Table I. List of the 244 proteins found among the 1116 quantified to significantly change during heat stress. Protein IDs are derived from gene models from version 3.1 of the Chlamydomonas genome sequence (16).
| Bin | Functional group | No of proteins in bin | Enrichment (p value)a | Ups (Cluster; maximum fold increase)b | Downs (Cluster; maximum percent decrease)c |
|---|---|---|---|---|---|
| 1 | Flagellar and basal body proteins | 38 | 1,0E+00 | - | FAP24(C;40.1), FAP103(D;11.3), FAP278(E;21.5), PF9(-;66.4) |
| 2.0 | Other proteins associated with light reactions | 19 | 6,1E-01 | LHCSR3(A;1.2), ULP1(B;2.7) | FNR1(E;9.4), TEF8(C;45.0) |
| 2.1 | Proteins associated with PS I | 11 | 4,0E-01 | PSAN(B;2.1), LHCA3(B;1.2) | LHCA5(E;16.9) |
| 2.2 | Proteins associated with PS II | 10 | 1,3E-01 | - | PSBO(D;19.1), PSBP1(C;30.7), LHCBM1(C;45.6), LHCBM3(C;35.5) |
| 3 | Proteins of photosynthetic and photorespiratory carbon metabolism | 30 | 2,2E-7 | - | SHMT1(D;25.9), SHMT2(C;13.8), SHMT3(E;9.8), GCST(C;7.1), GCSP(E;11.3), rbcL(D;11.4), RCA1(C;29.6), CP12(D;22.2), FBA3(E;8.1), TRK1(E;9.7), FBP1(E;10.9), SBP1(E;8.7), RPE1(C;26.5), TPIC(E;14.8), PRK1(E;5.9), LCIB(D;8.2), LCIC(D;10.3), LCI23(-;87.2), CAH4(D;12.9), PPD2(C;31.9) |
| 4 | Starch synthesis & degradation | 8 | 4,4E-01 | - | PHOA(D;17.5), PHOB(D;14.6) |
| 5 | Porphyrin biogenesis | 14 | 1,7E-01 | - | GSA(D;17.8), ALAD(D;12.7), UROD1(E;30.9), UROD2(-;82.0), CHLI1(C;18.8) |
| 6 | Carotenogenic enzymes | 5 | - | - | |
| 7 | Glycolysis and gluconeogenesis | 13 | 7,9E-01 | - | PGH1(D;10.0), PYK1(E;27.0) |
| 8 | TCA | 14 | 3,7E-01 | - | PDC1(D;19.1), IDH3(E;7.2), OGD1(D;19.7), OGD2(D;32.1) |
| 9 | Oxidative pentose phosphate pathway | 6 | 6,0E-01 | - | 101528(E;19.8) |
| 10 | Acetate metabolism/glyoxylate cycle | 10 | 6,4E-03 | - | ACS1(D;15.1), ACS3(D;10.4), ACH1(D;9.2), ICL1(D;21.0), MAS1(D;11.4), MDH1(D;10.8) |
| 11 | Fermentation | 6 | 2,8E-01 | - | PDC3(C;59.1), PFL1(C;67.2) |
| 12 | Glycerolipid metabolism | 22 | 5,8E-01 | - | BCR1(C;20.2), KAR1(E;18.2), ENR1(C;26.1), 190684(C;60.3), ATO1(D;29.7) |
| 13 | Mitochondrial electron transport chain and ATP synthase | 12 | 9,6E-01 | - | CYC(D;36.6) |
| 14 | N-metabolism | 7 | 3,3E-03 | - | GSF1(D;14.2), GSN1(C;32.8), GLN1(E;25.5), 194028(C;22.0), MDH5(E;20.4) |
| 15 | Amino acid metabolism | 47 | 1,8E-01 | - | 136279(E;42.5), 162449(D;21.3), 126232(E;29.0), HIS1(D;43.1), 140252(E;14.0), ASSD1(C;24.2), METE(C;58.6), THS1(D;19.8), AAD1(D;16.1), AAI1(C;22.5), ALSS1(C;17.6), LEU2(E;25.4), AGS1(D;12.3), CMPL1(D;16.7) |
| 16 | S-assimilation | 5 | 5,2E-01 | - | ATS1(C;60.5) |
| 17 | Metal handling | 3 | 2,8E-01 | - | SBD1(E;16.9) |
| 18 | C1 metabolism | 6 | 8,7E-03 | - | FDH1(D;80.2), 111330(C;15.0), METM(C;12.3), SAH1(D;21.6) |
| 19 | Vitamin biosynthesis | 7 | 3,7E-01 | THI4a(A;1.5) | PDX1(C;41.5) |
| 20.0 | Protein folding and abiotic stress | 8 | 7,9E-01 | 154979(A;2.5) | - |
| 20.1 | Small heat shock proteins | 3 | 0,0E+00 | HSP22A(B;21.4), HSP22C(B;26.0), HSP22E(B;13.2) | - |
| 20.2 | HSP60s | 15 | 6,4E-03 | CPN60A(B;4.1), CPN60B1(B;2.1), CPN60B2(B;4.0), CPN60C(A;1.3), CPN23(B;2.5), CPN20(B;2.5), CPN10(B;3.0), CPN11(B;2.5) | - |
| 20.3 | HSP70 and co-chaperones | 11 | 3,3E-04 | HSP70A(B;2.9), HSP70B(B;2.4), HSP70C(B;1.3), HSP70E(B;2.0), 150437(A;6.4), MOT53(-;3.2), DNJ1(A;2.3) | HSP70G(E;56.9) |
| 20.4 | HSP90 and co-chaperones | 5 | 3,0E-03 | HSP90A(B;5.2), HSP90B(B;1.4), HSP90C(B;3.4), HOP1(A;2.6) | - |
| 20.5 | HSP100 | 4 | 8,7E-03 | CLPB1(A;22.1), CLPB3(A;5.7), CLPB4(A;6.2) | - |
| 20.6 | FKBPs/Cyclophilins | 10 | 1,1E-03 | FKB62(B;11.5) | FKB12(D;17.7), FKB53(E;10.7), CYN19–2(C;43.4), CYN20–1(E;9.0), CYN20–3(C;46.7), CYN38(D;29.3) |
| 21 | Proteases/Peptidases | 53 | 1,0E+00 | - | 82208(E;7.5), 139416(D;18.0), UBC2(D;23.1), CDC48(D;16.8) |
| 22 | Redox regulation/oxidative stress response | 35 | 4,1E-01 | - | TRXH(C;15.4), CITRX(E;8.4), RB60(D;15.3), CCPR1(C;53.4), 165193(E;9.4), APX1(C;36.5), GPX5(E;16.8), FSD1(E;4.9), MSRA4(-;39.2) |
| 23 | Nucleotide metabolism | 26 | 1,0E+00 | - | 175039(D;28.7) |
| 24 | Sugar nucleotide metabolism | 10 | 1,3E-01 | - | 158152(C;23.6), SNE1(E;15.4), SNE6(C;10.8), UPTG1(D;17.6) |
| 25 | RNA processing/binding | 43 | 1,0E+00 | - | RSZ22(C;46.1), UAP56(E;6.0), NOP1(D;43.6), 184151(D;15.9), RB47(D;13.0), RB38(D;16.9) |
| 26 | DNA binding/transcription/chromatin remodeling | 65 | 1,0E+00 | 153995(-;3.3), 24073(B;1.5) | GBP1(E;27.1), 186410(C;33.5), 154370(E;16.5) |
| 27.1 | Protein biosynthesis (not ribosome) | 50 | 6,0E-01 | - | 186253(E;23.6), 82920(D;32.6), 38643(E;19.9), 145770(D;14.0), EFG2(D;13.6), EFT1a(C;64.4), tufA(D;13.2), EIF3K(D;19.7), 188942(C;13.9), EIF4E(C;17.1), EIF6A(D;23.4) |
| 27.2.0 | Protein biosynthesis | 4 | - | - | |
| 27.2.1 | Protein biosynthesis (LSU plastid) | 21 | 9,4E-01 | - | PRPL1(D;37.0), rpl2(E;10.7), PRPL9(E;10.2) |
| 27.2.2 | Protein biosynthesis (SSU plastid) | 15 | - | - | |
| 27.2.3 | Protein biosynthesis (LSU cytosol) | 40 | 1,4E-06 | - | RPP0(E;7.3), RPL3(D;21.1), RPL4(D;10.5), RPL5(E;5.9), RPL6(E;14.3), RPL7(D;20.6), RPL9(E;6.3), RPL10(D;16.9), RPL10a(D;11.4), RPL12(C;10.4), RPL13(D;13.3), RPL14(D;12.4), RPL18a(D;11.5), RPL19(E;10.3), RPL21(E;8.3), RPL22(E;11.1), RPL27(D;7.9), RPL28(C;14.9), RPL32(D;28.6), RPL35(D;14.1), RPL35a(D;18.9), RPL36(E;15.5), RPL40(E;31.2) |
| 27.2.4 | Protein biosynthesis (SSU cytosol) | 31 | 9,4E-09 | - | RPS2(D;26.9), RPS3(E;13.8), RPS3a(E;15.0), RPS4(D;31.4), RPS6(D;29.5), RPS7(D;26.2), RPS8(D;17.3), RPS9(E;27.1), RPS10(E;14.2), RPS14(C;17.4), RPS15(D;12.1), RPS15a(C;27.6), RPS16(D;18.8), RPS18(D;10.2), RPS19(E;9.2), RPS20(D;15.0), RPS23(D;35.4), RPS24(E;22.5), RPS25(D;17.0), RPS27-A(D;18.0), RPS28(D;13.3), RPS29(D;27.3) |
| 28 | Signal transduction | 58 | 1,0E+00 | CRT2(B;1.1), AKC2(-;2.0) | 184895(D;6.7), RACK1(E;7.3), PP2A-2r(E;21.5), RABC2(-;25.1), FTT1(D;15.2) |
| 29 | Pumps and transporters | 16 | 9,4E-01 | - | ATPvA1(D;16.2), ATPvB(D;10.4) |
| 30 | Vesicle transport | 22 | 9,5E-01 | - | COPE1(E;30.6), COPG1(C;17.1), VPS35(C;18.3) |
| 31 | Cytoskeleton | 9 | - | - | |
| 32 | Miscellaneous | 145 | 1,0E+00 | 193531(A;43.8), 148088(B;1.6) | SPS1(E;21.1), CPLD48(-;35.9), 190138(C;22.5), 190503(C;23.6), RCD2(C;26.0), 194623(C;20.0), 179100(D;54.5) |
| 33 | Proteins without functional annotation | 115 | 1,0E+00 | - | 144849(C;15.6), 178937(C;97.1), 95661(-;30.0), 192803(D;12.6), 137973(-;44.3), CGL13(-;20.7), 166509(-;33.5) |
| 34 | Protein sorting | 9 | 9,4E-02 | - | TIC40(D;46.6), TIC110(-;19.1), SRP19(C;32.6), IPB2(E;23.7) |
a Significant bin enrichment is given at p values below 1,0E-02.
b Cluster A = UP fast; B = UP delayed; C = DOWN fast; D = DOWN delayed; E = DOWN delayed, into steady state. Maximum fold increase was calculated by dividing protein quantification values for all time points with the value of the first available time point and selecting the quotient with the highest value for display.
c Maximum percent decrease was calculated by subtracting the quotients of protein quantification values from all time points and the first available time point from 1 and selecting the difference with the highest value for display.