耐久肠球菌C11菌株的环境胁迫耐受性及其低温适应相关基因的基因组学鉴定
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摘要
测定了耐久肠球菌C11菌株在不同环境胁迫条件下(温度、酸度、渗透压和人工胃肠液)的耐受性,并进行比较基因组学分析。结果显示,该菌株能够在15～25℃条件下生长,但是对酸(p H 2. 0～4. 0)、渗透压(质量分数为5. 0%～15. 0%的Na Cl、质量分数为0. 05%～0. 3%的胆盐),以及人工胃肠液均无显著耐受性;耐久肠球菌C11基因组含有33个菌株特异性基因,其中有26个编码功能未知的假设蛋白,7个编码功能蛋白。此外,还鉴定到大量与细胞膜不饱和脂肪酸合成、相容性溶质吸收或合成、环境应激调控等相关基因,可能与其低温适应性相关。
This study was constructed to dissect the tolerance of Enterococcus durans C11 to environmental stresses and possible molecular mechanisms of its ability to adapt low-temperature environment. Tolerance of E. durans C11 was determined under different temperatures,acidities,osmolality,and artificial gastrointestinal fluids,and comparative genomic analysis was also carried out. The results showed that E. durans C11 was able to grow at 15-25℃,but had no significant tolerances to acid( p H 2. 0-4. 0),osmotic pressure induced by 5. 0%-15. 0% NaCl and 0. 05%-0. 3% bile salt,as well as to artificial gastric and intestinal fluids. It was also revealed that E. durans C11 had 33 strain-specific genes,which encoded for 26 hypothetical proteins and 7 functional proteins. Moreover,a number of genes involved in synthesizing cell membrane unsaturated fatty acids,uptaking or synthesizing compatible solutes,and regulating environmental stresses were identified from E. durans C11 genome,which may be related to the low-temperature adaptation of the bacterium. This study provides some data supports for future study on low-temperature adaptation of E. durans.
This study was constructed to dissect the tolerance of Enterococcus durans C11 to environmental stresses and possible molecular mechanisms of its ability to adapt low-temperature environment. Tolerance of E. durans C11 was determined under different temperatures,acidities,osmolality,and artificial gastrointestinal fluids,and comparative genomic analysis was also carried out. The results showed that E. durans C11 was able to grow at 15-25℃,but had no significant tolerances to acid( p H 2. 0-4. 0),osmotic pressure induced by 5. 0%-15. 0% NaCl and 0. 05%-0. 3% bile salt,as well as to artificial gastric and intestinal fluids. It was also revealed that E. durans C11 had 33 strain-specific genes,which encoded for 26 hypothetical proteins and 7 functional proteins. Moreover,a number of genes involved in synthesizing cell membrane unsaturated fatty acids,uptaking or synthesizing compatible solutes,and regulating environmental stresses were identified from E. durans C11 genome,which may be related to the low-temperature adaptation of the bacterium. This study provides some data supports for future study on low-temperature adaptation of E. durans.
引文
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[2] LADERO V,LINARES D M,DEL R B,et al. Draft genome sequence of the tyramine producer Enterococcus durans strain IPLA 655[J]. Genome Announcements,2013,1(3):e00 265-13.
[3] AVRAMHANANEL,LIRAZ,JULIA,et al. E. durans strain M4-5 isolated from human colonic flora attenuates intestinal inflammation[J]. Diseases of the Colon and Rectum,2010,53(12):1 676-1 686.
[4] RAMAKRISHNAN V,GOVEAS L,CONCEPTA,et al. Kinetic modeling,production and characterization of an acidic lipase produced by Enterococcus durans NCIM5427 from fish waste[J]. Journal of Food Science and Technology,2015,52(3):1 328-1 338.
[5]黄坚,童京京,岳华,等.牦牛发酵酸奶中耐久肠球菌的筛选鉴定和益生特性[J].食品科学,2017,38(12):43-49.
[6] LIU Fei,LI Bailiang,DU Jincheng,et al. Complete genome sequence of Enterococcus durans KLDS6. 0930,a strain with probiotic properties[J]. Journal of Biotechnology,2016,217:49-50.
[7]隋馨瑶,王莹,张卫兵,等.低温乳酸菌的研究与应用现状[J].食品与发酵科技,2017,53(4):83-87.
[8] LI Ping,GU Qiang. Complete genome sequence of Lactobacillus plantarum LZ95,a potential probiotic strain producing bacteriocins and B-group vitamin riboflavin[J]. Journal of Biotechnology,2016,229:1-2.
[9] LI Junfeng,YUAN Xianjun,DESTA S T,et al. Characterization of Enterococcus faecalis JF85 and Enterococcus faecium Y83 isolated from Tibetan yak(Bos grunniens)for ensiling Pennisetum sinese[J]. Bioresource Technology,2018,257:76.
[10] XU Shuang,LIU Taigang,RADJI C A,et al. Isolation,identification,and evaluation of new lactic acid bacteria strains with both cellular antioxidant and bile salt hydrolase activities in vitro[J]. Journal of Food Protection,2016,79(11):1 919-1 928.
[11] ZHANG Bei,WANG Yanping,TAN Zhongfang,et al.Screening of probiotic activities of Lactobacilli strains isolated from traditional Tibetan Qula,a raw yak milk cheese[J]. Asian-Australasian Journal of Animal Sciences,2016,29(10):1 490-1 499.
[12] BROWN J,PIRRUNG M,MCCUE L A. FQC Dashboard.integrates Fast QC results into a web-based,interactive,and extensible FASTQ quality control tool[J]. Bioinformatics,2017,33(19):3 137-3 139.
[13] DELCHER A L,BRATKE K A,POWERS E C,et al. Identifying bacterial genes and endosymbiont DNA with Glimmer[J]. Bioinformatics,2007,23(6):673-679.
[14] LOWE T M,EDDY S R. tRNAscan-SE:a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Res,1997,25(5):955-964.
[15] LAGESEN K,HALLIN P,RODLAND E A,et al. RNAmmer:consistent and rapid annotation of ribosomal RNA genes[J]. Nucleic Acids Res,2007,35(9):3 100-3 108.
[16] GRISSA I,VERGNAUD G,POURCEL C. CRISPRFinder:a web tool to identify clustered regularly interspaced short palindromic repeats[J]. Nucleic Acids Research,2007,35:52-57.
[17] TATUSOVA T,DICUCCIO M,BADRETDIN A,et al. NCBI prokaryotic genome annotation pipeline[J]. Nucleic Acids Research,2016,44(14):6 614-6 624.
[18] MARCHLER-BAUER A,DERBYSHIRE M K,GONZALES N R,et al. CDD:NCBI's conserved domain database[J]. Nucleic Acids Research,2015,43:D222-226.
[19] PETERSEN T N,BRUNAK S,V HEIJNE G,et al. Signal P4. 0:discriminating signal peptides from transmembrane regions[J]. Nature Methods,2011,8(10):785-786.
[20] KROGH A,LARSSON B,VON H G,et al. Predicting transmembrane protein topology with a hidden Markov model:application to complete genomes[J]. Journal of Molecular Biology,2001,305(3):567-580.
[21] FU Limin,NIU Beifang,ZHU Zhengwei,et al. CD-HIT:accelerated for clustering the next-generation sequencing data[J]. Bioinformatics,2012,28(23):3 150-3 152.
[22] EDGAR R C. MUSCLE:multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Research,2004,32(5):1 792-1 797.
[23] GUINDON S,GASCUEL O. A simple,fast,and accurate algorithm to estimate large phylogenies by maximum likelihood[J]. Systematic Biology,2003,52(5):696.
[24] ZHANG Huangkai,GAO Shenghan,LERCHER M J,et al.Evol View,an online tool for visualizing,annotating and managing phylogenetic trees[J]. Nucleic Acids Research,2012,40:569-572.
[25] LI Bailiang,EVIVIE S E,JIN D,et al. Complete genome sequence of Enterococcus durans KLDS6. 0933,a potential probiotic strain with high cholesterol removal ability[J].Gut Pathogens,2018,10(1):32.
[26] WAN K H,YU C,PARK S,et al. Complete genome sequence of Enterococcus durans Oregon-R-modENCODE strain BDGP3,a lactic acid bacterium found in the Drosophila melanogaster gut[J]. Genome Announcements,2017,5(40):e01 041-01 017.
[27]祝进,白永凤,陆军,等.粪肠球菌毒力基因及耐药性分析[J].放射免疫学杂志,2012,25(3):276-279.
[28]辛玉华,周宇光,东秀珠.低温细菌与古菌的生物多样性及其冷适应机制[J].生物多样性,2013,21(4):468-480.
[29]余永红,马建荣,王海洪.细菌脂肪酸合成多样性的研究进展[J].微生物学杂志,2016,36(4):76-83.
[30] CASANUEVA A,TUFFIN M,CARY C,et al. Molecular adaptations to psychrophily:the impact of'omic'technologies[J]. Trends In Microbiology,2010,18(8):374-381.
[31] WELSH D T. Ecological significance of compatible solute accumulation by micro-organisms:from single cells to global climate[J]. FEMS Microbiology Reviews,2000,24(3):263-290.
[32] TAMARA H,ERHARD B. Protection of Bacillus subtilis against cold stress via compatible-solute acquisition[J].Journal of Bacteriology,2011,193(7):1 552-1 562.
[33] KREIL D P,OUZOUNIS C A. Identification of thermophilic species by the amino acid compositions deduced from their genomes[J]. Nucleic Acids Research,2001,29(7):1 608-1 615.
[34] KASANA R C,GULATI A. Cellulases from psychrophilic microorganisms:a review[J]. Journal of basic Microbiology,2011,51(6):572-579.
[35] PHADTARE S. Recent developments in bacterial coldshock response[J]. Current Issues in Molecular Biology,2004,6(2):125-136.
[36] CHATTOPADHYAY M K. Mechanism of bacterial adaptation to low temperature[J]. Journal of Biosciences(Bangalore),2006,31(1):157-165.
[37]刘芳明. 3株南极海洋石油烃低温降解菌(Shewanella sp. NJ49、Pseudoalteromonas sp. NJ289和Planococus sp.NJ41)基因组学及比较研究[D].青岛:中国科学院研究生院(海洋研究所),2016.
[38] KUHN E. Toward understanding life under subzero conditions:the significance of exploring psychrophilic"coldshock"proteins[J]. Astrobiology,2012,12(11):1 078-1 086.
[39] ZHU Chunhua,SUN Boyi,LIU Taigang,et al. Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins(Vpa Csp A and Vpa Csp D)in Vibrio parahaemolyticus CHN25 during low-temperature survival[J]. BMC Genomics,2017,18(1):436.
[40] BAKERMANS C,TOLLAKSEN S L,GIOMETTI C S,et al. Proteomic analysis of Psychrobacter cryohalolentis K5during growth at subzero temperatures[J]. Extremophiles:Life under Extreme Conditions,2007,11(2):343-354.