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Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch

A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragm...

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Autores principales: Zverkov, Oleg Anatolyevich, Seliverstov, Alexandr Vladislavovich, Lyubetsky, Vassily Alexandrovich
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810238/
https://www.ncbi.nlm.nih.gov/pubmed/26840333
http://dx.doi.org/10.3390/life6010007
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author Zverkov, Oleg Anatolyevich
Seliverstov, Alexandr Vladislavovich
Lyubetsky, Vassily Alexandrovich
author_facet Zverkov, Oleg Anatolyevich
Seliverstov, Alexandr Vladislavovich
Lyubetsky, Vassily Alexandrovich
author_sort Zverkov, Oleg Anatolyevich
collection PubMed
description A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed.
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spelling pubmed-48102382016-04-04 Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch Zverkov, Oleg Anatolyevich Seliverstov, Alexandr Vladislavovich Lyubetsky, Vassily Alexandrovich Life (Basel) Article A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed. MDPI 2016-01-29 /pmc/articles/PMC4810238/ /pubmed/26840333 http://dx.doi.org/10.3390/life6010007 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zverkov, Oleg Anatolyevich
Seliverstov, Alexandr Vladislavovich
Lyubetsky, Vassily Alexandrovich
Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
title Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
title_full Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
title_fullStr Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
title_full_unstemmed Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
title_short Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
title_sort regulation of expression and evolution of genes in plastids of rhodophytic branch
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810238/
https://www.ncbi.nlm.nih.gov/pubmed/26840333
http://dx.doi.org/10.3390/life6010007
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