The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer

Abstract

Transfer RNAs (tRNAs) require the absolutely conserved sequence motif at their 3′-ends, representing the site of aminoacylation. In the majority of organisms, this trinucleotide sequence is not encoded in the genome and thus has to be added post-transcriptionally by the CCA-adding enzyme, a specialized nucleotidyltransferase. In eukaryotic genomes this ubiquitous and highly conserved enzyme family is usually represented by a single gene copy. Analysis of published sequence data allows us to pin down the unusual evolution of eukaryotic CCA-adding enzymes. We show that the CCA-adding enzymes of animals originated from a horizontal gene transfer event in the stem lineage of Holozoa, i.e. Metazoa (animals) and their unicellular relatives, the Choanozoa. The tRNA nucleotidyltransferase, acquired from an α-proteobacterium, replaced the ancestral enzyme in Metazoa. However, in Choanoflagellata, the group of Choanozoa that is closest to Metazoa, both the ancestral and the horizontally transferred CCA-adding enzymes have survived. Furthermore, our data refute a mitochondrial origin of the animal tRNA nucleotidyltransferases.

Molecular evidence for the evolution of the eukaryotic mitochondrial arginyl‐tRNA synthetase from the prokaryotic suborder Cystobacterineae

“…It is unlikely to be coincidental that the and encoded in the Mito genome possess a yeast (Mito)‐like U20, to which the Mito enzyme is insensitive , whereas the nuclear‐encoded tRNA ACG has an A20 that is an essential identity element for recognition by the Cyto arginyl‐tRNA synthetase . It is notable that Monosiga and Salpingoeca are the only ones in a collection of 12 Choanozoans that also have two distinct genes for the essential tRNA‐modifying ‘CCA‐enzyme’ (CCA tRNA nucleotidyltransferase) .…”

“…Numbering is that of the yeast enzyme. of 12 Choanozoans that also have two distinct genes for the essential tRNA-modifying 'CCA-enzyme' (CCA tRNA nucleotidyltransferase) [28].…”

Divergent Evolution of Eukaryotic CC- and A-Adding Enzymes

“…At their 3 terminus, these molecules carry the invariant sequence cytidine-cytidine-adenosine (CCA), which is important for the attachment of the corresponding amino acid and for proper participation of the tRNA in translation [1][2][3]. In all Eukaryotes, most Archaea, and many Bacteria, the CCA triplet is not encoded in the tRNA genes [4][5][6][7][8] and has to be added post-transcriptionally by ATP(CTP):tRNA nucleotidyltransferases (CCA-adding enzymes). These enzymes belong to a family of specialized polymerases with a unique mechanism of polymerization without the need of a nucleic acid-based template [3, [9][10][11].…”

“…Recently, we showed in an extended phylogenetic analysis that metazoan CCA-adding enzymes originate from a horizontal gene transfer event (HGT) from Alphaproteobacteria to the common ancestor of Metazoa and their unicellular relatives, the Choanozoa [8]. In the course of evolution, the newly acquired alphaproteobacterial gene replaced the original ancestral eukaryotic gene ( Figure 1B).…”

“…Plants, Fungi, and Amoebozoa, however, carry the ancestral eukaryotic CCA-adding enzyme ( Figure 1B). Consequently, eukaryotic tRNA nucleotidyltransferases can be subdivided into acquired alphaproteobacterial-like and ancestral eukaryotic CCA-adding enzymes (a-type enzymes, e-type enzymes), both showing characteristic differences in their catalytic core motifs [8]. Surprisingly, in the choanoflagellates Salpingoeca rosetta and Monosiga brevicollis, both an a-type as well as an e-type enzyme are encoded in their genomes.…”