-
1
-
-
0025796711
-
Codon usage tabulated from the GenBank genetic sequence data
-
Wada K., et al. Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res. 19 Suppl. (1991) 1981-1986
-
(1991)
Nucleic Acids Res.
, vol.19
, Issue.SUPPL
, pp. 1981-1986
-
-
Wada, K.1
-
2
-
-
0031586223
-
Growth rate-optimised tRNA abundance and codon usage
-
Berg O.G., and Kurland C.G. Growth rate-optimised tRNA abundance and codon usage. J. Mol. Biol. 270 (1997) 544-550
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 544-550
-
-
Berg, O.G.1
Kurland, C.G.2
-
3
-
-
4644280499
-
Solving the riddle of codon usage preferences: a test for translational selection
-
dos Reis M., et al. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32 (2004) 5036-5044
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5036-5044
-
-
dos Reis, M.1
-
4
-
-
0031582214
-
Does Escherichia coli optimize the economics of the translation process?
-
Solomovici J., et al. Does Escherichia coli optimize the economics of the translation process?. J. Theor. Biol. 185 (1997) 511-521
-
(1997)
J. Theor. Biol.
, vol.185
, pp. 511-521
-
-
Solomovici, J.1
-
5
-
-
0028920684
-
Differential codon usage: a safeguard against inappropriate expression of specialized genes?
-
Saier Jr. M.H. Differential codon usage: a safeguard against inappropriate expression of specialized genes?. FEBS Lett. 362 (1995) 1-4
-
(1995)
FEBS Lett.
, vol.362
, pp. 1-4
-
-
Saier Jr., M.H.1
-
6
-
-
0025181355
-
Switches in species-specific codon preferences: the influence of mutation biases
-
Shields D.C. Switches in species-specific codon preferences: the influence of mutation biases. J. Mol. Evol. 31 (1990) 71-80
-
(1990)
J. Mol. Evol.
, vol.31
, pp. 71-80
-
-
Shields, D.C.1
-
7
-
-
0035220937
-
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
-
10.1186/gb-2001-2-4-research0010
-
Knight R.D., et al. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol 2 (2001). http://genomebiology.com 10.1186/gb-2001-2-4-research0010
-
(2001)
Genome Biol
, vol.2
-
-
Knight, R.D.1
-
8
-
-
0029931535
-
Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?
-
Eyre-Walker A. Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?. Mol. Biol. Evol. 13 (1996) 864-872
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 864-872
-
-
Eyre-Walker, A.1
-
9
-
-
33846786904
-
Synonymous codon usage in Escherichia coli: selection for translational accuracy
-
Stoletzki N., and Eyre-Walker A. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol. Biol. Evol. 24 (2007) 374-381
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 374-381
-
-
Stoletzki, N.1
Eyre-Walker, A.2
-
10
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond D.A., and Wilke C.O. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134 (2008) 341-352
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
11
-
-
0019474499
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
-
Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol. 146 (1981) 1-21
-
(1981)
J. Mol. Biol.
, vol.146
, pp. 1-21
-
-
Ikemura, T.1
-
12
-
-
0035941484
-
Codon bias at the 3′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli
-
Stenstrom C.M., et al. Codon bias at the 3′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli. Gene 263 (2001) 273-284
-
(2001)
Gene
, vol.263
, pp. 273-284
-
-
Stenstrom, C.M.1
-
13
-
-
0037123362
-
Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3′ side
-
Stenstrom C.M., and Isaksson L.A. Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3′ side. Gene 288 (2002) 1-8
-
(2002)
Gene
, vol.288
, pp. 1-8
-
-
Stenstrom, C.M.1
Isaksson, L.A.2
-
14
-
-
0023395492
-
Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli
-
Looman A.C., et al. Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli. EMBO J. 6 (1987) 2489-2492
-
(1987)
EMBO J.
, vol.6
, pp. 2489-2492
-
-
Looman, A.C.1
-
15
-
-
4944224262
-
A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli
-
Gonzalez de Valdivia E.I., and Isaksson L.A. A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli. Nucleic Acids Res. 32 (2004) 5198-5205
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5198-5205
-
-
Gonzalez de Valdivia, E.I.1
Isaksson, L.A.2
-
16
-
-
0035827918
-
Cooperative effects by the initiation codon and its flanking regions on translation initiation
-
Stenstrom C.M., et al. Cooperative effects by the initiation codon and its flanking regions on translation initiation. Gene 273 (2001) 259-265
-
(2001)
Gene
, vol.273
, pp. 259-265
-
-
Stenstrom, C.M.1
-
17
-
-
0036295371
-
Silent mutations affect in vivo protein folding in Escherichia coli
-
Cortazzo P., et al. Silent mutations affect in vivo protein folding in Escherichia coli. Biochem. Biophys. Res. Commun. 293 (2002) 537-541
-
(2002)
Biochem. Biophys. Res. Commun.
, vol.293
, pp. 537-541
-
-
Cortazzo, P.1
-
18
-
-
0032699491
-
Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation
-
Komar A.A., et al. Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett. 462 (1999) 387-391
-
(1999)
FEBS Lett.
, vol.462
, pp. 387-391
-
-
Komar, A.A.1
-
19
-
-
48249093081
-
Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host
-
Angov E., et al. Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLoS One 3 (2008) e2189
-
(2008)
PLoS One
, vol.3
-
-
Angov, E.1
-
20
-
-
34848845616
-
Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins
-
Zalucki Y.M., et al. Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins. Nucleic Acids Res. 35 (2007) 5748-5754
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5748-5754
-
-
Zalucki, Y.M.1
-
21
-
-
4444356342
-
Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli
-
Power P.M., et al. Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli. Biochem. Biophys. Res. Commun. 322 (2004) 1038-1044
-
(2004)
Biochem. Biophys. Res. Commun.
, vol.322
, pp. 1038-1044
-
-
Power, P.M.1
-
22
-
-
33847076187
-
Experimental confirmation of a key role for non-optimal codons in protein export
-
Zalucki Y.M., and Jennings M.P. Experimental confirmation of a key role for non-optimal codons in protein export. Biochem. Biophys. Res. Commun. 355 (2007) 143-148
-
(2007)
Biochem. Biophys. Res. Commun.
, vol.355
, pp. 143-148
-
-
Zalucki, Y.M.1
Jennings, M.P.2
-
23
-
-
37549050221
-
Secretory signal sequence non-optimal codons are required for expression and export of β-lactamase
-
Zalucki Y.M., et al. Secretory signal sequence non-optimal codons are required for expression and export of β-lactamase. Biochem. Biophys. Res. Commun. 366 (2008) 135-141
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.366
, pp. 135-141
-
-
Zalucki, Y.M.1
-
24
-
-
0036908375
-
Distribution of rare triplets along mRNA and their relation to protein folding
-
Makhoul C.H., and Trifonov E.N. Distribution of rare triplets along mRNA and their relation to protein folding. J. Biomol. Struct. Dyn. 20 (2002) 413-420
-
(2002)
J. Biomol. Struct. Dyn.
, vol.20
, pp. 413-420
-
-
Makhoul, C.H.1
Trifonov, E.N.2
-
25
-
-
0031475013
-
Evidence of rare codon clusters within Escherichia coli coding regions
-
Phoenix D.A., and Korotkov E. Evidence of rare codon clusters within Escherichia coli coding regions. FEMS Microbiol. Lett. 155 (1997) 63-66
-
(1997)
FEMS Microbiol. Lett.
, vol.155
, pp. 63-66
-
-
Phoenix, D.A.1
Korotkov, E.2
-
26
-
-
0029908504
-
Protein secondary structural types are differentially coded on messenger RNA
-
Thanaraj T.A., and Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci. 5 (1996) 1973-1983
-
(1996)
Protein Sci.
, vol.5
, pp. 1973-1983
-
-
Thanaraj, T.A.1
Argos, P.2
-
27
-
-
27144555357
-
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
-
Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361 (2005) 13-37
-
(2005)
Gene
, vol.361
, pp. 13-37
-
-
Kozak, M.1
-
28
-
-
14544308803
-
AU-rich sequences within 5′ untranslated leaders enhance translation and stabilize mRNA in Escherichia coli
-
Komarova A.V., et al. AU-rich sequences within 5′ untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J. Bacteriol. 187 (2005) 1344-1349
-
(2005)
J. Bacteriol.
, vol.187
, pp. 1344-1349
-
-
Komarova, A.V.1
-
29
-
-
0034405491
-
A story: unpaired adenosine bases in ribosomal RNAs
-
Gutell R.R., et al. A story: unpaired adenosine bases in ribosomal RNAs. J. Mol. Biol. 304 (2000) 335-354
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 335-354
-
-
Gutell, R.R.1
-
30
-
-
0020338446
-
Sequence of a 1.26-kb DNA fragment containing the structural gene for E. coli initiation factor IF3: presence of an AUU initiator codon
-
Sacerdot C., et al. Sequence of a 1.26-kb DNA fragment containing the structural gene for E. coli initiation factor IF3: presence of an AUU initiator codon. EMBO J. 1 (1982) 311-315
-
(1982)
EMBO J.
, vol.1
, pp. 311-315
-
-
Sacerdot, C.1
-
31
-
-
0036015649
-
Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU
-
Binns N., and Masters M. Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU. Mol. Microbiol. 44 (2002) 1287-1298
-
(2002)
Mol. Microbiol.
, vol.44
, pp. 1287-1298
-
-
Binns, N.1
Masters, M.2
-
33
-
-
0021856417
-
Signal sequences. The limits of variation
-
von Heijne G. Signal sequences. The limits of variation. J. Mol. Biol. 184 (1985) 99-105
-
(1985)
J. Mol. Biol.
, vol.184
, pp. 99-105
-
-
von Heijne, G.1
-
34
-
-
0033008601
-
Protein targeting to the bacterial cytoplasmic membrane
-
Fekkes P., and Driessen A.J. Protein targeting to the bacterial cytoplasmic membrane. Microbiol. Mol. Biol. Rev. 63 (1999) 161-173
-
(1999)
Microbiol. Mol. Biol. Rev.
, vol.63
, pp. 161-173
-
-
Fekkes, P.1
Driessen, A.J.2
-
35
-
-
0021099521
-
Effects of the complete removal of basic amino acid residues from the signal peptide on secretion of lipoprotein in Escherichia coli
-
Vlasuk G.P., et al. Effects of the complete removal of basic amino acid residues from the signal peptide on secretion of lipoprotein in Escherichia coli. J. Biol. Chem. 258 (1983) 7141-7148
-
(1983)
J. Biol. Chem.
, vol.258
, pp. 7141-7148
-
-
Vlasuk, G.P.1
-
36
-
-
0031043413
-
Positively charged lysine at the N-terminus of the signal peptide of the Escherichia coli alkaline phosphatase provides the secretion efficiency and is involved in the interaction with anionic phospholipids
-
Nesmeyanova M.A., et al. Positively charged lysine at the N-terminus of the signal peptide of the Escherichia coli alkaline phosphatase provides the secretion efficiency and is involved in the interaction with anionic phospholipids. FEBS Lett. 403 (1997) 203-207
-
(1997)
FEBS Lett.
, vol.403
, pp. 203-207
-
-
Nesmeyanova, M.A.1
-
37
-
-
33746878779
-
Whole genome analysis of non-optimal codon usage in secretory signal sequences of Streptomyces coelicolor
-
Li Y.D., et al. Whole genome analysis of non-optimal codon usage in secretory signal sequences of Streptomyces coelicolor. Biosystems 85 (2006) 225-230
-
(2006)
Biosystems
, vol.85
, pp. 225-230
-
-
Li, Y.D.1
-
38
-
-
0014666439
-
Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA
-
Steitz J.A. Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature 224 (1969) 957-964
-
(1969)
Nature
, vol.224
, pp. 957-964
-
-
Steitz, J.A.1
-
39
-
-
49349113285
-
Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization
-
Mitarai N., et al. Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. J. Mol. Biol. 382 (2008) 236-245
-
(2008)
J. Mol. Biol.
, vol.382
, pp. 236-245
-
-
Mitarai, N.1
-
40
-
-
33645399045
-
A model of protein translation including codon bias, nonsense errors, and ribosome recycling
-
Gilchrist M.A., and Wagner A. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J. Theor. Biol. 239 (2006) 417-434
-
(2006)
J. Theor. Biol.
, vol.239
, pp. 417-434
-
-
Gilchrist, M.A.1
Wagner, A.2
-
41
-
-
0024962419
-
Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
-
Curran J.F., and Yarus M. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J. Mol. Biol. 209 (1989) 65-77
-
(1989)
J. Mol. Biol.
, vol.209
, pp. 65-77
-
-
Curran, J.F.1
Yarus, M.2
-
42
-
-
0021731777
-
Escherichia coli ribosomes translate in vivo with variable rate
-
Pedersen S. Escherichia coli ribosomes translate in vivo with variable rate. EMBO J. 3 (1984) 2895-2898
-
(1984)
EMBO J.
, vol.3
, pp. 2895-2898
-
-
Pedersen, S.1
-
43
-
-
0021760637
-
Codon usage can affect efficiency of translation of genes in Escherichia coli
-
Robinson M., et al. Codon usage can affect efficiency of translation of genes in Escherichia coli. Nucleic Acids Res. 12 (1984) 6663-6671
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 6663-6671
-
-
Robinson, M.1
-
44
-
-
0024405193
-
Codon usage determines translation rate in Escherichia coli
-
Sorensen M.A., et al. Codon usage determines translation rate in Escherichia coli. J. Mol. Biol. 207 (1989) 365-377
-
(1989)
J. Mol. Biol.
, vol.207
, pp. 365-377
-
-
Sorensen, M.A.1
-
45
-
-
0026409389
-
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
-
Sorensen M.A., and Pedersen S. 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. J. Mol. Biol. 222 (1991) 265-280
-
(1991)
J. Mol. Biol.
, vol.222
, pp. 265-280
-
-
Sorensen, M.A.1
Pedersen, S.2
-
46
-
-
0023722029
-
Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro
-
Thomas L.K., et al. Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro. Proc. Natl. Acad. Sci. U. S. A. 85 (1988) 4242-4246
-
(1988)
Proc. Natl. Acad. Sci. U. S. A.
, vol.85
, pp. 4242-4246
-
-
Thomas, L.K.1
-
47
-
-
0020554080
-
Mechanisms of protein localization
-
Silhavy T.J., et al. Mechanisms of protein localization. Microbiol. Rev. 47 (1983) 313-344
-
(1983)
Microbiol. Rev.
, vol.47
, pp. 313-344
-
-
Silhavy, T.J.1
-
48
-
-
0023749045
-
Protein translocation across membranes
-
Verner K., and Schatz G. Protein translocation across membranes. Science 241 (1988) 1307-1313
-
(1988)
Science
, vol.241
, pp. 1307-1313
-
-
Verner, K.1
Schatz, G.2
-
49
-
-
0030832397
-
Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor
-
Powers T., and Walter P. Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor. EMBO J. 16 (1997) 4880-4886
-
(1997)
EMBO J.
, vol.16
, pp. 4880-4886
-
-
Powers, T.1
Walter, P.2
|