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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

Genome map of phage phiAxp-3.Representation of the open reading frame (ORF) (ORF 1 to 80) organisation of phage phiAxp-3. The predicted genes are indicated as arrows. Blue arrows, DNA regulation module; purple arrows, packaging module; yellow arrows, phage structural proteins; red arrows, host lysis proteins; green arrows, lysis/lysogeny module; black arrows, hypothetical proteins.
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f4: Genome map of phage phiAxp-3.Representation of the open reading frame (ORF) (ORF 1 to 80) organisation of phage phiAxp-3. The predicted genes are indicated as arrows. Blue arrows, DNA regulation module; purple arrows, packaging module; yellow arrows, phage structural proteins; red arrows, host lysis proteins; green arrows, lysis/lysogeny module; black arrows, hypothetical proteins.

Mentions: The order and arrangement of the open reading frames of the revised genome are the same as the previously sequenced version and were not affected by the reorganisation of the terminal regions of the genome. A total of 80 protein coding genes were predicted in the genome and ranged from 120 to 10,287 bp, 22 of which are leftward oriented while the others are rightward oriented (Fig. 4). N4-like phages are a class of virulent Podoviridae phages and members of this group are lytic against their hosts22. The phiAxp-3 genome sequence shares 51.6% and 50.4% nucleotide identity with JWAlpha and JWDelta, respectively. The three phages were isolated from samples obtained from two locations that are geographically far apart (phiAxp-3 was isolated in China, JWAlpha and JWDelta were isolated in Germany)14. For comparison, phiAxp-3 shares 40.8% nucleotide identity with phage N4. JWAlpha and JWDelta share 96.6% nucleotide sequence identity. The overall architecture of N4 is shared among all phages of this group. Based on our analysis, the annotated proteins of phiAxp-3 can be categorised into the following functional groups: Transcription (RNA polymerase; RNAP1, RNAP2, vRNAP), DNA metabolism (HNH endonuclease, dCTP deaminase, thymidylate synthase), lysis inhibition (rllA, rllB), DNA replication (NTP-PPase, DNA helicase, DNA polymerase, DNA primase, ssDNA-binding protein), virion morphogenesis (structural proteins, tail protein, major capsid protein, tape measure protein, portal protein), host lysis (N-acetylmuramidase, holin) and DNA packaging (large terminase subunit) (Fig. 4). No tRNA was identified in the phiAxp-3 genome; this indicates that upon entry into the host, the phage is completely reliant on the host tRNA for its protein synthesis. Table 2 shows a detailed comparison of phiAxp-3, N4, and JWAlpha and JWDelta proteins. In our analyses, 25 phage proteins were detected using LC/ESI/MS/MS, of which 10 had annotated functions (Table 3).


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)

Genome map of phage phiAxp-3.Representation of the open reading frame (ORF) (ORF 1 to 80) organisation of phage phiAxp-3. The predicted genes are indicated as arrows. Blue arrows, DNA regulation module; purple arrows, packaging module; yellow arrows, phage structural proteins; red arrows, host lysis proteins; green arrows, lysis/lysogeny module; black arrows, hypothetical proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Genome map of phage phiAxp-3.Representation of the open reading frame (ORF) (ORF 1 to 80) organisation of phage phiAxp-3. The predicted genes are indicated as arrows. Blue arrows, DNA regulation module; purple arrows, packaging module; yellow arrows, phage structural proteins; red arrows, host lysis proteins; green arrows, lysis/lysogeny module; black arrows, hypothetical proteins.
Mentions: The order and arrangement of the open reading frames of the revised genome are the same as the previously sequenced version and were not affected by the reorganisation of the terminal regions of the genome. A total of 80 protein coding genes were predicted in the genome and ranged from 120 to 10,287 bp, 22 of which are leftward oriented while the others are rightward oriented (Fig. 4). N4-like phages are a class of virulent Podoviridae phages and members of this group are lytic against their hosts22. The phiAxp-3 genome sequence shares 51.6% and 50.4% nucleotide identity with JWAlpha and JWDelta, respectively. The three phages were isolated from samples obtained from two locations that are geographically far apart (phiAxp-3 was isolated in China, JWAlpha and JWDelta were isolated in Germany)14. For comparison, phiAxp-3 shares 40.8% nucleotide identity with phage N4. JWAlpha and JWDelta share 96.6% nucleotide sequence identity. The overall architecture of N4 is shared among all phages of this group. Based on our analysis, the annotated proteins of phiAxp-3 can be categorised into the following functional groups: Transcription (RNA polymerase; RNAP1, RNAP2, vRNAP), DNA metabolism (HNH endonuclease, dCTP deaminase, thymidylate synthase), lysis inhibition (rllA, rllB), DNA replication (NTP-PPase, DNA helicase, DNA polymerase, DNA primase, ssDNA-binding protein), virion morphogenesis (structural proteins, tail protein, major capsid protein, tape measure protein, portal protein), host lysis (N-acetylmuramidase, holin) and DNA packaging (large terminase subunit) (Fig. 4). No tRNA was identified in the phiAxp-3 genome; this indicates that upon entry into the host, the phage is completely reliant on the host tRNA for its protein synthesis. Table 2 shows a detailed comparison of phiAxp-3, N4, and JWAlpha and JWDelta proteins. In our analyses, 25 phage proteins were detected using LC/ESI/MS/MS, of which 10 had annotated functions (Table 3).

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