Table S1: Stationary Phase Induced (Spi) Proteins

Table S1: Stationary phase induced (Spi) proteins. The table shows the protein spots whose induction at 48 h into stationary phase was statistically significant as calculated using a Student’s-T test to a confidence limit of P=0.05. Proteins are then further divided depending on their behaviour in stationary phase cultures of greater than 128 days old. Spi128: proteins with reduced synthesis levels at ≥128 d stationary phase compared with 48 h stationary phase. Spi128=: proteins with similar synthesis levels in 48 h and ≥128 d stationary phase. Spi128: proteins with higher synthesis levels at ≥128 d stationary phase than in 48 h stationary phase. -: Protein spot not present or not resolved. Quantities are given in mean ppm (parts per million)  se, and these were calculated by dividing the dpm counts of the spot by the total dpm of all the spots in that gel, and multiplying by 1,000,000 ppm. Where se is missing, the value is based on only one gel (because the spot was not resolved or absent in the other gels of the same condition). a The SSP (standard spot number) is the unique number that PDQuest assigns to each spot of the matchset. b Molecular weight (Mr). c Isoelectric point (pI) of the spot. SSP Mr pI exponential 48 h sp > 128 d sp phase (kDa) (ppm  se) (ppm  se) (ppm  se)

Spi128 8 8.4 6.6 179 3624  321 288  99 53 8.1 6.6 - 2210  682 - 534 37 6.8 157  19 349  53 - 2456 35 5.7 165 1025  242 508 3231 21 5.4 - 2821  512 1463 563 53 4.9 - 4232  1523 - 7546 36 4.6 733  262 3553  786 1106  582 Spi128= 2458 36 5.9 - 1976  402 1803  504 2621 49 5.7 420  60 1362  266 1415  454 4827 91 5.2 22 388  121 484 7734 55 4.7 - 550  161 438  116

Spi128 1633 47 6.0 57 196  13 1884  1469 2629 49 5.8 579  39 912  37 2565  805 2747 57 5.8 95  10 506  100 4080  1079 4024 13 5.3 50  15 3871  1014 7925  2744 6740 55 4.8 116  3 283  47 2508  681 Table S2: Proteins with expression levels maintained at exponential phase levels at 48 h stationary phase (Spm proteins). The expression of these proteins was maintained within 1.1 fold of the level in exponential phase. Spm128: proteins with lower synthesis levels at >128 d stationary phase than in either exponential or 48 h stationary phase. Spm128=: proteins with similar synthesis levels in exponential, 48 h and >128 d stationary phase. Spm128: proteins with higher synthesis levels at >128 d stationary phase than in both exponential and 48 h stationary phase. - value: protein spot not present or not resolved. See legend to Table 2 for column headings. SSP Mr pI exponential 48 h sp > 128 d sp phase (kDa) (ppm  se) (ppm  se) (ppm  se)

Spm128 408 36 6.5 511  147 556  299 - 713 60 6.6 180  22 184  65 - 2732 56 5.7 704  609 647  241 - 3025 9.7 5.6 5206  1536 5119  2057 1009  644 5030 9.5 5.2 1643  614 1569  664 264 5433 33 5.1 2081  827 2185  408 462 6853 73 4.7 532  224 509  240 397 Spm128= 1226 24 6.3 361  14 373  98 341  95 4025 12.3 5.3 1397  368 1382  385 1272  374 5525 37 4.9 4360  2204 4563  3404 6045  1361 7031 10.3 4.5 717  233 770  176 692  472

Spm128 1227 24 6.2 473  20 478  349 4345  2281 1737 56 6.0 607  454 707  114 6843  1410 2737 69 5.7 71 40  19 506  55 4442 36 5.3 960 524  43 4809  882 4533 37 5.3 3576  1688 3256  1048 6341  1901 5722 61 5.0 1295  265 1789  1271 6445  959 7928 122 4.7 1110  241 947  118 2395  402 Table S3: Stationary phase repressed (Spr) proteins. The repression in 48 h stationary phase compared with exponential phase was statistically significant for all protein spots shown (as calculated using a Student’s-T test to a confidence limit of

P=0.05) . Spr128: proteins with similar or reduced expression levels after >128 days in stationary phase compared with 48 h stationary phase. Spr128: proteins with increased expression levels after >128 days in stationary phase compared with 48 h stationary phase. See legend to Table for column headings. Rows shown in bold correspond to

Spr128 proteins that were subsequently identified (See Table 5). a b c SSP Mr pI exponential 48 h sp > 128 d sp phase (kDa) (ppm  se) (ppm  se) (ppm  se)

Spr128 1116 20 6.3 903  207 181  64 - 4023 13.8 5.3 1241  547 686 304 4134 19 5.4 543  46 142  38 - 4836 79 5.3 3204  463 580  172 - 5133 20 4.0 2616  278 695  259 - 6120 16 4.7 1815  237 510  162 -

Spr128 2620 46 5.8 1209  312 264  58 1432  358 2623 46 5.7 798  27 167  54 832  208 2728 53 5.8 1438  747 609  94 2434  385 3322 28 5.5 1597  422 357  156 3876  966 4121 16 5.3 586  151 133  35 3328  1275 4642 45 5.3 17671  11331 3021  583 10020  20 4746 64 5.3 1954  507 146  60 4007 4748 66 5.2 501  48 79  40 410 5834 91 5.0 402  130 1058  74 4025  635 7726 55 4.6 17178  14013 238  50 2812  1102 7734 26 4.7 1571  308 160 1530  206 7838 85 4.6 3099  1394 - 3059  1460 7840 76 4.5 1865  951 265  74 4148  1679