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 GSK2118436 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 Palbociclib 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, ADAMTS5 involved in DNA transformation       2163 ± 1242 $ 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). § see additional file 3: Competence DNA uptake machinery of B. subtilis and comparison with L. sakei. £ not found statistically differentially expressed in the microarray transcriptome experiment, checked by qPCR. Two genes coding for hypothetical proteins, LSA0409 and LSA0779, were down-regulated in the sigH Lsa overexpression strain. As sigma factors are usually positive regulators, we consider it likely that down-regulation of these genes is an indirect effect of sigH Lsa overexpression, e.g., this effect could correspond to σH-mediated activation of an unidentified repressor. The sole transcriptional regulator (LSA0421) listed as σH-activated in Table 2 is probably not responsible for this effect, since MerR-type regulators reportedly act as activators [34].