Function of ImuB-C is less clear, since it does not seem to have a enzyme-like pattern of conserved residues, but the authors suggest, based on genomic context, that it might be a DNA binding 1,1-Dimethylbiguanide hydrochlorideMedChemExpress 1,1-Dimethylbiguanide hydrochloride domain and play a role in the recognition of DNA damage. General considerations This work presents solid evidence for the connection between the YoqW and ImuB-C domains and the SOS network and DNA repair. It makes intelligent use of available data on structures and other experimental results to infer the molecular function of YoqW, thus leading to a very interesting and extended analogy to LexA. Addition of these domains to the known repertoire of SOS-related protein domains is of great interest to drive further experimental studies on this system. In conclusion, I believe this work is fit for publication but I have some minor PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28549975 corrections and suggestions that I suggest the authors to consider (see below).Authors’ responseThe paragraph that starts “Beyond the induction of SOS by various genotoxic stresses, it also appears to play a role” might read more clearly if rewritten like “Beyond the induction of SOS DNA-repair response by various genotoxic stresses, the SOS gene regulatory and protein interaction network also appears to play a role”.Authors’ responseWe have now modified that sentence so that it reads better. Although I have complied with it so far, I must voice against referring to the new thiol peptidase domain by the Bacillus gene name YoqW. Gene names that start with “y” are traditionally used in genome annotation to name computationally predicted genes not associated with any phenotype or as synonyms for other gene names and are based on the chromosomal map location of the gene (PMID: 9729612). Such gene names will, therefore refer to entirely different genes in different organisms, even if closely related. I would suggest renaming DUF159 to something like SOSAE for “SOS-associated enzyme” and let the standard peptidase nomenclature wait for experimental validation.Authors’ responseWe thank the referee for the positive evaluation of this work. Minor issues I ask the authors and the managers of Biology Direct submission system to investigate what happened to the bibliographic references in this submission. The PDF I downloaded from BD’s website contained only reference manager codes and no references. It forced me to search each reference I wanted to look at using last author name and year, a time consuming procedure I would not like to repeat.Authors’ responseWe agree this is a good suggestion. Using DUF159 or YoqW do not convey the clear functional implications of these proteins and are similarly opaque in this regard. Hence we have renamed the domain as SRAP for SOS response associated peptidase. In the sentence “small domain globular domain of about 80 residues” remove the first domain”.Authors’ responseWe have corrected this in the revised manuscript. With respect to the supplement, it would be of great value if the table of genomes contexts was sorted in some meaningful order, like by taxonomy, instead of an apparently random order. Also, redundancies in these tables should be removed.Authors’ responseWe believe there was some problem with the uploaded manuscript (as also noted by referee 2). We have now reformatted the revised manuscript and it should set this issue right. Considering the importance of the ImuAB-dnaE2 operon for this work, I believe it is fair to add at least one citation of the paper that first characterized thes.
