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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.