TABLE 2.

Genes identified by microarray analysis as downregulated by HrcA^a

Geneb	Differential expression in L. monocytogenes parent strain vs ΔhrcA strain		Protein function (specific gene name)
	Adjusted P value	Fold changec
lmo0117	0.0003	−1.8	LmaB, antigen B (lmaB)
lmo0124	0.0058	−1.5	Unknown
lmo0355	0.0013	−1.6	Similar to flavocytochrome C fumarate reductase chain A
lmo0641	0.0005	−1.9	Similar to heavy metal-transporting ATPase
lmo0669	0.0001	−2.0	Similar to oxidoreductase
lmo0670	0.0005	−1.7	Unknown
lmo1257	0.0010	−2.8	Unknown
lmo1293	0.0003	−1.9	Similar to glycerol 3-phosphate dehydrogenase (glpD)
lmo1407	0.0003	−1.8	Pyruvate formate lyase-activating enzyme (pflC)
lmo1474	0.0017	−3.1	Heat shock protein (grpE)
lmo1473	0.0017	−4.9	Heat shock protein (dnaK)
lmo1472	0.0003	−4.2	Heat shock protein (dnaJ)
lmo1471	0.0001	−3.1	Similar to ribosomal protein L11 methyltransferase
lmo1470	0.0027	−1.5	Unknown
lmo1634	0.0071	−1.9	Similar to alcohol-acetaldehyde dehydrogenase
lmo2069	0.0003	−7.0	Heat shock protein (groES)
lmo2068	0.0003	−5.4	Heat shock protein (groEL)
lmo2070	0.0185	−1.8	Unknown
lmo2161	0.0006	−1.5	Unknown
lmo2159	0.0010	−1.6	Similar to oxidoreductase
lmo2269	0.0039	−1.6	Unknown
lmo2460	0.0134	−1.5	Similar to B. subtilis CggR hypothetical transcriptional regulator
lmo2459	0.0046	−1.5	Glyceraldehyde 3-phosphate dehydrogenase (gap)
lmo2585	0.0004	−1.6	Similar to B. subtilis YrhD protein
lmo2637	0.0014	−2.1	Conserved lipoprotein

^aAll genes that showed lower transcript levels in the parent strain (i.e., an adjusted P value of <0.05 and n-fold change of ≤−1.5) in the microarray comparison are listed; these genes are either directly or indirectly downregulated by HrcA.

^bPutative operons are in bold font; gene names correspond to the gene designations for L. monocytogenes strain EGD-e (as listed on the ListiList server http://genolist.pasteur.fr/ListiList/).

^cA negative n-fold change indicates that the gene has lower transcript levels in the L. monocytogenes parent strain.