TABLE 2.
Comparison of gene expression levels measured by RNA-seq analysis of cells grown in GNB medium, GalNAc medium, and Gal mediuma
| Cluster | Locus tagb | Genbank_ID | Gene | Predicted function | Gal | GalNAc | GNB |
|---|---|---|---|---|---|---|---|
| Z-score | Z-score | Z-score | |||||
| A | RS03070 | WP_015764582.1 | glgB | 1,4-Alpha-glucan branching protein GlgB | 0.256 | 1.314 | 0.646 |
| A | RS03075* | WP_005687169.1 | Glucose-1-phosphate adenylyltransferase | 0.111 | 1.723 | 1.541 | |
| A | RS03080* | NA | glgD | Glucose-1-phosphate adenylyltransferase subunit GlgD | −0.035 | 1.482 | 1.737 |
| A | RS03085* | WP_005692826.1 | glgA | Glycogen synthase GlgA | −0.125 | 1.01 | 1.545 |
| A | RS03090 | WP_019728285.1 | Glycogen/starch/alpha-glucan phosphorylase | 0.034 | 0.457 | 1.106 | |
| A | RS03095 | WP_005692830.1 | Glycoside hydrolase family 13 protein | 0.128 | 0.426 | 0.982 | |
| B | RS04750* | WP_005689192.1 | lpdA | Dihydrolipoyl dehydrogenase | 0.47 | 1.549 | 1.949 |
| B | RS04755 | WP_015764445.1 | Dihydrolipoyllysine-residue acetyltransferase | 0.944 | 1.797 | 1.417 | |
| B | RS04760 | WP_005689188.1 | Pyruvate dehydrogenase subunit beta | 1.289 | 1.872 | 0.976 | |
| B | RS04765 | WP_005685622.1 | pdhA | Pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha | 1.096 | 1.499 | 0.405 |
| B | RS04770 | WP_005689186.1 | ATPase | −0.383 | 0.176 | 0.675 | |
| C | RS07800 | WP_005690692.1 | PTS sugar transporter subunit IIC | −0.465 | 2.318 | 1.407 | |
| C | RS07805* | WP_005690694.1 | PTS system mannose/fructose/sorbose family transporter subunit IID | −0.535 | 2.293 | 1.705 | |
| C | RS07810* | WP_005690696.1 | PTS sugar transporter subunit IIB | −0.574 | 1.991 | 2.228 | |
| C | RS07815* | WP_005690698.1 | MurR/RpiR family transcriptional regulator | −0.363 | 1.572 | 2.191 | |
| C | RS07820 | WP_015764772.1 | murQ | N-acetylmuramic acid 6-phosphate etherase | −0.539 | 1.356 | 1.988 |
| C | RS07825* | WP_005690702.1 | Serine hydrolase | −0.482 | 1.187 | 1.79 | |
| C | RS07830 | WP_005690704.1 | Serine hydrolase | −0.469 | 0.467 | 1.315 | |
| D | RS11890* | WP_019728333.1 | GntR family transcriptional regulator | 0.33 | 3.566 | 2.386 | |
| D | RS11895* | WP_005687616.1 | Phosphosugar isomerase | 0.368 | 3.728 | 2.446 | |
| D | RS11900* | WP_005687614.1 | nagA | N-acetylglucosamine-6-phosphate deacetylase | 0.407 | 3.775 | 2.598 |
| D | RS11905 | WP_014571082.1 | Phospho-beta-galactosidase | −0.311 | 2.096 | 1.038 | |
| D | RS11910 | WP_005687609.1 | PTS sugar transporter subunit IIB | 0.023 | 2.226 | 0.766 | |
| D | RS11915 | WP_005687608.1 | PTS sugar transporter subunit IIC | 0.062 | 2.385 | 0.698 | |
| D | RS11920 | WP_005691352.1 | PTS system mannose/fructose/sorbose family transporter subunit IID | 0.074 | 2.314 | 0.93 | |
| D | RS11925 | WP_005691354.1 | PTS sugar transporter subunit IIA | 0.067 | 2.085 | 1.225 | |
| E | RS13095 | WP_005690785.1 | Transaldolase | 2.508 | 3.353 | 2.343 | |
| E | RS13100 | WP_005714186.1 | PTS glucitol/sorbitol transporter subunit IIA | 2.479 | 3.487 | 2.089 | |
| E | RS13105 | WP_005690782.1 | PTS glucitol/sorbitol transporter subunit IIB | 2.511 | 3.662 | 2.258 | |
| E | RS13110 | WP_005687747.1 | PTS glucitol/sorbitol transporter subunit IIC | 2.85 | 3.98 | 2.375 | |
| E | RS13115 | WP_005690780.1 | Transcriptional regulator GutM | 2.802 | 3.996 | 2.315 | |
| E | RS13120 | WP_014571687.1 | HTH domain-containing protein | 3.472 | 4.523 | 2.281 | |
| E | RS13125 | WP_005690776.1 | Sorbitol-6-phosphate 2-dehydrogenase | 3.688 | 4.985 | 2.105 | |
| E | RS13130 | WP_220094871.1 | Cell wall protein with serine-rich repeat domain | 0.346 | 1.629 | 2.432 | |
| E | RS13135 | WP_015764686.1 | Glycosyltransferase | 1.272 | 1.802 | 2.665 | |
| E | RS13140 | WP_014571544.1 | Glycosyltransferase | 1.117 | 1.517 | 2.276 | |
| E | RS13145 | WP_005692417.1 | NAD-dependent succinate-semialdehyde dehydrogenase | 1.425 | 1.923 | 1.701 | |
| F | RS13565 | WP_155519883.1 | LPXTG cell wall anchor domain-containing protein | 0.074 | 1.193 | 2.266 | |
| F | RS13570* | WP_019728467.1 | Glycosyl transferase | 0.187 | 1.545 | 1.903 |
a
Fold changes against cells grown in the Glc medium were translated to Z-scores.
b
Locus tag identifier from the L. rhamnosus JCM 1136T genome sequence (AZCQ01000000). *Astarisks beside the locus tag numbers indicate 13 genes found by volcano plot analysis (FIG 4).