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The hypothesized role of YbeZ in 16S rRNA maturation

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Abstract

Ribosomes are the protein production machines in all living cells. Yet in contrast to our understanding of how the ribosome translates DNA information into life, the steps involved in ribosome biogenesis, the assembly of the ribosomal RNA (rRNA) and protein molecules that make up the ribosome, remain incomplete. YbeY is considered one of the most physiologically critical endoribonucleases and is implicated in numerous roles involving RNA including 16S rRNA maturation, yet our existing knowledge of its biochemical function fails to explain the phenotypes that manifest when it is lost. In bacteria, it is common for functionally associated genes to be found co-localized in the genome. Across phylogenetically diverse bacteria, the gene encoding ybeZ, encoding a PhoH domain protein, sits adjacent to ybeY. Recent experimental evidence has shown that PhoH domains are RNA helicases, suggesting that this is also the role of YbeZ. The role of an RNA helicase to support the function of YbeY would help explain its reported biochemistry; therefore, we propose a model for the function of YbeZ in 16S rRNA maturation, linking it with the most recent hypotheses on the function of YbeY, that YbeY together with other ribosomal proteins, and ribosome-associated proteins, plays a role in the biogenesis of the small ribosomal subunit. Our model provides a testable hypothesis to resolve the outstanding details surrounding ribosome biogenesis in bacteria.

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Fig. 1
Fig. 2

adapted from King et al. 1986) with the 3ʹ RNaseIII cleavage site, and mature 16S rRNA 3ʹ marked with arrows. The bold sequence between the 3ʹ RNaseIII cleavage site through to the 3ʹ terminus of mature 16S rRNA was modelled using the RNAfold server (http://rna.tbi.univie.ac.at/). (B) The resulting secondary structure prediction of the last of the unprocessed RNA sequence coloured by base-pairing probability (0–1) shows a stem-loop conformation

Fig. 3
Fig. 4

Abbreviations

rrn:

Ribosomal RNA operon

SSU:

Small ribosomal subunit

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Funding

This work is supported through the award of a grant from the Marsden Fund (VUW-18-050) to WMP.

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Authors and Affiliations

  1. Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand

    Emma S. V. Andrews & Wayne M. Patrick

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  1. Emma S. V. Andrews
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  2. Wayne M. Patrick
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Contributions

ESVA read and analysed the literature, developed the hypotheses, and wrote the manuscript. WMP provided funding to support this work and edited the manuscript.

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Correspondence to Emma S. V. Andrews.

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The authors declare that they have no competing interests.

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Communicated by Erko Stackebrandt.

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Andrews, E.S.V., Patrick, W.M. The hypothesized role of YbeZ in 16S rRNA maturation. Arch Microbiol 204, 114 (2022). https://doi.org/10.1007/s00203-021-02739-z

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