Domain may function as part of a DNA repair system, basedDomain may function as part

Domain may function as part of a DNA repair system, based
Domain may function as part of a DNA repair system, based on the different operons that it is found in. The authors conjecture that the domain may be a DNA binding domain, given its size and lack of obvious conserved catalytic residues. I can find no evidence to disagree with this statement, but I wonder if there could not be alternative functions for this domain, such as a protein interaction module?Authors’ responseWe have corrected this in the revised manuscript. There are also a few sentences where the PD150606 web scientific meaning is vague. If something is `strongly co-occurs’ what does that mean? Please support PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27107493 with numbers. Also, how was YoqW `transferred’ to eukaryotes? The authors should provide indicate where the HMMER search parameters were default.Authors’ responseIn principle, it is possible that the ImuB-C is involved in protein-protein interaction. However, several subtle domain architectural features weigh in favor of a DNAbinding function. First, it is found in association with a wide range of mechanistically distinct DNA repair systems (Network in Figure 2) but rarely if ever in any non-DNA repair related contexts. Second, it is primarily prokaryotic in its phyletic spread, and there is no evidence forThe first issue has been supported with numerical data in the revised manuscript. Regarding the transfer of YoqW to the eukaryotes: The superfamily is found across all major bacterial lineages suggesting that it was likely to have been present in the bacterial common ancestor. However, it is present only in less than 10 of the archaeal genomes and that too only in the euryarchaeal lineage. In eukaryotes it is present in most major eukaryotic lineages including the basal eukaryote Trichomonas. This phyletic pattern is most consistent with it being transferred from bacteria to eukaryotes, perhaps from early bacterial symbionts. The HMMER search parameters have been included in the revised version. They should also provide the version (or date) of the NR sequence database that was used.Aravind et al. Biology Direct 2013, 8:20 http://www.biology-direct.com/content/8/1/Page 10 ofAuthors’ responseThis has been done. Is the TASS package publicly available? If it is not, I am not sure why it mentioned.Authors’ responseIt has been removed in the revised manuscript.Reviewer 3: Gaspar Jekely (Max Planck Institute for developmental biology, Germany)In this paper Aravind and colleagues describe two novel components of the bacterial SOS response, the YoqW and the ImuB-C domains, identified by gene-neighborhood analysis. Sequence conservation analyses and analyses of available structures suggest that the YoqW proteins have proteolytic activity and undergo autoproteolysis. The YoqW domain may thus represent a novel type of thiol protease. This is a fascinating insight, based on sequence and structure analysis alone, and illustrates how careful sequence searches and information from structural genomics can suggest functions for uncharacterized proteins. The function of the second identified domain (ImuB-C domain) is less clear, but the authors suggest, based on genomic context analysis, that it may be involved in binding damaged DNA structures and help recruit downstream components. I find this a very nice paper, and recommend publication without hesitation.Authors’ responsethe methods that can be reproduced by anyone with access to the NCBI databases and tools. Regarding the in house perl scripts the main issue is that they are not in state for g.