1
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Baaziz H, Makhlouf R, McClelland M, Hsu BB. Bacterial resistance to temperate phage is influenced by the frequency of lysogenic establishment. iScience 2024; 27:109595. [PMID: 38623331 PMCID: PMC11016777 DOI: 10.1016/j.isci.2024.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Temperate phages can shape bacterial community dynamics and evolution through lytic and lysogenic life cycles. In response, bacteria that resist phage infection can emerge. This study explores phage-based factors that influence bacterial resistance using a model system of temperate P22 phage and Salmonella both inside and outside the mammalian host. Phages that remained functional despite gene deletions had minimal impact on lysogeny and phage resistance except for deletions in the immI region that substantially reduced lysogeny and increased phage resistance to levels comparable to that observed with an obligately lytic P22. This immI deletion does not make the lysogen less competitive but instead increases the frequency of bacterial lysis. Thus, subtle changes in the balance between lysis and lysogeny during the initial stages of infection can significantly influence the extent of phage resistance in the bacterial population. Our work highlights the complex nature of the phage-bacteria-mammalian host triad.
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Affiliation(s)
- Hiba Baaziz
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rita Makhlouf
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Bryan B. Hsu
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
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2
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Cui Y, Su X, Wang C, Xu H, Hu D, Wang J, Pei K, Sun M, Zou T. Bacterial MazF/MazE toxin-antitoxin suppresses lytic propagation of arbitrium-containing phages. Cell Rep 2022; 41:111752. [PMID: 36476854 DOI: 10.1016/j.celrep.2022.111752] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Temperate phages dynamically switch between lysis and lysogeny in their full life cycle. Some Bacillus-infecting phages utilize a quorum-sensing-like intercellular communication system, the "arbitrium," to mediate lysis-lysogeny decisions. However, whether additional factors participate in the arbitrium signaling pathway remains largely elusive. Here, we find that the arbitrium signal induces the expression of a functionally conserved operon downstream of the arbitrium module in SPbeta-like phages. SPbeta yopM and yopR (as well as phi3T phi3T_93 and phi3T_97) in the operon play roles in suppressing phage lytic propagation and promoting lysogeny, respectively. We further focus on phi3T_93 and demonstrate that it directly binds antitoxin MazE in the host MazF/MazE toxin-antitoxin (TA) module and facilitates the activation of MazF's toxicity, which is required for phage suppression. These findings show events regulated by the arbitrium system and shed light on how the interplay between phages and the host TA module affects phage-host co-survival.
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Affiliation(s)
- Yongqing Cui
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Su
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delei Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Pei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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3
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Tetz V, Tetz G. Novel prokaryotic system employing previously unknown nucleic acids-based receptors. Microb Cell Fact 2022; 21:202. [PMID: 36195904 PMCID: PMC9531389 DOI: 10.1186/s12934-022-01923-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/16/2022] [Indexed: 12/26/2022] Open
Abstract
The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named "TezRs", that form receptor's network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to "forget" preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.
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Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA.
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4
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Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A, Cui Y, Jiang X, Peng S, Li S, Tong Y. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR Genom Bioinform 2022; 4:lqac057. [PMID: 35937545 PMCID: PMC9346568 DOI: 10.1093/nargab/lqac057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.
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Affiliation(s)
- Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Ruohan Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Xiangcheng Xie
- College of Computer, National University of Defense Technology , Changsha 410073, People's Republic of China
| | - Yunjia Hu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
- School of Medicine, Shanghai University , Shanghai 200444, People's Republic of China
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Qiang Sun
- The 964th Hospital , Changchun 130021, People's Republic of China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University , Xi’an 710072, People's Republic of China
| | - Wei Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Shanwei Tong
- Bioinformatics Graduate Program, University of British Columbia , Vancouver BC V6T 1Z4, Canada
- Faculty of Health Sciences, Simon Fraser University , Burnaby , BC V5A 1S6, Canada
| | - Wei Yan
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Mengyao Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Shixiang Zhai
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071, People's Republic of China
| | - Cheng Sun
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Fangyi Wang
- Department of Statistics, the Ohio State University , Columbus, OH 43210, USA
| | - Qi Niu
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph , Guelph , ON N1G 2W1 , Canada
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Shaoliang Peng
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
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5
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Varming AK, Rasmussen KK, Zong Z, Thulstrup PW, Kilstrup M, Lo Leggio L. Flexible linker modulates the binding affinity of the TP901-1 CI phage repressor to DNA. FEBS J 2021; 289:1135-1148. [PMID: 34665941 DOI: 10.1111/febs.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/16/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Temperate bacteriophages can switch between two life cycles following infection of a host bacterium: the lytic or lysogenic life cycle. The choice between these is controlled by a bistable genetic switch. We investigated the genetic switch of the lactococcal temperate bacteriophage, TP901-1, which is controlled by two regulatory proteins, the Clear 1 (CI) repressor and modulator of repression (MOR) antirepressor. CI consists of a DNA-binding N-terminal domain and a C-terminal domain responsible for oligomerization, connected by a flexible interdomain linker. Full-length CI is hexameric, whereas the truncated version CI with 58 C-terminal residues truncated (CIΔ58), missing the second C-terminal subdomain, is dimeric, but binds with the same affinity as full-length CI to the OL operator site, responsible for lytic genes transcription repression. Three variants of CIΔ58 with shorter, longer, and PP substituted linkers were produced and confirmed by circular dichroism spectroscopy and nanodifferential scanning fluorimetry to be well folded. With small-angle X-ray scattering, we delineated the conformational space sampled by the variants and wild-type in solution and found that shortening and lengthening the linker decrease and increase this, respectively, as also substantiated by molecular dynamics and as intended. Isoelectric focusing electrophoresis confirmed that all variants are able to bind to the MOR antirepressor. However, using electrophoretic mobility shift assays, we showed that shortening and lengthening the linker lead to a 94 and 17 times decrease in affinity to OL , respectively. Thus, an appropriate linker length appears to be crucial for appropriate DNA-binding and subsequent TP901-1 genetic switch function.
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Affiliation(s)
| | | | - Zhiyou Zong
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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6
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Hao N, Agnew D, Krishna S, Dodd IB, Shearwin KE. Analysis of Infection Time Courses Shows CII Levels Determine the Frequency of Lysogeny in Phage 186. Pharmaceuticals (Basel) 2021; 14:ph14100998. [PMID: 34681220 PMCID: PMC8538670 DOI: 10.3390/ph14100998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 11/29/2022] Open
Abstract
Engineered phage with properties optimised for the treatment of bacterial infections hold great promise, but require careful characterisation by a number of approaches. Phage–bacteria infection time courses, where populations of bacteriophage and bacteria are mixed and followed over many infection cycles, can be used to deduce properties of phage infection at the individual cell level. Here, we apply this approach to analysis of infection of Escherichia coli by the temperate bacteriophage 186 and explore which properties of the infection process can be reliably inferred. By applying established modelling methods to such data, we extract the frequency at which phage 186 chooses the lysogenic pathway after infection, and show that lysogenisation increases in a graded manner with increased expression of the lysogenic establishment factor CII. The data also suggest that, like phage λ, the rate of lysogeny of phage 186 increases with multiple infections.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (N.H.); (D.A.); (I.B.D.)
- CSIRO Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia
| | - Dylan Agnew
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (N.H.); (D.A.); (I.B.D.)
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India;
| | - Ian B. Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (N.H.); (D.A.); (I.B.D.)
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (N.H.); (D.A.); (I.B.D.)
- Correspondence: ; Tel.: +61-8-83135361
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7
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Pei K, Zhang J, Zou T, Liu Z. AimR Adopts Preexisting Dimer Conformations for Specific Target Recognition in Lysis-Lysogeny Decisions of Bacillus Phage phi3T. Biomolecules 2021; 11:biom11091321. [PMID: 34572534 PMCID: PMC8464984 DOI: 10.3390/biom11091321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 12/04/2022] Open
Abstract
A bacteriophage switches between lytic and lysogenic life cycles. The AimR-AimP-AimX communication system is responsible for phage lysis-lysogeny decisions during the infection of Bacillus subtilis. AimX is a regulator biasing phage lysis, AimR is a transcription factor activating AimX expression, and AimP is an arbitrium peptide that determines phage lysogeny by deactivating AimR. A strain-specific mechanism for the lysis-lysogeny decisions is proposed in SPbeta and phi3T phages. That is, the arbitrium peptide of the SPbeta phage stabilizes the SPbeta AimR (spAimR) dimer, whereas the phi3T-derived peptide disassembles the phi3T AimR (phAimR) dimer into a monomer. Here, we find that phAimR does not undergo dimer-to-monomer conversion upon arbitrium peptide binding. Gel-filtration, static light scattering (SLS) and analytical ultracentrifugation (AUC) results show that phAimR is dimeric regardless of the presence of arbitrium peptide. Small-angle X-ray scattering (SAXS) reveals that the arbitrium peptide binding makes an extended dimeric conformation. Single-molecule fluorescence resonance energy transfer (smFRET) analysis reveals that the phAimR dimer fluctuates among two distinct conformational states, and each preexisting state is selectively recognized by the arbitrium peptide or the target DNA, respectively. Collectively, our biophysical characterization of the phAimR dynamics underlying specific target recognition provides new mechanistic insights into understanding lysis-lysogeny decisions in Bacillus phage phi3T.
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8
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Thomason LC, Schiltz CJ, Court C, Hosford CJ, Adams MC, Chappie JS, Court DL. Bacteriophage λ RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth. Mol Microbiol 2021; 116:1044-1063. [PMID: 34379857 DOI: 10.1111/mmi.14792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
Abstract
The CI and Cro repressors of bacteriophage λ create a bistable switch between lysogenic and lytic growth. In λ lysogens, CI repressor expressed from the PRM promoter blocks expression of the lytic promoters PL and PR to allow stable maintenance of the lysogenic state. When lysogens are induced, CI repressor is inactivated and Cro repressor is expressed from the lytic PR promoter. Cro repressor blocks PRM transcription and CI repressor synthesis to ensure that the lytic state proceeds. RexA and RexB proteins, like CI, are expressed from the PRM promoter in λ lysogens; RexB is also expressed from a second promoter, PLIT , embedded in rexA. Here we show that RexA binds CI repressor and assists the transition from lysogenic to lytic growth, using both intact lysogens and defective prophages with reporter genes under control of the lytic PL and PR promoters. Once lytic growth begins, if the bistable switch does return to the immune state, RexA expression lessens the probability that it will remain there, thus stabilizing the lytic state and activation of the lytic PL and PR promoters. RexB modulates the effect of RexA and may also help establish phage DNA replication as lytic growth ensues.
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Affiliation(s)
- Lynn C Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, 21702.,RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, 14850.,Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Carolyn Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
| | - Christopher J Hosford
- Department of Molecular Medicine, Cornell University, Ithaca, 14850.,New England Biolabs, Inc, Ipswich, MA, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, 14850
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, 14850
| | - Donald L Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
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9
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Silveira CB, Luque A, Rohwer F. The landscape of lysogeny across microbial community density, diversity and energetics. Environ Microbiol 2021; 23:4098-4111. [PMID: 34121301 DOI: 10.1111/1462-2920.15640] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022]
Abstract
Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low-density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive effects of coinfections, diversity and host energic status yield a bimodal distribution of lysogeny as a function of microbial densities. At high cell densities (above 106 cells ml-1 or g-1 ) and low diversity, coinfections by two or more phages are frequent and excess energy availability stimulates inefficient metabolism. Both mechanisms favour phage integration and characterize the Piggyback-the-Winner dynamic. At low densities (below 105 cells ml-1 or g-1 ), starvation represses lytic genes and extends the time window for lysogenic commitment, resulting in a higher frequency of coinfections that cause integration. This pattern follows the predictions of the refugium hypothesis. At intermediary densities (between 105 and 106 cells ml-1 or g-1 ), encounter rates and efficient energy metabolism favour lysis. This may involve Kill-the-Winner lytic dynamics and induction. Based on these three regimes, we propose a framework wherein phage integration occurs more frequently at both ends of the host density gradient, with distinct underlying molecular mechanisms (coinfections and host metabolism) dominating at each extreme.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33143, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
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10
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Cortes MG, Lin Y, Zeng L, Balázsi G. From Bench to Keyboard and Back Again: A Brief History of Lambda Phage Modeling. Annu Rev Biophys 2021; 50:117-134. [PMID: 33957052 DOI: 10.1146/annurev-biophys-082020-063558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellular decision making is the process whereby cells choose one developmental pathway from multiple possible ones, either spontaneously or due to environmental stimuli. Examples in various cell types suggest an almost inexhaustible plethora of underlying molecular mechanisms. In general, cellular decisions rely on the gene regulatory network, which integrates external signals to drive cell fate choice. The search for general principles of such a process benefits from appropriate biological model systems that reveal how and why certain gene regulatory mechanisms drive specific cellular decisions according to ecological context and evolutionary outcomes. In this article, we review the historical and ongoing development of the phage lambda lysis-lysogeny decision as a model system to investigate all aspects of cellular decision making. The unique generality, simplicity, and richness of phage lambda decision making render it a constant source ofmathematical modeling-aided inspiration across all of biology. We discuss the origins and progress of quantitative phage lambda modeling from the 1950s until today, as well as its possible future directions. We provide examples of how modeling enabled methods and theory development, leading to new biological insights by revealing gaps in the theory and pinpointing areas requiring further experimental investigation. Overall, we highlight the utility of theoretical approaches both as predictive tools, to forecast the outcome of novel experiments, and as explanatory tools, to elucidate the natural processes underlying experimental data.
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Affiliation(s)
- Michael G Cortes
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA; .,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Yiruo Lin
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA; .,Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA; .,Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
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11
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Murchland IM, Ahlgren-Berg A, Pietsch JMJ, Isabel A, Dodd IB, Shearwin KE. Instability of CII is needed for efficient switching between lytic and lysogenic development in bacteriophage 186. Nucleic Acids Res 2020; 48:12030-12041. [PMID: 33211866 PMCID: PMC7708051 DOI: 10.1093/nar/gkaa1065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 11/13/2022] Open
Abstract
The CII protein of temperate coliphage 186, like the unrelated CII protein of phage λ, is a transcriptional activator that primes expression of the CI immunity repressor and is critical for efficient establishment of lysogeny. 186-CII is also highly unstable, and we show that in vivo degradation is mediated by both FtsH and RseP. We investigated the role of CII instability by constructing a 186 phage encoding a protease resistant CII. The stabilised-CII phage was defective in the lysis-lysogeny decision: choosing lysogeny with close to 100% frequency after infection, and forming prophages that were defective in entering lytic development after UV treatment. While lysogenic CI concentration was unaffected by CII stabilisation, lysogenic transcription and CI expression was elevated after UV. A stochastic model of the 186 network after infection indicated that an unstable CII allowed a rapid increase in CI expression without a large overshoot of the lysogenic level, suggesting that instability enables a decisive commitment to lysogeny with a rapid attainment of sensitivity to prophage induction.
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Affiliation(s)
- Iain M Murchland
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alexandra Ahlgren-Berg
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Julian M J Pietsch
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alejandra Isabel
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Keith E Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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12
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Rijal K, Prasad A, Das D. Protein hourglass: Exact first passage time distributions for protein thresholds. Phys Rev E 2020; 102:052413. [PMID: 33327114 DOI: 10.1103/physreve.102.052413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Protein thresholds have been shown to act as an ancient timekeeping device, such as in the time to lysis of Escherichia coli infected with bacteriophage λ. The time taken for protein levels to reach a particular threshold for the first time is defined as the first passage time (FPT) of the protein synthesis system, which is a stochastic quantity. The first few moments of the distribution of first passage times were known earlier, but an analytical expression for the full distribution was not available. In this work, we derive an analytical expression for the first passage times for a long-lived protein. This expression allows us to calculate the full distribution not only for cases of no self-regulation, but also for both positive and negative self-regulation of the threshold protein. We show that the shape of the distribution matches previous experimental data on λ-phage lysis time distributions. We also provide analytical expressions for the FPT distribution with non-zero degradation in Laplace space. Furthermore, we study the noise in the precision of the first passage times described by coefficient of variation (CV) of the distribution as a function of the protein threshold value. We show that under conditions of positive self-regulation, the CV declines monotonically with increasing protein threshold, while under conditions of linear negative self-regulation, there is an optimal protein threshold that minimizes the noise in the first passage times.
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Affiliation(s)
- Krishna Rijal
- Physics Department, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ashok Prasad
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Dibyendu Das
- Physics Department, Indian Institute of Technology Bombay, Mumbai 400076, India
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13
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Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles. mSystems 2020; 5:5/5/e00353-20. [PMID: 32934113 PMCID: PMC7498681 DOI: 10.1128/msystems.00353-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities. Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections—a well-understood molecular mechanism of lysogenization—increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates). IMPORTANCE The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.
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14
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Trinh JT, Shao Q, Guan J, Zeng L. Emerging heterogeneous compartments by viruses in single bacterial cells. Nat Commun 2020; 11:3813. [PMID: 32732913 PMCID: PMC7393140 DOI: 10.1038/s41467-020-17515-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/06/2020] [Indexed: 11/17/2022] Open
Abstract
Spatial organization of biological processes allows for variability in molecular outcomes and coordinated development. Here, we investigate how organization underpins phage lambda development and decision-making by characterizing viral components and processes in subcellular space. We use live-cell and in situ fluorescence imaging at the single-molecule level to examine lambda DNA replication, transcription, virion assembly, and resource recruitment in single-cell infections, uniting key processes of the infection cycle into a coherent model of phage development encompassing space and time. We find that different viral DNAs establish separate subcellular compartments within cells, which sustains heterogeneous viral development in single cells. These individual phage compartments are physically separated by the E. coli nucleoid. Our results provide mechanistic details describing how separate viruses develop heterogeneously to resemble single-cell phenotypes. Here, the authors apply live-cell and in situ fluorescence imaging at the single-molecule level to examine lambda DNA replication in single cells, finding that individual phage DNAs sequester host factors to their own vicinity and confine their replicated DNAs into separate compartments, suggesting that phage decision-making transcripts are spatially organized in separate compartments to allow distinct subcellular decisions to develop.
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Affiliation(s)
- Jimmy T Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.,Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.,Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Jingwen Guan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.,Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA.,Molecular and Environmental Plant Science, Texas A&M University, College Station, TX, 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA. .,Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA. .,Molecular and Environmental Plant Science, Texas A&M University, College Station, TX, 77843, USA.
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15
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Li G, Cortez MH, Dushoff J, Weitz JS. When to be temperate: on the fitness benefits of lysis vs. lysogeny. Virus Evol 2020; 6:veaa042. [PMID: 36204422 PMCID: PMC9532926 DOI: 10.1093/ve/veaa042] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Bacterial viruses, that is ‘bacteriophage’ or ‘phage’, can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e. ‘temperate’ bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, that is the ‘prophage’, can induce and restart the lytic pathway. Here, we explore the relationship among infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage–bacteria dynamics spanning both explicit and implicit representations of intra-cellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses—notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.
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Affiliation(s)
- Guanlin Li
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael H Cortez
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON L8S 4L8, Canada
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Joshua S Weitz
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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16
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Cortes MG, Krog J, Balázsi G. Optimality of the spontaneous prophage induction rate. J Theor Biol 2019; 483:110005. [PMID: 31525321 DOI: 10.1016/j.jtbi.2019.110005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/30/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
Lysogens are bacterial cells that have survived after genomically incorporating the DNA of temperate bacteriophages infecting them. If an infection results in lysogeny, the lysogen continues to grow and divide normally, seemingly unaffected by the integrated viral genome known as a prophage. However, the prophage can still have an impact on the host's phenotype and overall fitness in certain environments. Additionally, the prophage within the lysogen can activate the lytic pathway via spontaneous prophage induction (SPI), killing the lysogen and releasing new progeny phages. These new phages can then lyse or lysogenize other susceptible nonlysogens, thereby impacting the competition between lysogens and nonlysogens. In a scenario with differing growth rates, it is not clear whether SPI would be beneficial or detrimental to the lysogens since it kills the host cell but also attacks nonlysogenic competitors, either lysing or lysogenizing them. Here we study the evolutionary dynamics of a mixture of lysogens and nonlysogens and derive general conditions on SPI rates for lysogens to displace nonlysogens. We show that there exists an optimal SPI rate for bacteriophage λ and explain why it is so low. We also investigate the impact of stochasticity and conclude that even at low cell numbers SPI can still provide an advantage to the lysogens. These results corroborate recent experimental studies showing that lower SPI rates are advantageous for phage-phage competition, and establish theoretical bounds on the SPI rate in terms of ecological and environmental variables associated with lysogens having a competitive advantage over their nonlysogenic counterparts.
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Affiliation(s)
- Michael G Cortes
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan Krog
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
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17
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Gallego Del Sol F, Penadés JR, Marina A. Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems. Mol Cell 2019; 74:59-72.e3. [PMID: 30745087 PMCID: PMC6458997 DOI: 10.1016/j.molcel.2019.01.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 10/28/2022]
Abstract
Bacillus phages use a communication system, termed "arbitrium," to coordinate lysis-lysogeny decisions. Arbitrium communication is mediated by the production and secretion of a hexapeptide (AimP) during lytic cycle. Once internalized, AimP reduces the expression of the negative regulator of lysogeny, AimX, by binding to the transcription factor, AimR, promoting lysogeny. We have elucidated the crystal structures of AimR from the Bacillus subtilis SPbeta phage in its apo form, bound to its DNA operator and in complex with AimP. AimR presents intrinsic plasticity, sharing structural features with the RRNPP quorum-sensing family. Remarkably, AimR binds to an unusual operator with a long spacer that interacts nonspecifically with the receptor TPR domain, while the HTH domain canonically recognizes two inverted repeats. AimP stabilizes a compact conformation of AimR that approximates the DNA-recognition helices, preventing AimR binding to the aimX promoter region. Our results establish the molecular basis of the arbitrium communication system.
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Affiliation(s)
- Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
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18
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Abstract
Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage "golden era," key recent developments, including advances in phage genomics, microscopy, and the discovery of the CRISPR-Cas anti-phage defense system, have sparked a renaissance in phage research in the past decade. This review highlights recently discovered unexpected complexities in phage biology, describes a new arsenal of phage genes that help them overcome bacterial defenses, and discusses advances toward documentation of the phage biodiversity on a global scale.
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Affiliation(s)
- Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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19
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Arbel-Goren R, Di Patti F, Fanelli D, Stavans J. Noise⁻Seeded Developmental Pattern Formation in Filamentous Cyanobacteria. Life (Basel) 2018; 8:life8040058. [PMID: 30423937 PMCID: PMC6316479 DOI: 10.3390/life8040058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/24/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Under nitrogen-poor conditions, multicellular cyanobacteria such as Anabaena sp. PCC 7120 undergo a process of differentiation, forming nearly regular, developmental patterns of individual nitrogen-fixing cells, called heterocysts, interspersed between intervals of vegetative cells that carry out photosynthesis. Developmental pattern formation is mediated by morphogen species that can act as activators and inhibitors, some of which can diffuse along filaments. We survey the limitations of the classical, deterministic Turing mechanism that has been often invoked to explain pattern formation in these systems, and then, focusing on a simpler system governed by birth-death processes, we illustrate pedagogically a recently proposed paradigm that provides a much more robust description of pattern formation: stochastic Turing patterns. We emphasize the essential role that cell-to-cell differences in molecular numbers—caused by inevitable fluctuations in gene expression—play, the so called demographic noise, in seeding the formation of stochastic Turing patterns over a much larger region of parameter space, compared to their deterministic counterparts.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Francesca Di Patti
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Dip. di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Firenze, Italy.
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Duccio Fanelli
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel.
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20
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Dou C, Xiong J, Gu Y, Yin K, Wang J, Hu Y, Zhou D, Fu X, Qi S, Zhu X, Yao S, Xu H, Nie C, Liang Z, Yang S, Wei Y, Cheng W. Structural and functional insights into the regulation of the lysis-lysogeny decision in viral communities. Nat Microbiol 2018; 3:1285-1294. [PMID: 30323253 DOI: 10.1038/s41564-018-0259-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/31/2018] [Indexed: 02/05/2023]
Abstract
Communication is vital for all organisms including microorganisms, which is clearly demonstrated by the bacterial quorum-sensing system. However, the molecular mechanisms underlying communication among viruses (phages) via the quorum-sensing-like 'arbitrium' system remain unclear. Viral or host densities are known to be related to an increased prevalence of lysogeny; however, how the switch from the lytic to the lysogenic pathway occurs is unknown. Thus, we sought to reveal mechanisms of communication among viruses and determine the lysogenic dynamics involved. Structural and functional analyses of the phage-derived SAIRGA and GMPRGA peptides and their corresponding receptors, phAimR and spAimR, indicated that SAIRGA directs the lysis-lysogeny decision of phi3T by modulating conformational changes in phAimR, whereas GMPRGA regulates the lysis-lysogeny pathway by stabilizing spAimR in the dimeric state. Although temperate viruses are thought to share a similar lytic-lysogenic cycle switch model, our study suggests the existence of alternative strain-specific mechanisms that regulate the lysis-lysogeny decision. Collectively, these findings provide insights into the molecular mechanisms underlying communication among viruses, offering theoretical applications for the treatment of infectious viral diseases.
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Affiliation(s)
- Chao Dou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jie Xiong
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yijun Gu
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai, China
| | - Kun Yin
- Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Disease, Jining, China
| | - Jinjing Wang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuehong Hu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Dan Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xianghui Fu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shiqian Qi
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xiaofeng Zhu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shaohua Yao
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Heng Xu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Chunlai Nie
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Zongan Liang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shengyong Yang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuquan Wei
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
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21
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Shao Q, Trinh JT, Zeng L. High-resolution studies of lysis-lysogeny decision-making in bacteriophage lambda. J Biol Chem 2018; 294:3343-3349. [PMID: 30242122 DOI: 10.1074/jbc.tm118.003209] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cellular decision-making guides complex development such as cell differentiation and disease progression. Much of our knowledge about decision-making is derived from simple models, such as bacteriophage lambda infection, in which lambda chooses between the vegetative lytic fate and the dormant lysogenic fate. This paradigmatic system is broadly understood but lacking mechanistic details, partly due to limited resolution of past studies. Here, we discuss how modern technologies have enabled high-resolution examination of lambda decision-making to provide new insights and exciting possibilities in studying this classical system. The advent of techniques for labeling specific DNA, RNA, and proteins in cells allows for molecular-level characterization of events in lambda development. These capabilities yield both new answers and new questions regarding how the isolated lambda genetic circuit acts, what biological events transpire among phages in their natural context, and how the synergy of simple phage macromolecules brings about complex behaviors.
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Affiliation(s)
- Qiuyan Shao
- From the Department of Biochemistry and Biophysics and.,the Center for Phage Technology, Texas A&M University, College Station, Texas 77843
| | - Jimmy T Trinh
- From the Department of Biochemistry and Biophysics and.,the Center for Phage Technology, Texas A&M University, College Station, Texas 77843
| | - Lanying Zeng
- From the Department of Biochemistry and Biophysics and .,the Center for Phage Technology, Texas A&M University, College Station, Texas 77843
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22
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Structural basis of the arbitrium peptide–AimR communication system in the phage lysis–lysogeny decision. Nat Microbiol 2018; 3:1266-1273. [DOI: 10.1038/s41564-018-0239-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 08/06/2018] [Indexed: 11/08/2022]
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23
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Golding I. Infection by bacteriophage lambda: an evolving paradigm for cellular individuality. Curr Opin Microbiol 2018; 43:9-13. [PMID: 29107897 PMCID: PMC5934347 DOI: 10.1016/j.mib.2017.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022]
Abstract
Since the earliest days of molecular biology, bacteriophage lambda has served to illuminate cellular function. Among its many roles, lambda infection is a paradigm for phenotypic heterogeneity among genetically identical cells. Early studies attributed this cellular individuality to random biochemical fluctuations, or 'noise'. More recently, however, attention has turned to the role played by deterministic hidden variables in driving single-cell behavior. Here, I briefly describe how studies in lambda are driving the shift in our understanding of cellular heterogeneity, allowing us to better appreciate the precision at which cells function.
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Affiliation(s)
- Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
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24
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Ralph M, Bednarchik M, Tomer E, Rafael D, Zargarian S, Gerlic M, Kobiler O. Promoting Simultaneous Onset of Viral Gene Expression Among Cells Infected with Herpes Simplex Virus-1. Front Microbiol 2017; 8:2152. [PMID: 29163436 PMCID: PMC5671993 DOI: 10.3389/fmicb.2017.02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/20/2017] [Indexed: 11/30/2022] Open
Abstract
Synchronous viral infection facilitates the study of viral gene expression, viral host interactions, and viral replication processes. However, the protocols for achieving synchronous infections were hardly ever tested in proper temporal resolution at the single-cell level. We set up a fluorescence-based, time lapse microscopy assay to study sources of variability in the timing of gene expression during herpes simplex virus-1 (HSV-1) infection. We found that with the common protocol, the onset of gene expression within different cells can vary by more than 3 h. We showed that simultaneous viral genome entry to the nucleus can be achieved with a derivative of the previously characterized temperature sensitive mutant tsB7, however, this did not improve gene expression synchrony. We found that elevating the temperature in which the infection is done and increasing the multiplicity of infection (MOI) significantly promoted simultaneous onset of viral gene expression among infected cells. Further, elevated temperature result in a decrease in the coefficient of variation (a standardized measure of dispersion) of viral replication compartments (RCs) sizes among cells as well as a slight increment of viral late gene expression synchrony. We conclude that simultaneous viral gene expression can be improved by simple modifications to the infection process and may reduce the effect of single-cell variability on population-based assays.
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Affiliation(s)
| | | | | | | | | | | | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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25
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Abstract
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates). These circuits offer the opportunity for a new class of antivirals that could lead to intrinsic combination-antiviral therapies within a single molecule-evolutionary escape from such circuit-disrupting antivirals would require simultaneous evolution of both the viral cis regulatory element (e.g., the DNA-binding site) and the trans element (e.g., the transcription factor) in order for the virus to recapitulate a circuit that would not be disrupted. We review the architectures of these fate-regulating master circuits in HIV-1 and the human herpesvirus cytomegalovirus along with potential circuit-disruption strategies that may ultimately enable escape-resistant antiviral therapies.
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Affiliation(s)
- Anand Pai
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158;
| | - Leor S Weinberger
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158; .,Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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Trinh JT, Székely T, Shao Q, Balázsi G, Zeng L. Cell fate decisions emerge as phages cooperate or compete inside their host. Nat Commun 2017; 8:14341. [PMID: 28165024 PMCID: PMC5303824 DOI: 10.1038/ncomms14341] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
The system of the bacterium Escherichia coli and its virus, bacteriophage lambda, is paradigmatic for gene regulation in cell-fate development, yet insight about its mechanisms and complexities are limited due to insufficient resolution of study. Here we develop a 4-colour fluorescence reporter system at the single-virus level, combined with computational models to unravel both the interactions between phages and how individual phages determine cellular fates. We find that phages cooperate during lysogenization, compete among each other during lysis, and that confusion between the two pathways occasionally occurs. Additionally, we observe that phage DNAs have fluctuating cellular arrival times and vie for resources to replicate, enabling the interplay during different developmental paths, where each phage genome may make an individual decision. These varied strategies could separate the selection for replication-optimizing beneficial mutations during lysis from sequence diversification during lysogeny, allowing rapid adaptation of phage populations for various environments.
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Affiliation(s)
- Jimmy T. Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Tamás Székely
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
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Munro PD, Ackers GK, Shearwin KE. Aspects of protein-DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ. Biophys Rev 2016; 8:331-345. [PMID: 28510022 DOI: 10.1007/s12551-016-0231-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/04/2016] [Indexed: 12/20/2022] Open
Abstract
Protein-DNA interactions are central to the control of gene expression across all forms of life. The development of approaches to rigorously model such interactions has often been hindered both by a lack of quantitative binding data and by the difficulty in accounting for parameters relevant to the intracellular situation, such as DNA looping and thermodynamic non-ideality. Here, we review these considerations by developing a thermodynamically based mathematical model that attempts to simulate the functioning of an Escherichia coli expression system incorporating two of the best characterised prokaryotic DNA binding proteins, Lac repressor and lambda CI repressor. The key aim was to reproduce experimentally observed reporter gene activities arising from the expression of either wild-type CI repressor or one of three positive-control CI mutants. The model considers the role of several potentially important, but sometimes neglected, biochemical features, including DNA looping, macromolecular crowding and non-specific binding, and allowed us to obtain association constants for the binding of CI and its variants to a specific operator sequence.
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Affiliation(s)
- Peter D Munro
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,, 2/159 Hardgrave Rd., West End, Brisbane, QLD 4101, Australia.
| | - Gary K Ackers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Keith E Shearwin
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
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