(3.238.173.209) 您好!臺灣時間:2021/05/17 12:25
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果

詳目顯示:::

我願授權國圖
: 
twitterline
研究生:林乃頌
研究生(外文):Nai-Sung Lin
論文名稱:Thermoanaerobacteriumsp.NTOU2之局部基因體序列解析與註解
論文名稱(外文):Analysis and annotation of the partial genome sequence of Thermoanaerobacterium sp. NTOU2
指導教授:鄒文雄
指導教授(外文):Wen-Shyong Tzou
學位類別:碩士
校院名稱:國立臺灣海洋大學
系所名稱:生物科技研究所
學門:生命科學學門
學類:生物科技學類
論文種類:學術論文
論文出版年:2008
畢業學年度:96
語文別:中文
論文頁數:51
中文關鍵詞:異營嗜高溫菌NTOU2龜山島海底熱泉
外文關鍵詞:Thermoanaerobacterium sp. NTOU2hydrothermal vent of Gueishan Island
相關次數:
  • 被引用被引用:7
  • 點閱點閱:256
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
Thermoanaerobacterium sp. NTOU2為龜山島海底熱泉中一株異營嗜高溫菌,革蘭氏染色上判斷為陰性,形狀為桿狀。根據pyrosequencing,在T. sp. NTOU2確認了625 contigs中的2,783,744個鹼基,共有2,707 Glimmer預測之open reading frame (ORF) ,其中1,851 (68.4 %) ORF發現與其他物種的有功能註解的蛋白質序列相似,856 (31.6 %) ORF沒有功能註解。與目前已完整解序的物種序列比對,T. sp. NTOU2蛋白質序列與Thermoanaerobacter sp. X514 (一球狀革蘭氏陽性異營嗜高溫菌) 最相似。跨物種(T. sp. NTOU2、 Thermoanaerobacter tengcongensis與Thermoanaerobacter pseudethanolicus ATCC33223) ORF蛋白質序列及代謝途經交叉分析顯示T. sp. NTOU2具有一些較獨特的碳水化合物代謝相關基因如beta-xylosidase、alpha-L-arabinofuranosidase, 2-keto-3-deoxy-6-phosphogluconate aldolase、altronate dehydratase、alpha-glucuronidase。此研究也發現T. sp. NTOU2具有完整的glycolysis、pentose phosphate pathway酵素基因與amino acid biosynthesis、purine metabolism、pyrimidine metabolism pathway相關的大部分酵素基因。
Thermoanaerobacterium sp. NTOU2 is a rod-shape, gram negative, anaerobic bacterium was enriched and isolated from the hydrothermal vent of Gueishan Island at Taiwan. Total 625 contigs (2,783,744 base pairs) were assembled by the pyrosequencing method. Through Glimmer method, total predicted 2,707 open reading frames (ORFs) were predicted. Among them, 1,851 (68.4 %) with functional annotation, but the remains 856 (31.6 %) ORF were not. Among all the known published complete sequenced species genome, ORF protein sequences of T. sp. NTOU2 are most related to Thermoanaerobacter sp. X514, a ball-shaped, gram-positive anaerobic bacterium. Carbohydrate metabolism-related enzymes which include beta-xylosidase, alpha-L-arabinofuranosidase, 2-keto-3-deoxy-6-phosphogluconate aldolase, altronate dehydratase, alpha-glucuronidase are found unique to T. sp. NTOU2 based on the cross-species analysis on the ORFs of T. sp. NTOU2, Thermoanaerobacter tengcongensis and Thermoanaerobacter pseudethanolicus ATCC33223. We also discovered that T. sp. NTOU2 encodes enzymes responsible for complete pathway of glycolysis, pentose phosphate and most of the pathway related to the amino acid biosynthesis, purine metabolism and pyrimidine metabolism.
目次
中文摘要 5
Abstract 6
一. 前言 7
二. 研究方法 11
(一) 工具介紹(BLAST, GLIMMER, perl, FreeBSD) 11
(二) BLASTX Open reading frame (ORF) 預測與註解 12
(三) GLIMMER Open reading frame (ORF) 預測與註解 12
(四) T. sp. NTOU2, T. tengcongensis,T. pseudethanolicus ATCC33223 ORF序列比較 13
(五) 熱適應探討 14
三. 結果 15
(一) T. sp. NTOU2 contigs長度分佈 15
(二) BLASTX Open reading frame (ORF) 預測與註解 15
(三) GLIMMER Open reading frame (ORF) 預測與註解 15
(四) T. sp. NTOU2、T. tengcongensis、T. pseudethanolicus ATCC33223物種ORF序列比較 23
(五) 熱適應探討 25
四. 討論 27
(一) BLASTX與GLIMMER預測ORF位置比較 27
(二) T. sp. NTOU2之基因註解 28
(三) 熱適應探討 30
五. 結論 33
六. 未來方向 34
表一. 物種生長溫度(℃)表 35
表二. T. sp. NTOU2, T. tengcongensis, T. pseudethanolicus ATCC33223 COGs功能分布(percent of category number) 36
表三. T. sp. NTOU2, T. tengcongensis, T. sp. X514, T. pseudethanolicus ATCC33223基因體序列資訊 37
圖二. T. sp. NTOU2 pentose phosphate pathway 39
圖三. T. sp. NTOU2 pyruvate metabolism 40
圖五. T. sp. NTOU2、T. tengcongensis、T. pseudethanolicus ATCC33223 ORF比對結果 41
圖六. T. sp. NTOU2、T. tengcongensis、T. pseudethanolicus ATCC33223 ORF比較之COGs carbohydrate metabolism 分類比例 42
圖七. 胺基酸組成與生長溫度相關性 43
圖八. BLASTX 與 GLIMMER預測位置比較 44
參考文獻 47
參考文獻
Altschul, S. F., W. Gish, et al. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-10.

Bao, Q., Y. Tian, et al. (2002). "A complete sequence of the T. tengcongensis ge-nome." Genome Res 12(5): 689-700.

Bronnenmeier, K., H. Meissner, et al. (1995). "alpha-D-glucuronidases from the xy-lanolytic thermophiles Clostridium stercorarium and Thermoanaerobacterium sac-charolyticum." Microbiology 141 ( Pt 9): 2033-40.

Burma, D. P. and B. L. Horecker (1958). "Pentose fermentation by Lactobacillus plantarum. III. Ribulokinase." J Biol Chem 231(2): 1039-51.

Cohen, S. (1953). "Studies on D-ribulose and its enzymatic conversion to D-arabinose." J Biol Chem 201(1): 71-84.

Conesa, A., S. Gotz, et al. (2005). "Blast2GO: a universal tool for annotation, visuali-zation and analysis in functional genomics research." Bioinformatics 21(18): 3674-6.

Conway, T., G. W. Sewell, et al. (1987). "Cloning and sequencing of the alcohol de-hydrogenase II gene from Zymomonas mobilis." J Bacteriol 169(6): 2591-7.

Cyr, D. M., T. Langer, et al. (1994). "DnaJ-like proteins: molecular chaperones and specific regulators of Hsp70." Trends Biochem Sci 19(4): 176-81.

Delcher, A. L., K. A. Bratke, et al. (2007). "Identifying bacterial genes and endosym-biont DNA with Glimmer." Bioinformatics 23(6): 673-9.

Francke, C., R. J. Siezen, et al. (2005). "Reconstructing the metabolic network of a bacterium from its genome." Trends Microbiol 13(11): 550-8.

Gilead, S. and Y. Shoham (1995). "Purification and characterization of al-pha-L-arabinofuranosidase from Bacillus stearothermophilus T-6." Appl Environ Mi-crobiol 61(1): 170-4.

Greaves, R. B. and J. Warwicker (2007). "Mechanisms for stabilisation and the main-tenance of solubility in proteins from thermophiles." BMC Struct Biol 7: 18.

Haney, P. J., J. H. Badger, et al. (1999). "Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species." Proc Natl Acad Sci U S A 96(7): 3578-83.

Hemmingsen, S. M., C. Woolford, et al. (1988). "Homologous plant and bacterial proteins chaperone oligomeric protein assembly." Nature 333(6171): 330-4.

Hickman, J. and G. Ashwell (1958). "Purification and properties of D-xylulokinase in liver." J Biol Chem 232(2): 737-48.

Hirata, H., T. Fukazawa, et al. (1986). "Structure of a beta-galactosidase gene of Ba-cillus stearothermophilus." J Bacteriol 166(3): 722-7.

Hochster, R. M. and R. W. Watson (1954). "Enzymatic isomerization of D-xylose to D-xylulose." Arch Biochem Biophys 48(1): 120-9.

Jornvall, H., B. Persson, et al. (1987). "Characteristics of alcohol/polyol dehydro-genases. The zinc-containing long-chain alcohol dehydrogenases." Eur J Biochem 167(2): 195-201.

Kanehisa, M. and S. Goto (2000). "KEGG: kyoto encyclopedia of genes and ge-nomes." Nucleic Acids Res 28(1): 27-30.

Kiryu, T., H. Nakano, et al. (2005). "Purification and characterization of a novel al-pha-glucuronidase from Aspergillus niger specific for O-alpha-D-glucosyluronic acid alpha-D-glucosiduronic acid." Biosci Biotechnol Biochem 69(3): 522-9.

Koga, J., T. Adachi, et al. (1991). "Molecular cloning of the gene for indolepyruvate decarboxylase from Enterobacter cloacae." Mol Gen Genet 226(1-2): 10-6.

Kramer, G., H. Patzelt, et al. (2004). "Trigger factor peptidyl-prolyl cis/trans isom-erase activity is not essential for the folding of cytosolic proteins in Escherichia coli." J Biol Chem 279(14): 14165-70.

Lee, D. Y., K. A. Kim, et al. (2004). "Substitution of aspartic acid with glutamic acid increases the unfolding transition temperature of a protein." Biochem Biophys Res Commun 320(3): 900-6.

Levy-Rimler, G., R. E. Bell, et al. (2002). "Type I chaperonins: not all are created equal." FEBS Lett 529(1): 1-5.

Liu, J., C. Huang, et al. (2005). "Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization." J Mol Biol 350(5): 987-96.

Meadow, N. D., D. K. Fox, et al. (1990). "The bacterial phosphoenolpyruvate: glycose phosphotransferase system." Annu Rev Biochem 59: 497-542.

Meloche, H. P. and W. A. Wood (1964). "Crystallization and Characteristics of 2-Keto-3-Deoxy-6-Phosphogluconic Aldolase." J Biol Chem 239: 3515-8.

Musto, H., H. Naya, et al. (2004). "Correlations between genomic GC levels and op-timal growth temperatures in prokaryotes." FEBS Lett 573(1-3): 73-7.

Natsumeda, Y., S. Ohno, et al. (1990). "Two distinct cDNAs for human IMP dehy-drogenase." J Biol Chem 265(9): 5292-5.

Nnyepi, M. R., Y. Peng, et al. (2007). "Inactivation of E. coli pyruvate formate-lyase: role of AdhE and small molecules." Arch Biochem Biophys 459(1): 1-9.

Onyenwoke, R. U., V. V. Kevbrin, et al. (2007). "Thermoanaerobacter pseudethano-licus sp. nov., a thermophilic heterotrophic anaerobe from Yellowstone National Park." Int J Syst Evol Microbiol 57(Pt 10): 2191-3.

Postma, P. W., J. W. Lengeler, et al. (1993). "Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria." Microbiol Rev 57(3): 543-94.

Prasad, T. K. and C. R. Stewart (1992). "cDNA clones encoding Arabidopsis thaliana and Zea mays mitochondrial chaperonin HSP60 and gene expression during seed germination and heat shock." Plant Mol Biol 18(5): 873-85.

Quevillon, E., V. Silventoinen, et al. (2005). "InterProScan: protein domains identi-fier." Nucleic Acids Res 33(Web Server issue): W116-20.

Roh, Y., S. V. Liu, et al. (2002). "Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado." Appl Environ Microbiol 68(12): 6013-20.

Russell, R. J., J. M. Ferguson, et al. (1997). "The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution." Bio-chemistry 36(33): 9983-94.

Saier, M. H., Jr. and J. Reizer (1992). "Proposed uniform nomenclature for the pro-teins and protein domains of the bacterial phosphoenolpyruvate: sugar phosphotrans-ferase system." J Bacteriol 174(5): 1433-8.

Saurin, W., M. Hofnung, et al. (1999). "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters." J Mol Evol 48(1): 22-41.

Shao, W. and J. Wiegel (1992). "Purification and characterization of a thermostable beta-xylosidase from Thermoanaerobacter ethanolicus." J Bacteriol 174(18): 5848-53.

Smiley, J. D. and G. Ashwell (1960). "Uronic acid metabolism in bacteria. III. Purifi-cation and properties of D-altronic acid and D-mannonic acid dehydrases in Es-cherichia coli." J Biol Chem 235: 1571-5.

Stephens, C. M. and R. Bauerle (1991). "Analysis of the metal requirement of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli." J Biol Chem 266(31): 20810-7.

Szurmant, H. and G. W. Ordal (2004). "Diversity in chemotaxis mechanisms among the bacteria and archaea." Microbiol Mol Biol Rev 68(2): 301-19.

Tatusov, R. L., E. V. Koonin, et al. (1997). "A genomic perspective on protein fami-lies." Science 278(5338): 631-7.

Tomazic, S. J. and A. M. Klibanov (1988). "Mechanisms of irreversible thermal inac-tivation of Bacillus alpha-amylases." J Biol Chem 263(7): 3086-91.

Vasiliou, V., A. Pappa, et al. (2000). "Role of aldehyde dehydrogenases in endogenous and xenobiotic metabolism." Chem Biol Interact 129(1-2): 1-19.

Vuralhan, Z., M. A. Morais, et al. (2003). "Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae." Appl Environ Microbiol 69(8): 4534-41.

Walker, G. E., B. Dunbar, et al. (1996). "Evidence for a novel class of microbial 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase in Streptomyces coelicolor A3(2), Streptomyces rimosus and Neurospora crassa." Microbiology 142 ( Pt 8): 1973-82.

Wang, H. C., E. Susko, et al. (2006). "On the correlation between genomic G+C con-tent and optimal growth temperature in prokaryotes: data quality and confounding factors." Biochem Biophys Res Commun 342(3): 681-4.

Williamson, V. M. and C. E. Paquin (1987). "Homology of Saccharomyces cerevisiae ADH4 to an iron-activated alcohol dehydrogenase from Zymomonas mobilis." Mol Gen Genet 209(2): 374-81.

Xue, Y., Y. Xu, et al. (2001). "Thermoanaerobacter tengcongensis sp. nov., a novel anaerobic, saccharolytic, thermophilic bacterium isolated from a hot spring in Teng-cong, China." Int J Syst Evol Microbiol 51(Pt 4): 1335-41.

Zeldovich, K. B., I. N. Berezovsky, et al. (2007). "Protein and DNA sequence deter-minants of thermophilic adaptation." PLoS Comput Biol 3(1): e5.

李世強 (2007) 龜山島海底熱泉分離之一株厭氧式高溫醣類分解菌之型態與特性分析。碩士論文。1-55頁。
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
無相關期刊