Biology subjects

Prince, C. R.

Publications and source records attributed to Prince, C. R..

6 recordsLinked to original sources

bioRxiv2026

A Novel Eukaryotic Ribosome Factor Enables Translation Restart Following Cellular Dormancy

Dormancy is a survival strategy employed by all domains of life to withstand prolonged nutrient deprivation and environmental stress that is marked by a global shutdown of protein synthesis. However, the molecular mechanisms driving ribosome inactivation and reactivation during and after dormancy in eukaryotes remain poorly understood. Here, we identify SNOR, a novel SBDS-like ribosome-associated factor in Schizosaccharomyces pombe, that is upregulated and associates with ribosomes during induced dormancy triggered by glucose depletion. SNOR contributes to protein synthesis repression by binding the ribosome to probe the peptidyl transferase center (PTC), block tRNA-binding sites, and cap the polypeptide exit tunnel (PET). Importantly, we show that SNOR is essential for the restart of protein synthesis upon glucose reintroduction and exit from dormancy. SNOR is evolutionarily conserved and specifically upregulated in response to glucose stress in fungi. These findings reveal a previously unrecognized ribosome-associated factor that links glucose stress and cellular dormancy to surveillance of protein synthesis and highlight the power of in situ structural biology to uncover stress-responsive regulators of translation.

biophysics↗

bioRxiv2025

Conservation of sporulation genes and a transmembrane-containing Spo0B variant in Paenibacillus

Sporulation is a strategy employed by many bacteria to survive harsh environmental conditions. The genus Paenibacillus includes spore-forming species notorious for spoiling pasteurized dairy products and causing fatal infections in honeybee larvae, leading to colony collapse. Here, we present a comprehensive survey of sporulation genes across 1460 high-quality Paenibacillus genomes. We find that all members of the sporulation-initiating phosphorelay are well-conserved, but that the Spo0B phosphotransferase contains a transmembrane domain that is unique to this genus. The transmembrane-domain-containing variant of Spo0B is present in 92% of surveyed Paenibacillus genomes. Consistent with this high level of conservation, we find that for Paenibacillus polymyxa Spo0B, the transmembrane domain is important for interaction with its phosphorelay partners Spo0A and Spo0F. Moreover, we find that Spo0B exhibits low sequence identity across Bacilli when compared to other members of the phosphorelay. Altogether, this work highlights the potential for diversity even within the highly conserved phosphorelay that initiates sporulation in Bacilli. ImportanceSpores are the most durable life-form, and the sporulation process serves as a paradigm of cellular development and differentiation. Sporulation is well-characterized in the model organism Bacillus subtilis, but we lack information about non-model spore-formers. The genus Paenibacillus includes spore-formers that negatively impact farming and food industries. Here, we present the first comprehensive search for sporulation genes in Paenibacillus and show that a unique transmembrane-domain-containing Spo0B is widespread throughout this genus.

microbiology↗

bioRxiv2024

YebC2 resolves ribosome stalling at polyprolines independent of EF-P and the ABCF ATPase YfmR

Polyproline motifs are essential structural features of many proteins, and recent evidence suggests that EF-P is one of several factors that facilitate their translation. For example, YfmR was recently identified as a protein that prevents ribosome stalling at proline-containing sequences in the absence of EF-P. Here, we show that the YebC-family protein YebC2 (formerly YeeI) functions as a translation factor in B. subtilis that resolves ribosome stalling at polyprolines. We demonstrate that YebC2, EF-P and YfmR act independently to support cellular fitness. Moreover, we show that YebC2 interacts directly with the 70S ribosome, supporting a direct role for YebC2 in translation. Finally, we assess the evolutionary relationship between YebC2 and other characterized YebC family proteins, and present evidence that transcription and translation factors within the YebC family have evolved separately. Altogether our work identifies YebC2 as a translation factor that resolves ribosome stalling and provides crucial insight into the relationship between YebC2, EF-P, and YfmR, three factors that prevent ribosome stalling at prolines.

microbiology↗

bioRxiv2024

The evolution and functional significance of the programmed ribosomal frameshift in prfB

When the ribosome reaches a stop codon, translation is terminated by a release factor. Bacteria encode two release factors, RF1 and RF2. In many bacteria, the gene encoding RF2 (prfB) contains an in-frame premature stop codon near the beginning of the open reading frame. A programmed ribosomal frameshift is therefore required to translate full-length RF2. While the molecular mechanism of the programmed ribosomal frameshift has been extensively characterized in Escherichia coli, bioinformatic analysis of the evolution and conservation of this motif has been limited to few genomes. By analyzing >12,000 bacterial genomes, we sought to thoroughly characterize the conserved frameshifting elements within the programmed frameshifting motif and identify genomic features of phyla that have lost the motif altogether. We find that the programmed ribosomal frameshift in prfB was likely present in the last common ancestor of bacteria and that the motif elements are almost completely conserved, including the identity of the internal stop codon. We find that loss of the programmed frameshift motif is highly correlated with RF2-specific stop codon usage, suggesting that stop codon usage has shaped the conservation of this regulatory mechanism. In support of this model, the programmed frameshift in prfB is entirely absent in Actinobacteriota, which have particularly high RF2 specific stop codon usage. Finally, we show that a model member of Actinobacteriota fails to produce full-length RF2 when provided with an allele of prfB that contains the programmed frameshifting motif. Altogether, our work provides a thorough characterization of RF2 regulation across the bacterial domain.

microbiology↗

bioRxiv2024

RqcH supports survival in the absence of non-stop ribosome rescue factors

Ribosomes frequently translate truncated or damaged mRNAs due to the extremely short half-life of mRNAs in bacteria. When ribosomes translate mRNA that lacks a stop codon (non-stop mRNA), specialized pathways are required to rescue the ribosome from the 3 end of the mRNA. The most highly conserved non-stop rescue pathway is trans-translation, which is found in greater than 95% of bacterial genomes. In all Proteobacteria that have been studied, the alternative non-stop ribosome rescue factors, ArfA and ArfB, are essential in the absence of trans-translation. Here, we investigate the interaction between non-stop rescue pathways and RqcH, a ribosome quality control factor that is broadly conserved outside of Proteobacteria. RqcH does not act directly on non-stop ribosomes but adds a degron tag to stalled peptides that obstruct the large ribosomal subunit, which allows the stalled peptide to be cleared from the ribosome by peptidyl-tRNA hydrolase (PTH). We show that Bacillus subtilis can survive without trans-translation and BrfA (Bacillus ArfA homolog), due to the presence of RqcH. We also show that expression of RqcH and its helper protein RqcP rescues the synthetic lethality of {Delta}ssrA{Delta}arfA in Escherichia coli. These results suggest that non-stop ribosome complexes can be disassembled and then cleared because of the tagging activity of RqcH, and that this process is essential in the absence of non-stop ribosome rescue pathways. Moreover, we surveyed the conservation of ribosome rescue pathways in >14,000 bacterial genomes. Our analysis reveals a broad distribution of non-stop rescue pathways, especially trans-translation and RqcH, and a strong co-occurrence between the ribosome splitting factor MutS2 and RqcH. Altogether, our results support a role for RqcH in non-stop ribosome rescue and provide a broad survey of ribosome rescue pathways in diverse bacterial species. ImportanceRibosome stalling on damaged mRNA is a major problem in bacteria. It is estimated that 2-4% of all translation reactions terminate with the ribosome stalled on a damaged mRNA lacking a stop codon. Mechanisms that rescue these ribosomes, such as trans-translation, are often essential for viability. We investigated the functional overlap between RqcH and the non-stop ribosome rescue systems (ArfA and trans-translation) that are present in both E. coli and B. subtilis. Since these two species are extremely distant relatives, our work is likely to have wider implications for understanding ribosome rescue in bacteria. Furthermore, we used a bioinformatics approach to examine the conservation and overlap of various ribosome rescue systems in >14,000 species throughout the bacterial domain. These results provide key insights into ribosome rescue in diverse phyla.

microbiology↗

bioRxiv2023

Identification of factors that prevent ribosome stalling during early elongation

Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, particularly polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in B. subtilis. YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes and that depleting YfmR from {Delta}efp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from {Delta}efp cells was lethal, and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P. SignificanceTranslation is one of the most ancient and energetically demanding processes that occurs in the cell. Ribosomes constitute more than 60% of cellular mass in actively growing cells, and ribosomes are a major target of antimicrobials and chemotherapeutics. Here, we identify YfmR as a translation factor that is essential in the absence of EF-P. YfmR is a member of the ABCF family of ATPases whose role in translation is only beginning to be understood. Given the broad distribution of ABCFs from bacteria to fungi, we expect our results to have implications for understanding translation elongation in diverse organisms.

biochemistry↗