Table 1.
Genes differentially expressed in S. sobrinus 6715 using interspecies microarrays.
| Unique ID (GenBank) |
Description | Difference (n-fold) of geom. means pH 5/ pH 7 |
Parametric P value |
|---|---|---|---|
| Up-regulated genes | |||
| Energy metabolism | |||
| SMU.137 | malolactic enzyme, mleS | 17.893 | 3.00E-07 |
| SMU.131 | putative lipoate-protein ligase, lplA | 14.891 | 3.00E-07 |
| SMU.127 | pyruvate/ acetoin dehydrogenase, E1 component α, adhA/acoA |
8.646 | 1.4E-06 |
| SMU.1528 | F0F1 membrane-bound proton- translocating ATPase, β subunit, atpD |
2.742 | 0.0032706 |
| SMU.1537 | glycogen biosynthesis protein, glgD | 2.405 | 0.0081713 |
| SMU.670 | aconitate hydratase aconitase, citB/acnA |
2.097 | 0.0146193 |
| SMU.275 | L-ribulose 5-phosphate 4-epimerase, rmpF |
1.857 | 0.0287093 |
| SMU.1115 | lactate dehydrogenase, ldh/lct | 1.850 | 0.0154089 |
| SMU.99 | fructose-1,6-biphosphate adolase, sorG/fbaA |
1.660 | 0.0285881 |
| SMU.1191 | 6-phosphofructokinase, pfkA | 1.593 | 0.0426727 |
| Transport and binding | |||
| SMU.602 | putative sodium-dependent transporter | 7.627 | 0.000666 |
| SMU.1668 | putative branched chain amino acid ABC transporter, livH |
2.892 | 0.001657 |
| SMU.248 | ABC transporter, membrane protein | 1.954 | 0.0072554 |
| SMU.827 | polysaccharide ABC transporter, permease protein, rgpCc |
1.953 | 0.0253459 |
| SMU.1927 | ABC transporter, ATP-binding protein, psaA |
1.880 | 0.0126816 |
| SMU.247 | putative ABC transporter, ATP-binding protein, yurY |
1.758 | 0.0380766 |
| SMU.1347 | ABC transporter permease protein, ylbB |
1.734 | 0.0286651 |
| Amino acid biosynthesis | |||
| SMU.873 | putative homocysteine methyltransferase methionine synthase II, metE/metC |
1.792 | 0.035998 |
| Regulatory functions | |||
| SMU.2044 | stringent response protein, ppGpp synthetase, relA |
2.959 | 0.0357087 |
| SMU.1515 | conserved hypothetical protein CovX (VicX), covX/vicX |
2.368 | 0.0063014 |
| SMU.479 | RNA polymerase-associated protein RpoZ, Ω subunit, rpoZ |
2.047 | 0.0113671 |
| Protein synthesis | |||
| SMU.1311 | asparaginyl-tRNA synthetase, asnS | 1.829 | 0.043923 |
| SMU.1272 | histidyl-tRNA synthase, hisZ/hisS | 1.818 | 0.0466654 |
| Central intermediary metabolism | |||
| SMU.249 | putative NifS protein homologue, class- V aminotransferase, nifS |
3.007 | 0.0005185 |
| SMU.1415 | putative phosphatases involved in N- acetyl-glucosamine catabolism, nagD/ylfH |
2.043 | 0.0240285 |
| DNA metabolism and repair | |||
| SMU.1649 | exodeoxyribonuclease III, exoA/smxA | 2.725 | 0.0006884 |
| SMU.1650 | endonuclease III (DNA repair), end3 | 1.789 | 0.0359052 |
| SMU.991 | similar to ribonucleotide reductase α subunit, nrdE |
2.267 | 0.0059736 |
| Detoxification | |||
| SMU.838 | glutathione reductase, gshR/gor | 1.791 | 0.021416 |
| SMU.1451 | putative alpha-acetolactate decarboxylase, aldB |
2.860 | 0.0018603 |
| Cell division | |||
| SMU.1713 | segregation and condensation protein A, scpA |
1.746 | 0.0334277 |
| SMU.15 | cell division protein FtsH, ftsH | 1.682 | 0.0443664 |
| Hypothetical proteins | |||
| SMU.1700 | hypothetical protein possible LrgB family protein |
3.200 | 0.0121089 |
| SMU.1755 | conserved hypothetical protein | 2.202 | 0.0036035 |
| SMU.573 | conserved hypothetical protein | 2.127 | 0.0468976 |
| SMU.564 | conserved hypothetical protein | 2.125 | 0.0349508 |
| SMU.591 | hypothetical protein | 1.850 | 0.0192613 |
| SMU.748 | hypothetical protein | 1.781 | 0.0370629 |
| SMU.173 | putative ppGpp-regulated growth inhibitor, mazF |
1.695 | 0.027644 |
| Down-regulated genes | |||
| Energy metabolism | |||
| SMU.671 | citrate synthase, citZ | 0.291 | 0.0003693 |
| SMU.1011 | putative CitG protein, citG | 0.171 | 0.0003965 |
| Transport and binding | |||
| SMU.998 | ABC transporter, periplasmic ferrichrome-binding protein, yclQ/fatB |
0.592 | 0.0415653 |
| SMU.568 | amino acid ABC transporter, ATP- binding protein, glnQ |
0.538 | 0.0313816 |
| SMU.2116 | osmoprotectant amino acid ABC transporter, ATP-binding, opuCA |
0.414 | 0.0034014 |
| SMU.460 | putative amino acid ABC transporter, permease |
0.374 | 0.0025901 |
| SMU.461 | putative amino acid ABC transporter, ATP-binding protein |
0.261 | 0.0006624 |
| SMU.933 | putative amino acid ABC transporter, periplasmic amino acid, atmA |
0.147 | 1.21E-05 |
| SMU.935 | putative amino acid ABC transporter | 0.135 | 5.18E-05 |
| Amino acid biosynthesis | |||
| SMU.1836 | DAHP synthase phosphor-2-dehydro- 3-deoxyphosphoheptonate adolase, aroG |
0.655 | 0.0427644 |
| SMU.317 | putative tetrahydrodipicolinate succinylase, ykuQ/ dapD |
0.569 | 0.0315775 |
| SMU.335 | argininosuccinate lyase, argH | 0.563 | 0.0445401 |
| SMU.1383 | 3-isopropylmalate dehydrogenase, leuB |
0.530 | 0.0105533 |
| SMU.1382 | 3-isopropylmalate dehydratase, large subunit, leuC |
0.499 | 0.014424 |
| SMU.784 | 5-enolpyruvylshikimate-3-phosphate synthase, aroA |
0.460 | 0.0314230 |
| SMU.990 | dihydrodipicolinate synthase, dapA | 0.385 | 0.0429038 |
| SMU.1653 | D-3-phosphoglycerate dehydrogenase, serA |
0.324 | 0.0001565 |
| Regulatory function | |||
| SMU.1037 | Putative histidine kinase, phoR | 0.613 | 0.0425196 |
| SMU.1958 | fructose-specific enzyme IIC component, levF |
0.149 | 0.0001353 |
| Biosynthesis of proteins/ purine ribonucleotides/cofactors | |||
| SMU.2003 | 30S ribosomal protein S13, rs13/rpsM | 0.613 | 0.0482857 |
| SMU.2157 | inosine monophosphate dehydrogenase, guaB/impH |
0.454 | 0.0077039 |
| SMU.465 | NAD(+) synthetase (nitrogen regulatory protein), nadE |
0.386 | 0.0011386 |
| Central intermediary metabolism | |||
| SMU.376 | putative aminotransferase | 0.366 | 0.0406214 |
| SMU.636 | N-acetylglucosamine-6-phosphate isomerase, nagB |
0.203 | 0.0026116 |
| DNA metabolism | |||
| SMU.1002 | DNA topoisomerase I, topA | 0.556 | 0.0220572 |
| Cell division | |||
| SMU.2165 | chromosome segregation protein, ParB-like nuclease domain, smc |
0.581 | 0.0303665 |
| Protein fate/chaperone | |||
| SMU.1929 | protease HtpX, heat shock protein, htpX |
0.563 | 0.0345522 |
| SMU.91 | peptidyl-prolyl isomerase RopA (trigger factor), ropA |
0.560 | 0.0455648 |
| SMU.539 | signal peptidase type IV, hopD | 0.439 | 0.0159205 |
| Hypothetical proteins | |||
| SMU.1151 | conserved hypothetical protein | 0.626 | 0.0484003 |
| SMU.607 | conserved hypothetical protein | 0.608 | 0.0403010 |
| SMU.1404 | conserved hypothetical protein | 0.600 | 0.0351768 |
| SMU.252 | hypothetical protein | 0.580 | 0.0251873 |
| SMU.383 | conserved hypothetical protein | 0.543 | 0.0491039 |
| SMU.1853 | conserved hypothetical protein | 0.529 | 0.0357836 |
| SMU.163 | hypothetical protein | 0.522 | 0.0464475 |
| SMU.295 | hypothetical protein | 0.508 | 0.0096429 |
| SMU.673 | conserved hypothetical protein | 0.503 | 0.0269833 |
| SMU.1089 | conserved hypothetical protein | 0.501 | 0.0385478 |
| SMU.1884 | hypothetical protein | 0.472 | 0.0267431 |
| SMU.462 | conserved hypothetical protein | 0.442 | 0.0195586 |
| SMU.1284 | conserved hypothetical protein | 0.436 | 0.0146092 |
| SMU.1703 | conserved hypothetical protein | 0.435 | 0.0119016 |
| SMU.201 | conserved hypothetical protein | 0.432 | 0.0165989 |
| SMU.919 | hypothetical protein, putative ATPase, confers aluminum resistance |
0.421 | 0.0229347 |
| SMU.1480 | hypothetical protein | 0.409 | 0.0289793 |
| SMU.195 | hypothetical protein | 0.388 | 0.0072813 |
| SMU.1956 | hypothetical protein | 0.383 | 0.0094685 |
| SMU.862 | hypothetical protein | 0.354 | 0.0151455 |
| SMU.213 | hypothetical protein | 0.327 | 0.0032760 |
| SMU.1220 | conserved hypothetical protein | 0.282 | 0.0013358 |
| SMU.1723 | conserved hypothetical protein | 0.236 | 0.0002403 |
| SMU.684 | hypothetical protein | 0.190 | 0.0008547 |
| SMU.940 | putative hemolysin III, patB | 0.382 | 0.0107347 |