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Table 4 List of putative STM 2683 CDS differentially regulated upon metal exposure

From: Genome-wide transcriptional responses of two metal-tolerant symbiotic Mesorhizobium isolates to Zinc and Cadmium exposure

Label*

CDS description and putative function

Zn / Control

Cd / Control

 

log2 Fold

FDR

log2 Fold

FDR

STM 4661 Homologs §

Transport

      

MESS2v1_p180001

Cation efflux system protein czcD-type (fragment)

1.97

2.5E-16

1.41

2E-08

MESS4v1_360039

MESS2v1_300037

ABC transporter, periplasmic binding protein, Zn import

−4.09

2E-60

2.54

1.3E-24

MESS4v1_520016

MESS2v1_300038

ABC transporter, permease protein, Zn import

−4.13

3E-116

2.49

4.5E-43

MESS4v1_520017

MESS2v1_300039

ABC transporter-related protein, Zn import

−4.37

2E-127

2.32

4E-24

MESS4v1_520018

MESS2v1_740030

Heavy metal-translocating P-type ATPase CadA

3.07

6.7E-21

2.2

2.2E-12

MESS4v1_360013

MESS2v1_980072

Transporter protein of unknown function

3.36

3E-42

2.2

4.9E-17

Not found

MESS2v1_980073

Zinc, cobalt and lead efflux system ZntA

4.65

2E-134

3.48

6E-131

MESS4v1_610026

MESS2v1_620035

Multidrug efflux system, subunit C, MdtC

0.93

0.0283

0.13

1

MESS4v1_690033

MESS2v1_620036

Multidrug efflux system, subunit A, MtdA

0.95

0.0116

0.0714

1

MESS4v1_690034

MESS2v1_730268

Putative cation efflux system protein (Cobalt-zinc-cadmium resistance CzcD-like), CDF family (fragment, part 1)

1.12

0.0182

0.67

0.69

MESS4v1_360039

MESS2v1_730269

Putative cation efflux system protein (Cobalt-zinc-cadmium resistance CzcD-like), CDF family (fragment, part 2)

1.26

0.00012

0.64

0.48

MESS4v1_360039

MESS2v1_320039

ABC transporter, permease protein, sugar transporter

0.44

1

0.82

0.0364

MESS4v1_530098

MESS2v1_730254

Efflux transporter, RND family, MFP subunit

−0.32

1

1.2

9.6E-05

Not found

Metal sequestration

     

MESS2v1_p180003

conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domain

2.01

4.4E-17

1.42

5.5E-08

MESS4v1_360040

MESS2v1_730267

conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domain

1.09

0.0263

0.58

1

MESS4v1_360040

MESS2v1_1150003

conserved and cytoplasmic protein of unknown function, contains 2 CPX Zn finger domain

−0.78

0.0792

−0.3

1

Not found

MESS2v1_310036

Cyclic beta-glucan succinyl transferase OpgC, cytoplasmic membrane

−0.14

1

0.76

0.0813

MESS4v1_520093

MESS2v1_1210019

Antibiotic biosynthesis monooxygenase, putative, involved in the biosynthesis of extracellular polysaccharides

−0.0992

1

0.77

0.0654

MESS4v1_160035

MESS2v1_740029

Cytochrome c biogenesis protein, transmembrane region CcdA, putative, involved in reduction as Zn or Cd Sulfides

3.04

6.2E-29

2.17

1.9E-30

MESS4v1_360014

MESS2v1_740015

Phosphoesterase PA-phosphatase-related (fragment), located in cytoplasmic membrane

1.19

3E-05

0.73

0.23

Not found

MESS2v1_740019

Signal peptidase II. Aspartic peptidase. MEROPS family A08, located in cytoplasmic membrane

1.64

1.5E-12

0.65

0.3

MESS4v1_360023

MESS2v1_440031

Rhodanese domain protein, putative, involved in reduction as sulfide

−0.0727

1

0.88

0.0481

MESS4v1_590053

MESS2v1_1160006

Transcription regulator, putative, involved in reduction as Cd Sulfides

0.0363

1

0.93

0.00391

MESS4v1_120164

MESS2v1_1660011

Putative cytochrome c biogenesis protein, involved in reduction as Cd sulfide, located in cytoplasmic membrane

0.1

1

1.59

2.9E-11

Not found

MESS2v1_1660012

Thioredoxin-related, putative, involved in reduction as Cd sulfide

−0.0234

1

1.68

9.2E-12

Not found

MESS2v1_160018

Serine endoprotease, periplasmic DegQ, putative, involved in Zn periplasmic binding

1.7

1.7E-10

0.24

1

MESS4v1_440007

MESS2v1_160022

Glutamate-ammonia-ligase adenylyltransferase GlnE, putative, involved in Zn periplasmic binding and participating to degQ activity

0.94

0.00988

0.33

1

MESS4v1_440011

MESS2v1_1530017

conserved exported protein of unknown function, putative metal-binding protein

−0.45

1

−1.58

3.9E-06

MESS4v1_830506

Regulation

      

MESS2v1_160020

putative Two-component transcriptional regulator; transcriptional regulator involved in heavy-metal (Cu/Zn) homeostasis

1.12

0.00012

0.0744

1

MESS4v1_440009

MESS2v1_160021

Sensor protein

0.87

0.0294

0.17

1

MESS4v1_440010

MESS2v1_300035

Transcriptional regulator, AsnC family

−0.38

1

1.12

0.00047

MESS4v1_520012

Oxidoreduction

      

MESS2v1_110046

Alpha/beta hydrolase fold protein

−0.87

0.0228

0.18

1

Not found

MESS2v1_620027

NAD(P)H:quinone oxidoreductase

1.1

0.00721

0.19

1

Not found

MESS2v1_1150002

Haloalkane dehalogenase

−0.83

0.0623

−0.74

0.21

Not found

MESS2v1_300036

conserved protein of unknown function, putative, hydrolase activity

−0.77

0.27

1.5

4.2E-07

MESS4v1_520015

MESS2v1_790137

conserved exported protein of unknown function, putative, succinate dehydrogenase/fumarate reductase, flavoprotein subunit

−0.26

1

1.08

0.00047

MESS4v1_830086

Others

      

MESS2v1_1590041

conserved protein of unknown function - N-acetyltransferase activity

−0.94

0.00626

−0.65

0.3

MESS4v1_830271

MESS2v1_10049

Protein folding- Stress - chaperonin groES

−0.91

0.0796

−0.51

1

MESS4v1_60077, MESS4v1_430231, MESS4v1_510195

MESS2v1_900005

transposase

−0.0531

1

0.95

0.0027

 

MESS2v1_980071

protein of unknown function, putative transposase

0.8

0.0689

−0.0345

1

Not found

MESS2v1_1530018

Nuclear export factor GLE1 (fragment)

−0.4

1

−1.54

2.6E-09

Not found

MESS2v1_1660010

conserved protein of unknown function, putative, antirestriction protein ArdC

−0.0576

1

0.89

0.00928

Not found

Unclassified

      

MESS2v1_p180002

protein of unknown function

2.02

1.8E-14

1.29

1.1E-06

Not found

MESS2v1_740028

exported protein of unknown function

2

3.1E-28

1.41

5E-07

Not found

MESS2v1_740031

protein of unknown function

2.17

2.4E-39

1.43

1.4E-09

Not found

MESS2v1_1030151

protein of unknown function

−1.5

2.7E-12

−1.75

2.1E-14

Not found

MESS2v1_1280026

protein of unknown function

1.73

6.8E-13

1.82

3.4E-13

Partial MESS4v1_220037

MESS2v1_1520011

protein of unknown function

−0.94

0.0626

−0.99

0.0116

Not found

MESS2v1_160019

protein of unknown function

1.71

1.1E-12

0.27

1

Not found

MESS2v1_280030

protein of unknown function

−0.79

0.0689

−0.66

0.29

Not found

MESS2v1_460011

protein of unknown function

0.79

0.0689

0.13

1

Not found

MESS2v1_620020

conserved exported protein of unknown function

−0.98

0.0834

0.12

1

Not found

MESS2v1_740027

protein of unknown function

1.18

3.5E-05

0.67

0.41

Not found

MESS2v1_980070

protein of unknown function

1.72

8.8E-08

0.92

0.62

Not found

MESS2v1_p110013

protein of unknown function

−0.72

0.73

−1.25

0.0192

Not found

MESS2v1_50011

protein of unknown function

−0.57

0.93

−0.99

0.0167

Not found

MESS2v1_310082

protein of unknown function

0.35

1

0.75

0.0813

Not found

MESS2v1_360012

protein of unknown function

−0.53

1

−0.77

0.0585

Not found

MESS2v1_600022

protein of unknown function

0.28

1

0.89

0.0833

Not found

MESS2v1_600023

conserved exported protein of unknown function

0.33

1

1.1

0.00014

MESS4v1_680074

MESS2v1_660006

protein of unknown function

−0.34

1

−0.75

0.0813

Not found

MESS2v1_730256

conserved protein of unknown function

−0.083

1

0.93

0.0049

Not found

MESS2v1_760133

protein of unknown function

−0.65

0.4

−0.75

0.0833

Not found

MESS2v1_1100024

conserved exported protein of unknown function

−0.41

1

0.94

0.0226

MESS4v1_120015

MESS2v1_1100025

conserved exported protein of unknown function

−0.12

1

1.05

0.00597

MESS4v1_120016

MESS2v1_1100026

conserved exported protein of unknown function

−0.22

1

1.05

0.00426

MESS4v1_120016

MESS2v1_1210020

conserved protein of unknown function

−0.71

0.44

1.36

5.1E-07

MESS4v1_160036

MESS2v1_1210021

conserved protein of unknown function

0.0842

1

1.2

0.00105

MESS4v1_160037

MESS2v1_1270078

conserved exported protein of unknown function

−0.0732

1

0.84

0.0503

MESS4v1_220001

MESS2v1_1530016

protein of unknown function

−0.42

1

−1.52

4.5E-05

Not found

MESS2v1_1660004

membrane protein of unknown function

0.16

1

1.04

0.00032

Not found

MESS2v1_1660005

conserved protein of unknown function

0.38

1

1.5

4.1E-12

Not found

  1. * Gene labels (CDS) were obtained from MaGe; CDS significantly regulated (FDR < 0.1) upon metal exposure in both STM 2683 and STM 4661 are in bold. MESS2v1_XXX are genes located on the chromosome and MESS2v1_pXXX are genes located on the plasmid.
  2. § When detected, STM 4661 homologs are indicated (See Methods for details).
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