Biology subjects

Lin, I. N.

Publications and source records attributed to Lin, I. N..

2 recordsLinked to original sources

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

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↗