Horizontal gene transfer of a Chlamydial tRNA-guanine transglycosylase gene to eukaryotic microbes

Highlights

• We present the evolutionary origin of a new class of tRNA-guanine transglycosylases.

• These enzymes horizontally acquired by eukaryotic microbes from Chlamydiae bacteria.

• Drugs have been developed against bacterial tRNA-guanine transglycosylases.

• The presence of these enzymes in pathogenic protozoa serve as putative drug targets.

• Horizontal gene transfer represents are untapped resource for possible drug targets.

Abstract

tRNA-guanine transglycosylases are found in all domains of life and mediate the base exchange of guanine with queuine in the anticodon loop of tRNAs. They can also regulate virulence in bacteria such as Shigella flexneri, which has prompted the development of drugs that inhibit the function of these enzymes. Here we report a group of tRNA-guanine transglycosylases in eukaryotic microbes (algae and protozoa) which are more similar to their bacterial counterparts than previously characterized eukaryotic tRNA-guanine transglycosylases. We provide evidence demonstrating that the genes encoding these enzymes were acquired by these eukaryotic lineages via horizontal gene transfer from the Chlamydiae group of bacteria. Given that the S. flexneri tRNA-guanine transglycosylase can be targeted by drugs, we propose that the bacterial-like tRNA-guanine transglycosylases could potentially be targeted in a similar fashion in pathogenic amoebae that possess these enzymes such as Acanthamoeba castellanii. This work also presents ancient prokaryote-to-eukaryote horizontal gene transfer events as an untapped resource of potential drug target identification in pathogenic eukaryotes.

Introduction

Base modification of tRNAs has been implicated in tRNA structure, aminoacyl tRNA synthetase interaction and influencing codon–anticodon base pairing (Jackman and Alfonzo, 2013). The function of the modification will depend on its type and the position of the modified base. For example, most bases that are modified within the anticodon loop (positions 34–36) of tRNAs are important for accurate translation by facilitating interactions with their cognate codons in mRNAs (Jackman and Alfonzo, 2013). One such modification that influences codon–anticodon base pairing is the incorporation of queuine within the anticodon loop.

Queuosine is a modified guanosine analogue found in tRNAs from all three domains of life. Despite its wide phylogenetic distribution, queuosine is only found in a select group of tRNAs (tRNA^His, tRNA^Asp, tRNA^Tyr and tRNA^Asn) (Katze et al., 1982). Reduced incorporation of queuosine in these tRNAs alters their codon recognition ability and has been linked to various cancers (Emmerich et al., 1985, Meier et al., 1985).

Queuosine modification of tRNA is mediated by tRNA-guanine transglycosylases (TGTases) (also known as queuine tRNA-ribosyltransferases). TGTases catalyze this modification via base exchange where the guanine at position 34 of the tRNA is post-transcriptionally removed and substituted with queuine or a queuine precursor (Garcia and Kittendorf, 2005). Eukaryotes are not capable of de novo queuine synthesis but acquire it through diet or their gastrointestinal microbiota (Vinayak and Pathak, 2010). After its acquisition, the eukaryotic TGTase (E-TGTase) mediates the replacement of guanine with queuine in the anticodon loop. In contrast, queuosine modification of bacterial tRNA is more complex. Prokaryotes use GTP-cyclohydrolase-like enzymes to synthesize a queuine precursor (e.g. preQ₁) from GTP. The bacterial TGTase (B-TGTase) then mediates the base exchange with guanine to incorporate preQ₁, unlike E-TGTases that use queuine itself as the substrate. This incorporated preQ₁ is then modified by S-adenosylmethionine tRNA ribosyltransferase to epoxyQ, which is further modified to form queuosine (Vinayak and Pathak, 2010). In addition to tRNA modification, B-TGTases play a role in regulating the expression of bacterial genes. TGTase mutants (vacC) in the bacterium Shigella flexneri exhibit reduced expression of the virG and ipaBCD genes, which encode virulence factors that facilitate the spread and invasion of the pathogen (Durand et al., 1994). This is a result of the VacC TGTase being required to modify a single base in virF mRNA, which encodes the transcriptional activator of virG and ipaBCD (Hurt et al., 2007). Thus, B-TGTases can modify substrates other than tRNA and are important mediators of bacterial virulence. As a result, B-TGTases have served as a target for the development of drugs that interfere with their function (Brenk et al., 2003). Here we report a new group of TGTases in eukaryotes that display significantly greater similarity to B-TGTases than E-TGTases; we hereby refer to these proteins as bacterial-like TGTases (BL-TGTases). In silico analysis identified 25 BL-TGTases in distinct protozoan and algal lineages and the reason for their similarity to B-TGTases is explored in this article.