Unraveling the function of the highly conserved Lrs14 proteins in the order of the Sulfolobales

The Lrs14 family is an archaea-specific family of DNA-binding proteins containing a wHTH domain. Initially, Lrs14 proteins were considered classical transcription factors, belonging to the Lrp/AsnC family. Yet, as the structural topology is completely different, they were classified as a separate family (Orell et al., 2013). Lrs14-like proteins are implicated in gene regulation in response to environmental changes. Yet, there are some indications that they may also be involved in chromatin-organization.

The Lrs14 protein, AbfR1 from Sulfolobus acidocaldarius, encoded by saci_0446 was shown to be involved in biofilm formation and cell motility and was therefore named Archaeal biofilm regulator 1 (AbfR1). DNA-binding assays demonstrated that AbfR1 binds DNA non-sequence specific (Orell et al., 2013). And it was also demonstrated that AbfR1 is upregulated upon heat shock. Homologs of AbfR1 can be found in the entire order of the Sulfolobales, including in Metallosphaera sedula, in which it is encoded by msed_2175. In literature, Msed_2175 was described as a specific regulator of the CO2 fixation pathway, yet experimental proof is limited. As opposed to AbfR1, Msed_2175 binds a specific DNA motif in the promotors of the CO2 pathway genes (Leyn et al., 2015).

Can two conserved proteins really differ so much in both the way they specifically bind DNA and their biological function? In this study, we aim at expanding our knowledge on these homologous DNA-binding proteins by in silico structural predictions and sequence analysis, in vitro DNA-binding assays and in vivo gene expression studies. To do so, the recombinant Msed_2175 and AbfR1 have been successfully purified, and their binding properties have been determined using different DNA probes. Both Msed_2175 and AbfR1 bind all tested DNA sequences. For AbfR1, this was expected, yet also Msed_2175 appears to bind DNA non-sequence specific. We conclude that Msed_2175 from M. sedula binds DNA with low sequence specificity. Further, we hypothesize that these homologs have a rather global gene regulatory function and potentially also a chromatin-organizing one instead of a specific regulatory role as was described before. This hypothesis was also postulated by Karr et al. (2017) for the entire Lrs14 family.