PEOPLE

Michael Ibba, Ph.D.
Dean, Schmid College of Science and Technology
Professor, Biological Sciences

Mike Ibba obtained an undergraduate degree in biochemistry from Imperial College in London and then went on to complete Ph.D. work in the field of microbial biochemistry at the University of Manchester. After graduating he undertook both industrial and academic post-docs in Switzerland and the US before going on to set up his own independent research group. After starting out as a faculty member in Copenhagen, Denmark, Mike moved to the Department of Microbiology at Ohio State University where he was the Chair of the Microbiology Department and served as the Associate Director for the Infectious Disease Institute at The Ohio State University. After 19 years at Ohio State, Mike moved to Chapman University to serve as the Dean of Schmid College of Science and Technology.

Whitney N. Wood, Ph.D.

Postdoctoral Researcher

Whitney completed her B.S. in Biochemistry at Texas State University in San Marcos, TX and she went on to earn her Ph.D. in Chemistry at Wayne State University in Detroit, MI. She is interested in studying bacterial persister cells and how the aminoacyl-tRNA syntheses influence persistence.

Arundhati Kavoor
Doctoral Student, Molecular Cellular and Developmental Biology Program, Ohio State

Arundhati completed her B.S. in Biotechnology at Christ University, India and earned her M.S. in Biotechnology at Indian Institute of Technology, Bombay, India. She is interested in studying translational quality control during stress responses.

Mary Agnes Cranley
Graduate student, Microbiology

Mary completed her B.S. in Microbiology at Ohio Wesleyan University. She is interested in studying the mechanism and rational for different modification states of EF-P.

Lorenzo Leiva
Post-doctoral fellow, Chapman University

PUBLICATIONS

SELECTED RECENT PUBLICATIONS

View the full list of publications by the Ibba Lab here: Google Scholar

Steiner RE, Ibba M. (2019) Regulation of tRNA-dependent translational quality control. IUBMB Life.

Steiner RE, Kyle AM, Ibba M (2019) Oxidation of phenylalanyl-tRNA synthetase positively regulates translational quality control. PNAS. 116, 10058-10063

Tollerson II R, Witzky A, Ibba M (2018) Elongation factor P is required to maintain proteome homeostasis at high growth rate. PNAS. 115, 11072-11077.

Sahai KS, Steiner RE, Au MG, Graham JM, Salamon N, Ibba M, Pierson TM (2018) FARS2 mutations presenting with pure spastic paraplegia and lesions of the dentate nuclei. Ann Clin Transl Neurol. 5, 1128-1133.

Steiner RE, Ibba M (2018) Bridging the gap between tRNA modifications and the respiratory chain. Biochem. 57, 2565-2566.

Witzky A, Hummels KR, Tollerson R II, Rajkovic A, Jones LA, Kearns DB, Ibba M (2018) EF-P post-translational modification has variable impact on polyproline translation in Bacillus subtilis. mBio. 9, e00306-18.

Mohler K, Mann R, Kyle A, Reynolds N, Ibba M (2018) Aminoacyl-tRNA quality control is required for efficient activation of the TOR pathway regulator Gln3p. RNA Biol. 15, 594-603.

Kelly P, Ibba M (2017) Aminoacyl-tRNA quality control provides a speedy solution to discriminate right from wrong. J Mol Biol. 5, 17-19.

Tollerson R II, Witzky A, Ibba M (2017) Elongation factor P interactions with the ribosome are independent of pausing. mBio. 8, e01056-17.

Hummels KR, Witzky A, Rajkovic A, Tollerson R 2nd, Jones LA, Ibba M, Kearns DB (2017) Carbonyl reduction by YmfI in Bacillus subtilis prevents accumulation of an inhibitory EF-P modification state. Mol Microbiol. 106, 236-251.

Mohler K, Mann R, Bulwinkle TJ, Hopkins K, Hwang L, Reynolds NM, Gassaway B, Aerni HR, RinehartJ, Polymenis M, Faull K, Ibba M (2017) Editing of misaminoacylated tRNA controls the sensitivity of amino acid stress responses in Saccharomyces cerevisiae. Nucelic Acids Res. 45, 3985-3996.

Mohler K, Aerni HR, Gassaway B, Ling J, Ibba M, Rinehart J (2017) MS-READ: Quantitative measurement of amino acid incorporation. Biochim Biophys Acta. S0304-4165, 30033-8.

Mohler K, Mann R, Ibba M (2017) Isoacceptor specific characterization of tRNA aminoacylation and misacylation in vivo. Methods. 113, 127-131.

Elgamal S, Artsimovich I, Ibba M (2016) Maintenance of transcription-translation coupling by elongation factor P. mBio. 7, e01373-16.

Moghal A, Hwang L, Faull K, Ibba M (2016) Multiple quality control pathways limit non-protein amino acid use by yeast cytoplasmic phenylalanyl-tRNA syntheses. J. Biol. Chem. 291, 15796-805.

Katz A, Elgamal S, Rajkovic A, Ibba M (2016). Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology. Mol. Microbiol. 101, 545-58.

Rajkovic A, Hummels KR, Witzky A, Erickson S, Gafken PR, Whitelegge JP, Faull KF, Kearns DB, Ibba M (2016). Translation control of swarming proficiency in Bacillus subitlis by 5-Aminopentanolylated Elongation Factor P. J. Biol. Chem. 291, 10976-85.

Bullwinkle T and Ibba M (2016) Translation quality control is critical for bacterial responses to amino acid stress. Proc. Natl. Acad. Sci. USA. 113, 2252-7.

Rajkovic A, Erickson S, Witzky A, Branson OE, Seo J, Gafken PR, Frietas MA, Whitelegge JP, Faull KF, Navarre W, Darwin AJ and Ibba M. (2015) Cyclic rhamnosylated elongation factor P establishes antibiotic resistance in Pseudomonas aeruginosa. mBio. 6, e00823-15.

Rajkovic A, Witzky A, Navarre W, Darwin AJ and Ibba M (2015) Elongation factor-P at the crossroads of the host-endosymbiont interface. Microbial Cell. 2, 360-362.

Shepherd J and Ibba M (2015) Bacterial transfer RNAs. FEMS Microbiol Rev. 39, 280-300.

Ibba M. (2015) Transfer RNA comes of age. RNA 21, 648-649.

Williams-Wagner RN, Grundy FJ, Raina M, Ibba M and Henkin TM (2015) The Bacillus subtilistyrZ gene encodes a highly selective tyrosyl-tRNA synthetase and is regulated by a MarR regulator and T box riboswitch. J. Bacteriol. 197, 1624-1631.

Elgamal S, Katz A, Hersch SJ, Newsom D, White P, Navarre WW and Ibba, M. (2014) EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genetics 10 e1004553.PDF

Bullwinkle TJ, Reynolds NM, Raina M, Moghal A, Matsa E, Rajkovic A., Kayadibi H, Fazlollahi F, Ryan C, Howitz N, Faull K, Lazazzera BA and Ibba M. (2014) Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code. eLife e02501.PDF

Bullwinkle TJ, Lazazzera BA and Ibba M. (2014) Quality control and infiltration of translation by amino acids outside of the genetic code. Annu. Rev. Genet. 48, 149-166. PDF

Hersch SJ, Elgamal S, Katz A, Ibba M and Navarre WW (2014) Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis. J. Biol. Chem. 289, 28160-28171.PDF

Shepherd J and Ibba M (2014) Relaxed substrate specificity leads to extensive tRNA mischarging by Streptococcus pneumoniae class I and class II aminoacyl-tRNA synthetases. mBio 5, e01656-14PDF

Raina M and Ibba M (2014) tRNAs as regulators of biological processes. Front. Genet. 5 171.PDF

Raina M, Moghal A, Kano A, Jerums M, Schnier PD, Luo S, Deshpande R, Bondarenko PV, Lin H and Ibba M. (2014) Reduced amino acid specificity of mammalian tyrosyl-tRNA synthetase is associated with elevated mistranslation of Tyr codons. J. Biol. Chem. 289, 17780-17790.PDF

Katz A, Solden L, Zou SB, Navarre WW and Ibba M. (2014) Molecular evolution of protein-RNA mimicry as a mechanism for translational control. Nucleic Acids Res. 42, 3261-3271.PDF

OTHER RELEVANT PUBLICATIONS

Bullwinkle TJ, Zou SB, Rajkovic A, Hersch SJ, Elgamal S, Robinson N, Smil D, Bolshan Y, Navarre WW and Ibba M. (2013) (R)-β-lysine modified elongation factor P functions in translation elongation. J. Biol. Chem 288, 4416-4423.PDF

Yadavalli SS and Ibba M. (2013) Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code. Nucleic Acids Res. 41, 1104-1112.PDF

Shepherd J and Ibba M (2013) Lipid II-independent trans editing of mischarged tRNAs by the penicillin resistance factor MurM. J. Biol. Chem. 288, 25915-25923.PDF

Elo, JM, Yadavalli SS, Euro L, Isohanni P, Götz A, Carroll C, Valanne L, Alkuraya FS, Uusimaa J, Paetau A, Caruso EM, Pihko H, Ibba M, Tyynismaa H & Suomalainen A (2012) Mitochondrial phenylalanyl-tRNA synthetase mutations underlie fatal infantile Alpers encephalopathy. Hum. Mol. Genet. 21, 4521-4529.

Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, Forsyth CJ, Navarre WW & Ibba M (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nat. Chem. Biol. 7, 667-669. Nature Research Highlight. OSU news.

Reynolds NM, Lazazzera BA & Ibba M. (2010) Cellular mechanisms that control mistranslation. Nat Rev Microbiol 8, 849-856.

Weygand-Durasevic I & Ibba M. (2010) New roles for codon usage. Science 329, 1473-1474.

Roy H & Ibba M. (2010) Bridging the gap between ribosomal and non-ribosomal protein synthesis. Proc Natl Acad Sci USA 107, 14517-14518.

Navarre WW, Zou S, Roy H, Xie JL, Savchenko A, Singer A, Evdokimova E, Prost LR, Kumar R, Ibba M & Fang FC. (2010) PoxA, YjeK and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica. Mol Cell 39, 209-221.

Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, Hamel P & Ibba M. (2010) Cell-specific differences in the requirements for translational quality control. Proc Natl Acad Sci USA 107, 4063-4068..

Ling J, So BR, Yadavalli SS, Roy H, Shoji S, Fredrick K, Musier-Forsyth K & Ibba M. (2009) Resampling and editing of mischarged tRNA prior to translation elongation. Mol Cell 33, 654-660.

Roy H & Ibba M. (2008) RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors. Proc Natl Acad Sci USA 105, 4667-4672.

Ling J, Roy H, Qin D, Rubio MA, Alfonzo JD, Fredrick K & Ibba M. (2007) Pathogenic mechanism of a human mitochondrial tRNA^Phe mutation associated with MERRF syndrome. Proc Natl Acad Sci USA 104, 15299-15304.

Ling J, Roy H & Ibba M. (2007) Mechanism of tRNA-dependent editing in translational quality control. Proc Natl Acad Sci USA 104, 72-77.

Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman W, Yates JR 3rd, Ibba M & Söll D. (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307, 1969-1972.

Roy H, Ling J, Irnov and Ibba M. (2004) Post-transfer editing in vitro and in vivo by the beta-subunit of phenylalanyl-tRNA synthetase. EMBO J. 23, 4639-4648.

Jester B, Levengood J, Roy H, Ibba M & Devine K. (2003) Non-orthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogs to the genetic code. Proc Natl Acad Sci USA 100, 14351-14356.

ALUMNI

Doctoral Students (thesis advisor)

Sandro Ataide (2002 – 2006)
Associate Professor, University of Sydney

Jeffrey Levengood (2002 – 2006)
Research Scientist, Case Western Reserve

Corinne Hausmann (2004 – 2008)
Specialist Leader, Deloitte Consulting

Jiqiang Ling (2004 – 2008)
Associate Professor, University of Maryland

Theresa Rogers (2006 – 2010)
Associate Professor, Cal. Lutheran University

Noah Reynolds (2006 – 2011)
Assistant Professor, Univ. Illinois Springfield

Samhita Yadavalli (2007 – 2012)
Assistant Professor, Rutgers University

Kiley Dare (2007 – 2012)
ProFile Discovery

Medha Raina (2009 – 2014)
Post-doc, NIH

Sara Elgamal (2011 – 2015)
Post-doc, Ohio State University

Adil Moghal (2012 – 2016)
Patent Lawyer, Washington, DC

Andrei Rajkovic (2012 – 2016)
Bioinformatics Developer, Nationwide Children’s Hospital

Kyle Mohler (2013 – 2017)
NCI Post-doc, Yale University

Anne Witzky (2015 – 2019)
Assistant Professor, Ohio Dominican Univ.

Rebecca Steiner (2016 – 2019)
Assistant Professor, Lake Erie College of Osteopathic Medicine

Rodney Tollerson (2016 – 2019)
Post-doc, California Institute of Technology

Paul Kelly (2015 – 2020)
Post-doc, Elanco

Nien-Ching Han (2017 – 2021)
Post-doc, The Salk Institute

Masters Students (thesis advisor)

Amanda Monthan (2000)
Scientist, Swedish Dairy Association

Marla Gilreath (2009 – 2011)
Regulatory Specialist, Nexeo Solutions

Mengchi Wang (2011 – 2013)
Bioinformatician, Illumina

Rachel Simari (2013 – 2014)
Clinical microbiologist, Utah

Sarah Erickson (2014 – 2015)
Graduate student, Boston College

Post-doctoral Fellows

Nina Mejlhede (2000 – 2001)
Scientist, State Serum Institute, Denmark

Mette Prætorius (2001 – 2005)
Assistant Professor, Ohio State University

Hervé Roy (2003 – 2011)
Associate Professor, Univ of Central Florida

Shiming Wang (2004 – 2006)
Assistant Professor, Nanjing University

Rajat Banerjee (2008 – 2010)
Associate Professor, University of Calcutta

Assaf Katz (2011 – 2014)
Assistant Professor, University of Chile

Jennifer Shepherd (2011 – 2015)
Prime Global Medical Communications

Tammy Bullwinkle (2010 – 2016)
Assistant Professor, Ohio State University

Miguel-Angel Rubio Gomez (2017 – 2019)
Scientist, Sevilla, Spain

Rodney Tollerson (2020)
Post-doc, California Institute of Technology

Paul Kelly (2020)
Post-doc, Elanco

Research

Our research is directed towards understanding the mechanisms that determine how cells ensure the accurate translation of the genetic code, and how changes in the underlying processes impact cellular health and contribute to microbial pathogenesis and disease. Many of these processes are essential and unique to particular systems, making them ideal potential drug targets.

Quality control in protein synthesis: Ribosomes are the protein synthesis factories of the cell that translate the codons of mRNA into amino acids. Protein synthesis proceeds by delivery to the ribosome of aminoacyl-tRNAs, which pair with the corresponding mRNA sequences. Aminoacyl-tRNAs are made by the aminoacyl-tRNA synthetases, a family of twenty proteins each of which pairs a particular amino acid with the correct tRNA. Accurate aminoacyl-tRNA synthesis often requires an additional editing activity intrinsic to many aaRSs. The editing activity significantly decreases the level of mistakes in aminoacyl-tRNA synthesis in vitro and in vivo, although quantitative analysis of its contribution to the overall fidelity of translation has not been performed. The overall aim of our work is to develop experimental systems to quantitatively measure the frequency of aaRS-dependent misincorporation for several amino acids and evaluate the contribution of aaRS editing to overall translational fidelity in vivo.

Translational control of antibiotic resistance: In responses to different environmental stresses, such as the presence of antibiotics, microbes direct resources away from translation to a variety of pathways that contribute to resistance. Elongation factor P (EF-P). EF-P is a protein that mimics the structure and function of a tRNA and binds ribosomes. Aminoacylation of EF-P is required for optimal growth under a variety of conditions, for example at key points during Salmonella infection. We are interested in understanding how EF-P mimics tRNA at the molecular level and how this provides a novel mechanism for the post-transcriptional control of gene expression.

FIGURE 1: The role of EF-P in M. aeruginosavorus during host invasion.

The far left panel depicts P. aeruginosa drawn in purple and M. aeruginosavorus in yellow.
(A) The image illustrates a breach in the outer membrane allowing for dTDP-L-rhamnose to diffuse into M. aeruginosavorus where EF-P (red) is then modified by EarP (white).
(B) As a result of EF-P being modified ribosomes (grey and purple) can effectively translate mRNA (blue) with a poly-proline stretch.
(C) On the other hand during the attack phase EF-P is unmodified and therefore poly-proline translation is absent.
(Rajkovic et al. 2015)