Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins |
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Authors: | Varinia López-Ramírez Luis D Alcaraz Gabriel Moreno-Hagelsieb Gabriela Olmedo-Álvarez |
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Institution: | 1.Departamento de Ingeniería Genética de Plantas,Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato,Irapuato,Mexico;2.Department of Genomics and Health,Centro Superior de Investigación en Salud Pública,Valencia,Spain;3.Department of Biology,Wilfrid Laurier University,Waterloo,Canada |
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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. |
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