Pneumococcal RNase R globally impacts protein synthesis by regulating the amount of actively translating ribosomes

Abstract

Ribosomes are macromolecular machines that carry out protein synthesis. After each round of translation, ribosome recycling is essential for reinitiating protein synthesis. Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyse the transient split of the 70S ribosome into subunits. This splitting is then stabilized by initiation factor 3 (IF3), which functions as an anti-association factor. The correct amount of these factors ensures the precise level of 70S ribosomes in the cell. RNase R is a highly conserved exoribonuclease involved in the 3ʹ to 5ʹ degradation of RNAs. In this work we show that pneumococcal RNase R directly controls the expression levels of frr, fusA and infC mRNAs, the corresponding transcripts of RRF, EF-G and IF3, respectively. We present evidences showing that accumulation of these factors leads to a decreased amount of 70S active particles, as demonstrated by the altered sucrose gradient ribosomal pattern in the RNase R mutant strain. Furthermore, the single deletion of RNase R is shown to have a global impact on protein synthesis and cell viability, leading to a~50% reduction in bacterial CFU/ml. We believe that the fine-tuned regulation of these transcripts by RNase R is essential for maintaining the precise amount of active ribosomal complexes required for proper mRNA translation and thus we propose RNase R as a new auxiliary factor in ribosome reassociation. Considering the overall impact of RNase R on protein synthesis, one of the main targets of antibiotics, this enzyme may be a promising target for antimicrobial treatment. ARTICLE HISTORY

Bacterial ribonucleases and their roles in RNA metabolism

“…RNase R also is important for mRNA decay (Cheng and Deutscher 2005; Andrade et al 2006; Figure 4), particularly of regions in the mRNA with extensive secondary structure, such as REP elements (Cheng and Deutscher 2005). RNase R also plays an important role in removing mRNA during trans -translation (Richards et al 2006; Liang and Deutscher 2013; Domingues et al 2015), and in regulating the amount of translating ribosomes (Barria et al 2019).…”

Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation

“…RNAs bearing 2′- O -methylations show enhanced stability ( 19–21 ) and increased resistance to degradation by some Ribonuclease Rs (RNase R) ( 22 ). RNase R from Escherichia coli ( Ec R) and a number of mycoplasma species such as Mycoplasma genitalium ( Mg R), Mycoplasma hyor ( Mh R), Mycoplasma canis ( Mc R), are a major type of 3′-5′ exoribonucleases belonging to the RNase II/ RNB family that are involved in RNA degradation ( 23 ), maturation ( 24 ) and quality control ( 25 , 26 ) in all kingdoms of life. Prototypical of members of the family also include E. coli RNase II ( Ec II), yeast Rrp44 and human Dis3-like proteins.…”

A Novel Cold-Adapted and Salt-Tolerant RNase R from Antarctic Sea-Ice Bacterium Psychrobacter sp. ANT206

“…In Escherichia coli ( E. coli ), eight distinct RNases involved in different aspects of RNA metabolism were identified. RNase R, originally termed as vacB in Shigella flexneri [3], was found in Aeromonas hydrophila [4], Legionella pneumophila [5], and Pneumoniae [6]. RNase R participates in an essential cell function besides its role in virulence [3].…”