Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism
- University of Washington, United States
Abstract
Bacterial survival is fraught with antagonism, including that deriving from viruses and competing bacterial cells. It is now appreciated that bacteria mount complex antiviral responses; however, whether a coordinated defense against bacterial threats is undertaken is not well understood. Previously we showed that Pseudomonas aeruginosa possess a danger sensing pathway that is a critical fitness determinant during competition against other bacteria. Here, we conducted genome-wide screens in P. aeruginosa that reveal three conserved and widespread interbacterial antagonism resistance clusters (arc1-3). We find that although arc1-3 are coordinately activated by the Gac/Rsm danger sensing system, they function independently and provide idiosyncratic defense capabilities, distinguishing them from general stress response pathways. Our findings demonstrate that Arc3 family proteins provide specific protection against phospholipase toxins by preventing the accumulation of lysophospholipids in a manner distinct from previously characterized membrane repair systems. These findings liken the response of P. aeruginosa to bacterial threats to that of eukaryotic innate immunity, wherein threat detection leads to the activation of specialized defense systems.
Data availability
Sequence data associated with this study is available from the Sequence Read Archive at BioProject PRJNA754428 (http://www.ncbi.nlm.nih.gov/bioproject/754428).
Article and author information
Author details
Funding
National Institutes of Health (AI080609)
- Joseph D Mougous
National Institutes of Health (DK089507)
- Stephen J. Salipante
National Institutes of Health (R01AI136979)
- Libin Xu
Cystic Fibrosis Foundation (SINGH19R0)
- Stephen J. Salipante
National Institutes of Health (S10OD026741)
- Stephen J. Salipante
Howard Hughes Medical Institute
- Joseph D Mougous
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Ting et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,493
- views
-
- 363
- downloads
-
- 8
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism
eLife 11:e74658.
https://doi.org/10.7554/eLife.74658
Further reading
-
- Evolutionary Biology
- Microbiology and Infectious Disease
When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.
-
- Microbiology and Infectious Disease
Viruses are ubiquitous in nature and play key roles in various ecosystems. Notably, some viruses (e.g. bacteriophage) exhibit alternative life cycles, such as chronic infections without cell lysis. However, the impact of chronic infections and their interactions with the host organisms remains largely unknown. Here, we found for the first time that polysaccharides induced the production of multiple temperate phages infecting two deep-sea Lentisphaerae strains (WC36 and zth2). Through physiological assays, genomic analysis, and transcriptomics assays, we found these bacteriophages were released via a chronic style without host cell lysis, which might reprogram host polysaccharide metabolism through the potential auxiliary metabolic genes. The findings presented here, together with recent discoveries made on the reprogramming of host energy-generating metabolisms by chronic bacteriophages, shed light on the poorly explored marine virus–host interaction and bring us closer to understanding the potential role of chronic viruses in marine ecosystems.
