Ribosome-Associated Quality Control in Bacteria

Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuelae

RNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA sequencing to explore the impact of RNase III and RNase J on the transcriptome of Streptomyces venezuelae. Differential expression analysis comparing wild-type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant, this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting a link between RNA metabolism and a regulator that bridges primary and specialized metabolism. We connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical for S. venezuelae development and specialized metabolism.

IMPORTANCE

RNA processing and metabolism are mediated by ribonucleases and are fundamental processes in all cells. In the morphologically complex and metabolically sophisticated Streptomyces bacteria, RNase III and RNase J influence both development and metabolism through poorly understood mechanisms. Here, we show that both ribonucleases are required for the proper expression of the BldD developmental pathway and contribute to the control of chloramphenicol production, with an interesting connection to phosphate regulation for RNase III. Additionally, we show that both RNases have the potential to impact translation through distinct mechanisms and can function cooperatively in degrading specific transcripts. This study advances our understanding of RNases in Streptomyces biology by providing insight into distinct contributions made by these enzymes and the intriguing interplay between them.

In vivo evaluation of phage therapy against Klebsiella pneumoniae using the Galleria mellonella model and molecular characterization of a novel Drulisvirus phage species

Multidrug-resistant (MDR) Klebsiella pneumoniae is challenging to treat with conventional antibiotic regimens, posing a threat to healthcare systems. Phage therapy presents a promising alternative treatment strategy; however, characterization of its efficacy and safety is required. Here, we describe the microbiological and molecular characterization of a novel bacteriophage with activity against MDR K. pneumoniae using a greater wax moth (Galleria mellonella) model system. A bacteriophage was isolated from hospital wastewater. Viral kinetics and phage stability were evaluated under varied pH and temperature conditions. The therapeutic efficacy of the phage was evaluated using MDR Klebsiella-infected G. mellonella larvae as an in vivo model. Phage titers and larva survival were compared in phage-treated and control groups. Genomic sequencing (Nanopore and Illumina) was used to classify the bacteriophage and identify any resistance genes or virulence factors present in its genome. Functional characterization demonstrated effective lytic activity, favorable burst size (161 PFU/cell), and an optimal MOI of 0.1. The phage demonstrated stability across a wide range of temperatures (8°C-40°C) and pH levels (4-8). Experiments using the G. mellonella model showed improved larval survival with phage treatment. The novel bacteriophage was identified as a new species within the genus Drulisvirus with no lysogeny-associated, antimicrobial resistance, or virulence genes detected. The new Drulisvirus phage identified is a promising candidate for treatment of infections caused by MDR K. pneumoniae.IMPORTANCEThe study describes a bacteriophage with potential for use in phage therapy against Klebsiella pneumoniae, one of the most clinically significant bacterial pathogens today. Microbiological and genomic characterization of the phage revealed advantageous properties for therapeutic applications, while also identifying a novel species within the Drulisvirus genus. These findings significantly contribute to our understanding of bacteriophage diversity and their utility in combating antibiotic-resistant infections. Moreover, the authors developed an in vivo preclinical model of MDR infection using Galleria mellonella larvae and successfully applied it to study the bacteriophage's therapeutic efficacy. This model offers a robust and efficient platform for preclinical testing.

Peptidyl-tRNA hydrolase is the nascent chain release factor in bacterial ribosome-associated quality control

Rescuing stalled ribosomes often involves their splitting into subunits. In many bacteria, the resultant large subunits bearing peptidyl-tRNAs are processed by the ribosome-associated quality control (RQC) apparatus that extends the C termini of the incomplete nascent polypeptides with polyalanine tails to facilitate their degradation. Although the tailing mechanism is well established, it is unclear how the nascent polypeptides are cleaved off the tRNAs. We show that peptidyl-tRNA hydrolase (Pth), the known role of which has been to hydrolyze ribosome-free peptidyl-tRNA, acts in concert with RQC factors to release nascent polypeptides from large ribosomal subunits. Dislodging from the ribosomal catalytic center is required for peptidyl-tRNA hydrolysis by Pth. Nascent protein folding may prevent peptidyl-tRNA retraction and interfere with the peptide release. However, oligoalanine tailing makes the peptidyl-tRNA ester bond accessible for Pth-catalyzed hydrolysis. Therefore, the oligoalanine tail serves not only as a degron but also as a facilitator of Pth-catalyzed peptidyl-tRNA hydrolysis.

trans-translation system is important for maintaining genome integrity during DNA damage in bacteria

DNA integrity in bacteria is regulated by various factors that act on the DNA. trans-translation has previously been shown to be important for the survival of Escherichia coli cells exposed to certain DNA-damaging agents. However, the mechanisms underlying this sensitivity are poorly understood. In this study, we explored the involvement of the trans-translation system in the maintenance of genome integrity using various DNA-damaging agents and mutant backgrounds. Relative viability assays showed that SsrA-defective cells were sensitive to DNA-damaging agents, such as nalidixic acid (NA), ultraviolet radiation (UV), and methyl methanesulfonate (MMS). The viability of SsrA-defective cells was rescued by deleting sulA, although the expression of SulA was not more pronounced in SsrA-defective cells than in wild-type cells. Live cell imaging using a Gam-GFP fluorescent reporter showed increased double-strand breaks (DSBs) in SsrA-defective cells during DNA damage. We also showed that the ribosome rescue function of SsrA was sufficient for DNA damage tolerance. DNA damage sensitivity can be alleviated by partial uncoupling of transcription and translation by using sub-lethal concentrations of ribosome inhibiting antibiotic (tetracycline) or by mutating the gene coding for RNase H (rnhA). Taken together, our results highlight the importance of trans-translation system in maintaining genome integrity and bacterial survival during DNA damage.

Dual metabolic pathways co-determine the efficient aerobic biodegradation of phenol in Cupriavidus nantongensis X1

Phenol, as an important chemical raw material, often exists in wastewater from chemical plants and pollutes soil and groundwater. Aerobic biodegradation is a promising method for remediation of phenolic wastewater. In this study, degradation characteristics and mechanisms of phenol in Cupriavidus nantongensis X1 were explored. Strain X1 could completely degrade 1.5 mM phenol within 32 h and use it as the sole carbon source for growth. The optimal degradation temperature and pH for phenol by strain X1 were 30 °C and 7.0. The detection of 3-oxoadipate and 4-hydroxy-2-oxopentanoate indicated that dual metabolic pathways coexist in strain X1 for phenol degradation, ortho- and meta-pathway. Genome and transcriptome sequencing revealed the whole gene clusters for phenol biomineralization, in which C12O and C23O were key enzymes in two metabolic pathways. The ribosome proteins were also involved in the regulation of phenol degradation. Meanwhile, the degradation activities of enzyme C23O was 188-fold higher than that of C12O in vitro, which indicated that the meta-pathway was more efficient than ortho-pathway for catechol degradation in strain X1. This study provides an efficient strain resource for phenol degradation, and the discovery of dual metabolic pathways provides new insight into the aerobic biological metabolism and bioremediation of phenol.