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PMID:23593293

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Citation

Simoliūnas, E, Kaliniene, L, Truncaitė, L, Zajančkauskaitė, A, Staniulis, J, Kaupinis, A, Ger, M, Valius, M and Meškys, R (2013) Klebsiella phage vB_KleM-RaK2 - a giant singleton virus of the family Myoviridae. PLoS ONE 8:e60717

Abstract

At 346 kbp in size, the genome of a jumbo bacteriophage vB_KleM-RaK2 (RaK2) is the largest Klebsiella infecting myovirus genome sequenced to date. In total, 272 out of 534 RaK2 ORFs lack detectable database homologues. Based on the similarity to biologically defined proteins and/or MS/MS analysis, 117 of RaK2 ORFs were given a functional annotation, including 28 RaK2 ORFs coding for structural proteins that have no reliable homologues to annotated structural proteins in other organisms. The electron micrographs revealed elaborate spike-like structures on the tail fibers of Rak2, suggesting that this phage is an atypical myovirus. While head and tail proteins of RaK2 are mostly myoviridae-related, the bioinformatics analysis indicate that tail fibers/spikes of this phage are formed from podovirus-like peptides predominantly. Overall, these results provide evidence that bacteriophage RaK2 differs profoundly from previously studied viruses of the Myoviridae family.

Links

PubMed PMC3622015 Online version:10.1371/journal.pone.0060717

Keywords

Bacteriolysis; Gene Order; Genome, Viral; Host-Pathogen Interactions; Klebsiella/virology; Molecular Sequence Data; Myoviridae/physiology; Myoviridae/ultrastructure; Nucleotides/metabolism; Open Reading Frames; RNA, Transfer/metabolism; Viral Proteins/genetics; Viral Proteins/metabolism; Viral Tropism; Virion/ultrastructure; Virus Replication

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Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

9CAUD:H6X3M8

GO:0019012: virion

ECO:0007184 :

C

Table S3 shows that gp071 has a molecular mass of 131.63 kDa and cellular components were determined via bioinformatics and MS/MS-based proteomics. This protein is not specifically shown in figure 5.

Organism: Klebsiella Phage vB_KleM-RaK2

complete
CACAO 13534

9CAUD:H6X4Y9

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp532 (ORF 532), Putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 532 has a molecular mass of 87.315 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete
CACAO 13530

9CAUD:H6X3J8

GO:0019012: virion

ECO:0007184:

C

Table S3 shows that gp041 has a molecular mass of 97.19 kDa and cellular components were determined via bioinformatics and MS/MS-based proteomics. Protein was not shown in fig. 5.

Organism: Klebsiella Phage vB_KleM-RaK2

complete
CACAO 13532

9CAUD:H6X3Q5

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp098 (098, orf098, uncharacterized protein, RaK2 00098) has a molecular weight of 62.869 kDa in Enterobacteria phage vB_KleM-RaK2.

complete
CACAO 13535

9CAUD:H6X3K7

GO:0019012: virion

ECO:0007184:

C

Through Mass Spectroscopy, Table S3 states that gp050 (Gene Rak2_00050) proposed function in Enterobacteria Phage vB_KleM-Rak2 is identified as a Conserved Phage protein with a Molecular Weight of 33.576.

complete
CACAO 13536

9CAUD:H6X4Y5

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp528w (528, orf528, uncharacterized protein, RaK2 00528) has a molecular weight of 121.755 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3G7

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp010 (ORF 010), Putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 010 has a molecular mass of 13.932 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3J9

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp042 (ORF 042), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 042 has a molecular mass of 24.950 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete
CACAO 13542

9CAUD:H6X3K0

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp043 (ORF 043), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 043 has a molecular mass of 28.720 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3G8

GO:0019012: virion

ECO:0007184: protein mass spectrometry evidence used in manual assertion

C

Figure 5 shows that gp 011 (ORF 011), a putative virion protein, of Klebsiella Phage vB_KleM-RaK2, produces a protein residue. Table S3 determines that gp 011 has a molecular mass of 12.065 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

complete
CACAO 13544

9CAUD:H6X3K4

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp047 (ORF 047), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 047 has a molecular mass of 23.356 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3K5

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp048 (ORF 048), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 048 has a molecular mass of 20.374 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3J5

GO:0019012: virion

ECO:0007184 :

C

Figure 5 shows that gp 038 (ORF 038), a neck protein, of Klebsiella Phage vB_KleM-RaK2, produces a protein residue. Table S3 determines that gp 038 has a molecular mass of 30.294 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

complete

9CAUD:H6X3K6

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp049 (ORF 049), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 049 has a molecular mass of 34.878 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3K8

GO:0019012: virion

ECO:0007184: protein mass spectrometry evidence used in manual assertion

C

Figure 5 and Table S3 show that gp 051 (ORF 051), a conserved phage protein, of Klebsiella Phage vB_KleM-RaK2, produces a protein residue. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

complete
CACAO 13549

9CAUD:H6X3M9

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp072 (072, orf072, uncharacterized protein, RaK2 00072) has a molecular weight of 15.024 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X4Z1

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp534(ORF534) produces a protein residue via SDS-PAGE. Table S3 states that gp534 is a putative virion protein with a molecular weight of 70.781 due to bioinformatics. Organism: Klebsiella Phage vB_KleM-Rak2

complete
CACAO 13581

9CAUD:H6X4Y3

GO:0019012: virion

ECO:0007184:

C

Through MS/MS, Figure 5 shows that gp526w(ORF526w), a putative tail protein, is a protein residue via SDS-PAGE. Through bioinformatics, shown in Table S3, the protein was determined to be a putative tail protein and has a molecular weight of 63.021. Organism: Klebsiella PhagevB_KleM-Rak2.

complete
CACAO 13585

9CAUD:H6X4Y4

GO:0019012: virion

ECO:0007184:

C

Through MS/MS, shown in figure 5, it is determined that gp527w(ORF527w) is present in mature virus particles via SDS-PAGE. Through bioinformatics, shown in Table S3, the protein was determined to be a putative tail fiber protein with a molecular weight of 79.449 in Klebsiella Phage vB_KleM-RaK2.

complete
CACAO 13586

9CAUD:H6X4Y7

GO:0019012: virion

ECO:0007184:

C

Figure 5 identifies the protein gp530w through Mass spectrometry and it is defined as a putative tail protein through bioinformatics in table S3. Gp530w is a structural protein of Klebsiella Phage vB_KleM-RaK.

complete

9CAUD:H6X3Q1

GO:0098017: viral capsid, major subunit

ECO:0000318:

UniProtKB:P04535 (CAPSH_BPT4)


C

Fig. 7 shows that gp 094, major capsid protein, of Klebsiella Phage vB_KleM-RaK2, shows phylogenetic similarity to Enterobacteria phage T4 major capsid protein gp23.

complete
CACAO 13590

9CAUD:H6X3Q1

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp 094, major capsid protein, of Klebsiella Phage vB_KleM-RaK2, produces a protein residue. Table S3 determines that gp 094 has a molecular mass of 42.725 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X478

GO:0019012: virion

ECO:0007184:

C

Through Mass spectrometry, Figure 5 identifies the protein gp 531w(ORF531w), a structural protein, via SDS-PAGE. It is defined as a putative tail protein through bioinformatics in table S3 with a molecular weight of 97.727. Gp531w is a structural protein of Klebsiella Phage vB_KleM-RaK.

complete
CACAO 13589

9CAUD:H6X3R2

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp105(ORF105), a putative tail protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 27.854.

complete
CACAO 13621

9CAUD:H6X3R3

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp106(ORF106w), a putative tail protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 24.651 through bioinformatics.

complete
CACAO 13622

9CAUD:H6X3R4

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp107(ORF107), a putative virion protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 21.133.

complete
CACAO 13623

9CAUD:H6X3U2

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp135(ORF135), a putative virion protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 23.259.

complete

9CAUD:H6X3S0

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp113 (ORF113), a putative single-stranded binding protein, produces a residue via SDS PAGE. Table S3 determines that gp113 has a molecular mass of 40.488 kDa. Cellular components were determined via MS/MS -based proteomics. Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3P6

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp089 (ORF089), a portal vertex protein, produces a residue via SDS PAGE. Table S3 determines that gp089 has a molecular mass of 64.744 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics. Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3P9

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp92 (ORF92), a prohead core scaffolding protein and protease, produces a residue via SDS PAGE. Table S3 determines that gp92 has a molecular mass of 22.870 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics. Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3Y9

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp182 (ORF182), putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 182 has a molecular mass of 13.142 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X4W3

GO:0019012: virion

ECO:0007184:

C

Table S3 show that gp506 (ORF 506), hypothetical protein, has a molecular mass of 53.675 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3V2

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp145w (ORF145w), uncharacterized protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 145w has a molecular mass of 25.061 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X4V3

GO:0019012: virion

ECO:0007184:

C

Fig. 5 shows that gp496 (ORF496), putative structural protein, produces a protein residue via SDS PAGE. Table S3 determines that gp 496 has a molecular mass of 22.787 kDa. Cellular components were determined via bioinformatics and MS/MS -based proteomics.

Organism: Klebsiella Phage vB_KleM-RaK2

complete

9CAUD:H6X3N6

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp079w (079, orf079w, uncharacterized protein, RaK2 00079) has a molecular weight of 87.857 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3N8

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp081w (081, orf081w, uncharacterized protein, RaK2 00081) has a molecular weight of 27.44 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3P8

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp091 (091, orf091, uncharacterized protein, RaK2 00091) has a molecular weight of 28.209 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3V8

GO:0019012: virion

ECO:0007184: protein mass spectrometry evidence used in manual assertion

C

Table S3 and Figure 5 say that gp151(151, orf151, uncharacterized protein, RaK2 00151) has a molecular weight of 20.561 kDa in Enterobacteria phage vB_KleM-RaK2.

complete
CACAO 13693

9CAUD:H6X3W3

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp156 (156, orf156, uncharacterized protein, RaK2 00156) has a molecular weight of 34.198 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3W7

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp160 (160, orf160 uncharacterized protein, RaK2 00160) has a molecular weight of 87.718 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3Y2

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp175 (175, orf175, uncharacterized protein, RaK2 00175) has a molecular weight of 21.079 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3L7

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp060w(ORF060w), a putative virion protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 56.225(KDa). Uniprot: Uncharacterized protein, RaK2_00060

complete
CACAO 13701

9CAUD:H6X440

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp233 (233, orf233, uncharacterized protein, RaK2 00233) has a molecular weight of 30.971 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X482

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp275 (275, orf275, uncharacterized protein, RaK2 00275) has a molecular weight of 64.095 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X4V0

GO:0019012: virion

ECO:0007184:

C

Table S3 and Figure 5 say that gp493 (493, orf493, uncharacterized protein, RaK2 00493) has a molecular weight of 21.475 kDa in Enterobacteria phage vB_KleM-RaK2.

complete

9CAUD:H6X3L8

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp061w(ORF61w), a putative virion protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 12.577(KDa). Uniprot: Uncharacterized protein, RaK2_00061

complete
CACAO 13707

9CAUD:H6X3M2

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp065(ORF065), a putative virion protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 45.317 (KDa). Uniprot: Uncharacterized protein, RaK2_00065

complete

9CAUD:H6X3M5

GO:0019012: virion

ECO:0007184:

C

Fig 5 shows that gp068w(ORF068), a putative virion protein of Klebsiella Phage vB_KleM-RaK2, is a protein residue via SDS-PAGE. Table S3 states that the proposed function is a putative virion protein with a molecular weight of 56.144 (KDa). Uniprot: Uncharacterized protein, RaK2_00068

complete

Notes

See also

References

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