-
1
-
-
33644876507
-
The tmRDB and SRPDB resources
-
Andersen, E.S., Rosenblad, M.A., Larsen, N., Westergaard, J.C., Burks, J., Wower, I.K., Wower, J., Gorodkin, J., Samuelsson, T., and Zwieb, C. 2006. The tmRDB and SRPDB resources. Nucleic Acids Res. 34: D163-D168.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Andersen, E.S.1
Rosenblad, M.A.2
Larsen, N.3
Westergaard, J.C.4
Burks, J.5
Wower, I.K.6
Wower, J.7
Gorodkin, J.8
Samuelsson, T.9
Zwieb, C.10
-
2
-
-
0034646235
-
Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli
-
Barends, S., Wower, J., and Kraal, B. 2000. Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli. Biochemistry 39: 2652-2658.
-
(2000)
Biochemistry
, vol.39
, pp. 2652-2658
-
-
Barends, S.1
Wower, J.2
Kraal, B.3
-
3
-
-
0035900548
-
Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA
-
Barends, S., Karzai, A.W., Sauer, R.T., Wower, J., and Kraal, B. 2001. Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA. J. Mol. Biol. 314: 9-21.
-
(2001)
J. Mol. Biol
, vol.314
, pp. 9-21
-
-
Barends, S.1
Karzai, A.W.2
Sauer, R.T.3
Wower, J.4
Kraal, B.5
-
4
-
-
34347233462
-
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
-
Bessho, Y., Shibata, R., Sekine, S., Murayama, K., Higashijima, K., Hori-Takemoto, C., Shirouzu, M., Kuramitsu, S., and Yokoyama, S. 2007. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc. Natl. Acad. Sci. 104: 8293-8298.
-
(2007)
Proc. Natl. Acad. Sci
, vol.104
, pp. 8293-8298
-
-
Bessho, Y.1
Shibata, R.2
Sekine, S.3
Murayama, K.4
Higashijima, K.5
Hori-Takemoto, C.6
Shirouzu, M.7
Kuramitsu, S.8
Yokoyama, S.9
-
5
-
-
26444443117
-
Comparative 3D modeling of tmRNA
-
Burks, J., Zwieb, C., Muller, F., Wower, I., and Wower, J. 2005. Comparative 3D modeling of tmRNA. BMC Mol. Biol. 6: 14-29.
-
(2005)
BMC Mol. Biol
, vol.6
, pp. 14-29
-
-
Burks, J.1
Zwieb, C.2
Muller, F.3
Wower, I.4
Wower, J.5
-
6
-
-
0031014984
-
Probing the structure of the Escherichia coli 10Sa RNA (tmRNA)
-
Felden, B., Himeno, H., Muto, A., McCutcheon, J.P., Atkins, J.F., and Gesteland, R.F. 1997. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). RNA 3: 89-103.
-
(1997)
RNA
, vol.3
, pp. 89-103
-
-
Felden, B.1
Himeno, H.2
Muto, A.3
McCutcheon, J.P.4
Atkins, J.F.5
Gesteland, R.F.6
-
7
-
-
0036566827
-
Two-piece tmRNA in cyanobacteria and its structural analysis
-
Gaudin, C., Zhou, X., Williams, K.P., and Felden, B. 2002. Two-piece tmRNA in cyanobacteria and its structural analysis. Nucleic Acids Res. 30: 2018-2024.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2018-2024
-
-
Gaudin, C.1
Zhou, X.2
Williams, K.P.3
Felden, B.4
-
8
-
-
0346494971
-
The tmRNA website: Reductive evolution of tmRNA in plastids and other endosymbionts
-
Gueneau de Novoa, P. and Williams, K.P. 2004. The tmRNA website: Reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res. 32: D104-D108.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Gueneau de Novoa, P.1
Williams, K.P.2
-
9
-
-
2942755867
-
Pre-binding of small protein B to a stalled ribosome triggers trans-translation
-
Hallier, M., Ivanova, N., Rametti, A., Pavlov, M., Ehrenberg, M., and Felden, B. 2004. Pre-binding of small protein B to a stalled ribosome triggers trans-translation. J. Biol. Chem. 279: 25978-25985.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 25978-25985
-
-
Hallier, M.1
Ivanova, N.2
Rametti, A.3
Pavlov, M.4
Ehrenberg, M.5
Felden, B.6
-
10
-
-
33645802168
-
Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation
-
Hallier, M., Desreac, J., and Felden, B. 2006. Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation. Nucleic Acids Res. 34: 1935-1943.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1935-1943
-
-
Hallier, M.1
Desreac, J.2
Felden, B.3
-
11
-
-
21344471643
-
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA
-
Ivanova, N., Pavlov, M.Y., Bouakaz, E., Ehrenberg, M., and Schiavone, L.H. 2005. Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res. 33: 3529-3539.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3529-3539
-
-
Ivanova, N.1
Pavlov, M.Y.2
Bouakaz, E.3
Ehrenberg, M.4
Schiavone, L.H.5
-
12
-
-
0345465673
-
SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)
-
Karzai, A.W., Susskind, M.M., and Sauer, R.T. 1999. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 18: 3793-3799.
-
(1999)
EMBO J
, vol.18
, pp. 3793-3799
-
-
Karzai, A.W.1
Susskind, M.M.2
Sauer, R.T.3
-
13
-
-
33750838456
-
Cryo-EM visualization of transfer-messenger RNA with two SmpBs in a stalled ribosome
-
Kaur, S., Gillet, R., Li, W., Gursky, R., and Frank, J. 2006. Cryo-EM visualization of transfer-messenger RNA with two SmpBs in a stalled ribosome. Proc. Natl. Acad. Sci. 103: 16484-16489.
-
(2006)
Proc. Natl. Acad. Sci
, vol.103
, pp. 16484-16489
-
-
Kaur, S.1
Gillet, R.2
Li, W.3
Gursky, R.4
Frank, J.5
-
14
-
-
0034608854
-
tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter
-
Keiler, K.C., Shapiro, L., and Williams, K.P. 2000. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc. Natl. Acad. Sci. 97: 7778-7783.
-
(2000)
Proc. Natl. Acad. Sci
, vol.97
, pp. 7778-7783
-
-
Keiler, K.C.1
Shapiro, L.2
Williams, K.P.3
-
15
-
-
0034852587
-
Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities
-
Kelley, S.T., Harris, J.K., and Pace, N.R. 2001. Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities. RNA 7: 1310-1316.
-
(2001)
RNA
, vol.7
, pp. 1310-1316
-
-
Kelley, S.T.1
Harris, J.K.2
Pace, N.R.3
-
16
-
-
0028124122
-
A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli
-
Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K., and Inokuchi, H. 1994. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl. Acad. Sci. 91: 9223-9227.
-
(1994)
Proc. Natl. Acad. Sci
, vol.91
, pp. 9223-9227
-
-
Komine, Y.1
Kitabatake, M.2
Yokogawa, T.3
Nishikawa, K.4
Inokuchi, H.5
-
17
-
-
34748881977
-
A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation
-
Konno, T., Kurita, D., Takada, K., Muto, A., and Himeno, H. 2007. A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA 13: 1723-1731.
-
(2007)
RNA
, vol.13
, pp. 1723-1731
-
-
Konno, T.1
Kurita, D.2
Takada, K.3
Muto, A.4
Himeno, H.5
-
18
-
-
0034951396
-
Determinants on tmRNA for initiating efficient and precise trans-translation: Some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro
-
Lee, S., Ishii, M., Tadaki, T., Muto, A., and Himeno, H. 2001. Determinants on tmRNA for initiating efficient and precise trans-translation: Some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro. RNA 7: 999-1012.
-
(2001)
RNA
, vol.7
, pp. 999-1012
-
-
Lee, S.1
Ishii, M.2
Tadaki, T.3
Muto, A.4
Himeno, H.5
-
19
-
-
0032539857
-
39 Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli
-
Li, Z., Pandit, S., and Deutscher, M.P. 1998. 39 Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl. Acad. Sci. 95: 2856-2861.
-
(1998)
Proc. Natl. Acad. Sci
, vol.95
, pp. 2856-2861
-
-
Li, Z.1
Pandit, S.2
Deutscher, M.P.3
-
20
-
-
4544289260
-
Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules
-
McGinness, K.E. and Sauer, R.T. 2004. Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules. Proc. Natl. Acad. Sci. 101: 13454-13459.
-
(2004)
Proc. Natl. Acad. Sci
, vol.101
, pp. 13454-13459
-
-
McGinness, K.E.1
Sauer, R.T.2
-
21
-
-
17844381357
-
Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation
-
Metzinger, L., Hallier, M., and Felden, B. 2005. Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation. Nucleic Acids Res. 33: 2384-2394.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2384-2394
-
-
Metzinger, L.1
Hallier, M.2
Felden, B.3
-
22
-
-
48249108321
-
The role of upstream sequences in selecting the reading frame on tmRNA
-
Miller, M.R., Heally, D.W., Robison, S.G., Dewey, J.D., and Buskirk, A.R. 2008. The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol. 6: 29-38.
-
(2008)
BMC Biol
, vol.6
, pp. 29-38
-
-
Miller, M.R.1
Heally, D.W.2
Robison, S.G.3
Dewey, J.D.4
Buskirk, A.R.5
-
23
-
-
34247103448
-
The tmRNA system for translational surveillance and ribosome rescue
-
Moore, S.D. and Sauer, R.T. 2007. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76: 101-124.
-
(2007)
Annu. Rev. Biochem
, vol.76
, pp. 101-124
-
-
Moore, S.D.1
Sauer, R.T.2
-
24
-
-
0033568555
-
An NMR and mutational analysis of an RNA pseudoknot of Escherichia coli tmRNA involved in trans-translation
-
Nameki, N., Chattopadhyay, P., Himeno, H., Muto, A., and Kawai, G. 1999a. An NMR and mutational analysis of an RNA pseudoknot of Escherichia coli tmRNA involved in trans-translation. Nucleic Acids Res. 27: 3667-3675.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3667-3675
-
-
Nameki, N.1
Chattopadhyay, P.2
Himeno, H.3
Muto, A.4
Kawai, G.5
-
25
-
-
0033605218
-
Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA
-
Nameki, N., Felden, B., Atkins, J.F., Gesteland, R.F., Himeno, H., and Muto, A. 1999b. Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA. J. Mol. Biol. 286: 733-744.
-
(1999)
J. Mol. Biol
, vol.286
, pp. 733-744
-
-
Nameki, N.1
Felden, B.2
Atkins, J.F.3
Gesteland, R.F.4
Himeno, H.5
Muto, A.6
-
26
-
-
0034737453
-
Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs
-
Nameki, N., Tadaki, T., Himeno, H., and Muto, A. 2000. Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs. FEBS Lett. 470: 345-349.
-
(2000)
FEBS Lett
, vol.470
, pp. 345-349
-
-
Nameki, N.1
Tadaki, T.2
Himeno, H.3
Muto, A.4
-
27
-
-
0032840381
-
Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu
-
Rudinger-Thirion, J., Giege, R., and Felden, B. 1999. Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. RNA 5: 989-992.
-
(1999)
RNA
, vol.5
, pp. 989-992
-
-
Rudinger-Thirion, J.1
Giege, R.2
Felden, B.3
-
28
-
-
0023953676
-
Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro
-
Sampson, J.R. and Uhlenbeck, O.C. 1988. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc. Natl. Acad. Sci. 85: 1033-1037.
-
(1988)
Proc. Natl. Acad. Sci
, vol.85
, pp. 1033-1037
-
-
Sampson, J.R.1
Uhlenbeck, O.C.2
-
29
-
-
4344705601
-
A third lineage with two-piece tmRNA
-
Sharkady, S.M. and Williams, K.P. 2004. A third lineage with two-piece tmRNA. Nucleic Acids Res. 32: 4531-4538.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 4531-4538
-
-
Sharkady, S.M.1
Williams, K.P.2
-
30
-
-
0024241761
-
Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension
-
Stern, S., Moazed, D., and Noller, H.F. 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
-
31
-
-
36849093840
-
Functional SmpB-ribosome interactions require tmRNA
-
Sundermeier, T.R. and Karzai, A.W. 2007. Functional SmpB-ribosome interactions require tmRNA. J. Biol. Chem. 282: 34779-34786.
-
(2007)
J. Biol. Chem
, vol.282
, pp. 34779-34786
-
-
Sundermeier, T.R.1
Karzai, A.W.2
-
32
-
-
33744505213
-
Genetic analysis of the structure and function of transfer-messenger RNA pseudoknot 1
-
Tanner, D.R., Dewey, J.D., Miller, M.R., and Buskirk, A.R. 2006. Genetic analysis of the structure and function of transfer-messenger RNA pseudoknot 1. J. Biol. Chem. 281: 10561-10566.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 10561-10566
-
-
Tanner, D.R.1
Dewey, J.D.2
Miller, M.R.3
Buskirk, A.R.4
-
33
-
-
1942533456
-
tRNA slippage at the tmRNA resume codon
-
Trimble, M.J., Minnicus, A., and Williams, K.P. 2004. tRNA slippage at the tmRNA resume codon. RNA 10: 805-812.
-
(2004)
RNA
, vol.10
, pp. 805-812
-
-
Trimble, M.J.1
Minnicus, A.2
Williams, K.P.3
-
34
-
-
0242515749
-
Visualizing tmRNA entry into a stalled ribosome
-
Valle, M., Gillet, R., Kaur, S., Henne, A., Ramakrishnan, V., and Frank, J. 2003. Visualizing tmRNA entry into a stalled ribosome. Science 300: 127-130.
-
(2003)
Science
, vol.300
, pp. 127-130
-
-
Valle, M.1
Gillet, R.2
Kaur, S.3
Henne, A.4
Ramakrishnan, V.5
Frank, J.6
-
35
-
-
0026350896
-
Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase
-
Varshney, U., Lee, C.P., and RajBhandary, U.L. 1991. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J. Biol. Chem. 266: 24712-24718.
-
(1991)
J. Biol. Chem
, vol.266
, pp. 24712-24718
-
-
Varshney, U.1
Lee, C.P.2
RajBhandary, U.L.3
-
36
-
-
0036567510
-
Descent of a split RNA
-
Williams, K.P. 2002. Descent of a split RNA. Nucleic Acids Res. 30: 2025-2030.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2025-2030
-
-
Williams, K.P.1
-
37
-
-
0029907105
-
Phylogenetic analysis of tmRNA secondary structure
-
Williams, K.P. and Bartel, D.P. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2: 1306-1310.
-
(1996)
RNA
, vol.2
, pp. 1306-1310
-
-
Williams, K.P.1
Bartel, D.P.2
-
38
-
-
0033215307
-
Resuming translation on tmRNA: A unique mode of determining a reading frame
-
Williams, K.P., Martindale, K.A., and Bartel, D.P. 1999. Resuming translation on tmRNA: A unique mode of determining a reading frame. EMBO J. 18: 5423-5433.
-
(1999)
EMBO J
, vol.18
, pp. 5423-5433
-
-
Williams, K.P.1
Martindale, K.A.2
Bartel, D.P.3
-
39
-
-
0034423519
-
Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome
-
Wower, I.K., Zwieb, C.W., Guven, S.A., and Wower, J. 2000. Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome. EMBO J. 19: 6612-6621.
-
(2000)
EMBO J
, vol.19
, pp. 6612-6621
-
-
Wower, I.K.1
Zwieb, C.W.2
Guven, S.A.3
Wower, J.4
-
40
-
-
0037118708
-
SmpB: A protein that binds to double-stranded segments in tmRNA and tRNA
-
Wower, J., Zwieb, C.W., Hoffman, D.W., and Wower, I.K. 2002. SmpB: A protein that binds to double-stranded segments in tmRNA and tRNA. Biochemistry 41: 8826-8836.
-
(2002)
Biochemistry
, vol.41
, pp. 8826-8836
-
-
Wower, J.1
Zwieb, C.W.2
Hoffman, D.W.3
Wower, I.K.4
-
41
-
-
11144236530
-
Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation
-
Wower, I.K., Zwieb, C., and Wower, J. 2004. Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation. J. Biol. Chem. 279: 54202-54209.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 54202-54209
-
-
Wower, I.K.1
Zwieb, C.2
Wower, J.3
-
42
-
-
17844398246
-
Transfer-messenger RNA unfolds as it transits the ribosome
-
Wower, I.K., Zwieb, C., and Wower, J. 2005. Transfer-messenger RNA unfolds as it transits the ribosome. RNA 11: 668-673.
-
(2005)
RNA
, vol.11
, pp. 668-673
-
-
Wower, I.K.1
Zwieb, C.2
Wower, J.3
-
43
-
-
0033983838
-
tmRDB (tmRNA database)
-
Zwieb, C. and Wower, J. 2000. tmRDB (tmRNA database). Nucleic Acids Res. 28: 169-170.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 169-170
-
-
Zwieb, C.1
Wower, J.2
-
44
-
-
0033562579
-
Comparative sequence analysis of tmRNA
-
Zwieb, C., Wower, I., and Wower, J. 1999. Comparative sequence analysis of tmRNA. Nucleic Acids Res. 27: 2063-2071.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2063-2071
-
-
Zwieb, C.1
Wower, I.2
Wower, J.3
|