Table 3.
Small RNA species detected reliably by RNA-Seq and confirmed by RT-qPCR. Differential expression in biofilms and during swarming motility
| Genomic Coordinates | Name | Size bp | Identity Gomez-Lozano, et al. | Identity Wurtzel, et al. | Complementarity (potential binding sites within other transcripts) | Fold change in biofilms | Fold change in swarming motility |
|---|---|---|---|---|---|---|---|
| 143,349–143,517 | PA0123.1 | 169 | pant15 | Not identified | None | 1 | 10 |
| 326,875–327,066 | PA0290.1 | 192 | pant37 | PA14sr_012 | pilW, plcH | −9 | 1 |
| 334,491–334,686 | PA0296.1 | 196 | Not identified | P1 | rne | −2 | 1 |
| 354,527–354,742 | PA0314.1 | 216 | pant42 | Not identified | None | −5 | 1 |
| 586,867–586,990 | PA0527.11 | 124 | rsmY | rsmY | None | 4 | 11 |
| 720,091–720,345 | PA0667.1 | 255 | Not identified | Not identified | PA3505, PA2897, PA0690 | −3 | 1 |
| 798,865–799,255 | PA0730.1 | 391 | pant80 | PA14sr_122 | None | −3 | 44 |
| 883,307–883,582 | PA0805.1 | 276 | pant89 | PA14sr_119PA14sr_120 | None | −5 | −5 |
| 1,045,414–1,045,733 | PA0958.1 | 320 | pant103 | PA14sr_112 | None | −6 | 2 |
| 1,182,820–1,183,057 | PA1091.1 | 238 | pant119 | Not identified | PA0588 | 3 | 5 |
| 1,254,432–1,254,698 | PA1156.1 | 267 | pant125 | PA14sr_105 | PA1123, phuR | 1 | 1 |
| 2,761,459–2,761,704 | PA2461.1 | 246 | pant225, | PA14sr_076, | PA2460, PA2458 | −8 | −3 |
| 2,761,599–2,761,911 | PA2461.2 | 313 | pant226 | PA14sr_077 | PA2460, PA2458 | −5 | 1 |
| 2,964,898–2,965,137 | PA2461.3 | 240 | pant233 | Not identified | PA5134 | −2 | 3 |
| 2,977,373–2,977,611 | PA2633.1 | 239 | pant235 | PA14sr_067 | PA3672, recJ, nrdG, PA3522, PA3949, PA5325 | 5 | 8 |
| 3,312,577–3,312,693 | PA2952.1 | 117 | Not identified | PA14sr_061 | PA4629 | −2 | 2 |
| 3,545,572–3,545,872 | PA3159.1 | 301 | pant292 | no PA14 ortholog | None | −2 | 3 |
| 3,697,226–3,697,433 | PA3299.1 | 208 | Not identified | Not identified | PA0690, cyoB | 2 | 1 |
| 3,930,282–3,930,639 | PA3514.1 | 358 | pant326 | no PA14 ortholog | tagF1 | 10 | 1 |
| 4,012,653–4,012,735 | PA3580.1 | 83 | pant337 | Not identified | None | −4 | 1 |
| 4,536,541–4,536,848 | PA4055.1 | 308 | pant373 | Not identified | PA2728, mfd, chpA, PA3641 | −3 | −2 |
| 5,080,450–5,080,630 | PA4539.1 | 181 | pant415 | Not identified | wzz | 2 | 10 |
| 5,207,898–5,208,463 | PA4639.1 | 566 | pant428 | PA14sr_139 | PA5156, PA2502, PA4510, aruI, PA0475, PA0558, PA1025 | 5 | n/a |
| 5,224,568–5,224,795 | PA4656.1 | 228 | pant430 | Not identified | PA2038, PA3517, PA2152, pslE, PA2472, PA2750 | −4 | 3 |
| 5,283,960–5,284,110 | PA4704.11 | 151 | prrF1 | prrF1 | prrF2 | 12 | 217 |
| 5,284,172–5,284,319 | PA4704.21 | 148 | prrF2 | prrF2 | prrF1 | 20 | 141 |
| 5,283,960–5,284,319 | prrH 1 | 360 | prrH | prrH | prrF1, prrF2 | 13 | 163 |
| 5,309,047–5,309,325 | PA4726.3 | 279 | pant439 | PA14sr_141 | ispA, hepA, PA2018, PA3461 | −5 | 1 |
| 5,718,503–5,718,753 | PA5078.1 | 251 | pant465 | Not identified | PA0312, kds | −6 | 3 |
| 5,973,539–5,973,681 | PA5304.1 | 143 | pant487 | Not identified | None | 1 | 5 |
| 5,986,186–5,986,427 | PA5316.2 | 242 | pant488 | PA14sr_154 | PA1302, PA2933, gcp, PA0241, PA0364, pilJ, hsiC2, PA2325, PA3037, rnhB, pchF, recD, algP | −7 | −2 |
1RsmY and PrrF1–2, included as controls, were previously known to be up-regulated during the biofilm mode of growth [24]. The two small RNAs named PrrF1 and PrrF2 are adjacent and very similar in sequence and have been reported to also form a single transcript named PrrH
2n/a indicates that no consistent amplification or expression of that transcript was detectable under the given adaptive condition in three biological replicates. Expression was observed under mid logarithmic growth conditions
Four other putative sRNAs (68,836–69,271, 707,395–707,685, 830,970–831,031, and 99,801–100,048) could not be confirmed by RT-qPCR