The Lrs14 family of DNA-binding proteins as an archaea-specific class of nucleoid-associated proteins

Organization of archaeal chromatin combines bacterial, eukaryotic and unique characteristics. While some archaeal lineages harbor eukaryotic histone-like proteins for genome organization, in other lineages, such as the Crenarchaeota, histones are lacking. The latter rely on a wide diversity of bacterial-like nucleoid-associated proteins (NAPs), which are small DNA-organizing proteins (Peeters et al., 2015). In the order of the Sulfolobales, representing the Crenarchaeota, Sul7d, Cren7, Sul10a, Sul12a are well-characterized chromatin proteins. However, a large number of small DNA-binding proteins, of which the function is still unclear, are predicted to be encoded in the genome of Sulfolobus acidocaldarius, the model species of the Sulfolobales (Chen et al., 2005). One family of such small DNA-binding proteins are the Lrs14 proteins.
The Lrs14 family is an archaea-specific family of DNA-binding proteins containing a wHTH domain. Initially, Lrs14 proteins were considered classical transcription factors having a gene regulatory role in specific cellular processes, such as cell motility and biofilm formation (Orell et al., 2013). However, early studies, combined with novel ideas, also provide evidence that Lrs14-type proteins do not only harbor a transcriptional regulator function but also act as NAPs (Chen et al., 2004; Napoli et al., 2001; Fiorentino et al., 2003). In this study, we aim to explore the functional role(s) of the Lrs14 family of DNA-binding proteins, as well as their phylogenetic conservation within Sulfolobales and their structural and functional similarities with other NAP families.
It was previously observed that Lrs14 dimers bind DNA non-sequence specifically, albeit with a preference for AT-rich regions, including promoter regions. Whereas dimers usually bind somewhat less than 40 nt, the binding is highly cooperative, leading to extended regions of DNA binding (Orell et al., 2013; Li et al., 2017). Based on phylogenetic and structural analysis, we found that the Lrs14 proteins can be divided into 5 clusters with small differences in topology and conserved residues, potentially leading to slightly different biological functions. We used fluorescence microscopy and DAPI-staining to look at the nucleoid structure of E. coli, while heterotrophically overexpressing an Lrs14-protein. The expression of the Lrs14 protein compacts the nucleoid showing that Lrs14 proteins have an influence on DNA structure, even in another domain of life, which underscores again the sequence aspecific binding of Lrs14 proteins to DNA. Studying published transcriptomics data showed that the genes encoding Lrs14 proteins in S. acidocaldarius are differentially expressed upon diverse stress conditions. This implicates a potential regulatory role for these proteins upon stress. Moreover, it was observed that Lrs14s are post-translationally modified by acetylation and phosphorylation (Cao et al., 2019; Li et al., 2017), both epigenetic mechanisms that may play a role in this regulation. Taking together, we postulate that members of the Lrs14 family can be considered as nucleoid-associated proteins in Sulfolobales that combine a DNA-structuring role with a global gene expression role in response to stress conditions.