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Table 3 Small RNA species detected reliably by RNA-Seq and confirmed by RT-qPCR. Differential expression in biofilms and during swarming motility

From: High-throughput detection of RNA processing in bacteria

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
  1. 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
  2. 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
  3. 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