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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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Map of the genome of 0305φ8-36 showing distribution of features. The features are from ref. [1]. The scale is in kilobase pairs. Arrows – orfs color coded as: green – encodes virion protein, dark green – encodes high copy virion protein, grey – implied virion protein by sequence analysis only, blue – non-structural, and red – non structural in terminal repeat. The orf number for every 10th orf is given, with the exception of numbers that are not consecutive, for which each orf is labelled. Purple rectangles – tRNA-like sequences of unclear significance. Abbreviations include: TMP – tape measure protein; thy. kinase – thymidine kinase; mreB – mreB-like rod determination protein; hsdM – HsdM, Type I restriction-modification system methyltransferase subunit; nrd – ribonucleoside reductase; rec. exo – DNA repair exonuclease; UDG – uracil-DNA glycosylase. Italic indicates a tentative assignment. Noncoding regions greater than 40 bp are marked above the orfs in cyan if they do, or brown if they do not, contain a promoter candidate of the class described in Figure 6.
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Figure 1: Map of the genome of 0305φ8-36 showing distribution of features. The features are from ref. [1]. The scale is in kilobase pairs. Arrows – orfs color coded as: green – encodes virion protein, dark green – encodes high copy virion protein, grey – implied virion protein by sequence analysis only, blue – non-structural, and red – non structural in terminal repeat. The orf number for every 10th orf is given, with the exception of numbers that are not consecutive, for which each orf is labelled. Purple rectangles – tRNA-like sequences of unclear significance. Abbreviations include: TMP – tape measure protein; thy. kinase – thymidine kinase; mreB – mreB-like rod determination protein; hsdM – HsdM, Type I restriction-modification system methyltransferase subunit; nrd – ribonucleoside reductase; rec. exo – DNA repair exonuclease; UDG – uracil-DNA glycosylase. Italic indicates a tentative assignment. Noncoding regions greater than 40 bp are marked above the orfs in cyan if they do, or brown if they do not, contain a promoter candidate of the class described in Figure 6.

Mentions: The gene organization of phage 0305φ8-36 [1,2] is shown in Figure 1. The transcriptional orientation of most orfs converges on the center of the genome, dividing it into a left arm and a right arm. The left arm bears a relationship to a string of phage-like genes in a contig [GenBank:NZ_AAJM01000001] from the draft sequence of B. thuringiensis israelensis. This phage-like chromosomal region is called BtI1. BtI1 contains the closest known homologues for 1) many 0305φ8-36 structure and morphogenesis genes, and 2) four non-structure genes on the left arm (orf180, a primase, a helicase, and recB) [1]. The homology relationships of the right arm (discussed below) are completely unlike the left arm. The difference in relationships of the left and right arms combined with their opposite transcriptional orientations are the first of several indications that the 0305φ8-36 genome plan may have been created by the fusion of separate left and right arm ancestors.


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)

Map of the genome of 0305φ8-36 showing distribution of features. The features are from ref. [1]. The scale is in kilobase pairs. Arrows – orfs color coded as: green – encodes virion protein, dark green – encodes high copy virion protein, grey – implied virion protein by sequence analysis only, blue – non-structural, and red – non structural in terminal repeat. The orf number for every 10th orf is given, with the exception of numbers that are not consecutive, for which each orf is labelled. Purple rectangles – tRNA-like sequences of unclear significance. Abbreviations include: TMP – tape measure protein; thy. kinase – thymidine kinase; mreB – mreB-like rod determination protein; hsdM – HsdM, Type I restriction-modification system methyltransferase subunit; nrd – ribonucleoside reductase; rec. exo – DNA repair exonuclease; UDG – uracil-DNA glycosylase. Italic indicates a tentative assignment. Noncoding regions greater than 40 bp are marked above the orfs in cyan if they do, or brown if they do not, contain a promoter candidate of the class described in Figure 6.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Map of the genome of 0305φ8-36 showing distribution of features. The features are from ref. [1]. The scale is in kilobase pairs. Arrows – orfs color coded as: green – encodes virion protein, dark green – encodes high copy virion protein, grey – implied virion protein by sequence analysis only, blue – non-structural, and red – non structural in terminal repeat. The orf number for every 10th orf is given, with the exception of numbers that are not consecutive, for which each orf is labelled. Purple rectangles – tRNA-like sequences of unclear significance. Abbreviations include: TMP – tape measure protein; thy. kinase – thymidine kinase; mreB – mreB-like rod determination protein; hsdM – HsdM, Type I restriction-modification system methyltransferase subunit; nrd – ribonucleoside reductase; rec. exo – DNA repair exonuclease; UDG – uracil-DNA glycosylase. Italic indicates a tentative assignment. Noncoding regions greater than 40 bp are marked above the orfs in cyan if they do, or brown if they do not, contain a promoter candidate of the class described in Figure 6.
Mentions: The gene organization of phage 0305φ8-36 [1,2] is shown in Figure 1. The transcriptional orientation of most orfs converges on the center of the genome, dividing it into a left arm and a right arm. The left arm bears a relationship to a string of phage-like genes in a contig [GenBank:NZ_AAJM01000001] from the draft sequence of B. thuringiensis israelensis. This phage-like chromosomal region is called BtI1. BtI1 contains the closest known homologues for 1) many 0305φ8-36 structure and morphogenesis genes, and 2) four non-structure genes on the left arm (orf180, a primase, a helicase, and recB) [1]. The homology relationships of the right arm (discussed below) are completely unlike the left arm. The difference in relationships of the left and right arms combined with their opposite transcriptional orientations are the first of several indications that the 0305φ8-36 genome plan may have been created by the fusion of separate left and right arm ancestors.

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