Phage defence loci of Streptococcus thermophilus-tip of the anti-phage iceberg?

Autor:	Kelleher P; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland., Ortiz Charneco G; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland., Kampff Z; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland., Diaz-Garrido N; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland., Bottacini F; Department of Biological Sciences, Munster Technological University, Cork, Ireland., McDonnell B; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland., Lugli GA; Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, and Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy., Ventura M; Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, and Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy., Fomenkov A; New England Biolabs, Ipswich, MA, USA., Quénée P; Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France., Kulakauskas S; Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France., de Waal P; DSM-Firmenich, Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands., van Peij NNME; DSM-Firmenich, Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands., Cambillau C; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.; Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France., Roberts RJ; New England Biolabs, Ipswich, MA, USA., van Sinderen D; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland., Mahony J; School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Sep 24. Date of Electronic Publication: 2024 Sep 24.
DOI:	10.1093/nar/gkae814
Abstrakt:	Bacteria possess (bacterio)phage defence systems to ensure their survival. The thermophilic lactic acid bacterium, Streptococcus thermophilus, which is used in dairy fermentations, harbours multiple CRISPR-Cas and restriction and modification (R/M) systems to protect itself against phage attack, with limited reports on other types of phage-resistance. Here, we describe the systematic identification and functional analysis of the phage resistome of S. thermophilus using a collection of 27 strains as representatives of the species. In addition to CRISPR-Cas and R/M systems, we uncover nine distinct phage-resistance systems including homologues of Kiwa, Gabija, Dodola, defence-associated sirtuins and classical lactococcal/streptococcal abortive infection systems. The genes encoding several of these newly identified S. thermophilus antiphage systems are located in proximity to the genetic determinants of CRISPR-Cas systems thus constituting apparent Phage Defence Islands. Other phage-resistance systems whose encoding genes are not co-located with genes specifying CRISPR-Cas systems may represent anchors to identify additional Defence Islands harbouring, as yet, uncharacterised phage defence systems. We estimate that up to 2.5% of the genetic material of the analysed strains is dedicated to phage defence, highlighting that phage-host antagonism plays an important role in driving the evolution and shaping the composition of dairy streptococcal genomes. (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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