메뉴 건너뛰기




Volumn 8, Issue 11, 2012, Pages 913-919

Discovery and biological characterization of geranylated RNA in bacteria

Author keywords

[No Author keywords available]

Indexed keywords

CARBON 13; NITROGEN 15; NUCLEIC ACID; NUCLEOTIDE; RNA; SULFUR; TRANSFER RNA;

EID: 84867673706     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1070     Document Type: Article
Times cited : (96)

References (45)
  • 1
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • DOI 10.1038/nrg1379
    • He, L. & Hannon, G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5, 522-531 (2004). (Pubitemid 38868508)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.7 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 2
    • 34548778155 scopus 로고    scopus 로고
    • Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins
    • DOI 10.1038/nrg2172, PII NRG2172
    • Serganov, A. & Patel, D.J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat. Rev. Genet. 8, 776-790 (2007). (Pubitemid 47429208)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.10 , pp. 776-790
    • Serganov, A.1    Patel, D.J.2
  • 4
    • 77956170809 scopus 로고    scopus 로고
    • RNA-based antiviral immunity
    • Ding, S.W. RNA-based antiviral immunity. Nat. Rev. Immunol. 10, 632-644 (2010).
    • (2010) Nat. Rev. Immunol. , vol.10 , pp. 632-644
    • Ding, S.W.1
  • 5
    • 78651335915 scopus 로고    scopus 로고
    • Te RNA modifcation database RNAMDB: 2011 update
    • Cantara, W.A. et al. Te RNA Modifcation Database, RNAMDB: 2011 update. Nucleic Acids Res. 39, D195-D201 (2011).
    • (2011) Nucleic Acids Res. , vol.39
    • Cantara, W.A.1
  • 6
    • 77949820848 scopus 로고    scopus 로고
    • Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
    • Ikeuchi, Y. et al. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat. Chem. Biol. 6, 277-282 (2010).
    • (2010) Nat. Chem. Biol. , vol.6 , pp. 277-282
    • Ikeuchi, Y.1
  • 7
    • 77649263055 scopus 로고    scopus 로고
    • Agmatidine, a modifed cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine
    • Mandal, D. et al. Agmatidine, a modifed cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Proc. Natl. Acad. Sci. USA 107, 2872-2877 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 2872-2877
    • Mandal, D.1
  • 8
    • 29544452864 scopus 로고    scopus 로고
    • Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions
    • DOI 10.1016/j.molcel.2005.11.001, PII S1097276505017612
    • Ikeuchi, Y., Shigi, N., Kato, J., Nishimura, A. & Suzuki, T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol. Cell 21, 97-108 (2006). (Pubitemid 43017852)
    • (2006) Molecular Cell , vol.21 , Issue.1 , pp. 97-108
    • Ikeuchi, Y.1    Shigi, N.2    Kato, J.-I.3    Nishimura, A.4    Suzuki, T.5
  • 9
    • 79956306359 scopus 로고    scopus 로고
    • Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modifcation
    • Miles, Z.D., McCarty, R.M., Molnar, G. & Bandarian, V. Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modifcation. Proc. Natl. Acad. Sci. USA 108, 7368-7372 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 7368-7372
    • Miles, Z.D.1    McCarty, R.M.2    Molnar, G.3    Bandarian, V.4
  • 10
    • 33646778150 scopus 로고    scopus 로고
    • Biosynthesis of wybutosine, a hyper-modifed nucleoside in eukaryotic phenylalanine tRNA
    • Noma, A., Kirino, Y., Ikeuchi, Y. & Suzuki, T. Biosynthesis of wybutosine, a hyper-modifed nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25, 2142-2154 (2006).
    • (2006) EMBO J. , vol.25 , pp. 2142-2154
    • Noma, A.1    Kirino, Y.2    Ikeuchi, Y.3    Suzuki, T.4
  • 11
    • 66049158949 scopus 로고    scopus 로고
    • A Chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA
    • Kowtoniuk, W.E., Shen, Y., Heemstra, J.M., Agarwal, I. & Liu, D.R. A Chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Proc. Natl. Acad. Sci. USA 106, 7768-7773 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 7768-7773
    • Kowtoniuk, W.E.1    Shen, Y.2    Heemstra, J.M.3    Agarwal, I.4    Liu, D.R.5
  • 13
    • 0030825580 scopus 로고    scopus 로고
    • How were porphyrins and lipids synthesized in the RNA world?
    • DOI 10.1016/S0040-4039(97)01143-X, PII S004040399701143X
    • Scott, A.I. How were porphyrins and lipids synthesized in the RNA world? Tetrahedr. Lett. 38, 4961-4964 (1997). (Pubitemid 27345027)
    • (1997) Tetrahedron Letters , vol.38 , Issue.28 , pp. 4961-4964
    • Scott, A.I.1
  • 14
    • 0023664535 scopus 로고
    • Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities
    • Hagervall, T.G., Edmonds, C.G., McCloskey, J.A. & Bjork, G.R. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. J. Biol. Chem. 262, 8488-8495 (1987).
    • (1987) J. Biol. Chem. , vol.262 , pp. 8488-8495
    • Hagervall, T.G.1    Edmonds, C.G.2    McCloskey, J.A.3    Bjork, G.R.4
  • 15
    • 0037417771 scopus 로고    scopus 로고
    • Mnma and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli
    • DOI 10.1021/bi026536+
    • Kambampati, R. & Lauhon, C.T. MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 42, 1109-1117 (2003). (Pubitemid 36159546)
    • (2003) Biochemistry , vol.42 , Issue.4 , pp. 1109-1117
    • Kambampati, R.1    Lauhon, C.T.2
  • 16
    • 0031907784 scopus 로고    scopus 로고
    • Active drug substance impurity profiling. Part II. LC/MS/MS fingerprinting
    • DOI 10.1016/S0731-7085(97)00132-5, PII S0731708597001325
    • Nicolas, E.C. & Scholz, T.H. Active drug substance impurity profling part II. LC/MS/MS fngerprinting. J. Pharm. Biomed. Anal. 16, 825-836 (1998). (Pubitemid 28097410)
    • (1998) Journal of Pharmaceutical and Biomedical Analysis , vol.16 , Issue.5 , pp. 825-836
    • Nicolas, E.C.1    Scholz, T.H.2
  • 17
    • 20044392729 scopus 로고    scopus 로고
    • A 'gain of function' mutation in a protein mediates production of novel modified nucleosides
    • DOI 10.1038/sj.emboj.7600666
    • Chen, P., Crain, P.F., Nasvall, S.J., Pomerantz, S.C. & Bjork, G.R.A. "Gain of function" mutation in a protein mediates production of novel modifed nucleosides. EMBO J. 24, 1842-1851 (2005). (Pubitemid 40769503)
    • (2005) EMBO Journal , vol.24 , Issue.10 , pp. 1842-1851
    • Chen, P.1    Crain, P.F.2    Nasvall, S.J.3    Pomerantz, S.C.4    Bjork, G.R.5
  • 18
    • 58149191272 scopus 로고    scopus 로고
    • TRNAdb 2009: Compilation of tRNA sequences and tRNA genes
    • Jühling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159-D162 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Jühling, F.1
  • 19
    • 0016733670 scopus 로고
    • Te nucleotide sequences of the two glutamine transfer ribonucleic acids from Escherichia coli
    • Yaniv, M. & Folk, W.R. Te nucleotide sequences of the two glutamine transfer ribonucleic acids from Escherichia coli. J. Biol. Chem. 250, 3243-3253 (1975).
    • (1975) J. Biol. Chem. , vol.250 , pp. 3243-3253
    • Yaniv, M.1    Folk, W.R.2
  • 20
    • 77951276163 scopus 로고    scopus 로고
    • Optimization of the hybridization-based method for purifcation of thermostable tRNAs in the presence of tetraalkylammonium salts
    • Yokogawa, T., Kitamura, Y., Nakamura, D., Ohno, S. & Nishikawa, K. Optimization of the hybridization-based method for purifcation of thermostable tRNAs in the presence of tetraalkylammonium salts. Nucleic Acids Res. 38, e89 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Yokogawa, T.1    Kitamura, Y.2    Nakamura, D.3    Ohno, S.4    Nishikawa, K.5
  • 21
    • 0242717401 scopus 로고
    • On the structure of ribonucleic acids. 2. Te products of ribonuclease action
    • Volkin, E. & Cohn, W.E. On the structure of ribonucleic acids. 2. Te products of ribonuclease action. J. Biol. Chem. 205, 767-782 (1953).
    • (1953) J. Biol. Chem. , vol.205 , pp. 767-782
    • Volkin, E.1    Cohn, W.E.2
  • 22
    • 44049123270 scopus 로고
    • Tandem mass spectrometry of small, multiply charged oligonucleotides
    • Mcluckey, S.A., Vanberkel, G.J. & Glish, G.L. Tandem mass spectrometry of small, multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom. 3, 60-70 (1992).
    • (1992) J. Am. Soc. Mass Spectrom. , vol.3 , pp. 60-70
    • McLuckey, S.A.1    Vanberkel, G.J.2    Glish, G.L.3
  • 23
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • DOI 10.1006/jmbi.1996.0428
    • Dong, H., Nilsson, L. & Kurland, C.G. Co-variation of tRNA abundance and codon usage in Escherichia coli at diferent growth rates. J. Mol. Biol. 260, 649-663 (1996). (Pubitemid 26270960)
    • (1996) Journal of Molecular Biology , vol.260 , Issue.5 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 24
    • 0021173799 scopus 로고
    • Quantities of individual aminoacyl-tRNA families and their turnover in Escherichia coli
    • Jakubowski, H. & Goldman, E. Quantities of individual aminoacyl-tRNA families and their turnover in Escherichia coli. J. Bacteriol. 158, 769-776 (1984). (Pubitemid 14088588)
    • (1984) Journal of Bacteriology , vol.158 , Issue.3 , pp. 769-776
    • Jakubowski, H.1    Goldman, E.2
  • 25
    • 0345826117 scopus 로고    scopus 로고
    • Functional diversity of the rhodanese homology domain: The Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase
    • DOI 10.1074/jbc.M310442200
    • Wolfe, M.D. et al. Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase. J. Biol. Chem. 279, 1801-1809 (2004). (Pubitemid 38084447)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.3 , pp. 1801-1809
    • Wolfe, M.D.1    Ahmed, F.2    Lacourciere, G.M.3    Lauhon, C.T.4    Stadtman, T.C.5    Larson, T.J.6
  • 26
    • 0023395492 scopus 로고
    • Infuence of the codon following the AUG initiation codon on the expression of a modifed lacZ gene in Escherichia coli
    • Looman, A.C. et al. Infuence of the codon following the AUG initiation codon on the expression of a modifed lacZ gene in Escherichia coli. EMBO J. 6, 2489-2492 (1987).
    • (1987) EMBO J. , vol.6 , pp. 2489-2492
    • Looman, A.C.1
  • 27
    • 0026409389 scopus 로고
    • Absolute in vivo translation rates of individual codons in Escherichia coli: The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate
    • Sørensen, M.A. & Pedersen, S. Absolute in vivo translation rates of individual codons in Escherichia coli. Te two glutamic acid codons GAA and GAG are translated with a threefold diference in rate. J. Mol. Biol. 222, 265-280 (1991). (Pubitemid 121004006)
    • (1991) Journal of Molecular Biology , vol.222 , Issue.2 , pp. 265-280
    • Sorensen, M.A.1    Pedersen, S.2
  • 28
    • 0024361792 scopus 로고
    • Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: Purification, codon specificity and translational activity
    • Wittwer, A.J. & Ching, W.M. Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: purifcation, codon specifcity and translational activity. Biofactors 2, 27-34 (1989). (Pubitemid 19209816)
    • (1989) BioFactors , vol.2 , Issue.1 , pp. 27-34
    • Wittwer, A.J.1    Ching, W.-M.2
  • 29
    • 0242473140 scopus 로고    scopus 로고
    • Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli
    • DOI 10.1093/emboj/cdg561
    • Gurvich, O.L. et al. Sequences that direct signifcant levels of frameshifing are frequent in coding regions of Escherichia coli. EMBO J. 22, 5941-5950 (2003). (Pubitemid 37408829)
    • (2003) EMBO Journal , vol.22 , Issue.21 , pp. 5941-5950
    • Gurvich, O.L.1    Baranov, P.V.2    Zhou, J.3    Hammer, A.W.4    Gesteland, R.F.5    Atkins, J.F.6
  • 31
    • 19444374782 scopus 로고    scopus 로고
    • Biosynthesis and function of tRNA wobble modifcations
    • ed. Grosjean, H. Springer, Berlin/Heidelberg
    • Suzuki, T. Biosynthesis and function of tRNA wobble modifcations. in Fine-Tuning of RNA Functions by Modifcation and Editing, Vol. 12 (ed. Grosjean, H.) 23-69 (Springer, Berlin/Heidelberg, 2005).
    • (2005) Fine-Tuning of RNA Functions by Modifcation and Editing , vol.12 , pp. 23-69
    • Suzuki, T.1
  • 32
    • 33846269602 scopus 로고    scopus 로고
    • TRNA's wobble decoding of the genome: 40 years of modification
    • DOI 10.1016/j.jmb.2006.11.046, PII S0022283606015865
    • Agris, P.F., Vendeix, F.A. & Graham, W.D. tRNA's wobble decoding of the genome: 40 years of modifcation. J. Mol. Biol. 366, 1-13 (2007). (Pubitemid 46123342)
    • (2007) Journal of Molecular Biology , vol.366 , Issue.1 , pp. 1-13
    • Agris, P.F.1    Vendeix, F.A.P.2    Graham, W.D.3
  • 35
    • 0027273985 scopus 로고
    • A 2-thiouridine derivative in tRNA(Glu) is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase
    • Glu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 32, 3836-3841 (1993). (Pubitemid 23126971)
    • (1993) Biochemistry , vol.32 , Issue.15 , pp. 3836-3841
    • Sylvers, L.A.1    Rogers, K.C.2    Shimizu, M.3    Ohtsuka, E.4    Soll, D.5
  • 36
    • 0344026255 scopus 로고    scopus 로고
    • Single atom modifcation (O→S) of tRNA confers ribosome binding
    • Ashraf, S.S. et al. Single atom modifcation (O→S) of tRNA confers ribosome binding. RNA 5, 188-194 (1999).
    • (1999) RNA , vol.5 , pp. 188-194
    • Ashraf, S.S.1
  • 37
    • 0034619490 scopus 로고    scopus 로고
    • LysUUU species
    • LysUUU species. Biochemistry 39, 13390-13395 (2000).
    • (2000) Biochemistry , vol.39 , pp. 13390-13395
    • Yarian, C.1
  • 38
    • 0002561141 scopus 로고    scopus 로고
    • Historical perspectives on RNA nucleoside modifcations
    • eds. Grosjean, H. & Benne, R. ASM Press
    • Lane, B.G. Historical Perspectives on RNA Nucleoside Modifcations. in Modifcation and Editing of RNA (eds. Grosjean, H. & Benne, R.) 1-20 (ASM Press, 1998).
    • (1998) Modifcation and Editing of RNA , pp. 1-20
    • Lane, B.G.1
  • 39
    • 0026594057 scopus 로고
    • Sequence requirements for efcient translational frameshifing in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon
    • Tsuchihashi, Z. & Brown, P.O. Sequence requirements for efcient translational frameshifing in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev. 6, 511-519 (1992).
    • (1992) Genes Dev. , vol.6 , pp. 511-519
    • Tsuchihashi, Z.1    Brown, P.O.2
  • 42
    • 78650683942 scopus 로고    scopus 로고
    • A quantitative systems approach reveals dynamic control of tRNA modifcations during cellular stress
    • Chan, C.T. et al. A quantitative systems approach reveals dynamic control of tRNA modifcations during cellular stress. PLoS Genet. 6, e1001247 (2010).
    • (2010) PLoS Genet. , vol.6
    • Chan, C.T.1
  • 43
    • 79954570710 scopus 로고    scopus 로고
    • RNA localization in bacteria
    • Keiler, K.C. RNA localization in bacteria. Curr. Opin. Microbiol. 14, 155-159 (2011).
    • (2011) Curr. Opin. Microbiol. , vol.14 , pp. 155-159
    • Keiler, K.C.1
  • 45
    • 59049093107 scopus 로고    scopus 로고
    • Efects of linker sequences on vesicle fusion mediated by lipid-anchored DNA oligonucleotides
    • Chan, Y.H., van Lengerich, B. & Boxer, S.G. Efects of linker sequences on vesicle fusion mediated by lipid-anchored DNA oligonucleotides. Proc. Natl. Acad. Sci. USA 106, 979-984 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 979-984
    • Chan, Y.H.1    Van Lengerich, B.2    Boxer, S.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.