TABLE 1.
List of primers used in this study
| Objective of primer construction | Primer name | Nucleotide sequence (5′-3′) | Size (bp) of PCR product | Gene or structure on which primer was designed | PVL phage(s) | Location(s) of primer(s) |
|---|---|---|---|---|---|---|
| For screening of fosmid library | int-R2 | CATTTTAATTGCCAGCATCTTA | 558 | int | φSa2958 | 1547-1525 |
| int-F2 | ATGTTTTCGAGTTTTTGAGTTAG | int | 989-1011 | |||
| PVL-F | ATGTCTGGACATGATCCAA | 970 | lukS-PV | 45386-45404 | ||
| PVL-R | AACTATCTCTGCCATATGGT | lukF-PV | 46356-46337 | |||
| For long-range PCR to amplify entire structure of φSa2958 | ||||||
| From chromosome to integrase | phiMW2-DN1 | GCAGAAAAAGATGCGATTGAA | (2.5 kb) | Chromosome of JCSC2958 | φSa2958 | Upstream of φ2958PVL |
| intR | AGGATATCGAAAAAGATGAATC | int | 1655-1634 | |||
| From integrase to DNA polymerase | intc | TTTGTAGTGTCTTTGTATCCG | 9,214 | int | 1376-1396 | |
| MW1425-R | TTGTTGCCATTTTTCAAGATC | pol | 10589-10569 | |||
| From DNA polymerase to ORF JP030 | MW1425-F | CTAAAGTAGATAATGAGCCTT | 8,060 | pol | 10237-10257 | |
| 2958-1405R1 | TCCCTTTTCTTGCTTCATTTC | JP030 | 18296-18276 | |||
| From virulence-associated protein E to portal protein | CF35 | ACGAAGACGATTTTATCAAGG | 6,097 | por | 17509-17529 | |
| 2958-portalR1 | CACTATATCTTCAGAGACATA | virE | 23605-23585 | |||
| From terminase large subunit to tail length tape measure protein | CF47 | AAAGTTATCTAATTCGATGGC | 10,480 | terL | 22990-23010 | |
| CF67 | GGGCTCTTGAATACATATCT | mtp | 33469-33450 | |||
| From tail length tape measure protein to ORF JP052 | 2958-1392-F10 | ATACTGAAAAGTGGTGGAATG | 8,741 | mtp | 32807-32827 | |
| phi-M-TR1 | GACTTCCTAAGTCGAAATAG | JP052 | 41547-41528 | |||
| From ORF JP052 to lukF-PV gene | phi-M-T1 | TGGATTAACTAAATCTAGTCG | 4,877 | JP052 | 41480-41500 | |
| PVL-R | AACTATCTCTGCCATATGGT | lukF-PV | 46356-46337 | |||
| From ORF JP058 to chromosome | LukS-RR | TGGTCAACTATATCGTGGTTTT | (2 kb) | JP058 | 44574-44595 | |
| phiMW-UP | TCGCCACGTTTAGCAATTTTAT | Chromosome of JCSC2958 | Downstream of φSa2958 | |||
| For classifying phages | ||||||
| PCR-1 (for identifying φ108PVL and φPVL) | portal-1F | ACACGTGATAAAACAGGAGAA | 569 | por | φ108PVL | 21069-21089 |
| portal-1R | TCTAAATTAGCATCCGTGATAC | por | 21637-21616 | |||
| tail-1R | ATAATTGGGATAGCAACGCAA | 489 | mtp | 31237-31257 | ||
| tail-1F | CTTGATTAGACTCAACCAAACT | mtp | 31725-31704 | |||
| PCR-2 (for identifying φ2958PVL, φSLT, and φSa2mw) | portal-2F | GATGGCTAGTTTGCCCTTGA | 656 | por | φSa2958 | 23005-23024 |
| portal-2R | CTGAGGGCAATTGAAAAACG | por | 23660-23641 | |||
| tail-2F | CATAGCGCTAATGTCGCAAA | 468 | mtp | 30040-30059 | ||
| tail-2R | AGCCTCCATTGTTTGTTTGG | mtp | 30507-30488 | |||
| PCR-3 (for identifying the gene lineage between genes of φ108PVL and φPVL, and lukS-PV) | lukSR1 | ACGAAGTAGCAATAGGAGTGA | 10,497 | lukS-PV | φ108PVL | 42326-42306 |
| teil-ico-F | AGATTTAGAAGAGGAGGCACGA | mtp | 31830-31851 | |||
| PCR-4 (for identifying the gene lineage between genes of φSa2958, φSa2mw, and φSLT, and lukS-PV) | lukSR1 | ACGAAGTAGCAATAGGAGTGA | 9,483 | lukS-PV | φSa2958 | 44861-44841 |
| For identifying each PVL phage | ||||||
| PCR-5 (for identifying φPVL and φ108PVL) | intF2 | ATGTTTTCGAGTTTTTGAGTTAG | 4,340 | int | φ108PVL, φPVL | 393-415, 24310-24332 |
| 108-aR | TCAAATCCGTAATCACTCATTCT | ant | φ108PVL | 4732-4710 | ||
| PVL-aR | TTCACTAACTAAACCTATCATTGT | 1,411 | JP030 | φPVL | 25720-25697 | |
| PCR-6 (for identifying φSa2958) | int-F2 | ATGTTTTCGAGTTTTTGAGTTAG | 2,238 | int | φSa2958 | 989-1011 |
| 2958-aR | TGGTAATCAACCATTCACTTATGA | JP004 | 3226-3203 | |||
| PCR-7 (for identifying φSa2mw) | int-F2 | ATGTTTTCGAGTTTTTGAGTTAG | 4,065 | int | φSa2mw | 1574920-1574898 |
| MW2-aR | TAAGTTCCTGGTGTCATTCCTAAT | cro | 1570856-1570879 | |||
| PCR-8 (for identifying φSLT) | int-F2 | ATGTTTTCGAGTTTTTGAGTTAG | 8,770 | int | φSLT | 123-145 |
| SLT-aR | TCTTACCAAATGCAACACAACGAAT | ssb | 8892-8868 |