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JBacusmo Dissertation_FINAL.pdf (21.28 MB)

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Proline Codon Translational Fidelity in Rhodopseudomonas palustris: Characterization of Novel Trans-editing Factor ProXp-abu

Bacusmo, Jo Marie
http://rave.ohiolink.edu/etdc/view?acc_num=osu1397747141

Abstract Details

2014, Doctor of Philosophy, Ohio State University, Chemistry.
Ribosomal protein synthesis is a core biological process essential to all living systems. Proteomic aberrations caused by translational inaccuracies lead to cellular dysfunction and in certain cases, cell death. Aminoacyl-tRNA synthetases (aaRSs) play a central role in protein synthesis. They are responsible for covalent attachment of the correct amino acid to their cognate tRNA substrates. However, this process is inherently error prone due to the isosteric nature of amino acids thus quality control mechanisms have evolved to maintain translational fidelity. In the case of bacterial prolyl-tRNA synthetase (ProRS), a triple-sieve editing mechanism is generally employed, which consists of the ProRS active site that discriminates amino acids based primarily on volume and size, a cis-editing domain (INS) that hydrolyzes Ala-tRNAPro, and a trans-editing factor, YbaK, which clears Cys-tRNAPro. Extensive genomic analysis revealed five distinct trans-editing domains homologous to the INS domain. While a subset of these factors correct ProRS-dependent errors, recent studies have revealed distinct substrate specificities and tRNA recognition capabilities that extend beyond Ala- and Cys-tRNAPro. All known editing mechanisms clear standard non-cognate amino acids; how non-protein amino acids are prevented from misincorporation is unclear. Non-protein amino acids are found in many foods and have the potential to adversely affect human health. The non-protein amino acid aminobutyrate (Abu) is a metabolite involved in various cellular processes. Due to Abu’s similarity to Ala and Val, it is recognized and misactivated by several aaRSs. The metabolically versatile bacterium Rhodopseudomonas palustris (Rp) encodes for a ProRS containing a catalytically inactive, truncated INS domain, in addition to two distinct INS homologs: YbaK, which deacylates Cys-tRNAPro, and ProXp-x of unknown function. Comparison of known crystal structures reveals that the catalytic pocket of ProXp-x is larger than that of INS, which suggests substrates larger than Ala are preferred. Indeed, ProXp-x weakly deacylates tRNAs charged with Ile and Val, but robustly edits Abu mischarged onto tRNAPro, tRNAVal, and tRNAIle. Semi-promiscuous editing may offer advantages to cells and our data suggest ProXp-x may act as a general Abu-tRNA deacylase. Rp ProRS specificity for activation of Pro over Abu is only about 1,000:1, which strongly suggests that editing of Abu-tRNAPro is required in vivo. Taken together, these data suggest that Abu-tRNA editing by the trans-editing factor ProXp-x, now renamed ProXp-abu, is likely to be a critical checkpoint to ensure high fidelity in codon translation.
Karin Musier-Forsyth (Committee Member)
Michael Ibba (Committee Member)
Thomas Magliery (Committee Member)
136 p.
Biochemistry; Chemistry; Molecular Biology
translation, protein synthesis, aminoacyl-tRNA Synthetase, post-transfer editing, trans-editing, non-protein amino acid, Rhodopseudomonas palustris,

Recommended Citations

Citations

  • Bacusmo, J. M. (2014). Proline Codon Translational Fidelity in Rhodopseudomonas palustris: Characterization of Novel Trans-editing Factor ProXp-abu [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397747141

    APA Style (7th edition)

  • Bacusmo, Jo Marie. Proline Codon Translational Fidelity in Rhodopseudomonas palustris: Characterization of Novel Trans-editing Factor ProXp-abu. 2014. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1397747141.

    MLA Style (8th edition)

  • Bacusmo, Jo Marie. "Proline Codon Translational Fidelity in Rhodopseudomonas palustris: Characterization of Novel Trans-editing Factor ProXp-abu." Doctoral dissertation, Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397747141

    Chicago Manual of Style (17th edition)

osu1397747141
260
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This open access ETD is published by The Ohio State University and OhioLINK.