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研究生:江弈芯
研究生(外文):Yi Hsin Jiang
論文名稱:鑑定由副血鏈球菌FW213染色體重覆序列產生的小RNA
論文名稱(外文):Identification of a regulatory small RNA encoded from
指導教授:陳怡原
指導教授(外文):Y. Y. Chen
學位類別:碩士
校院名稱:長庚大學
系所名稱:生物醫學研究所
學門:生命科學學門
學類:生物化學學類
論文種類:學術論文
論文出版年:2014
畢業學年度:102
論文頁數:62
中文關鍵詞:副血鏈球菌小RNA基因調控北方墨漬法全面性調控子
外文關鍵詞:Streptococcus parasanguinis FW213small RNAintergenic regionsNorthern analysisglobal regulator
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指導教授推薦書…………………………………………………………i
口試委員會審定書……………………………………………………ii
誌謝………………………………………………………………………………iii
中文摘要………………………………………………………………………iv
ABSTRACT……………………………………………………………………v
TABLE OF CONTENENTS………………………………………vi
LIST OF TABLES……………………………………………………vii
LIST OF FIGURES…………………………………………………viii
INTRODUCTION…………………………………………………………-1-
MATERIALS AND METHODS…………………………………-10-
RESULTS………………………………………………………………………-16-
DISCUSSION………………………………………………………………-22-
TABLES…………………………………………………………………………-27-
FIGURES………………………………………………………………………-39-
REFERENCES…………………………………………………………………-49-

1. Acebo, P., A. J. Martin-Galiano, S. Navarro, A. Zaballos, and M. Amblar. 2012. Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae. RNA 18:530-46.
2. An, S. Q., G. T. Lu, H. Z. Su, R. F. Li, Y. Q. He, B. L. Jiang, D. J. Tang, and J. L. Tang. 2011. Systematic mutagenesis of all predicted gntR genes in Xanthomonas campestris pv. campestris reveals a GntR family transcriptional regulator controlling hypersensitive response and virulence. Mol Plant Microbe Interact 24:1027-39.
3. Argaman, L., R. Hershberg, J. Vogel, G. Bejerano, E. G. Wagner, H. Margalit, and S. Altuvia. 2001. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11:941-50.
4. Axmann, I. M., P. Kensche, J. Vogel, S. Kohl, H. Herzel, and W. R. Hess. 2005. Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol 6:R73.
5. Backofen, R., and W. R. Hess. 2010. Computational prediction of sRNAs and their targets in bacteria. RNA Biol 7:33-42.
6. Barrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D. A. Romero, and P. Horvath. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-12.
7. Bejerano-Sagie, M., and K. B. Xavier. 2007. The role of small RNAs in quorum sensing. Curr Opin Microbiol 10:189-98.
8. Bohn, C., C. Rigoulay, and P. Bouloc. 2007. No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus. BMC Microbiol 7:10.
9. Boisset, S., T. Geissmann, E. Huntzinger, P. Fechter, N. Bendridi, M. Possedko, C. Chevalier, A. C. Helfer, Y. Benito, A. Jacquier, C. Gaspin, F. Vandenesch, and P. Romby. 2007. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 21:1353-66.
10. Bouvier, M., C. M. Sharma, F. Mika, K. H. Nierhaus, and J. Vogel. 2008. Small RNA binding to 5' mRNA coding region inhibits translational initiation. Mol Cell 32:827-37.
11. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-54.
12. Burnette-Curley, D., V. Wells, H. Viscount, C. L. Munro, J. C. Fenno, P. Fives-Taylor, and F. L. Macrina. 1995. FimA, a major virulence factor associated with Streptococcus parasanguis endocarditis. Infect Immun 63:4669-74.
13. Carpousis, A. J., B. F. Luisi, and K. J. McDowall. 2009. Endonucleolytic initiation of mRNA decay in Escherichia coli. Prog Mol Biol Transl Sci 85:91-135.
14. Casneuf, T., Y. Van de Peer, and W. Huber. 2007. In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics 8:461.
15. Chen, Q., H. Wu, and P. M. Fives-Taylor. 2004. Investigating the role of secA2 in secretion and glycosylation of a fimbrial adhesin in Streptococcus parasanguis FW213. Mol Microbiol 53:843-56.
16. Chen, S., E. A. Lesnik, T. A. Hall, R. Sampath, R. H. Griffey, D. J. Ecker, and L. B. Blyn. 2002. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65:157-77.
17. Chen, Y. Y., M. J. Betzenhauser, and R. A. Burne. 2002. cis-Acting elements that regulate the low-pH-inducible urease operon of Streptococcus salivarius. Microbiology 148:3599-608.
18. Chen YY, S. H., Chang YC. 2013. The Expression of the fim Operon Is Crucial for the Survival of Streptococcus parasanguinis FW213 within Macrophages but Not Acid Tolerance. PLoS One 8:e66163.
19. Cole, R. M., G. B. Calandra, E. Huff, and K. M. Nugent. 1976. Attributes of potential utility in differentiating among "group H" streptococci or Streptococcus sanguis. J Dent Res 55:A142-53.
20. Davis, B. M., M. Quinones, J. Pratt, Y. Ding, and M. K. Waldor. 2005. Characterization of the small untranslated RNA RyhB and its regulon in Vibrio cholerae. J Bacteriol 187:4005-14.
21. Dunny, G. M., L. N. Lee, and D. J. LeBlanc. 1991. Improved electroporation and cloning vector system for gram-positive bacteria. Appl Environ Microbiol 57:1194-201.
22. Eklund, A. C., L. R. Turner, P. Chen, R. V. Jensen, G. deFeo, A. R. Kopf-Sill, and Z. Szallasi. 2006. Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol 24:1071-3.
23. Fenno, J. C., A. Shaikh, G. Spatafora, and P. Fives-Taylor. 1995. The fimA locus of Streptococcus parasanguis encodes an ATP-binding membrane transport system. Mol Microbiol 15:849-63.
24. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick, and et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
25. Froeliger, E. H., and P. Fives-Taylor. 2001. Streptococcus parasanguis fimbria-associated adhesin fap1 is required for biofilm formation. Infect Immun 69:2512-9.
26. Geng, J., C. H. Chiu, P. Tang, Y. Chen, H. R. Shieh, S. Hu, and Y. Y. Chen. 2012. Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms. PLoS One 7:e34769.
27. Gerdes, K., A. Nielsen, P. Thorsted, and E. G. Wagner. 1992. Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs. J Mol Biol 226:637-49.
28. Giomarelli, B., L. Visai, K. Hijazi, S. Rindi, M. Ponzio, F. Iannelli, P. Speziale, and G. Pozzi. 2006. Binding of Streptococcus gordonii to extracellular matrix proteins. FEMS Microbiol Lett 265:172-7.
29. Gottesman, S. 2004. The small RNA regulators of Escherichia coli: roles and mechanisms*. Annu Rev Microbiol 58:303-28.
30. Gottesman, S., C. A. McCullen, M. Guillier, C. K. Vanderpool, N. Majdalani, J. Benhammou, K. M. Thompson, P. C. FitzGerald, N. A. Sowa, and D. J. FitzGerald. 2006. Small RNA regulators and the bacterial response to stress. Cold Spring Harb Symp Quant Biol 71:1-11.
31. Gruber, A. R., S. Findeiss, S. Washietl, I. L. Hofacker, and P. F. Stadler. 2010. Rnaz 2.0: Improved Noncoding Rna Detection. Pac Symp Biocomput 15:69-79.
32. Heidrich, N., A. Chinali, U. Gerth, and S. Brantl. 2006. The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol Microbiol 62:520-36.
33. Ikeda, Y., M. Yagi, T. Morita, and H. Aiba. 2011. Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Mol Microbiol 79:419-32.
34. Kawamoto, H., T. Morita, A. Shimizu, T. Inada, and H. Aiba. 2005. Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. Genes Dev 19:328-38.
35. Lau, P. C., C. K. Sung, J. H. Lee, D. A. Morrison, and D. G. Cvitkovitch. 2002. PCR ligation mutagenesis in transformable streptococci: application and efficiency. J Microbiol Methods 49:193-205.
36. Le Rhun, A., and E. Charpentier. 2012. Small RNAs in streptococci. RNA Biol 9:414-26.
37. Lee, H. J., and S. H. Hong. 2012. Analysis of microRNA-size, small RNAs in Streptococcus mutans by deep sequencing. FEMS Microbiol Lett 326:131-6.
38. Lenz, D. H., K. C. Mok, B. N. Lilley, R. V. Kulkarni, N. S. Wingreen, and B. L. Bassler. 2004. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118:69-82.
39. Liu, M. Y., G. Gui, B. Wei, J. F. Preston, 3rd, L. Oakford, U. Yuksel, D. P. Giedroc, and T. Romeo. 1997. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 272:17502-10.
40. Livny, J. 2007. Efficient annotation of bacterial genomes for small, noncoding RNAs using the integrative computational tool sRNAPredict2. Methods Mol Biol 395:475-88.
41. Livny, J., A. Brencic, S. Lory, and M. K. Waldor. 2006. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 34:3484-93.
42. Livny, J., M. A. Fogel, B. M. Davis, and M. K. Waldor. 2005. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 33:4096-105.
43. Loman, N. J., C. Constantinidou, J. Z. Chan, M. Halachev, M. Sergeant, C. W. Penn, E. R. Robinson, and M. J. Pallen. 2012. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10:599-606.
44. Mann, B., T. van Opijnen, J. Wang, C. Obert, Y. D. Wang, R. Carter, D. J. McGoldrick, G. Ridout, A. Camilli, E. I. Tuomanen, and J. W. Rosch. 2012. Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog 8:e1002788.
45. Marsh, P. D. 1995. The role of microbiology in models of dental caries. Adv Dent Res 9:244-54; discussion 255-69.
46. Mason, D. J., A. Dietz, and R. M. Smith. 1961. Actinospectacin, a new antibiotic. I. Discovery and biological properties. Antibiot Chemother (Northfield Ill) 11:118-22.
47. Masse, E., and S. Gottesman. 2002. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99:4620-5.
48. Mey, A. R., S. A. Craig, and S. M. Payne. 2005. Characterization of Vibrio cholerae RyhB: the RyhB regulon and role of ryhB in biofilm formation. Infect Immun 73:5706-19.
49. Mogens Kilian, L. M. a. J. H. 1989. Taxonomic Study of Viridans Streptococci: Description of Streptococcus gordonii sp. nov. and Emended Descriptions of Streptococcus sanguis (White and Niven 1946), Streptococcus oralis (Bridge and Sneath 1982), and Streptococcus mitis (Andrewes and Horder 1906). Int J Syst Bacteriol 39:471-484.
50. Morita, T., K. Maki, and H. Aiba. 2005. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19:2176-86.
51. Mortazavi, A., B. A. Williams, K. McCue, L. Schaeffer, and B. Wold. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-8.
52. Oetjen, J., P. Fives-Taylor, and E. H. Froeliger. 2002. The divergently transcribed Streptococcus parasanguis virulence-associated fimA operon encoding an Mn(2+)-responsive metal transporter and pepO encoding a zinc metallopeptidase are not coordinately regulated. Infect Immun 70:5706-14.
53. Okoniewski, M. J., and C. J. Miller. 2006. Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 7:276.
54. Oliver, H. F., R. H. Orsi, L. Ponnala, U. Keich, W. Wang, Q. Sun, S. W. Cartinhour, M. J. Filiatrault, M. Wiedmann, and K. J. Boor. 2009. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10:641.
55. Paik, S., L. Senty, S. Das, J. C. Noe, C. L. Munro, and T. Kitten. 2005. Identification of virulence determinants for endocarditis in Streptococcus sanguinis by signature-tagged mutagenesis. Infect Immun 73:6064-74.
56. Papenfort, K., and J. Vogel. 2009. Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level. Res Microbiol 160:278-87.
57. Parkhomchuk, D., T. Borodina, V. Amstislavskiy, M. Banaru, L. Hallen, S. Krobitsch, H. Lehrach, and A. Soldatov. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37:e123.
58. Passalacqua, K. D., A. Varadarajan, B. D. Ondov, D. T. Okou, M. E. Zwick, and N. H. Bergman. 2009. Structure and complexity of a bacterial transcriptome. J Bacteriol 191:3203-11.
59. Peng, Z., P. Fives-Taylor, T. Ruiz, M. Zhou, B. Sun, Q. Chen, and H. Wu. 2008. Identification of critical residues in Gap3 of Streptococcus parasanguinis involved in Fap1 glycosylation, fimbrial formation and in vitro adhesion. BMC Microbiol 8:52.
60. Perkins, T. T., R. A. Kingsley, M. C. Fookes, P. P. Gardner, K. D. James, L. Yu, S. A. Assefa, M. He, N. J. Croucher, D. J. Pickard, D. J. Maskell, J. Parkhill, J. Choudhary, N. R. Thomson, and G. Dougan. 2009. A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet 5:e1000569.
61. Pfeiffer, V., K. Papenfort, S. Lucchini, J. C. Hinton, and J. Vogel. 2009. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16:840-6.
62. Postic, G., I. Dubail, E. Frapy, M. Dupuis, J. Dieppedale, A. Charbit, and K. L. Meibom. 2012. Identification of a novel small RNA modulating Francisella tularensis pathogenicity. PLoS One 7:e41999.
63. Ramirez-Pena, E., J. Trevino, Z. Liu, N. Perez, and P. Sumby. 2010. The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript. Mol Microbiol 78:1332-47.
64. Rasmussen, S., H. B. Nielsen, and H. Jarmer. 2009. The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73:1043-57.
65. Rigali, S., A. Derouaux, F. Giannotta, and J. Dusart. 2002. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 277:12507-15.
66. Rivas, E., R. J. Klein, T. A. Jones, and S. R. Eddy. 2001. Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:1369-73.
67. Romby, P., and E. Charpentier. 2010. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci 67:217-37.
68. Romby, P., F. Vandenesch, and E. G. Wagner. 2006. The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol 9:229-36.
69. Sa-Nogueira, I., and L. J. Mota. 1997. Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene. J Bacteriol 179:1598-608.
70. Sapranauskas, R., G. Gasiunas, C. Fremaux, R. Barrangou, P. Horvath, and V. Siksnys. 2011. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39:9275-82.
71. Selinger, D. W., K. J. Cheung, R. Mei, E. M. Johansson, C. S. Richmond, F. R. Blattner, D. J. Lockhart, and G. M. Church. 2000. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18:1262-8.
72. Sepkowitz, K. A. 2002. Opportunistic infections in patients with and patients without Acquired Immunodeficiency Syndrome. Clin Infect Dis 34:1098-107.
73. Sharma, C. M., F. Darfeuille, T. H. Plantinga, and J. Vogel. 2007. A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 21:2804-17.
74. Sharma, C. M., and J. Vogel. 2009. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 12:536-46.
75. Shaw, W. V. 1975. Chloramphenicol acetyltransferase from chloramphenicol-resistant bacteria. Methods Enzymol 43:737-55.
76. Shaw, W. V., D. G. Brenner, S. F. LeGrice, S. E. Skinner, and A. R. Hawkins. 1985. Chloramphenicol acetyltransferase gene of staphylococcal plasmid pC221. Nucleotide sequence analysis and expression studies. FEBS Lett 179:101-6.
77. Shearwin, K. E., B. P. Callen, and J. B. Egan. 2005. Transcriptional interference--a crash course. Trends Genet 21:339-45.
78. Shenep, J. L. 2000. Viridans-group streptococcal infections in immunocompromised hosts. Int J Antimicrob Agents 14:129-35.
79. Silvaggi, J. M., J. B. Perkins, and R. Losick. 2006. Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol 188:532-41.
80. Sobek, L., D. Di Lorenzo, M. Oettel, and G. Kaufmann. 1994. Normal and stable transfected cancer cell lines: tools for a screening of progestogenic, antiprogestogenic and antiglucocorticoid substances. Methods Find Exp Clin Pharmacol 16:545-51.
81. Spatafora, G., N. Van Hoeven, K. Wagner, and P. Fives-Taylor. 2002. Evidence that ORF3 at the Streptococcus parasanguis fimA locus encodes a thiol-specific antioxidant. Microbiology 148:755-62.
82. Toledo-Arana, A., F. Repoila, and P. Cossart. 2007. Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol 10:182-8.
83. Voss, B., J. Georg, V. Schon, S. Ude, and W. R. Hess. 2009. Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 10:123.
84. Wassarman, K. M., F. Repoila, C. Rosenow, G. Storz, and S. Gottesman. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637-51.
85. Waters, L. S., and G. Storz. 2009. Regulatory RNAs in bacteria. Cell 136:615-28.
86. Ween, O., P. Gaustad, and L. S. Havarstein. 1999. Identification of DNA binding sites for ComE, a key regulator of natural competence in Streptococcus pneumoniae. Mol Microbiol 33:817-27.
87. Wilderman, P. J., N. A. Sowa, D. J. FitzGerald, P. C. FitzGerald, S. Gottesman, U. A. Ochsner, and M. L. Vasil. 2004. Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc Natl Acad Sci U S A 101:9792-7.
88. Wu, H., S. Bu, P. Newell, Q. Chen, and P. Fives-Taylor. 2007. Two gene determinants are differentially involved in the biogenesis of Fap1 precursors in Streptococcus parasanguis. J Bacteriol 189:1390-8.
89. Wu, H., and P. M. Fives-Taylor. 1999. Identification of dipeptide repeats and a cell wall sorting signal in the fimbriae-associated adhesin, Fap1, of Streptococcus parasanguis. Mol Microbiol 34:1070-81.
90. Wu, H., K. P. Mintz, M. Ladha, and P. M. Fives-Taylor. 1998. Isolation and characterization of Fap1, a fimbriae-associated adhesin of Streptococcus parasanguis FW213. Mol Microbiol 28:487-500.
91. Wu, H., M. Zeng, and P. Fives-Taylor. 2007. The glycan moieties and the N-terminal polypeptide backbone of a fimbria-associated adhesin, Fap1, play distinct roles in the biofilm development of Streptococcus parasanguinis. Infect Immun 75:2181-8.
92. Ye ZS. 21013. Functional analysis of the collagen binding homologoues of Streptococcus parasanguinis FW213.
93. Yoder-Himes, D. R., P. S. Chain, Y. Zhu, O. Wurtzel, E. M. Rubin, J. M. Tiedje, and R. Sorek. 2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 106:3976-81.
94. Yoshida, K. I., Y. Fujita, and S. D. Ehrlich. 2000. An operon for a putative ATP-binding cassette transport system involved in acetoin utilization of Bacillus subtilis. J Bacteriol 182:5454-61.



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