TABLE 2.
Primers
| Primer | Length (mer) | Sequence (5′–3′)a, location, and relevant properties | Reference or source |
|---|---|---|---|
| Used in fsrB deletion mutagenesis | |||
| BDF1 | 31 | AAA GAG CTC GAA AGG GAT GAG TGA ACA AAT G, from bp −839 to −818 to start codon of fsrB, outer primer used for amplification of fsrB 5′ region | This study |
| BDR1 | 31 | CCG AAT TCC TTT GTC CAT TGT GTT TTT CCT G, from bp 78 to 56 in fsrB, inner primer used for amplification of fsrB 5′ region | This study |
| BDF2 | 31 | CCG AAT TCT GGA TGG GAC AAA CTG AAA AAC A, from bp 54 to 23 before fsrB stop codon, inner primer used for amplification of fsrB 3′ region | This study |
| BDR2 | 31 | CCG GTA CCT AGC CAA CAA ACG AAT CAC AAC C, from bp 1020 to 999 after fsrB stop codon, outer primer used for amplification of fsrB 3′ region | This study |
| Used for cotranscription study | |||
| fsrARTF1 | 22 | ACA ATA CTT CTA ACG CTT TTG C, from bp 70 to 49 after fsrA start codon | This study |
| orf1RTR1 | 20 | TAG TGG CGT GAC CTA CAT TG, from bp 28 to 9 before orf1 stop codon | This study |
| fsrBRTF1 | 21 | GAT CTT CCT GAT CCA TAT CCA, from bp 52 to 32 after fsrB start codon | This study |
| fsrARTR1 | 23 | CAA GGC ACT ATT TCT TAC TTA GG, from bp 22 before fsrA stop codon to bp 1 after fsrA stop codon | This study |
| fsrCRTF1 | 21 | ACT CGT AAA AAG ACA AAA ACG, from bp 71 to 51 after fsrC start codon | This study |
| fsrBRTR1 | 20 | TGA TGG TGT GGG AAC TAA GC, from bp 103 to 84 before fsrB stop codon | This study |
| gelERTF1 | 21 | AGT ATT GCT TTA TCC TCC CTA, from bp 51 to 71 before gelE start codon | This study |
| fsrCRTR1 | 21 | CTA AAA GTA ATC CAG AAG AGC, from bp 164 to 144 before fsrC stop codon | This study |
| sprERTF1 | 22 | ATC AGA AAC AAA AAA CCA GCA C, from bp 74 to 53 after sprE start codon | This study |
| gelERTR1 | 19 | CTC GTG ATG CGA TGC TTG C, from bp 148 to 130 before gelE stop codon | This study |
| Used for primer extension study | |||
| APE1 | 22 | ACA ATA CTT CTA ACG CTT TTG C, from bp 70 to 49 after fsrA start codon | This study |
| BPE2 | 21 | TAA GCC AGA AAA ATA AAC GGT, from bp 108 to 88 after fsrB start codon | This study |
| EPE2 | 21 | CCA ACA AAG ATG CCT GTA CCT, from bp 50 to 30 after gelE start codon | This study |
| Used for study of promoter activity | |||
| APRF1 | 32 | CGG GAT CCT CTC AAG AAG ATA TAA AAT TAC AC, from bp −6 to −29 to fsrA start codon, used for amplification of fsrA promoter | This study |
| APRR1 | 28 | CGG AAT TCG CGA CTC ATT CAA CAG GAA G, from bp −406 to −387 to fsrA start codon, used for amplification of fsrA promoter | This study |
| BPRF1 | 29 | CGG GAT CCT CCT CTT CAA GTA TTG CAC TA, from bp −8 to −28 to fsrB start codon, used for amplification of fsrB promoter | This study |
| BPRR1 | 30 | CGG AAT TCC AAG GCA CTA TTT CTT ACT TAG, from bp −110 to −89 to fsrB start codon, used for amplification of fsrB promoter | This study |
| EPRF1 | 30 | CGG GAT CCT TCC CCA GTT TCC TTT TAT TTC, from bp −16 to −37 to gelE start codon, used for amplification of gelE promoter | This study |
| EPRR1 | 29 | CGG AAT TCG CTA TGG TAT TGA GTT ATG AG, from bp −218 to −198 to gelE start codon, used for amplification of gelE promoter | This study |
| BMP1 | 28 | CGG AAT TCA GGG AGG GAT AAT GAC TAA T, from bp −90 to −71 to fsrB start codon | This study |
| BMP2 | 32 | CGG AAT TCA TTA AGG AAT TAT CTA TCT ATT AG, from bp −72 to −49 to fsrB start codon | This study |
| BMP4 | 57 | CGG AAT TCG GGA TAA TGA CTA ATT AAG GAA TTA TCT ATC TAT TAG TCG CTA TAT TCG, from bp −85 to −37 to fsrB start codon | This study |
| BMP5 | 63 | CGG AAT TCT AGG GAG GGA TAA TGA CTA ATA TTC CTT TTA TCT ATC TAT TAG TCG CTA TAT TCG, from bp −91 to −37 to fsrB start codon, bp −70 to −64 sequence TAA GGA A was changed to ATT CCT T | This study |
| BMP6 | 62 | CGG AAT TCA GGG AAA AAT GTC GGC TGA TTA AGG AAT TAT CTA TCT ATT AGT CGC TAT ATT CG, from bp −188 to −170 to gelE start codon and from bp −72 to −37 to fsrB start codon | This study |
| EMP1 | 27 | CGG AAT TCA GGG AAA AAT GTC GGC TGA, from bp −188 to −170 to gelE start codon | This study |
| EMP2 | 30 | CGG AAT TCA TTA AGG AAT TTA GAT AGT GCC, from bp −170 to −149 to gelE start codon | This study |
| EMP5 | 55 | CGG AAT TCA GGG AAA AAT GTC GGC TGA TTT TCC TTT TTA GAT AGT GCC GGT TAG G, from bp −188 to −142 to gelE start codon, bp −167 to −162 sequence AAG GAA was changed to TTC CTT | This study |
| EMP6 | 56 | CGG AAT TCT AGG GAG GGA TAA TGA CTA ATT AAG GAA TTT AGA TAG TGC CGG TTA GG, from bp −91 to −73 to fsrB start codon and bp −170 to −142 to gelE start codon | This study |
| Vlac1 | 23 | GTT GAA TAA CAC TTA TTC CTA TC, flanking pTCV-lac cloning sites, used for sequencing inserts in pTCV-lac | 20 |
| Vlac2 | 21 | CTT CCA CAG TAG TTC ACC ACC, flanking pTCV-lac cloning sites, used for sequencing inserts in pTCV-lac | 20 |
| Others | |||
| lytF1 | 20 | ACA CCA ACC ACA GAA ACT AC, from bp 226 to 245 in E. faecalis autolysin gene | This study |
| lytR1 | 20 | GGC AAT AAA TTC TGA AGG AC, from bp 555 to 536 in E. faecalis autolysin gene | This study |
| gelEF1 | 21 | TGG TTG TGA TTC GTT TGT TGG, from bp −508 to −561 to gelE start codon | This study |
| GBR2 | 22 | TGA CCA GAA CAG ATT CAC TTG G, from bp 9 to 30 before gelE stop codon | This study |
a
Linker sequences are underlined.