Biology subjects

Juozapaitis, J.

Publications and source records attributed to Juozapaitis, J..

6 recordsLinked to original sources

bioRxiv2026

Characterization of six environmental coli-phages isolated in Astana, Kazakhstan, during the School of Molecular and Theoretical Biology

Bacteriophage (phage) collections are essential resources for studying virus-host interactions in bacterial species. Here, we report six Escherichia coli-infecting phages that expand the Lund Collection of Bacteriophages. These phages were isolated in 2025 within the framework of the School of Molecular and Theoretical Biology for high-school students, from samples collected in Lake Taldykol, Astana, Kazakhstan, using E. coli strains MG1655{Delta}RM and EV36 as hosts. The isolated phages comprise Taldykol (LuPh6), a member of the genus Kagunavirus; Aidakhar (LuPh7) of the genus Phapecoctavirus; Samruk (LuPh8) of the genus Tequintavirus; the T-odd-like phage Baiterek (LuPh9) of the genus Vequintavirus; and two T-even-like phages Tulpar (LuPh10) and Shurale (LuPh11) that belong to the Tequatrovirus genus. This expanded phage collection enhances the toolkit for investigating phage-host interactions and their molecular mechanisms and highlights the use of phage isolation as a component of high school research education. ImportancePhage collections are a key resource for studying phage biology, phage-bacteria interactions and bacterial immune systems. Here, we extend the Lund Phage Collection through the isolation and characterisation of six E. coli-infecting phages, including three novel species (LuPh6, LuPh8 and LuPh11) as well as a member of the genus Phapecoctavirus that not represented in widely used collections such as BASEL (LuPh7). This study expands the resources available for probing phage-host interactions and demonstrates an example of integrating phage research into education of high school students.

microbiology↗

bioRxiv2026

Thirty years of Achromobacter ruhlandii evolution reveal pathways to epidemic lineages

BackgroundAchromobacter spp. are emerging opportunistic pathogens, associated with chronic infections, antimicrobial resistance, and poor clinical outcomes. The Danish epidemic strain (DES) of A. ruhlandii is highly drug-resistant and adapted to the cystic fibrosis (CF) airway, yet its evolutionary history and defining genomic features remain poorly understood. MethodsWe analysed genome and antibiotic susceptibility testing data for 58 longitudinally collected DES isolates sampled over 21 years at Rigshospitalet, Denmark. We combined these with 79 publicly available A. ruhlandii genomes and applied phylogenomics to infer DES emergence and transmission, and genome-wide association studies (GWAS) to identify lineage-specific and adaptive genomic features. ResultsDES forms a distinct monophyletic clade within A. ruhlandii, estimated to have emerged around 1990, with no evidence of dissemination beyond Denmark. GWAS identified key lineage-defining traits, including acquisition of large mobile genetic elements, plasmid integration events, and enrichment of resistance and iron acquisition genes. In addition, we detected other epidemic A. ruhlandii lineages with evidence of long-term persistence and inter-country spread, sharing similar genetic signatures of adaptation. ConclusionsThis study elucidates the genomic features associated with chronic infection and epidemic potential in A. ruhlandii. The DES lineage illustrates how extensive horizontal gene transfer, high intrinsic resistance potential, and enhanced host-adaptation traits, such as increased iron acquisition, can facilitate the emergence and persistence of successful epidemic lineages. These findings highlight shared evolutionary signatures of epidemic A. ruhlandii and underscore the need for continued genomic surveillance to detect and monitor emerging high-risk lineages in chronic infections.

bioinformatics↗

bioRxiv2026

Viral SSB-bound ssDNA activates the bacterial anti-phage defense system DARNA

To protect themselves against phage infection, bacteria employ diverse defense systems that are typically activated specifically upon infection. However, the mechanisms of activation and self versus non-self discrimination for most systems remain poorly understood. Here, we show that the bacterial immunity protein DARNA, once activated, cleaves a subset of host tRNAs, thereby inhibiting phage propagation. Although phages escape DARNA-mediated defense through mutations in the gene encoding single-stranded DNA-binding protein (SSB), we find that phage SSBs do not directly stimulate DARNA. Instead, DARNA is activated by single-stranded DNA presented by phage SSB, but not by the host SSB. The recognition of an endogenous nucleic acid signal promoted by a viral protein ensures that DARNA can detect and respond to a broad range of viruses while avoiding auto-immunity.

microbiology↗

bioRxiv2026

Deoxydinucleotides activate the bacterial anti-phage defense system ApeA

Bacteria and archaea encode diverse antiviral defense systems, many of which rely on toxic effector proteins that are activated specifically upon bacteriophage infection. However, the mechanisms by which infection is recognized and coupled to effector activation remain poorly understood for most antiviral systems. Here, we focus on ApeA, a HEPN-domain antiviral protein that confers immunity through cleavage of host tRNAs within their anticodon loops. We show that ApeA proteins form large doughnut-shaped oligomers that are activated upon ligand binding in a conserved protein pocket distinct from the catalytic center. In the Ec2ApeA variant, this pocket specifically recognizes 5'-phosphorylated deoxydinucleotides that likely arise as intermediates of host genome degradation by viral nucleases, thereby enabling Ec2ApeA to achieve a broad protection profile. Together, our results reveal how small-molecule products of virus-induced host cell destruction function as signals that activate bacterial immune defenses.

molecular biology↗

bioRxiv2025

Characterization of five environmental phages infecting Escherichia coli K-12 isolated during a phage biology training course

Phage collections are essential tools for discovering and dissecting bacterial anti-phage defense systems. Here, we report the isolation and characterization of five environmental Escherichia coli-infecting phages, obtained during the 2023 Fundamentals of Basic and Applied Phage Biology course at Lund University. The phages were isolated using a motile E. coli K-12 BW25113 strain, whose motility is conferred by an IS5 insertion upstream of the flhDC operon, the master regulator of flagellar synthesis. The isolated Escherichia phages include Lubas (LuPh1) and Lucat (LuPh2) of the genus Tequatrovirus; Lupin (LuPh3) and Lucris (LuPh4) of the genus Tequintavirus; and Kompetensportalen (LuPh5) of the genus Chivirus. Transmission electron microscopy confirmed myovirus and siphovirus morphologies consistent with these genera. As expected for phages in the flagellotropic Chivirus genus, LuPh5 failed to infect a poorly motile BW25113 strain lacking the IS5 element upstream of flhDC. By testing a panel of eight previously described anti-phage defense systems, we found that LuPh1 and LuPh2 are inhibited by the toxin-antitoxin-chaperone CmdTAC system; LuPh5 is inhibited by both the restriction-modification system EcoRI and the abortive infection reverse transcriptase AbiK; and all five phages are sensitive to the hybrid artificial CmdTA-HigC system. Collectively, our findings expand the toolkit for probing phage-host interactions and underscore the pedagogical value of incorporating phage isolation into practical training for emerging researchers.

microbiology↗

bioRxiv2023

Astonishing diversity and multifaceted biological connections of Type IV restriction-modification systems

A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote CoCoNuTs (coiled-coil nuclease tandems) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with 3 distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.

microbiology↗