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For: Deana A, Ehrlich R, Reiss C. Synonymous codon selection controls in vivo turnover and amount of mRNA in Escherichia coli bla and ompA genes. J Bacteriol 1996;178:2718-20. [PMID: 8626345 PMCID: PMC178002 DOI: 10.1128/jb.178.9.2718-2720.1996] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
Number Cited by Other Article(s)
1
Ballard A, Bieniek S, Carlini DB. The fitness consequences of synonymous mutations in Escherichia coli: Experimental evidence for a pleiotropic effect of translational selection. Gene 2019;694:111-120. [PMID: 30738968 DOI: 10.1016/j.gene.2019.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/21/2018] [Accepted: 01/22/2019] [Indexed: 01/06/2023]
2
Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E. Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics 2018;33:2487-2495. [PMID: 28398465 DOI: 10.1093/bioinformatics/btx207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/05/2017] [Indexed: 01/21/2023]  Open
3
Komar AA. The Yin and Yang of codon usage. Hum Mol Genet 2016;25:R77-R85. [PMID: 27354349 DOI: 10.1093/hmg/ddw207] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/24/2016] [Indexed: 01/07/2023]  Open
4
Codon influence on protein expression in E. coli correlates with mRNA levels. Nature 2016;529:358-363. [PMID: 26760206 DOI: 10.1038/nature16509] [Citation(s) in RCA: 294] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/01/2015] [Indexed: 02/06/2023]
5
The Art of Gene Redesign and Recombinant Protein Production: Approaches and Perspectives. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
6
The effects of codon context on in vivo translation speed. PLoS Genet 2014;10:e1004392. [PMID: 24901308 PMCID: PMC4046918 DOI: 10.1371/journal.pgen.1004392] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/04/2014] [Indexed: 11/19/2022]  Open
7
Aslam F, Gardner QTAA, Zain H, Nadeem MS, Ali M, Rashid N, Akhtar M. Studies on the expression and processing of human proinsulin derivatives encoded by different DNA constructs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013;1834:2116-23. [DOI: 10.1016/j.bbapap.2013.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 07/01/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
8
Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet 2013;9:e1003527. [PMID: 23737754 PMCID: PMC3667748 DOI: 10.1371/journal.pgen.1003527] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/08/2013] [Indexed: 11/19/2022]  Open
9
Schenk MF, Szendro IG, Krug J, de Visser JAGM. Quantifying the adaptive potential of an antibiotic resistance enzyme. PLoS Genet 2012;8:e1002783. [PMID: 22761587 PMCID: PMC3386231 DOI: 10.1371/journal.pgen.1002783] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 05/09/2012] [Indexed: 12/30/2022]  Open
10
Nocadello S, Swennen EF. The new pLAI (lux regulon based auto-inducible) expression system for recombinant protein production in Escherichia coli. Microb Cell Fact 2012;11:3. [PMID: 22222111 PMCID: PMC3274441 DOI: 10.1186/1475-2859-11-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/05/2012] [Indexed: 11/26/2022]  Open
11
Chung DH, Min Z, Wang BC, Kushner SR. Single amino acid changes in the predicted RNase H domain of Escherichia coli RNase G lead to complementation of RNase E deletion mutants. RNA (NEW YORK, N.Y.) 2010;16:1371-1385. [PMID: 20507976 PMCID: PMC2885686 DOI: 10.1261/rna.2104810] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 04/12/2010] [Indexed: 05/29/2023]
12
Dreyfus M. Killer and protective ribosomes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009;85:423-66. [PMID: 19215779 DOI: 10.1016/s0079-6603(08)00811-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
13
Marin M. Folding at the rhythm of the rare codon beat. Biotechnol J 2008;3:1047-57. [PMID: 18624343 DOI: 10.1002/biot.200800089] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
14
Yamanishi H, Yonesaki T. RNA cleavage linked with ribosomal action. Genetics 2005;171:419-25. [PMID: 16020788 PMCID: PMC1456760 DOI: 10.1534/genetics.105.042515] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
15
Otsuka Y, Yonesaki T. A novel endoribonuclease, RNase LS, in Escherichia coli. Genetics 2005;169:13-20. [PMID: 15677746 PMCID: PMC1448878 DOI: 10.1534/genetics.104.033290] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
16
Giacani L, Sun ES, Hevner K, Molini BJ, Van Voorhis WC, Lukehart SA, Centurion-Lara A. Tpr homologs in Treponema paraluiscuniculi Cuniculi A strain. Infect Immun 2004;72:6561-76. [PMID: 15501788 PMCID: PMC523035 DOI: 10.1128/iai.72.11.6561-6576.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
17
Power PM, Jones RA, Beacham IR, Bucholtz C, Jennings MP. Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli. Biochem Biophys Res Commun 2004;322:1038-44. [PMID: 15336569 DOI: 10.1016/j.bbrc.2004.08.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Indexed: 11/21/2022]
18
Duan J, Antezana MA. Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J Mol Evol 2004;57:694-701. [PMID: 14745538 DOI: 10.1007/s00239-003-2519-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2003] [Accepted: 06/30/2003] [Indexed: 11/29/2022]
19
Chamary JV, Hurst LD. Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol Biol Evol 2004;21:1014-23. [PMID: 15014158 DOI: 10.1093/molbev/msh087] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
20
Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. 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 2002;99:9697-702. [PMID: 12119387 PMCID: PMC124983 DOI: 10.1073/pnas.112318199] [Citation(s) in RCA: 638] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2002] [Indexed: 11/18/2022]  Open
21
Lesnik T, Solomovici J, Deana A, Ehrlich R, Reiss C. Ribosome traffic in E. coli and regulation of gene expression. J Theor Biol 2000;202:175-85. [PMID: 10640436 DOI: 10.1006/jtbi.1999.1047] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
22
Deana A, Ehrlich R, Reiss C. Silent mutations in the Escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo. Nucleic Acids Res 1998;26:4778-82. [PMID: 9753749 PMCID: PMC147888 DOI: 10.1093/nar/26.20.4778] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
23
Berlyn MK. Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol Mol Biol Rev 1998;62:814-984. [PMID: 9729611 PMCID: PMC98936 DOI: 10.1128/mmbr.62.3.814-984.1998] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
24
Thanaraj TA, Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci 1996;5:1973-83. [PMID: 8897597 PMCID: PMC2143259 DOI: 10.1002/pro.5560051003] [Citation(s) in RCA: 130] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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