Table 1.
List of selected intergenic regions of S. aureus for expression studies
| Rsaa | Start-end (size) | Startb | Flanking genes | Strand | Selection criteriac | Commentsd |
|---|---|---|---|---|---|---|
| RsaA | 637111–637250 (139) | RT, 5′RACE | SA0543/SA0544 | < > < | RNAsim, ΔG, Term | E<<S (BHI, NZM), Staphylococci |
| RsaB | 1778009–1778068 (60) | RT, 5′3′RACE | SA1552/fhs | < > < | RNAsim | E<<S (BHI), S. aureus |
| RsaC | 679909–680452 (544) | 5′3′RACE | SA0586/SA0587 | < > > | ΔG, RNAsim, Term | E<<S (BHI, NZM), S. aureus |
| RsaD | 695867–696043 (177) | RT | SA0600/SA0601 | > < > | RNAsim, Term | E<<S (BHI, NZM), Staphylococci |
| RsaE | 975383–975482 (100) | RT, 5′RACE | SA0859/SA0860 | > > < | RNAsim, Term | E<<S (BHI, NZM), Bacillaceae |
| RsaF | 975461–975564 (104) | 5′RACE | SA0859/SA0860 | > > < | ΔG, RNAsim | E<<S (BHI, NZM), S. aureus |
| RsaG | 254702–254895 (194) | RT, 5′RACE | uhpT/SA0215 | > > < | HMM, ΔG, Term | S (BHI), S. aureus |
| RsaH | 829511–829634 (124) | RT, 5′3′RACE | SA0724/SA0725 | < > > | ΔG, RNAsim, Term | E<<S (BHI), Staphylococci |
| RsaI | 2367918–2368061 (144) | RT, 5′RACE | SA2104/SA2105 | < < > | RNAsim, Term | E<<S (BHI), Staphylococci |
| RsaJ | 2486806–2487092 (287) | nd | bioD/SA2216 | < > < | RNAsim, ΔG, Term | E<<S (BHI), S. aureus |
| RsaK | 216920–217128 (209) | RT | glcA/SA0184 | > > < | RNAsim, Term | Cis-acting leader of glcA |
| RsaX01 | 43000–43600 | SA0035/SA0036 | HMM, RNAsim | – | ||
| RsaX02 | 81706–81855 | kdpC/SA0072 | RNAsim, Term | (23) | ||
| RsaX03 | 95295–95689 | SA0084–SA0085 | RNAsim, Term | (22) | ||
| RsaX04 | 149756–149850 | SA0129–SA0130 | RNAsim, Term | – | ||
| RsaX05 | 470600–470900 | SA0410/ndhF | Prom, Term | Cis-acting leader of ndhF? | ||
| RsaX06 | 659823–659968 | SA0565/SA0566 | RNAsim | – | ||
| RsaX07 | 666122–666257 | SA0575/sarA | RNAsim, Term | – | ||
| RsaX08 | 761087–761230 | SA0667/SA0668 | RNAsim, Term | PreQ1 riboswitch, (22) | ||
| RsaX09 | 905650–905835 | SA0801/SA0802 | Term | Cis-acting leader of SA0802? | ||
| RsaX10 | 1138640–1138848 | SA1005/SA1006 | RNAsim, Term | – | ||
| RsaX11 | 1175489–1175753 | SA1037/lsp | HMM, RNAsim, Term | – | ||
| RsaX12 | 1399044–1399209 | SA1224/lysC | RNAsim, HMM | Upstream of lysine riboswitch | ||
| RsaX13 | 1421983–1422128 | odhA/arlS | Term | UCCC motif | ||
| RsaX14 | 1801062–1801380 | SA1570/SA1571 | RNAsim, Term | – | ||
| RsaX15 | 1839300–1839600 | SA1602/trunc.SA | HMM, RNAsim, Term | – | ||
| RsaX16 | 1914236–1914464 | SA1676/tnp | RNAsim, Term | – | ||
| RsaX17 | 1992090–1992414 | SA1738/SAS056 | HMM, RNAsim, Term | (11) | ||
| RsaX18 | 2436200–2436800 | SA2168–SA2169 | RNAsim, ΔG | (11) | ||
| RsaX19 | 2440668–2440850 | scrA/gltT | HMM, RNAsim, Term | Repeat motifs, STAR | ||
| RsaX20 | 2473450–2473566 | SA2203/SA2204 | RNAsim, ΔG, Term | UCCC motif, sORF upstream | ||
| RsaX21 | 2544796–2545113 | SA2268/SA2269 | Term | – | ||
| RsaX22 | 2586551–2586821 | SA2301/SA2302 | RNAsim | – | ||
| RsaX23 | 2590928–2591046 | fbp/SA2305 | RNAsim, Term | sprA3 (8) | ||
| RsaX24 | 2649194–2649400 | isaA/SA2357 | RNAsim, Term | – | ||
| RsaX25 | 2769241–2769725 | SA2457/icaR | HMM, RNAsim, Term | UCCCC motif |
aThe Rsa sRNAs have been referred in GenBank under the accession numbers: GQ403615 (RsaA), GQ403616 (RsaB), GQ403617 (RsaC), GQ403618 (RsaD), GQ403619 (RsaE), GQ403620 (RsaF), GQ403621 (RsaG), GQ403622 (RsaH), GQ403623 (RsaI), GQ403624 (RsaJ) and GQ403625 (RsaK). RsaD, E, H and I were predicted by Livny et al. (23) and RsaI was also found expressed in the S. aureus N315 strain (22). In RN6390, no significant expression was detected for RsaX01 to RsaX26. sORF is for small open reading frame.
bThe 5′ start of Rsa RNAs was determined by primer extension (RT), and Rapid Amplification of cDNA Ends (RACE); 5′3′RACE was done on circularized RNA; nd is for not determined.
cTerm is for Rho-independent terminator.
dThe expression of RsaA to RsaK was analyzed at the exponential (E) and the stationary (S) phase of growth in various S. aureus strains.