ArticleJournal of molecular evolution2011
Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins.
Article in Journal of molecular evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
- DDX RNA helicases: key players in cellular homeostasis and innate antiviral immunity.Journal of virology · 2024Review
- RNase R vs. PNPase: selecting the best-suited exoribonuclease for environmental adaptation.Extremophiles : life under extreme conditions · 2024Review
- Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria.Nucleic acids research · 2024Article
- Role of DEAD-box RNA helicases in low-temperature adapted growth of AntarcticMicrobiology spectrum · 2024Article
- Metagenomic Analysis of Antarctic Biocrusts Unveils a Rich Range of Cold-Shock Proteins.Microorganisms · 2023Article
- The DEAD-box RNA helicase RhlE2 is a global regulator of Pseudomonas aeruginosa lifestyle and pathogenesis.Nucleic acids research · 2021Article
- Genera specific distribution of DEAD-box RNA helicases in cyanobacteria.Microbial genomics · 2021Article
- FGMP: assessing fungal genome completeness.BMC bioinformatics · 2019Article
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- The DEAD-Box RNA Helicases ofFrontiers in microbiology · 2018Article
- Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus.Journal of bacteriology · 2017Article
- Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein.RNA (New York, N.Y.) · 2016Article
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- RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains.Molecular genetics and genomics : MGG · 2015Article
- Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes.PLoS genetics · 2014Article
- RNA helicases: diverse roles in prokaryotic response to abiotic stress.RNA biology · 2013Review
- An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7.PloS one · 2013Article
- Roles of four putative DEAD-box RNA helicase genes in growth of Listeria monocytogenes EGD-e under heat, pH, osmotic, ethanol, and oxidative stress conditions.Applied and environmental microbiology · 2012Article
- A Listeria monocytogenes RNA helicase essential for growth and ribosomal maturation at low temperatures uses its C terminus for appropriate interaction with the ribosome.Journal of bacteriology · 2012Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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