Abstract
ABSTRACTBacterial competence, which can be natural or induced, allows the uptake of exogenous double stranded DNA (dsDNA) into a competent bacterium. This process is known as transformation. A multiprotein assembly binds and processes the dsDNA to import one strand and degrade another yet the underlying molecular mechanisms are relatively poorly understood. Here distant relationships of domains in Competence protein EC (ComEC) of Bacillus subtilis (Uniprot: P39695) were characterized. DNA‐protein interactions were investigated in silico by analyzing models for structural conservation, surface electrostatics and structure‐based DNA binding propensity; and by data‐driven macromolecular docking of DNA to models. Our findings suggest that the DUF4131 domain contains a cryptic DNA‐binding OB fold domain and that the β‐lactamase‐like domain is the hitherto cryptic competence nuclease. Proteins 2016; 84:1431–1442. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Highlights
Natural transformation is the uptake of free environmental double stranded DNA that has been secreted by other bacteria or is the product of cell lysis.[1,2] Bacterial competence is the physiological state in which DNA uptake is possible, and can be natural or induced
We have described compelling evidence of an OB fold in the Domain of Unknown Function 4131 (DUF4131) domain of Competence protein EC (ComEC)
Despite the equivocal results obtained with structurebased DNA-binding function predictors, it is very likely that it functions to bind ssDNA in ComEC, especially as this is in such obvious agreement with the broad functional context of ComEC
Summary
Natural transformation is the uptake of free environmental double stranded DNA (dsDNA) that has been secreted by other bacteria or is the product of cell lysis.[1,2] Bacterial competence is the physiological state in which DNA uptake is possible, and can be natural or induced Transformation facilitates both inter- and intraspecies DNA transfer.[3,4] The benefits of bacterial DNA uptake by competence can result from either the acquisition and incorporation of exogenous genetic material into their genome or its use as a food resource of carbon, nitrogen, and phosphorus.[4,5,6] It has been suggested that environmental DNA from closely related species can act as templates for DNA repair.[4].
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