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DNA-intercalating antiphage molecules trigger abortive infection through ‘mutual destruction’ and synergize with bacterial immunity

ABSTRACT: Bacteria deploy diverse antiphage defense systems, including small bioactive molecules providing protection at the multicellular level. DNA-intercalating anthracyclines such as daunorubicin exhibit broad antiphage activity, but the underlying mechanism had remained elusive. Here, we systematically screened the Escherichia coli BASEL phage collection to elucidate the mode of action of daunorubicin. We identified taxonomically distinct clusters of susceptible viral groups and demonstrate that daunorubicin blocks infection of T5-like phages (Markadamsvirinae) after first-step transfer (FST) as revealed by long-read sequencing. Continued expression of pre-early genes leads to abortive infection via ‘mutual destruction’, where both phage and host succumb. Analogous phenotypes of abortive infection were observed for taxonomically diverse phages with different DNA-intercalating antiphage molecules. Notably, we show that daunorubicin synergizes with downstream nucleic acid-targeting defences underscoring context dependency in the observed defense phenotype. Our findings reveal how chemical defense contributes to the multilayered antiviral immunity and highlight the intricate interplay between mechanistic inhibition and infection outcome.

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ORGANISM(S): Escherichia Coli Escherichia Phage Hildybeyeler

SUBMITTER: Timo Glatter

LAB HEAD: Timo Glatter

PROVIDER: PXD070949 | Pride | 2026-05-13

REPOSITORIES: Pride

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Project description:Metabolism is fundamental to life, all life activities are sustained through metabolism. Metabolic engineering, while modifying host endogenous metabolic network or introducing heterologous pathway for biotechnological applications, often results in unfitness and suboptimal characteristics, because of the lack of full knowledge on host metabolism. Adaptive laboratory evolution (ALE), harnessing the nature of life -- evolution, has become a potent approach in phenotype optimization, environmental adaptation, and cell biology study1–3. Through ALE, alternative pathways of β-alanine biosynthesis4, pyridoxal 5’-phosphate (PLP) biosynthesis5, isoleucine biosynthesis6, as well as ATP generation7 have been uncovered; E. coli aerobic citrate utilization8,9 and various synthetic C1-trophy10–14 have been realized. In this study, we describe E. coli recruits the same workforce, Sad, in evolution through various strategies, i.e., catalytic efficiency improvement, gene dose increase, and gene expression regulations, to overcome metabolic damages (Fig. 1). Sad, i.e. NAD(P)+-dependent succinate semialdehyde dehydrogenase (SSADH), is an aldehyde dehydrogenase (ALDH) family protein. Sad oxidizes succinate semialdehyde to succinate, preventing accumulation of the toxic aldehyde intermediate in nitrogen metabolism, such as putrescine, arginine and γ-aminobutyrate (GABA) degradations15–17. Some bacteria, for example E. coli, possess also a NADP+-dependent SSADH, GabD15,18. SSADH is ubiquitous in both prokaryotes and eukaryotes. In human, it involves in catabolism of GABA, a major neurotransmitter, its malfunction leads to a disorder SSADH deficiency19. In plants, SSADH involves in leaf development and morphogenesis20 as well as defense of abiotic stress21. And in cyanobacteria, SSADH is an essential enzyme of its uncanonical tricarboxylic acid cycle. SSADH was also found to be able to oxidize glutarate semialdehyde, participating in lysine catabolism in bacteria.

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DNA-intercalating antiphage molecules trigger abortive infection through ‘mutual destruction’ and synergize with bacterial immunity

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