메뉴 건너뛰기




Volumn 17, Issue 1, 2011, Pages 45-53

Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases

Author keywords

5 methyluridine; Archaea; Horizontal gene transfer; MALDI MS; RRNA modification

Indexed keywords

METHYLTRANSFERASE; RIBOSOME RNA; RNA 23S; TRANSFER RNA;

EID: 78650489654     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2323411     Document Type: Article
Times cited : (30)

References (46)
  • 1
    • 0037088598 scopus 로고    scopus 로고
    • Characterization of the 23S ribosomal RNA m5U1939 methyltransferase from Escherichia coli
    • Agarwalla S, Kealey JT, Santi DV, Stroud RM. 2002. Characterization of the 23S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J Biol Chem 277: 8835-8840.
    • (2002) J Biol Chem , vol.277 , pp. 8835-8840
    • Agarwalla, S.1    Kealey, J.T.2    Santi, D.V.3    Stroud, R.M.4
  • 2
    • 1242309517 scopus 로고    scopus 로고
    • Decoding the genome: A modified view
    • Agris PF. 2004. Decoding the genome: a modified view. Nucleic Acids Res 32: 223-238.
    • (2004) Nucleic Acids Res , vol.32 , pp. 223-238
    • Agris, P.F.1
  • 3
    • 44349185734 scopus 로고    scopus 로고
    • Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases
    • Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J. 2008. Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases. Proc Natl Acad Sci 105: 6876-6881.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 6876-6881
    • Alian, A.1    Lee, T.T.2    Griner, S.L.3    Stroud, R.M.4    Finer-Moore, J.5
  • 4
    • 33646806139 scopus 로고    scopus 로고
    • YebU is a m5C methyltransferase specific for 16S rRNA nucleotide 1407
    • Andersen NM, Douthwaite S. 2006. YebU is a m5C methyltransferase specific for 16S rRNA nucleotide 1407. J Mol Biol 359: 777-786.
    • (2006) J Mol Biol , vol.359 , pp. 777-786
    • Andersen, N.M.1    Douthwaite, S.2
  • 5
    • 2442686628 scopus 로고    scopus 로고
    • A novel partial modification at 2501 in Escherichia coli 23S ribosomal RNA
    • Andersen TE, Porse BT, Kirpekar F. 2004. A novel partial modification at 2501 in Escherichia coli 23S ribosomal RNA. RNA 10: 907-913.
    • (2004) RNA , vol.10 , pp. 907-913
    • Andersen, T.E.1    Porse, B.T.2    Kirpekar, F.3
  • 6
    • 34547107631 scopus 로고    scopus 로고
    • Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase
    • Auxilien S, El Khadali F, Rasmussen A, Douthwaite S, Grosjean H. 2007. Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase. J Biol Chem 282: 18711-18721.
    • (2007) J Biol Chem , vol.282 , pp. 18711-18721
    • Auxilien, S.1    El Khadali, F.2    Rasmussen, A.3    Douthwaite, S.4    Grosjean, H.5
  • 7
    • 0017030513 scopus 로고
    • New approach to the cultivation of methanogenic bacteria: 2-Mercaptoethanesulfonic acid (HS-CoM)- dependent growth of Methanobacterium ruminantium in a pressurized atmosphere
    • Balch WE, Wolfe RS. 1976. New approach to the cultivation of methanogenic bacteria: 2-Mercaptoethanesulfonic acid (HS-CoM)- dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl Environ Microbiol 32: 781-791.
    • (1976) Appl Environ Microbiol , vol.32 , pp. 781-791
    • Balch, W.E.1    Wolfe, R.S.2
  • 8
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4A ̊ resolution
    • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4A ̊ resolution. Science 289: 905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 10
    • 25144485401 scopus 로고    scopus 로고
    • Nanoarchaea: Representatives of a novel archaeal phylum or a fastevolving euryarchaeal lineage related to Thermococcales?
    • doi: 10.1186/gb-2005-6-5-r42
    • Brochier C, Gribaldo S, ZiVanovic Y, Confalonieri F, Forterre P. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fastevolving euryarchaeal lineage related to Thermococcales? Genome Biol 6: R42. doi: 10.1186/gb-2005-6-5-r42.
    • (2005) Genome Biol , vol.6
    • Brochier, C.1    Gribaldo, S.2    Zivanovic, Y.3    Confalonieri, F.4    Forterre, P.5
  • 11
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • doi: 10.1186/ 1471-2105-3-2
    • Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, et al. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2. doi: 10.1186/ 1471-2105-3-2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.J.1    Subramanian, S.2    Schnare, M.N.3    Collett, J.R.4    D'Souza, L.M.5    Du, Y.6    Feng, B.7    Lin, N.8    Madabusi, L.V.9    Muller, K.M.10
  • 12
    • 34248663955 scopus 로고    scopus 로고
    • The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: Twenty-something years on
    • Chomczynski P, Sacchi N. 2006. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protoc 1: 581-585.
    • (2006) Nat Protoc , vol.1 , pp. 581-585
    • Chomczynski, P.1    Sacchi, N.2
  • 13
    • 35648960799 scopus 로고    scopus 로고
    • Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications
    • Chow CS, Lamichhane TN, Mahto SK. 2007. Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications. ACS Chem Biol 2: 610-619.
    • (2007) ACS Chem Biol , vol.2 , pp. 610-619
    • Chow, C.S.1    Lamichhane, T.N.2    Mahto, S.K.3
  • 14
    • 0018462013 scopus 로고
    • Role of ribothymidine in the thermal stability of transfer RNA as monitored by proton magnetic resonance
    • DaVanloo P, Sprinzl M, Watanabe K, Albani M, Kersten H. 1979. Role of ribothymidine in the thermal stability of transfer RNA as monitored by proton magnetic resonance. Nucleic Acids Res 6: 1571-1581.
    • (1979) Nucleic Acids Res , vol.6 , pp. 1571-1581
    • Davanloo, P.1    Sprinzl, M.2    Watanabe, K.3    Albani, M.4    Kersten, H.5
  • 15
    • 34648840096 scopus 로고    scopus 로고
    • Comparative RNomics and modomics in Mollicutes: Prediction of gene function and evolutionary implications
    • de Crécy-Lagard V, Marck C, Brochier-Armanet C, Grosjean H. 2007. Comparative RNomics and modomics in Mollicutes: Prediction of gene function and evolutionary implications. IUBMB Life 59: 634-658.
    • (2007) IUBMB Life , vol.59 , pp. 634-658
    • De Crécy-Lagard, V.1    Marck, C.2    Brochier-Armanet, C.3    Grosjean, H.4
  • 16
    • 0036629250 scopus 로고    scopus 로고
    • RRNA modifications and ribosome function
    • Decatur WA, Fournier MJ. 2002. rRNA modifications and ribosome function. Trends Biochem Sci 27: 344-351.
    • (2002) Trends Biochem Sci , vol.27 , pp. 344-351
    • Decatur, W.A.1    Fournier, M.J.2
  • 17
    • 33749032381 scopus 로고    scopus 로고
    • 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
    • 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci 103: 14003-14008.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 14003-14008
    • Grilley, D.1    Soto, A.M.2    Draper, D.E.3
  • 19
    • 38649122634 scopus 로고    scopus 로고
    • Detection of enzymatic activity of transfer RNA modification enzymes using radiolabelled tRNA substrates
    • (ed. JM Gott), Elsevier, New York
    • Grosjean H, Droogmans L, Roovers M, Keith G. 2007. Detection of enzymatic activity of transfer RNA modification enzymes using radiolabelled tRNA substrates. In RNA modification (ed. JM Gott), pp. 57-101. Elsevier, New York.
    • (2007) RNA Modification , pp. 57-101
    • Grosjean, H.1    Droogmans, L.2    Roovers, M.3    Keith, G.4
  • 20
    • 0029786633 scopus 로고    scopus 로고
    • Recognition of the T-arm of tRNA by tRNA m5U54 -methyltransferase is not sequence specific
    • Gu X, IVanetich KM, Santi DV. 1996. Recognition of the T-arm of tRNA by tRNA m5U54 -methyltransferase is not sequence specific. Biochemistry 35: 11652-11659.
    • (1996) Biochemistry , vol.35 , pp. 11652-11659
    • Gu, X.1    Ivanetich, K.M.2    Santi, D.V.3
  • 22
    • 33845984589 scopus 로고    scopus 로고
    • Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: A structural perspective
    • Hur S, Stroud RM, Finer-Moore J. 2006. Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective. J Biol Chem 281: 38969-38973.
    • (2006) J Biol Chem , vol.281 , pp. 38969-38973
    • Hur, S.1    Stroud, R.M.2    Finer-Moore, J.3
  • 24
    • 0032827799 scopus 로고    scopus 로고
    • A simple and efficient method to reduce nontemplated nucleotide addition at the 39-terminus of RNAs transcribed by T7 RNA polymerase
    • Kao C, Zheng M, Rudisser S. 1999. A simple and efficient method to reduce nontemplated nucleotide addition at the 39-terminus of RNAs transcribed by T7 RNA polymerase. RNA 5: 1268-1272.
    • (1999) RNA , vol.5 , pp. 1268-1272
    • Kao, C.1    Zheng, M.2    Rudisser, S.3
  • 25
    • 0028650333 scopus 로고
    • Enzymatic mechanism of tRNA m5U54 methyltransferase
    • Kealey JT, Gu X, Santi DV. 1994. Enzymatic mechanism of tRNA m5U54 methyltransferase. Biochimie 76: 1133-1142.
    • (1994) Biochimie , vol.76 , pp. 1133-1142
    • Kealey, J.T.1    Gu, X.2    Santi, D.V.3
  • 26
    • 0033950924 scopus 로고    scopus 로고
    • Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry
    • Kirpekar F, Douthwaite S, Roepstorff P. 2000. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 6: 296-306.
    • (2000) RNA , vol.6 , pp. 296-306
    • Kirpekar, F.1    Douthwaite, S.2    Roepstorff, P.3
  • 27
    • 33748582906 scopus 로고    scopus 로고
    • Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements
    • Korostelev A, Trakhanov S, Laurberg M, Noller HF. 2006. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126: 1065-1077.
    • (2006) Cell , vol.126 , pp. 1065-1077
    • Korostelev, A.1    Trakhanov, S.2    Laurberg, M.3    Noller, H.F.4
  • 28
    • 0037439087 scopus 로고    scopus 로고
    • Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII
    • Lebars I, Yoshizawa S, Stenholm AR, Guittet E, Douthwaite S, Fourmy D. 2003. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J 22: 183-192.
    • (2003) EMBO J , vol.22 , pp. 183-192
    • Lebars, I.1    Yoshizawa, S.2    Stenholm, A.R.3    Guittet, E.4    Douthwaite, S.5    Fourmy, D.6
  • 29
    • 14844293080 scopus 로고    scopus 로고
    • A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function
    • Lee TT, Agarwalla S, Stroud RM. 2005. A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120: 599-611.
    • (2005) Cell , vol.120 , pp. 599-611
    • Lee, T.T.1    Agarwalla, S.2    Stroud, R.M.3
  • 30
    • 0345306616 scopus 로고    scopus 로고
    • Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry
    • Madsen CT, Mengel-Jorgensen J, Kirpekar F, Douthwaite S. 2003. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res 31: 4738-4746.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4738-4746
    • Madsen, C.T.1    Mengel-Jorgensen, J.2    Kirpekar, F.3    Douthwaite, S.4
  • 31
    • 0036295964 scopus 로고    scopus 로고
    • The linkage between magnesium binding and RNA folding
    • Misra VK, Draper DE. 2002. The linkage between magnesium binding and RNA folding. J Mol Biol 317: 507-521.
    • (2002) J Mol Biol , vol.317 , pp. 507-521
    • Misra, V.K.1    Draper, D.E.2
  • 32
    • 0021158357 scopus 로고
    • Structure of ribosomal RNA
    • Noller HF. 1984. Structure of ribosomal RNA. Annu Rev Biochem 53: 119-162.
    • (1984) Annu Rev Biochem , vol.53 , pp. 119-162
    • Noller, H.F.1
  • 33
    • 0034130606 scopus 로고    scopus 로고
    • Identification of the TRM2 gene encoding the tRNA(m5U54)- methyltransferase of Saccharomyces cerevisiae
    • Nordlund ME, Johansson JO, von Pawel-Rammingen U, Byström AS. 2000. Identification of the TRM2 gene encoding the tRNA(m5U54)- methyltransferase of Saccharomyces cerevisiae. RNA 6: 844-860.
    • (2000) RNA , vol.6 , pp. 844-860
    • Nordlund, M.E.1    Johansson, J.O.2    Von Pawel-Rammingen, U.3    Byström, A.S.4
  • 34
    • 0024289294 scopus 로고
    • Purification of transfer RNA m5U54-methyltransferase from Escherichia coli. association with RNA
    • Ny T, Lindström HR, Hagervall TG, Björk GR. 1988. Purification of transfer RNA m5U54-methyltransferase from Escherichia coli. association with RNA. Eur J Biochem 177: 467-475.
    • (1988) Eur J Biochem , vol.177 , pp. 467-475
    • Ny, T.1    Lindström, H.R.2    Hagervall, T.G.3    Björk, G.R.4
  • 36
    • 52949109757 scopus 로고    scopus 로고
    • YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962
    • Purta E, O'Connor M, Bujnicki JM, Douthwaite S. 2008. YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J Mol Biol 383: 641-651.
    • (2008) J Mol Biol , vol.383 , pp. 641-651
    • Purta, E.1    O'Connor, M.2    Bujnicki, J.M.3    Douthwaite, S.4
  • 37
    • 65949090299 scopus 로고    scopus 로고
    • YgdE is the 29-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA
    • Purta E, O'Connor M, Bujnicki JM, Douthwaite S. 2009. YgdE is the 29-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol 72: 1147-1158.
    • (2009) Mol Microbiol , vol.72 , pp. 1147-1158
    • Purta, E.1    O'Connor, M.2    Bujnicki, J.M.3    Douthwaite, S.4
  • 40
    • 0024241761 scopus 로고
    • Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension
    • Stern S, Moazed D, Noller HF. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol 164: 481-489.
    • (1988) Methods Enzymol , vol.164 , pp. 481-489
    • Stern, S.1    Moazed, D.2    Noller, H.F.3
  • 41
    • 52949092370 scopus 로고    scopus 로고
    • Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes
    • Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J. 2008. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol 383: 652-666.
    • (2008) J Mol Biol , vol.383 , pp. 652-666
    • Sunita, S.1    Tkaczuk, K.L.2    Purta, E.3    Kasprzak, J.M.4    Douthwaite, S.5    Bujnicki, J.M.6    Sivaraman, J.7
  • 43
    • 22844445708 scopus 로고    scopus 로고
    • Identification of a novel gene encoding a flavin-dependent tRNA:M5U methyltransferase in bacteria-evolutionary implications
    • Urbonavičius J, Skouloubris S, Myllykallio H, Grosjean H. 2005. Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria-evolutionary implications. Nucleic Acids Res 33: 3955-3964.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3955-3964
    • Urbonavičius, J.1    Skouloubris, S.2    Myllykallio, H.3    Grosjean, H.4
  • 44
    • 34548740836 scopus 로고    scopus 로고
    • In vitro detection of the enzyme activity of folate-dependent tRNA(U54, C5)-methyltransferase
    • (ed. JM Gott), Elsevier, New York
    • Urbonavičius J, Brochier-Armanet C, Skouloubris S, Myllykallio H, Grosjean H. 2007. In vitro detection of the enzyme activity of folate-dependent tRNA(U54, C5)-methyltransferase. In RNA modification (ed. JM Gott), Vol. 425, pp. 103-119. Elsevier, New York.
    • (2007) RNA Modification , vol.425 , pp. 103-119
    • Urbonavičius, J.1    Brochier-Armanet, C.2    Skouloubris, S.3    Myllykallio, H.4    Grosjean, H.5
  • 46
    • 35548979485 scopus 로고    scopus 로고
    • Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA
    • Ying BW, Fourmy D, Yoshizawa S. 2007. Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA. RNA 13: 2042-2050.
    • (2007) RNA , vol.13 , pp. 2042-2050
    • Ying, B.W.1    Fourmy, D.2    Yoshizawa, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.