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Table 1 Selected Synechocystis sRNAs for two-step RT-PCR analysis and relative abundance (ranked by sRNA abundance)

From: Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803

sRNA

Location

Dir*

∆G (kcal/mol)

5′ gene

Annotation

Distance (bp)

3′ gene

Annotation

Distance (bp)

Relative abundance

E24

E48

 

nc64

1,832,231–1,832,345

<>>

−40.6

sll1382

Ferredoxin

302

slr1474

Hypothetical protein

15

Nc64 (4.5S rRNA)

1.01

0.51

 

nc18

552,943–553,017

<<<

−16.8

sll1635

FAD-dependent thymidylate synthase

76

sml0005

Photosystem II reaction center protein K

48

Nc18 (Ncl0200)

0.965

0.837

 

nc1

2948–3061

<><

−14.1

sll0558

Hypothetical protein

75

sll1214

Magnesium-protoporphyrin IX monomethyl ester cyclase

131

Nc1

0.881

1.274

 

nc121

3,316,752–3,317,151

><<

−108.3

slr1464

Hypothetical protein

17

ssl2667

NifU protein

212

Nc121 (tmRNA)

1.315

0.646

 

nc81

2,250,490–2,250,580

><>

−34.9

ssr3307

Preprotein translocase subunit SecG

16

slr1946

Hypothetical protein

131

Nc81

1.133

3.577

 

nc110

3,138,648–3,138,738

<<<

−18.2

sll0737

Hypothetical protein

44

sll0048

Hypothetical protein

179

Nc110 (SyR5)

1.19

2.171

 

nc26

842,648–842,758

<<>

−40.5

sll1799

50S ribosomal protein L3

35

slr1894

Hypothetical protein

347

Nc26

1.201

0.635

 

nc41

1,190,736–1,190,822

<>>

−22.2

sll1783

Hypothetical protein

353

slr1852

Hypothetical protein

45

Nc41 (Ncr0480)

0.678

1.053

 

nc70

1,886,895–1,887,070

>><

−47.8

slr1288

Hypothetical protein

158

sll1166

Hypothetical protein

89

Nc70 (6S rRNA)

0.743

0.701

 

nc7

219,563–219,783

<<<

−66.9

sll1029

Carbon dioxide concentrating mechanism protein CcmK

46

sll1027

NADH-glutamate synthase small subunit

196

Nc7

1.303

0.632

 

nc122

3,323,090–3,323,230

<>>

−25.8

sll0629

Photosystem I subunit X

327

slr0653

RNA polymerase sigma factor RpoD

45

Nc122 (Ncr1650)

1.042

0.848

 

nc60

1,748,923–1,749,070

<<>

−44.8

sll1247

Hypothetical protein

30

slr1351

UDP-N-acetylmuramoylalanyl-d-glutamyl-2,6-diamino-pimelate-d-alanyl-d-alanine ligase

76

Nc60 (SyR7)

0.912

1.229

 

nc117

3,250,549–3,250,647

>>>

−10.1

slr0550

Dihydrodipicolinate synthase

262

slr0551

Hypothetical protein

353

Nc117 (Ncr1600)

1.519

1.67

 

nc33

1,004,885–1,005,121

<<<

−40.2

sll1454

Nitrate reductase

108

sll1453

Nitrate transport protein NrtD

60

Nc33

1.607

0.815

 

nc85

2,383,750–2,383,875

>><

−42.3

slr0381

Hypothetical protein

114

sll0330

3-Ketoacyl-ACP reductase

74

Nc85

1.13

2.111

 

nc65

1,840,822–1,840,980

<><

−25.4

sll1376

Bifunctional sterol desaturase/short chain dehydrogenase

331

sll1374

Melibiose carrier protein

76

Nc65

1.068

1.089

 

sRNA

E72

B24

B48

B72

H24

H48

H72

S24

S48

S72

N24

N48

N72

nc64

1.519

1.254

0.709

2.69

1.387

0.609

1.572

2.061

1.09

2.143

0.674

0.387

1.131

nc18

0.834

1.289

1.001

0.596

0.972

0.634

0.221

0.366

0.298

0.278

0.111

0.048

0.05

nc1

0.858

0.927

1.584

0.804

0.72

0.844

0.548

0.642

0.993

0.748

0.189

0.188

0.115

nc121

0.853

1.452

0.36

1.469

2.311

0.544

1.534

1.107

0.853

1.626

0.888

0.768

3.146

nc81

0.882

1.641

7.166

1.058

1.326

1.784

0.381

0.691

1.021

0.261

2.293

4.651

1.237

nc110

1.04

1.335

2.358

1.799

3.616

1.22

0.647

1.097

1.398

0.538

1.276

3.595

3.599

nc26

0.64

0.852

0.76

0.653

0.75

0.813

0.489

2.159

1.544

1.709

0.587

0.225

0.163

nc41

0.973

0.959

0.955

0.665

0.969

1.249

0.619

0.207

0.314

0.296

0.319

0.209

0.149

nc70

1.635

0.896

0.465

1.346

1.511

0.577

1.472

1.005

0.865

1.809

1.086

0.876

2.212

nc7

1.178

1.08

0.454

0.981

1.001

0.572

1.259

1.193

1.054

2.444

0.398

0.311

1.158

nc122

1.031

0.864

0.968

0.823

0.723

0.875

1.059

0.58

0.768

0.677

1.531

1.263

1.962

nc60

1.078

0.504

0.73

0.506

0.979

0.512

0.365

0.179

0.201

0.26

1.438

0.965

0.573

nc117

1.293

1.743

1.623

1.035

1.101

0.851

0.866

2.083

1.12

1.12

0.875

1.061

1.404

nc33

1.282

2.254

0.773

1.172

1.239

0.905

0.788

4.606

2.041

3.843

3.152

3.674

4.558

nc85

1.39

1.305

2.13

1.212

0.898

0.964

0.472

1.077

1.402

0.769

4.358

4.151

3.34

nc65

0.927

1.165

1.148

0.987

1.223

0.99

0.857

1.044

1.129

0.94

1.392

1.526

1.364

  1. * Direction of sRNA and adjacent genes