*Article* **Interactions among Redox Regulators and the CtrA Phosphorelay in** *Dinoroseobacter shibae* **and** *Rhodobacter capsulatus*

#### **Sonja Koppenhöfer and Andrew S. Lang \***

Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada; skoppenhofer@mun.ca

**\*** Correspondence: aslang@mun.ca

Received: 11 March 2020; Accepted: 10 April 2020; Published: 14 April 2020

**Abstract:** Bacteria employ regulatory networks to detect environmental signals and respond appropriately, often by adjusting gene expression. Some regulatory networks influence many genes, and many genes are a ffected by multiple regulatory networks. Here, we investigate the extent to which regulatory systems controlling aerobic–anaerobic energetics overlap with the CtrA phosphorelay, an important system that controls a variety of behavioral processes, in two metabolically versatile alphaproteobacteria, *Dinoroseobacter shibae* and *Rhodobacter capsulatus*. We analyzed ten available transcriptomic datasets from relevant regulator deletion strains and environmental changes. We found that in *D. shibae*, the CtrA phosphorelay represses three of the four aerobic–anaerobic Crp/Fnr superfamily regulator-encoding genes (*fnrL*, *dnrD*, and especially *dnrF*). At the same time, all four Crp/Fnr regulators repress all three phosphorelay genes. Loss of *dnrD* or *dnrF* resulted in activation of the entire examined CtrA regulon, regardless of oxygen tension. In *R. capsulatus* FnrL, in silico and ChIP-seq data also suggested regulation of the CtrA regulon, but it was only with loss of the redox regulator RegA where an actual transcriptional e ffect on the CtrA regulon was observed. For the first time, we show that there are complex interactions between redox regulators and the CtrA phosphorelays in these bacteria and we present several models for how these interactions might occur.

**Keywords:** Alphaproteobacteria; Rhodobacteraceae; nitric oxide; quorum sensing; gene transfer agent; motility; Crp/Fnr; Dnr; RegA; ChpT
