长双歧杆菌XY01的基因组学和蛋白质组学分析
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摘要
目的探究长双歧杆菌XY01(B. longum XY01)的基因组和蛋白质组特点。方法基于基因组学和蛋白质组学测序,比较分析B. longum XY01与常规菌株B. longum NCC2705的碳水化合物代谢特点。通过液相色谱-串联质谱联用技术鉴定该菌株的蛋白质图谱。结果与结论与B. longum NCC2705相比,B. longum XY01的基因组更大,含有一个2 480 603 bp的环状染色体,并含有381个特异编码序列,其中5个与岩藻糖代谢相关,即岩藻糖酸脱水酶(GS08_09530和GS08_01695)、岩藻糖异构酶(GS08_01710)、α-L-岩藻糖苷酶(GS08_01715)和L-岩藻糖通透酶(GS08_09520)。利用液相色谱-串联质谱联用技术鉴定出B. longum XY01菌株含有1365种蛋白(占预测蛋白组的71. 8%),确定了B. longum XY01的bifid shunt过程和糖酵解通路相关的酶。
Objective To explore the genomic and proteomic characteristics of Bifidobacterium longum XY01( B. longum XY01). Methods Genomics and proteomic sequencing were applied to compare the carbohydrate metabolism characteristics of B. longum XY01 and normal B. longum NCC2705. Moreover,liquid chromatography coupled with tandem mass spectrometry( LC-MS/MS) was used to draw the protein profiles. Results and Conclusion Compared with B. longum NCC2705,B. longum XY01 was found to have a larger circular chromosome of 2 480 603 bp and 381 specific protein coding sequences,five of which were related to fucose metabolism. They are fucose dehydrase( GS08 _09530 and GS08_01695),fucose isomerase( GS08_01710),α-L-fucosidase( GS08_01715) and L-fucose permease( GS08_09520).Meanwhile,1365 proteins( 71. 8% of the predicted protein group) and the enzymes related to the bifid shunt process and glycolysis pathway of B. longum XY01 have been identified by LC-MS/MS.
Objective To explore the genomic and proteomic characteristics of Bifidobacterium longum XY01( B. longum XY01). Methods Genomics and proteomic sequencing were applied to compare the carbohydrate metabolism characteristics of B. longum XY01 and normal B. longum NCC2705. Moreover,liquid chromatography coupled with tandem mass spectrometry( LC-MS/MS) was used to draw the protein profiles. Results and Conclusion Compared with B. longum NCC2705,B. longum XY01 was found to have a larger circular chromosome of 2 480 603 bp and 381 specific protein coding sequences,five of which were related to fucose metabolism. They are fucose dehydrase( GS08 _09530 and GS08_01695),fucose isomerase( GS08_01710),α-L-fucosidase( GS08_01715) and L-fucose permease( GS08_09520).Meanwhile,1365 proteins( 71. 8% of the predicted protein group) and the enzymes related to the bifid shunt process and glycolysis pathway of B. longum XY01 have been identified by LC-MS/MS.
引文
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[3]Bottacini F,Ventura M,van Sinderen D,et al.Diversity,ecology and intestinal function of bifidobacteria[J].Microb Cell Fact,2014,13(Suppl 1):S4.
[4]Schell MA,Karmirantzou M,Snel B,et al.The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract[J].Proc Natl Acad Sci USA,2002,99(22):14422-14427.
[5]Lin MY,Chang FJ.Antioxidative effect of intestinal bacteria Bifidobacterium longum ATCC 15708 and Lactobacillus acidophilus ATCC 4356[J].Dig Dis Sci,2000,45(8):1617-1622.
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[7]Yuan J,Zhu L,Liu X,et al.A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705[J].Mol Cell Proteomics,2006,5(6):1105-1118.
[8]Rakoff-Nahoum S,Paglino J,Eslami-Varzaneh F,et al.Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis[J].Cell,2004,118(2):229-241.
[9]Stappenbeck TS,Hooper LV,Gordon JI.Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells[J].Proc Natl Acad Sci USA,2002,99(24):15451-15455.
[10]Benesova E,Lipovova P,Dvorakova H,et al.α-L-fucosidase from Paenibacillus thiaminolyticus:its hydrolytic and transglycosylation abilities[J].Glycobiology,2013,23(9):1052-1065.
[11]Osanjo G,Dion M,Drone J,et al.Directed evolution of the alphaL-fucosidase from Thermotoga maritima into an alpha-L-transfucosidase[J].Biochemistry,2007,46(4):1022-1033.
[12]Moriwaki K,Miyoshi E.Fucosylation and gastrointestinal cancer[J].World J Hepatol,2010,2(4):151-161.
[13]Hyatt D,Chen GL,Locascio PF,et al.Prodigal:prokaryotic gene recognition and translation initiation site identification[J].BMCBioinformatics,2010,11:119.
[14]Mount DW.Using the basic local alignment search tool(BLAST)[J].CSH Protoc,2007,2007:p17.
[15]Rutherford K,Parkhill J,Crook J,et al.Artemis:sequence visualization and annotation[J].Bioinformatics,2000,16(10):944-945.
[16]Haft DH,Selengut JD,White O.The TIGRFAMs database of protein families[J].Nucleic Acids Res,2003,31(1):371-373.
[17]Finn RD,Mistry J,Tate J,et al.The Pfam protein families database[J].Nucleic Acids Res,2010,38(Database issue):D211-D222.
[18]Kanehisa M,Araki M,Goto S,et al.KEGG for linking genomes to life and the environment[J].Nucleic Acids Res.2008,36(Database issue):D480-D484.
[19]Tatusov RL,Galperin MY,Natale DA,et al.The COG database:a tool for genome-scale analysis of protein functions and evolution[J].Nucleic Acids Res,2000,28(1):33-36.
[20]Preising J,Philippe D,Gleinser M,et al.Selection of bifidobacteria based on adhesion and anti-inflammatory capacity in vitro for amelioration of murine colitis[J].Appl Environ Microbiol,2010,76(9):3048-3051.
[21]Gao F,Zhang CT.GC-Profile:a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences[J].Nucleic Acids Res,2006,34(Web Server issue):W686-W691.
[22]Abbott JC,Aanensen DM,Bentley SD.Web ACT:an online genome comparison suite[J].Methods Mol Biol,2007,395:57-74.
[23]Albrethsen J,Knol JC,Piersma SR,et al.Subnuclear proteomics in colorectal cancer:identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression[J].Mol Cell Proteomics,2010,9(5):988-1005.
[24]Altschul SF,Madden TL,Schaffer AA,et al.Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J].Nucleic Acids Res,1997,25(17):3389-3402.
[25]Yu NY,Wagner JR,Laird MR,et al.PSORTb 3.0:improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes[J].Bioinformatics,2010,26(13):1608-1615.
[26]Petersen TN,Brunak S,von Heijne G,et al.SignalP 4.0:discriminating signal peptides from transmembrane regions[J].Nat Methods,2011,8(10):785-786.
[27]Zhou M,Boekhorst J,Francke C,et al.LocateP:genome-scale subcellular-location predictor for bacterial proteins[J].BMCBioinformatics,2008,9:173.
[28]Pokusaeva K,Fitzgerald GF,van Sinderen D.Carbohydrate metabolism in bifidobacteria[J].Genes Nutr,2011,6(3):285-306.
[29]Turroni F,Bottacini F,Foroni E,et al.Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging[J].Proc Natl Acad Sci USA,2010,107(45):19514-19519.
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