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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