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Table 2 Genome-wide transcriptome profiling of SigHLsa overexpression in L.sakei 23 K

From: Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei

Functional category and CDS

Gene Name

Product

Pvalue (Bonferroni)

common variance model

Pvalue (FDR) varmixt model

Expression sigH(hy)*/

ratio$ sigH(wt)*

     

microarray

qPCR

Competence

LSA0492

comFA

DNA uptake machinery §

1.54E-02

> threshold

1.5 ± 0.4

286 ± 88

LSA0493

comFC

DNA uptake machinery

0

3.56E-03

2.2 ± 0.2

 

LSA1069

comEC

DNA uptake machinery

9.52E-10

1.31E-02

1.9 ± 0.2

 

LSA1071

comEA

DNA uptake machinery

0

7.23E-03

2.5 ± 0.3

261 ± 115

LSA1301

comGF

DNA uptake machinery

0

2.71E-04

3 ± 2

 

LSA1302

comGE

DNA uptake machinery

0

1.44E-06

3.7 ± 0.5

 

LSA1303

comGD

DNA uptake machinery

0

2.21E-04

2.8 ± 0.3

 

LSA1304

comGC

DNA uptake machinery

0

5.62E-12

7 ± 2

421 ± 104

LSA1305

comGB

DNA uptake machinery

1.02E-10

3.57E-02

2.0 ± 0.3

 

LSA1306

comGA

DNA uptake machinery

3.17E-09

7.25E-03

1.9 ± 0.2

 

LSA1771

comC

DNA uptake machinery

0

4.10E-06

3.2 ± 0.2

608 ± 199

DNA metabolism: replication, repair, recombination, RM

LSA0008

ssb

Single-stranded DNA binding protein

> threshold

3.88E-02

1.4 ± 0.1

1.2 ± 0.3

LSA0146

 

Putative DNA methyltransferase (apparently stand-alone)

1.55E-04

> threshold

1.6 ± 0.4

 

LSA1299

 

Putative DNA methyltransferase (apparently stand-alone)

2.48E-08

> threshold

1.9 ± 0.4

 

LSA1338

exoA

Exodeoxyribonuclease III

1.36E-07

> threshold

1.8 ± 0.3

 

Purines, pyrimidines, nucleosides and nucleotides

LSA0533

iunh2

Inosine-uridine preferring nucleoside hydrolase

1.14E-05

> threshold

1.7 ± 0.4

 

Energy metabolism

LSA1298

ack2

Acetate kinase

4.27E-09

> threshold

1.9 ± 0.4

 

Translation

LSA0009

rpsR

Ribosomal protein

1.67E-02

> threshold

1.5 ± 0.4

 

Regulatory function

LSA0421

 

Putative transcriptional regulator, MerR family

0

3.56E-03

2.5 ± 0.5

 

Hypothetical protein

LSA0040

 

Hypothetical protein, conserved in some lactobacilli

0

3.56E-03

2.5 ± 0.5

 

LSA0409

 

Hypothetical integral membrane protein

3.02E-05

7.25E-03

0.61 ± 0.01

 

LSA0536

 

Hypothetical protein with putative NAD-binding domain, NmrA structural superfamily

6.28E-06

3.32E-02

1.6 ± 0.4

 

LSA0779

 

Hypothetical protein, peptidase S66 superfamily

4.77E-05

> threshold

0.6 ± 0.1

 

LSA0991

 

Hypothetical protein with putative NAD-binding domain, NmrA structural superfamily

1.02E-04

> threshold

1.6 ± 0.2

 

LSA1475

 

Hypothetical protein, conserved in bacteria

1.62-12

> threshold

2.1 ± 0.5

 

CDS £

Gene Name

Product

   

qPCR

LSA0487

recA

DNA recombinase A

   

2.7 ± 0.7

LSA0992

dprA

DNA protecting protein, involved in DNA transformation

   

2163 ± 1242

  1. $ Expression ratios represent the fold change in amounts of transcripts in the strain overexpressing SigH relative to the WT control strain. For the microarray experiment they were calculated from log2ratio; for the qPCR they were calculated by the 2-ΔΔCt method described in Methods. Genes underexpressed in the context of SigH overexpression have a ratio < 1. Standard deviation is indicated (weak accuracy for qPCR experiments may be due to Ct at the detection limit for basal level).
  2. § see additional file 3: Competence DNA uptake machinery of B. subtilis and comparison with L. sakei.
  3. £ not found statistically differentially expressed in the microarray transcriptome experiment, checked by qPCR.
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BMC Microbiology

ISSN: 1471-2180

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