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Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 2024; 32:557-572.e6. [PMID: 38402614 PMCID: PMC11009048 DOI: 10.1016/j.chom.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.
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Affiliation(s)
- Yi Wu
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anne van den Hurk
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Simran Krishnakant Kushwaha
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Claire M King
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yaqing Ou
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Thomas C Todeschini
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Franklin L Nobrega
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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Erken R, Loukachov V, van Dort K, van den Hurk A, Takkenberg RB, de Niet A, Jansen L, Willemse S, Reesink H, Kootstra N. Quantified integrated hepatitis B virus is related to viral activity in patients with chronic hepatitis B. Hepatology 2022; 76:196-206. [PMID: 35073596 PMCID: PMC9305117 DOI: 10.1002/hep.32352] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/20/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS HBV can integrate in the host genome of the hepatocyte and recent findings suggest that integrated HBV contributes to the persistent production of viral proteins. Here, we quantified the levels of integrated HBV in patients with chronic hepatitis B (CHB) and analyzed the relation between HBV integration, virological activity (plasma HBV DNA and HBsAg levels), and clinical outcomes. APPROACH AND RESULTS We developed and validated a multistep Arthrobacter luteus (Alu)-PCR that specifically amplifies integrated HBV and RT-Alu-PCR detecting mRNA transcripts derived from integrated HBV. Pretreatment liver biopsy samples and baseline characteristics of 124 patients with CHB either treated for 48 weeks with pegylated interferon plus adefovir or tenofovir or receiving no treatment were available for analysis. Integrated HBV sequences containing open reading frame S and X (but not C) and S and X mRNA transcripts derived from integrated HBV could be detected and quantified in liver biopsies. Integrated HBV levels correlated with HBV DNA, HBsAg, alanine aminotransferase plasma levels, and the liver histology activity index but not to levels of intrahepatic covalently closed circular DNA (cccDNA), plasma pregenomic RNA, or hepatitis B core-related antigen. Multivariable logistic regression analysis showed that lower baseline HBV integration levels were independently associated with HBsAg loss (functional cure) within 5 years follow-up. CONCLUSIONS Integrated HBV levels are strongly correlated with surrogate markers for virological activity but not to cccDNA levels and are predictive for HBsAg loss. Our data suggest that integrated HBV is closely related to HBV replication and may therefore be an important tool in the evaluation and development of treatment modalities aiming to cure CHB.
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Affiliation(s)
- Robin Erken
- Department of Experimental ImmunologyAmsterdam UMC, location AMCAmsterdam Infection & Immunity InstituteUniversity of AmsterdamAmsterdamthe Netherlands,Department of Gastroenterology and HepatologyAmsterdam Gastroenterology Endocrinology MetabolismAmsterdam UMC, location AMCAmsterdamthe Netherlands
| | - Vladimir Loukachov
- Department of Experimental ImmunologyAmsterdam UMC, location AMCAmsterdam Infection & Immunity InstituteUniversity of AmsterdamAmsterdamthe Netherlands
| | - Karel van Dort
- Department of Experimental ImmunologyAmsterdam UMC, location AMCAmsterdam Infection & Immunity InstituteUniversity of AmsterdamAmsterdamthe Netherlands
| | - Anne van den Hurk
- Department of Experimental ImmunologyAmsterdam UMC, location AMCAmsterdam Infection & Immunity InstituteUniversity of AmsterdamAmsterdamthe Netherlands
| | - R. Bart Takkenberg
- Department of Gastroenterology and HepatologyAmsterdam Gastroenterology Endocrinology MetabolismAmsterdam UMC, location AMCAmsterdamthe Netherlands
| | - Anniki de Niet
- Department of Gastroenterology and HepatologyAmsterdam Gastroenterology Endocrinology MetabolismAmsterdam UMC, location AMCAmsterdamthe Netherlands
| | - Louis Jansen
- Department of Gastroenterology and HepatologyAmsterdam Gastroenterology Endocrinology MetabolismAmsterdam UMC, location AMCAmsterdamthe Netherlands
| | - Sophie Willemse
- Department of Gastroenterology and HepatologyAmsterdam Gastroenterology Endocrinology MetabolismAmsterdam UMC, location AMCAmsterdamthe Netherlands
| | - Henk Reesink
- Department of Gastroenterology and HepatologyLeiden University Medical CenterLeidenthe Netherlands
| | - Neeltje Kootstra
- Department of Experimental ImmunologyAmsterdam UMC, location AMCAmsterdam Infection & Immunity InstituteUniversity of AmsterdamAmsterdamthe Netherlands
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