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

Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia
Author to whom correspondence should be addressed.
Academic Editor: Alexander Bolshoy
Received: 17 December 2015 / Revised: 20 January 2016 / Accepted: 25 January 2016 / Published: 29 January 2016
(This article belongs to the Special Issue Structure and Evolution of Genome)
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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 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. View Full-Text
Keywords: plastid; protein; transcription factor; translation initiation; clustering plastid; protein; transcription factor; translation initiation; clustering

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Zverkov, O.A.; Seliverstov, A.V.; Lyubetsky, V.A. Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch. Life 2016, 6, 7.

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