Article
Version 1
Preserved in Portico This version is not peer-reviewed
Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species
Version 1
: Received: 24 March 2024 / Approved: 25 March 2024 / Online: 25 March 2024 (08:53:51 CET)
A peer-reviewed article of this Preprint also exists.
Farookhi, H.; Xia, X. Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species. Microorganisms 2024, 12, 768. Farookhi, H.; Xia, X. Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species. Microorganisms 2024, 12, 768.
Abstract
Different bacterial species have dramatically different generation times, from 20-30 minutes in Escherichia coli to about two weeks in Mycobacterium leprae. The translation machinery in a cell needs to synthesize all proteins for a new cell in each generation. The three subprocesses of translation, i.e., initiation, elongation, and termination, are expected to be under stronger selection pressure to optimize in short-generation bacteria (SGB) such as Vibrio natriegens than in the long-generation Mycobacterium leprae. The initiation efficiency depends on the start codon decoded by the initiation tRNA, the optimal Shine-Dalgarno (SD) decoded by the anti-SD (aSD) sequence on small subunit rRNA, and the secondary structure that may embed the initiation signals and prevent them from being decoded. The elongation efficiency depends on the tRNA pool and codon usage. The termination efficiency in bacteria depends mainly on the nature of the stop codon and the nucleotide immediately downstream of the stop codon. By contrasting SGB with long-generation bacteria (LGB), we predict that 1) SGB to have more ribosome RNA operons to produce ribosomes, and more tRNA genes for carrying amino acid to ribosomes, 2) SGB to have a higher percentage of genes using AUG as start codon and UAA as stop codon than LGB, 3) SGB to exhibit better codon and anticodon adaptation than LGB, and 4) SGB to have weaker secondary structure near translation initiation signals than LGB. These differences between SGB and LGB should be more pronounced in highly expressed genes than lowly expressed genes. We present empirical evidence in support of these predictions.
Keywords
Mycobacterium leprae; Mycobacterium tuberculosis; translation efficiency; translation initiation; translation elongation; translation termination; RNA secondary structure; rrn operons; tRNA
Subject
Biology and Life Sciences, Ecology, Evolution, Behavior and Systematics
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Comments (0)
We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.
Leave a public commentSend a private comment to the author(s)
* All users must log in before leaving a comment