| Summary: | Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In <i>Pseudomonas</i> spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In <i>Xanthomonas</i> spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from <i>Pseudomonas</i> ColS and <i>Xanthomonas</i> RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to <i>raxRH</i> are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple <i>Xanthomonas</i> spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the <i>Xanthomonas</i> RaxH-RaxR system is orthologous to the <i>Pseudomonas</i> ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to <i>Xanthomonas</i> spp., and that the Vgr, Rax, and Det designations be used instead.
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