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 endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions perfo...

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Autores principales:	James T. Van Leuven, Meng Mao, Denghui D. Xing, Gordon M. Bennett, John P. McCutcheon
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	endosymbionts evolutionary biology genomics RNAseq symbiosis tRNA maturation Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/cfd241f92a9d49cc96593cb9f46ad0d4
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spelling	oai:doaj.org-article:cfd241f92a9d49cc96593cb9f46ad0d42021-11-15T15:55:25ZCicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery10.1128/mBio.01950-182150-7511https://doaj.org/article/cfd241f92a9d49cc96593cb9f46ad0d42019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01950-18https://doaj.org/toc/2150-7511ABSTRACT Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, “Candidatus Hodgkinia cicadicola” (Alphaproteobacteria) and “Ca. Sulcia muelleri” (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original “Ca. Hodgkinia cicadicola” genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” 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 found that most “Ca. Hodgkinia cicadicola” and “Ca. Sulcia muelleri” tRNAs exist as tRNA halves. We hypothesize that “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” tRNAs function in bacterial translation but require host-encoded enzymes to do so. IMPORTANCE The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5′ and 3′ ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities.James T. Van LeuvenMeng MaoDenghui D. XingGordon M. BennettJohn P. McCutcheonAmerican Society for Microbiologyarticleendosymbiontsevolutionary biologygenomicsRNAseqsymbiosistRNA maturationMicrobiologyQR1-502ENmBio, Vol 10, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	endosymbionts evolutionary biology genomics RNAseq symbiosis tRNA maturation Microbiology QR1-502
spellingShingle	endosymbionts evolutionary biology genomics RNAseq symbiosis tRNA maturation Microbiology QR1-502 James T. Van Leuven Meng Mao Denghui D. Xing Gordon M. Bennett John P. McCutcheon Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
description	ABSTRACT Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, “Candidatus Hodgkinia cicadicola” (Alphaproteobacteria) and “Ca. Sulcia muelleri” (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original “Ca. Hodgkinia cicadicola” genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” 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 found that most “Ca. Hodgkinia cicadicola” and “Ca. Sulcia muelleri” tRNAs exist as tRNA halves. We hypothesize that “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” tRNAs function in bacterial translation but require host-encoded enzymes to do so. IMPORTANCE The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5′ and 3′ ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities.
format	article
author	James T. Van Leuven Meng Mao Denghui D. Xing Gordon M. Bennett John P. McCutcheon
author_facet	James T. Van Leuven Meng Mao Denghui D. Xing Gordon M. Bennett John P. McCutcheon
author_sort	James T. Van Leuven
title	Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
title_short	Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
title_full	Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
title_fullStr	Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
title_full_unstemmed	Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
title_sort	cicada endosymbionts have trnas that are correctly processed despite having genomes that do not encode all of the trna processing machinery
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/cfd241f92a9d49cc96593cb9f46ad0d4
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Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery

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