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Table 4 Upregulated and downregulated genes in CaAc and NaAc condition (gene expression ≥ 100, fold change ≥ 2, and p value ≤ .05)

From: Enhanced calcium carbonate-biofilm complex formation by alkali-generating Lysinibacillus boronitolerans YS11 and alkaliphilic Bacillus sp. AK13

Locus taq

Gene symbol

Product

Strand

CaAc RPKM

NaAc RPKM

CaAc/NaAc

Genes upregulated by high Ca2+

 Branched chain amino acid synthesis

  LBYS11_13585

 

Acetolactate synthase small subunit

−

144.04

14

10.29

  LBYS11_13570

leuB

3-Isopropylmalate dehydrogenase

−

124.41

12.67

9.82

  LBYS11_13580

 

Ketol-acid reductoisomerase

−

263.2

27.42

9.6

  LBYS11_13560

leuD

3-Isopropylmalate dehydratase small subunit

−

116.42

12.75

9.13

  LBYS11_13565

leuC

3-Isopropylmalate dehydratase large subunit

−

144.46

17.55

8.23

  LBYS11_13575

 

2-Isopropylmalate synthase

−

165.84

20.78

7.98

  LBYS11_13590

ilvB

Acetolactate synthase large subunit IlvB1

−

131.49

18.13

7.25

  LBYS11_13595

ilvD

Dihydroxy-acid dehydratase

−

223.6

41.14

5.44

 Branched chain fatty acid synthesis

  LBYS11_00205

 

Hypothetical protein (NCBI blast: 3-oxoacyl-(Acyl-carrier-protein (ACP)) synthase III)

+

1150.45

113.55

10.13

  LBYS11_00220

 

Phosphopantetheine-binding protein

+

1044.75

125.49

8.33

  LBYS11_00200

 

Hypothetical protein: holo-[acyl-carrier-protein] synthase

+

956.13

115.3

8.29

  LBYS11_00230

 

Hypothetical protein: holo-[acyl-carrier-protein] synthase

+

1028.85

125.53

8.2

 Lysine synthesis

  LBYS11_00215

lysA

Diaminopimelate decarboxylase

+

1089.26

118.57

9.19

 Might serve as radioprotective agent

  LBYS11_06125

 

Glutathionylspermidine synthase

+

315.38

82.76

3.81

 Protease involved genes

  LBYS11_00265

 

Uncharacterized zinc protease YmfH

+

754.93

96.72

7.81

  LBYS11_00260

 

Zinc protease

+

685.49

90.94

7.54

  LBYS11_06700

 

n|Uncharacterized protein YuaG

+

560.04

124.56

4.5

  LBYS11_16935

hflK

FtsH protease activity modulator HflK|Protein HflK

−

605.83

146.1

4.15

  LBYS11_16930

hflC

Protease modulator HflC|Protein HflC

−

887.2

231.43

3.83

  LBYS11_17070

sppA

Signal peptide peptidase SppA|Putative signal peptide peptidase SppA

−

139.57

36.6

3.81

 Multidrug efflux pump and swarming motility involved genes

  LBYS11_00190

 

Multidrug export protein AcrF Cobalt-zinc-cadmium resistance protein CzcA

+

336.58

42.35

7.95

  LBYS11_00195

 

Swarming motility protein SwrC

+

800.18

106.83

7.49

  LBYS11_00255

 

Hypothetical protein Multi antimicrobial extrusion protein (Na(+)/drug antiporter)

+

376.26

51.85

7.26

  LBYS11_00250

 

Hypothetical protein Multi antimicrobial extrusion protein (Na(+)/drug antiporter)

+

265.05

37.79

7.01

 TCA cycle involved genes

  LBYS11_00240

 

Acyl-CoA dehydrogenase

+

1676.26

217.77

7.7

  LBYS11_07645

 

NADP-specific glutamate dehydrogenase

−

453.98

112.24

4.04

 Hydantoinase

  LBYS11_08510

 

N-methyl hydantoinase

+

162.46

21.19

7.67

  LBYS11_08515

 

Hydantoinase subunit beta

+

225.3

32.87

6.85

 Membrane proteins

  LBYS11_13515

 

Uncharacterized membrane protein YceF

+

664.23

68.7

9.67

  LBYS11_06695

 

Uncharacterized membrane protein YuaF

+

432.69

89.78

4.82

  LBYS11_17065

 

RDD family protein|Uncharacterized membrane protein YteJ

−

362.02

93.05

3.89

  LBYS11_20665

 

Hypothetical protein|UPF0699 transmembrane protein YdbS

−

148.94

39.48

3.77

 Hypothetical proteins

  LBYS11_00210

 

Hypothetical protein

+

1190.22

124.33

9.57

  LBYS11_00225

 

Hypothetical protein

+

1021.86

116.54

8.77

  LBYS11_00235

 

Hypothetical protein

+

1193.34

140.21

8.51

  LBYS11_00245

 

Hypothetical protein

+

1002.8

129.52

7.74

  LBYS11_09000

 

Hypothetical protein

+

232.67

38.56

6.03

  LBYS11_09005

 

Hypothetical protein

+

186.62

33.96

5.5

  LBYS11_09815

 

Hypothetical protein

+

153.15

32.91

4.65

  LBYS11_21200

 

Hypothetical protein

−

143.8

32.67

4.4

  LBYS11_19760

 

Hypothetical protein|Uncharacterized protein YvlA

+

133.72

33.88

3.95

  LBYS11_06120

 

Hypothetical protein|Uncharacterized serine-rich protein C21513

+

413.46

112.58

3.67

Genes downregulated by high Ca2+

 LBYS11_19235

 

Copper amine oxidase

−

63.11

224.53

.28

 LBYS11_08750

 

Copper amine oxidase

+

52.07

239.12

.22

 LBYS11_20870

 

Zinc transporter ZupT

−

133.27

521.26

.26

 LBYS11_01430

 

Divalent metal cation transporter

−

8.88

211.74

.04

 LBYS11_20140

 

Guanine/hypoxanthine permease

−

9.31

157.38

.06