Bacterial transfer RNAs

Abstract

Transfer RNA is an essential adapter molecule that is found across all three domains of life. The primary role of transfer RNA resides in its critical involvement in the accurate translation of messenger RNA codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. This review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer RNAs. Codon recognition at the ribosome as well as the ever-increasing number of alternative roles for transfer RNA outside of translation will be discussed in the specific context of bacterial cells.

Keywords: aminoacylation; codon; modification; protein synthesis; tRNA; translation.

Graphical Abstract Figure.

This review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer RNAs.

Figure 1.

The typical life cycle of a bacterial transfer RNA. The numbering system corresponds to the specific sections of this review. Abbreviations include aminoacyl-tRNA synthetase (aaRS), inorganic pyrophosphate (PPi), amino acid (aa) and elongation factor-TU (EF-Tu).

Figure 2.

Known modifications and their positions in E. coli tRNA. The information presented in this figure was adapted from El Yacoubi, Bailly and de Crecy-Lagard, (2012). Abbreviations for specific groups include m-, c-, n-, o-, t-, i-, K-, r- and s- for methyl, carbon, amino, oxy, threonine, isopentyl, lysine, ribose and thio groups, respectively. Other abbreviations include acp: 3-amino-3-carboxypropyl, D: dihydrouridine, I: inosine, Ψ: pseudouridine, Q: queuosine. Other capital letters refer to the appropriate bases uracil, cytosine, guanine and adenine. An index and an exponent indicate the number and the position of the substitution, for example 6-dimethyladenosine is written as m⁶₂A.

Figure 3.

Formation of an aminoacylated-tRNA molecule by an aaRS. An amino acid (blue) is activated by an aaRS to form an aminoacyl-adenylate. This process requires ATP and results in the release of PPi. Following tRNA binding to the aaRS, the activated amino acid is transferred to the 3′ end of the tRNA molecule forming aminoacyl-tRNA with concurrent release of adenosine monophosphate (AMP). The aminoacyl-tRNA product is released from the aaRS and is either subject to binding by EF-Tu for delivery to the ribosome or hijacking by other factors for diversion into biosynthetic pathways outside of translation. Figure reproduced from Reynolds, Lazazzera and Ibba (2010).

Figure 4.

Indirect tRNA aminoacylation pathways. (A) The indirect pathways for generation of Gln-tRNA^Gln and Asn-tRNA^Asn by transamidation. Abbreviations include AdT for amidotransferase. (B) The selenocysteine tRNA modification pathway. (C) The formylation pathway for initiator Met-tRNAf^Met. Abbreviations include FMT for methionyl-tRNA_f^Met transformylase, FTHF for N-10 formyltetrahydrofolate and IF2 for initiation factor 2.

Figure 5.

Quality control steps during the formation of a non-cognate aminoacyl-tRNA. After activation of a non-cognate amino acid (red), the aminoacyl adenylate may be hydrolyzed and released. A non-cognate aminoacyl-tRNA may be translocated into the editing site of the aaRS for hydrolysis. If the mischarged aminoacyl-tRNA is released from the aaRS without being edited, it is subjected to editing by trans-editing factors or through resampling by the aaRS. Some non-cognate aminoacyl-tRNAs are discriminated against by EF-Tu, which either binds them too tightly or too weakly for efficient delivery and release in the ribosome. Figure reproduced from Reynolds, Lazazzera and Ibba (2010).