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瘤胃细菌GH48家族糖苷水解酶基因多样性 被引量:5

Gene diversity of the bacterial 48 family glycoside hydrolase (GH48) in rumen environment
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摘要 【目的】了解瘤胃细菌第48家族糖苷水解酶基因(GH48)多样性,为木质纤维素高效降解提供新的基因资源。【方法】通过基因序列比对,设计gh48的简并引物;同时提取两个瘤胃样品的总DNA和总RNA,并将总RNA逆转录成cDNA。以总DNA和cDNA为模板,通过PCR扩增分别建立克隆文库并对克隆文库进行测序;对所得序列进行out种类划分和聚类分析。【结果】本研究共得到了455条编码GH48家族蛋白的基因序列,核苷酸序列之间的相似性为58.65%-100%。对序列的进一步分析表明,89%可以作为区分其种类的界定标准。以此为依据确定所得到的基因序列分别编码66种不同的GH48家族蛋白,分别聚为5个相对独立的类群,其中新类群C中OTU65所代表的序列是cDNA克隆文库中的优势序列,分别占两个cDNA克隆文库的36.4%和19.5%。我们的结果揭示瘤胃细菌gh48基因具有丰富的多样性,同时,其中也存在优势表达的GH48家族蛋白。 [Objective]The gene diversity of the bacterial 48 family glycoside hydrolase(GH48) in rumen environment was studied and new gene resources for efficient cellulose degradation were provided.[Methods]A pair of gh48 degenerate primers was designed through sequences alignment of the gh48 gene sequences from ruminal Ruminococcus.The total DNA and RNA were extracted from two rumen samples and cDNA was synthetized through reverse transcription from total RNA. Four gh48 gene clone libraries were constructed and analyzed.[Results]In total 455 gh48 gene sequences were obtained from the 4clone libraries. Sequence similarity among the 455 gene sequences varies between 58.65% and 100%.They fell into 66 species with the sequence similarity ≥89%,and divided into 5 different clusters.OTU65 in cluster Crepresents an abundant gh48 gene which in both DNA and cDNA clones libraries,accounting for 36.4% and 19.5% respectively.Our studyrevealsrich gene diversity of the 48 family glycoside hydrolase and provided new gene resources for cellulose degradation.
出处 《微生物学报》 CAS CSCD 北大核心 2014年第1期53-61,共9页 Acta Microbiologica Sinica
基金 国家"863计划"(2011CB100804)~~
关键词 瘤胃细菌 木质纤维素降解 GH48 糖苷水解酶 多样性 rumen bacteria lignocellulose degradation 48 family glycoside hydrolase gene diversity
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  • 1Olson DG, Tripathi SA, Giannone RJ, Lo J, Caiazza NC, Hogsett DA, Hettich RL, Guss AM, Dubrovsky G, Lynd LR. Deletion of the Ce148S cellulase from Clostridium thermocellum. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(41) : 17727-17732.
  • 2Steenbakkers PJ, Freelove A, Van Cranenbroek B, Sweegers BM, Harhangi HR, Vogels GD, Hazlewood GP, Gilbert H J, Op den Camp HJ. The major component of the cellulosomes of anaerobic fungi from the genus Piromyces is a family 48 glycoside hydrolase. DNA sequence: the Journal of DNA Sequencing and Mapping, 2002, 13(6) : 313-320.
  • 3Devillard E, Goodheart DB, Karnati SK, Bayer EA, Lamed R, Miron J, Nelson KE, Morrison M. Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Ce148A and CeI9B, both of which possess a novel modular architecture. Journal of Bacteriology, 2004, 186 ( 1 ) : 1 '~6-145_.
  • 4Sukharnikov LO, Alahuhta M, Brunecky R, Upadhyay A, Himmel ME, Lunin VV, Zhulin IB. Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. The Journal of Biological Chemistry, 2012, 287(49): 41068-41077.
  • 5Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(6): 1948-1953.
  • 6Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM. Metagenomic discovery of biomass- degrading genes and genomes from cow rumen. Science, 2011, 331(6016) : 463-467.
  • 7Dai X, Zhu Y, Luo Y, Song L, Liu D, Liu L, Chen F, WangM, Li J, Zeng X, Dong Z, Hu S, Li L, Xu J, Huang L, Dong X. Metagenomic insights into thefibrolytic microbiome in yak rumen. PLoS One, 2012, 7 (7) : e40430.
  • 8Qi M, Wang P, O'Toole N, Barboza PS, Ungerfe|d E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach. PLoS One, 2011, 6(5): e20521.
  • 9Lin C, Raskin L, Stahl DA. Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA~targeted oligonucleotide probes. FEMS Microbiology Ecology, 1997, 22(4) : 281- 294.
  • 10Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_ X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 1997, 25(24) : 4876-4882.

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  • 1谭婉新,刘利,胡亚林,段承杰,唐纪良,冯家勋.一个新的内切葡聚糖酶基因umcel5K的克隆、表达及其表达产物的酶学特性[J].广西农业生物科学,2008,27(1):7-13. 被引量:6
  • 2祁茹,温建新,程明,汪文鑫,肖宇,褚永康,林英庭.不同外源寡糖对崂山奶山羊瘤胃微生物区系的影响[J].动物营养学报,2012,24(2):349-357. 被引量:21
  • 3高山,欧剑虹,肖凯.R语言与Bioconductor生物信息学应用[M].天津:天津科技翻译出版公司,2014:158-18.
  • 4BUDDLE B M, DENIS M, ATTWOOD G T, et al. Strategies to reduce methane emissions from farmed ruminants grazing on pasture [ J ]. The Veterinary Journal,2011,188( 1 ) : 11-17.
  • 5NAGALAKSHMI U, WANG Z, WAERN K, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing [ J ]. Science, 2008,320 ( 5881 ) : 1344-1349.
  • 6WILHELM B T, MARGUERAT S, WATT S, et al.Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution [ J ]. Nature, 2008,453(7199) : 1239-1243.
  • 7CARVALHAIS L C, DENNIS P G, TYSON G W, et al. Application of metatranscriptomics to soil envi- ronments [ J ]. Journal of Microbiological Methods, 2012,91(2) :246-251.
  • 8LU T T, LUG J, FAN D L, et al. Function annota- tion of rice transcriptome at single nucleotide resolu- tion by RNA-Seq [ J ]. Genome Research, 2010,20 (9) : 1238-1249.
  • 9DAVID L A, MAURICE C F, CARMODY R N, et al. Diet rapidly and reproducibly alters the human gut microbiome[J]. Nature, 2013,505 ( 7484 ) : 559 - 563.
  • 10ROSENTHAL A Z, MATSON E G, ELDAR A, et al. RNA-Seq reveals cooperative metabolic interac- tions between two termite-gut spirochete species in co-culture[J]. The ISME Journal, 2011, 5 ( 7 ) : 1133-1142.

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