title: Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins.
abstract: 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.
authors: 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.
authors: Varinia
authors: V
authors: López-Ramírez
authors: Luis D
authors: LD
authors: Alcaraz
authors: Gabriel
authors: G
authors: Moreno-Hagelsieb
authors: Gabriela
authors: G
authors: Olmedo-Álvarez
mesh_terms: D001412:Bacillus subtilis / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics*; D001499:Bayes Theorem; D053487:DEAD-box RNA Helicases / Q000145:classification / Q000235:genetics*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics; D008390:Markov Chains; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D053487:DEAD-box RNA Helicases