-
1
-
-
66849109240
-
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins
-
Kramer G, Boehringer D, Ban N, Bukau B, (2009) The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol 16: 589–597. doi: 10.1038/nsmb.1614 19491936
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 589-597
-
-
Kramer, G.1
Boehringer, D.2
Ban, N.3
Bukau, B.4
-
2
-
-
84925553022
-
Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo
-
Pechmann S, Chartron JW, Frydman J, (2014) Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat Struct Mol Biol 21: 1100–1105. doi: 10.1038/nsmb.2919 25420103
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 1100-1105
-
-
Pechmann, S.1
Chartron, J.W.2
Frydman, J.3
-
3
-
-
79551690253
-
Folding at the birth of the nascent chain: coordinating translation with co-translational folding
-
Zhang G, Ignatova Z, (2011) Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr Opin Struct Biol 21: 25–31. doi: 10.1016/j.sbi.2010.10.008 21111607
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 25-31
-
-
Zhang, G.1
Ignatova, Z.2
-
4
-
-
0015907492
-
The dynamics of nucleic-acid single-strand conformation changes. Oligo- and polyriboadenylic acids
-
Porschke D, (1973) The dynamics of nucleic-acid single-strand conformation changes. Oligo- and polyriboadenylic acids. European journal of biochemistry / FEBS 39: 117–126. 4770785
-
(1973)
European journal of biochemistry / FEBS
, vol.39
, pp. 117-126
-
-
Porschke, D.1
-
5
-
-
84893427735
-
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
-
Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, et al. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505: 696–700. doi: 10.1038/nature12756 24270811
-
(2014)
Nature
, vol.505
, pp. 696-700
-
-
Ding, Y.1
Tang, Y.2
Kwok, C.K.3
Zhang, Y.4
Bevilacqua, P.C.5
-
6
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, et al. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467: 103–107. doi: 10.1038/nature09322 20811459
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
Wan, Y.2
Mazor, E.3
Rinn, J.L.4
Nutter, R.C.5
-
7
-
-
84871887837
-
Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome
-
Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, et al. (2012) Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 24: 4346–4359. doi: 10.1105/tpc.112.104232 23150631
-
(2012)
Plant Cell
, vol.24
, pp. 4346-4359
-
-
Li, F.1
Zheng, Q.2
Vandivier, L.E.3
Willmann, M.R.4
Chen, Y.5
-
8
-
-
84893351549
-
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
-
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS, (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505: 701–705. doi: 10.1038/nature12894 24336214
-
(2014)
Nature
, vol.505
, pp. 701-705
-
-
Rouskin, S.1
Zubradt, M.2
Washietl, S.3
Kellis, M.4
Weissman, J.S.5
-
9
-
-
84925777836
-
Structural imprints in vivo decode RNA regulatory mechanisms
-
Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, et al. (2015) Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519: 486–490. doi: 10.1038/nature14263 25799993
-
(2015)
Nature
, vol.519
, pp. 486-490
-
-
Spitale, R.C.1
Flynn, R.A.2
Zhang, Q.C.3
Crisalli, P.4
Lee, B.5
-
10
-
-
84925799191
-
hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1
-
Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, et al. (2015) hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature 519: 491–494. doi: 10.1038/nature14280 25799984
-
(2015)
Nature
, vol.519
, pp. 491-494
-
-
Sugimoto, Y.1
Vigilante, A.2
Darbo, E.3
Zirra, A.4
Militti, C.5
-
11
-
-
84893358533
-
Landscape and variation of RNA secondary structure across the human transcriptome
-
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, et al. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505: 706–709. doi: 10.1038/nature12946 24476892
-
(2014)
Nature
, vol.505
, pp. 706-709
-
-
Wan, Y.1
Qu, K.2
Zhang, Q.C.3
Flynn, R.A.4
Manor, O.5
-
12
-
-
84925301356
-
The RNA structurome: transcriptome-wide structure probing with next-generation sequencing
-
Kwok CK, Tang Y, Assmann SM, Bevilacqua PC, (2015) The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem Sci 40: 221–232. doi: 10.1016/j.tibs.2015.02.005 25797096
-
(2015)
Trends Biochem Sci
, vol.40
, pp. 221-232
-
-
Kwok, C.K.1
Tang, Y.2
Assmann, S.M.3
Bevilacqua, P.C.4
-
13
-
-
79953052296
-
mRNA helicases: the tacticians of translational control
-
Parsyan A, Svitkin Y, Shahbazian D, Gkogkas C, Lasko P, et al. (2011) mRNA helicases: the tacticians of translational control. Nat Rev Mol Cell Biol 12: 235–245. doi: 10.1038/nrm3083 21427765
-
(2011)
Nat Rev Mol Cell Biol
, vol.12
, pp. 235-245
-
-
Parsyan, A.1
Svitkin, Y.2
Shahbazian, D.3
Gkogkas, C.4
Lasko, P.5
-
14
-
-
11844292767
-
mRNA helicase activity of the ribosome
-
Takyar S, Hickerson RP, Noller HF, (2005) mRNA helicase activity of the ribosome. Cell 120: 49–58. 15652481
-
(2005)
Cell
, vol.120
, pp. 49-58
-
-
Takyar, S.1
Hickerson, R.P.2
Noller, H.F.3
-
15
-
-
84928210758
-
RNA: Detailed probing of RNA structure in vivo
-
Burgess DJ, (2015) RNA: Detailed probing of RNA structure in vivo. Nature reviews Genetics 16: 255. doi: 10.1038/nrg3939 25854184
-
(2015)
Nature reviews Genetics
, vol.16
, pp. 255
-
-
Burgess, D.J.1
-
16
-
-
77649169870
-
mRNA secondary structures fold sequentially but exchange rapidly in vivo
-
Mahen EM, Watson PY, Cottrell JW, Fedor MJ, (2010) mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol 8: e1000307. doi: 10.1371/journal.pbio.1000307 20161716
-
(2010)
PLoS Biol
, vol.8
, pp. 1000307
-
-
Mahen, E.M.1
Watson, P.Y.2
Cottrell, J.W.3
Fedor, M.J.4
-
17
-
-
0037162469
-
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
-
Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN, (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99: 9697–9702. 12119387
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 9697-9702
-
-
Bernstein, J.A.1
Khodursky, A.B.2
Lin, P.H.3
Lin-Chao, S.4
Cohen, S.N.5
-
18
-
-
85027939461
-
Dynamics of translation by single ribosomes through mRNA secondary structures
-
Chen C, Zhang H, Broitman SL, Reiche M, Farrell I, et al. (2013) Dynamics of translation by single ribosomes through mRNA secondary structures. Nat Struct Mol Biol 20: 582–588. doi: 10.1038/nsmb.2544 23542154
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 582-588
-
-
Chen, C.1
Zhang, H.2
Broitman, S.L.3
Reiche, M.4
Farrell, I.5
-
19
-
-
41149155366
-
Following translation by single ribosomes one codon at a time
-
Wen JD, Lancaster L, Hodges C, Zeri AC, Yoshimura SH, et al. (2008) Following translation by single ribosomes one codon at a time. Nature 452: 598–603. doi: 10.1038/nature06716 18327250
-
(2008)
Nature
, vol.452
, pp. 598-603
-
-
Wen, J.D.1
Lancaster, L.2
Hodges, C.3
Zeri, A.C.4
Yoshimura, S.H.5
-
20
-
-
62049083910
-
Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
-
Zhang G, Hubalewska M, Ignatova Z, (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol 16: 274–280. doi: 10.1038/nsmb.1554 19198590
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 274-280
-
-
Zhang, G.1
Hubalewska, M.2
Ignatova, Z.3
-
21
-
-
84942284143
-
Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate
-
Gorochowski TE, Ignatova Z, Bovenberg RA, Roubos JA, (2015) Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res 43: 3022–3032. doi: 10.1093/nar/gkv199 25765653
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 3022-3032
-
-
Gorochowski, T.E.1
Ignatova, Z.2
Bovenberg, R.A.3
Roubos, J.A.4
-
22
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer M, (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897–907. 1752426
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
23
-
-
84921690520
-
Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation
-
Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, et al. (2014) Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol Syst Biol 10: 770. doi: 10.15252/msb.20145524 25538139
-
(2014)
Mol Syst Biol
, vol.10
, pp. 770
-
-
Pop, C.1
Rouskin, S.2
Ingolia, N.T.3
Han, L.4
Phizicky, E.M.5
-
24
-
-
84879654928
-
Efficient translation initiation dictates codon usage at gene start
-
Bentele K, Saffert P, Rauscher R, Ignatova Z, Bluthgen N, (2013) Efficient translation initiation dictates codon usage at gene start. Mol Syst Biol 9: 675. doi: 10.1038/msb.2013.32 23774758
-
(2013)
Mol Syst Biol
, vol.9
, pp. 675
-
-
Bentele, K.1
Saffert, P.2
Rauscher, R.3
Ignatova, Z.4
Bluthgen, N.5
-
25
-
-
84886302057
-
Causes and effects of N-terminal codon bias in bacterial genes
-
Goodman DB, Church GM, Kosuri S, (2013) Causes and effects of N-terminal codon bias in bacterial genes. Science 342: 475–479. doi: 10.1126/science.1241934 24072823
-
(2013)
Science
, vol.342
, pp. 475-479
-
-
Goodman, D.B.1
Church, G.M.2
Kosuri, S.3
-
26
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS, (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218–223. doi: 10.1126/science.1168978 19213877
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
27
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621–628. doi: 10.1038/nmeth.1226 18516045
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
28
-
-
0026559344
-
Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site
-
Ehretsmann CP, Carpousis AJ, Krisch HM, (1992) Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev 6: 149–159. 1730408
-
(1992)
Genes Dev
, vol.6
, pp. 149-159
-
-
Ehretsmann, C.P.1
Carpousis, A.J.2
Krisch, H.M.3
-
29
-
-
0028341449
-
A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage
-
McDowall KJ, Lin-Chao S, Cohen SN, (1994) A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J Biol Chem 269: 10790–10796. 7511606
-
(1994)
J Biol Chem
, vol.269
, pp. 10790-10796
-
-
McDowall, K.J.1
Lin-Chao, S.2
Cohen, S.N.3
-
30
-
-
0142240435
-
Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs
-
Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U, (2003) Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9: 1308–1314. 14561880
-
(2003)
RNA
, vol.9
, pp. 1308-1314
-
-
Moll, I.1
Afonyushkin, T.2
Vytvytska, O.3
Kaberdin, V.R.4
Blasi, U.5
-
31
-
-
84861121932
-
Global analysis of RNA secondary structure in two metazoans
-
Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, et al. (2012) Global analysis of RNA secondary structure in two metazoans. Cell Rep 1: 69–82. doi: 10.1016/j.celrep.2011.10.002 22832108
-
(2012)
Cell Rep
, vol.1
, pp. 69-82
-
-
Li, F.1
Zheng, Q.2
Ryvkin, P.3
Dragomir, I.4
Desai, Y.5
-
32
-
-
84924584607
-
Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
-
Incarnato D, Neri F, Anselmi F, Oliviero S, (2014) Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol 15: 491. 25323333
-
(2014)
Genome Biol
, vol.15
, pp. 491
-
-
Incarnato, D.1
Neri, F.2
Anselmi, F.3
Oliviero, S.4
-
33
-
-
33646838978
-
A periodic pattern of mRNA secondary structure created by the genetic code
-
Shabalina SA, Ogurtsov AY, Spiridonov NA, (2006) A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res 34: 2428–2437. 16682450
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2428-2437
-
-
Shabalina, S.A.1
Ogurtsov, A.Y.2
Spiridonov, N.A.3
-
34
-
-
33749125440
-
DEAD-box RNA helicases in Escherichia coli
-
Iost I, Dreyfus M, (2006) DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Res 34: 4189–4197. 16935881
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4189-4197
-
-
Iost, I.1
Dreyfus, M.2
-
35
-
-
78751667727
-
Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA
-
Resch A, Vecerek B, Palavra K, Blasi U, (2010) Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA. RNA Biol 7: 796–802. 21045550
-
(2010)
RNA Biol
, vol.7
, pp. 796-802
-
-
Resch, A.1
Vecerek, B.2
Palavra, K.3
Blasi, U.4
-
36
-
-
84901634173
-
Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures
-
Vakulskas CA, Pannuri A, Cortes-Selva D, Zere TR, Ahmer BM, et al. (2014) Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures. Mol Microbiol 92: 945–958. doi: 10.1111/mmi.12606 24708042
-
(2014)
Mol Microbiol
, vol.92
, pp. 945-958
-
-
Vakulskas, C.A.1
Pannuri, A.2
Cortes-Selva, D.3
Zere, T.R.4
Ahmer, B.M.5
-
37
-
-
84925998694
-
mRNA-programmed translation pauses in the targeting of E. coli membrane proteins
-
Fluman N, Navon S, Bibi E, Pilpel Y, (2014) mRNA-programmed translation pauses in the targeting of E. coli membrane proteins. Elife 3.
-
(2014)
Elife
, vol.3
-
-
Fluman, N.1
Navon, S.2
Bibi, E.3
Pilpel, Y.4
-
38
-
-
1542358892
-
Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins
-
Woolhead CA, McCormick PJ, Johnson AE, (2004) Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 116: 725–736. 15006354
-
(2004)
Cell
, vol.116
, pp. 725-736
-
-
Woolhead, C.A.1
McCormick, P.J.2
Johnson, A.E.3
-
39
-
-
0031280034
-
Controlling messenger RNA stability in bacteria: strategies for engineering gene expression
-
Carrier TA, Keasling JD, (1997) Controlling messenger RNA stability in bacteria: strategies for engineering gene expression. Biotechnol Prog 13: 699–708. 9413129
-
(1997)
Biotechnol Prog
, vol.13
, pp. 699-708
-
-
Carrier, T.A.1
Keasling, J.D.2
-
40
-
-
84871321022
-
RNase E: at the interface of bacterial RNA processing and decay
-
Mackie GA, (2013) RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol 11: 45–57. doi: 10.1038/nrmicro2930 23241849
-
(2013)
Nat Rev Microbiol
, vol.11
, pp. 45-57
-
-
Mackie, G.A.1
-
41
-
-
84920786962
-
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli
-
Clarke JE, Kime L, Romero AD, McDowall KJ, (2015) Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res 42: 11733–11751.
-
(2015)
Nucleic Acids Res
, vol.42
, pp. 11733-11751
-
-
Clarke, J.E.1
Kime, L.2
Romero, A.D.3
McDowall, K.J.4
-
42
-
-
0036786891
-
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures
-
Ma J, Campbell A, Karlin S, (2002) Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol 184: 5733–5745. 12270832
-
(2002)
J Bacteriol
, vol.184
, pp. 5733-5745
-
-
Ma, J.1
Campbell, A.2
Karlin, S.3
-
43
-
-
0021760395
-
The influence of messenger RNA secondary structure on expression of an immunoglobulin heavy chain in Escherichia coli
-
Wood CR, Boss MA, Patel TP, Emtage JS, (1984) The influence of messenger RNA secondary structure on expression of an immunoglobulin heavy chain in Escherichia coli. Nucleic Acids Res 12: 3937–3950. 6328446
-
(1984)
Nucleic Acids Res
, vol.12
, pp. 3937-3950
-
-
Wood, C.R.1
Boss, M.A.2
Patel, T.P.3
Emtage, J.S.4
-
44
-
-
84871766345
-
Comparison of mRNA features affecting translation initiation and reinitiation
-
Osterman IA, Evfratov SA, Sergiev PV, Dontsova OA, (2013) Comparison of mRNA features affecting translation initiation and reinitiation. Nucleic Acids Res 41: 474–486. doi: 10.1093/nar/gks989 23093605
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 474-486
-
-
Osterman, I.A.1
Evfratov, S.A.2
Sergiev, P.V.3
Dontsova, O.A.4
-
45
-
-
0026532777
-
Translation initiation in Escherichia coli: sequences within the ribosome-binding site
-
Ringquist S, Shinedling S, Barrick D, Green L, Binkley J, et al. (1992) Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol 6: 1219–1229. 1375310
-
(1992)
Mol Microbiol
, vol.6
, pp. 1219-1229
-
-
Ringquist, S.1
Shinedling, S.2
Barrick, D.3
Green, L.4
Binkley, J.5
-
46
-
-
33645965566
-
Unfolding of mRNA secondary structure by the bacterial translation initiation complex
-
Studer SM, Joseph S, (2006) Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell 22: 105–115. 16600874
-
(2006)
Mol Cell
, vol.22
, pp. 105-115
-
-
Studer, S.M.1
Joseph, S.2
-
47
-
-
0042166100
-
Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA
-
de Smit MH, van Duin J, (2003) Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA. J Mol Biol 331: 737–743. 12909006
-
(2003)
J Mol Biol
, vol.331
, pp. 737-743
-
-
de Smit, M.H.1
van Duin, J.2
-
48
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis HM, Mirsky EA, Voigt CA, (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27: 946–950. doi: 10.1038/nbt.1568 19801975
-
(2009)
Nat Biotechnol
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
49
-
-
84892773271
-
Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation
-
Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, et al. (2013) Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol 11: e1001731. doi: 10.1371/journal.pbio.1001731 24339747
-
(2013)
PLoS Biol
, vol.11
, pp. 1001731
-
-
Duval, M.1
Korepanov, A.2
Fuchsbauer, O.3
Fechter, P.4
Haller, A.5
-
50
-
-
0035834062
-
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA
-
Sengupta J, Agrawal RK, Frank J, (2001) Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA. Proc Natl Acad Sci U S A 98: 11991–11996. 11593008
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 11991-11996
-
-
Sengupta, J.1
Agrawal, R.K.2
Frank, J.3
-
51
-
-
0029153552
-
The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae
-
Bonetti B, Fu L, Moon J, Bedwell DM, (1995) The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol 251: 334–345. 7650736
-
(1995)
J Mol Biol
, vol.251
, pp. 334-345
-
-
Bonetti, B.1
Fu, L.2
Moon, J.3
Bedwell, D.M.4
-
52
-
-
0029923751
-
Structure of the C-terminal end of the nascent peptide influences translation termination
-
Bjornsson A, Mottagui-Tabar S, Isaksson LA, (1996) Structure of the C-terminal end of the nascent peptide influences translation termination. The EMBO journal 15: 1696–1704. 8612594
-
(1996)
The EMBO journal
, vol.15
, pp. 1696-1704
-
-
Bjornsson, A.1
Mottagui-Tabar, S.2
Isaksson, L.A.3
-
53
-
-
1342286071
-
The major 5' determinant in stop codon read-through involves two adjacent adenines
-
Tork S, Hatin I, Rousset JP, Fabret C, (2004) The major 5' determinant in stop codon read-through involves two adjacent adenines. Nucleic Acids Res 32: 415–421. 14736996
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 415-421
-
-
Tork, S.1
Hatin, I.2
Rousset, J.P.3
Fabret, C.4
-
54
-
-
27144495430
-
Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover
-
Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, et al. (2005) Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437: 1187–1191. 16237448
-
(2005)
Nature
, vol.437
, pp. 1187-1191
-
-
Callaghan, A.J.1
Marcaida, M.J.2
Stead, J.A.3
McDowall, K.J.4
Scott, W.G.5
-
55
-
-
48349130534
-
The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation
-
Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, et al. (2008) The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation. Structure 16: 1238–1244. doi: 10.1016/j.str.2008.04.017 18682225
-
(2008)
Structure
, vol.16
, pp. 1238-1244
-
-
Koslover, D.J.1
Callaghan, A.J.2
Marcaida, M.J.3
Garman, E.F.4
Martick, M.5
-
56
-
-
84876161665
-
A simple assay for the ribonuclease activity of ribonucleases in the presence of ethidium bromide
-
Tripathy DR, Dinda AK, Dasgupta S, (2013) A simple assay for the ribonuclease activity of ribonucleases in the presence of ethidium bromide. Anal Biochem 437: 126–129. doi: 10.1016/j.ab.2013.03.005 23499964
-
(2013)
Anal Biochem
, vol.437
, pp. 126-129
-
-
Tripathy, D.R.1
Dinda, A.K.2
Dasgupta, S.3
-
58
-
-
0015915047
-
Movement of ribosomes over messenger RNA in polysomes of rel + and rel—Escherichia coli strains
-
Cozzone AJ, Stent GS, (1973) Movement of ribosomes over messenger RNA in polysomes of rel + and rel—Escherichia coli strains. J Mol Biol 76: 163–179. 4578097
-
(1973)
J Mol Biol
, vol.76
, pp. 163-179
-
-
Cozzone, A.J.1
Stent, G.S.2
-
59
-
-
77955644289
-
Mammalian microRNAs predominantly act to decrease target mRNA levels
-
Guo H, Ingolia NT, Weissman JS, Bartel DP, (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835–840. doi: 10.1038/nature09267 20703300
-
(2010)
Nature
, vol.466
, pp. 835-840
-
-
Guo, H.1
Ingolia, N.T.2
Weissman, J.S.3
Bartel, D.P.4
-
60
-
-
0037336121
-
Definition of the Escherichia coli MC4100 genome by use of a DNA array
-
Peters JE, Thate TE, Craig NL, (2003) Definition of the Escherichia coli MC4100 genome by use of a DNA array. J Bacteriol 185: 2017–2021. 12618467
-
(2003)
J Bacteriol
, vol.185
, pp. 2017-2021
-
-
Peters, J.E.1
Thate, T.E.2
Craig, N.L.3
-
61
-
-
84896748566
-
DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest
-
Zhang Y, Mooney RA, Grass JA, Sivaramakrishnan P, Herman C, et al. (2014) DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest. Mol Cell 53: 766–778. doi: 10.1016/j.molcel.2014.02.005 24606919
-
(2014)
Mol Cell
, vol.53
, pp. 766-778
-
-
Zhang, Y.1
Mooney, R.A.2
Grass, J.A.3
Sivaramakrishnan, P.4
Herman, C.5
-
62
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, et al. (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6: 26. doi: 10.1186/1748-7188-6-26 22115189
-
(2011)
Algorithms Mol Biol
, vol.6
, pp. 26
-
-
Lorenz, R.1
Bernhart, S.H.2
Honer Zu Siederdissen, C.3
Tafer, H.4
Flamm, C.5
-
63
-
-
84860231100
-
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
-
Li GW, Oh E, Weissman JS, (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484: 538–541. doi: 10.1038/nature10965 22456704
-
(2012)
Nature
, vol.484
, pp. 538-541
-
-
Li, G.W.1
Oh, E.2
Weissman, J.S.3
-
64
-
-
50649097486
-
The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA
-
Soper TJ, Woodson SA, (2008) The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14: 1907–1917. doi: 10.1261/rna.1110608 18658123
-
(2008)
RNA
, vol.14
, pp. 1907-1917
-
-
Soper, T.J.1
Woodson, S.A.2
-
65
-
-
0028928471
-
Secondary structures of Escherichia coli antisense micF RNA, the 5'-end of the target ompF mRNA, and the RNA/RNA duplex
-
Schmidt M, Zheng P, Delihas N, (1995) Secondary structures of Escherichia coli antisense micF RNA, the 5'-end of the target ompF mRNA, and the RNA/RNA duplex. Biochemistry 34: 3621–3631. 7534474
-
(1995)
Biochemistry
, vol.34
, pp. 3621-3631
-
-
Schmidt, M.1
Zheng, P.2
Delihas, N.3
-
66
-
-
0018936473
-
Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence
-
Woese CR, Magrum LJ, Gupta R, Siegel RB, Stahl DA, et al. (1980) Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 8: 2275–2293. 6159576
-
(1980)
Nucleic Acids Res
, vol.8
, pp. 2275-2293
-
-
Woese, C.R.1
Magrum, L.J.2
Gupta, R.3
Siegel, R.B.4
Stahl, D.A.5
-
67
-
-
0036600570
-
The accuracy of ribosomal RNA comparative structure models
-
Gutell RR, Lee JC, Cannone JJ, (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12: 301–310. 12127448
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 301-310
-
-
Gutell, R.R.1
Lee, J.C.2
Cannone, J.J.3
-
68
-
-
0035805213
-
Crystal structure of the ribosome at 5.5 A resolution
-
Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, et al. (2001) Crystal structure of the ribosome at 5.5 A resolution. Science 292: 883–896. 11283358
-
(2001)
Science
, vol.292
, pp. 883-896
-
-
Yusupov, M.M.1
Yusupova, G.Z.2
Baucom, A.3
Lieberman, K.4
Earnest, T.N.5
|