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Table 1 Sequence motifs identified in regulatory regions of the genes differentially expressed in the rosR mutant and the wild-type strain, which show a significant similarity to the RosR-box sequence

From: Transcriptome profiling of a Rhizobium leguminosarum bv. trifolii rosR mutant reveals the role of the transcriptional regulator RosR in motility, synthesis of cell-surface components, and other cellular processes

Gene

Putative function of encoded protein product

COG

Log2 fold change

Sequence motif (5’-3’)a

Identity (%)

Distance to translation start site (nt)

Rt617_78

Amino acid ABC transporter substrate-binding protein

E

5.097

TGAAATCCATATCGACACTTCT

72.2

0

Rt620_77

Urea ABC transporter ATP-binding protein

E

3.502

CGGCTTCAAGGCGCTGAATTCG

66.7

61

Rt619_162

ABC-type dipeptide/oligopeptide transport system, permease

EP

−4.011

CAGAATCCGGCGGTGC-TTCCG

68.2

−153

Rt619_164

Peptide ABC transporter ATPase

EP

−4.438

CGCATTCTTCTCCTCTATATCG

66.7

−281

Rt648_25

LacI family transcriptional regulator

G

3.147

CGGCGGATAATCCTTGATCTCG

66.7

−176

Rt794_16

ABC transporter ATP-binding protein

G

2.968

GCGCTTCGTGGCGTGGATTTCG

66.7

56

Rt794_99

Sugar ABC transporter

G

2.053

CGGATTCCAGTAGGGATTTTCG

72.2

85

Rt643_15

Sugar ABC transporter substrate-binding protein

G

−3.744

CGGGGTCAGCAACTGCATTTCG

72.2

−83

Rt620_14

Glycerol 3-phosphate ABC transporter

G

2.133

CGAAATTTCTCTAAATATTTCC

66.7

−174

Rt657_260

Cell division protein FtsK

D

−3.211

CGGCGTCGAGATCTCGACATCG

66.7

−216

Rt634_26

Flagellar biosynthesis repressor FlbT

N

−3.247

CGCAAGGTCGCGCTGGAATTCC

66.7

74

Rt634_27

Flagellar basal body rod modification protein FlgD

N

−3.391

CAGAAGGCAACGCTGAATTACG

66.7

65

Rt634_13

Flagellin B

N

−4.601

TCCGATCTCGATTTAGCTTTCT

66.7

−170

Rt634_5

Flagellar basal body P-ring biosynthesis protein FlgA

N

−3.438

GGAAATCACCGAGCTGATCTCG

59.1

−99

Rt628_11

Flagellar motor switch protein FliN

NU

−4.579

CCGGCTGCGGGCATGGATTTCG

66.7

−13

Rt761_94

Methyl-accepting chemotaxis protein

NT

−3.966

CGCAAACGCAGTGTGTATTTGA

54.5

−124

Rt628_20

Chemotaxis protein CheD

NT

−2.353

CGAATTGGAAGATTGGCTGTCG

66.7

145

Rt792_47

Chemotaxis protein

NT

−2.587

CGGAATGCAGCTATCCATTCCC

66.7

−36

Rt647_8

Chemotaxis protein

NT

−3.651

TAAATTCTACGCCAAGATCGCC

66.7

127

Rt628_24

Chemotaxis protein CheW

NT

−3.050

CGGAGTCCAGCCCGGATTTCG

72.7

98

Rt628_25

Chemotaxis protein CheA

NT

−2.793

CGGAGTCCAGCCCCGGATTTCG

72.7

98

Rt792_70

Chemotaxis protein

NT

−3.025

CGGATGACATCAGAGGATTTCG

72.2

−298

Rt628_22

Chemotaxis protein CheB

NT

−3.030

CGGCGTCTATGAATGGGTGGAG

66.7

−40

Rt620_4

Glycosyl transferase

M

5.444

CGAATACCAAAGCCTGATTTCG

66.7

−76

Rt620_5

Polysaccharide biosynthesis protein

M

5.090

CTGGCGCGACTGCTCGATTTCG

66.7

59

Rt794_35

Polysaccharide biosynthesis protein

M

2.433

CGGCATCGGCCGGTAGATGACG

66.7

−191

Rt768_57

Peptidoglycan hydrolase

M

−2.657

CCGCATCGGCACGATGATTTCG

66.7

−243

Rt679_3

Glycosyl transferase

M

−3.806

CCGATTCACTATCTCGATCTCG

66.7

−137

Rt621_6

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase

M

−2.028

CGAAATCCGCTGCGAGATATAA

66.7

130

Rt623_92

Glycosyl transferase

M

−2.450

TGAAGTCTTGGGACTGACATCA

66.7

−106

Rt780_45

Polysaccharide biosynthesis protein

M

7.890

TTGAAACGA-GCCTGGATTACG

63.6

291

Rt627_76

Polysaccharide biosynthesis protein GelA

M

2.218

CGGATCGAAGCG-TG-AATTCG

63.6

22

Rt620_62

Exopolysaccharide biosynthesis protein PssA

M

−1.170

CGAAATGCTGTTGTTTAGTTCC

54.5

11

Rt772_12

Glycosyl transferase PssC

M

−1.451

CTGAAGCTCCGGGGCGAAGCTCG

63.6

−125

Rt780_150

Signal peptide protein

H

3.925

ATGCATCAAATACTGCATGTCG

66.7

−239

Rt622_32

Ubiquinol oxidase subunit II

C

−6.942

CGAAAAATCCTTCTTGATTTCA

66.7

−231

Rt620_122

Iron transporter

P

−2.510

CGGAAGGCAGCGATGGTGTTCT

66.7

73

Rt772_17

PrsD component of type I secretion system

MU

2.252

CTGCAGCTACGGGTCCATCAAG

59.1

−50

Rt646_16

Acyl-homoserine-lactone synthase (RaiI)

T

6.049

AGCAATCTATGAATGGAATCGT

66.7

64

Rt628_39

Histidine kinase (PhoR)

T

3.583

GGTAATCTAGCACCGTAATTTG

66.7

−200

Rt620_2

Crp/Fnr family transcriptional regulator

T

7.049

TTTCAACTAAATGTAGACTTGA

66.7

−129

Rt628_38

Chemotaxis protein CheY

T

4.010

GAGGATCTCGCCGGGGATTTCC

66.7

−299

Rt628_26

Chemotaxis protein CheY

T

−3.129

CGGAACCAATGTCAGCATTGAG

66.7

81

Rt782_109

Nitrogen regulatory protein P-II

TE

3.152

CGGTATTCAGGGGCTGAC—-CG

63.6

80

Rt648_50

PhoB family transcriptional regulator

TK

3.900

GGTCGTCAAGGTGTTGAACCAG

50.0

−167

Rt783_97

Transcriptional regulator

K

4.442

CGGTGTCGGCCATCGGCTTTCG

66.7

−224

Rt794_73

TetR family transcriptional regulator

K

3.385

CGTCATCTCGATGACCATTTCG

66.7

49

Rt764_77

TetR family transcriptional regulator

K

2.774

TGAAATCTCCGCAGCCGTTCCA

66.7

40

Rt780_87

AraC family transcriptional regulator

K

2.340

GCAAATCAATCGATCGATCTCG

66.7

117

Rt792_156

LysR family transcriptional regulator

K

2.246

CAGGATCTGGAAGCCGATATCG

66.7

131

Rt641_47

LysR family transcriptional regulator

K

2.237

CGGAAGGTGTTTTCGGATGCCG

66.7

−267

Rt636_12

GntR family transcriptional regulator

K

2.044

CCGAAACTATCAGCGCGCTTCG

66.7

−45

Rt764_77

TetR family transcriptional regulator

K

2.774

TGAAATCTCCGCAGCCGTTCCA

66.7

40

Rt634_21

Transcriptional regulator

K

−1.776

TCAAATCGCTACCCAGATCTTA

66.7

−126

Rt780_42

Membrane protein

S

5.363

CGATATTTAATGATGGATACCA

66.7

−64

  

RosR-box sequence

 

CGGAATCTAGGGGTGGATTTCG

-

-

  1. aIdentity of sequence motifs to the RosR-box was determined using 22-nt long sequences with the exception of their 4 nt in the middle of the sequence