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Hvid U, Mitarai N. Competitive advantages of T-even phage lysis inhibition in response to secondary infection. PLoS Comput Biol 2024; 20:e1012242. [PMID: 38976747 PMCID: PMC11257392 DOI: 10.1371/journal.pcbi.1012242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/18/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
T-even bacteriophages are known to employ lysis inhibition (LIN), where the lysis of an infected host is delayed in response to secondary adsorptions. Upon the eventual burst of the host, significantly more phage progenies are released. Here, we analysed the competitive advantage of LIN using a mathematical model. In batch culture, LIN provides a bigger phage yield at the end of the growth where all the hosts are infected due to an exceeding number of phage particles and, in addition, gives a competitive advantage against LIN mutants with rapid lysis by letting them adsorb to already infected hosts in the LIN state. By simulating plaque formation in a spatially structured environment, we show that, while LIN phages will produce a smaller zone of clearance, the area over which the phages spread is actually comparable to those without LIN. The analysis suggests that LIN induced by secondary adsorption is favourable in terms of competition, both in spatially homogeneous and inhomogeneous environments.
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Affiliation(s)
- Ulrik Hvid
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Bacteriophage self-counting in the presence of viral replication. Proc Natl Acad Sci U S A 2021; 118:2104163118. [PMID: 34916284 DOI: 10.1073/pnas.2104163118] [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] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases because of replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that instead of hindering lambda's decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wild-type phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision-lysis upon single-phage infection and lysogeny at higher MOI.
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3
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Smith MW, Herfort L, Rivers AR, Simon HM. Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary. Front Microbiol 2019; 10:2475. [PMID: 31749780 PMCID: PMC6848030 DOI: 10.3389/fmicb.2019.02475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
In fast-flowing, river-dominated estuaries, “hotspots” of microbial biogeochemical cycling can be found within areas of extended water retention. Lateral bays located off of the North and South channels of the Columbia River estuary are proposed to be such hotspots. Previous metagenomic studies on water samples indicated that these regions function both as sources and sinks of biogenic particles, with potential to impact organic matter fluxes in the estuary. To extend this work, we analyzed 11 sediment metagenomes from three disparate bays: the freshwater Cathlamet Bay, and the brackish Youngs Bay and more saline Baker Bay located nearer the mouth to the south and north of the main channel, respectively. Samples were collected from upper layers of sediments in August of 2011 and 2013 for DNA extraction and metagenome sequencing. All metagenomes were dominated by bacterial sequences, although diatom sequences as high as 26% of the total annotated sequences were observed in the higher salinity samples. Unsupervised 2D hierarchical clustering analysis resulted in the eleven metagenome samples clustered into four groups by microbial taxonomic composition, with Bacteroides, diatom, and phage levels driving most of the grouping. Results of functional gene clustering further indicated that diatom bloom degradation stage (early vs. late) was an important factor. While the Flavobacteriia and Cytophagia classes were well represented in metagenomes containing abundant diatoms, taxa from the Bacteroidia class, along with certain members of the Sphingobacteriia class, were particularly abundant in metagenomes representing later stages of diatom decomposition. In contrast, the sediment metagenomes with low relative abundance of diatom and Bacteroidetes sequences appeared to have a metabolic potential biased toward microbial growth under nutrient limitation. While differences in water salinity clearly also influenced the microbial community composition and metabolic potential, our results highlight a central role for allochthonous labile organic matter (i.e., diatom detritus), in shaping bacterial taxonomic and functional properties in the Columbia River estuary lateral bay sediments. These results suggest that in fast-flowing, river-dominated estuaries, sediment microbial communities in areas of extended water retention, such as the lateral bays, may contribute disproportionately to estuarine organic matter degradation and recycling.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States
| | - Lydie Herfort
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, United States
| | - Adam R Rivers
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Holly M Simon
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, United States
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4
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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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5
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Sinha V, Goyal A, Svenningsen SL, Semsey S, Krishna S. In silico Evolution of Lysis-Lysogeny Strategies Reproduces Observed Lysogeny Propensities in Temperate Bacteriophages. Front Microbiol 2017; 8:1386. [PMID: 28798729 PMCID: PMC5526970 DOI: 10.3389/fmicb.2017.01386] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/10/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages play key roles as shapers of ecosystems and drivers of bacterial evolution. Temperate phages can choose between (i) lysis: exploiting their bacterial hosts by producing multiple phage particles and releasing them by lysing the host cell, and (ii) lysogeny: establishing a potentially mutually beneficial relationship with the host by integrating their chromosome into the host cell's genome. Temperate phages exhibit lysogeny propensities in the curiously narrow range of 5–15%. For some temperate phages, the propensity is further regulated by the multiplicity of infection, such that single infections go predominantly lytic while multiple infections go predominantly lysogenic. We ask whether these observations can be explained by selection pressures in environments where multiple phage variants compete for the same host. Our models of pairwise competition, between phage variants that differ only in their propensity to lysogenize, predict the optimal lysogeny propensity to fall within the experimentally observed range. This prediction is robust to large variation in parameters such as the phage infection rate, burst size, decision rate, as well as bacterial growth rate, and initial phage to bacteria ratio. When we compete phage variants whose lysogeny strategies are allowed to depend upon multiplicity of infection, we find that the optimal strategy is one which switches from full lysis for single infections to full lysogeny for multiple infections. Previous attempts to explain lysogeny propensity have argued for bet-hedging that optimizes the response to fluctuating environmental conditions. Our results suggest that there is an additional selection pressure for lysogeny propensity within phage populations infecting a bacterial host, independent of environmental conditions.
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Affiliation(s)
- Vaibhhav Sinha
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences-TIFRBangalore, India.,Manipal UniversityManipal, India
| | - Akshit Goyal
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences-TIFRBangalore, India
| | | | - Szabolcs Semsey
- Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences-TIFRBangalore, India
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Mitarai N, Brown S, Sneppen K. Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli. J Bacteriol 2016; 198:1783-93. [PMID: 27068593 PMCID: PMC4886755 DOI: 10.1128/jb.00965-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/05/2016] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Bacteria living in physically structured habitats are exposed heterogeneously to both resources and different types of phages. While there have been numerous experimental approaches to examine spatially distributed bacteria exposed to phages, there is little theory to guide the design of these experiments, interpret their results, or expand the inferences drawn to a broader ecological and evolutionary context. Plaque formation provides a window into understanding phage-bacterium interactions in physically structured populations, including surfaces, semisolids, and biofilms. We develop models to address the plaque dynamics for a temperate phage and its virulent mutants. The models are compared with phage λ-Escherichia coli system to quantify their applicability. We found that temperate phages gave an increasing number of gradually smaller colonies as the distance increased from the plaque center. For low-lysogen frequency this resulted in plaques with most of the visible colonies at an intermediate distance between the center and periphery. Using spot inoculation, where phages in excess of bacteria were inoculated in a circular area, we measured the frequency and spatial distribution of lysogens. The spot morphology of cII-negative (cII(-)) and cIII(-) mutants of phage λ displays concentric rings of high-density lysogenic colonies. The simplest of these ring morphologies was reproduced by including multiplicity of infection (MOI) sensitivity in lysis-lysogeny decisions, but its failure to explain the occasional observation of multiple rings in cIII(-) mutant phages highlights unknown features of this phage. Our findings demonstrated advantages of temperate phages over virulent phages in exploiting limited resources in spatially distributed microbial populations. IMPORTANCE Phages are the most abundant organisms on earth, and yet little is known about how phages and bacterial hosts are influencing each other in density and evolution. Phages can be either virulent or temperate, a difference that is highlighted when a spatially structured bacterial population is infected. Phage λ is a temperate phage, with a capacity for dormancy that can be modified by single gene knockouts. The stochastic bias in the lysis-lysogeny decision's probability is reflected in plaque morphologies on bacterial lawns. We present a model for plaque morphology of both virulent and temperate phages, taking into account the underlying survival of bacterial microcolonies. It reproduces known plaque morphologies and speaks to advantages of temperate phages in a spatially structured environment.
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Affiliation(s)
- Namiko Mitarai
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University
| | - Stanley Brown
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University
| | - Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University
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7
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Broussard GW, Hatfull GF. Evolution of genetic switch complexity. BACTERIOPHAGE 2014; 3:e24186. [PMID: 23819104 PMCID: PMC3694055 DOI: 10.4161/bact.24186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/03/2013] [Indexed: 12/20/2022]
Abstract
The circuitry of the phage λ genetic switch determining the outcome of lytic or lysogenic growth is well-integrated and complex, raising the question as to how it evolved. It is plausible that it arose from a simpler ancestral switch with fewer components that underwent various additions and refinements, as it adapted to vast numbers of different hosts and conditions. We have recently identified a new class of genetic switches found in mycobacteriophages and other prophages, in which immunity is dependent on integration. These switches contain only three genes (integrase, repressor and cro) and represent a major departure from the λ-like circuitry, lacking many features such as xis, cII and cIII. These small self-contained switches represent an unrealized, elegant circuitry for controlling infection outcome. In this addendum, we propose a model of possible events in the evolution of a complex λ-like switch from a simpler integration-dependent switch.
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Affiliation(s)
- Gregory W Broussard
- Department of Biological Sciences; University of Pittsburgh; Pittsburgh, PA USA
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Lehmann M, Sneppen K. Genetic regulatory networks that count to 3. J Theor Biol 2013; 329:15-9. [PMID: 23567648 DOI: 10.1016/j.jtbi.2013.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 01/29/2013] [Accepted: 03/27/2013] [Indexed: 10/27/2022]
Abstract
Sensing a graded input and differentiating between its different levels is at the core of many developmental decisions. Here, we want to examine how this can be realized for a simple system. We model gene regulatory circuits that reach distinct states when setting the underlying gene copy number to 1, 2 and 3. This distinction can be considered as counting the copy number. We explore different circuits that allow for counting and keeping memory of the count after resetting the copy number to 1. For this purpose, we sample different architectures and parameters, only considering circuits that contain repressive links, which we model by Michaelis-Menten terms. Interestingly, we find that counting to 3 does not require a hierarchy in Hill coefficients, in contrast to counting to 2, which is known from lambda phage. Furthermore, we find two main circuit architectures: one design also found in the vertebrate neural tube in a development governed by the sonic hedgehog morphogen and the more robust design of a repressilator supplemented with a weak repressilator acting in the opposite direction.
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Affiliation(s)
- Malte Lehmann
- Niels Bohr Institute/CMOL, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen, Denmark
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9
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Thattai M. Using topology to tame the complex biochemistry of genetic networks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110548. [PMID: 23277605 PMCID: PMC3538440 DOI: 10.1098/rsta.2011.0548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Living cells are controlled by networks of interacting genes, proteins and biochemicals. Cells use the emergent collective dynamics of these networks to probe their surroundings, perform computations and generate appropriate responses. Here, we consider genetic networks, interacting sets of genes that regulate one another's expression. It is possible to infer the interaction topology of genetic networks from high-throughput experimental measurements. However, such experiments rarely provide information on the detailed nature of each interaction. We show that topological approaches provide powerful means of dealing with the missing biochemical data. We first discuss the biochemical basis of gene regulation, and describe how genes can be connected into networks. We then show that, given weak constraints on the underlying biochemistry, topology alone determines the emergent properties of certain simple networks. Finally, we apply these approaches to the realistic example of quorum-sensing networks: chemical communication systems that coordinate the responses of bacterial populations.
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Affiliation(s)
- Mukund Thattai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bellary Road, Bangalore 560065, India.
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10
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Abstract
Bacteriophage λ, rediscovered in the early 1950s, has served as a model in molecular biology studies for decades. Although currently more complex organisms and more complicated biological systems can be studied, this phage is still an excellent model to investigate principles of biological processes occurring at the molecular level. In fact, very few other biological models provide possibilities to examine regulations of biological mechanisms as detailed as performed with λ. In this chapter, recent advances in our understanding of mechanisms of bacteriophage λ development are summarized and discussed. Particularly, studies on (i) phage DNA injection, (ii) molecular bases of the lysis-versus-lysogenization decision and the lysogenization process itself, (iii) prophage maintenance and induction, (iv), λ DNA replication, (v) phage-encoded recombination systems, (vi) transcription antitermination, (vii) formation of the virion structure, and (viii) lysis of the host cell, as published during several past years, will be presented.
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Avlund M, Krishna S, Semsey S, Dodd IB, Sneppen K. Minimal gene regulatory circuits for a lysis-lysogeny choice in the presence of noise. PLoS One 2010; 5:e15037. [PMID: 21188148 PMCID: PMC3004801 DOI: 10.1371/journal.pone.0015037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 10/13/2010] [Indexed: 11/18/2022] Open
Abstract
Gene regulatory networks (GRNs) that make reliable decisions should have design features to cope with random fluctuations in the levels or activities of biological molecules. The phage λ GRN makes a lysis-lysogeny decision informed by the number of phages infecting the cell. To analyse the design of decision making GRNs, we generated random in silico GRNs comprised of two or three transcriptional regulators and selected those able to perform a λ-like decision in the presence of noise. Various two-protein networks analogous to the λ CI-Cro GRN worked in noise-less conditions but failed when noise was introduced. Adding a λ CII-like protein significantly improved robustness to noise. CII relieves the CI-like protein of its 'decider' function, allowing CI to be optimized as a decision 'maintainer'. CII's lysogenic decider function was improved by its instability and rapid removal once the decision was taken, preventing its interference with maintenance. A more reliable decision also resulted from simulated co-transcription of the genes for CII and the Cro-like protein, which correlates fluctuations in these opposing decider functions and makes their ratio less noisy. Thus, the λ decision network contains design features for reducing and resisting noise.
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Affiliation(s)
- Mikkel Avlund
- Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
| | - Sandeep Krishna
- Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
- National Centre for Biological Sciences, Bangalore, India
| | - Szabolcs Semsey
- Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
| | - Ian B. Dodd
- Molecular and Biomedical Sciences (Biochemistry), University of Adelaide, Adelaide, Australia
| | - Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
- * E-mail:
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