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1
Mattingly JM, Nguyen HA, Roy B, Fredrick K, Dunham CM. Structural analysis of noncanonical translation initiation complexes. J Biol Chem 2024;300:107743. [PMID: 39222680 PMCID: PMC11497404 DOI: 10.1016/j.jbc.2024.107743] [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: 05/03/2024] [Revised: 08/14/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]  Open
2
Gemler BT, Warner BR, Bundschuh R, Fredrick K. Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea. RNA (NEW YORK, N.Y.) 2024;30:1264-1276. [PMID: 39043438 PMCID: PMC11404451 DOI: 10.1261/rna.080091.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024]
3
Warner BR, Fredrick K. Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome. RNA (NEW YORK, N.Y.) 2024;30:770-778. [PMID: 38570183 PMCID: PMC11182017 DOI: 10.1261/rna.079960.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/23/2024] [Indexed: 04/05/2024]
4
Naeem FM, Gemler BT, McNutt ZA, Bundschuh R, Fredrick K. Analysis of programmed frameshifting during translation of prfB in Flavobacterium johnsoniae. RNA (NEW YORK, N.Y.) 2024;30:136-148. [PMID: 37949662 PMCID: PMC10798248 DOI: 10.1261/rna.079721.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
5
Warner BR, Bundschuh R, Fredrick K. Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit. Nucleic Acids Res 2023;51:5242-5254. [PMID: 37102690 PMCID: PMC10250234 DOI: 10.1093/nar/gkad316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023]  Open
6
McNutt ZA, Roy B, Gemler BT, Shatoff EA, Moon KM, Foster L, Bundschuh R, Fredrick K. Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae. Nucleic Acids Res 2023;51:1927-1942. [PMID: 36727479 PMCID: PMC9976891 DOI: 10.1093/nar/gkad047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 02/03/2023]  Open
7
Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022;376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
8
McNutt ZA, Gandhi MD, Shatoff EA, Roy B, Devaraj A, Bundschuh R, Fredrick K. Comparative Analysis of anti-Shine- Dalgarno Function in Flavobacterium johnsoniae and Escherichia coli. Front Mol Biosci 2021;8:787388. [PMID: 34966783 PMCID: PMC8710568 DOI: 10.3389/fmolb.2021.787388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/08/2021] [Indexed: 12/03/2022]  Open
9
Shatoff EA, Gemler BT, Bundschuh R, Fredrick K. Maturation of 23S rRNA includes removal of helix H1 in many bacteria. RNA Biol 2021;18:856-865. [PMID: 34812116 PMCID: PMC8782170 DOI: 10.1080/15476286.2021.2000793] [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] [Indexed: 11/17/2022]  Open
10
del Peso Santos T, Alvarez L, Sit B, Irazoki O, Blake J, Warner BR, Warr AR, Bala A, Benes V, Waldor MK, Fredrick K, Cava F. BipA exerts temperature-dependent translational control of biofilm-associated colony morphology in Vibrio cholerae. eLife 2021;10:e60607. [PMID: 33588990 PMCID: PMC7886329 DOI: 10.7554/elife.60607] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022]  Open
11
Jha V, Roy B, Jahagirdar D, McNutt ZA, Shatoff EA, Boleratz BL, Watkins DE, Bundschuh R, Basu K, Ortega J, Fredrick K. Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Nucleic Acids Res 2021;49:547-567. [PMID: 33330920 PMCID: PMC7797042 DOI: 10.1093/nar/gkaa1195] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022]  Open
12
Chen M, Fredrick K. RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time. J Mol Biol 2020;432:3981-3986. [PMID: 32198117 DOI: 10.1016/j.jmb.2020.03.018] [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: 01/22/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 01/19/2023]
13
Ying L, Zhu H, Fosso MY, Garneau-Tsodikova S, Fredrick K. Modified Aminoglycosides Bind Nucleic Acids in High-Molecular-Weight Complexes. Antibiotics (Basel) 2020;9:antibiotics9020093. [PMID: 32098020 PMCID: PMC7168264 DOI: 10.3390/antibiotics9020093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/05/2022]  Open
14
Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Res 2019;47:10477-10488. [PMID: 31602466 PMCID: PMC6847099 DOI: 10.1093/nar/gkz855] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022]  Open
15
Hoffer ED, Maehigashi T, Fredrick K, Dunham CM. Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Nucleic Acids Res 2019;47:1557-1563. [PMID: 30476222 PMCID: PMC6379664 DOI: 10.1093/nar/gky1178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 01/18/2023]  Open
16
Hoffer ED, Maehigashi T, Fredrick K, Dunham CM. Ribosomal ambiguity ( ram ) mutations promote 30S domain closure and thereby increase miscoding. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.628.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
17
Ying L, Zhu H, Shoji S, Fredrick K. Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation. RNA (NEW YORK, N.Y.) 2019;25:247-254. [PMID: 30413565 PMCID: PMC6348987 DOI: 10.1261/rna.068460.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/06/2018] [Indexed: 05/18/2023]
18
Zhao D, Baez WD, Fredrick K, Bundschuh R. RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling. Bioinformatics 2018;35:1486-1493. [DOI: 10.1093/bioinformatics/bty854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 09/03/2018] [Accepted: 10/09/2018] [Indexed: 11/14/2022]  Open
19
Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. Publisher Correction: ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018;560:E35. [PMID: 29925958 DOI: 10.1038/s41586-018-0271-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
20
Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018;557:510-515. [PMID: 29769718 PMCID: PMC5973781 DOI: 10.1038/s41586-018-0137-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/09/2018] [Indexed: 11/29/2022]
21
Gibbs MR, Fredrick K. Roles of elusive translational GTPases come to light and inform on the process of ribosome biogenesis in bacteria. Mol Microbiol 2017;107:445-454. [PMID: 29235176 DOI: 10.1111/mmi.13895] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022]
22
Roy B, Liu Q, Shoji S, Fredrick K. IF2 and unique features of initiator tRNAfMet help establish the translational reading frame. RNA Biol 2017;15:604-613. [PMID: 28914580 DOI: 10.1080/15476286.2017.1379636] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
23
Dai X, Zhu M, Warren M, Balakrishnan R, Patsalo V, Okano H, Williamson JR, Fredrick K, Wang YP, Hwa T. Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth. Nat Microbiol 2016;2:16231. [PMID: 27941827 PMCID: PMC5346290 DOI: 10.1038/nmicrobiol.2016.231] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 10/17/2016] [Indexed: 01/13/2023]
24
Ying L, Fredrick K. Epistasis analysis of 16S rRNA ram mutations helps define the conformational dynamics of the ribosome that influence decoding. RNA (NEW YORK, N.Y.) 2016;22:499-505. [PMID: 26873598 PMCID: PMC4793206 DOI: 10.1261/rna.054486.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
25
Liu Q, Fredrick K. Intersubunit Bridges of the Bacterial Ribosome. J Mol Biol 2016;428:2146-64. [PMID: 26880335 DOI: 10.1016/j.jmb.2016.02.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 02/02/2023]
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