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Table 1 Bacillus subtilis OKB105 genes differentially expressed in response to rice seedlings

From: Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings

Gene

Annotation

Fold-change ratio

q-value (%)

Up-regulated genes

   

Cell wall (3.85%)

   

yngB

UTP-glucose-1-phosphate uridylytransferase

2.631

0

dacA

Penicillin-binding protein 5

2.2647

0

Transport/binding and lipoproteins (15.38%)

   

ydgH

Putative drug exporter of the RND superfamily

16.1482

0

mtlA

PTS mannitol-specific enzyme II CB component

5.7777

0

yhcA

Multidrug resistance protein

5.2704

0

ykoY

Transporter

3.8449

0

yxkD

Efflux transporter

2.7977

0

yflA

Amino acid carrier protein

2.1064

0

ydfM

Cation efflux system

2.083

0

yflS

2-Oxoglutarate/malate translocator

2.0806

0

Sensors (signal transduction) (3.85%)

   

yclJ

Two-component response regulator YclK

2.4004

0

yclK

Two-component sensor histidine kinase

2.3307

0

Sporulation (1.92%)

   

rapF

Response regulator aspartate phosphatase

2.408

0

Metabolism of carbohydrates and related molecules (11.54%)

   

mtlD

Mannitol-1-phosphate dehydrogenase

5.5707

0

ywkA

Malate dehydrogenase

4.12

0

araA

L-arabinose isomerase

2.7149

0

galE

UDP-glucose 4-epimerase

2.6384

0

yngB

UTP-glucose-1-phosphate uridylytransfarase

2.631

0

mmgD

Citrate synthase III

2.0082

 

Metabolism of amino acids and related molecules (9.62%)

   

proB

Glutamate-5-kinase

2.5409

0

ald

L-alanine dehydrogenase

2.3522

0

speA

Arginine decarboxylase

2.2631

0

yrpC

Glutamate racemase

2.0801

0

hutH

histidase

2.0154

0

Metabolism of lipids (1.92%)

   

yngG

Hydroxymethylglutary-COA lyase

2.2458

0

RNA regulation (13.46%)

   

ydgG

MarR family transcriptional regulator

13.515

0

yhbI

Transcriptional regulator (MarR family)

7.9016

0

yhgD

Transcriptional regulator (TerR/AcrR family)

7.5195

 

yhcB

Trp repressor binding protein

2.5366

0

fruR

Transcriptional repressor of the fructose operon

2.4164

0

yugG

Lrp/Asnc family transcriptional regulator

2.2458

0

yusO

MarR family transcriptional regulator

2.1994

0

Protein synthesis (1.92%)

   

pheS

Phenylalanyl-tRNA synthetase

2.0356

0

Protein modification (1.92%)

   

yxaL

Serine/threonine protein kinase

2.3234

0

Adaptation to atypical conditions (1.92%)

   

rsbX

Serine phosphatase

2.1821

0

Detoxification (1.92%)

   

ykoY

Toxic anion resistance protein

3.4438

0

Phage-related functions (1.92%)

   

yhgE

Phage infection protein

5.0703

0

Unknown (28.85%)

   

ydfK

Putative integral inner membrane protein

3.8449

0

yvpB

Putative hydrolase

3.5212

0

yneF

Hypothetical protein

3.0863

0

yrkO

Putative integral inner membrane protein

2.6702

0

yngA

Putative conserved membrane protein

2.4775

0

yhaJ

Putative bacteriocin

2.4261

0

yfkA

Putative Fe-S oxidoreductase

2.4164

0

yfhE

Hypothetical protein

2.3804

0

ykcB

Putative integral inner membrane protein

2.2993

0

ywkB

Putative transporter

2.2629

0

yaaT

Hypothetical protein

2.2497

0

ykaA

Putative Pit accessory protein

2.0901

0

ydhB

Putative integral inner membrane protein

2.0405

0

ykyB

Hypothetical protein

2.0219

0

Down-regulated

   

Cell wall (8.06%)

   

tuaD

Biosynthesis of teichuronic acid

0.4536

0

tuaA

Biosynthesis of teichuronic acid

0.4382

0

lytD

N-Acetylglucosaminidase

0.4371

0

tuaC

Biosynthesis of teichuronic acid

0.435

 

tuaF

Biosynthesis of teichuronic acid

0.3949

0

tuaG

Biosynthesis of teichuronic acid

0.3922

0

tuaB

Biosynthesis of teichuronic acid

0.3855

0

pbpE

Penicillin-binding protein 4

0.3219

0

tuaH

Biosynthesis of teichuronic acid

0.319

0

tuaE

Biosynthesis of teichuronic acid

0.2841

0

Transport/binding proteins and lipoproteins (8.87%)

   

opuD

Glycine betaine transporter

0.491

0

gabP

γ-Aminobutyrate permease

0.4897

0

ydhF

Lipoproteins

0.4892

0

iolF

Inositol transport protein

0.4687

0

yxlG

ABC transporter permease

0.4536

0

yxlF

ABC transporter

0.3579

0

glpF

Glycerol uptake facilitor

0.3393

0

yteP

Transmembrane lipoprotein

0.3054

0

ytcQ

Lipoprotein

0.221

0

ytcP

ABC transporter

0.2021

0

yybF

Antibotic resistance protein

0.1847

0

Mobility and chemotaixs (6.45%)

   

fliL

Flagellar protein required for flagellar formation

  

yvyG

Flagellar protein

0.4886

0

flgK

Flagellar hook-associated protein 1 (HAP1)

0.4395

0

hag

Flagellin protein

0.3963

0

fliK

Flagellar hook-length control

0.3692

0

flgL

Flagellar hook-associated protein # (HAP3)

0.361

0

cheV

Modulation of cheA activity in response to attractants

0.3404

0

fliJ

Flagellar protein required for formation of basal body

0.2175

0

Sporulation (8.06%)

   

spmA

Spore maturation protein

0.4981

0

phrC

Phosphatase regulator

0.4976

0

cgeD

Matyration of the outermost layer of the spore

0.4922

0

usd

Required for translation of spoIII D

0.4893

0

rapG

Response regulator aspartate phosphatase

0.4844

0

tlp

Small acid-soluble spore protein

0.4354

0

phrE

Phosphatase regulator

0.4216

0

phrG

Response regulator aspartate phosphatase

0.3595

0

ywcE

Protein required for proper spore morphogenesis and germination

0.1561

0

csfB

Forespore-specific protein

0.2353

0

Metabolism of carbohydrates and related molecules (9.68%)

   

abnA

Arabinan-endo-1,5-α-L-arabinase

0.4833

0

pdhB

Pyruvate dehydrogenase

0.4766

0

bglH

β-Glucosidase

0.4239

0

iolH

Myo-inositol catabolism

0.4076

0

iolG

Myo-inositol catabolism

0.3885

0

glpK

Glycerol kinase

0.3478

0

yteT

Rhamnogalacturonyl dehydrogenase

0.299

0

iolE

Myo-inositol catabolism

0.2972

0

iolD

Myo-inositol catabolism

0.2712

0

iolB

Myo-inositol catabolism

0.2634

0

iolC

Myo-inositol catabolism

0.2609

0

yteR

Unsaturated rhamnogalacturonyl hydrolase

0.2221

0

Metabolism of amino acids and related molecules (9.68%)

   

argG

Argininosuccinate synthase

0.49

0

leuA

2-Isopropylmalate synthase

0.4795

0

yuxL

Acylaminoacyl-peptidase

0.4718

0

vpr

Minor extracellular serine protease

0.4661

0

leuD

3-Isopropylmalate dehydratase

0.462

0

ymfH

Processing protease

0.4612

0

leuB

3-Inospropylmalate dehydratase

0.4476

0

epr

Minor extracellular serine protease

0.429

0

argC

N-Acetylornithine aminotransferase

0.394

0

racX

Amino acid racemase

0.3608

0

ilvC

Ketol-acid dehydratase

0.3524

0

yaaO

Lysine decarboxylase

0.2553

0

Metabolism of nucleotides and nucleic acids (4.03%)

   

purF

Glutamine phosphoribosylpyrophosphate aminotransferase

0.4532

0

purM

Phosphoribosylglycinamidezole synthetase

0.4313

0

purD

Phosphoribosylglycinamide synthetase

0.4158

0

purH

Phosphoribosylglycinamide carboxy formyl formyltransferase

0.4008

0

purN

Phosphoribosylglycinamide formyltransferase

0.3243

0

Metabolism of lipids (2.42%)

   

yusK

Acetyl-CoA C-acyltransferase

0.4973

0

glpQ

Glycerophosphoryl diester phosphodiesterase

0.4721

0

yvaG

3-Oxoacyl-acyl-carrier protein reductase

0.4424

0

Metabolism of coenzymes and prosthetic groups (0.81%)

   

folC

Folyl-polyglutamate synthetase

0.3952

0

RNA synthesis (4.84%)

   

spo0A

Two-component response regulator central for the initiation of sporulation

0.4924

0

sigA

RNA polymerase major sigma factor

0.4332

0

abh

Transcriptional regulator of transition state genes

0.4266

0

yozG

Transcriptional regulator

0.3154

0

sigY

RNA polymerase ECF-type sigma factor

0.2552

0

ykoM

Transcriptional regulator

0.2517

0

Protein synthesis (2.42%)

   

yxlE

Negative regulator of sigma-Y antivity

0.2727

0

yxlD

Sigma-Y antisigma factor component

0.2629

0

yxlC

Sigma-Y antisigma factor

0.2276

0

Aminoacyl-tRNA synthetases (1.61%)

   

ileS

Isoleucyl-tRNA synthetase

0.4435

0

valS

Valy-tRNA synthetase

0.3497

0

Detoxification (1.61%)

   

ybfO

Erythromycin esterase

0.4784

0

yndN

Fosfomycin resistance protein

0.4711

0

Unknown (31.45%)

   

yisT

Hypothetical protein

0.4827

0

yukJ

Hypothetical protein

0.4766

0

ysdB

Hypothetical protein

0.474

0

ylxF

Putative kinesin-like protein

0.473

0

yrzF

Putative serine/threonine-protein kinase

0.4723

0

ywqH

Hypothetical protein

0.4715

0

ykpC

Hypothetical protein

0.4711

0

ypiB

Hypothetical protein

0.4647

0

yitR

Hypothetical protein

0.4627

0

yvfG

Hypothetical protein

0.4602

0

yhfM

Hypothetical protein

0.4522

0

yvaG

Putative oxidoreductase

0.4424

0

yqhO

Hypothetical protein

0.4406

0

ytzD

Hypothetical protein

0.4349

0

ywnF

Hypothetical protein

0.4316

0

yfmB

Hypothetical protein

0.4297

0

ypiF

Hypothetical protein

0.4239

0

yqhL

Hypothetical protein

0.4205

0

yjfB

Hypothetical protein

0.4165

0

yocB

Hypothetical protein

0.4042

0

yyaB

Putative integral inner membrane protein

0.4036

0

ytbQ

Putative nucleoside-diphosphate-sugar epimerase

0.3851

0

ybgB

Hypothetical protein

0.3787

0

yxbC

Hypothetical protein

0.3598

0

yrzL

Hypothetical protein

0.3565

0

yuiB

Hypothetical protein

0.3557

0

ykrP

Putative integral inner membrane protein

0.3394

0

yhzC

Hypothetical protein

0.3291

0

yyaO

Hypothetical protein

0.2553

0

yxbB

Putative S-adenosylmethionine-dependent methyltransferase

0.2325

0

yuiA

Hypothetical protein

0.2091

0

yxnB

Hypothetical protein

0.1604

0

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BMC Microbiology

ISSN: 1471-2180

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