Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic categories CD, CE, DNA, E, L, Mi, Nt, and P.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05 and |fold change|>1 for at least one sampling time) and RT-qPCR (<i>P</i><0.05) experiments.</p

Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic category CH.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05 and |fold change|>1 for at least one sampling time) and RT-qPCR (<i>P</i><0.05) experiments.</p

Time-course of <i>P. freudenreichii</i> CIRM-BIA1^T metabolic activity over a 40 h-incubation at 30°C followed by a further 9 days at 4°C.

<p>Lactate was added at 64 h (<b>↓</b>) to mimic cheese ripening conditions. <b>A</b>, growth monitored by optical density (650 nm) measurements (black circle), lactate consumption (cross), production of acetate (white triangle) and propionate (black triangle); <b>B</b>, production of pyruvate (white rhombus) and succinate (black rhombus), consumption of aspartate (white triangle) and asparagine (black triangle); <b>C</b>, production of methylbutanoate (sum of 2-methyl- and 3-methylbutanoate acids). ¥: sampling times for microarray experiments.</p

Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic category Ph and PM.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05).</p

Schematic representation of carbon metabolism in <i>P. freudenreichii</i> CIRM-BIA1^T during storage at 4°C and relevant for this study.

<p>Protein and gene names are written in plain and in italic fonts, respectively. The color indicates the change in expression at 4°C, compared to reference time (exponential growth at 30°C, 20 h): in red, genes up-regulated at 4°C using microarray and RT-qPCR data and protein present at larger amounts; in pink, genes up-regulated at 4°C using microarray results only; in blue, genes down-regulated at 4°C using microarray and RT-qPCR data; in green, genes up-regulated at 4°C using microarray data only; in black, genes not being differentially expressed at 4°C using microarray data. * genes up-regulated using RT-qPCR data, but not significantly affected using microarray experiments. Red lines emphasize the metabolic pathways that seem to be favored at 4°C in <i>P. freudenreichii</i> considering the proteomic and transcriptomic results. Plain lines are used to symbolize one reaction, dotted lines several reactions (intermediary products not detailed). Gene and protein abbreviations are as follow: <i>acn</i> (aconitase), Ald/<i>ald</i> (alanine dehydrogenase), AspA2/<i>aspA2</i> (aspartate ammonia-lyase), Cat/<i>cat</i> (coenzyme A transferase), <i>dld</i> (D-lactate dehydrogenase), Eno1/e<i>no1</i> (enolase 1), <i>fba2</i> (fructose-bisphosphate aldolase class I), FumC/<i>fumC</i> (fumarate hydratase class-II), <i>glgA</i> (glycosyltransferase), <i>glgC</i> (glucose-1-P adenylyltransferase), <i>gltA1,2</i> (citrate synthases), <i>icd</i> (putative isocitrate/isopropylmalate dehydrogenase), <i>ldh</i> (L-lactate dehydrogenase), <i>mdh</i> (malate dehydrogenase), MmdA/<i>mmdA</i> (methylmalonyl-CoA carboxytransferase 12S subunit), MutA/<i>mutA</i> (methylmalonyl-CoA mutase small subunit), MutB/<i>mutB</i> (methylmalonyl-CoA mutase large subunit), <i>pccB</i> (propionyl-CoA carboxylase β-chain), Pgi/<i>pgi</i> (glucose-6-P isomerase), Pgm1/<i>pgm1</i> (phosphoglucomutase), PpdK/<i>ppdk</i> (pyruvate phosphate dikinase), <i>ptsI</i> (PTS enzyme I), <i>sdaA</i> (L-serine dehydratase), <i>sdhA</i> (succinate dehydrogenase, subunit A), <i>sdhA3</i> (succinate dehydrogenase, flavoprotein subunit), <i>sdhB</i> (succinate dehydrogenase, subunit B), <i>sdhB3</i> (succinate dehydrogenase), <i>sdhC1</i> (succinate dehydrogenase, subunit C), <i>sdhC2</i> (succinate dehydrogenase, cytochrome B-558 subunit), ?: undefined protein (probable phosphoenolpyruvic carboxylase).</p

Figure 2

<p>Two-dimensional analysis of proteins produced during <i>P. freudenreichii</i> CIRM-BIA1^T growth (<b>A</b>) at 30°C (reference time 20 h) and then (<b>B</b>) at 4°C (3 days). Numbers identify spots which volume decreased at 4°C (<b>A</b>), or increased at 4°C (<b>B</b>). The identification by MS/MS of each spot can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a>.</p

Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic categories A, AA and C.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05 and |fold change|>1 for at least one sampling time) and RT-qPCR (<i>P</i><0.05) experiments.</p

Indicators of <i>P. freudenreichii</i> CIRM-BIA1^T strain metabolism during a 40 h-incubation at 30°C followed by 9 days at 4°C.

a<p>Methylbutanoate is sum of 2-methylbutanoate and 3-methylbutanoate.</p>b<p>Not detected.</p>c<p>Values at 30°C and 4°C significantly differed at <i>P</i> = 0.09.</p>d<p>Values at 30°C and 4°C significantly differed at P = 0.12.</p><p>Values are means and standard deviations of three independent experiments.</p