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Table 1 Candidate promoters with different strengths selected based on omics datasets

From: Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

Gene ID

Gene name

Operon

Gene function

Array

RNA-Seq

Proteomics

EGFP/opmCherry (log phase)

EGFP/opmCherry (sta phase)

Candidate promoters with strong strength

 ZMO0177

gap

 

Glyceraldehyde-3-phosphate dehydrogenase, type I

15.06

11.2

9.23

0.38 ± 0.0202

0.47 ± 0.0191

 ZMO1360

pdc

 

Thiamine pyrophosphate protein TPP binding domain-containing protein

14.52

11.78

8.59

0.24 ± 0.0220

0.22 ± 0.0086

 ZMO0516

Tuf

ND

Elongation factor Tu

15.33

11.58

8.08

0.24 ± 0.0162

0.30 ± 0.0148

 ZMO1608

eno

 

Phosphopyruvate hydratase

15.22

13.2

8.97

0.23 ± 0.0145

0.34 ± 0.0093

 ZMO0997

eda

Yes

2-Dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

14.97

14.6

8.46

0.18 ± 0.0178

0.15 ± 0.0167

 ZMO0367

zwf

 

Glucose-6-phosphate 1-dehydrogenase

14.92

11.19

7.38

0.16 ± 0.0057

0.14 ± 0.0124

 ZMO1719

frk

 

ROK family protein

15.06

12.2

6.85

0.12 ± 0.0038

0.17 ± 0.0098

 ZMO1609

  

Hypothetical protein

15.26

12.77

5.78

0.12 ± 0.0061

0.14 ± 0.0038

 ZMO0689

gfo

 

Oxidoreductase domain-containing protein

14.49

11.68

6.38

0.10 ± 0.0075

0.13 ± 0.0130

 ZMO1721

gloA3

ND

Glyoxalase/bleomycin resistance protein/dioxygenase

14.35

12.66

5.97

0.09 ± 0.0044

0.11 ± 0.0022

 ZMO0514

rpsG

Yes

30S ribosomal protein S7

15.31

10.79

5.54

0.07 ± 0.0062

0.07 ± 0.0015

 ZMO0515

 

Yes

Elongation factor G

15.07

11.14

5.83

0.07 ± 0.0062

0.07 ± 0.0015

 ZMO1596

adhB

 

Iron-containing alcohol dehydrogenase

15.32

10.98

7.07

0.07 ± 0.0084

0.07 ± 0.0030

 ZMO1141

ilvC

Yes

Ketol-acid reductoisomerase

15.41

12.39

6.76

0.05 ± 0.0012

0.04 ± 0.0006

 ZMO0241

atpD

Yes

F0F1 ATP synthase subunit beta

15.09

11.73

7.77

0.05 ± 0.0030

0.04 ± 0.0029

 ZMO0244

  

Histone family protein DNA-binding protein

14.79

12.98

6.1

0.04 ± 0.0013

0.04 ± 0.0007

 Po1721

      

0.04 ± 0.0020

0.03 ± 0.0007

 ZMO0493

glnA

Yes

Glutamine synthetase, type I

14.53

10.02

6.17

0.03 ± 0.0023

0.03 ± 0.0005

 ZMO1779

 

Yes

Antibiotic biosynthesis monooxygenase

15.08

11.24

7.52

0.02 ± 0.0005

0.02 ± 0.0008

Candidate promoters with medium strength

 ZMO1351

clcD1

Yes

Carboxymethylenebutenolidase

12.93

6.81

3.14

0.14 ± 0.0064

0.16 ± 0.0036

 ZMO0056

glmS

 

Glucosamine–fructose-6-phosphate aminotransferase

12.93

6.91

2.45

0.12 ± 0.0021

0.11 ± 0.0024

 ZMO0559

  

Hypothetical protein

12.68

6.75

3.1

0.11 ± 0.0064

0.08 ± 0.0039

 ZMO1385

  

Toxic anion resistance family protein

12.83

6.93

2.55

0.06 ± 0.0012

0.05 ± 0.0018

 ZMO0127

 

Yes

S1/P1 nuclease

12.84

7.11

3.13

0.05 ± 0.0015

0.05 ± 0.0014

 ZMO1100

 

Yes

Nucleotidyl transferase

12.58

7.18

2.82

0.05 ± 0.0012

0.05 ± 0.0023

 ZMO1392

  

Hypothetical protein

12.46

7.43

2.45

0.04 ± 0.0012

0.04 ± 0.0012

 ZMO0326

  

7-cyano-7-deazaguanine reductase

12.65

7.41

2.7

0.03 ± 0.0018

0.04 ± 0.0012

 ZMO0570

prmA

 

Ribosomal L11 methyltransferase

12.38

7.32

2.45

0.03 ± 0.0030

0.04 ± 0.0013

Candidate promoters with weak strength

 ZMO1231

recJ

 

Single-stranded-DNA-specific exonuclease RecJ

11.03

5.7

0.07

0.08 ± 0.0023

0.07 ± 0.0029

 ZMO1980

gidB

Yes

Methyltransferase GidB

10.59

5.27

0.07

0.05 ± 0.0025

0.05 ± 0.0029

 ZMO1484

  

UvrD/REP helicase

10.93

5.4

0.07

0.05 ± 0.0013

0.05 ± 0.0026

 ZMO0145

 

Yes

Peptidase M28

11.37

4.98

0.07

0.04 ± 0.0018

0.04 ± 0.0006

 ZMO0101

  

NAD-dependent epimerase/dehydratase

10.61

5.05

0.07

0.04 ± 0.0013

0.04 ± 0.0014

 ZMO1194

dprA

Yes

DNA protecting protein DprA

10.7

4.77

0.07

0.04 ± 0.0011

0.03 ± 0.0006

 ZMO1644

  

DEAD/DEAH box helicase domain-containing protein

10.61

4.98

0.07

0.03 ± 0.0013

0.03 ± 0.0007

 ZMO1582

  

Uracil-DNA glycosylase superfamily protein

10.33

4.63

0.07

0.03 ± 0.0004

0.03 ± 0.0003

 ZMO0005

cysD

Yes

Sulfate adenylyltransferase subunit 2

11.5

5.28

0.07

0.03 ± 0.0012

0.03 ± 0.0009

 ZMO0300

xseA

 

Exodeoxyribonuclease VII large subunit

11.6

4.71

0.07

0.03 ± 0.0010

0.03 ± 0.0013

  1. The operon information is predicted by DOOR2 prediction server. The values of array, RNA-Seq and proteomics of each gene are the average log2-transformed values under different growth conditions
  2. ND non-determined, Log phase exponential phase, Sta phase stationary phase
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Biotechnology for Biofuels and Bioproducts

ISSN: 2731-3654

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