TABLE 2.
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 |
The 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.
Ratio of the gene abundance measured using RNA extracted after separation of cells to the abundance measured using RNA extracted directly from cheese.
The threshold values of the two protocols were significantly different (P < 0.05).