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Table 1 sRNA-encoding genes in Erwinia amylovora identified by RNA-seq

From: Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function

IDa

Strandb

Startc

Endc

Sized

Adjacent genese

Orientationf

Rfam (E-value)g

RI terminatorh

Northerni

Mutationj

5’ RACEk

Δ hfq/Ea1189 6 hr (%)l

Δ hfq/Ea1189 12 hr (%)m

spf (spot42)

+

52654

52816

163

polA/engB

> > <

RF00021 (3.2E-25)

Yes

NT

Yes

 

12.5

7.2

hrs1

+

130070

130143

74

cpxP/fief

> > >

N/A

Yes

Yes

No

 

21.2

13.9

hrs2

+

245012

245077

66

metE/ysgA

> > <

N/A

Yes

NT

No

 

8.5

4.5

hrs3

+

834512

834619

108

EAM0472/EAM0473

< > <

N/A

Yes

NT

No

 

33.3

0.0

micM (sroB)

+

1149210

1149296

87

EAM1042/EAM1043

< > <

RF00368 (7.5E-10)

Yes

NT

Yes

 

10.0

0.0

hrs4

-

1252343

1252249

95

mtr/fur

> < <

 

Yes

NT

No

 

86.9

76.4

hrs5

-

1408551

1408436

116

EAM1295/EAM1296

< < <

RF00110 (1.2E-10)

Yes

Yes

Yes

1408551

15.9

10.8

rprA

-

1771945

1771835

111

ppsA/EAM1647

> < <

RF00034 (1.9E-12)

Yes

Yes

Yes

 

2.5

5.5

hrs6 (rmaA)

+

1783452

1783564

113

sufE/lpp

> > <

N/A

Yes

Yes

Yes

 

76.7

50.4

hrs7

-

1964168

1964063

78

palI/EAM1824

< < <

N/A

Yes

NT

No

 

8.7

0.0

ryhB

-

1981794

1981655

140

pspF/sapA

> < >

RF00057 (6.9E-13)

Yes

Yes

Yes

 

2.7

2.1

hrs8

-

2132995

2132831

165

EAM1984/EAM1985

< < <

RF00111 (1.1E-24)

Yes

Yes

Yes

2132931

24.2

15.2

hrs9

-

2315585

2315491

95

EAM2160/galE

< < <

RF01707 (2.5E-11)

Yes

Yes

No

2315684; 2315585

29.6

39.2

hrs10

+

2356621

2356768

148

EAM2188/EAM2189

> > >

N/A

Yes

Yes

Yes

2356641

24.0

42.1

hrs11

-

2399219

2399091

129

spr/rtn

> < >

N/A

Yes

ND

Yes

2399299

18.6

29.2

hrs12

+

2438083

2438169

87

ompC/EAM2260

< > >

RF00033 (6.3E-3)

Yes

Yes

Yes

2438075

3.5

5.2

hrs13

-

2610835

2610754

82

ansP/EAM2411

< < <

N/A

Yes

Yes

Yes

 

0.3

11.2

micA

+

2872049

2872162

114

luxS/gshA

< > <

RF00078 (5.6E-13)

Yes

NT

Yes

 

68.5

26.3

gcvB

+

2962739

2962947

209

gcvA/EAM2720

< > <

RF00022 (3.4E-33)

Yes

Yes

No

 

2.1

0.5

omrAB

-

3009426

3009347

80

EAM2752/EAM2753

< < >

RF00079 (1.4E-14)

Yes

Yes

Yes

 

28.0

4.8

arcZ (ryhA)

+

3399347

3399550

204

mtgA/arcB

< > <

RF00081 (8.4E-16)

Yes

Yes

Yes

 

3.1

1.6

hrs15

-

3573610

3573476

135

EAM3277/EAM3278

< < >

RF00057 (5.0E-13)

Yes

NT

Yes

 

5.9

6.3

hrs16

+

3790560

3790675

116

EAM3469/EAM3470

> > >

N/A

Yes

NT

No

 

0.0

0.0

hrs17

+

83003

83246

244

EAM0051/EAM0052

< > >

N/A

No

NT

No

 

31.1

18.2

hrs18

+

500345

500429

85

dcuA/aspA

< > <

N/A

No

NT

No

 

51.0

36.5

hrs19

+

1119874

1119949

76

EAM1011/EAM1012

< > <

N/A

No

Yes

No

 

57.4

73.3

hrs20

-

1212602

1212522

81

EAM1116/EAM1117

> < >

N/A

No

NT

Yes

 

16.5

42.9

hrs21

-

1267525

1267392

134

gltA/sdhC

< < >

N/A

No

Yes

Yes

1267597; 1267524

10.9

2.2

hrs23

+

1767030

1767167

138

hmuS/EAM1643

< > <

N/A

No

NT

No

 

38.1

62.1

hrs24

-

1794862

1794772

91

EAM1664/EAM1665

< < >

N/A

No

NT

No

 

2.4

0.0

hrs25

-

1894012

1893924

89

EAM1754/EAM1755

< < >

N/A

No

NT

No

 

24.1

11.8

hrs26

-

1909866

1909756

111

pepT/EAM1768

> < <

N/A

No

NT

No

 

11.1

3.3

hrs27

+

1922305

1922405

101

EAM1774/fnr

< > >

N/A

No

Yes

Yes

 

0.0

0.0

hrs28

-

1929971

1929863

109

EAM1781/ydgI

> < >

N/A

No

NT

No

 

5.0

3.4

hrs29

+

2391802

2392008

207

nfo/fruA

> > <

N/A

No

NT

Yes

 

13.3

28.6

hrs30

+

2493229

2493312

84

EAM2298/EAM2299

< > <

N/A

No

NT

No

 

59.1

44.6

hrs31

-

2556693

2556613

81

ccmA/EAM2395

< < >

N/A

No

Yes

Yes

 

65.2

3.5

hrs32

+

2649467

2649520

54

EAM2427/EAM2428

< > <

N/A

No

NT

No

 

40.0

69.2

hrs33

-

2857326

2857206

121

EAM2616/EAM2617

> < >

N/A

No

NT

No

 

58.5

50.0

hrs34

-

3356002

3355930

73

EAM3063/EAM3064

< < >

N/A

No

NT

Yes

 

18.2

46.7

  1. aGene names of E. amylovora sRNAs.
  2. bThe strand (+:clockwise; -:counterclockwise strand of the chromosome) that the sRNA is encoded.
  3. cGenome locations of the sRNA genes.
  4. dPutative sizes of the sRNAs detected by deep sequencing.
  5. eFlanking genes of the intergenic region in which the sRNA is encoded.
  6. fThe orientation of the flanking genes and sRNA gene (middle).
  7. gThe Rfam database match. Rfam accession number and E-value are provided if a match was found. N/A means no match found in the Rfam database.
  8. hWhether Rho-independent terminator sequences are present at the 3’ end of the sRNA.
  9. iWhether the expression and size of the sRNA were confirmed by Northern blot. See Figure 2 and [39]. ND: not detected, NT: not tested.
  10. jWhether deletion mutant of the sRNA gene was constructed.
  11. kWhether the transcription start site of the sRNA was mapped by the 5’ RACE assay. The number indicates the nucleotide on the E. amylovora genome from which the transcription of the sRNA starts.
  12. lThe percentage of sRNA depth in Δhfq mutant compared to Ea1189 at 6 hr post-induction in Hrp-inducing MM.
  13. mThe percentage of sRNA depth in Δhfq mutant compared to Ea1189 at 12 hr post-induction in Hrp-inducing MM.
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BMC Genomics

ISSN: 1471-2164

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