Publications

  1. Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit. Warner BR, Bundschuh R, Fredrick K. Nucleic Acids Research. 2023 April 13;gkad316 doi: 10.1093/nar/gkad316.
  2. Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae. McNutt ZA, Roy B, Gemler BT, Shatoff EA, Moon KM, Foster LJ, Bundschuh R, Fredrick K. Nucleic Acids Research. 2023 Feb  2;gkad047. doi: 10.1093/nar/gkad047.
  3. Comparative Analysis of anti-Shine- Dalgarno Function in Flavobacterium johnsoniae and Escherichia coli. McNutt ZA, Gandhi MD, Shatoff EA, Roy B, Devaraj A, Bundschuh R, Fredrick K.Front Mol Biosci. 2021 Dec 13;8:787388. doi: 10.3389/fmolb.2021.787388. eCollection 2021.
  4. Maturation of 23S rRNA includes removal of helix H1 in many bacteria. Shatoff EA, Gemler BT, Bundschuh R, Fredrick K.RNA Biol. 2021 Nov 12;18(sup2):856-865. doi: 10.1080/15476286.2021.2000793. Epub 2021 Nov 23.
  5. BipA exerts temperature-dependent translational control of biofilm-associated colony morphology in Vibrio cholerae. 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. Elife. 2021 Feb 12;10:e60607. doi: 10.7554/eLife.60607.
  6. Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Jha V, Roy B, Jahagirdar D, McNutt ZA, Shatoff EA, Boleratz BL, Watkins DE, Bundschuh R, Basu K, Ortega J, Fredrick K. Nucleic Acids Res. 2021 Jan 11;49(1):547-567. doi: 10.1093/nar/gkaa1195.
  7. Functional Analysis of BipA in E. coli Reveals the Natural Plasticity of 50S Subunit Assembly. Gibbs MR, Moon KM, Warner BR, Chen M, Bundschuh R, Foster LJ, Fredrick K. J Mol Biol. 2020 Sep 4;432(19):5259-5272. doi: 10.1016/j.jmb.2020.07.013. Epub 2020 Jul 22.
  8. RNA Polymerase’s Relationship with the Ribosome: Not So Physical, Most of the Time. Chen M, Fredrick K. J Mol Biol. 2020 Jun 26;432(14):3981-3986. doi: 10.1016/j.jmb.2020.03.018. Epub 2020 Mar 19.
  9. Modified Aminoglycosides Bind Nucleic Acids in High-Molecular-Weight Complexes. Ying L, Zhu H, Fosso MY, Garneau-Tsodikova S, Fredrick K. Antibiotics (Basel). 2020 Feb 21;9(2):93. doi: 10.3390/antibiotics9020093.
  10. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Nucleic Acids Res. 2019 Oct 11. pii: gkz855. doi: 10.1093/nar/gkz855
  11. Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Hoffer ED, Maehigashi T, Fredrick K, Dunham CM. Nucleic Acids Res. 2019 Feb 20;47(3):1557-1563. doi: 10.1093/nar/gky1178
  12. Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation. Ying L, Zhu H, Shoji S, Fredrick K. RNA. 2019 Feb;25(2):247-254. doi: 10.1261/rna.068460.118. Epub 2018 Nov 9.
  13. RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling. Zhao D, Baez WD, Fredrick K, Bundschuh R. Bioinformatics. 2019 May 1;35(9):1486-1493. doi: 10.1093/bioinformatics/bty854.
  14. Measures of single- versus multiple-round translation argue against a mechanism to ensure coupling of transcription and translation. Chen M, Fredrick K. Proc Natl Acad Sci U S A. 2018 Oct 1. pii: 201812940.
  15. Publisher Correction: ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR 3rd, Fredrick K, Schimmel P, Ackerman SL. Nature. 2018 Aug;560(7720):E35.
  16. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR 3rd, Fredrick K, Schimmel P, Ackerman SL. Nature. 2018 May;557(7706):510-515.
  17. Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress. Dai X, Zhu M, Warren M, Balakrishnan R, Okano H, Williamson JR, Fredrick K, Hwa T. MBio. 2018 Feb 13;9(1).
  18. Roles of elusive translational GTPases come to light and inform on the process of ribosome biogenesis in bacteria. Gibbs MR, Fredrick K. Molecular microbiology. 2018; 107(4):445-454.
  19.  Conserved GTPase LepA (Elongation Factor 4) functions in biogenesis of the 30S subunit of the 70S ribosome. Gibbs MR, Moon KM, Chen M, Balakrishnan R, Foster LJ, Fredrick K. Proceedings of the National Academy of Sciences of the United States of America. 2017; 114(5):980-985.
  20. Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth. Dai X, Zhu M, Warren M, Balakrishnan R, Patsalo V, Okano H, Williamson JR, Fredrick K, Wang YP, Hwa T. Nature microbiology. 2016; 2:16231.
  21. Intersubunit Bridges of the Bacterial Ribosome. Liu Q, Fredrick K. Journal of molecular biology. 2016; 428(10 Pt B):2146-64.
  22. Epistasis analysis of 16S rRNA ram mutations helps define the conformational dynamics of the ribosome that influence decoding. Ying L, Fredrick K. RNA (New York, N.Y.). 2016; 22(4):499-505.
  23. A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Fleming IM, Paris Z, Gaston KW, Balakrishnan R, Fredrick K, Rubio MA, Alfonzo JD.
  24. Roles of helix H69 of 23S rRNA in translation initiation. Liu Q, Fredrick K. Proceedings of the National Academy of Sciences of the United States of America. 2015; 112(37):11559-64.
  25. Tobramycin Variants with Enhanced Ribosome-Targeting Activity. Fosso MY, Zhu H, Green KD, Garneau-Tsodikova S, Fredrick K. Chembiochem : a European journal of chemical biology. 2015; 16(11):1565-70.
  26. Another look at mutations in ribosomal protein S4 lends strong support to the domain closure model. Fredrick K. Journal of bacteriology. 2015; 197(6):1014-6.
  27. In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state. McGinnis JL, Liu Q, Lavender CA, Devaraj A, McClory SP, Fredrick K, Weeks KM. Proceedings of the National Academy of Sciences of the United States of America. 2015; 112(8):2425-30.
  28. The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli. Balakrishnan R, Oman K, Shoji S, Bundschuh R, Fredrick K. Nucleic acids research. 2014; 42(21):13370-83.
  29. Direct measurement of the mechanical work during translocation by the ribosome. Liu T, Kaplan A, Alexander L, Yan S, Wen JD, Lancaster L, Wickersham CE, Fredrick K, Noller H, Tinoco I, Bustamante CJ. eLife. 2014; 3:e03406.
  30. Distinct functional classes of ram mutations in 16S rRNA. McClory SP, Devaraj A, Fredrick K. RNA (New York, N.Y.). 2014; 20(4):496-504.
  31. The ABCs of the ribosome. Fredrick K, Ibba M. Nature structural & molecular biology. 2014; 21(2):115-6.
  32. Bifacial PNA complexation inhibits enzymatic access to DNA and RNA. Xia X, Piao X, Fredrick K, Bong D. Chembiochem : a European journal of chemical biology. 2014; 15(1):31-6.
  33. Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state. Fagan CE, Dunkle JA, Maehigashi T, Dang MN, Devaraj A, Miles SJ, Qin D, Fredrick K, Dunham CM. Proceedings of the National Academy of Sciences of the United States of America. 2013; 110(24):9716-21.
  34. Contribution of intersubunit bridges to the energy barrier of ribosomal translocation. Liu Q, Fredrick K. Nucleic acids research. 2013; 41(1):565-74.
  35. Analysis of polysomes from bacteria. Qin D, Fredrick K. Methods in enzymology. 2013; 530:159-72.
  36. Role of helix 44 of 16S rRNA in the fidelity of translation initiation. Qin D, Liu Q, Devaraj A, Fredrick K. RNA (New York, N.Y.). 2012; 18(3):485-95.
  37. Short spacing between the Shine-Dalgarno sequence and P codon destabilizes codon-anticodon pairing in the P site to promote +1 programmed frameshifting. Devaraj A, Fredrick K. Molecular microbiology. 2010; 78(6):1500-9
  38. Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection. McClory SP, Leisring JM, Qin D, Fredrick K. RNA (New York, N.Y.). 2010; 16(10):1925-34.
  39. How the sequence of a gene can tune its translation. Fredrick K, Ibba M. Cell. 2010; 141(2):227-9.
  40. Translation factor LepA contributes to tellurite resistance in Escherichia coli but plays no apparent role in the fidelity of protein synthesis. Shoji S, Janssen BD, Hayes CS, Fredrick K. Biochimie. 2010; 92(2):157-63
  41. RNase II is important for A-site mRNA cleavage during ribosome pausing. Garza-Sánchez F, Shoji S, Fredrick K, Hayes CS. Molecular microbiology. 2009; 73(5):882-97
  42. Contribution of ribosomal residues to P-site tRNA binding. Shoji S, Abdi NM, Bundschuh R, Fredrick K. Nucleic acids research. 2009; 37(12):4033-42.
  43. Resampling and editing of mischarged tRNA prior to translation elongation. Ling J, So BR, Yadavalli SS, Roy H, Shoji S, Fredrick K, Musier-Forsyth K, Ibba M. Molecular cell. 2009; 33(5):654-60
  44. Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA. Qin D, Fredrick K. Molecular microbiology. 2009; 71(5):1239-49
  45. Ribosomal translocation: one step closer to the molecular mechanism. Shoji S, Walker SE, Fredrick K. ACS chemical biology. 2009; 4(2):93-107.
  46. A role for the 30S subunit E site in maintenance of the translational reading frame. Devaraj A, Shoji S, Holbrook ED, Fredrick K. RNA (New York, N.Y.). 2009; 15(2):255-65.
  47. Protein synthesis: Errors rectified in retrospect. Fredrick K, Ibba M. Nature. 2009; 457(7226):157-8.
  48. Structural basis for hygromycin B inhibition of protein biosynthesis. Borovinskaya MA, Shoji S, Fredrick K, Cate JH. RNA (New York, N.Y.). 2008; 14(8):1590-9.
  49. Role of hybrid tRNA-binding states in ribosomal translocation. Walker SE, Shoji S, Pan D, Cooperman BS, Fredrick K. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(27):9192-7.
  50. Preparation and evaluation of acylated tRNAs. Walker SE, Fredrick K. Methods (San Diego, Calif.). 2008; 44(2):81-6.
  51. Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation. Qin D, Abdi NM, Fredrick K. RNA (New York, N.Y.). 2007; 13(12):2348-55.
  52. Pathogenic mechanism of a human mitochondrial tRNAPhe mutation associated with myoclonic epilepsy with ragged red fibers syndrome. Ling J, Roy H, Qin D, Rubio MA, Alfonzo JD, Fredrick K, Ibba M. Proceedings of the National Academy of Sciences of the United States of America. 2007; 104(39):15299-304.
  53. A steric block in translation caused by the antibiotic spectinomycin. Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JHD. ACS chemical biology. 2007; 2(8):545-552
  54. Reverse translocation of tRNA in the ribosome. Shoji S, Walker SE, Fredrick K. Molecular cell. 2006; 24(6):931-42.
  55. Paternal chromosome segregation during the first mitotic division determines Wolbachia-induced cytoplasmic incompatibility phenotype. Tram U, Fredrick K, Werren JH, Sullivan W. Journal of cell science. 2006; 119(Pt 17):3655-63.
  56. Recognition and positioning of mRNA in the ribosome by tRNAs with expanded anticodons. Walker SE, Fredrick K. Journal of molecular biology. 2006; 360(3):599-609.
  57. Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome. McGarry KG, Walker SE, Wang H, Fredrick K. Molecular cell. 2005; 20(4):613-22
  58. Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics. Yassin A, Fredrick K, Mankin AS. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102(46):16620-5.
  59. Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli. Abdi NM, Fredrick K. RNA (New York, N.Y.). 2005; 11(11):1624-32.