Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803.

Soumaya Laalami,Harald Putzer,Carine Chagneau,Marina Cavaiuolo

doi:10.3389/fmicb.2020.01055

Abstract

mRNA levels result from an equilibrium between transcription and degradation. Ribonucleases (RNases) facilitate the turnover of mRNA, which is an important way of controlling gene expression, allowing the cells to adjust transcript levels to a changing environment. In contrast to the heterotrophic model bacteria Escherichia coli and Bacillus subtilis, RNA decay has not been studied in detail in cyanobacteria. Synechocystis sp. PCC6803 encodes orthologs of both E. coli and B. subtilis RNases, including RNase E and RNase J, respectively. We show that in vitro Sy RNases E and J have an endonucleolytic cleavage specificity that is very similar between them and also compared to orthologous enzymes from E. coli, B. subtilis, and Chlamydomonas. Moreover, Sy RNase J displays a robust 5′-exoribonuclease activity similar to B. subtilis RNase J1, but unlike the evolutionarily related RNase J in chloroplasts. Both nucleases are essential and gene deletions could not be fully segregated in Synechocystis. We generated partially disrupted strains of Sy RNase E and J that were stable enough to allow for their growth and characterization. A transcriptome analysis of these strains partially depleted for RNases E and J, respectively, allowed to observe effects on specific transcripts. RNase E altered the expression of a larger number of chromosomal genes and antisense RNAs compared to RNase J, which rather affects endogenous plasmid encoded transcripts. Our results provide the first description of the main transcriptomic changes induced by the partial depletion of two essential ribonucleases in cyanobacteria.

Highlights

Frequent environmental changes require bacteria to reprogram gene expression, often by adjusting mRNA amounts
The catalytic domain of the Sy RNase E contains the four typical subdomains identified in the “large” domain of E. coli (Ec) RNase E (Callaghan et al, 2005), but it lacks the “small” domain classifying the protein as type IV RNase E (Ait-Bara and Carpousis, 2015)
We have investigated and compared the enzymatic activities of RNases E and J and studied their role in RNA metabolism in the cyanobacteria Synechocystis

Summary

Introduction

Frequent environmental changes require bacteria to reprogram gene expression, often by adjusting mRNA amounts. RNases E, J, and Y are likely the key players that define bacterial mRNA decay strategies and all prokaryotes have at least one or any combination of these three ribonucleases (Laalami and Putzer, 2011) The characterization of these very disparate enzymes has revealed a surprisingly similar endonucleolytic cleavage specificity and suggests that the major mRNA decay pathways in bacteria initiate with an internal cleavage event. This can be summarized by “different enzymes-similar strategies” (Laalami et al, 2014). Despite this convergent evolution toward a similar ribonucleolytic activity there is ample room for species specific strategies of mRNA metabolism, including the formation of degradosome complexes, subcellular compartmentalization and the presence of one or more of these key ribonucleases

Methods

Results

Conclusion