Overview of tRNA Modifications in Chloroplasts

Abstract

The chloroplast is a promising platform for biotechnological innovation due to its compact translation machinery. Nucleotide modifications within a minimal set of tRNAs modulate codon–anticodon interactions that are crucial for translation efficiency. However, a comprehensive assessment of these modifications does not presently exist in chloroplasts. Here, we synthesize all available information concerning tRNA modifications in the chloroplast and assign translation efficiency for each modified anticodon–codon pair. In addition, we perform a bioinformatics analysis that links enzymes to tRNA modifications and aminoacylation in the chloroplast of Chlamydomonas reinhardtii. This work provides the first comprehensive analysis of codon and anticodon interactions of chloroplasts and its implication for translation efficiency.

Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii

“…For the quartet boxes, the unmodified U 34 nucleotide efficiently pairs with U‐ and A‐ending codons, while a G 3 :U 34 wobble base is unstable and C‐ending codons are not read efficiently (Grosjean & Westhof, 2016 ). Anticodons containing an unknown modification of U 34 were hypothesized to lead to higher translation efficiency of A‐ and U‐ending codons within quartet boxes in the chloroplast of C. reinhardtii and in M. capricolum , in accordance with Ikemura's second rule (Fages‐Lartaud & Hohmann‐Marriott, 2022 ; Grosjean & Westhof, 2016 ). These codon–anticodon affinities, plus the mutational bias, explain the strong codon usage bias toward NNU/A codons in quartet boxes across all gene expression groups (Figure 8 ).…”

“…Pairing affinity is highly dependent on the identity of the anticodon, the respective nucleotide modifications, and tRNA secondary structures. In order to verify the applicability of Ikemura's second rule to codon selection in the chloroplast, we collated bioinformatics analysis with available experimental data to build a comprehensive picture of the current knowledge concerning tRNA modifications in the chloroplast (Figure 7 ) (Fages‐Lartaud & Hohmann‐Marriott, 2022 ). The results of this study are used to infer codon–anticodon affinity and translation efficiency.…”

“… Principal modifications of the tRNA anticodon loop. The principal modifications of the tRNA anticodon loop are shown in connection to their position (Figure from Fages‐Lartaud & Hohmann‐Marriott, 2022 , submitted). Each nucleotide position of the anticodon loop is associated with corresponding modifications depending on the type of original nucleotide.…”

“…The last row contains the tRNA modifications of anticodon position 34 and other important modifications. The codon–anticodon pairing efficiency is represented with the same color code as Wij (from Fages‐Lartaud & Hohmann‐Marriott, 2022 ). Base 34 of each anticodon is represented directly below the codon it recognizes by Watson–Crick pairing (whenever it is possible).…”

“…The chloroplastic tRNA set resembles the one of M. capricolum analyzed by Grosjean et al in terms of tRNA modifications, the ability of U 34 to read an entire quartet box, and a relatively similar GC content (Grosjean & Westhof, 2016). Substituents such as Um, cmnm 5 , and cmnm 5 s 2 on U 34 restrict anticodon pairing to NNA/G boxes with a strong preference for A-ending codons (Fages-Lartaud & Hohmann-Marriott, 2022;Grosjean et al, 2010;Kurata et al, 2008;Lim, 1994;Takai & Yokoyama, 2003). Such a large difference in codon-anticodon affinity explains the omnipresence of NNA codons for duet boxes regardless of the expression groups (Figure 8).…”