Table 1

Genes differentially expressed in the transcriptome data as a result of bldA mutation1

Gene2

Annotated function3

P-value4

Mean pfp value5

Up/down in bldA6

Potential reason for absence in proteomic data7


SCO0072

possible secreted protein

N/A

0.055*

down

Secreted

    SCO0247

conserved hypothetical protein

3.29E-06

N/A

down

Predicted 1 transmembrane domain

    SCO0248

hypothetical protein

1.76E-05

N/A

down

Predicted pI = 11.6

    SCO0297

secreted protein

8.25E-05

0.033

down

Secreted

SCO0472

possible secreted protein

N/A

0.076*

down

Secreted

SCO0499

possible formyltransferase

9.76E-04

N/A

down

SCO0759

hypothetical protein

0.000976

N/A

down

Predicted 1 transmembrane domain

SCO0760

probable methyltransferase

0.000796

0.083

down

Predicted pI = 10.9

    SCO0762

protease inhibitor precursor

0.0262

0.012

down

Secreted

    SCO0990

integral membrane protein

7.72E-03

N/A

down

Predicted 7 transmembrane domains

SCO0991

conserved hypothetical protein

0.00772

N/A

down

Predicted transmembrane domain

SCO0994

integral membrane protein

0.0317

N/A

down

Predicted 9 transmembrane domains

SCO0995

probable methyltransferase

9.76E-04

N/A

down

Predicted 2 transmembrane domains

SCO1089

unknown

N/A

0*

up

None

SCO1815

probable 3-oxacyl-(acyl-carrier-protein) reductase

N/A

0.084*

down

Predicted 2 transmembrane domains

SCO1845

possible low-affinity phosphate transport protein

N/A

0*

up

Predicted 10 transmembrane domains

SCO1968

probable secreted hydrolase

N/A

0*

down

Secreted

    SCO2435

hypothetical protein

0.00589

N/A

down

None

SCO3088

hypothetical protein

0.000415

N/A

up

Predicted pI = 9.7, mwt = 8377 Da

SCO3285

large gly/ala rich protein

7.72E-03

N/A

up

SCO3286

secreted protein

0.00772

0.05

up

Secreted

SCO3428

50S ribosomal protein

N/A

0.082*

down

Predicted pI = 10.8, mwt = 6416 Da

SCO3608

hypothetical protein

N/A

0.1*

up

Predicted 3 transmembrane domains

SCO3717

probable cation transport system component

N/A

0.068

up

Predicted 7 transmembrane domains

SCO3718

probable cation transport system component

N/A

0

up

Predicted 11 transmembrane domains

    SCO4131

integral membrane protein

0.0389

N/A

down

Predicted 2 transmembrane domains

SCO4173

unknown

N/A

0.088*

down

Predicted 1 transmembrane domains

SCO4174

possible integral membrane protein

N/A

0.088*

down

Predicted 1 transmembrane domains; predicted pI = 11.0

SCO4187

putative membrane protein

0.0404

0.1

down

Predicted pI = 9.5, mwt = 6268 Da

SCO4246

hypothetical protein

5.89E-03

N/A

down

Predicted pI = 9.7

    SCO4252

hypothetical protein

3.29E-06

0.017

down

    SCO4253

conserved hypothetical protein

5.93E-05

5.66E-03

down

    SCO4256

possible hydrolytic protein

0.00772

N/A

down

None

    SCO4262

hypothetical protein

0.000976

0.083

down

Predicted pI = 11.7, mwt = 12884 Da

    SCO4295

Cold shock protein scoF4

0.00126

0.053

down

Predicted mwt = 7387 Da

SCO4442

hypothetical protein

0.00608

0.09*

down

Predicted mwt = 6484 Da

SCO4653

50S ribosomal protein

N/A

0.097*

down

None

SCO4661

elongation factor G

N/A

0.088*

down

None

SCO4677

possible regulatory protein

N/A

0.038*

down

SCO4703

50S ribosomal protein

N/A

0.076*

down

Predicted pI = 10.0

SCO4704

50S ribosomal protein

N/A

0.044*

down

Predicted pI = 10.6

SCO4705

50S ribosomal protein

N/A

0.087*

down

Predicted pI = 11.3

SCO4706

30S ribosomal protein

N/A

0.095*

down

Predicted pI = 10.8

SCO4707

50S ribosomal protein

N/A

0.091*

down

Predicted pI = 10.2

SCO4712

50S ribosomal protein

N/A

0.087*

down

Predicted pI = 10.2

SCO4713

50S ribosomal protein

N/A

0.076*

down

Predicted pI = 10.3

SCO4714

50S ribosomal protein

N/A

0.088*

down

Predicted pI = 9.6

SCO4716

30S ribosomal protein

N/A

0.077*

down

Predicted pI = 9.6

SCO4717

50S ribosomal protein

N/A

0.043*

down

Predicted pI = 9.8

SCO4718

50S ribosomal protein

N/A

0.074*

down

Predicted pI = 10.6

SCO4719

30S ribosomal protein

N/A

0.071*

down

Predicted pI = 10.1

    SCO4994

hypothetical protein

0.0136

N/A

down

Predicted 1 transmembrane domain

SCO5013

secreted protein

0.0479

N/A

down

Secreted

SCO5073

possible oxidoreductase

4.79E-02

0*

down

SCO5074

possible dehydratase

N/A

0*

down

Predicted pI = 8.6; secreted

SCO5079

conserved hypothetical protein

N/A

0*

down

    SCO5123

membrane protein

0.000415

N/A

down

Predicted pI = 8.2, mwt = 6622 Da

    SCO5124

hypothetical protein

0.00512

N/A

down

Predicted pI = 7.12, mwt = 7054 Da

SCO5125

hypothetical protein

0.000788

N/A

down

None

SCO5166

putative helicase

5.12E-03

N/A

up

Predicted pI = 9.5

SCO5225

ribonucleotide-diphosphate reductase small chain

N/A

0.007*

up

Predicted 2 transmembrane domains

SCO5624

30S ribosomal protein S2

N/A

0.089*

down

None

SCO5649

unknown

N/A

0.1*

down

None

    SCO6197

secreted protein

3.29E-06

0.063

down

Secreted

SCO6198

secreted protein

8.09E-03

N/A

down

Secreted

SCO6346

hypothetical protein

6.08E-03

N/A

down

None

    SCO6362

Probable two-component sensor

0.00589

N/A

down

Predicted 6 transmembrane domains; pI = 10.43

    SCO6637

hypothetical protein

0.000788

N/A

down

    SCO6638

hypothetical protein

0.000415

N/A

down

SCO6808

possible ArsR-family regulator

0.00219

N/A

down

Predicted mwt = 13271 Da

SCO6958

putative membrane protein

0.036

N/A

up

Predicted 3 transmembrane domains; pI= 8.7; mwt = 11304 Da

SCO7510

peptidyl-prolyl cis-trans isomerase

N/A

0.01*

up

None

SCO7511

glyceraldehyde 3-phosphate dehydrogenase

N/A

0*

up

    SCO7657

secreted protein

1.76E-05

0.066*

down

Secreted


1 presented in more detail in Additional File 8.

2 genes in bold were also found to be different in the proteome analysis detailed in Additional File 5. Underlined genes were more highly expressed during all stages of growth in M600 relative to the bldA mutant. Q-RT-PCR was performed with the 16 RNA samples from replicate 3 time courses, using specific primers and probes covering 50–150 bp, for each of the following genes: SCO4295, SCO5013, SCO6808, and SCO7657; five genes up-regulated in the bldA mutant – SCO3088, SCO3285, SCO3286, SCO5166, SCO6958; the TTA-containing gene SCO6638; and the ribosomal protein genes SCO4648, SCO4702, SCO4705, SCO4717. See Additional File 2 for these results.

3from ScoDB [55]

4 from a Welch t-test applying the Benjamini and Hochberg multiple testing correction

5 average pfp (Probability of False Prediction) values from time-point comparisons outputted from Rank Product Analysis. * denotes those genes found differentially expressed at one time point only.

6determined from a visual inspection of expression profiles in Additional File 1

7 pI and Mwt values from ScoDB [55]: transmembrane domain predictions from TmPred [56]

Hesketh et al. BMC Genomics 2007 8:261   doi:10.1186/1471-2164-8-261

Open Data