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Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage.

Hardies SC, Thomas JA, Serwer P - Virol. J. (2007)

Bottom Line: Other segments were best described as multigene units engaged in modular horizontal exchange.Genomic organization at a level higher than individual gene sequence comparison can be analyzed to aid in understanding large phage genomes.Methods of analysis include 1) applying a time scale, 2) augmenting blast scores with positional information, 3) categorizing genomic rearrangements into one of several processes with characteristic rates and outcomes, and 4) correlating apparent transcript sizes with genomic position, gene content, and promoter motifs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA. hardies@uthscsa.edu

ABSTRACT

Background: The recently sequenced 218 kb genome of morphologically atypical Bacillus thuringiensis phage 0305phi8-36 exhibited only limited detectable homology to known bacteriophages. The only known relative of this phage is a string of phage-like genes called BtI1 in the chromosome of B. thuringiensis israelensis. The high degree of divergence and novelty of phage genomes pose challenges in how to describe the phage from its genomic sequences.

Results: Phage 0305phi8-36 and BtI1 are estimated to have diverged 2.0 - 2.5 billion years ago. Positionally biased Blast searches aligned 30 homologous structure or morphogenesis genes between 0305phi8-36 and BtI1 that have maintained the same gene order. Functional clustering of the genes helped identify additional gene functions. A conserved long tape measure gene indicates that a long tail is an evolutionarily stable property of this phage lineage. An unusual form of the tail chaperonin system split to two genes was characterized, as was a hyperplastic homologue of the T4gp27 hub gene. Within this region some segments were best described as encoding a conservative array of structure domains fused with a variable component of exchangeable domains. Other segments were best described as multigene units engaged in modular horizontal exchange. The non-structure genes of 0305phi8-36 appear to include the remnants of two replicative systems leading to the hypothesis that the genome plan was created by fusion of two ancestral viruses. The case for a member of the RNAi RNA-directed RNA polymerase family residing in 0305phi8-36 was strengthened by extending the hidden Markov model of this family. Finally, it was noted that prospective transcriptional promoters were distributed in a gradient of small to large transcripts starting from a fixed end of the genome.

Conclusion: Genomic organization at a level higher than individual gene sequence comparison can be analyzed to aid in understanding large phage genomes. Methods of analysis include 1) applying a time scale, 2) augmenting blast scores with positional information, 3) categorizing genomic rearrangements into one of several processes with characteristic rates and outcomes, and 4) correlating apparent transcript sizes with genomic position, gene content, and promoter motifs.

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Alignment of 0305φ8-36 orf99 to diagnostic motifs of the RNA-dependent RNA polymerase family Pfam05183. The motifs [34] are represented by segments of the sequence logo obtained from Pfam. The orf99 sequences aligned according to SAM.
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Figure 5: Alignment of 0305φ8-36 orf99 to diagnostic motifs of the RNA-dependent RNA polymerase family Pfam05183. The motifs [34] are represented by segments of the sequence logo obtained from Pfam. The orf99 sequences aligned according to SAM.

Mentions: A potential factor in the transcriptional organization of 0305φ8-36 is that orf99 appears to be a phage-encoded RNA polymerase. This gene was initially found as a weak Blast match to a portion of eucaryotic RNA-directed RNA polymerases involved in amplifying RNA during an RNAi response (Pfam05183). We expanded the Pfam domain model into a complete sequence alignment and HMM model using SAM. SAM then detected 0305φ8-36 orf99 with E = 10-100 and aligned it from end to end. Segments of the Pfam sequence logo described as definitive of this family [34] are shown in Figure 5 with the gp99 sequence aligned according to SAM. The family has been characterized [34] as having no detectable sequence similarity to virus-encoded RNA-directed RNA polymerases or any DNA-directed RNA polymerases. However, a role for an RNA-directed RNA polymerase in 0305φ8-36 would require it to be involved in some unprecedented process for a DNA phage. Alternatively, we tentatively assume that gp99 is a DNA-directed RNA polymerase, possibly representing the function of the ancestor of this polymerase family. Other than the obvious potential for involvement in gene expression, there is also the possibility that the polymerase is involved in some aspect of injection. However, the precedent for RNA polymerase-mediated injection is that it would probably be too slow to be used exclusively on a genome of this length [35].


Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage.

Hardies SC, Thomas JA, Serwer P - Virol. J. (2007)

Alignment of 0305φ8-36 orf99 to diagnostic motifs of the RNA-dependent RNA polymerase family Pfam05183. The motifs [34] are represented by segments of the sequence logo obtained from Pfam. The orf99 sequences aligned according to SAM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2147016&req=5

Figure 5: Alignment of 0305φ8-36 orf99 to diagnostic motifs of the RNA-dependent RNA polymerase family Pfam05183. The motifs [34] are represented by segments of the sequence logo obtained from Pfam. The orf99 sequences aligned according to SAM.
Mentions: A potential factor in the transcriptional organization of 0305φ8-36 is that orf99 appears to be a phage-encoded RNA polymerase. This gene was initially found as a weak Blast match to a portion of eucaryotic RNA-directed RNA polymerases involved in amplifying RNA during an RNAi response (Pfam05183). We expanded the Pfam domain model into a complete sequence alignment and HMM model using SAM. SAM then detected 0305φ8-36 orf99 with E = 10-100 and aligned it from end to end. Segments of the Pfam sequence logo described as definitive of this family [34] are shown in Figure 5 with the gp99 sequence aligned according to SAM. The family has been characterized [34] as having no detectable sequence similarity to virus-encoded RNA-directed RNA polymerases or any DNA-directed RNA polymerases. However, a role for an RNA-directed RNA polymerase in 0305φ8-36 would require it to be involved in some unprecedented process for a DNA phage. Alternatively, we tentatively assume that gp99 is a DNA-directed RNA polymerase, possibly representing the function of the ancestor of this polymerase family. Other than the obvious potential for involvement in gene expression, there is also the possibility that the polymerase is involved in some aspect of injection. However, the precedent for RNA polymerase-mediated injection is that it would probably be too slow to be used exclusively on a genome of this length [35].

Bottom Line: Other segments were best described as multigene units engaged in modular horizontal exchange.Genomic organization at a level higher than individual gene sequence comparison can be analyzed to aid in understanding large phage genomes.Methods of analysis include 1) applying a time scale, 2) augmenting blast scores with positional information, 3) categorizing genomic rearrangements into one of several processes with characteristic rates and outcomes, and 4) correlating apparent transcript sizes with genomic position, gene content, and promoter motifs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA. hardies@uthscsa.edu

ABSTRACT

Background: The recently sequenced 218 kb genome of morphologically atypical Bacillus thuringiensis phage 0305phi8-36 exhibited only limited detectable homology to known bacteriophages. The only known relative of this phage is a string of phage-like genes called BtI1 in the chromosome of B. thuringiensis israelensis. The high degree of divergence and novelty of phage genomes pose challenges in how to describe the phage from its genomic sequences.

Results: Phage 0305phi8-36 and BtI1 are estimated to have diverged 2.0 - 2.5 billion years ago. Positionally biased Blast searches aligned 30 homologous structure or morphogenesis genes between 0305phi8-36 and BtI1 that have maintained the same gene order. Functional clustering of the genes helped identify additional gene functions. A conserved long tape measure gene indicates that a long tail is an evolutionarily stable property of this phage lineage. An unusual form of the tail chaperonin system split to two genes was characterized, as was a hyperplastic homologue of the T4gp27 hub gene. Within this region some segments were best described as encoding a conservative array of structure domains fused with a variable component of exchangeable domains. Other segments were best described as multigene units engaged in modular horizontal exchange. The non-structure genes of 0305phi8-36 appear to include the remnants of two replicative systems leading to the hypothesis that the genome plan was created by fusion of two ancestral viruses. The case for a member of the RNAi RNA-directed RNA polymerase family residing in 0305phi8-36 was strengthened by extending the hidden Markov model of this family. Finally, it was noted that prospective transcriptional promoters were distributed in a gradient of small to large transcripts starting from a fixed end of the genome.

Conclusion: Genomic organization at a level higher than individual gene sequence comparison can be analyzed to aid in understanding large phage genomes. Methods of analysis include 1) applying a time scale, 2) augmenting blast scores with positional information, 3) categorizing genomic rearrangements into one of several processes with characteristic rates and outcomes, and 4) correlating apparent transcript sizes with genomic position, gene content, and promoter motifs.

Show MeSH
Related in: MedlinePlus