Table 3

Genes performing significant altered transcription in the deletion mutant of SO1377 gene

Gene

Symbol

Putative Function

Expression

AVG

SE

P-value


    Energy metabolism


SO0397

fdrC

fumarate reductase cytochrome B subunit

+3.445

0.729

*

SO0398

frdA

fumarate reductase flavoprotein subunit

+3.409

0.711

*

SO0399

frdB

fumarate reductase iron-sulfur protein

+1.895

0.336

**


SO1017

nuoF

NADH dehydrogenase I, F subunit

+9.606

2.178

*

SO2098

hyaB

quinone-reactive Ni/Fe hydrogenase, large subunit

+3.506

0.937

**


SO2361

ccoP

cytochrome c oxidase, cbb3-type, subunit III

-2.079

0.036

*****

SO2362

ccoQ

cytochrome c oxidase, cbb3-type, CcoQ subunit

-6.711

0.099

****

SO2363

ccoO

cytochrome c oxidase, cbb3-type, subunit II

-27.027

0.046

****

SO2364

ccoN

cytochrome c oxidase, cbb3-type, subunit I

-7.042

0.033

*****


SO3034

ferric iron reductase protein, putative

-2.227

0.040

*****

SO3980

cytochrome c552 nitrite reductase

+3.346

0.770

*

SO4513

formate dehydrogenase, alpha subunit

+2.408

0.370

***

    Transport and binding protiens

SO0530

transporter, LysE family

+8.483

1.561

**


SO3030

alcA

siderophore biosynthesis protein

-2.457

0.038

*****

SO3031

siderophore biosynthesis protein, putative

-1.534

0.070

*

SO3032

siderophore biosynthesis protein, putative

-2.033

0.038

*****

SO3033

ferric alcaligin siderophore receptor

-2.079

0.071

***


SO3134

dctP

C4-dicarboxylate-binding periplasmic protein

-3.165

0.048

*****

SO3135

C4-dicarboxylate transporter, putative

-2.793

0.037

*****

SO3136

dctM

C4-dicarboxylate transport protein

-1.969

0.051

*****


    Cellular process

SO3065

colicin V production protein

+3.219

0.580

*

SO4405

katG-2

catalase/peroxidase HPI

+5.409

1.310

*

    DNA metabolism

SO2081

ATP-dependent helicase, DinG family

+5.111

1.493

*

    Cell envelope

SO4676

kdtA

3-deoxy-D-manno-octulosonic-acid (KDO) transferase

+2.225

0.475

**

    Biosynthesis ofcofactors, prosthetic groups, and carriers


SO4723

molybdopterin biosynthesis MoeA protein, putative

+1.748

0.183

***

SO4724

molvbdenum cofactor biosynthesis protein A

+2.000

0.132

****


    Amino acid biosynthesis

SO4054

metF

5, 10-methylenetetrahydrofolate reductase

+2.061

0.451

*

    Central intermediary metabolism

SO3505

nagA

N-acetylglucosamine-6-phosphate deacetylase

+2.720

0.264

*****

SO3628

glycerate dehydrogenase, degenerate

+4.349

1.469

*

    Signal transduction

SO2366

response regulator

-30.303

0.028

*****

    Unknown function

SO0796

GGDEF family protein

+7.824

1.795

*

SO1312

TolB domain protein

+4.079

1.690

*

SO2005

dskA-type zinc finger protein

+3.096

0.503

***

SO3506

SIS domain protein

+3.049

0.667

**


SO4671

glpG

glpG protein

+2.189

0.216

*****

SO4672

g1pE

glpE protein

+1.574

0.142

**


1. The average (AVG) expression ratio of the mutant sample to the wild-type control was calculated from 12 replicates together with the respective standard error (SE), a standard t-test result (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; *****, P < 0.00001 probability in Student's t-test).

2. All genes shown in here have expression change ratio between the mutant and the wild-type more than 2.0-fold, except for several ones if they belong to an operon with a gene performing expression ratio of more than 2.0-fold.

3. Fold increases is marked as (+) and decreases (-). Expression changes of greater than 2.0-fold are shown in bold font.

4. Genes belonging to a same operon are framed in a rectangle.

Gao et al. BMC Genomics 2006 7:76   doi:10.1186/1471-2164-7-76

Open Data