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Isolation and molecular characterisation of Achromobacter phage phiAxp-3, an N4-like bacteriophage.

Ma Y, Li E, Qi Z, Li H, Wei X, Lin W, Zhao R, Jiang A, Yang H, Yin Z, Yuan J, Zhao X - Sci Rep (2016)

Bottom Line: Using proteomics, we identified 25 viral proteins from purified phiAxp-3 particles.Notably, investigation of the phage phiAxp-3 receptor on the surface of the host cell revealed that lipopolysaccharide serves as the receptor for the adsorption of phage phiAxp-3.Our findings advance current knowledge about A. xylosoxidans phages in an age where alternative therapies to combat antibiotic-resistant bacteria are urgently needed.

View Article: PubMed Central - PubMed

Affiliation: College of Food Science, Henan Institute of Science and Technology, Xinxiang, 453003, China.

ABSTRACT
Achromobacter xylosoxidans, an opportunistic pathogen, is responsible for various nosocomial and community-acquired infections. We isolated phiAxp-3, an N4-like bacteriophage that infects A. xylosoxidans, from hospital waste and studied its genomic and biological properties. Transmission electron microscopy revealed that, with a 67-nm diameter icosahedral head and a 20-nm non-contractile tail, phiAxp-3 has features characteristic of Podoviridae bacteriophages (order Caudovirales). With a burst size of 9000 plaque-forming units and a latent period of 80 min, phiAxp-3 had a host range limited to only four A. xylosoxidans strains of the 35 strains that were tested. The 72,825 bp phiAxp-3 DNA genome, with 416-bp terminal redundant ends, contains 80 predicted open reading frames, none of which are related to virulence or drug resistance. Genome sequence comparisons place phiAxp-3 more closely with JWAlpha and JWDelta Achromobacter phages than with other N4 viruses. Using proteomics, we identified 25 viral proteins from purified phiAxp-3 particles. Notably, investigation of the phage phiAxp-3 receptor on the surface of the host cell revealed that lipopolysaccharide serves as the receptor for the adsorption of phage phiAxp-3. Our findings advance current knowledge about A. xylosoxidans phages in an age where alternative therapies to combat antibiotic-resistant bacteria are urgently needed.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree based on the virion RNA polymerase (a) and large terminase subunits (b) of N4-like bacteriophages for which genome sequences are available. The 26 virion RNA polymerase and large terminase subunits were compared using the ClustalW program, and the phylogenetic tree was generated with the neighbour-joining method and 1000 bootstrap replicates (CLC Genomics Workbench 6).
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f5: Phylogenetic tree based on the virion RNA polymerase (a) and large terminase subunits (b) of N4-like bacteriophages for which genome sequences are available. The 26 virion RNA polymerase and large terminase subunits were compared using the ClustalW program, and the phylogenetic tree was generated with the neighbour-joining method and 1000 bootstrap replicates (CLC Genomics Workbench 6).

Mentions: Phage N4 employs at least three genes encoding RNAPs for the transcription of genes in different stages of its life cycle23. The most remarkable and highly conserved signature is the virion RNA polymerase (vRNAP), which is by far the largest protein described among all known phages23. vRNAP is packed into the capsid and is injected into the host cell together with phage DNA, which makes N4 the only known phage that does not depend on host RNAP for transcription of its early genes24. As an N4 like virus, phiAxp-3 also harbours three different RNAPs, suggesting the same transcription strategy as that used by N4. The large 3428 amino acid vRNAP (ORF54), which represents approximately 14% of the whole genome length of phiAxp-3, contains no cysteine residues. The vRNAP of phiAxp-3 shares amino acid 82% sequence identity with JWAlpha and JWDelta. Phylogenetic analysis of vRNAP from different N4 viruses revealed that phiAxp-3, JWAlpha, and JWDelta formed a separate clade from the other N4-like viruses (Fig. 5a). Besides vRNAP, phiAxp-3 possesses two different RNA polymerase subunits for transcription of phage middle genes: RNAP1 (ORF14) and RNAP2 (ORF17). RNAP1 and RNAP2 are transcribed in the opposite direction to vRNAP. In the N4 genome the RNAP1 gene is followed directly by RNAP2, but in the phiAxp-3 genome insertions of two small genes (ORF15 and ORF16) occur between RNAP1 and RNAP2. This situation differs from JWAlpha and JWDelta as they encode two RNAP2 in their genomes14.


Isolation and molecular characterisation of Achromobacter phage phiAxp-3, an N4-like bacteriophage.

Ma Y, Li E, Qi Z, Li H, Wei X, Lin W, Zhao R, Jiang A, Yang H, Yin Z, Yuan J, Zhao X - Sci Rep (2016)

Phylogenetic tree based on the virion RNA polymerase (a) and large terminase subunits (b) of N4-like bacteriophages for which genome sequences are available. The 26 virion RNA polymerase and large terminase subunits were compared using the ClustalW program, and the phylogenetic tree was generated with the neighbour-joining method and 1000 bootstrap replicates (CLC Genomics Workbench 6).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837373&req=5

f5: Phylogenetic tree based on the virion RNA polymerase (a) and large terminase subunits (b) of N4-like bacteriophages for which genome sequences are available. The 26 virion RNA polymerase and large terminase subunits were compared using the ClustalW program, and the phylogenetic tree was generated with the neighbour-joining method and 1000 bootstrap replicates (CLC Genomics Workbench 6).
Mentions: Phage N4 employs at least three genes encoding RNAPs for the transcription of genes in different stages of its life cycle23. The most remarkable and highly conserved signature is the virion RNA polymerase (vRNAP), which is by far the largest protein described among all known phages23. vRNAP is packed into the capsid and is injected into the host cell together with phage DNA, which makes N4 the only known phage that does not depend on host RNAP for transcription of its early genes24. As an N4 like virus, phiAxp-3 also harbours three different RNAPs, suggesting the same transcription strategy as that used by N4. The large 3428 amino acid vRNAP (ORF54), which represents approximately 14% of the whole genome length of phiAxp-3, contains no cysteine residues. The vRNAP of phiAxp-3 shares amino acid 82% sequence identity with JWAlpha and JWDelta. Phylogenetic analysis of vRNAP from different N4 viruses revealed that phiAxp-3, JWAlpha, and JWDelta formed a separate clade from the other N4-like viruses (Fig. 5a). Besides vRNAP, phiAxp-3 possesses two different RNA polymerase subunits for transcription of phage middle genes: RNAP1 (ORF14) and RNAP2 (ORF17). RNAP1 and RNAP2 are transcribed in the opposite direction to vRNAP. In the N4 genome the RNAP1 gene is followed directly by RNAP2, but in the phiAxp-3 genome insertions of two small genes (ORF15 and ORF16) occur between RNAP1 and RNAP2. This situation differs from JWAlpha and JWDelta as they encode two RNAP2 in their genomes14.

Bottom Line: Using proteomics, we identified 25 viral proteins from purified phiAxp-3 particles.Notably, investigation of the phage phiAxp-3 receptor on the surface of the host cell revealed that lipopolysaccharide serves as the receptor for the adsorption of phage phiAxp-3.Our findings advance current knowledge about A. xylosoxidans phages in an age where alternative therapies to combat antibiotic-resistant bacteria are urgently needed.

View Article: PubMed Central - PubMed

Affiliation: College of Food Science, Henan Institute of Science and Technology, Xinxiang, 453003, China.

ABSTRACT
Achromobacter xylosoxidans, an opportunistic pathogen, is responsible for various nosocomial and community-acquired infections. We isolated phiAxp-3, an N4-like bacteriophage that infects A. xylosoxidans, from hospital waste and studied its genomic and biological properties. Transmission electron microscopy revealed that, with a 67-nm diameter icosahedral head and a 20-nm non-contractile tail, phiAxp-3 has features characteristic of Podoviridae bacteriophages (order Caudovirales). With a burst size of 9000 plaque-forming units and a latent period of 80 min, phiAxp-3 had a host range limited to only four A. xylosoxidans strains of the 35 strains that were tested. The 72,825 bp phiAxp-3 DNA genome, with 416-bp terminal redundant ends, contains 80 predicted open reading frames, none of which are related to virulence or drug resistance. Genome sequence comparisons place phiAxp-3 more closely with JWAlpha and JWDelta Achromobacter phages than with other N4 viruses. Using proteomics, we identified 25 viral proteins from purified phiAxp-3 particles. Notably, investigation of the phage phiAxp-3 receptor on the surface of the host cell revealed that lipopolysaccharide serves as the receptor for the adsorption of phage phiAxp-3. Our findings advance current knowledge about A. xylosoxidans phages in an age where alternative therapies to combat antibiotic-resistant bacteria are urgently needed.

No MeSH data available.


Related in: MedlinePlus