Conserved and specific molecular principles involved in the ribosome life cycle

Ribosomes are universally conserved large ribonucleoprotein particles ensuring protein synthesis in every cell. The universal conservation of ribosome function and structure offers a unique paradigm for understanding how RNP assembly mechanisms and function have evolved. Our research aim to contribute to a better characterization of conserved and specific molecular principles involved in the ribosome life cycle.

To do so we are using comparative functional analysis across various model (micro-)organisms to provide molecular mechanistic insights into common rules and specific principles involved in the life cycle of the translation machinery. 

Our current research mostly focus on the analysis of RNA metabolism in the model archaea H. volcanii and S. acidocaldarius (e.g. Knüppel et al., 2018; Jüttner et al., 2020; Knüppel et al., 2021), but, we also exploit additional model organisms like E. coli (e.g. Knüppel et al., 2021) and/or S. cerevisiae (e.g. Knüppel et al., 2018).

Ribosome homeostasis in Archaea

Our research focus on the analysis of key principles of archaeal ribosome homeostasis. We are investing ribosome synthesis, assembly, function, degradation, the subcellular organization of these processes, and the underlying regulatory mechanisms controlling them. Moreover, to better understand the functional conservation of these molecular principles, we use functional comparative analysis across different archaeal model organisms, in addition to well established bacterial and eukaryotic model organisms.

Over the past years our studies have provided additional in vivo insights on archaeal small ribosomal subunit biogenesis. Notably our work has provided in vivo functional evidence of similarities between the late steps of archaeal and eukaryotic small ribosomal subunit biogenesis (Knüppel et al., 2018), as well as functional specifities of the archaeal ribosome biogenesis (Jüttner et al., 2020; Schwarz et al., 2020; Knüppel et al., 2021).

Based on these studies we are further expanding our comparative structure/function analysis of archaeal ribosome homeostasis and its regulation.

Defining the Archaeal RNA binding-proteome

The systematic identification of RNA-binding proteins, and determination of their respective functional contribution to cellular RNA metabolism has been applied in bacterial and eukaryotic model organisms, however, such comprehensive view has not been obtained for any archaeal organisms.

Using tailor-made RNA/RNP-interactome capture strategies we aim to contribute to:

1) define the core archaeal RNA-binding protein landscape and its dynamic across multiple conditions,

2) functionally characterize conserved and specific features of the archaeal RNA metabolism, and

3) explore structural and functional innovations of archaeal RNPs.

Expanding the archaeal toolbox

In part due to their late discovery and specific growth conditions, several otherwise “well established” key methodological tools for the analysis of gene expression have not been applied or adapted to the study of archaeal biology. To fill-up some of these technological gaps we are continuously adapting various methologies facilitating the analysis of (r)RNA metabolism and gene expression in archaea.

Over the last years, we have optimized utilization of nucleotide- and amino acid-analogs (Knüppel et al., 2017; Knüppel et al., 2021) as well as in vivo RNA structure analysis using SHAPE reagents (Knüppel et al., 2020; Knüppel et al., 2021), in the model archaea Haloferax volcanii and/or Sulfolobus acidocaldarius.

Recently, we have also explored Nanopore sequencing technology to analyse ribosomal RNA processing and modifications (Grünberger et al., BioRxiv).