Table 4.
List of validated sRNA genes located close to virulence-related genes
| Candidate | sRNA | Origin | Loc.a | 5′-endb | 3′-endc | Typed | Target genese | Target function | O. g.f | ExPEC specific?g | Scoreh N/ kcal/mol |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Escherichia coli | |||||||||||
| SQ8164 | IntP4R | E. c. 536 | PAI-II | 4 735 462 | 4 735 232 | asRNA | intP4 | PAI DNA mobility | < > | No | 10 / −26.28 |
| SQ7560 | PrfR | E. c. 536 | PAI-II | 4 747 389 | 4 747 630 | asRNA | prfF | Adhesion | > < | Yes | 3 / −12.64 |
| SQ7575 | HlyR | E. c. 536 | PAI-II | 4 763 726 | 4 763 963 | asRNA | hlyA | Hemolysis | > < | Yes | 2 / −5.76 |
| SQ7606 | HaeR | E. c. 536 | PAI-II | 4 783 731 | 4 783 731 | asRNA | ECP_4580 | Filamentous haemagglutinin | > < | Yes | 9 / −6.52 |
| SQ8017 | FimR | E. c. 536 | Core | 4 852 969* | 4 852 518 | asRNA | fimD | Adhesion | < > | No | 15 / −8.49 |
| SQ109 | AfaR | E. c. AL862 | PAI-I | 56 564* | 56 332 | IGR | afa8 | Adhesion | > < | Yes | 2 / −5.2 |
| SQ19 | IntR | E. c. AL862 | PAI-I | 58 845 | 59 076 | asRNA | Int | PAI DNA mobility | < > | No | 12 / −14.94 |
| Streptococcus agalactiae | |||||||||||
| SQ18 | SQ18 | S. a. NEM316 | Core | 47 857* | 47 734 | asRNA | gbs0031 | Surface exposed protein | > < | N.A. | 3 / −10 |
| SQ340 | SQ340 | S. a. NEM316 | PAI-X | 1 163 702* | 1 163 779 | IGR | gbs1118 | Transposase of TnGBS2 | > < | N.A. | 3 / −10.5 |
| SQ893 | SQ893 | S. a. NEM316 | Core | 13 00 661 | 1 300 360 | IGR | gbs1263 | Fibronectin binding protein | < > | N.A. | 3 / −4 |
| SQ407 | SQ407 | S. a. NEM316 | PAI-XII | 1 350 419 | 1 350 658 | asRNA | Lmb | Laminin binding protein | > < | N.A. | 11 / −11.5 |
| SQ485 | SQ485 | S. a. NEM316 | Core | 1 655 610 | 1 655 852 | asRNA | gbs1588/ gbs1589 | Putative ABC transporter | > < | N.A. | 9 / −10.3 |
| SQ1004 | SQ1004 | S. a. NEM316 | PAI-XIII | 2 052 153 | 2 052 383 | IGR | gbs1987 | Streptomycin resistance | > < | N.A. | 3 / −7.6 |
aLocalization of the sRNA gene. Core, core genome; PAI, pathogenicity islands.
bThe 5′-end of the sRNA candidate is arbitrarily located 200 bp upstream from the first nucleotide of the predicted RIT. An asterisk indicates the 5′ triphosphates RNA end determined by 5′ RACE. The 5′ ends of SQ109 (E. coli AL862) and SQ340 (S. agalactiae NEM316) sRNAs were determined in another study (C.P., personal communication).
cThe 3′-end of the sRNA candidate is defined as the last nucleotide of the RIT poly-uracil tail.
dType of sRNA candidate gene locus. IGR, intergenic region; asRNA, sRNA antisense to a CDS.
eAntisense sRNA predicted target mRNA. The sRNA genes located in an IGR may regulate adjacent genes by an antisense mechanism.
fO. g., Orientation of genes (order sRNA/mRNA).
gSpecificity was determined by FASTA analysis against the Genbank database.
hN, number of covariations identified/RIT score in kcal/mol.
E.c., Escherichia coli; S.a., Streptococcus agalactiae