Cicada endosymbionts have tRNAs that are correctly processed despite having genomes that do not encode all of the tRNA processing machinery

Abstract

Gene loss and genome reduction are defining characteristics of nutritional endosymbiotic bacteria. In extreme cases, even essential genes related to core cellular processes such as replication, transcription, and translation are lost from endosymbiont genomes. Computational predictions on the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, \"Candidatus Hodgkinia cicadicola\" (Alphaproteobacteria) and \"Ca. Sulcia muelleri\" (Betaproteobacteria), find only 26 and 16 tRNA, and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original \"Ca. Hodgkinia\" genome annotation is missing several essential genes involved in tRNA processing, such as RNase P and CCA tRNA nucleotidyltransferase, as well as several RNA editing enzymes required for tRNA maturation. How \"Ca. Sulcia\" and \"Ca. Hodgkinia\" preform basic translation-related processes without these genes remains unknown. Here, by sequencing eukaryotic mRNA and total small RNA, we show that the limited tRNA set predicted by computational annotation of \"Ca. Sulcia\" and \"Ca. Hodgkinia\" is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5 and 3 ends, and seem to undergo nucleotide modification. Surprisingly, we find that most \"Ca. Hodgkinia\"and \"Ca. Sulcia\" tRNAs exist as tRNA halves. Finally, and in contrast with other related insects, we show that cicadas have experienced little horizontal gene transfer that might complement the activities missing from the endosymbiont genomes. We conclude that \"Ca. Sulcia\" and \"Ca. Hodgkinia\" tRNAs likely function in bacterial translation, but require host-encoded enzymes to do so.