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Dahan Y, Wingreen NS, Meir Y. The value of information gathering in phage-bacteria warfare. PNAS NEXUS 2024; 3:pgad431. [PMID: 38196923 PMCID: PMC10776245 DOI: 10.1093/pnasnexus/pgad431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Phages-viruses that infect bacteria-have evolved over billions of years to overcome bacterial defenses. Temperate phage, upon infection, can "choose" between two pathways: lysis-in which the phage create multiple new phage particles, which are then liberated by cell lysis, and lysogeny-where the phage's genetic material is added to the bacterial DNA and transmitted to the bacterial progeny. It was recently discovered that some phages can read information from the environment related to the density of bacteria or the number of nearby infection attempts. Such information may help phage make the right choice between the two pathways. Here, we develop a theoretical model that allows an infecting phage to change its strategy (i.e. the ratio of lysis to lysogeny) depending on an outside signal, and we find the optimal strategy that maximizes phage proliferation. While phages that exploit extra information naturally win in competition against phages with a fixed strategy, there may be costs to information, e.g. as the necessary extra genes may affect the growth rate of a lysogen or the burst size of new phage for the lysis pathway. Surprisingly, even when phages pay a large price for information, they can still maintain an advantage over phages that lack this information, indicating the high benefit of intelligence gathering in phage-bacteria warfare.
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Affiliation(s)
- Yuval Dahan
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yigal Meir
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
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2
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Floccari VA, Dragoš A. Host control by SPβ phage regulatory switch as potential manipulation strategy. Curr Opin Microbiol 2023; 71:102260. [PMID: 36580707 DOI: 10.1016/j.mib.2022.102260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022]
Abstract
The interaction between temperate phages and their bacterial hosts has always been one of the most controversial in nature. As genetic parasites, phages need their hosts to propagate, while the host may take advantage of the genetic arsenal carried in the phage genome. This intriguing host-parasite interplay with an evident mutualistic implication could be challenged by recent discoveries of alternative phage lifestyles and regulatory systems that seem to support a manipulative strategy pursued by the phage. Through two fascinating novel mechanisms concerning the active lysogeny and a phage-encoded quorum sensing system, referred as 'Arbitrium', employed by SPβ-like phages of Bacilli, we propose the parasite manipulation as ecological relationship between certain temperate phages and bacteria.
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Affiliation(s)
- Valentina A Floccari
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia.
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3
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Zeynali kelishomi F, Khanjani S, Fardsanei F, Saghi Sarabi H, Nikkhahi F, Dehghani B. Bacteriophages of Mycobacterium tuberculosis, their diversity, and potential therapeutic uses: a review. BMC Infect Dis 2022; 22:957. [PMID: 36550444 PMCID: PMC9773572 DOI: 10.1186/s12879-022-07944-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) is a highly infectious disease and worldwide health problem. Based on the WHO TB report, 9 million active TB cases are emerging, leading to 2 million deaths each year. The recent emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) strains emphasizes the necessity to improve novel therapeutic plans. Among the various developing antibacterial approaches, phage therapy is thought to be a precise hopeful resolution. Mycobacteriophages are viruses that infect bacteria such as Mycobacterium spp., containing the M. tuberculosis complex. Phages and phage-derived proteins can act as promising antimicrobial agents. Also, phage cocktails can broaden the spectrum of lysis activity against bacteria. Recent researches have also shown the effective combination of antibiotics and phages to defeat the infective bacteria. There are limitations and concerns about phage therapy. For example, human immune response to phage therapy, transferring antibiotic resistance genes, emerging resistance to phages, and safety issues. So, in the present study, we introduced mycobacteriophages, their use as therapeutic agents, and their advantages and limitations as therapeutic applications.
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Affiliation(s)
- Fatemeh Zeynali kelishomi
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Susan Khanjani
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Fatemeh Fardsanei
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hediyeh Saghi Sarabi
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farhad Nikkhahi
- grid.412606.70000 0004 0405 433XMedical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Behzad Dehghani
- grid.412571.40000 0000 8819 4698Department of Bacteriology-Virology, Shiraz University of Medical Sciences, Shiraz, Iran
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Butala M, Dragoš A. Unique relationships between phages and endospore-forming hosts. Trends Microbiol 2022; 31:498-510. [PMID: 36535834 DOI: 10.1016/j.tim.2022.11.009] [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: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
As part of their survival strategy under harsh environmental conditions, endospore-forming bacteria can trigger a sporulation developmental program. Although the regulatory cascades that precisely control the transformation of vegetative bacteria into mother cells and resilient spores have been described in detail, less is known about how bacteriophages that prey on endospore-formers exploit sporulation. Herein, we argue that phages infecting these bacteria have evolved several specific molecular mechanisms, not yet known in other bacteria, that manifest from the phage-driven alliance to negative effects on the host. We anticipate that the relationships between phages and endospore-formers outlined here will inspire studies on phage ecology and evolution, and could facilitate important advances in the development of phage therapies against pathogenic spore-formers.
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Affiliation(s)
- Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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5
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Mechanisms of interactions between bacteria and bacteriophage mediate by quorum sensing systems. Appl Microbiol Biotechnol 2022; 106:2299-2310. [PMID: 35312824 DOI: 10.1007/s00253-022-11866-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/02/2022]
Abstract
Bacteriophage (phage) and their host bacteria coevolve with each other over time. Quorum sensing (QS) systems play an important role in the interaction between bacteria and phage. In this review paper, we summarized the function of QS systems in bacterial biofilm formation, phage adsorption, lysis-lysogeny conversion of phage, coevolution of bacteria and phage, and information exchanges in phage, which may provide reference to future research on alternative control strategies for antibiotic-resistant and biofilm-forming pathogens by phage. KEY POINTS: • Quorum sensing (QS) systems influence bacteria-phage interaction. • QS systems cause phage adsorption and evolution and lysis-lysogeny conversion. • QS systems participate in biofilm formation and co-evolution with phage of bacteria.
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Boldin B. The importance of ecological dynamics in evolutionary processes: a host-bacteriophage model revisited. J Theor Biol 2022; 539:111057. [PMID: 35181286 DOI: 10.1016/j.jtbi.2022.111057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
A recent study of adaptive dynamics of lysis propensity in temperate phages suggested that full lysogeny emerges as the outcome of bacteriophage evolution in a simple host-phage system. The conclusion is based on the premise that mutant strains necessarily appear in equilibrium host-phage environments. Revisiting the model, we show that the ecological system exhibits richer asymptotic dynamics and that, in a certain parameter regime, evolution may in fact drive lysis propensity towards an evolutionary singularity in which a non-zero proportion of phages initiate infection in a lytic cycle. These singularities act as points of evolutionary diversification, leading to periodic coexistence of two distinct phage strains on the evolutionary time-scale. One of the two strains in the dimorphic evolutionary singularity is fully lysogenic (in the sense that cell infection always leads to lysogeny), while the other is partially lytic. Our study thus highlights the importance of ecological interactions as a driver of evolution.
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Affiliation(s)
- Barbara Boldin
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia.
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Shivam S, Li G, Lucia-Sanz A, Weitz JS. OUP accepted manuscript. Virus Evol 2022; 8:veac037. [PMID: 35615104 PMCID: PMC9126285 DOI: 10.1093/ve/veac037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/14/2022] [Accepted: 04/19/2022] [Indexed: 11/14/2022] Open
Abstract
Temperate phage can initiate lysis or lysogeny after infecting a bacterial host. The genetic switch between lysis and lysogeny is mediated by phage regulatory genes as well as host and environmental factors. Recently, a new class of decision switches was identified in phage of the SPbeta group, mediated by the extracellular release of small, phage-encoded peptides termed arbitrium. Arbitrium peptides can be taken up by bacteria prior to infection, modulating the decision switch in the event of a subsequent phage infection. Increasing the concentration of arbitrium increases the chance that a phage infection will lead to lysogeny, rather than lysis. Although prior work has centered on the molecular mechanisms of arbitrium-induced switching, here we focus on how selective pressures impact the benefits of plasticity in switching responses. In this work, we examine the possible advantages of near-term adaptation of communication-based decision switches used by the SPbeta-like group. We combine a nonlinear population model with a control-theoretic approach to evaluate the relationship between a putative phage reaction norm (i.e. the probability of lysogeny as a function of arbitrium) and the extent of phage reproduction at a near-term time horizon. We measure phage reproduction in terms of a cellular-level metric previously shown to enable comparisons of near-term phage fitness across a continuum from lysis to latency. We show the adaptive potential of communication-based lysis–lysogeny responses and find that optimal switching between lysis and lysogeny increases the near-term phage reproduction compared to fixed responses, further supporting both molecular- and model-based analyses of the putative benefits of this class of decision switches. We further find that plastic responses are robust to the inclusion of cellular-level stochasticity, variation in life history traits, and variation in resource availability. These findings provide further support to explore the long-term evolution of plastic decision systems mediated by extracellular decision-signaling molecules and the feedback between phage reaction norms and ecological context.
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Affiliation(s)
| | - Guanlin Li
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Adriana Lucia-Sanz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Bruce JB, Lion S, Buckling A, Westra ER, Gandon S. Regulation of prophage induction and lysogenization by phage communication systems. Curr Biol 2021; 31:5046-5051.e7. [PMID: 34562385 PMCID: PMC8612742 DOI: 10.1016/j.cub.2021.08.073] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/20/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022]
Abstract
Many viruses cause both lytic infections, where they release viral particles, and dormant infections, where they await future opportunities to reactivate.1 The benefits of each transmission mode depend on the density of susceptible hosts in the environment.2-4 Some viruses infecting bacteria use molecular signaling to respond plastically to changes in host availability.5 These viruses produce a signal during lytic infection and regulate, based on the signal concentration in the environment, the probability with which they switch to causing dormant infections.5,6 We present an analytical framework to examine the adaptive significance of plasticity in viral life-history traits in fluctuating environments. Our model generalizes and extends previous theory7 and predicts that host density fluctuations should select for plasticity in entering lysogeny as well as virus reactivation once signal concentrations decline. Using Bacillus subtilis and its phage phi3T, we experimentally confirm the prediction that phages use signal to make informed decisions over prophage induction. We also demonstrate that lysogens produce signaling molecules and that signal is degraded by hosts in a density-dependent manner. Declining signal concentrations therefore potentially indicate the presence of uninfected hosts and trigger prophage induction. Finally, we find that conflict over the responses of lysogenization and reactivation to signal is resolved through the evolution of different response thresholds for each trait. Collectively, these findings deepen our understanding of the ways viruses use molecular communication to regulate their infection strategies, which can be leveraged to manipulate host and phage population dynamics in natural environments.
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Affiliation(s)
- John B Bruce
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Exeter, UK.
| | - Sébastien Lion
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Exeter, UK
| | - Edze R Westra
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Exeter, UK.
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
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