1887

Abstract

Mycobacteriophage Tweety is a newly isolated phage of . It has a viral morphology with an isometric head and a long flexible tail, and forms turbid plaques from which stable lysogens can be isolated. The Tweety genome is 58 692 bp in length, contains 109 protein-coding genes, and shows significant but interrupted nucleotide sequence similarity with the previously described mycobacteriophages Llij, PMC and Che8. However, overall the genome possesses mosaic architecture, with gene products being related to other mycobacteriophages such as Che9d, Omega and Corndog. A gene encoding an integrase of the tyrosine-recombinase family is located close to the centre of the genome, and a putative site has been identified within a short intergenic region immediately upstream of . This Tweety cassette was used to construct a new set of integration-proficient plasmid vectors that efficiently transform both fast- and slow-growing mycobacteria through plasmid integration at a chromosomal locus containing a tRNA gene. These vectors are maintained well in the absence of selection and are completely compatible with integration vectors derived from mycobacteriophage L5, enabling the simple construction of complex recombinants with genes integrated simultaneously at different chromosomal positions.

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2007-08-01
2019-10-18
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Alignment of Tweety genes and with Che8 gene . The Che8 gene sequence is shown in green, and Tweety and in red and blue respectively. A single nucleotide deletion in Tweety (boxed) results in a frameshift to generate the truncated Tweety gp20. [ PDF] (620 kb) Sequence chromatograms confirming a nucleotide deletion in the Tweety genome relative to the homologous segment in phage Llij (which is identical to Che8 in this region). [ PDF] (1 kb) (larger version). Map of the Tweety genome and comparison to maps of Che8, Llij, PMC and Che9d. Genomes are represented by horizontal lines with putative genes shown as boxes above (transcribed rightwards) or below (transcribed leftwards) each genome; the number of each gene is shown within each box. The diagonal arrow indicates a programmed translational frameshift between Tweety genes and . All genes have been assorted into phamilies (Phams) of related sequences using the computer program 'Phamerator' (S. Cresawn, R. W. Hendrix & G. F. Hatfull, unpublished data); the phamily number is displayed above each gene and the boxes colour-coordinated accordingly. Note that the Pham numbers differ from those described previously (Hatfull , 2006). Putative gene functions are noted. [ PDF] (2771 kb) Nucleotide repeats in Tweety gene 54 [ PDF] (12 kb) Repeated sequences in phages Tweety gp54, Che8 gp57 and PMC gp51 [ PDF] (13 kb)

PDF

Alignment of Tweety genes and with Che8 gene . The Che8 gene sequence is shown in green, and Tweety and in red and blue respectively. A single nucleotide deletion in Tweety (boxed) results in a frameshift to generate the truncated Tweety gp20. [ PDF] (620 kb) Sequence chromatograms confirming a nucleotide deletion in the Tweety genome relative to the homologous segment in phage Llij (which is identical to Che8 in this region). [ PDF] (1 kb) (larger version). Map of the Tweety genome and comparison to maps of Che8, Llij, PMC and Che9d. Genomes are represented by horizontal lines with putative genes shown as boxes above (transcribed rightwards) or below (transcribed leftwards) each genome; the number of each gene is shown within each box. The diagonal arrow indicates a programmed translational frameshift between Tweety genes and . All genes have been assorted into phamilies (Phams) of related sequences using the computer program 'Phamerator' (S. Cresawn, R. W. Hendrix & G. F. Hatfull, unpublished data); the phamily number is displayed above each gene and the boxes colour-coordinated accordingly. Note that the Pham numbers differ from those described previously (Hatfull , 2006). Putative gene functions are noted. [ PDF] (2771 kb) Nucleotide repeats in Tweety gene 54 [ PDF] (12 kb) Repeated sequences in phages Tweety gp54, Che8 gp57 and PMC gp51 [ PDF] (13 kb)

PDF

Alignment of Tweety genes and with Che8 gene . The Che8 gene sequence is shown in green, and Tweety and in red and blue respectively. A single nucleotide deletion in Tweety (boxed) results in a frameshift to generate the truncated Tweety gp20. [ PDF] (620 kb) Sequence chromatograms confirming a nucleotide deletion in the Tweety genome relative to the homologous segment in phage Llij (which is identical to Che8 in this region). [ PDF] (1 kb) (larger version). Map of the Tweety genome and comparison to maps of Che8, Llij, PMC and Che9d. Genomes are represented by horizontal lines with putative genes shown as boxes above (transcribed rightwards) or below (transcribed leftwards) each genome; the number of each gene is shown within each box. The diagonal arrow indicates a programmed translational frameshift between Tweety genes and . All genes have been assorted into phamilies (Phams) of related sequences using the computer program 'Phamerator' (S. Cresawn, R. W. Hendrix & G. F. Hatfull, unpublished data); the phamily number is displayed above each gene and the boxes colour-coordinated accordingly. Note that the Pham numbers differ from those described previously (Hatfull , 2006). Putative gene functions are noted. [ PDF] (2771 kb) Nucleotide repeats in Tweety gene 54 [ PDF] (12 kb) Repeated sequences in phages Tweety gp54, Che8 gp57 and PMC gp51 [ PDF] (13 kb)

PDF

Alignment of Tweety genes and with Che8 gene . The Che8 gene sequence is shown in green, and Tweety and in red and blue respectively. A single nucleotide deletion in Tweety (boxed) results in a frameshift to generate the truncated Tweety gp20. [ PDF] (620 kb) Sequence chromatograms confirming a nucleotide deletion in the Tweety genome relative to the homologous segment in phage Llij (which is identical to Che8 in this region). [ PDF] (1 kb) (larger version). Map of the Tweety genome and comparison to maps of Che8, Llij, PMC and Che9d. Genomes are represented by horizontal lines with putative genes shown as boxes above (transcribed rightwards) or below (transcribed leftwards) each genome; the number of each gene is shown within each box. The diagonal arrow indicates a programmed translational frameshift between Tweety genes and . All genes have been assorted into phamilies (Phams) of related sequences using the computer program 'Phamerator' (S. Cresawn, R. W. Hendrix & G. F. Hatfull, unpublished data); the phamily number is displayed above each gene and the boxes colour-coordinated accordingly. Note that the Pham numbers differ from those described previously (Hatfull , 2006). Putative gene functions are noted. [ PDF] (2771 kb) Nucleotide repeats in Tweety gene 54 [ PDF] (12 kb) Repeated sequences in phages Tweety gp54, Che8 gp57 and PMC gp51 [ PDF] (13 kb)

PDF

Alignment of Tweety genes and with Che8 gene . The Che8 gene sequence is shown in green, and Tweety and in red and blue respectively. A single nucleotide deletion in Tweety (boxed) results in a frameshift to generate the truncated Tweety gp20. [ PDF] (620 kb) Sequence chromatograms confirming a nucleotide deletion in the Tweety genome relative to the homologous segment in phage Llij (which is identical to Che8 in this region). [ PDF] (1 kb) (larger version). Map of the Tweety genome and comparison to maps of Che8, Llij, PMC and Che9d. Genomes are represented by horizontal lines with putative genes shown as boxes above (transcribed rightwards) or below (transcribed leftwards) each genome; the number of each gene is shown within each box. The diagonal arrow indicates a programmed translational frameshift between Tweety genes and . All genes have been assorted into phamilies (Phams) of related sequences using the computer program 'Phamerator' (S. Cresawn, R. W. Hendrix & G. F. Hatfull, unpublished data); the phamily number is displayed above each gene and the boxes colour-coordinated accordingly. Note that the Pham numbers differ from those described previously (Hatfull , 2006). Putative gene functions are noted. [ PDF] (2771 kb) Nucleotide repeats in Tweety gene 54 [ PDF] (12 kb) Repeated sequences in phages Tweety gp54, Che8 gp57 and PMC gp51 [ PDF] (13 kb)

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