Biology subjects

Yang, A. L. J.

Publications and source records attributed to Yang, A. L. J..

2 recordsLinked to original sources

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↗

bioRxiv2024

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses

Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) the targeted bacterial defense system. Here, we uncover a mechanism by which the T7 bacteriophage broadly counteracts bacterial defenses using protein phosphorylation. We show that the T7 protein kinase (T7K), which was believed to specifically redirect the function of a few host proteins, is in fact a hyper-promiscuous, dual-specificity kinase enacting a massive wave of phosphorylation on virtually all host and phage proteins during infection. The scale of phosphorylation vastly exceeds the number of previously known phosphorylation events in E. coli, has no sequence motif specificity, and results in a higher proteome-wide phosphorylation density than that of mammalian cells which encode [~] 500 kinases. Stoichiometry analysis of phosphorylation sites revealed a strong bias of T7K activity towards nucleic acid-binding substrates, which we show is mediated by its C-terminal DNA-binding domain. This specificity for highly stoichiometric phosphorylation of nucleic acid-binding proteins enables the deactivation of DNA-targeting or - containing bacterial defense systems. We provide mechanistic insight into how T7K weakens two such defense systems, Retron-Eco9 and DarTG1, through specific phosphorylation events, with single phosphomimetic mutations in key sites of the toxins abolishing defense. Finally, by screening a large collection of E. coli strains, we provide evidence of broad counter-defense capacities for T7K in nature, as strains counteracted contain diverse bacterial defense systems.

microbiology↗