Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid

ABSTRACT Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps1...

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Autores principales:	Vojtěch David, Pavel Flegontov, Evgeny Gerasimov, Goro Tanifuji, Hassan Hashimi, Maria D. Logacheva, Shinichiro Maruyama, Naoko T. Onodera, Michael W. Gray, John M. Archibald, Julius Lukeš
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/cece96b2c0254a7580ba024afffa4004
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spelling	oai:doaj.org-article:cece96b2c0254a7580ba024afffa40042021-11-15T15:41:24ZGene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid10.1128/mBio.01498-152150-7511https://doaj.org/article/cece96b2c0254a7580ba024afffa40042015-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01498-15https://doaj.org/toc/2150-7511ABSTRACT Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts. IMPORTANCE Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.Vojtěch DavidPavel FlegontovEvgeny GerasimovGoro TanifujiHassan HashimiMaria D. LogachevaShinichiro MaruyamaNaoko T. OnoderaMichael W. GrayJohn M. ArchibaldJulius LukešAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 6 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Vojtěch David Pavel Flegontov Evgeny Gerasimov Goro Tanifuji Hassan Hashimi Maria D. Logacheva Shinichiro Maruyama Naoko T. Onodera Michael W. Gray John M. Archibald Julius Lukeš Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid
description	ABSTRACT Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts. IMPORTANCE Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.
format	article
author	Vojtěch David Pavel Flegontov Evgeny Gerasimov Goro Tanifuji Hassan Hashimi Maria D. Logacheva Shinichiro Maruyama Naoko T. Onodera Michael W. Gray John M. Archibald Julius Lukeš
author_facet	Vojtěch David Pavel Flegontov Evgeny Gerasimov Goro Tanifuji Hassan Hashimi Maria D. Logacheva Shinichiro Maruyama Naoko T. Onodera Michael W. Gray John M. Archibald Julius Lukeš
author_sort	Vojtěch David
title	Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid
title_short	Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid
title_full	Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid
title_fullStr	Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid
title_full_unstemmed	Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid
title_sort	gene loss and error-prone rna editing in the mitochondrion of <italic toggle="yes">perkinsela</italic>, an endosymbiotic kinetoplastid
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/cece96b2c0254a7580ba024afffa4004
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Gene Loss and Error-Prone RNA Editing in the Mitochondrion of <italic toggle="yes">Perkinsela</italic>, an Endosymbiotic Kinetoplastid

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