基于基因组学分析嗜热链球菌KLDS SM的蛋白质水解系统和氨基酸合成途径
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摘要
为从遗传水平上探究嗜热链球菌KLDS SM蛋白质水解和氨基酸合成的能力,首先基于Illumina Hiseq 2500与Pacbio RSII测序平台对嗜热链球菌KLDS SM进行全基因组测序并绘制基因组图谱;随后从胞外蛋白酶、转运系统、胞内肽酶以及氨基酸合成等方面所涉及的基因进行生物信息学分析;最后对15株已完成全基因组测序的嗜热链球菌的氨基酸合成能力进行比较基因组学研究。结果表明:菌株KLDS SM的基因组由一个1 856 787 bp环状染色体组成,GC含量为39.08%,含有1 732个蛋白质编码基因;菌株KLDS SM具有完整的蛋白水解系统和8种氨基酸的合成能力;15株嗜热链球菌在氨基酸合成方面上相对保守,仅在组氨酸合成途径存在较大的差异。本研究为该菌株氮代谢能力的挖掘提供了理论依据,并在将其开发为发酵剂方面上具有一定指导意义。
The purpose of this study was to gain genomic insights into the proteolysis system and amino acid biosynthesis in Streptococcus thermophilus KLDS SM. Firstly, whole genome sequencing was performed using combination of Illumina Hiseq 2500 sequencing and Pacific Biosciences RSII sequencing and the circular genomic map was constructed; subsequently, in silico bioinformatics analysis was carried out with respect to extracellular proteinase, peptide transport system, intracellular peptidase and amino acid biosynthesis; finally, comparative genomics of amino acid biosynthesis between strain KLDS SM and 14 other S. thermophilus strains, all of which have had the whole genome sequenced, was performed. The results showed that the genome of S. thermophilus KLDS SM consisted of a circular chromosome(1 856 787 bp) with GC content of 39.08%. A total of 1 732 protein-encoding genes were predicted. S. thermophilus KLDS SM had a complete proteolytic system and could biosynthesize eight amino acids. Furthermore, comparative genomics analysis showed that the amino acid biosynthesis abilities of 15 strains were relatively conservative except for a large difference in histidine biosynthesis among different strains. The results of this study can provide a theoretical basis for better understanding of nitrogen metabolism in S. thermophilus KLDS SM and are of important significance to exploiting it as a starter culture.
The purpose of this study was to gain genomic insights into the proteolysis system and amino acid biosynthesis in Streptococcus thermophilus KLDS SM. Firstly, whole genome sequencing was performed using combination of Illumina Hiseq 2500 sequencing and Pacific Biosciences RSII sequencing and the circular genomic map was constructed; subsequently, in silico bioinformatics analysis was carried out with respect to extracellular proteinase, peptide transport system, intracellular peptidase and amino acid biosynthesis; finally, comparative genomics of amino acid biosynthesis between strain KLDS SM and 14 other S. thermophilus strains, all of which have had the whole genome sequenced, was performed. The results showed that the genome of S. thermophilus KLDS SM consisted of a circular chromosome(1 856 787 bp) with GC content of 39.08%. A total of 1 732 protein-encoding genes were predicted. S. thermophilus KLDS SM had a complete proteolytic system and could biosynthesize eight amino acids. Furthermore, comparative genomics analysis showed that the amino acid biosynthesis abilities of 15 strains were relatively conservative except for a large difference in histidine biosynthesis among different strains. The results of this study can provide a theoretical basis for better understanding of nitrogen metabolism in S. thermophilus KLDS SM and are of important significance to exploiting it as a starter culture.
引文
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[2]DE VUYST L,WECKX S,RAVYTS F E D E,et al.New insights into the exopolysaccharide production of Streptococcus thermophilus[J].International Dairy Journal,2011,21(9):586-591.DOI:10.1016/j.idairyj.2011.03.016.
[3]GALIA W,PERRIN C,GENAY M,et al.Variability and molecular typing of Streptococcus thermophilus strains displaying different proteolytic and acidifying properties[J].International Dairy Journal,2009,19(2):89-95.DOI:10.1016/j.idairyj.2008.08.004.
[4]ZOTTA T,RICCIARDI A,CIOCIA F,et al.Diversity of stress responses in dairy thermophilic streptococci[J].International Journal of Food Microbiology,2008,124(1):34-42.DOI:10.1016/j.ijfoodmicro.2008.02.024.
[5]HOLS P,HANCY F E D E,FONTAINE L,et al.New insights in the molecular biology and physiology of Streptococcus thermophilusrevealed by comparative genomics[J].FEMS Microbiology Reviews,2005,29(3):435-463.DOI:10.1016/j.femsre.2005.04.008.
[6]LI W,BIAN X,EVIVIE S E,et al.Comparative analysis of clustered regularly interspaced short palindromic repeats(CRISPR)of Streptococcus thermophilus St-I and its bacteriophage-insensitive mutants(BIM)derivatives[J].Current Microbiology,2016,73(3):393-400.DOI:10.1007/s00284-016-1076-y.
[7]COUVIGNY B,THéRIAL C,GAUTIER C,et al.Streptococcus thermophilus biofilm formation:a remnant trait of ancestral commensal life?[J].PLo S ONE,2015,10(6):e128099.DOI:10.1371/journal.pone.0128099.
[8]白风翎,张柏林,赵宏飞.乳酸菌蛋白代谢研究进展[J].食品科学,2010,31(19):381-384.
[9]郑华军.保加利亚乳酸杆菌工业生产菌株2038的基因组学分析[D].上海:复旦大学,2010.
[10]MAKAROVA K,SLESAREV A,WOLF Y,et al.Comparative genomics of the lactic acid bacteria[J].Proceedings of the National Academy of Sciences of the United States of America,2007,189(4):1199-1208.DOI:10.1073/pnas.0607117103.
[11]SUN Z,CHEN X,WANG J,et al.Complete genome sequence of Streptococcus thermophilus strain ND03[J].Journal of Bacteriology,2011,193(3):793.DOI:10.1128/JB.01374-10.
[12]KANG X,LING N,SUN G,et al.Complete genome sequence of Streptococcus thermophilus Strain MN-ZLW-002[J].Journal of Bacteriology,2012,194(16):4428-4429.DOI:10.1128/JB.00740-12.
[13]WU Q,TUN H M,LEUNG C C,et al.Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275[J].Scientific Reports,2014,4(7500):4974.DOI:10.1038/srep04974.
[14]SHI Y,CHEN Y,LI Z,et al.Complete genome sequence of Streptococcus thermophilus MN-BM-A02,a rare strain with a high acid-producing rate and low post-acidification ability[J].Genome Announcements,2015,3(5):2090-2094.DOI:10.1128/genome A.00979-15.
[15]LABRIE S J,TREMBLAY D M,PLANTE P L,et al.Complete genome sequence of Streptococcus thermophilus SMQ-301,a model strain for phage-host interactions[J].Genome Announcements,2015,3(3):1-2.DOI:10.1128/genome A.00480-15.
[16]BAI Y,SUNA E,SHI Y,et al.Complete genome sequence of Streptococcus thermophilus MN-BM-A01,a strain with high exopolysaccharides production[J].Journal of Biotechnology,2016,224:45-46.DOI:10.1016/j.jbiotec.2016.03.003.
[17]DELORME C,BARTHOLINI C,LURASCHI M,et al.Complete genome sequence of the pigmented Streptococcus thermophilusstrain JIM8232[J].Journal of Bacteriology,2011,193(19):5581.DOI:10.1128/JB.05404-11.
[18]EVIVIE S E,LI B,DING X,et al.Complete genome sequence of Streptococcus thermophilus KLDS 3.1003,a strain with high antimicrobial potential against foodborne and vaginal pathogens[J].Frontiers in Microbiology,2017,8:1-4.DOI:10.3389/fmicb.2017.01238.
[19]CHIN C,ALEXANDER D H,MARKS P,et al.Nonhybrid,finished microbial genome assemblies from long-read SMRT sequencing data[J].Nature Methods,2013,10(6):563-569.DOI:10.1038/nmeth.2474.
[20]LI R,LI Y,FANG X,et al.SNP detection for massively parallel whole-genome resequencing[J].Genome Research,2009,19(6):1124-1132.DOI:10.1101/gr.088013.108.
[21]LI S,LI R,LI H,et al.SOAPindel:efficient identification of indels from short paired reads[J].Genome Research,2013,23(1):195-200.DOI:10.1101/gr.132480.111.
[22]TATUSOVA T,DICUCCIO M,BADRETDIN A,et al.NCBI prokaryotic genome annotation pipeline[J].Nucleic Acids Research,2016,44(14):6614-6624.DOI:10.1093/nar/gkw569.
[23]AZIZ R K,BARTELS D,BEST A A,et al.The RAST Server:rapid annotations using subsystems technology[J].BMC Genomics,2008,9(1):75.DOI:10.1186/1471-2164-9-75.
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[28]APWEILER R,BAIROCH A,WU C H,et al.Uni Prot:the universal protein knowledge base[J].Nucleic Acids Research,2004,32(Suppl 1):D115-D119.DOI:10.1093/nar/gkh131.
[29]刘文俊.嗜热链球菌和保加利亚乳杆菌产酸,风味特性及其功能基因分型和表达研究[D].呼和浩特:内蒙古农业大学,2014.
[30]张文羿,孟和,张和平.乳酸菌基因组学研究进展[J].微生物学报,2008,48(9):1270-1275.DOI:10.3321/j.issn:0001-6209.2008.09.023.
[31]PASTINK M I,TEUSINK B,HOLS P,et al.Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria[J].Applied and Environmental Microbiology,2009,75(11):3627-3633.DOI:10.1128/AEM.00138-09.
[32]FLAHAUT N A,WIERSMA A,VAN DE BUNT B,et al.Genome-scale metabolic model for Lactococcus lactis MG1363and its application to the analysis of flavor formation[J].Applied Microbiology and Biotechnology,2013,97(19):8729-8739.DOI:10.1007/s00253-013-5140-2.
[33]VENDRAMIN V,TREU L,CAMPANARO S,et al.Genome comparison and physiological characterization of eight Streptococcus thermophilus strains isolated from Italian dairy products[J].Food Microbiology,2017,63:47-57.DOI:10.1016/j.fm.2016.11.002.
[34]GOH Y J,GOIN C,O’FLAHERTY S,et al.Specialized adaptation of a lactic acid bacterium to the milk environment:the comparative genomics of Streptococcus thermophilus LMD-9[J].Microbial Cell Factories,2011,10(1):S22.DOI:10.1186/1475-2859-10-S1-S22.