Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in Halobacterium salinarum

Abstract

Halobacterium salinarum NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed loci. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of gvpA1b, gvpC1b, gvpN1b, and gvpO1b); archaellum formation (due to down-regulation of arlI, arlB1, arlB2, and arlB3); and glycerol metabolism (due to up-regulation of glpA1, glpB, and glpC). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight rpl15e, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery.

Involvement of ArlI, ArlJ, and CirA in Archaeal Type-IV Pilin-Mediated Motility Regulation

“…However, a study in another halophilic species found that while protein abundance changes for the archaella biosynthetic proteins in the tested experimental conditions were not found, transcriptional analysis was able to identify differences in the regulation of arl genes 35 .…”

“…While differences in protein abundance of ArlI or ArlJ were not observed in wild type or JK3 25 , the abundance of archaella biosynthetic components could be below the detection level of quantitative proteomics experiment, consistent with the absence of any ArlI or ArlJ peptides identified in the Archaeal Proteome Project (ArcPP) database 34 . However, a study in another halophilic species found that while protein abundance changes for the archaella biosynthetic proteins in the tested experimental conditions were not found, transcriptional analysis was able to identify differences in the regulation of arl genes 35 . Furthermore, another study reported that sessile, disk-shaped biofilm-derived cells can exhibit a decreased expression of arl genes 36 .…”

Discovery of transcription start, transcription termination and transcript processing sites in Halobacterium salinarum NRC-1 using dRNA-seq

“…The work from Onga and other coauthors that does not include the author of this thesis (Onga et al, 2022), draw one of their main conclusions supported by the TPS map provided by (Ibrahim et al, 2021). In their Figure 3b (Ibrahim et al, 2021) on a third party work (Onga et al 2022). The gene on focus is rpl15e (see text for details).…”

“…(b) screenshot of a GGB use to visualize public Ribo-seq data and TPS also presented as a resource in (Ibrahim et al, 2021). (c) screenshot of Figure 3 at page 7 from (Onga et al 2022) where the direct usage of visualization (b) was made (see text for details and refer to their paper for full biological interpretation).…”

“…Figure (4-6-1): Usage of the main contribution of this PhD thesis(Ibrahim et al, 2021) on a third party work(Onga et al 2022). The gene on focus is rpl15e (see text for details).…”