caa a22 4500 445821418 CHVBK 20180317145245.0 cr unu---uuuuu 170323e20110401xx s 000 0 eng 10.1007/s00239-011-9441-8 doi (NATIONALLICENCE)springer-10.1007/s00239-011-9441-8 Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins [Elektronische Daten] [Varinia López-Ramírez, Luis Alcaraz, Gabriel Moreno-Hagelsieb, Gabriela Olmedo-Álvarez] DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this study, we analyzed the distribution and architecture of DEAD-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. We identified 1,848 unique DEAD-box proteins from 563 bacterial genomes. Bacterial genomes can possess a single copy DEAD-box gene, or up to 12 copies of the gene, such as in Shewanella. The alignment of 1,208 sequences allowed us to perform a robust analysis of the hallmark motifs of DEAD-box proteins and determine the residues that occur at high frequency, some of which were previously overlooked. Bacterial DEAD-box proteins do not generally contain a conserved C-terminal domain, with the exception of some members that possess a DbpA RNA-binding domain (RBD). Phylogenetic analysis showed a separation of DbpA-RBD-containing and DbpA-RBD-lacking sequences and revealed a group of DEAD-box protein genes that expanded mainly in the Proteobacteria. Analysis of DEAD-box proteins from Firmicutes and γ-Proteobacteria, was used to deduce orthologous relationships of the well-studied DEAD-box proteins from Escherichia coli and Bacillus subtilis. These analyses suggest that DbpA-RBD is an ancestral domain that most likely emerged as a specialized domain of the RNA-dependent ATPases. Moreover, these data revealed numerous events of gene family expansion and reduction following speciation. The Author(s), 2011 DEAD-box proteins nationallicence RNA helicases nationallicence Evolutionary history nationallicence Comparative genomics nationallicence Gene family nationallicence López-Ramírez Varinia Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821, Irapuato, Guanajuato, Mexico aut Alcaraz Luis Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821, Irapuato, Guanajuato, Mexico aut Moreno-Hagelsieb Gabriel Department of Biology, Wilfrid Laurier University, 75 University Ave. W., N2L 3C5, Waterloo, ON, Canada aut Olmedo-Álvarez Gabriela Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821, Irapuato, Guanajuato, Mexico aut Journal of Molecular Evolution Springer-Verlag 72/4(2011-04-01), 413-431 0022-2844 72:4<413 2011 72 239 https://doi.org/10.1007/s00239-011-9441-8 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00239-011-9441-8 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- López-Ramírez Varinia Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821, Irapuato, Guanajuato, Mexico aut NATIONALLICENCE 700 1- Alcaraz Luis Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821, Irapuato, Guanajuato, Mexico aut NATIONALLICENCE 700 1- Moreno-Hagelsieb Gabriel Department of Biology, Wilfrid Laurier University, 75 University Ave. W., N2L 3C5, Waterloo, ON, Canada aut NATIONALLICENCE 700 1- Olmedo-Álvarez Gabriela Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821, Irapuato, Guanajuato, Mexico aut NATIONALLICENCE 773 0- Journal of Molecular Evolution Springer-Verlag 72/4(2011-04-01), 413-431 0022-2844 72:4<413 2011 72 239 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer