Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins
Abstract
Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.
- Authors:
-
[3];
[1];
[2];
[4]
- Univ. of California, Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States). Innovative Genomics Inst.
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States). Innovative Genomics Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF); National Center for Advancing Translational Sciences
- OSTI Identifier:
- 1773739
- Alternate Identifier(s):
- OSTI ID: 1777972
- Grant/Contract Number:
- AC02-05CH11231; S10RR025622; S10RR029668; S10RR027303; OD018174; DGE 1752814
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 15; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Bacterial genetics; functional genomics; microbial ecology; soil microbiology
Citation Formats
Carim, Sean, Azadeh, Ashley L., Kazakov, Alexey E., Price, Morgan N., Walian, Peter J., Lui, Lauren M., Nielsen, Torben N., Chakraborty, Romy, Deutschbauer, Adam M., Mutalik, Vivek K., and Arkin, Adam P. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. United States: N. p., 2021.
Web. doi:10.1038/s41396-021-00921-1.
Carim, Sean, Azadeh, Ashley L., Kazakov, Alexey E., Price, Morgan N., Walian, Peter J., Lui, Lauren M., Nielsen, Torben N., Chakraborty, Romy, Deutschbauer, Adam M., Mutalik, Vivek K., & Arkin, Adam P. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. United States. https://doi.org/10.1038/s41396-021-00921-1
Carim, Sean, Azadeh, Ashley L., Kazakov, Alexey E., Price, Morgan N., Walian, Peter J., Lui, Lauren M., Nielsen, Torben N., Chakraborty, Romy, Deutschbauer, Adam M., Mutalik, Vivek K., and Arkin, Adam P. Mon .
"Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins". United States. https://doi.org/10.1038/s41396-021-00921-1. https://www.osti.gov/servlets/purl/1773739.
@article{osti_1773739,
title = {Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins},
author = {Carim, Sean and Azadeh, Ashley L. and Kazakov, Alexey E. and Price, Morgan N. and Walian, Peter J. and Lui, Lauren M. and Nielsen, Torben N. and Chakraborty, Romy and Deutschbauer, Adam M. and Mutalik, Vivek K. and Arkin, Adam P.},
abstractNote = {Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.},
doi = {10.1038/s41396-021-00921-1},
journal = {The ISME Journal},
number = ,
volume = 15,
place = {United States},
year = {Mon Mar 01 00:00:00 EST 2021},
month = {Mon Mar 01 00:00:00 EST 2021}
}
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Characteristic features of the SERA multigene family in the malaria parasite
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New species in Dictyosporium, new combinations in Dictyocheirospora and an updated backbone tree for Dictyosporiaceae
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Loss of a chloroplast encoded function could influence species range in kelp
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Characterization of the complete chloroplast genome of a critically endangered decaploid rose species, Rosa praelucens (Rosaceae)
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Admixture analyses and phylogeographic relationships reveal complete genetic distinctiveness of Polish farm and wild red foxes ( Vulpes vulpes ) and the North American origin of farm‐bred individuals
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The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence
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Barcoding Analysis of Paraguayan Squamata
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Ecomorphological adaptation in three mudskippers (Teleostei: Gobioidei: Gobiidae) from the Persian Gulf and the Gulf of Oman
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Algicoccus marinus gen. nov. sp. nov., a marine bacterium isolated from the surface of brown seaweed Laminaria japonica
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Two new entomopathogenic species of Ophiocordyceps in Thailand
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Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems
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Interspecific delimitation and relationships among four Ostrya species based on plastomes
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Ophiostomatoid fungi associated with Ips subelongatus, including eight new species from northeastern China
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Whitefly predation and extensive mesonotum color polymorphism in an Acletoxenus population from Singapore (Diptera, Drosophilidae)
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Biological invasions increase the richness of arbuscular mycorrhizal fungi from a Hawaiian subtropical ecosystem
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Shedding light on the polyphyletic behavior of the genus Sterkiella: The importance of ontogenetic and molecular phylogenetic approaches
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Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira
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Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat
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New different origins and evolutionary processes of AP2/EREBP transcription factors in Taxus chinensis
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Population genetic structure and phylogenetic analysis of gray’s pipefish, Halicampus grayi in the South China Sea
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Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach
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An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)
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Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber
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Moth tails divert bat attack: Evolution of acoustic deflection
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The complete chloroplast genome of Korean endemic species, Cirsium rhinoceros (H.Lév. & vaniot) Nakai (Asteraceae)
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Global diversity and distribution of close relatives of apicomplexan parasites: Diversity and distribution of apicomplexan parasites
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Molecular homology and multiple-sequence alignment: an analysis of concepts and practice
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Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly
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Hymenoscyphus pusillus , a new species on leaves of Fraxinus pennsylvanica in Poland
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Did aculeate silk evolve as an antifouling material?
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Computational approaches to study the effects of small genomic variations
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The complete mitochondrial genome of the Xinyuan honey bee, Apis mellifera sinisxinyuan (Insecta: Hymenoptera: Apidae)
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Characterization of the lytic archaeal virus Drs3 infecting Methanobacterium formicicum
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Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans: BODY SIZE EVOLUTION IN CAENORHABDITIS
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Evolution and development of the adelphophagic, intracapsular Schmidt’s larva of the nemertean Lineus ruber
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Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus – Contributors to Cellular Detoxification
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The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
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Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services
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The Quantification of Representative Sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia
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The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species
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Computational studies of human class V alcohol dehydrogenase - the odd sibling
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Duplication and Remolding of tRNA Genes in the Mitochondrial Genome of Reduvius tenebrosus (Hemiptera: Reduviidae)
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Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina
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Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae)
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Genome Sequences of Akhmeta Virus, an Early Divergent Old World Orthopoxvirus
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Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species
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Poliovirus serotype 2 and coxsackievirus A promote the natural recombination of poliovirus
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Reconstructing the genetic history of late Neanderthals
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Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic
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Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup
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Diversity and Hidden Host Specificity of Chytrids Infecting Colonial Volvocacean Algae
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- Van den Wyngaert, Silke; Rojas-Jimenez, Keilor; Seto, Kensuke
- Journal of Eukaryotic Microbiology, Vol. 65, Issue 6
Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia
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- Microbiology, Vol. 89, Issue 3
Interlaboratory Comparison of Six Real-Time PCR Assays for Detection of Bovine Leukemia Virus Proviral DNA
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The complete chloroplast genome of Rosa berberifolia
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- Zhang, Shu-Dong; Zhang, Chao; Ling, Li-Zhen
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Diversification patterns in the CES clade (Brassicaceae tribes Cremolobeae, Eudemeae, Schizopetaleae) in Andean South America
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A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples
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- Cannon, Matthew V.; Bogale, Haikel; Rutt, Lindsay
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Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data
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OD-seq: outlier detection in multiple sequence alignments
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Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair
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A continuous morphological approach to study the evolution of pollen in a phylogenetic context: An example with the order Myrtales
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Complete chloroplast genome of Exacum affine (Gentianaceae): the first plastome of the tribe Exaceae in the family Gentianaceae
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Prevotella intermedia produces two proteins homologous to Porphyromonas gingivalis HmuY but with different heme coordination mode
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The complete chloroplast genome and phylogenetic analysis of Begonia pulchrifolia , a near endangered Begoniaceae plant
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Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria
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Spatial transmission of H5N6 highly pathogenic avian influenza viruses among wild birds in Ibaraki Prefecture, Japan, 2016–2017
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