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Wright BW, Ruan J, Molloy MP, Jaschke PR. Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction. ACS Synth Biol 2020; 9:3079-3090. [PMID: 33044064 DOI: 10.1021/acssynbio.0c00323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sequence overlap between two genes is common across all genomes, with viruses having high proportions of these gene overlaps. Genome modularization and refactoring is the process of disrupting natural gene overlaps to separate coding sequences to enable their individual manipulation. The biological function and fitness effects of gene overlaps are not fully understood, and their effects on gene cluster and genome-level refactoring are unknown. The bacteriophage φX174 genome has ∼26% of nucleotides involved in encoding more than one gene. In this study we use an engineered φX174 phage containing a genome with all gene overlaps removed to show that gene overlap is critical to maintaining optimal viral fecundity. Through detailed phenotypic measurements we reveal that genome modularization in φX174 causes virion replication, stability, and attachment deficiencies. Quantitation of the complete phage proteome across an infection cycle reveals 30% of proteins display abnormal expression patterns. Taken together, we have for the first time comprehensively demonstrated that gene modularization severely perturbs the coordinated functioning of a bacteriophage replication cycle. This work highlights the biological importance of gene overlap in natural genomes and that reducing gene overlap disruption should be an integral part of future genome engineering projects.
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Affiliation(s)
- Bradley W. Wright
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Juanfang Ruan
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Mark P. Molloy
- Kolling Institute, Northern Clinical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Paul R. Jaschke
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Malekpour SA, Pakzad P, Foroughmand-Araabi MH, Goliaei S, Tusserkani R, Goliaei B, Sadeghi M. Modeling the probability distribution of the bacterial burst size via a game-theoretic approach. J Bioinform Comput Biol 2018; 16:1850012. [PMID: 30051743 DOI: 10.1142/s0219720018500129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Based on previous studies, empirical distribution of the bacterial burst size varies even in a population of isogenic bacteria. Since bacteriophage progenies increase linearly with time, it is the lysis time variation that results in the bacterial burst size variations. Here, the burst size variation is computationally modeled by considering the lysis time decisions as a game. Each player in the game is a bacteriophage that has initially infected and lysed its host bacterium. Also, the payoff of each burst size strategy is the average number of bacteria that are solely infected by the bacteriophage progenies after lysis. For calculating the payoffs, a new version of ball and bin model with time dependent occupation probabilities (TDOP) is proposed. We show that Nash equilibrium occurs for a range of mixed burst size strategies that are chosen and played by bacteriophages, stochastically. Moreover, it is concluded that the burst size variations arise from choosing mixed lysis strategies by each player. By choosing the lysis time and also the burst size stochastically, the released bacteriophage progenies infect a portion of host bacteria in environment and avoid extinction. The probability distribution of the mixed burst size strategies is also identified.
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Affiliation(s)
- Seyed Amir Malekpour
- * School of Mathematics, Statistics and Computer Science, University of Tehran, Tehran 1417466191, Iran.,** School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Parsa Pakzad
- † Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Sama Goliaei
- § Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Ruzbeh Tusserkani
- ¶ School of computer Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Bahram Goliaei
- † Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mehdi Sadeghi
- ∥ Department of Medical Biochemistry, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.,** School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
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Constrained evolvability of interferon suppression in an RNA virus. Sci Rep 2016; 6:24722. [PMID: 27098004 PMCID: PMC4838867 DOI: 10.1038/srep24722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/04/2016] [Indexed: 02/05/2023] Open
Abstract
Innate immunity responses controlled by interferon (IFN) are believed to constitute a major selective pressure shaping viral evolution. Viruses encode a variety of IFN suppressors, but these are often multifunctional proteins that also play essential roles in other steps of the viral infection cycle, possibly limiting their evolvability. Here, we experimentally evolved a vesicular stomatitis virus (VSV) mutant carrying a defect in the matrix protein (M∆51) that abolishes IFN suppression and that has been previously used in the context of oncolytic virotherapy. Serial transfers of this virus in normal, IFN-secreting cells led to a modest recovery of IFN blocking capacity and to weak increases in viral fitness. Full-genome ultra-deep sequencing and phenotypic analysis of population variants revealed that the anti-IFN function of the matrix protein was not restored, and that the Mdelta51 defect was instead compensated by changes in the viral phosphoprotein. We also show that adaptation to IFN-secreting cells can be driven by the selection of fast-growing viruses with no IFN suppression capacity, and that these population variants can be trans-complemented by other, IFN-suppressing variants. Our results thus suggest that virus-virus interactions and alternative strategies of innate immunity evasion can determine the evolution of IFN suppression in a virus.
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Baker CW, Miller CR, Thaweethai T, Yuan J, Baker MH, Joyce P, Weinreich DM. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174. G3 (BETHESDA, MD.) 2016; 6:939-55. [PMID: 26921293 PMCID: PMC4825663 DOI: 10.1534/g3.115.024075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 02/02/2016] [Indexed: 11/18/2022]
Abstract
Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages) has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones' phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.
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Affiliation(s)
- Christopher W Baker
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Craig R Miller
- Department of Mathematics, University of Idaho, Moscow, Idaho 83844 Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho 83844
| | - Tanayott Thaweethai
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Jeffrey Yuan
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Meghan Hollibaugh Baker
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Paul Joyce
- Department of Mathematics, University of Idaho, Moscow, Idaho 83844
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912 Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912
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Miller CR, Lee KH, Wichman HA, Ytreberg FM. Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection. PLoS One 2014; 9:e112988. [PMID: 25405628 PMCID: PMC4236103 DOI: 10.1371/journal.pone.0112988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 10/23/2014] [Indexed: 11/29/2022] Open
Abstract
Previous studies have shown that most random amino acid substitutions destabilize protein folding (i.e. increase the folding free energy). No analogous studies have been carried out for protein-protein binding. Here we use a structure-based model of the major coat protein in a simple virus, bacteriophage φX174, to estimate the free energy of folding of a single coat protein and binding of five coat proteins within a pentameric unit. We confirm and extend previous work in finding that most accessible substitutions destabilize both protein folding and protein-protein binding. We compare the pool of accessible substitutions with those observed among the φX174-like wild phage and in experimental evolution with φX174. We find that observed substitutions have smaller effects on stability than expected by chance. An analysis of adaptations at high temperatures suggests that selection favors either substitutions with no effect on stability or those that simultaneously stabilize protein folding and slightly destabilize protein binding. We speculate that these mutations might involve adjusting the rate of capsid assembly. At normal laboratory temperature there is little evidence of directional selection. Finally, we show that cumulative changes in stability are highly variable; sometimes they are well beyond the bounds of single substitution changes and sometimes they are not. The variation leads us to conclude that phenotype selection acts on more than just stability. Instances of larger cumulative stability change (never via a single substitution despite their availability) lead us to conclude that selection views stability at a local, not a global, level.
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Affiliation(s)
- Craig R. Miller
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
- Department of Mathematics, University of Idaho, Moscow, Idaho
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho
| | - Kuo Hao Lee
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho
| | - F. Marty Ytreberg
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho
- Department of Physics, University of Idaho, Moscow, Idaho
- * E-mail:
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A new Microviridae phage isolated from a failed biotechnological process driven by Escherichia coli. Appl Environ Microbiol 2014; 80:6992-7000. [PMID: 25192988 DOI: 10.1128/aem.01365-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are present in every environment that supports bacterial growth, including man made ecological niches. Virulent phages may even slow or, in more severe cases, interrupt bioprocesses driven by bacteria. Escherichia coli is one of the most widely used bacteria for large-scale bioprocesses; however, literature describing phage-host interactions in this industrial context is sparse. Here, we describe phage MED1 isolated from a failed industrial process. Phage MED1 (Microviridae family, with a single-stranded DNA [ssDNA] genome) is highly similar to the archetypal phage phiX174, sharing >95% identity between their genomic sequences. Whole-genome phylogenetic analysis of 52 microvirus genomes from public databases revealed three genotypes (alpha3, G4, and phiX174). Phage MED1 belongs to the phiX174 group. We analyzed the distribution of single nucleotide variants in MED1 and 18 other phiX174-like genomes and found that there are more missense mutations in genes G, B, and E than in the other genes of these genomes. Gene G encodes the spike protein, involved in host attachment. The evolution of this protein likely results from the selective pressure on phages to rapidly adapt to the molecular diversity found at the surface of their hosts.
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Ally D, Wiss VR, Deckert GE, Green D, Roychoudhury P, Wichman HA, Brown CJ, Krone SM. The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress. PLoS One 2014; 9:e88702. [PMID: 24533140 PMCID: PMC3922989 DOI: 10.1371/journal.pone.0088702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/10/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially. METHODOLOGY/PRINCIPAL FINDINGS We serially transferred bacteriophage populations growing at high temperatures (40°C) on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved. CONCLUSIONS/SIGNIFICANCE Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide evidence that some substitutions exclude each other.
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Affiliation(s)
- Dilara Ally
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Valorie R. Wiss
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Gail E. Deckert
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Danielle Green
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Pavitra Roychoudhury
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Stephen M. Krone
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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Roychoudhury P, Shrestha N, Wiss VR, Krone SM. Fitness benefits of low infectivity in a spatially structured population of bacteriophages. Proc Biol Sci 2013; 281:20132563. [PMID: 24225463 DOI: 10.1098/rspb.2013.2563] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
For a parasite evolving in a spatially structured environment, an evolutionarily advantageous strategy may be to reduce its transmission rate or infectivity. We demonstrate this empirically using bacteriophage (phage) from an evolution experiment where spatial structure was maintained over 550 phage generations on agar plates. We found that a single substitution in the major capsid protein led to slower adsorption of phage to host cells with no change in lysis time or burst size. Plaques formed by phage isolates containing this mutation were not only larger but also contained more phage per unit area. Using a spatially explicit, individual-based model, we showed that when there is a trade-off between adsorption and diffusion (i.e. less 'sticky' phage diffuse further), slow adsorption can maximize plaque size, plaque density and overall productivity. These findings suggest that less infective pathogens may have an advantage in spatially structured populations, even when well-mixed models predict that they will not.
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Affiliation(s)
- Pavitra Roychoudhury
- Department of Mathematics, University of Idaho, , Moscow, ID, USA, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, , Moscow, ID, USA, Department of Biological Sciences, University of Idaho, , Moscow, ID, USA
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