Biology subjects

Rudner, A. D.

Publications and source records attributed to Rudner, A. D..

3 recordsLinked to original sources

bioRxiv2026

Municipal Wastewater in Ottawa, Canada contains a reservoir of bacteriophages with clinically relevant Escherichia coli and Klebsiella pneumoniae Hosts

The recent rise of antimicrobial resistant bacteria in health care and environmental settings has been detrimental to the feasibility of antibiotic treatments for patients and agricultural applications. Along with this escalating issue, a resurgence of bacteriophage research has occurred, and phage therapy is proving to be a powerful case-specific alternative. However, a centralized source of phages that are accessible, abundant, and characterized as candidates for potential use in therapeutic applications remains to be fully established. This study aims to identify the range of bacteriophages available in municipal wastewater from Ottawa, Ontario that can infect and lyse Escherichia coli O1:K1:H7 and Klebsiella pneumoniae K3 hosts. Building-level sewer shed, influent, and primary sludge samples were screened for the presence of these phages which were then isolated through several rounds of plaque purification, sequenced by Nanopore technology, and annotated. Ten phages belonging to the genus Kayfunavirus, Vectrevirus, Kuravirus, or Sugarlandvirus were identified and bio-banked from different types of wastewater at several time points. These phages are 96-99% identical to phages isolated in Germany, Switzerland, and Spain, but contain divergent structural and metabolic genes. This work contributes to the ever-growing database of sequenced phages, provided with a physical archive of the organisms, and helps uncover the extent of phage biodiversity at different levels of wastewater treatment facilities that are readily available for screening in phage therapy applications.

microbiology↗

bioRxiv2025

Comparative genomic analysis of Cluster AZ Arthrobacter phages

Bacteria in the Arthrobacter genus belong to the phylum Actinobacteria and are primarily soil-dwelling. Over 600 bacteriophages infecting Arthrobacter hosts have been isolated and sequenced, and genomic analyses show these phages to be highly diverse with mosaic genome architectures. We describe here a group of 32 Arthrobacter phages grouped in Cluster AZ, isolated on four different Arthrobacter strains all with siphoviral morphologies. The Cluster AZ phages exhibit a spectrum of diversity and can be subdivided into four subclusters. The diversity in minor tail protein and endolysin genes correlates partly with isolation host strain and may be predictive of the host range of these phages. Most of the Cluster AZ phages are temperate, form stable lysogens, and encode an integrase; however, an immunity repressor gene has not been identified. The intracluster diversity was analyzed in-depth at the whole genome level and through individual genes. As more Arthrobacter phages are isolated and analyzed they continue to provide new insights into phage evolution.

genomics↗

bioRxiv2025

Identification of polyphosphate-binding proteins in E. coli uncovers targets involved in translation control and ribosome biogenesis

In many bacteria, polyphosphate kinase (PPK) enzymes use ATP to synthesize polyphosphate (polyP) in response to cellular stress. These chains of inorganic phosphates are joined by high-energy bonds and can reach hundreds of residues in length. PolyP plays diverse functions in helping bacteria adjust to changing environmental conditions. However, the molecular mechanisms underlying these functions are poorly understood. In eukaryotic cells, polyacidic serine- and lysine-rich (PASK) motifs of proteins can mediate binding to polyP chains. Whereas PASK motifs are relatively common in yeast and human cells, we report that these sequences are rare in bacteria commonly used for polyP research. Thus, to identify novel polyP-binding proteins in Escherichia coli, we carried out an untargeted screen and identified 7 novel targets with links to translation control and ribosome biogenesis. For two targets, the GTPase activating protein YihI and the ribonuclease Rnr, we mapped the regions of polyP interaction to non-PASK sequences and identified lysine residues critical for binding. We found that deletion of rnr suppressed the slow growth phenotype of {Delta}ppk mutants grown on minimal media. Conversely, ppk deletion resulted in decreased Rnr protein expression. These phenotypes were dependent on the polyP binding region of Rnr but independent of polyP binding itself, suggesting a complex interplay between PPK and Rnr function in E. coli. Overall, our work provides new insights into the scope of polyP binding proteins and extends the connections between polyP and the regulation of protein translation in E. coli.

molecular biology↗