Table 2.
Novel sRNAs implicated in the desiccation stress response in Salmonella enterica. Known sRNA similarities, sRNA conservation, predicted structural complexity, flanking/overlapping genes, putative targets, and expressions in stationary phase, 24 hr desiccated, and 72 hr desiccated cell samples are indicated.
| sRNAa | Conservation, sRNA Similarityb | Structurec | Flanking Genes & Overlapd | Putative Targets – IntaRNAe | Exp. In Stationaryf | Exp. In 24 hr Df | Exp. In 72 hr Df |
|---|---|---|---|---|---|---|---|
| sRNA294677 | WC, RF00391 | HS | rRNA; tRNAAsp; dkgB-1 | - | 25 | 117.7 | 78.8 |
| sRNA458139 | WC | HS | tsaA-1(3ʹ); yajB-1 | - | 16.2 | 31.4 | 13.6 |
| sRNA466762 | WC | HS | STnc1060(3ʹ); tsx-1 | - | 29.2 | 33.7 | 18.5 |
| sRNA539269 | WC | HS | priC-1 | - | 3.7 | 6.4 | 3.6 |
| sRNA539528 | WC | HS | apt-1 | - | 3.9 | 4.4 | 1.5 |
| sRNA898738 | WC | HS | ybiF-1; ompX-1(5ʹ) | - | 45.6 | 56 | 19 |
| sRNA901248 | WC, RF00110 | HS | ybiP-1; RybA(5ʹ); CBW16908 | - | 154.6 | 210.1 | 90.7 |
| sRNA978535 | WC | HS | cspD-1(3ʹ); clpS-1 | cspD | 32.3 | 19.1 | 7.6 |
| sRNA982124 | WC | HS | tnp-1(3ʹ) | - | 71.5 | 108.9 | 56.5 |
| sRNA982481 | WC, RF02902 | HS | CBW16982 | - | 1.9 | 16.7 | 17.2 |
| sRNA997533 | WC | HS | ftsK-1(3ʹ) | - | 2.7 | 9.3 | 14.3 |
| sRNA997685 | WC | HS | ftsK-1(3ʹ) | oadA1 | 5.6 | 15.8 | 7.9 |
| sRNA998116 | WC | HS | ftsK-1; lolA-1(5ʹ) | - | 9.1 | 10.1 | 3.6 |
| sRNA1000215 | - | HS | ycaJ-1; serS-1 | - | 9.8 | 9.8 | 4 |
| sRNA1118334 | WC | HS | ompA-1(3ʹ); sulA-1 | ompA | 24.9 | 28.3 | 15.2 |
| sRNA1227667 | WC | HS | rne-1(3ʹ) | ribonuclease E | 7 | 6 | 2.7 |
| sRNA1227716 | WC, RF00040 | HS | rne-1 | ribonuclease E | 16 | 13.5 | 6 |
| sRNA1290392 | WC, RF02076 | HS | tRNA-Arg; STnc520 | RatA | 42 | 19.8 | 11.1 |
| sRNA1291223 | - | HS | pliC-1(3ʹ) | lysozyme inhibitor | 26.8 | 37.1 | 11.8 |
| sRNA1291436 | - | HS | pliC-1 | - | 27 | 25.3 | 10.6 |
| sRNA1291652 | - | HP | CBW17281 | SsaE; Dcp | 32.4 | 18 | 6.5 |
| sRNA1320429 | WC | HS | yeaG-1(3ʹ) | - | 38 | 581.9 | 582.9 |
| sRNA1320654 | WC | HS | yeaG-1 | PrkA | 43.7 | 250 | 82.1 |
| sRNA1440272 | WC, RF00391 | HS | ssaE-1; sseA-1 | CpxP-like | 120.1 | 252.1 | 186.4 |
| sRNA1440474 | - | HP | ssaE-1; sseA-1(5ʹ); sseBa-1 | - | 31.6 | 18.5 | 6.2 |
| sRNA1448803 | - | HS | ssaK-1(3ʹ); ssaL-1; STnc1220 | - | 11.1 | 14 | 5.6 |
| sRNA1866912 | - | HS | CBW17833(3ʹ); ycgN-1 | - | 547.2 | 1420.8 | 603 |
| sRNA1886080 | WC | HS | CBW17853(5ʹ) | - | 23.7 | 25.2 | 6.6 |
| sRNA1922930 | - | HS | CBW17896; CBW17897 | endonuclease | 1.7 | 6.5 | 2.4 |
| sRNA1954465 | WC | HS | aspS-1; yecD-1 | aspS | 8.7 | 11.5 | 4 |
| sRNA1954754 | - | HS | yecD-1(3ʹ) | - | 7.2 | 10.3 | 3.4 |
| sRNA1996414 | WC | HS | sirA-1 (3ʹ) | dbrr | 22.9 | 8.1 | 2.8 |
| sRNA1996681 | WC | HS | yecF-1; sirA-1 | - | 4.8 | 2.8 | 1.9 |
| sRNA2111563 | WC, RF00174 | HS | cbiA-1; pag | ProP effector protein | 10.9 | 3.6 | 1.8 |
| sRNA2111772 | - | HS | cbiA-1; pocR-1 | - | 7.2 | 1.3 | 0.9 |
| sRNA2437186 | WC | HS | nuoA-1(3ʹ) | nuoA | 15.8 | 17.6 | 6.1 |
| sRNA2437382 | WC | HP | nuoA-1; CBW184000 | lytictransglycosylase; patatin family protein |
26.3 | 14.8 | 7.6 |
| sRNA2495587 | WC | HS | sixA-1(3ʹ); fadJ-1 | sixA | 100 | 162.4 | 82.9 |
| sRNA2499697 | WC | HS | yfcZ-1(3ʹ) | - | 24.9 | 21.3 | 7.9 |
| sRNA2499837 | WC | HS | fadL-1; yfcZ-1 | - | 5.6 | 18.3 | 9.6 |
| sRNA2522653 | WC | HS | nupC-1; mntH-1(3ʹ) | mntH | 4.7 | 24.3 | 7.4 |
| sRNA2522758 | - | HS | nupC-1; mntH-1 | treR; CysZ | 6.3 | 23.1 | 6.7 |
| sRNA2522977 | WC | HS | nupC-1(5ʹ) | - | 3.6 | 23.2 | 8 |
| sRNA2828025 | WC, RF00391 | HS | rimM-1; rps16-1(3ʹ); ffh-1 | 30S ribosomal protein S16 | 7.9 | 21.7 | 10.2 |
| sRNA2828147 | WC | HS | rps16-1; ffh-1 | ABC transporter; RecF; pncA |
3.9 | 13.7 | 5.5 |
| sRNA2828280 | WC | HS | rps16-1; ffh-1(5ʹ) | - | 8.6 | 26.1 | 10.3 |
| sRNA2948961 | - | HS | pipB2-1 | glgX; Kdul; HyaE; nrdD | 19.4 | 73.8 | 37.3 |
| sRNA2950404 | - | HP | pipB2-1(3ʹ) | pipB2 | 7.3 | 9.6 | 3.3 |
| sRNA2950578 | WC | HP | pipB2-1 | murC; SDR | 20.6 | 7.6 | 4.4 |
| sRNA2969551 | WC | HS | ygaP-1; stpA-1 | - | 9.8 | 14 | 9.3 |
| sRNA3393373 | - | HS | ygiH-1; gcp-1 | - | 26 | 63.5 | 38.3 |
| sRNA3395090 | WC, RF02818 | HS | rpsU-1; dnaG-1(5ʹ) | - | 7 | 25.3 | 9 |
| sRNA3417448 | WC | HS | yqjC-1(3ʹ); yqjE-1 | ferredoxin | 80 | 405.6 | 151.6 |
| sRNA3417670 | WC | HS | yqjC-1; yqjE-1 | ybbK; oadA1 | 64.7 | 484 | 218 |
| sRNA3435592 | WC, RF00010 | HP | gark-1 | - | 4254.2 | 2399.9 | 1744.1 |
| sRNA3435639 | WC, RF00010 | HS | gark-1 | - | 11178.2 | 7799 | 5212.6 |
| sRNA3758077 | WC | HS | rpoH-1(3ʹ); ftsX-1 | rpoH | 123.6 | 132.5 | 58.9 |
| sRNA3857685 | WC, RF01766 | HS | yiaG-1; cspA-1(5ʹ) | - | 452.4 | 1577 | 563.7 |
| sRNA3981754 | WC | HS | slsA-1(3ʹ); cigR-1 | - | 187.6 | 75.8 | 21.6 |
| sRNA3981945 | WC, RF00391 | HS | sciZ-1; yafV-1 | - | 106.6 | 250.6 | 166.6 |
| sRNA4066303 | WC | HS | dnaA-1(3ʹ) | DnaA | 12.6 | 19.9 | 7.7 |
| sRNA4066490 | - | HS | dnaA-1 | UmuD | 15.5 | 13.5 | 6.4 |
| sRNA4318787 | - | HS | yiiU-1(3ʹ); menG-1 | ilvD; NirC; kup; manY |
64.7 | 114.2 | 50.4 |
| sRNA4433610 | WC | HS | metH-1; yjbB-1(5ʹ) | - | 21.7 | 72.7 | 34 |
| sRNA4534936 | WC | HS | yjcH-1; acs-1(5ʹ) | rtcA | 3.7 | 26.9 | 13.5 |
| sRNA4626941 | WC | HS | hflX-1; hflK-1(5ʹ) | CreC; rpiA | 12.9 | 47.7 | 20.6 |
| sRNA4662099 | - | HS | cpdB-1; cysQ-1 | cpdB | 10.1 | 16.6 | 7.9 |
| sRNA4662318 | WC | HS | cpdB-1; cysQ-1(5ʹ) | - | 7.2 | 25.3 | 10.2 |
| sRNA4663946 | WC | HS | ytfK-1(5ʹ); ytfL-1 | - | 83 | 98.2 | 50.6 |
| sRNA4837237 | WC | HS | osmY-1; yjjU-1 | ndk; epmA | 43.8 | 203.2 | 108.5 |
| sRNA4876851 | WC | HS | arcA-1; yjjY-1(3ʹ) | - | 19.7 | 29.6 | 11.2 |
asRNA – name refers to the starting nucleotide position of the putative sRNA sequence on the SL1344 chromosome.
bConservation, sRNA Similarity – (WC), ‘well-conserved’ sRNAs are at least 80% identical over their entire length to a genomic sequence found within at least one other distinct bacterial genus. RF number refer to RFAM sequence family significantly aligning to indicated sRNA.
cStructure – Hairpin (HP), simple sRNA secondary structure containing one hairpin predicted with Mfold; Highly structured (HS), possesses more than one hairpin or simple structural element within predicted secondary structure.
dFlanking genes and Overlap determined by alignment in Ensembl – (5′) indicates that sRNA overlaps 5′-end of CDS; (3′) indicates that sRNA overlaps 3′-end of CDS.
ePutative Targets determined by IntaRNA, assuming a fdr cut-off of 0.1.
fExp. In Stationary – normalized number of transcripts per million (TPM) at sRNA location during normal stationary-phase growth; Exp. In 24 hr D – normalized TPM at sRNA location after 24 h of desiccation; Exp. In 72 hr D – normalized TPM at sRNA location after 72 h of desiccation.