Table 2.
Summary of sRNA candidates identified in silico
| Strain | Disease | IGR | asRNA | 5′ asRNA | 3′ asRNA | 5′ & 3′ asRNA | 5′ UTR | 3′ UTR | sense RNA |
|---|---|---|---|---|---|---|---|---|---|
| Escherichia coli | |||||||||
| MG1655 | L. S. | 195 | 452 | 74 | 142 | 73 | 89 | 199 | 643 |
| UTI89 | Cys. | 199 | 398 | 66 | 95 | 77 | 96 | 170 | 527 |
| 536 | Pyl. | 191 | 388 | 66 | 107 | 54 | 73 | 140 | 496 |
| AL862 | Sep. | 9 | 6 | 2 | 2 | 0 | 3 | 3 | 4 |
| S88 | Men. | 212 | 430 | 63 | 103 | 85 | 90 | 154 | 532 |
| Streptococcus agalactiae | |||||||||
| NEM316 | Sep. | 41 | 63 | 12 | 24 | 6 | 5 | 21 | 25 |
IGR, intergenic region; asRNA, sRNA antisense to a CDS; 5′ asRNA, antisense to the 5′-end of a CDS ; 3′ asRNA, antisense to the 3′-end of a CDS; 5′ UTR, 5′ untranslated region of a CDS; 3′ UTR, 3′ untranslated region of a CDS. For classification of the sRNA candidates into one of these categories, the first nucleotide of the RIT was used as the position reference of the candidate. This nucleotide had to be on the opposite DNA strand, between nucleotides −50 nt to +15 nt around the ATG codon (5′ asRNA), from position +15 nt with respect to the ATG codon to position –50 nt near the stop codon (asRNA) or from –50 nt to +15 nt around the stop codon (3′ asRNA). When candidates were on the same DNA strand as the CDS, the window around the first RIT nucleotide was < –100 nt before the ATG codon (5′ UTR), < +200 nt after the stop codon (3′ UTR) and from +50 nt after the ATG to –50 nt before the stop codon (seRNA). All candidates outside a CDS not included in a previous category are referred to IGR candidates. All candidates had to have a RIT with a score of ΔG°37 < -4 kcal/mol and at least two covariations had to be present in the RNA structure including the stem of the RIT. For asRNA and seRNA candidates, ΔG°37 had to be below -8 kcal/mol. L. S., laboratory strain; Cys., cystitis; Pyl., pyelonephritis; Sep., sepsis; Men., meningitis. Only the PAI-IAL862 sequence of the AL862 strain was analyzed.