Table 1 Genes involved in metabolic processes differentially regulated by fmt deletion in S. aureus RN4220 under (A) aerobic or (B) anaerobic growth conditions

A

Reduced expression in Δ fmt compared to wild type:

Amino acid metabolism

01452

ald

alanine dehydrogenase

103.1

00008

hutH

histidine ammonia-lyase

67.1

01451

ilvA

threonine dehydratase

39.8

00899

argG

argininosuccinate synthase

22.5

00435

gltB

glutamate synthase, large subunit, putative

21.8

02468

alsS

acetolactate synthase

14.1

00558

acetyl-CoA acetyltransferase, putative

12.2

01497

ansA

L-asparaginase, putative

7.6

01450

amino acid permease*

6.4

00081

HPCH-HPAI aldolase family protein*

4.6

02287

leuC

3-isopropylmalate dehydratase, large subunit

4.4

02574

NAD-NADP octopine-nopaline dehydrogenase family protein*

3.8

01450

amino acid permease*

3.2

02281

ilvD

dihydroxy-acid dehydratase

3.2

02839

L-serine dehydratase, iron-sulfur-dependent, alpha subunit

2.9

00510

cysE

serine acetyltransferase, putative

2.8

00147

acetylglutamate kinase, putative

2.5

02563

ureF

urease accessory protein, putative

2.3

02723

glycerate kinase, putative

2.2

Protein biosynthesis

01183

fmt

methionyl tRNA formyltransferase

585.8

01182

def2*

polypeptide deformylase (def2*)

6.3

01839

tyrS

tyrosyl-tRNA synthetase

2.8

00324

ribosomal-protein-serine acetyltransferase, putative

2.4

01738

hisS

histidyl-tRNA synthetase

2.4

Folic acid metabolism

01183

fmt

methionyl tRNA formyltransferase

585.8

02374

aminobenzoyl-glutamate utilization protein B, putative

4.5

02610

hutG

formiminoglutamase

3.4

Fermentation

00188

pflA

formate acetyltransferase activating enzyme

604.5

02830

ddh

D-lactate dehydrogenase, putative

263.6

00187

pflB

formate acetyltransferase (pyruvate-formate-lyase)

99.0

00608

adh1

alcohol dehydrogenase I, putative

74.0

00113

adhE

alcohol dehydrogenase, iron-containing

40.8

02467

budA2

alpha-acetolactate decarboxylase

2.6

02875

L-lactate dehydrogenase, putative

2.3

Purine metabolism

02553

inosine-uridine preferring nucleoside hydrolase*

3.3

00211

inosine-uridine preferring nucleoside hydrolase*

3.3

Lipid biosynthesis

01278

glpD

aerobic glycerol-3-phosphate dehydrogenase

14.7

Transport systems

00748

iron compound ABC transporter, ATP-binding protein, putative*

15.0

03019

ABC transporter, ATP-binding protein, putative

7.2

01991

ABC transporter, permease protein, putative

7.1

00155

PTS system, glucose-specific component

5.0

00424

ABC transporter, permease protein, putative

3.9

02154

ABC transporter, ATP-binding protein, putative

2.6

00844

ABC transporter, substrate-binding protein*

2.2

00215

PTS system component, putative

2.1

Urea metabolism

00899

argG

argininosuccinate synthase

22.5

02563

ureF

urease accessory protein, putative

2.3

energy production and conversion/electrone transfer

00412

ndhF

NADH dehydrogenase subunit 5, putative

359.0

00302

NADH-dependent flavin oxidoreductase, Oye family*

5.2

Higher expression in Δ fmt compared to wild type:

Amino acid metabolism

02971

aur

aureolysin, putative

3.4

B

Gene ID ^a,b

Name ^b

Gene product ^b

x-fold change

Reduced expression in Δ fmt compared to wild type:

Amino acid metabolism

00836

gcvH

glycine cleavage system H protein

2.4

00151

branched-chain amino acid transport system II carrier protein

2.4

01452

ald

alanine dehydrogenase

2.3

01450

amino acid permease*

2.1

00510

cysE

serine acetyltransferase, putative

2.1

01451

ilvA

threonine dehydratase

2.1

Protein biosynthesis

01183

fmt

methionyl-tRNA formyltransferase

158.3

01182

def2*

polypeptide deformylase (def2*)

4

01788

thrS

threonyl-tRNA synthetase

3.7

00009

serS

seryl-tRNA synthetase

2.4

01839

tyrS

tyrosyl-tRNA synthetase

2.3

01159

ilsS

isoleucyl-tRNA synthetase

2.1

Folic acid metabolism

01183

fmt

methionyl-tRNA formyltransferase

158.3

00836

gcvH

glycine cleavage system H protein

2.4

Lipid biosynthesis

01310

cardiolipin synthetase, putative

2.8

Fermentation

02830

ddh

D-lactate dehydrogenase, putative

9.8

00206

L-lactate dehydrogenase

2.3

00113

adhE

alcohol dehydrogenase, iron-containing

2

Increased expression in Δ fmt compared to wild type:

Amino acid metabolism

02840

L-serine dehydratase, iron-sulfur-dependent, beta subunit

4.3

Protein biosynthesis

01725

tRNA methyl transferase, putative

2.1

Purine metabolism

01012

purQ

phosphoribosylformylglycinamidine synthase I

4.2

01014

purF

amidophosphoribosyltransferase

3.6

00372

xprT

xanthine phosphoribosyltransferase

3.2

Purine metabolism (continued)

00375

guaA

GMP synthase, putative

2

Lipid biosynthesis

01260

pgsA

CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase

2.1

03006

lipase

2.7

Carbohydrate metabolism

01794

gap

glyceraldehyde-3-phosphate dehydrogenase, type I

6.3

00239

ribokinase, putative

2.1

Riboflavin metabolism

01886

riboflavin synthase, beta subunit

25

01888

riboflavin synthase, alpha subunit

5.7

01889

ribD

riboflavin biosynthesis protein RibD

4.5