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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| Format: | Article |
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MDPI AG
2016-01-01
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| Series: | Life |
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| Online Access: | http://www.mdpi.com/2075-1729/6/1/7 |
| _version_ | 1811185897838739456 |
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| author | Oleg Anatolyevich Zverkov Alexandr Vladislavovich Seliverstov Vassily Alexandrovich Lyubetsky |
| author_facet | Oleg Anatolyevich Zverkov Alexandr Vladislavovich Seliverstov Vassily Alexandrovich Lyubetsky |
| author_sort | Oleg Anatolyevich Zverkov |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T13:37:08Z |
| format | Article |
| id | doaj.art-ffac737faa5c46d6a96a7e7875d7e852 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-04-11T13:37:08Z |
| publishDate | 2016-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-ffac737faa5c46d6a96a7e7875d7e8522022-12-22T04:21:26ZengMDPI AGLife2075-17292016-01-0161710.3390/life6010007life6010007Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic BranchOleg Anatolyevich Zverkov0Alexandr Vladislavovich Seliverstov1Vassily Alexandrovich Lyubetsky2Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, RussiaA 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.http://www.mdpi.com/2075-1729/6/1/7plastidproteintranscription factortranslation initiationclustering |
| spellingShingle | Oleg Anatolyevich Zverkov Alexandr Vladislavovich Seliverstov Vassily Alexandrovich Lyubetsky Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch Life plastid protein transcription factor translation initiation clustering |
| 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 | plastid protein transcription factor translation initiation clustering |
| url | http://www.mdpi.com/2075-1729/6/1/7 |
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