TABLE 2.

Measurement of gene expression in cheese incubated for 15 h at 30°C using RNA directly extracted from cheese or after separation of cells

Gene	Gene product	Threshold valuea			Gene expression ratiob
		Direct RNA extraction	RNA extraction after separation of cells	Difference
adhE	Alcohol-acetaldehyde dehydrogenase	22.70 ± 0.30	23.00 ± 0.12	0.30	0.82
aldB	Alpha-acetolactate decarboxylase	22.04 ± 0.22	21.53 ± 0.23	0.51	1.40
als	Alpha-acetolactate synthase	19.44 ± 0.34	19.66 ± 0.06	−0.22	0.87
busAA	Betaine ABC transporter ATP-binding protein	25.58 ± 0.37	19.69 ± 0.33	5.89c	51.51
butB	2,3-Butanediol dehydrogenase	23.33 ± 0.38	23.81 ± 0.19	−0.48	0.73
citD	Citrate lyase acyl-carrier protein	19.10 ± 0.20	19.73 ± 0.26	−0.63	0.66
citF	Citrate lyase alpha chain	16.78 ± 0.10	16.92 ± 0.35	−0.14	0.91
codY	Transcriptional repressor	24.56 ± 0.24	22.31 ± 0.30	2.25c	4.46
cspD	Cold shock protein D	19.20 ± 0.35	16.14 ± 0.28	3.06c	6.71
cspE	Cold shock protein E	19.92 ± 0.07	18.06 ± 0.35	1.87c	3.30
cysS	Cysteinyl-tRNA synthetase	26.43 ± 0.11	23.97 ± 0.34	2.46c	9.77
cysK	Cysteine synthase	18.92 ± 0.17	18.73 ± 0.07	0.19	1.13
deoB	Phosphopentomutase	18.73 ± 0.12	19.31 ± 0.37	−0.58	0.68
dnaK	Molecular chaperone	16.85 ± 0.21	16.98 ± 0.32	−0.13	0.91
gapB	Glyceraldehyde 3-phosphate dehydrogenase	15.70 ± 0.12	16.40 ± 0.39	−0.70	0.64
glnQ	Glutamine ABC transporter ATP-binding protein	25.89 ± 0.47	21.62 ± 0.37	4.28c	16.13
groEL	Chaperonin	20.58 ± 0.22	20.58 ± 0.11	0.00	1.00
gyrA	DNA gyrase subunit A	20.83 ± 0.06	19.67 ± 0.06	1.17c	2.10
ldh	l-Lactate dehydrogenase	18.33 ± 0.06	18.27 ± 0.26	0.07	1.04
ldhB	l-Lactate dehydrogenase	24.36 ± 0.10	25.07 ± 0.57	−0.71	0.64
metA	Homoserine O-succinyltransferase	30.72 ± 0.21	27.71 ± 0.27	3.01c	6.23
metB1	Cystathionine gamma-synthase	29.97 ± 0.17	26.77 ± 0.16	3.20c	7.67
mleS	Malolactic enzyme	27.50 ± 0.28	25.54 ± 0.18	1.96c	3.51
pfl	Pyruvate-formate lyase	25.10 ± 0.14	23.99 ± 0.25	1.12c	2.03
purM	Phosphoribosylaminoimidazole synthetase	24.99 ± 0.04	22.75 ± 0.03	2.24c	4.85
rpiA	Ribose-5-phosphate isomerase A	24.02 ± 0.23	24.03 ± 0.18	−0.01	1.00
tuf	Elongation factor Tu	17.44 ± 0.12	17.89 ± 0.21	−0.45	0.75
16S rRNA	16S rRNA	9.60 ± 0.19	9.92 ± 0.12	−0.32	0.81
23S rRNA	23S rRNA	10.83 ± 0.15	11.10 ± 0.22	−0.27	0.84

^aThe values are means ± standard deviations for three repetitions (separate RNA extractions) using the same cheese sample. Reverse transcription was standardized using an RNA concentration of 15 ng/μl, and real-time PCR were done using a 25-fold dilution, except for 16S rRNA and 23S rRNA, for which a 125-fold dilution was used.

^bRatio of the gene abundance measured using RNA extracted after separation of cells to the abundance measured using RNA extracted directly from cheese.

^cThe threshold values of the two protocols were significantly different (P < 0.05).