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Gottlieb P, Alimova A. The Establishment of the ϕ6 Genome Packaging Assay. Viruses 2023; 16:22. [PMID: 38257723 PMCID: PMC10818532 DOI: 10.3390/v16010022] [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: 10/27/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
This editorial describes the efforts to establish a genome packaging assay for the ϕ6 bacteriophage, which were performed in the laboratory of Leonard Mindich, Ph [...].
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Affiliation(s)
- Paul Gottlieb
- School of Medicine, The City University of New York (CUNY), New York, NY 10530, USA;
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2
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Singhal S, Leon Guerrero CM, Whang SG, McClure EM, Busch HG, Kerr B. Adaptations of an RNA virus to increasing thermal stress. PLoS One 2017; 12:e0189602. [PMID: 29267297 PMCID: PMC5739421 DOI: 10.1371/journal.pone.0189602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
Environments can change in incremental fashions, where a shift from one state to another occurs over multiple organismal generations. The rate of the environmental change is expected to influence how and how well populations adapt to the final environmental state. We used a model system, the lytic RNA bacteriophage Φ6, to investigate this question empirically. We evolved viruses for thermostability by exposing them to heat shocks that increased to a maximum temperature at different rates. We observed increases in the ability of many heat-shocked populations to survive high temperature heat shocks. On their first exposure to the highest temperature, populations that experienced a gradual increase in temperature had higher average survival than populations that experienced a rapid temperature increase. However, at the end of the experiment, neither the survival of populations at the highest temperature nor the number of mutations per population varied significantly according to the rate of thermal change. We also evaluated mutations from the endpoint populations for their effects on viral thermostability and growth. As expected, some mutations did increase viral thermostability. However, other mutations decreased thermostability but increased growth rate, suggesting that benefits of an increased replication rate may have sometimes outweighed the benefits of enhanced thermostability. Our study highlights the importance of considering the effects of multiple selective pressures, even in environments where a single factor changes.
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Affiliation(s)
- Sonia Singhal
- Department of Biology, University of Washington, Seattle, WA, United States of America
| | | | - Stella G Whang
- Department of Biology, University of Washington, Seattle, WA, United States of America
| | - Erin M McClure
- Department of Biology, University of Washington, Seattle, WA, United States of America
| | - Hannah G Busch
- Department of Biology, University of Washington, Seattle, WA, United States of America
| | - Benjamin Kerr
- Department of Biology, University of Washington, Seattle, WA, United States of America
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3
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Ford BE, Sun B, Carpino J, Chapler ES, Ching J, Choi Y, Jhun K, Kim JD, Lallos GG, Morgenstern R, Singh S, Theja S, Dennehy JJ. Frequency and fitness consequences of bacteriophage φ6 host range mutations. PLoS One 2014; 9:e113078. [PMID: 25409341 PMCID: PMC4237377 DOI: 10.1371/journal.pone.0113078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Viruses readily mutate and gain the ability to infect novel hosts, but few data are available regarding the number of possible host range-expanding mutations allowing infection of any given novel host, and the fitness consequences of these mutations on original and novel hosts. To gain insight into the process of host range expansion, we isolated and sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found at least 17 unique suites of mutations among these 69 mutants. We assayed fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the standard laboratory host, P. phaseolicola. Mutants exhibited significantly lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola. Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P. phaseolicola compared to wildtype Φ6, confirming the prevalence of antagonistic pleiotropy during host range expansion. Further experiments revealed that the mechanistic basis of these fitness differences was likely variation in host attachment ability. In addition, using computational protein modeling, we show that host-range expanding mutations occurred in hotspots on the surface of the phage's host attachment protein opposite a putative hydrophobic anchoring domain.
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Affiliation(s)
- Brian E. Ford
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
- The Graduate Center of the City University of New York, New York, New York, United States of America
| | - Bruce Sun
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - James Carpino
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Elizabeth S. Chapler
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Jane Ching
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Yoon Choi
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Kevin Jhun
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Jung D. Kim
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Gregory G. Lallos
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Rachelle Morgenstern
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Shalini Singh
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Sai Theja
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - John J. Dennehy
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
- * E-mail:
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4
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Joseph SB, Peck KM, Burch CL. Dominance effects of deleterious and beneficial mutations in a single gene of the RNA virus ϕ6. PLoS One 2014; 9:e97717. [PMID: 24945910 PMCID: PMC4063744 DOI: 10.1371/journal.pone.0097717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/22/2014] [Indexed: 11/23/2022] Open
Abstract
Most of our knowledge of dominance stems from studies of deleterious mutations. From these studies we know that most deleterious mutations are recessive, and that this recessivity arises from a hyperbolic relationship between protein function (i.e., protein concentration or activity) and fitness. Here we investigate whether this knowledge can be used to make predictions about the dominance of beneficial and deleterious mutations in a single gene. We employed a model system--the bacteriophage φ6--that allowed us to generate a collection of mutations in haploid conditions so that it was not biased toward either dominant beneficial or recessive deleterious mutations. Screening for the ability to infect a bacterial host that does not permit infection by the wildtype φ6, we generated a collection of mutations in P3, a gene involved in attachment to the host and in phage particle assembly. The resulting collection contained mutations with both deleterious and beneficial effects on fitness. The deleterious mutations in our collection had additive effects on fitness and the beneficial mutations were recessive. Neither of these observations were predicted from previous studies of dominance. This pattern is not consistent with the hyperbolic (diminishing returns) relationship between protein function and fitness that is characteristic of enzymatic genes, but could have resulted from a curve of increasing returns.
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Affiliation(s)
- Sarah B. Joseph
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kayla M. Peck
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christina L. Burch
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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5
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Qiao J, Qiao X, Sun Y, Mindich L. Role of host protein glutaredoxin 3 in the control of transcription during bacteriophage Phi2954 infection. Proc Natl Acad Sci U S A 2010; 107:6000-4. [PMID: 20231437 PMCID: PMC2851929 DOI: 10.1073/pnas.1000383107] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage Phi2954 contains three dsRNA genomic segments, designated L, M, and S. The RNA is located inside a core particle composed of multiple copies of a major structural protein, an RNA-dependent RNA polymerase, a hexameric NTPase, and an auxiliary protein. The core particle is covered by a shell of protein P8, and this structure is enclosed within a lipid-containing membrane. We have found that normal infection of the host Pseudomonas syringae is dependent on the action of a host protein, glutaredoxin 3 (GrxC). GrxC removes the P8 shell from the infecting particle and binds to the inner core. Removal of P8 activates the transcription of segments S and M, whereas binding of GrxC to the core particle activates the transcription of segment L. The differences in transcription behavior are due to the preference of the polymerase for G as the first base of the transcript. Transcripts of segments S and M begin with GCAA, whereas those of segment L begin with ACAA. The binding of GrxC to the particle results in changes in polymerase activity. Mutations resulting in independence of GrxC are found in the gene for protein P1, the major structural protein of the inner core particle.
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Affiliation(s)
- Jian Qiao
- Public Health Research Institute Center, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
| | - Xueying Qiao
- Public Health Research Institute Center, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
| | - Yang Sun
- Public Health Research Institute Center, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
| | - Leonard Mindich
- Public Health Research Institute Center, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
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6
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Interaction of a host protein with core complexes of bacteriophage phi6 to control transcription. J Virol 2010; 84:4821-5. [PMID: 20164238 DOI: 10.1128/jvi.00026-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages of the family Cystoviridae have genomes consisting of three double-stranded RNA (dsRNA) segments, L, S, and M, packaged within a polyhedral capsid along with RNA polymerase. Transcription of genomic segment L is activated by the interaction of host protein YajQ with the capsid structure. Segment L codes for the proteins of the inner capsid, which are expressed early in infection. Green fluorescent protein (GFP) fusions with YajQ produce uniform fluorescence in uninfected cells and in cells infected with viruses not dependent on YajQ. Punctate fluorescence develops when cells are infected with YajQ-dependent viruses. It appears that the host protein binds to the infecting particles and remains with them during the entire infection period.
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7
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Joseph SB, Hanley KA, Chao L, Burch CL. Coinfection rates in Φ6 bacteriophage are enhanced by virus-induced changes in host cells. Evol Appl 2009; 2:24-31. [PMID: 25567844 PMCID: PMC3352419 DOI: 10.1111/j.1752-4571.2008.00055.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 11/26/2008] [Indexed: 11/28/2022] Open
Abstract
Two or more viruses infecting the same host cell can interact in ways that profoundly affect disease dynamics and control, yet the factors determining coinfection rates are incompletely understood. Previous studies have focused on the mechanisms that viruses use to suppress coinfection, but recently the phenomenon of enhanced coinfection has also been documented. In the experiments described here, we explore the hypothesis that enhanced coinfection rates in the bacteriophage Φ6 are achieved by virus-induced upregulation of the Φ6 receptor, which is the bacterial pilus. First, we confirmed that coinfection enhancement in Φ6 is virus-mediated by showing that Φ6 attaches significantly faster to infected cells than to uninfected cells. Second, we explored the hypothesis that coinfection enhancement in Φ6 depends upon changes in the expression of an inducible receptor. Consistent with this hypothesis, the closely related phage, Φ12, that uses constitutively expressed lipopolysaccharide as its receptor, attaches to infected and uninfected cells at the same rate. Our results, along with the previous finding that coinfection in Φ6 is limited to two virions, suggest that viruses may closely regulate rates of coinfection through mechanisms for both coinfection enhancement and exclusion.
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Affiliation(s)
- Sarah B Joseph
- Department of Biology, University of North Carolina Chapel Hill, NC, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University Las Cruces, NM, USA
| | - Lin Chao
- Division of Biological Sciences, University of California San Diego, CA, USA
| | - Christina L Burch
- Department of Biology, University of North Carolina Chapel Hill, NC, USA
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8
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Qiao X, Sun Y, Qiao J, Mindich L. Temporal control of message stability in the life cycle of double-stranded RNA bacteriophage phi8. J Virol 2009; 83:633-9. [PMID: 18971268 PMCID: PMC2612379 DOI: 10.1128/jvi.01766-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 10/16/2008] [Indexed: 11/20/2022] Open
Abstract
The cystoviruses have genomes of three double-stranded RNA segments. The genes of the L transcript are expressed early in infection, while those of M and S are expressed late. In all cystovirus groups but one, the quantity of the L transcript late in infection is lower than those of the other two because of transcriptional control. In bacteriophage Phi8 and its close relatives, transcription of L is not controlled; instead, the L transcript is turned over rapidly late in infection. The three messages are produced in approximately equal amounts early in infection, but the amount of L is less than 10% of the amounts of the others late in infection. The decay of the Phi8 L message depends upon the production of protein Hb, which is encoded in segment L. It also depends upon a target site within the H gene region. Phage mutants lacking either the Hb gene or the target region do not show the late control of L message quantity. In addition to having a role as a negative regulator, Hb functions to neutralize the activity of protein J, encoded by segment S, which causes the degradation of all viral transcripts.
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Affiliation(s)
- Xueying Qiao
- Department of Microbiology, the Public Health Research Institute, Newark, New Jersey 07103, USA
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9
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Qiao J, Qiao X, Mindich L. In vivo studies of genomic packaging in the dsRNA bacteriophage Phi8. BMC Microbiol 2005; 5:10. [PMID: 15762996 PMCID: PMC1079848 DOI: 10.1186/1471-2180-5-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Accepted: 03/11/2005] [Indexed: 11/10/2022] Open
Abstract
Background Φ8 is a bacteriophage containing a genome of three segments of double-stranded RNA inside a polyhedral capsid enveloped in a lipid-containing membrane. Plus strand RNA binds and is packaged by empty procapsids. Whereas Φ6, another member of the Cystoviridae, shows high stringency, serial dependence and precision in its genomic packaging in vitro and in vivo, Φ8 packaging is more flexible. Unique sequences (pac) near the 5' ends of plus strands are necessary and sufficient for Φ6 genomic packaging and the RNA binding sites are located on P1, the major structural protein of the procapsid. Results In this paper the boundaries of the Φ8 pac sequences have been explored by testing the in vivo packaging efficacy of transcripts containing deletions or changes in the RNA sequences. The pac sequences have been localized to the 5' untranslated regions of the viral transcripts. Major changes in the pac sequences are either tolerated or ameliorated by suppressor mutations in the RNA sequence. Changes in the genomic packaging program can be established as a result of mutations in P1, the major structural protein of the procapsid and the determinant of RNA binding specificity. Conclusion Although Φ8 is distantly related to bacteriophage Φ6, and does not show sequence similarity, it has a similar genomic packaging program. This program, however, is less stringent than that of Φ6.
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Affiliation(s)
- Jian Qiao
- Department of Microbiology, The Public Health Research Institute. Newark, New Jersey 07103, USA
| | - Xueying Qiao
- Department of Microbiology, The Public Health Research Institute. Newark, New Jersey 07103, USA
| | - Leonard Mindich
- Department of Microbiology, The Public Health Research Institute. Newark, New Jersey 07103, USA
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10
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Abstract
RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, phi 6, containing a beta-lactamase (bla) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another beta-lactam antibiotic, cefotaxime, due to mutations in the virus-borne bla gene. We monitored the changes in bla cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of bla sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for beta-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins.
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Affiliation(s)
- Eugene V Makeyev
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Finland
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11
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Abstract
Bacteriophage Phi8 has a genome of three dsRNA segments. It is able to acquire plasmid transcripts of cDNA copies of the genomic segments as replacements of its resident chromosomes. It is also able to effect recombination between the plasmid transcripts and the resident chromosomes. Depending upon the extent of sequence identity between the plasmid transcript and the resident chromosome, the recombination can be homologous or heterologous. Homologous recombination has not previously been reported for viruses with double-stranded RNA genomes.
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Affiliation(s)
- S Onodera
- Department of Microbiology, Public Health Research Institute, New York, New York 10016, USA
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12
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Mindich L. Precise packaging of the three genomic segments of the double-stranded-RNA bacteriophage phi6. Microbiol Mol Biol Rev 1999; 63:149-60. [PMID: 10066834 PMCID: PMC98960 DOI: 10.1128/mmbr.63.1.149-160.1999] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage phi6 has a genome of three segments of double-stranded RNA. Each virus particle contains one each of the three segments. Packaging is effected by the acquisition, in a serially dependent manner, of the plus strands of the genomic segments into empty procapsids. The empty procapsids are compressed in shape and expand during packaging. The packaging program involves discrete steps that are determined by the amount of RNA inside the procapsid. The steps involve the exposure and concealment of binding sites on the outer surface of the procapsid for the plus strands of the three genomic segments. The plus strand of segment S can be packaged alone, while packaging of the plus strand of segment M depends upon prior packaging of S. Packaging of the plus strand of L depends upon the prior packaging of M. Minus-strand synthesis begins when the particle has a full complement of plus strands. Plus-strand synthesis commences upon the completion of minus-strand synthesis. All of the reactions of packaging, minus-strand synthesis, and plus-strand synthesis can be accomplished in vitro with isolated procapsids. Live-virus constructions that are in accord with the model have been prepared. Mutant virus with changes in the packaging program have been isolated and analyzed.
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Affiliation(s)
- L Mindich
- Department of Microbiology, The Public Health Research Institute New York, New York 10016, USA.
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13
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Paatero AO, Mindich L, Bamford DH. Mutational analysis of the role of nucleoside triphosphatase P4 in the assembly of the RNA polymerase complex of bacteriophage phi6. J Virol 1998; 72:10058-65. [PMID: 9811745 PMCID: PMC110533 DOI: 10.1128/jvi.72.12.10058-10065.1998] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/1998] [Accepted: 08/25/1998] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage phi6 is a complex enveloped double-stranded RNA virus with a segmented genome and replication strategy quite similar to that of the Reoviridae. An in vitro packaging and replication system using purified components is available. The positive-polarity genomic segments are translocated into a preformed polymerase complex (procapsid) particle. This particle is composed of four proteins: the shell-forming protein P1, the RNA polymerase P2, and two proteins active in packaging. Protein P7 is involved in stable packaging, and protein P4 is a homomultimeric potent nucleoside triphosphatase that provides the energy for the RNA translocation event. In this investigation, we used mutational analysis to study P4 multimerization and assembly. P4 is assembled onto a preformed particle containing proteins P2 and P7 in addition to P1. Only simultaneous production of P1 and P4 in the same cell leads to P4 assembly on P1 alone, whereas the P1 shell is incompetent for accepting P4 if produced separately. The C-terminal part of P4 is essential for particle assembly but not for multimerization or enzymatic activity. Altering the P4 nucleoside triphosphate binding site destroys the ability to form multimers.
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Affiliation(s)
- A O Paatero
- Department of Biosciences, Biocenter, FIN-00014, University of Helsinki, Finland
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14
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Ulycznyj PI, Salmon KA, Douillard H, DuBow MS. Characterization of the Pseudomonas aeruginosa transposable bacteriophage D3112 A and B genes. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1264:249-53. [PMID: 8547306 DOI: 10.1016/0167-4781(95)00186-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The left end DNA of Mu-like transposable bacteriophage D3112 was sequenced from bp 2521 to bp 5483. Two large open reading frames were identified: ORF A (bp 2539-4611) and ORF B (bp 4626-5378). ORF A can encode a 690 amino acid, 78 kDa protein which is 44.4% similar to Mu transposase and ORF B can encode a 250 amino acid, 27 kDa protein, which is 46.4% similar to, though 62 amino acids shorter than, the Mu B protein. The cloned D3112 A gene exhibited activity on a mini-D3112-containing plasmid in Pseudomonas aeruginosa.
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Affiliation(s)
- P I Ulycznyj
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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15
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Johnson MD, Mindich L. Plasmid-directed assembly of the lipid-containing membrane of bacteriophage phi 6. J Bacteriol 1994; 176:4124-32. [PMID: 8021194 PMCID: PMC205612 DOI: 10.1128/jb.176.13.4124-4132.1994] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The nucleocapsid of bacteriophage phi 6 is enveloped within a lipid-containing membrane. The membrane is composed of proteins P3, P6, P9, P10, and P13 and phospholipids. The relationship between membrane protein P9 and morphogenetic protein P12 was studied in the absence of phage infection. cDNA copies of genes 9 and 12 were expressed on plasmids in Pseudomonas syringae pv. phaseolicola. Immunoblotting demonstrated the presence of protein P9 in strains carrying both gene 9 and gene 12 but not in strains with gene 9 alone. In the absence of P12, P9 was found to be unstable. Simultaneous synthesis of proteins P9 and P12 led to the formation of a low-density P9 particle having a buoyant density similar to that of precursor structures composed of phospholipid and proteins isolated from phi 6-infected cells. These results are consistent with results of previous genetic experiments suggesting that P9 and P12 are necessary and sufficient for the formation of the phi 6 envelope. Extensions of P9 at the C terminus do not impair particle formation; however, N-terminal extensions or C-terminal deletions that extend into the hydrophobic region of P9 do impair particle formation.
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Affiliation(s)
- M D Johnson
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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16
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Johnson MD, Mindich L. Isolation and characterization of nonsense mutations in gene 10 of bacteriophage phi 6. J Virol 1994; 68:2331-8. [PMID: 8139018 PMCID: PMC236709 DOI: 10.1128/jvi.68.4.2331-2338.1994] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Nonsense mutants of bacteriophage phi 6 were isolated by a procedure that involved directed mutagenesis of a cDNA copy of genomic segment M, transcription of this segment, in vitro packaging into procapsids, and transfection of spheroplasts to form viable mutant phage. Recombinant phi 6 viruses that contained amber mutations in two open reading frames, ORF 10 and ORF D, of genomic segment M were isolated. We show that phi 6 protein P10 is the gene product of ORF 10. Further characterization of the phi 6 ORF 10(Am) mutant revealed that phi 6 membrane-associated protein P10 is not required to make enveloped phage particles in infected cells. Enveloped phage particles isolated from a phi 6 ORF 10(Am) infection contained extremely low levels of phi 6 membrane-associated proteins P6 and P3. The low abundance is due to the very low level of P6 synthesis in phi 6 ORF 10(Am)-infected cells. The results suggest that P10 might play a role in regulating the translation of gene 6. Protein P10 was found to be required for host lysis.
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Affiliation(s)
- M D Johnson
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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17
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Onodera S, Qiao X, Gottlieb P, Strassman J, Frilander M, Mindich L. RNA structure and heterologous recombination in the double-stranded RNA bacteriophage phi 6. J Virol 1993; 67:4914-22. [PMID: 8331732 PMCID: PMC237879 DOI: 10.1128/jvi.67.8.4914-4922.1993] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Bacteriophage phi 6 has a genome of three segments of double-stranded RNA, designated L, M, and S. A 1.2-kbp kanamycin resistance gene was inserted into segment M but was shown to be genetically unstable because of a high recombination rate between segment M and the 3' ends of segments S and L. The high rate of recombination is due to complementary homopolymer tracts bounding the kan gene. Removal of one arm of this potential hairpin stabilizes the insertion. The insertion of a 241- or 427-bp lacZ' gene into segment M leads to a stable Lac+ phage. The insertion of the same genes bounded by complementary homopolymer arms leads to recombinational instability. A stable derivative of this phage was shown to have lost one of the homopolymer arms. Several other conditions foster recombination. The truncation of a genomic segment at the 3' end prevents replication, but such a damaged molecule can be rescued by recombination. Similarly, insertion of the entire 3-kb lacZ gene prevents normal formation of virus, but the viral genes can be rescued by recombination. It appears that conditions leading to the retardation or absence of replication of a particular genomic segment facilitate recombinational rescue.
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MESH Headings
- Bacteriophage T7/enzymology
- Bacteriophage phi 6/genetics
- Base Sequence
- Cloning, Molecular
- DNA
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Directed RNA Polymerases/metabolism
- Electrophoresis, Agar Gel
- Models, Genetic
- Models, Structural
- Molecular Sequence Data
- Oligodeoxyribonucleotides
- Pseudomonas/genetics
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/isolation & purification
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- RNA, Viral/metabolism
- Recombination, Genetic
- Restriction Mapping
- Transcription, Genetic
- Viral Plaque Assay
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Affiliation(s)
- S Onodera
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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18
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Ojala PM, Juuti JT, Bamford DH. Protein P4 of double-stranded RNA bacteriophage phi 6 is accessible on the nucleocapsid surface: epitope mapping and orientation of the protein. J Virol 1993; 67:2879-86. [PMID: 7682630 PMCID: PMC237613 DOI: 10.1128/jvi.67.5.2879-2886.1993] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Protein P4, an early protein of double-stranded RNA bacteriophage phi 6, is a component of the virion-associated RNA polymerase complex and possesses a nucleoside triphosphate (NTP) phosphohydrolase activity. We have produced and characterized a panel of 20 P4-specific monoclonal antibodies. Epitope mapping using truncated molecules of recombinant P4 revealed seven linear epitopes. The accessibility of the epitopes on the phi 6 nucleocapsid (NC) surface showed that at least the C terminus and an internal domain, containing the consensus sequence for NTP binding, protrude the NC shell. Four of the NC-binding antibodies distorted the integrity of the NC by releasing protein P4 and the major NC surface protein P8. This finding suggests a close contact between these two proteins. The dissociation of the NC led to the activation of the virion-associated RNA polymerase. The multimeric status of the recombinant P4 was similar to that of the virion-associated P4, indicating that no accessory virus proteins are needed for its multimerization.
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Affiliation(s)
- P M Ojala
- Department of Genetics, University of Helsinki, Finland
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19
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Pagratis NC, Revel HR. Broad host range, regulated expression system utilizing bacteriophage T7 RNA polymerase and promoter. Biotechnol Bioeng 1993; 41:837-45. [DOI: 10.1002/bit.260410902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Kenney JM, Hantula J, Fuller SD, Mindich L, Ojala PM, Bamford DH. Bacteriophage phi 6 envelope elucidated by chemical cross-linking, immunodetection, and cryoelectron microscopy. Virology 1992; 190:635-44. [PMID: 1519356 DOI: 10.1016/0042-6822(92)90901-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bacteriophage phi 6 is an enveloped dsRNA virus which infects the plant pathogenic Pseudomonas syringae bacterium. Using low dose cryoelectron microscopy we show that the nucleocapsid, spikeless virion, and intact virion have radii of 29, 35, and 43 nm, respectively. Thus, the membrane is 6 nm thick and the surface spikes of the receptor binding protein P3 extend 8 nm from the membrane surface. Cross-linking, immunological, and complementation evidence suggest that the spikes are formed of multimeric P3 molecules and that P3 is associated with membrane-bound protein P6. We observe that the envelope can accommodate up to 400 molecules of P3 but that the average virion contains less than one-fourth of this amount. Assembly of a very small number of P3 or truncated P3 molecules onto inactive virions restores infectivity, showing that only a few spikes are necessary for receptor binding and membrane fusion.
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Affiliation(s)
- J M Kenney
- Biological Structures and Biocomputing Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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21
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Kopelowitz J, Hampe C, Goldman R, Reches M, Engelberg-Kulka H. Influence of codon context on UGA suppression and readthrough. J Mol Biol 1992; 225:261-9. [PMID: 1375653 DOI: 10.1016/0022-2836(92)90920-f] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We studied the influence of the codon context on UGA suppression by a suppressor tRNA and on UGA readthrough by a normal tRNA in Escherichia coli. This was done by a series of constructs where only the immediate context of the TGA codon was varied by only one nucleotide at a time. For both UGA suppression and UGA readthrough the codon context had a similar influence according to the following rules. (1) The nature of the nucleotide immediately adjacent to the 3' side of the UGA is an important determinant; at that position the level of UGA translation is influenced by the nucleotides in the order A greater than G greater than C greater than U. (2) At extremely high or low levels of UGA translation this influence of the adjacent 3' nucleotide is not seen. (3) In all cases, the nature of both the nucleotide immediately adjacent to the 5' side of the codon and that following the base adjacent to the 3' side of the codon have little effect, if any, on UGA translation. The varying influence of the codon context effect on UGA translation is discussed in relation to its role in gene expression.
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Affiliation(s)
- J Kopelowitz
- Department of Molecular Biology, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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22
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Gottlieb P, Strassman J, Qiao X, Frilander M, Frucht A, Mindich L. In vitro packaging and replication of individual genomic segments of bacteriophage phi 6 RNA. J Virol 1992; 66:2611-16. [PMID: 1560520 PMCID: PMC241014 DOI: 10.1128/jvi.66.5.2611-2616.1992] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The genome of bacteriophage phi 6 contains three segments of double-stranded RNA. Procapsid structures whose formation was directed by cDNA copies of the large genomic segment are capable of packaging the three viral message sense RNAs in the presence of ATP. Addition of UTP, CTP, and GTP results in the synthesis of minus strands to form double-stranded RNA. In this report, we show that procapsids are capable of taking up any of the three plus-strand single-stranded RNA segments independently of the others. In manganese-containing buffers, synthesis of the corresponding minus strand takes place. In magnesium-containing buffers, individual message sense viral RNA segments were packaged, but minus-strand replication did not take place unless all three viral single-stranded RNA segments were packaged. Since the conditions of packaging in magnesium buffer more closely resemble those in vivo, these results indicated that there is no specific order or dependence in packaging and that replication is regulated so that it does not begin until all segments are in place.
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Affiliation(s)
- P Gottlieb
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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23
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Mindich L, Qiao X, Onodera S, Gottlieb P, Strassman J. Heterologous recombination in the double-stranded RNA bacteriophage phi 6. J Virol 1992; 66:2605-10. [PMID: 1560519 PMCID: PMC241013 DOI: 10.1128/jvi.66.5.2605-2610.1992] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bacteriophage phi 6 contains three double-stranded RNA genomic segments. We have constructed a virus with an insertion of a kanamycin resistance gene in genomic RNA segment M. The virus forms small, turbid plaques, and its genome is unstable. Virus from a single plaque contained from about 0.1 to 10% large clear-plaque forms of the virus; these were usually missing the kanamycin resistance gene, and in many cases, the resulting segment M was larger or smaller than its normal size. Sequence analysis of the genomic RNA of the apparent deletions showed that they were formed by recombination events between segment M and either segment S or L. These heterologous recombination events resulted in the loss of the kanamycin resistance gene from segment M and the replacement of the 3' end of segment M with the 3' end of segment S or L. Although the 3' ends of the single-stranded RNA transcripts of the genomic segments appear to have extensive secondary structure, the sequences at the 3' ends are not involved in the specificity of genomic packaging.
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Affiliation(s)
- L Mindich
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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24
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Onodera S, Olkkonen VM, Gottlieb P, Strassman J, Qiao XY, Bamford DH, Mindich L. Construction of a transducing virus from double-stranded RNA bacteriophage phi6: establishment of carrier states in host cells. J Virol 1992; 66:190-6. [PMID: 1727482 PMCID: PMC238275 DOI: 10.1128/jvi.66.1.190-196.1992] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteriophage phi 6 contains three double-stranded RNA (dsRNA) genomic segments. We have constructed a plasmid that contains a cDNA copy of the middle (M) segment, with a gene for kanamycin resistance (kan) inserted into the PstI site. A transcript of this cDNA was incorporated in vitro into procapsids along with natural transcripts of the S and L segments. The procapsids were coated with nucleocapsid surface protein P8 and transfected into Pseudomonas syringae pv. phaseolicola. The resulting infectious virus, phi 6 K1, was found to contain an M segment that was 1.2 kbp larger than the normal 4.1 kbp. K1 formed small, turbid plaques, and its genome was unstable. Preparations of K1 contained from about 0.1 to 10% large, clear-plaque forms of the virus which were usually missing the kan gene, and in some cases, the resulting segment M was smaller than its normal size. Cells picked from lawns of host cells infected with K1 yielded colonies that were resistant to kanamycin (Kan). These colonies could be passaged on kanamycin-containing medium. The cells were found to contain large amounts of dsRNA corresponding to the viral genomic segments. Some strains continued to produce viable phage, while others lost this ability. One strain completely lost the small genomic segment S. Approximately 1 in 10,000 infected cells acquired the carrier state with the original phage isolate K1. However, we isolated a viral mutant that was able to induce the carrier state in 10 to 20% of the infected cells. The ability to use drug resistance as a test for the carrier state makes this system very useful for the study of the mechanisms of induction of persistent infections.
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Affiliation(s)
- S Onodera
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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25
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Olkkonen VM, Ojala PM, Bamford DH. Generation of infectious nucleocapsids by in vitro assembly of the shell protein on to the polymerase complex of the dsRNA bacteriophage phi 6. J Mol Biol 1991; 218:569-81. [PMID: 2016747 DOI: 10.1016/0022-2836(91)90702-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A method for the in vitro uncoating of the phi 6 nucleocapsid (NC) was developed. The resulting particle, designated as the NC core, containing the genomic double-stranded (ds) RNA segments and the proteins P1, P2, P4 and P7, was not infectious but had a highly enhanced in vitro transcriptase activity compared to that of the intact NC. The NC shell protein P8 was purified by immunoaffinity chromatography, and it was shown to self-assemble to shell-like structures upon addition of calcium ions. The conditions for the self-assembly of the shell were optimized. Shell reassembly on to the NC cores restored the infectivity but resulted in a decrease of transcriptase activity. No reassembly of the shell on to RNA-less cores (procapsids) produced from a cDNA construction in Escherichia coli was observed. Our results suggest that the intracellular uncoating of the NC is the event activating the phi 6 dsRNA transcriptase and that the NC shell is necessary for infectivity, probably for the passage of the NC through the host cytoplasmic membrane. Packaging of the dsRNA segments into the procapsid appears to be a prerequisite for NC shell assembly.
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Affiliation(s)
- V M Olkkonen
- Department of Genetics, University of Helsinki, Finland
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26
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Olkkonen VM, Gottlieb P, Strassman J, Qiao XY, Bamford DH, Mindich L. In vitro assembly of infectious nucleocapsids of bacteriophage phi 6: formation of a recombinant double-stranded RNA virus. Proc Natl Acad Sci U S A 1990; 87:9173-7. [PMID: 2251260 PMCID: PMC55126 DOI: 10.1073/pnas.87.23.9173] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A system is described for assembling infectious bacteriophage phi 6 nucleocapsids in vitro. Procapsids encoded by cDNA copies of genomic segment L in Escherichia coli were used to package and replicate viral RNA segments. The resulting filled particles were shown to be capable of infecting host cell spheroplasts after incubation with purified nucleocapsid shell protein P8. The infected spheroplasts yielded infectious virions. A modified cDNA-derived RNA segment was inserted into virions by this method. The resulting infectious virions contained the same 4-base-pair deletion as the modified cDNA. These findings support the contention that the preformed procapsids are the "machine" that replicates the phi 6 genome, by showing that the cDNA-derived procapsids are competent to package and replicate RNA properly.
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Affiliation(s)
- V M Olkkonen
- Department of Genetics, University of Helsinki, Finland
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27
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Gottlieb P, Strassman J, Qiao XY, Frucht A, Mindich L. In vitro replication, packaging, and transcription of the segmented double-stranded RNA genome of bacteriophage phi 6: studies with procapsids assembled from plasmid-encoded proteins. J Bacteriol 1990; 172:5774-82. [PMID: 2211512 PMCID: PMC526894 DOI: 10.1128/jb.172.10.5774-5782.1990] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA (dsRNA). We prepared cDNA copies of the viral genome and cloned this material in plasmids that replicate in Escherichia coli and Pseudomonas phaseolicola, the natural host of phi 6. These plasmids direct the formation of viral proteins and the assembly of structures similar to viral procapsids containing proteins P1, P2, P4, and P7. We found that these particles are capable of taking up viral single-stranded RNA and synthesizing the minus strands to produce dsRNA structures. Once the dsRNA is formed, it is then used as a template for the production of viral plus strands in a reaction that resembles normal transcription. The particles were also capable of directly transcribing exogenous dsRNA. The replicase reactions were specific for phi 6 RNA, were specific for procapsids, and resulted in substantial incorporation of product dsRNA into particles. These results offer strong support to a model in which genomic packaging is done by preformed procapsids.
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Affiliation(s)
- P Gottlieb
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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28
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Ktistakis NT, Kao CY, Lang D. In vitro assembly of the outer shell of bacteriophage phi 6 nucleocapsid. Virology 1988; 166:91-102. [PMID: 3046121 DOI: 10.1016/0042-6822(88)90150-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Following dissociation of bacteriophage phi 6 nucleocapsid (NC) by EDTA, a particle composed of protein P8 and corresponding to the outer shell of the NC was assembled in vitro in the presence of Ca2+ and Mg2+. Assembly was obtained from soluble protein constituents above 100 micrograms/ml and was optimal within a temperature range of 22-30 degrees. Assembly did not require the presence of genomic RNA. Crosslinking results of intact NCs and in vitro-assembled outer shells suggested that protein P8 dimers are the structural subunits of the shell. Analysis of the assembly kinetics by electron microscopy suggested that ring-like particles of uniform size, packed in flat hexagonal arrays, are intermediates in outer shell assembly.
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Affiliation(s)
- N T Ktistakis
- Molecular and Cell Biology Program, University of Texas at Dallas, Richardson 75083-0688
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29
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Nemeroff ME, Pietras DF, Bruenn JA. Construction of full-length cDNA copies of viral double-stranded RNA. Virus Genes 1988; 1:243-53. [PMID: 3072756 DOI: 10.1007/bf00572703] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A method is described for the construction of full-length cDNA clones of dsRNAs. All dsRNA viruses have a capsid-associated transcriptase that is responsible for synthesis of the plus strand that is then extruded from viral particles. We have used in vitro transcripts synthesized by the segmented Saccharomyces cerevisiae virus (ScV) as templates for first-strand cDNA synthesis. Synthesis was primed by a 33-base synthetic oligonucleotide. This contained 27 nucleotides complementary to the 3' end of the plus strand from one ScV viral dsRNA segment (S14), and 6 additional nucleotides encoding an XbaI restriction site at the 5' end. The second cDNA strand was synthesized using a similar XbaI linker-synthetic oligonucleotide and the ds cDNA was cloned by standard ligation techniques. All four cDNA plasmid isolates characterized by sequence analysis contained the complete 5' end sequence of S14. Two of these were complete at the 3' end, and one lacked a single base here. Of these four clones, one also retained the XbaI sites at either end. Preparing full-length cDNA clones with unique restriction-site linkers by the use of synthetic oligonucleotides allows for easier screening for complete cDNA clones if neither the vector nor the cDNA has the chosen restriction site. It also provides for easier sequence analysis and manipulation of the genome for later studies, such as cloning into expression vectors. This method is more efficient than any previously described for production of full-sized cDNA clones.
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Affiliation(s)
- M E Nemeroff
- Department of Biological Sciences, State University of New York, Buffalo 14260
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30
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Mindich L, Nemhauser I, Gottlieb P, Romantschuk M, Carton J, Frucht S, Strassman J, Bamford DH, Kalkkinen N. Nucleotide sequence of the large double-stranded RNA segment of bacteriophage phi 6: genes specifying the viral replicase and transcriptase. J Virol 1988; 62:1180-5. [PMID: 3346944 PMCID: PMC253125 DOI: 10.1128/jvi.62.4.1180-1185.1988] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA. We determined the nucleotide sequence of cDNA derived from the largest RNA segment (L). This segment specifies the procapsid proteins necessary for transcription and replication of the phi 6 genome. The coding sequences of the four proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through analysis of isolated proteins. This report completes the sequence analysis of phi 6. This constitutes the first complete sequence of a double-stranded RNA genome virus.
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Affiliation(s)
- L Mindich
- Department of Microbiology, Public Health Research Institute of the City of New York, Inc., New York
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31
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Gottlieb P, Metzger S, Romantschuk M, Carton J, Strassman J, Bamford DH, Kalkkinen N, Mindich L. Nucleotide sequence of the middle dsRNA segment of bacteriophage phi 6: placement of the genes of membrane-associated proteins. Virology 1988; 163:183-90. [PMID: 3347997 DOI: 10.1016/0042-6822(88)90245-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA. We have determined the nucleotide sequence of cDNA derived from the middle-size RNA segment. The coding sequences of three proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through the analysis of isolated proteins. In contrast to our results with the small phi 6 dsRNA segment, the open reading frames are not tightly clustered. The homologous terminal noncoding regions between the middle and small dsRNA segments are found to be more extensive than RNA sequencing had previously indicated.
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Affiliation(s)
- P Gottlieb
- Department of Microbiology, Public Health Research Institute of the City of New York, Inc., New York 10016
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32
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Mindich L. Bacteriophage phi 6: a unique virus having a lipid-containing membrane and a genome composed of three dsRNA segments. Adv Virus Res 1988; 35:137-76. [PMID: 3068964 DOI: 10.1016/s0065-3527(08)60710-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- L Mindich
- Department of Microbiology, Public Health Research Institute, New York, New York 10016
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33
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Gottlieb P, Strassman J, Bamford DH, Mindich L. Production of a polyhedral particle in Escherichia coli from a cDNA copy of the large genomic segment of bacteriophage phi 6. J Virol 1988; 62:181-7. [PMID: 3275432 PMCID: PMC250517 DOI: 10.1128/jvi.62.1.181-187.1988] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A polyhedral particle that resembles in composition and structure the procapsid of bacteriophage phi 6 was produced in Escherichia coli containing cDNA copies of the entire large genomic segment inserted into expression vector plasmids under the control of lac or tac promoters. The particles were composed of proteins P1, P2, P4, and P7 in the same stoichiometry as in the intact virion. In electron micrographs of negatively stained samples, the particles appeared as hexagons, stars, or rings of 10 knobs, which are characteristic of the five-, three-, and twofold axes of symmetry characteristic of phi 6 procapsids. Stable particles were also produced from cDNA deletions that produce only P1 and P4. Other cDNA deletions producing P1 and P7 and P1 alone resulted in unstable particles which could only be visualized in electron micrographs of thin sections of E. coli transformed by the recombinant plasmids. Our results indicate that the assembly of the phi procapsid is independent of other phage proteins and of normal phage RNA.
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Affiliation(s)
- P Gottlieb
- Department of Microbiology, Public Health Research Institute of the City of New York, Inc., New York 10016
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34
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Revel HR, Ewen ME, Brusslan J, Pagratis N. Generation of cDNA clones of the bacteriophage phi 6 segmented dsRNA genome: characterization and expression of L segment clones. Virology 1986; 155:402-17. [PMID: 3024396 DOI: 10.1016/0042-6822(86)90203-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bacteriophage phi 6 has three dsRNA genome segments of about 3.0, 4.0, and 6.4 kbp. More than 90% of the segmented phi 6 dsRNA genome has been cloned as subchromosomal cDNA fragments, generated by reverse transcription of denatured polyadenylated dsRNA, RNA removal, annealing, filling, size fractionation, tailing, and insertion at the PstI site of pBR322. All of the large (L) segment is represented by five overlapping fragments, 98% of the small (S) segment is present in three fragments, and 67% of the medium (M) segment is contained in two fragments. Fragments have been aligned in linear arrays by Southern blot hybridization and restriction enzyme analysis. The orientation of the ordered fragments with respect to genomic RNA and phi 6 transcriptional direction was determined by comparison of terminal DNA sequences with RNA sequences at the genomic ends of phi 6 RNA. Expression of L segment clones using both Escherichia coli minicells and T7 polymerase/promoter vectors indicate that the order of known phi 6 genes on the large chromosome is: 5'--gene 7, gene 2, gene 4, gene 1--3'. cDNA complementation of a ts mutant, ts411, has located this mutation in gene 4.
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35
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McGraw T, Mindich L, Frangione B. Nucleotide sequence of the small double-stranded RNA segment of bacteriophage phi 6: novel mechanism of natural translational control. J Virol 1986; 58:142-51. [PMID: 3754015 PMCID: PMC252886 DOI: 10.1128/jvi.58.1.142-151.1986] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The lipid-containing bacteriophage phi 6 has a genome composed of three segments of double-stranded RNA. We determined the nucleotide sequence of a cDNA copy of the smallest RNA segment. The coding sequences of the four proteins on this segment were identified. These sequences were clustered. Three of the genes had overlapping initiation-termination codons. All noncoding sequences were at the ends of the molecule. The genes of the small double-stranded RNA segment comprised two translational polarity groups. We propose that the translational coupling is the result of an inability of ribosomes to bind independently to two of the four genes. Translation of these genes occurred when ribosomes were delivered to them by translation of an upstream gene.
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