modulation of RpoS levels must occur via post-transcriptional regulation (Figure 4). It is also possible that YmdB modulates other rpoS transcription factor(s), although we have not identified which other transcription factors are required for this response. Overall, the data suggest that YmdB and RpoS are co-regulators of biofilm formation (Figure 5). The identification of a novel role for YmdB is not altogether surprising, since eukaryotic macrodomain proteins can have multiple roles [43, 44], and YmdB has additional functions in bacteria [45, 46]. For instance, in E. coli YmdB deacetylates the sirtuin product of O-acetyl-ADP-ribose and reforms ADP ribose Ubiquitin inhibitor . The present study reveals that YmdB modulates the expression of genes involved in physiologically important pathways (Table 1); hence, YmdB could
act as a general regulator in a variety of cellular processes. Further examination of such a potential role for YmdB and its family members in bacteria is necessary. YmdB is also required to be coexpressed for the complementation of a function of ClsC, a recently identified cardiolipin synthase in E. coli. ClsC utilizes phosphatidylethanolamines (PE) as the phosphatidyl donor to phosphatidylglycine (PG) to form cardiolipin https://www.selleckchem.com/products/Ispinesib-mesilate(SB-715992).html (CL) . While YmdB is apparently not a direct modulator of that pathway (since changes in clsC (ymdC) gene expression in the microarrays were negligible (a 1.1-fold increase only); (data not shown), it may modulate it indirectly via the action of the fatty acid biosynthesis gene, fabD
(Table 1), on the CL synthesis-regulating gene; however, such a role has not been confirmed. The ectopic expression of YmdB almost completely regulates RNase III activity with respect to several targets, including pnp, rnc and ribosomal RNA processing (Additional file 1: selleck compound Figure S2) ; however, biofilm formation is not solely dependent Monoiodotyrosine upon YmdB-directed RNase III regulation, suggesting that gene expression data will be useful for identifying unknown RNase III-independently regulated YmdB functions. Several trans-acting factors that modulate the RNase activity of both exo- and endo-RNases have been identified in E. coli[15–18, 47, 48]. Among these four trans-acting regulatory proteins for endo-RNase activity have been well characterized in E. coli: RraA  and RraB  for RNase E, and bacteriophage T7 protein kinase  and YmdB  for RNase III. The presence of homologs in other species suggests such regulation of endo-RNase activity is generally required for bacterial physiology. Recently, gene expression profiling revealed a role for RraA in regulating the SOS response, a mechanism which responds to the stress caused by DNA damage [15, 49]. RNase III modulates approximately 12% (592 genes) of the E.