Table 2.

L. monocytogenes 10430S operons differentially transcribed after acid treatment of cells grown at 37°C to log or stationary phase^a

Locus tag (gene name)	Gene functionb	Fold change after acid treatment of cells inc:				Putative binding site(s)d
		Log phase		Stationary phase
		5 min	15 min	5 min	15 min
lmo0113	Similar to protein gp35 from bacteriophage A118				−1.81*
lmo0114	Similar to putative repressor C1 from lactococcal bacteriophage Tuc2009				−1.57*
lmo0136	Similar to oligopeptide ABC transporter, permease protein	2.27**	2.10**
lmo0137	Similar to oligopeptide ABC transporter, permease protein	1.64**	1.54*			B
lmo0180	Similar to sugar ABC transporter, permease protein	1.71*	1.80*
lmo0181	Similar to sugar ABC transporter, sugar-binding protein	1.75*	1.87**			h
lmo0230	Similar to Bacillus subtilis YacH protein	1.53*	1.56*			B, i
lmo0231	Similar to arginine kinase		1.60**
lmo0232 (clpC)	Endopeptidase Clp ATP-binding chain C	1.59**	1.67**
lmo0680	Similar to flagellum-associated protein FlhA	−1.59**	−1.87***
lmo0681	Similar to flagellar biosynthesis protein FlhF	−1.54*	−1.84**
lmo0683	Similar to chemotactic methyltransferase CheR	−2.16**	−2.68**
lmo0806	Similar to transcription regulator		2.03*			i
lmo0808	Similar to spermidine/putrescine ABC transporter, permease protein	1.87*	2.08*
lmo0809	Similar to spermidine/putrescine ABC transporter, permease protein	1.90**	2.07**
lmo0810	Similar to spermidine/putrescine-binding protein	2.27**	2.25***
lmo0811	Similar to carbonic anhydrase	2.55**	2.78**
lmo0847	Similar to glutamine ABC transporter (binding and transport protein)	2.27**	2.29**
lmo0848	Similar to amino acid ABC transporter, ATP-binding protein	1.82**	1.91**
lmo1041	Similar to molybdate ABC transporter binding protein				−1.66*
lmo1046	Molybdenum cofactor biosynthesis protein C				−1.58*
lmo1089 (tagD)	Highly similar to glycerol-3-phosphate cytidylyltransferase, CDP-glycerol pyrophosphorylase (teichoic acid biosynthesis protein D)	−1.86***	−2.03***
lmo1090	Similar to glycosyltransferases	−1.51**	−1.64***			b, h
lmo1406 (pflB)	Pyruvate-formate lyase	−4.03*	−4.30*
lmo1407 (pflC)	Pyruvate-formate lyase activating enzyme	−2.86*	−2.72*
lmo1474 (grpE)	Heat shock protein GrpE	1.84**	1.71**
lmo1475 (hrcA)	Transcription repressor of class I heat shock gene HrcA	1.83**	1.76**			B, I, III
lmo1541	Similar to unknown protein			1.60*	1.57**
lmo1542 (rplU)	Ribosomal protein L21			1.51*	1.69***
lmo1556 (hemC)	Highly similar to porphobilinogen deaminases (hydroxymethylbilane synthase)		−1.59*			h
lmo1557 (hemA)	Highly similar to glutamyl-tRNA reductase	−1.72***	−1.87***
lmo1589 (argB)	Highly similar to N-acetylglutamate 5-phosphotransferase		−4.37*			b
lmo1590 (argJ)	Highly similar to ornithine acetyltransferase and amino acid acetyltransferases	−6.76*	−4.84*
lmo1591 (argC)	Similar to N-acetylglutamate gamma-semialdehyde dehydrogenases	−25.44*	−11.04*
lmo1833 (pyrD)	Highly similar to dihydroorotase dehydrogenase		1.57**			h
lmo1835 (pyrAB)	Highly similar to carbamoyl-phosphate synthetase (catalytic subunit)	1.83*	1.91**
lmo1929 (ndk)	Similar to nucleoside diphosphate kinase				−1.73***
lmo1932	Heptaprenyl diphosphate synthase component I				−1.51*
lmo2040 (ftsL)	Similar to cell division protein FtsL		−1.51***
lmo2041	Similar to unknown proteins		−1.68***
lmo2114	Similar to ABC transporter (ATP-binding protein)	2.28**	2.25**
lmo2115	Similar to ABC transporter (permease)	2.23**	2.16**
lmo2260	Similar to unknown proteins	1.87*	1.78*
lmo2261	Similar to unknown proteins	1.63*
lmo2293	Protein gp10 (bacteriophage A118)	−2.34*
lmo2295	Protein gp8 (bacteriophage A118)	−2.88*	−2.39*
lmo2296	Similar to coat protein (bacteriophage SPP1)	−2.32*
lmo2362	Similar to amino acid antiporter (acid resistance)	−2.97**	−2.80**
lmo2363	Similar to glutamate decarboxylase	−2.59*	−2.28*
lmo2408	Similar to repressor protein	−1.61***	−1.94***
lmo2409	Unknown	−3.28**	−4.21***			h
lmo2484	Similar to B. subtilis YvlD protein		2.11*			B
lmo2487	Similar to B. subtilis YvlB protein	1.56*	1.74**
lmo2625 (rplP)	Ribosomal protein L16				1.69*
lmo2630 (rplW)	Ribosomal protein L23				1.50*
lmo2632 (rplC)	Ribosomal protein L3				1.50*
lmo2633 (rpsJ)	Ribosomal protein S10				1.64*

^aOperons with at least two genes showing a fold change with an absolute value of ≥1.5 after acid treatment and an adjusted P value of ≤0.05 after acid treatment. Gene names are from ListiList (http://genolist.pasteur.fr/ListiList), and operon predictions are from ListiList and reference 59. Acid treatment was done at 37°C in BHI adjusted to pH 3.5 with HCl.

^bBased on annotation provided by TIGR (http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi).

^cAdjusted P values are indicated as follows: ***, <0.001; **, <0.01; *, ≤0.05.

^dPutative binding sites for σ^B (B, b), σ^H (H, h), σ^L (L, l), CtsR (III, iii), and HrcA (I, i) are based on the hidden Markov model results reported by Hu et al. (27, 28), Raengpradub et al. (46), and Chaturongakul et al. (10). Hits were considered significant if they had an E value of ≤0.02 and were ≤300 bp upstream of the respective coding sequence. Uppercase denotes genes for which regulation has been confirmed by experimental studies (i.e., differential transcription in an isogenic deletion mutant versus the wild type).