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Ana Senčilo,
Deborah Jacobs-Sera, Daniel A Russell,
Ching-Chung Ko,
Charles A Bowman,
Nina S Atanasova,
Eija Osterlund,
Hanna M Oksanen,
Dennis H Bamford,
Graham F Hatfull,
Elina Roine,
Roger W Hendrix
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ABSTRACT: The complete genome sequences of archaeal tailed viruses are currently highly underrepresented in sequence databases. Here, we report the genomic sequences of 10 new tailed viruses infecting different haloarchaeal hosts. Among these, only two viral genomes are closely related to each other and to previously described haloviruses HF1 and HF2. The approximately 760 kb of new genomic sequences in total shows no matches to CRISPR/Cas spacer sequences in haloarchaeal host genomes. Despite their high divergence, we were able to identify virion structural and assembly genes as well as genes coding for DNA and RNA metabolic functions. Interestingly, we identified many genes and genomic features that are shared with tailed bacteriophages, consistent with the hypothesis that haloarchaeal and bacterial tailed viruses share common ancestry, and that a viral lineage containing archaeal viruses, bacteriophages and eukaryotic viruses predates the division of the three major domains of non-viral life. However, as in tailed viruses in general and in haloarchaeal tailed viruses in particular, there are still a considerable number of predicted genes of unknown function.
RNA biology 03/2013; 10(5). · 5.56 Impact Factor
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ABSTRACT: Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by electron cryo-microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to ∼10 Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein in the capsid lattice.
Journal of Virology 01/2013; · 5.40 Impact Factor
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Welkin H Pope,
Christina M Ferreira,
Deborah Jacobs-Sera,
Robert C Benjamin,
Ariangela J Davis,
Randall J DeJong,
Sarah C R Elgin,
Forrest R Guilfoile,
Mark H Forsyth,
Alexander D Harris, [......],
John T Wertz,
Kathleen A Weston-Hafer,
Kurt E Williamson,
Bo Zhang,
Steven G Cresawn,
Paras Jain,
Mariana Piuri,
William R Jacobs,
Roger W Hendrix,
Graham F Hatfull
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ABSTRACT: Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them--with the exception of TM4--form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.
PLoS ONE 01/2011; 6(10):e26750. · 4.09 Impact Factor
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Welkin H Pope,
Deborah Jacobs-Sera, Daniel A Russell,
Craig L Peebles,
Zein Al-Atrache,
Turi A Alcoser,
Lisa M Alexander,
Matthew B Alfano,
Samantha T Alford,
Nichols E Amy, [......],
Hannah S Wirtshafter,
Theresa W Wong,
Phillip Wu,
Yun jeong Yang,
Brandon C Yee,
David A Zaidins,
Bo Zhang,
Melina Y Zúniga,
Roger W Hendrix,
Graham F Hatfull
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ABSTRACT: Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.
PLoS ONE 01/2011; 6(1):e16329. · 4.09 Impact Factor
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Graham F Hatfull,
Deborah Jacobs-Sera,
Jeffrey G Lawrence,
Welkin H Pope, Daniel A Russell,
Ching-Chung Ko,
Rebecca J Weber,
Manisha C Patel,
Katherine L Germane,
Robert H Edgar, [......],
Thuy T Pham,
Matthew B O'Brien,
Amy M Vogelsberger,
Andrew J Hryckowian,
Jessica L Wynalek,
Helen Donis-Keller,
Matt W Bogel,
Craig L Peebles,
Steven G Cresawn,
Roger W Hendrix
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ABSTRACT: Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.
Journal of Molecular Biology 03/2010; 397(1):119-43. · 4.00 Impact Factor
