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Identification and molecular characterization of bacteriophage phiAxp-2 of Achromobacter xylosoxidans

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ABSTRACT

A novel Achromobacter xylosoxidans bacteriophage, phiAxp-2, was isolated from hospital sewage in China. The phage was morphologically and microbiologically characterized, and its one-step growth curve, host range, genomic sequence, and receptor were determined. Its morphology showed that phiAxp-2 belongs to the family Siphoviridae. Microbiological characterization demonstrated that pH 7 is most suitable for phage phiAxp-2; its titer decreased when the temperature exceeded 50 °C; phiAxp-2 is sensitive to ethanol and isopropanol; and the presence of calcium and magnesium ions is necessary to accelerate cell lysis and improve the formation of phiAxp-2 plaques. Genomic sequencing and a bioinformatic analysis showed that phage phiAxp-2 is a novel bacteriophage, consisting of a circular, double-stranded 62,220-bp DNA molecule with a GC content of 60.11% that encodes 86 putative open reading frames (ORFs). The lipopolysaccharide of A. xylosoxidans is involved in the adsorption of phiAxp-2.

No MeSH data available.


Multiple genome alignment constructed with the Mauve software (http://asap.ahabs.wisc.edu/mauve/) and the chromosomes of related phages.Similarity is represented by the heights of the bars, which correspond to the average level of conservation in that region of the genomic sequence. Completely white regions represent fragments that were not aligned or contained sequence elements specific to a particular genome. Boxes with identical colors represent local colinear blocks (LCB), indicating homologous DNA regions shared by two or more chromosomes without sequence rearrangements. LCBs indicated below the horizontal black line represent reverse complements of the reference LCB.
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f5: Multiple genome alignment constructed with the Mauve software (http://asap.ahabs.wisc.edu/mauve/) and the chromosomes of related phages.Similarity is represented by the heights of the bars, which correspond to the average level of conservation in that region of the genomic sequence. Completely white regions represent fragments that were not aligned or contained sequence elements specific to a particular genome. Boxes with identical colors represent local colinear blocks (LCB), indicating homologous DNA regions shared by two or more chromosomes without sequence rearrangements. LCBs indicated below the horizontal black line represent reverse complements of the reference LCB.

Mentions: The left half of the phiAxp-2 genome (ORF1–ORF29) has a similar genomic structure and encodes proteins most similar to each of the Burkholderia phage AH2 (JN564907) proteins from ORF78–ORF50 (the right half of the AH2 genome; excluding nine proteins) in the reverse transcription direction (Fig. 4 and Table 2). However, the range of overall similarity was as low as 29–57% at the amino acid level, and genomic comparisons with AH2 showed that in many instances, only small parts or domains of the ORFs were conserved. The most similar of these protein was the portal protein (57% identity with AH2 gp65) and the least similar was the decorator protein (24% identity with AH2 gp63) (Table 2). Phage AH2 is most closely related to Burkholderia phage BcepNazgul (NC005091)10, and a multiple genome alignment of the chromosomes of phiAxp-2, AH2, and BcepNazgul confirmed their relatedness (Fig. 5). Despite the similarities in their virion morphologies (the AH2 virion also has a noncontractile tail of approximately 220 nm and a capsid approximately 60 nm in diameter10), a phylogenetic analysis of the DNA polymerase and the terminase large subunit predicted that phiAxp-2 is most closely related to AH2 (Fig. 6a,b). Because the proteins of phiAxp-2 have largely uncharacterized functions, its genome must encode several new viral proteins. We predict that the large-scale genomic rearrangement in phiAxp-2 was mediated by transposase genes. However, we did not identify any transposase gene. Such genomic rearrangements may have caused the genomic diversity observed in the phages, resulting in the biological differences that distinguish them.


Identification and molecular characterization of bacteriophage phiAxp-2 of Achromobacter xylosoxidans
Multiple genome alignment constructed with the Mauve software (http://asap.ahabs.wisc.edu/mauve/) and the chromosomes of related phages.Similarity is represented by the heights of the bars, which correspond to the average level of conservation in that region of the genomic sequence. Completely white regions represent fragments that were not aligned or contained sequence elements specific to a particular genome. Boxes with identical colors represent local colinear blocks (LCB), indicating homologous DNA regions shared by two or more chromosomes without sequence rearrangements. LCBs indicated below the horizontal black line represent reverse complements of the reference LCB.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037462&req=5

f5: Multiple genome alignment constructed with the Mauve software (http://asap.ahabs.wisc.edu/mauve/) and the chromosomes of related phages.Similarity is represented by the heights of the bars, which correspond to the average level of conservation in that region of the genomic sequence. Completely white regions represent fragments that were not aligned or contained sequence elements specific to a particular genome. Boxes with identical colors represent local colinear blocks (LCB), indicating homologous DNA regions shared by two or more chromosomes without sequence rearrangements. LCBs indicated below the horizontal black line represent reverse complements of the reference LCB.
Mentions: The left half of the phiAxp-2 genome (ORF1–ORF29) has a similar genomic structure and encodes proteins most similar to each of the Burkholderia phage AH2 (JN564907) proteins from ORF78–ORF50 (the right half of the AH2 genome; excluding nine proteins) in the reverse transcription direction (Fig. 4 and Table 2). However, the range of overall similarity was as low as 29–57% at the amino acid level, and genomic comparisons with AH2 showed that in many instances, only small parts or domains of the ORFs were conserved. The most similar of these protein was the portal protein (57% identity with AH2 gp65) and the least similar was the decorator protein (24% identity with AH2 gp63) (Table 2). Phage AH2 is most closely related to Burkholderia phage BcepNazgul (NC005091)10, and a multiple genome alignment of the chromosomes of phiAxp-2, AH2, and BcepNazgul confirmed their relatedness (Fig. 5). Despite the similarities in their virion morphologies (the AH2 virion also has a noncontractile tail of approximately 220 nm and a capsid approximately 60 nm in diameter10), a phylogenetic analysis of the DNA polymerase and the terminase large subunit predicted that phiAxp-2 is most closely related to AH2 (Fig. 6a,b). Because the proteins of phiAxp-2 have largely uncharacterized functions, its genome must encode several new viral proteins. We predict that the large-scale genomic rearrangement in phiAxp-2 was mediated by transposase genes. However, we did not identify any transposase gene. Such genomic rearrangements may have caused the genomic diversity observed in the phages, resulting in the biological differences that distinguish them.

View Article: PubMed Central - PubMed

ABSTRACT

A novel Achromobacter xylosoxidans bacteriophage, phiAxp-2, was isolated from hospital sewage in China. The phage was morphologically and microbiologically characterized, and its one-step growth curve, host range, genomic sequence, and receptor were determined. Its morphology showed that phiAxp-2 belongs to the family Siphoviridae. Microbiological characterization demonstrated that pH 7 is most suitable for phage phiAxp-2; its titer decreased when the temperature exceeded 50 °C; phiAxp-2 is sensitive to ethanol and isopropanol; and the presence of calcium and magnesium ions is necessary to accelerate cell lysis and improve the formation of phiAxp-2 plaques. Genomic sequencing and a bioinformatic analysis showed that phage phiAxp-2 is a novel bacteriophage, consisting of a circular, double-stranded 62,220-bp DNA molecule with a GC content of 60.11% that encodes 86 putative open reading frames (ORFs). The lipopolysaccharide of A. xylosoxidans is involved in the adsorption of phiAxp-2.

No MeSH data available.