Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms

Abstract

Error-free protein synthesis relies on the precise recognition by the aminoacyl-tRNA synthetases of their cognate tRNAs in order to attach the corresponding amino acid. A concept of universal tRNA identity elements requires the aminoacyl-tRNA synthetases provided by the genome of an organism to match the identity elements found in the cognate tRNAs in an evolution-independent manner. Identity elements tend to cluster in the tRNA anticodon and acceptor stem regions. However, in the arginine system, in addition to the anticodon, the importance of nucleotide A20 in the tRNA D-loop for cognate enzyme recognition has been a sustained feature for arginyl-tRNA synthetase in archaea, bacteria and in the nuclear-encoded cytosolic form in mammals and plants. However, nuclear-encoded mitochondrial arginyl-tRNA synthetase, which can be distinguished from its cytosolic form by the presence or absence of signature motifs, dispenses with the A20 requirement. An examination of several hundred non-metazoan organisms and their corresponding tRNA^Arg substrates has confirmed this general concept to a large extent and over numerous phyla. However, some Stramenopiles, and in particular, Diatoms (Bacillariophyta) present a notable exception. Unusually for non-fungal organisms, the nuclear genome encodes tRNA^Arg isoacceptors with C or U at position 20. In this case one of two nuclear-encoded cytosolic arginyl-tRNA synthetases has evolved to become insensitive to the nature of the D-loop identity element. The other, with a binding pocket that is compatible with tRNA^Arg-A20 recognition, is targeted to organelles that encode solely such tRNAs.

Keywords: Aminoacyl-tRNA synthetase; Bacillariophyta; Diatoms; Identity element; Non-metazoan eukaryotic evolution; tRNA.

Fig. 1

Alignment of Bacillariophyta arginyl-tRNA synthetase tRNA D-loop binding regions (Panels A and B) and of the conserved “KMSK” catalytic region (Panel C). For orientation, segments from the E.coli and S.cerevisiae enzymes and the numbering of their critical residues is given. The species order is that given by the CLUSTAL Ω alignment and results in the two distinct clusters. Amino acid identity is shown as Red > 95%; Green 80–95%, Blue 60–80% (Color figure online)

Fig. 2

Cloverleaf depiction of tRNA^Arg isoacceptors that either require recognition by an arginyl-tRNA synthetase, which is indifferent to the nucleotide at position 20, or possessing A20 as a potential identity element. Shown are consensus sequences derived for all available Bacillariophyta tRNA^Arg isoacceptors encoded either by the mitochondrion, 22 sequences (A) or by the nucleus, 33 sequences (B). Nucleotide 20 is circled in each case and the anticodon is underlined. Nucleotides are given according to the IUPAC convention; Y, pyrimidine; R, purine; S, G or C; K, G or U. For recording consensus sequences, upper case denotes > 95% identity, lower case denotes 80–95% identity. • represents greater variability. Nucleotide numbering follows the convention established for tRNAs (Sprinzl et al. 1998)

Fig. 3

Clustering of Bacillariophyta arginyl-tRNA synthetase gene products in two groups. Alignments were performed by CLUSTALΩ and the resulting phylogenetic tree depicted in DENDROSCOPE (Huson and Scornavacca 2012)

Fig. 4

A comparison of the Bacillariophyta clusters of arginyl-tRNA synthetases with bacteria and yeast. Amino acids involved in the binding of the tRNA variable pocket that includes the identity element at position 20 are listed and the structure of the binding pocket in the E.coli crystallographic arginyl-tRNA synthetase/tRNA complex (Stephen et al. 2018), extracted from the Protein Data Bank (5YYN) and depicted in DISCOVERY STUDIO 4.0 is shown