Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea

Abstract

Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.

Ribosome Biogenesis in Archaea

“…Overall, these observations suggest that the relative amount of rRNA modifications and their diversity may reflect organismspecific adaptation to their respective environmental conditions and/or organism-specific evolutionary trajectories (Dennis et al, 2015;Seistrup et al, 2017;Sas-Chen et al, 2020;Knüppel et al, 2021). The functional significance of the variability in rRNA modifications, of the presence of different modification machineries on the ribosome biogenesis pathway in archaea, and how these machineries have contributed to (re-)shape the ribosome assembly pathway remains to be determined.…”

“…Remarkably, among all the known stand-alone enzymes, the SSU dimethyltransferase KsgA/Dim1 carrying the dimethylation of two universally conserved adenosines at the 3 end of the SSU rRNA is the only almost universally conserved factor involved in ribosome biogenesis (Lafontaine et al, 1994;Connolly et al, 2008;Seistrup et al, 2017;Knüppel et al, 2021). Despite its widespread distribution, several functional aspects of the KsgA/Dim1 biology, such as assembly/release mechanisms and the modification process itself (e.g., completion) strikingly diverge between different organisms and across the different domain of life (Van Buul et al, 1984;Formenoy et al, 1994;Lafontaine et al, 1994;Connolly et al, 2008;Zorbas et al, 2015;Ghalei et al, 2017;Seistrup et al, 2017;Knüppel et al, 2021;.…”

“…Most of these characterized factors are sequence homologs of genuine eukaryotic ribosome biogenesis factors [see Ebersberger et al (2014) for a complete list of candidates]. Among them, the dimethyltransferase KsgA/Dim1 [see above and Grünberger et al (2020); Knüppel et al (2021)], or the Rio ATPase/Kinase family members are implicated in the late steps of SSU maturation, where they probably play a role similar to their eukaryotic counterparts (Knüppel et al, 2018). Similarly, the endonuclease Nob1 is implicated in the maturation of the 16S rRNA 3 end in vitro (Veith et al, 2012;Qi et al, 2020; Figure 2).…”

Growth temperature is the principal driver of chromatinization in archaea

“…T. kodakarensis TrmBL2 stands out as having a much higher relative abundance than its homologs in other proteomes. (Jevtić et al 2019;Knüppel et al 2021). Note that the single H. volcanii histone (HstA) and MC1 are >10-fold less abundant than the novel NAP candidate HVO_1577.…”

“…CC-BY 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is (Jevtić et al 2019;Knüppel et al 2021). Note that the single H. volcanii histone (HstA) and MC1 are >10-fold less abundant than the novel NAP candidate HVO_1577.…”