Table 1.
Summary of the newly identified small RNAs
| sRNA gene | Screen typea | Minutes | Adjacent genes | Strandb | 5′ endc | 3′ endd | Lengthe | Conservationf | Comments |
|---|---|---|---|---|---|---|---|---|---|
| isrA (isrP1) | Conservation | 7.0 | STM0294.1n/STM0295 | → → → | 339338 | 339760 | 423 | A | |
| isrB-1 (isrP6) | Terminator (B) | 22.7 | sbcA/STM1010 | ← → ← | 1104173, 79 | 1104266 | 88, 94 | B | Identical to isrB-2 |
| isrC (isrP7) | Conservation | 27.4 | envF/msgA | ← → ← | 1329145 | 1329432 | 288 | A, B, C, D | |
| isrD (isrP9) | Terminator (B) | 27.7 | STM1261/STM1263 | → ← → | 1345788 | 1345738 | 51 | A, B, C, D | |
| isrE(isrP10) | Terminator (B) | 27.8 | STM1273/STM1274 | → ← → | 1352972 | 1352875 | 98 | A, B, C, D | RyhB ortholog |
| isrF(isrP11) | Terminator (C) | 33.6 | STM1552/STM1554 | → ← ← | 1630160 | 1629871 | 290 | ||
| isrG (isrP14) | Terminator (A) | 48.3 | STM2243/STM2244 | ← → → | 2344732 | 2345013 | 282 | C, D | |
| isrH-1 (isrP15) | Terminator (B) | 49.3 | glpC/STM2287 | → ← → | 2394753 | 2394303 | 451 | A, B, C, D | |
| isrH-2 (isrP15) | Terminator (B) | 49.3 | glpC/STM2287 | → ← → | 2394582 | 2394303 | 280 | A, B, C, D | |
| isrI(isrP16) | Terminator (C) | 56.8 | STM2614/STM2616 | → ← ← | 2761576 | 2761329 | 248 | 62 aa ORFg | |
| isrJ(isrP17) | Conservation | 56.9 | STM2614/STM2616 | → ← ← | 2762030 | 2761957 | 74 | B | |
| isrK(isr18) | Conservation | 56.9 | STM2616/STM2617 | ← ← ← | 2762867 | 2762791 | 77 | E, F, G, H | |
| isrB-2 (isrP19) | Terminator (B) | 57 | STM2631/sbcA | → ← → | 2770959, 65 | 2770872 | 88, 94 | B | Identical to isrB-1 |
| isrL (isrP20) | Terminator (B) | 58.4 | smpB/STM2690 | → ← → | 2839399 | 2839055 | 345 | A, B, C, D | |
| isrM(isrP22) | Terminator (A) | 59.8 | STM2762/STM2763 | ← → → | 2905050 | 2905378 | 329 | A | |
| isrN(isrP23) | Conservation | 59.8 | STM2764/STM2765 | ← → ← | 2906925 | 2907067 | 143 | I, J, K | |
| isrO (isrP25) | Terminator (A) | 65.8 | STM3038/STM3039 | ← → → | 3198380 | 3198580 | 201 | A, B, C, D | |
| isrP (isrP27) | Terminator (B) | 88.7 | STM4097/STM4098 | ← → ← | 4306719 | 4306866 | 148 | A, B, C, D | |
| isrQ (isrP28) | Terminator (A) | 98.0 | STM4508/STM4509 | ← → → | 4762991, 97 | 4763158 | 162, 168 |
asRNAs were predicted based on conservation or based on the presence of rho-independent transcription terminators. Three types of terminators were considered (see Figure 1).
bThe middle arrow represents the sRNA gene, while the flanking arrows indicate the orientation of the adjacent genes, respectively. Genes present on the strand given in the S. typhimurium genome database are indicated by (→), and genes present on the complementary strand are indicated by (←).
cDetermined by primer extension. The additional number represents a second, close start site.
dGiven is the position of the last uridine at the end of the terminator.
eGiven is the length in nucleotides.
fConservation of sRNAs genes in other genomes: (A) S. enterica paratyphi ATCC, (B) S. enterica choleraesius, (C) S. typhi, (D) S. typhi Ty2, (E) E. coli O157:H7, (F) S. dysenteriae. (G) S. flexneri, (H) S. sonnei, (I) E. coli 536, (J) E. coli CFT073, (K) E. coli UTI89.
gRNA transcript predicted to encode 62 aa ORF (No other transcripts were predicted to encode an ORF).