Biology subjects

Strock, R.

Publications and source records attributed to Strock, R..

3 recordsLinked to original sources

bioRxiv2026

Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation, or conflict remains fundamentally unknown. One potential window into archaeal-bacterial conflict is to ask whether some of the molecular weapons bacteria wield to kill other bacteria are present in archaea, and vice versa. Here, to start to address this question, we carry out a phylogenomic survey of bacteriocins in archaeal genomes and archaeocins in bacterial genomes. We find that more than 20% of known bacteriocins - proteins deployed by bacteria against other bacteria - have at least one homolog in archaea. Typically, these archaeal homologs are related to bacteriocins targeting (and encoded by) monoderm bacteria. Based on conservation of functionally critical residues, protein structure, and accessory genes critical for bacteriocin biosynthesis, we highlight homologs of subtilosin A, encoded in some Thermococcus archaea, as promising candidates for experimental follow- up work. We also show that halocin C8, originally described in Natrinema archaea, is comparatively common in bacterial genomes, including a number of skin-resident Staphylococcus species. Our results suggest that bacteriocins/archaeocins are shared across Domain boundaries with some regularity. While many instances are phylogenetically isolated - raising doubts about their functional importance and integration into host physiology - some bacteriocins are present in multiple related genomes and embedded in broader biosynthetic gene clusters that are also found in the original producers, suggesting that archaea and bacteria periodically use the same weapon systems in conflicts with other microbes. Further study of these systems might elucidate cross-Domain conflict and the nature of archaeal-bacterial interactions in different environments.

microbiology↗

bioRxiv2026

A Bactericidal Phospholipase from Archaea

Archaea kill bacteria, at least on occasion. The molecular underpinnings of these lethal interactions are barely understood. Here, we describe cinquedea, an /{beta} hydrolase secreted by the halophilic archaeon Haloferax larsenii s5a-1. Cinquedea exhibits bactericidal activity in the nanomolar range, killing halophilic Pontibacillus bacteria. Bacterial death is accompanied by gross morphological abnormalities, indicative of severe damage to the cell envelope. We predict, and confirm in vitro, that cinquedea is a phospholipase, with structural similarities to a phospholipase A1 enzyme isolated from hornet venom. Exposing lipids extracted from a cinquedea-sensitive Pontibacillus strain to the enzyme leads to accumulation of lysophosphatidylglycerol, a cleavage product of phospholipase A activity. This is consistent with direct activity of cinquedea against the Pontibacillus membrane, which we show is chiefly composed of phosphatidylglycerol. Considered alongside recent findings that some archaea encode bactericidal peptidoglycan hydrolases, these results suggest that archaea can kill bacteria in mechanistically diverse ways. Our work provides a template for future experimental discovery and characterization of bactericidal proteins of archaeal origin and reinforces an emerging view that archaea represent a substantial reservoir for the discovery of new antibacterial compounds.

microbiology↗

bioRxiv2024

Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria

The social life of archaea is poorly understood. In particular, even though competition and conflict are common themes in microbial communities, there is scant evidence documenting antagonistic interactions between archaea and their abundant prokaryotic brethren: bacteria. Do archaea specifically target bacteria for destruction? If so, what molecular weaponry do they use? Here, we present an approach to infer antagonistic interactions between archaea and bacteria from genome sequence. We show that a large and diverse set of archaea encode peptidoglycan hydrolases, enzymes that recognize and cleave a structure - peptidoglycan - that is a ubiquitous component of bacterial cell walls but absent from archaea. We predict the bacterial targets of archaeal peptidoglycan hydrolases using a structural homology approach and demonstrate that the predicted target bacteria tend to inhabit a similar niche to the archaeal producer, indicative of ecologically relevant interactions. Using a heterologous expression system, we demonstrate that two peptidoglycan hydrolases from the halophilic archaeaon Halogranum salarium B-1 kill the halophilic bacterium Halalkalibacterium halodurans, a predicted target, and do so in a manner consistent with peptidoglycan hydrolase activity. Our results suggest that, even though the tools and rules of engagement remain largely unknown, archaeal-bacterial conflicts are likely common, and we present a roadmap for the discovery of additional antagonistic interactions between these two domains of life. Our work has implications for understanding mixed microbial communities that include archaea and suggests that archaea might represent a large untapped reservoir of novel antibacterials.

microbiology↗