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Pereira-Santana A, Gamboa-Tuz SD, Zhao T, Schranz ME, Vinuesa P, Bayona A, Rodríguez-Zapata LC, Castano E. Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PLoS Comput Biol 2020; 16:e1008318. [PMID: 33075080 PMCID: PMC7608942 DOI: 10.1371/journal.pcbi.1008318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/03/2020] [Accepted: 09/07/2020] [Indexed: 12/26/2022] Open
Abstract
Fibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and high conservation of fibrillarins, there little is known about the evolutionary dynamics of this small gene family. We applied a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins across the Tree of Life. We identified 1063 non-redundant FIB sequences across 1049 completely sequenced genomes from Viruses, Bacteria, Archaea, and Eukarya. FIB is a highly conserved single-copy gene through Archaea and Eukarya lineages, except for plants, which have a gene family expansion due to paleopolyploidy and tandem duplications. We found a high conservation of the FIB genomic context during plant evolution. Surprisingly, FIB in mammals duplicated after the Eutheria split (e.g., ruminants, felines, primates) from therian mammals (e.g., marsupials) to form two main groups of sequences, the FIB and FIB-like groups. The FIB-like group transposed to another genomic context and remained syntenic in all the eutherian mammals. This transposition correlates with differences in the expression patterns of FIB-like proteins and with elevated Ks values potentially due to reduced evolutionary constraints of the duplicated copy. Our results point to a unique evolutionary event in mammals, between FIB and FIB-like genes, that led to non-redundant roles of the vital processes in which this protein is involved.
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Affiliation(s)
- Alejandro Pereira-Santana
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Samuel David Gamboa-Tuz
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Tao Zhao
- Bioinformatics and Evolutionary Genomics, VIB-UGent Center for Plant Systems Biology, Gent, Belgium
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Andrea Bayona
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | | | - Enrique Castano
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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Davidian A, Koshel E, Dyomin A, Galkina S, Saifitdinova A, Gaginskaya E. On some structural and evolutionary aspects of rDNA amplification in oogenesis of Trachemys scripta turtles. Cell Tissue Res 2020; 383:853-864. [PMID: 32897424 DOI: 10.1007/s00441-020-03282-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and reaches hundreds by the lampbrush chromosome stage (pre-vitellogenesis). RNA-polymerase I, fibrillarin, and PCNA immunodetection in the amplified nucleoli and FISH of the 5'ETS probe to the oocyte nuclear content suggest pre-rRNA and rDNA synthesis in the nucleoli at all stages studied. This implies a continuous reproduction of the nucleoli during oocyte development from early diplotene up to vitellogenesis. The data obtained offer a different way for rDNA amplification and formation of extrachromosomal nucleoli in turtle oocytes compared with the amplified nucleoli formation in amphibian and fish oocytes. In the Sauropsida clade of Archelosauria, which includes turtles, crocodiles, and birds, rDNA function is known to be suppressed in avian oogenesis during the lampbrush stage (Gaginskaya et al. in Cytogenet Genome Res 124:251-267, 2009).
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Affiliation(s)
- Asya Davidian
- St Petersburg University, St Petersburg, 199034, Russia
| | | | - Alexander Dyomin
- St Petersburg University, St Petersburg, 199034, Russia.,Saratov State Medical University, Saratov, 410000, Russia
| | | | - Alsu Saifitdinova
- Herzen State Pedagogical University of Russia, St Petersburg, 191186, Russia
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