50 2.93 3517 Phosphomevalonate kinase 1005 494 270 220 367 504 -3.72 -2.73 6308 Diphosphomevalonate decarboxylase 2146 1521 4628 2509 5598 1347 2.16 2.61   Redox Metabolism                 4401 Hypothetical oxidoreductase 6305 1432 1034 1014 1432 561 -6.10 -4.40 3606 Putative protein Cu-oxidase 741 92 184 195 1198 691 -4.04 1.62 5202 SDR family 2593 668 342 91 3515 418 -7.59 1.36 5208 Alcohol dehydrogenase 2564 1239 1008 1032 S63845 molecular weight 1607 578 -2.54 -1.60 4713 Monooxygenase 3930 522 4267 1706 5044 500 1.09 1.28 5703   4713 612 6594 2637 8287 916 1.40 1.76 5315 Cytochrome P450 10876 4259 16346 15386 6649 4692

1.50 -1.64 7108 Mn SOD 12020 3850 18262 13048 11032 1547 1.52 -1.09   Amino Acid Metabolism                 8604 Seryl-tRNA synthetase 783 87 2517 1567 3861 203 3.21 4.93 7209 PCI-34051 solubility dmso Methionyl-tRNA formyltransferase 912 290 28686 4392 17584 6195 31.44 19.27 7210   4348 1880 15379 2474 9085 2322 3.54 2.09 7816 Kynurenine 3-monooxygenase 111 73 726 424 811 64 6.56 7.33 7817   114 119 1139 751 1367 206 10.02 Raf inhibitor 12.03 7819   130 84 1625 1134 1797 821 12.50 13.82 6821 Aspartyl-tRNA synthetase 156 81 395 76 1532 796 2.54 9.84 6828   580 11 2001 1020 2199 706 3.45 3.79 5410 Probable acetylornithine aminotransferase 4766 986 1794 1531 2615 447 -2.66

-1.82 2517 Phenylalanyl-tRNA synthetase beta chain 3325 375 813 639 2104 1397 -4.09 -1.58 5409 Glutamate dehydrogenase 2194 1506 2738 930 6893 2363 1.25 3.14   Unknown                 2709 Conserved hypothetical protein 5609 2745 1227 889 4692 657 -4.57 -1.20 2710   2584 1482 1157 1630 1465 1413 -2.23 -1.76 6603 Hypothetical protein 3640 575 1014 1091 2985 120 -3.59 -1.22 7306 Hypothetical protein 2652 601 795 253 3569 2539 -3.34 1.35 6110 YALI0D17292p 10346 2105 1204 1434 8343 763 -8.59 -1.24 3503 Predicted protein 2670 367 906 897 735 650 -2.95 -3.63 a SSP numbers were assigned by PDQuest software analysis. b Identifications were obtained using the

Swiss-Prot and KEGG Pathways databases and contigs of X. dendrorhous PRKD3 genomic DNA. c Data derived from PDQuest estimation. d Mean fold changes compared with the 24 h cultures. Bold values indicate p < 0.01, italic p < 0.02 and underlined values indicate p < 0.05. Avg., average; SD, standard deviation. Most of the differentially regulated proteins (63%) fell within three functional groups (metabolism, genetic information processing and cellular processes), while 13% had unknown functions (Table 1). In addition, we observed similar patterns of intensities between proteins with multiple spots, such as myosin-associated protein and Golgi transport protein (Table 1, Figure 5). Figure 5 Fold changes of differentially expressed proteins. Proteins with more than two-fold changes (see Table 1) were plotted according to their fold change in exponential phase (left graph) or stationary phase (right graph) relative to their abundance in lag phase.