title: Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria?
abstract: Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that predicts the ΔG° of any tRNA to EF-Tu using the sequence of its three T-stem base pairs. Despite dramatic differences in T-stem sequences, the predicted ΔG° values for the majority of tRNA classes are similar in all bacteria and closely match the ΔG° values determined for E. coli tRNAs. Each individual tRNA class has evolved to have a characteristic ΔG° value to EF-Tu, but different T-stem sequences are used to achieve this ΔG° value in different bacteria. Thus, the compensatory relationship between the affinity of the tRNA body and the affinity of the esterified amino acid is universal among bacteria. Additionally, we predict and validate a small number of aa-tRNAs that bind more weakly to EF-Tu than expected and thus are candidates for acting as activated amino acid donors in processes outside of translation.
authors: Department of Molecular Biosciences, Northwestern University, Hogan 2-100, Evanston, IL 60208, USA.
authors: Jared M
authors: JM
authors: Schrader
authors: Olke C
authors: OC
authors: Uhlenbeck
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D020029:Base Pairing; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics; D008958:Models, Molecular; D010444:Peptide Elongation Factor Tu / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D016963:Thermus thermophilus / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012346:RNA, Transfer, Amino Acyl; D010444:Peptide Elongation Factor Tu