of sequences was performed against the closest-related strains, JDM1 and DOMLa, in order to identify the unmatched DNA regions of GB-LP1, and was detected using ACT [27]. Regarding each ortholog gene, the dN (rate of non-synonymous substitution) and dS (rate of synonymous substitution) values were calculated using codeml of PAML4 with the maximum-likelihood method [28]. Evolutionarily accelerated genes were estimated using the branch-site model.

성능/효과

1 and Table 1). From the total of 2,899 OFSs, 2,327 genes (80.3%) were annotated as functional genes, while the remaining 572 genes were predicted as hypothetical and functionally unknown genes. The distribution of predicted ORFs resulting from COG functional categorization and SEED subsystem categorization is presented in Fig.
00%. The topology of the ANI tree revealed that GB-LP1 belongs to the closest monophyletic group I consisting of three strains: Zhang-LL, DOMLa, and JDM1. Within group I, the closest neighbor of LP1 was Zhang-LL, but it was not congruent with the phylogenetic tree using orthologous genes.

후속연구

JDM1 has been proven safe, and is a commonly used probiotic for humans and various animals such as pigs [31]. These findings suggest GB-LP1 for use as a probiotic supplement, although further research is needed to identify bacterial traits or the impact on the host at the genomic level. We performed genomic analysis using different bioinformatics approaches based on evolutionary history in order to judge GB-LP1’s suitability as a probiotic bacterium.

참고문헌 (44)

Baumler AJ, Sperandio V. 2016. Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535: 85-93.

상세보기
Kostic AD, Xavier RJ, Gevers D. 2014. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146: 1489-1499.

상세보기
Virgin HW. 2014. The virome in mammalian physiology and disease. Cell 157: 142-150.

상세보기
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. 2014. Human genetics shape the gut microbiome. Cell 159: 789-799.

상세보기
Macfarlane S, Steed H, Macfarlane GT. 2009. Intestinal bacteria and inflammatory bowel disease. Crit. Rev. Clin. Lab. Sci. 46: 25-54.

상세보기
Paolillo R, Carratelli CR, Sorrentino S, Mazzola N, Rizzo A. 2009. Immunomodulatory effects of Lactobacillus plantarum on human colon cancer cells. Int. Immunopharmacol. 9: 1265-1271.

상세보기
Parvez S, Malik KA, Ah Kang S, Kim HY. 2006. Probiotics and their fermented food products are beneficial for health. J. Appl. Microbiol. 100: 1171-1185.

상세보기
Shah N, Patel A, Ambalam P, Holst O, Ljungh A, Prajapati J. 2016. Determination of an antimicrobial activity of Weissella confusa, Lactobacillus fermentum, and Lactobacillus plantarum against clinical pathogenic strains of Escherichia coli and Staphylococcus aureus in co-culture. Ann. Microbiol. 66: 1137-1143.

상세보기
Nomoto K. 2005. Prevention of infections by probiotics. J. Biosci. Bioeng. 100: 583-592.

상세보기
Stewart PS, William Costerton J. 2001. Antibiotic resistance of bacteria in biofilms. Lancet 358: 135-138.

상세보기
Eaton TJ, Gasson MJ. 2001. Molecular screening of Enterococcus virulence determinants and potential for genetic exchange between food and medical isolates. Appl. Environ. Microbiol. 67: 1628-1635.

상세보기
Mah T-F, Pitts B, Pellock B, Walker GC, Stewart PS, O’Toole GA. 2003. A genetic basis for Pseudomonas aeruginosa biofilm antibiotic resistance. Nature 426: 306-310.

상세보기
Morelli L. 2007. In vitro assessment of probiotic bacteria: from survival to functionality. Int. Dairy J. 17: 1278-1283.

상세보기
Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, et al. 2005. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 102: 11064-11069.

상세보기
Singh G, Sharma D, Singh V, Rani J, Marotta F, Kumar M, et al. 2017. In silico functional elucidation of uncharacterized proteins of Chlamydia abortus strain LLG. Future Sci. OA 3: FSO169.

상세보기
Siezen RJ, van Enckevort FH, Kleerebezem M, Teusink B. 2004. Genome data mining of lactic acid bacteria: the impact of bioinformatics. Curr. Opin. Biotechnol. 15: 105-115.

상세보기
Liu W-H, Yang C-H, Lin C-T, Li S-W, Cheng W-S, Jiang Y-P, et al. 2015. Genome architecture of Lactobacillus plantarum PS128, a probiotic strain with potential immunomodulatory activity. Gut Pathog. 7: 22.

상세보기
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.

상세보기
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.

상세보기
Bose T, Haque MM, Reddy C, Mande SS. 2015. COGNIZER: a framework for functional annotation of metagenomic datasets. PLoS One 10: e0142102.

상세보기
Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. 2009. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120.

상세보기
Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131.

상세보기
Kim KM, Sung S, Caetano-Anolles G, Han JY, Kim H. 2008. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 36: e110.

상세보기
Loytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635.

상세보기
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577.

상세보기
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729.

상세보기
Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J. 2005. ACT: the Artemis comparison tool. Bioinformatics 21: 3422-3423.

상세보기
Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.

상세보기
Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35: W52-W57.

상세보기
Wolf YI, Makarova KS, Yutin N, Koonin EV. 2012. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct 7: 46.

상세보기
Zhang Z-Y, Liu C, Zhu Y-Z, Wei Y-X, Tian F, Zhao G-P, et al. 2012. Safety assessment of Lactobacillus plantarum JDM1 based on the complete genome. Int. J. Food Microbiol. 153: 166-170.

상세보기
Hacker J, Carniel E. 2001. Ecological fitness, genomic islands and bacterial pathogenicity. EMBO Rep. 2: 376-381.

상세보기
Roberts AP, Kreth J. 2014. The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome.
Wiedenbeck J, Cohan FM. 2011. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol. Rev. 35: 957-976.

상세보기
Allali N, Afif H, Couturier M, Van Melderen L. 2002. The highly conserved TldD and TldE proteins of Escherichia coli are involved in microcin B17 processing and in CcdA degradation. J. Bacteriol. 184: 3224-3231.

상세보기
Yang S-C, Lin C-H, Sung CT, Fang J-Y. 2014. Antibacterial activities of bacteriocins: application in foods and pharmaceuticals. Front. Microbiol. 5: 241.
Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, et al. 2013. Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome 1: 20.

상세보기
Glenn K, Smith KS. 2015. Allosteric regulation of Lactobacillus plantarum xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp). J. Bacteriol. 197: 1157-1163.

상세보기
Pan Y, Ni R, Deng Q, Huang X, Zhang Y, Lu C, et al. 2013. Glyoxylate reductase/hydroxypyruvate reductase: a novel prognostic marker for hepatocellular carcinoma patients after curative resection. Pathobiology 80: 155-162.

상세보기
Duan X, Hu S, Zhou P, Zhou Y, Liu Y, Jiang Z. 2014. Characterization and crystal structure of a first fungal glyoxylate reductase from Paecilomyes thermophila. Enzyme Microb. Technol. 60: 72-79.

상세보기
Knight J, Wood KD, Lange JN, Assimos DG, Holmes RP. 2016. Oxalate formation from glyoxal in erythrocytes. Urology 88: 226.e11-226.e15.

상세보기
Abratt VR, Reid SJ. 2010. Oxalate-degrading bacteria of the human gut as probiotics in the management of kidney stone disease. Adv. Appl. Microbiol. 72: 63-87.

상세보기
Lahm A, Paolini C, Pallaoro M, Nardi M, Jones P, Neddermann P, et al. 2007. Unraveling the hidden catalytic activity of vertebrate class IIa histone deacetylases. Proc. Natl. Acad. Sci. USA 104: 17335-17340.

상세보기
Tanaka Y, Kasahara K, Hirose Y, Murakami K, Kugimiya R, Ochi K. 2013. Activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpoB) mutations in actinomycetes. J. Bacteriol. 195: 2959-2970.

상세보기

저자의 다른 논문 :

LOADING...

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증