메뉴 건너뛰기




Volumn 9, Issue 12, 2003, Pages 1502-1515

Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus

Author keywords

Phylogenetic conservation; RNA folding; RNA secondary structure; RNA tertiary structure; Translation control

Indexed keywords

DNA; MAGNESIUM ION; OLIGONUCLEOTIDE; PROTEIN; PYRIMIDINE; RNA; TRYPTOPHAN; TRYPTOPHAN RNA BINDING ATTENUATION PROTEIN; UNCLASSIFIED DRUG;

EID: 0344874264     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5149603     Document Type: Article
Times cited : (4)

References (37)
  • 3
    • 0033575897 scopus 로고    scopus 로고
    • Structure of the trp RNA-binding attenuation protein TRAP bound to RNA
    • Antson, A.A., Dodson, E.J., Dodson, G., Greaves, R.B., Chen, X., and Gollnick, P. 1999. Structure of the trp RNA-binding attenuation protein TRAP bound to RNA. Nature 401: 235-242.
    • (1999) Nature , vol.401 , pp. 235-242
    • Antson, A.A.1    Dodson, E.J.2    Dodson, G.3    Greaves, R.B.4    Chen, X.5    Gollnick, P.6
  • 4
    • 0034810138 scopus 로고    scopus 로고
    • Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure
    • Babitzke P. and Gollnick, P. 2001. Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J. Bacteriol. 183: 5795-5802.
    • (2001) J. Bacteriol. , vol.183 , pp. 5795-5802
    • Babitzke, P.1    Gollnick, P.2
  • 5
    • 0027458419 scopus 로고
    • Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein
    • Babitzke, P. and Yanofsky, C. 1993. Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein. Proc. Natl. Acad. Sci. 90: 133-137.
    • (1993) Proc. Natl. Acad. Sci. , vol.90 , pp. 133-137
    • Babitzke, P.1    Yanofsky, C.2
  • 6
    • 0029018202 scopus 로고
    • Structural features of L-tryptophan required for activation of TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis
    • -. 1995. Structural features of L-tryptophan required for activation of TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis. J. Biol. Chem. 270: 12452-12456.
    • (1995) J. Biol. Chem. , vol.270 , pp. 12452-12456
  • 7
    • 0028361572 scopus 로고
    • TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcripts
    • Babitzke, P., Stults, J.T., Shire, S.J., and Yanofsky, C. 1994. TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcripts. J. Biol. Chem. 269: 16597-16604.
    • (1994) J. Biol. Chem. , vol.269 , pp. 16597-16604
    • Babitzke, P.1    Stults, J.T.2    Shire, S.J.3    Yanofsky, C.4
  • 8
    • 0029839067 scopus 로고    scopus 로고
    • Interaction of the trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis with RNA: Effects of the number of GAG repeats, the nucleotides separating adjacent repeats, and RNA secondary structure
    • Babitzke, P., Yealy, J., and Campanelli, D. 1996. Interaction of the trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis with RNA: Effects of the number of GAG repeats, the nucleotides separating adjacent repeats, and RNA secondary structure. J. Bacteriol. 178: 5159-5163.
    • (1996) J. Bacteriol. , vol.178 , pp. 5159-5163
    • Babitzke, P.1    Yealy, J.2    Campanelli, D.3
  • 9
    • 0041757737 scopus 로고    scopus 로고
    • Role of RNA structure in transcription attenuation in Bacillus subtilis: The trpEDCFBA operon as a model system
    • in press
    • Babitzke, P., Schaak, J.E., Yakhnin, A.V., and Bevilacqua, P.C. 2003. Role of RNA structure in transcription attenuation in Bacillus subtilis: The trpEDCFBA operon as a model system. Methods Enzymol. (in press).
    • (2003) Methods Enzymol.
    • Babitzke, P.1    Schaak, J.E.2    Yakhnin, A.V.3    Bevilacqua, P.C.4
  • 10
    • 0032506045 scopus 로고    scopus 로고
    • Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin
    • Bevilacqua, J.M. and Bevilacqua, P.C. 1998. Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin. Biochemistry 37: 15877-15884.
    • (1998) Biochemistry , vol.37 , pp. 15877-15884
    • Bevilacqua, J.M.1    Bevilacqua, P.C.2
  • 12
    • 0033022150 scopus 로고    scopus 로고
    • Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus
    • Chen, X., Antson, A.A., Yang, M., Li, P., Baumann, C., Dodson, E.J., Dodson, G.G., and Gollnick, P. 1999. Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus. J. Mol. Biol. 289: 1003-1016.
    • (1999) J. Mol. Biol. , vol.289 , pp. 1003-1016
    • Chen, X.1    Antson, A.A.2    Yang, M.3    Li, P.4    Baumann, C.5    Dodson, E.J.6    Dodson, G.G.7    Gollnick, P.8
  • 13
    • 0028341904 scopus 로고
    • RNAs with dual specificity and dual RNAs with similar specificity
    • Connell, G.J. and Yarus, M. 1994. RNAs with dual specificity and dual RNAs with similar specificity. Science 264: 1137-1141.
    • (1994) Science , vol.264 , pp. 1137-1141
    • Connell, G.J.1    Yarus, M.2
  • 14
    • 0032493809 scopus 로고    scopus 로고
    • trp RNA-binding attenuation protein-mediated long distance RNA refolding regulates translation of trpE in Bacillus subtilis
    • Du, H. and Babitzke, P. 1998. trp RNA-binding attenuation protein-mediated long distance RNA refolding regulates translation of trpE in Bacillus subtilis. J. Biol. Chem. 273: 20494-20503.
    • (1998) J. Biol. Chem. , vol.273 , pp. 20494-20503
    • Du, H.1    Babitzke, P.2
  • 15
    • 0030934761 scopus 로고    scopus 로고
    • The trp RNA-binding attenuation protein regulates TrpG synthesis by binding to the trpG ribosome binding site of Bacillus subtilis
    • Du, H., Tarpey, R., and Babitzke, P. 1997. The trp RNA-binding attenuation protein regulates TrpG synthesis by binding to the trpG ribosome binding site of Bacillus subtilis. J. Bacteriol. 179: 2582-2586.
    • (1997) J. Bacteriol. , vol.179 , pp. 2582-2586
    • Du, H.1    Tarpey, R.2    Babitzke, P.3
  • 16
    • 0025254630 scopus 로고
    • The mtr locus is a two-gene operon required for transcription attenuation in the trp operon of Bacillus subtilis
    • Gollnick, P., Ishino, S., Kuroda, M.I., Henner, D.J., and Yanofsky, C. 1990. The mtr locus is a two-gene operon required for transcription attenuation in the trp operon of Bacillus subtilis. Proc. Natl. Acad. Sci. 87: 8726-8730.
    • (1990) Proc. Natl. Acad. Sci. , vol.87 , pp. 8726-8730
    • Gollnick, P.1    Ishino, S.2    Kuroda, M.I.3    Henner, D.J.4    Yanofsky, C.5
  • 18
    • 0028906665 scopus 로고
    • The mtrB gene of Bacillus pumilus encodes a protein with sequence and functional homology to the trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis
    • Hoffman, R.J. and Gollnick, P. 1995. The mtrB gene of Bacillus pumilus encodes a protein with sequence and functional homology to the trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis. J. Bacteriol. 177: 839-842.
    • (1995) J. Bacteriol. , vol.177 , pp. 839-842
    • Hoffman, R.J.1    Gollnick, P.2
  • 19
    • 0024041531 scopus 로고
    • cis-acting sites in the transcript of the Bacillus subtilis trp operon regulate expression of the operon
    • Kuroda, M.I., Henner, D., and Yanofsky, C. 1988. cis-acting sites in the transcript of the Bacillus subtilis trp operon regulate expression of the operon. J. Bacteriol. 170: 3080-3088.
    • (1988) J. Bacteriol. , vol.170 , pp. 3080-3088
    • Kuroda, M.I.1    Henner, D.2    Yanofsky, C.3
  • 20
    • 0028237035 scopus 로고
    • Stabilization of RNA structure by Mg ions. Specific and nonspecific effects
    • Laing, L.G., Gluick, T.C., and Draper, D.E. 1994. Stabilization of RNA structure by Mg ions. Specific and nonspecific effects. J. Mol. Biol. 237: 577-587.
    • (1994) J. Mol. Biol. , vol.237 , pp. 577-587
    • Laing, L.G.1    Gluick, T.C.2    Draper, D.E.3
  • 21
    • 0030747007 scopus 로고    scopus 로고
    • Unusual dynamics and pK(a) shift at the active site of a lead-dependent ribozyme
    • Legault, P. and Pardi, A. 1997. Unusual dynamics and pK(a) shift at the active site of a lead-dependent ribozyme. J. Am. Chem. Soc. 119: 6621-6628.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 6621-6628
    • Legault, P.1    Pardi, A.2
  • 22
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 23
    • 0028871292 scopus 로고
    • trp RNA-binding attenuation protein (TRAP)- trp leader RNA interactions mediate translational as well as transcriptional regulation of the Bacillus subtilis trp operon
    • Merino, E., Babitzke, P., and Yanofsky, C. 1995. trp RNA-binding attenuation protein (TRAP)- trp leader RNA interactions mediate translational as well as transcriptional regulation of the Bacillus subtilis trp operon. J. Bacteriol. 177: 6362-6370.
    • (1995) J. Bacteriol. , vol.177 , pp. 6362-6370
    • Merino, E.1    Babitzke, P.2    Yanofsky, C.3
  • 24
    • 0027509047 scopus 로고
    • MtrB from Bacillus subtilis binds specifically to trp leader RNA in a tryptophan-dependent manner
    • Otridge, J. and Gollnick, P. 1993. MtrB from Bacillus subtilis binds specifically to trp leader RNA in a tryptophan-dependent manner. Proc. Natl. Acad. Sci. 90: 128-132.
    • (1993) Proc. Natl. Acad. Sci. , vol.90 , pp. 128-132
    • Otridge, J.1    Gollnick, P.2
  • 26
    • 0034719109 scopus 로고    scopus 로고
    • Adenine protonation in domain B of the hairpin ribozyme
    • Ravindranathan, S., Butcher, S.E., and Feigon, J. 2000. Adenine protonation in domain B of the hairpin ribozyme. Biochemistry 39: 16026-16032.
    • (2000) Biochemistry , vol.39 , pp. 16026-16032
    • Ravindranathan, S.1    Butcher, S.E.2    Feigon, J.3
  • 27
    • 0034115502 scopus 로고    scopus 로고
    • A Bacillus subtilis gene of previously unknown function, yhaG, is translationally regulated by tryptophan-activated TRAP and appears to be involved in tryptophan transport
    • Sarsero, J.P., Merino, E., and Yanofsky, C. 2000. A Bacillus subtilis gene of previously unknown function, yhaG, is translationally regulated by tryptophan-activated TRAP and appears to be involved in tryptophan transport. J. Bacteriol. 182: 2329-2331.
    • (2000) J. Bacteriol. , vol.182 , pp. 2329-2331
    • Sarsero, J.P.1    Merino, E.2    Yanofsky, C.3
  • 28
    • 0042736855 scopus 로고    scopus 로고
    • 2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding
    • 2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding. J. Mol. Biol. 32: 555-574.
    • (2003) J. Mol. Biol. , vol.32 , pp. 555-574
    • Schaak, J.E.1    Yakhnin, H.2    Bevilacqua, P.C.3    Babitzke, P.4
  • 29
    • 0022570121 scopus 로고
    • Novel form of transcription attenuation regulates expression the Bacillus subtilis tryptophan operon
    • Shimotsu, H., Kuroda, M.I., Yanofsky, C., and Henner, D.J. 1986. Novel form of transcription attenuation regulates expression the Bacillus subtilis tryptophan operon. J. Bacteriol. 166: 461-471.
    • (1986) J. Bacteriol. , vol.166 , pp. 461-471
    • Shimotsu, H.1    Kuroda, M.I.2    Yanofsky, C.3    Henner, D.J.4
  • 30
    • 0025942760 scopus 로고
    • Nucleotide sequence of trpE, anthranilate synthase I gene, of Bacillus caldotenax
    • Shiratsuchi, A. and Sato, S. 1991. Nucleotide sequence of trpE, anthranilate synthase I gene, of Bacillus caldotenax. Biochim. Biophys. Acta 1090: 348-350.
    • (1991) Biochim. Biophys. Acta , vol.1090 , pp. 348-350
    • Shiratsuchi, A.1    Sato, S.2
  • 31
    • 0032882591 scopus 로고    scopus 로고
    • A 5′ RNA stem-loop participates in the transcription attenuation mechanism that controls expression of the Bacillus subtilis trpEDCFBA operon
    • Sudershana, S., Du, H., Mahalanabis, M., and Babitzke, P. 1999. A 5′ RNA stem-loop participates in the transcription attenuation mechanism that controls expression of the Bacillus subtilis trpEDCFBA operon. J. Bacteriol. 181: 5742-5749.
    • (1999) J. Bacteriol. , vol.181 , pp. 5742-5749
    • Sudershana, S.1    Du, H.2    Mahalanabis, M.3    Babitzke, P.4
  • 33
    • 0344289737 scopus 로고    scopus 로고
    • Thermodynamics of formation of secondary structure in nucleic acids
    • Oxford University Press, New York
    • Tinoco Jr., I. and Schmitz, M. 2000. Thermodynamics of formation of secondary structure in nucleic acids. In Thermodynamics in biology, pp. 131-176. Oxford University Press, New York.
    • (2000) Thermodynamics in Biology , pp. 131-176
    • Tinoco Jr., I.1    Schmitz, M.2
  • 34
    • 0000141714 scopus 로고
    • Nitrogen- 15-labeled oligodeoxynucleotides. 3. Protonation of the adenine N1 in the A.C and A.G mispairs of the duplexes (D[Cg(N-15(1))Agaattcccg])2 and (D[Cgggaattc(N-15(1)Acg])2
    • Wang, C., Gao, H., Gaffney, B.L., and Jones, R.A. 1991. Nitrogen- 15-labeled oligodeoxynucleotides. 3. Protonation of the adenine N1 in the A.C and A.G mispairs of the duplexes (D[Cg(N-15(1))Agaattcccg])2 and (D[Cgggaattc(N-15(1)Acg])2. J. Am. Chem. Soc. 113: 5486-5488.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 5486-5488
    • Wang, C.1    Gao, H.2    Gaffney, B.L.3    Jones, R.A.4
  • 35
    • 0037143667 scopus 로고    scopus 로고
    • NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro
    • Yakhnin, A.V. and Babitzke, P. 2002. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro. Proc. Natl. Acad. Sci. 99: 11067-11072.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 11067-11072
    • Yakhnin, A.V.1    Babitzke, P.2
  • 36
    • 0029120844 scopus 로고
    • Translation of trpG in Bacillus subtilis is regulated by the trp RNA-binding attenuation protein (TRAP)
    • Yang, M., de Saizieu, A., van Loon, A.P., and Gollnick, P. 1995. Translation of trpG in Bacillus subtilis is regulated by the trp RNA-binding attenuation protein (TRAP). J. Bacteriol. 177: 4272-4278.
    • (1995) J. Bacteriol. , vol.177 , pp. 4272-4278
    • Yang, M.1    De Saizieu, A.2    Van Loon, A.P.3    Gollnick, P.4
  • 37
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • NATO ASI Series, Kluwer Academic Publishers, Boston
    • Zuker, M., Mathews, D.H., and Turner, D.H. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA biochemistry and biotechnology, NATO ASI Series, Kluwer Academic Publishers, Boston.
    • (1999) RNA Biochemistry and Biotechnology
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.