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For: Yang C, Hockenberry AJ, Jewett MC, Amaral LAN. Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent. G3 (Bethesda) 2016;6:3467-74. [PMID: 27605518 DOI: 10.1534/g3.116.032227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Roots CT, Barrick JE. CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611466. [PMID: 39282447 PMCID: PMC11398486 DOI: 10.1101/2024.09.05.611466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
2
Ghosh A, Bharmal MHM, Ghaleb AM, Nandana V, Schrader JM. Initiator AUGs Are Discriminated from Elongator AUGs Predominantly through mRNA Accessibility in C. crescentus. J Bacteriol 2023;205:e0042022. [PMID: 37092987 PMCID: PMC10210977 DOI: 10.1128/jb.00420-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023]  Open
3
Enhanced extracellular raw starch-degrading α-amylase production in Bacillus subtilis through signal peptide and translation efficiency optimization. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
4
Bahiri Elitzur S, Cohen-Kupiec R, Yacobi D, Fine L, Apt B, Diament A, Tuller T. Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts. RNA Biol 2021;18:684-698. [PMID: 34586043 DOI: 10.1080/15476286.2021.1978767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]  Open
5
Zhao L, Fu G, Cui Y, Xu Z, Cai T, Zhang D. Compensating Complete Loss of Signal Recognition Particle During Co-translational Protein Targeting by the Translation Speed and Accuracy. Front Microbiol 2021;12:690286. [PMID: 34305852 PMCID: PMC8299109 DOI: 10.3389/fmicb.2021.690286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 11/23/2022]  Open
6
Liu SS, Hockenberry AJ, Jewett MC, Amaral LAN. A novel framework for evaluating the performance of codon usage bias metrics. J R Soc Interface 2019;15:rsif.2017.0667. [PMID: 29386398 DOI: 10.1098/rsif.2017.0667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/04/2018] [Indexed: 11/12/2022]  Open
7
Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO. Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function. Mol Biol Evol 2019;35:2487-2498. [PMID: 30085185 DOI: 10.1093/molbev/msy150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
8
Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs. PLoS One 2018;13:e0202768. [PMID: 30138485 PMCID: PMC6107199 DOI: 10.1371/journal.pone.0202768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 11/19/2022]  Open
9
Abrahams L, Hurst LD. Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts. Mol Biol Evol 2018;34:3064-3080. [PMID: 28961919 PMCID: PMC5850271 DOI: 10.1093/molbev/msx223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
10
Hockenberry AJ, Stern AJ, Amaral LAN, Jewett MC. Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands. Mol Biol Evol 2017;35:582-592. [PMID: 29220489 PMCID: PMC5850609 DOI: 10.1093/molbev/msx310] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
11
Jia B, Qi H, Li BZ, Pan S, Liu D, Liu H, Cai Y, Yuan YJ. Orthogonal Ribosome Biofirewall. ACS Synth Biol 2017;6:2108-2117. [PMID: 28783349 DOI: 10.1021/acssynbio.7b00148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
12
Nakagawa S, Niimura Y, Gojobori T. Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes. Nucleic Acids Res 2017;45:3922-3931. [PMID: 28334743 PMCID: PMC5397173 DOI: 10.1093/nar/gkx124] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/11/2017] [Indexed: 02/01/2023]  Open
13
Synonymous codon bias as a basis for novel antibiotic design: from nucleotide wobble constraint to ribosomal garrotte. Future Med Chem 2017;9:1377-1400. [PMID: 28771025 DOI: 10.4155/fmc-2017-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
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