TABLE 1.

Transcripts showing a ≥3-fold change in abundance during sulfur deprivationa

Clone (Fig. 3 panel)bACEcNameGene annotationDirection of change in transcript levelTranscript level (fold increase) for
CC425sac1 mutant
CC425dsac1d2 h4 h8 h12 h24 h0 h2 h4 h8 h12 h24 h
Sulfur metabolism
    ′963038E011936 ARSI Arylsulfatase +++++ ...... 8.517.5242.8141.593.391.321.10.80.770.99NA
    ′894069D019009 SIRI Sulfite reductase +++++ −+.++. 1.481.632.052.623.160.393.301.421.241.471.20
    ′963038A064494Sulfite reductase +++++ .+++++ 2.692.483.183.592.390.752.371.851.761.911.89
    ′963042H108444 SIR3 Sulfite reductase, bacterial type ..... .+.−.. 0.941.031.110.960.990.932.16NAe0.491.72NA
    ′894033F10[7588] ATS1 ATP sulfurylase +++++ .++++. 4.925.298.6210.587.691.052.652.432.041.70.9
    ′963046C091668 ATS2 ATP sulfurylase +++++ ...... 3.634.695.918.647.740.91.611.230.851.350.42
    ′894044E129443 APR 5′-Adenylylsulfate reductase +++++ ...... 2.351.571.311.901.341.010.900.850.991.210.97
    ′894077C011669 AKN2 APS kinase ...+. ...... 0.771.170.701.421.070.57NANANANANA
    ′963045D113138 SAT1 Serine O-acetyltransferase +++++ −.+.++ 6.696.2510.5914.779.060.881.771.441.241.442.18
    ′963024B058367 OASTL4 O-Acetylserine(thiol)lyase +++++ −++++. 6.017.0010.039.168.30.772.342.292.592.231.17
    ′963076G106009 CDO1 Cysteine dioxygenase +++++ −++++. 5.945.687.758.97.540.712.291.922.012.010.71
    ′963035D068168 SQDI UDP-SQi synthase +++++ .+++++ 5.636.647.739.59.570.974.432.42.452.364.2
    ′894101C06Nonef SQD2a UDP-SQj; diacylglycerol SQj transferase +++++ −++++. 5.166.138.448.316.890.831.692.351.91.751.12
    ′963017H04[5161] ECP76 Extracellular polypeptide 76 +++++ −...++ 4.839.4934.0722.1421.450.851.120.781.281.411.28
    ′894020C125894 SBDP Selenium-binding protein +++++ ++++++ 7.895.529.668.235.191.291.71.531.391.521.6
    ′963027A095894 SBDP Selenium-binding protein +++++ −+.++. 12.7214.1616.1320.415.710.741.751.531.571.860.89
    ′963046G027825SACI-like proteins (2 overlapping genes) +++++ −+++++ 27.5218.0640.3845.926.560.773.662.131.862.411.63
    ′894081F11[7825]SAC1-like protein +++++ −++.+. 60.8348.8937.0984.4653.560.641.622.122.342.951.23
Photosynthesis
    ′963024B11 (C)5736 LHCA1 Light-harvesting complex, PS I .++−− −−−−−− 1.211.381.20.70.390.380.410.250.250.260.06
    ′963047H05 (C)2886 LHCA2 Light-harvesting complex, PS I ...−− −−−−−− 1.271.161.10.580.30.390.20.160.150.090.03
    ′894033H06 (C)4209 LHCA3 Light-harvesting complex, PS I ...−− −−−−−− 1.041.131.090.550.220.370.310.220.170.120.01
    ′963042A01 (C)9189 LHCA5 Light-harvesting complex, PS I +++.− −−−−−− 1.551.671.280.850.390.340.380.280.260.160.02
    ′894041D11 (C)7340 LHCA5 Light-harvesting complex, PS I ...−− −−−−−− 1.221.671.190.690.450.660.370.290.290.320.22
    ′894087C09 (C)4579 LHCA8 Light-harvesting complex, PS I +++.− −−−−−. 1.461.421.360.840.360.860.560.330.370.420.41
    ′894044B07 (C)5739 LHCA6 Light-harvesting complex, PS I +++−− −−−−−− 1.21.151.210.680.410.690.570.390.320.260.1
    ′894078C01 (C)′[6907] LHCA9 Light-harvesting complex, PS I +++−− .−−−−− 1.281.271.220.790.260.780.340.390.330.180.01
    ′894076B06 (C)7340 LHCA9 Light-harvesting complex, PS I +..−− −−−−−. 1.21.131.180.670.370.470.190.130.110.1NA
    ′963069C06 (C)′[8250] LHCBM1 Light-harvesting complex, PS II +++.− −−−−−− 1.261.461.331.110.410.540.190.230.170.070.00
    ′894080G01 (C)1951 LHCBM3 Light-harvesting complex, PS II .+−.− −−−−−− NA1.180.790.840.520.570.250.190.140.090.01
    ′894062E07 (C)7231 LHCB4 Light-harvesting complex, PS II +++.− −−−−−− 1.381.341.490.950.730.820.520.360.470.390.07
    ′894052A01 (C)1436 LHCB5 CP26, minor light-harvesting complex, PS II +++−− −−−−−− 1.211.31.360.690.630.550.280.220.220.180.07
    ′894097E05 (E)5770 LhcSR2 Light-harvesting family polypeptide +++++ .+.... 10.2213.9419.9920.5422.380.821.40.67NA1.62NA
    ′894005B12′[8181] LIL Light-harvesting family polypeptide +..−. .....− 1.550.970.850.580.941.000.70.740.870.720.38
    ′963047E03 (A)′[2510] PSAD PS I subunit IV ....− −−−−−− 1.161.131.181.010.650.840.450.430.440.290.03
    ′894083B07 (A)′[3606] PSAE PS I subunit V ...−− −−−−−− 1.030.91.000.690.240.750.360.360.440.280.03
    ′894041H01 (A)1029 PSAF PS I subunit III .++.− −−−−−− 1.071.211.310.910.420.690.570.490.440.370.08
    ′894065A07 (A)′[4807] PSAG PS I subunit G .−−−− −−−−−− 1.050.880.960.570.240.630.240.230.170.10.03
    ′894100A05 (A)′[4807] PSAG PS I subunit G ...−− −−−−−− 1.031.151.010.630.270.630.270.240.170.110.05
    ′894014A05 (A)6118 PSAH. PS I subunit H +++.− .−−−−− 1.171.261.210.860.360.740.490.630.60.40.16
    ′894086C09 (A)4991 PSAK PS I subunit K ...−− .−−.−− 0.990.70.980.570.411.030.510.540.510.420.39
    ′894004A09 (A)′[7107] PSAL PS I subunit L ...−− −−−−−− 1.091.11.130.80.40.550.390.390.330.320.16
    ′894019E07 (A)683 PSAO PS I subunit O ...−−. .−−−−−− 1.191.131.190.650.270.810.310.30.240.160.03
    ′894068A11 (B)3356 PSBO OEE1, oxygen evolution enhancer 1 .++.− −−−−−− 1.081.221.180.90.580.690.360.350.420.320.09
    ′894006E05 (B)7935 PSBP1 OEE2, oxygen evolution enhancer 2 ...−− −−−−−− 1.021.000.940.640.660.780.270.260.320.230.07
    ′963041E04 (B)[5978] PSBQ OEE3, oxygen evolution enhancer 3 ..+−. −.−−−− 0.931.091.220.860.930.750.150.40.480.310.07
    ′894035D062796 PSBP3 Similar to OEE2 −.−.− .+.... 0.730.840.810.990.821.041.141.001.041.081.02
    ′894084F07′[3599] PSBR 10-kDa PS II polypeptide ...+. ...... 1.241.191.311.671.371.131.311.261.211.251.25
    ′894069B116084 PSBW PS II reaction center W protein ..+.− .−−−−− 0.971.211.271.010.681.060.530.520.610.460.14
    ′894072A03′[2051] PSB28 Ycf79, also called PsbW-like −−−−− ..−−−− 0.780.760.560.640.771.020.900.840.780.810.79
    ′894100F04 (D)′[5600] PETC Cytochrome b6fRieske subunit +..−− ...−−− 1.221.010.850.490.470.830.650.540.470.430.33
    ′963053C08 (D)9358 PETM Cytochrome b6f M subunit ...−− ...−−− 1.271.451.250.60.421.490.570.680.510.430.15
    ′894089E08 (D)5858 PETN Cytochrome b6f N subunit ...−− ..−−−− 1.031.100.840.480.371.110.830.630.570.460.36
    ′963092G08 (D)5888 PETO Cytochrome b6f subunit V −−−−− −−−−−. 0.860.780.550.340.50.740.380.230.230.1NA
    ′894002C07 (D)5888 PETO Cytochrome b6f subunit V .−−−−− −−−−− 0.940.750.640.380.460.610.360.230.240.120.02
    ′894069E01 (D)5927 PETE Plastocyanin (PCY1) −.−−− .−−−−− 0.80.810.640.580.180.760.380.270.160.10.02
    ′894017C09 (D)1713 PETF1 Ferredoxin −−−−− +−−−−− 0.770.620.390.230.21.340.280.330.260.180.04
    ′963046B11 (D)4881 PETF5 Ferredoxin −−−−−. −−−−−− 0.040.050.040.040.050.130.090.230.180.080.06
    ′963025F07 (D)6292 FNR Ferredoxin-NADP reductase ..−−− −−−−−− 1.080.870.630.260.210.60.320.170.20.120.15
    ′963048F017947 FTRV Ferredoxin-thioredoxin reductase variable chain −−−−− .−−−−− 0.830.670.670.620.541.040.210.540.60.520.25
    ′894006G058211 ATPC ATP synthase gamma chain, short transcript ++.−− .−−−−− 1.181.271.050.670.590.870.850.780.710.740.64
    ′894041H066174 ATPC ATP synthase gamma chain, longer transcript +..−− .−...− 1.231.050.970.360.410.710.54NANANA0.38
    ′894073D058211 ATPC ATP synthase gamma chain, longer transcript +.−−− −−.−−− 1.211.020.910.350.490.880.680.780.640.600.50
    ′963039D066174 ATPC ATP synthase gamma chain, longest transcript +..−− ....−. 1.521.111.130.690.600.891.690.530.440.44NA
    ′894021B01′[6167] ATPD ATP synthase delta chain +++−− +.+.−. 1.391.551.400.490.661.390.961.261.010.810.90
    ′963089H03302 ATPG ATP synthase CFO subunit II +++−− +−..−− 1.741.631.350.590.451.490.901.110.840.590.42
Carbon metabolism
    ′894022H122613 PRK Phosphoribulokinase ..−−− .−−−−− 1.111.000.760.370.371.040.430.350.440.340.05
    ′963079E12′[8511] RBCS1/2 Ribulose bisphosphate carboxylase small chain .++.− +−−−−− NA1.251.281.030.631.990.760.760.750.450.19
    ′894098E091399 TPI Chloroplast triosephosphate isomerase −−−−− −−−.−− 0.570.550.510.690.610.570.60.470.270.470.41
    ′963014G056790SERA, putative d-3-phosphoglycerate dehydrogenase +++++ −+.++. 2.062.774.035.153.30.651.711.091.471.840.61
    ′963028B116790SERA, putative d-3-phosphoglycerate dehydrogenase +++++ .+.++− 2.062.664.464.383.10.351.930.961.51.880.47
    ′894006B024808ALD3, fructose-1,6-bisphosphate aldolase ++++. ++++.. 2.052.693.63.081.221.351.82.142.071.250.9
    ′894040F039404 PGK Phosphoglycerate kinase −−−−− .−−−−− 0.820.810.730.590.60.910.320.270.270.180.05
    ′894082E076137Putative transketolase ..−−− −−−−−− 0.960.910.610.470.530.670.450.370.410.450.22
    ′894022G035947 PCK Phosphoenolpyruvate carboxykinase ++.−− ....−− 1.311.121.070.50.351.030.810.910.740.470.16
    ′963017B07′[6111] GND 6-Phosphogluconate dehydrogenase +++++ .+++++ 2.253.074.476.766.551.414.953.934.855.635.33
    ′894037H054431 TAL1 Transaldolase +++.− −..−−. 2.983.162.381.140.590.810.860.920.50.28NA
    ′894029C086695Similar to PGLS (6-phosphogluconolactonase) +++++ −..−.− 2.873.233.784.442.610.580.850.760.860.960.67
    ′894080B031974 GAP1 Cytosolic glyceraldehyde 3-P dehydrogenase −−+++ +−+++− 0.420.691.792.441.841.290.511.692.312.130.37
    ′963029F056610 SHMT1 Serine hydroxymethyltransferase +++++ .+++++ 1.391.41.331.321.50.81.712.291.981.882.49
    ′963036C036493GLX1, putative glyoxal oxidase −−−−− −−−−−. 0.030.090.040.040.050.110.040.030.020.02NA
    ′963070H06′[9345]SDC1, serine decarboxylase +.−.. −−−−−− 1.240.950.780.810.970.440.40.380.340.370.31
    ′963045H045544ACS3, putative acetyl-coenzyme A (CoA) synthetase +++−− ++++.− 3.152.581.470.780.31.681.551.431.140.680.08
    ′894038D077098PFL, pyruvate formate lyase −−−−− −−−−−− 0.210.210.310.340.320.250.060.30.420.310.06
    ′963048D101813 STA2 Granule-bound starch synthase I +++++ ....+− 3.254.046.164.965.070.851.411.51.41.580.19
    ′894008B027333 GLPV Glycogen/starch phosphorylase .++++ ..++++ 0.991.252.343.114.170.841.071.822.072.082.08
Respiration alternative electron transfer pathways, ATPases, transporters
    ′894024D078491 COX2a Cytochrome oxidase subunit IIa, N terminus −.++− −−..−− 0.771.031.411.380.930.770.40.810.920.730.38
    ′894102D01′[7853] COX2a Cytochrome oxidase subunit IIb, C terminus −.+++ +.+++− 0.761.021.101.511.181.171.141.371.401.190.88
    ′894076G106296 COX90 Cytochrome oxidase, Chlamydomonas-specific subunit −..+− −−−−−− 0.721.031.091.280.760.930.430.720.670.660.27
    ′963044H031715 ATP6 Subunit 6 mitochondrial ATP synthase −..−− −−−−−− 0.860.940.990.820.530.510.480.640.680.680.37
    ′894008C031860 AOX4 Chloroplast plastoquinol-oxygen oxidoreductase +++++ ++++++ 2.12.243.283.339.521.585.686.397.527.354.16
    ′894076B104448 HYD1 Chloroplast Fe-hydrogenase −−−−− −−−−−− 0.270.250.190.230.220.560.160.170.240.140.22
    ′894044F098476 AOX1 Mitochondrial alternative oxidase −−−.. .−−−−− 0.570.590.770.891.140.760.250.50.660.580.2
    ′894072B06′[4402]Mitochondrial fatty acid carrier/uncoupling protein ++.−− ++++.. 2.833.481.410.670.295.3510.565.291.890.67NA
    ′894059B10′[3328]MPC1, mitochondrial phosphate transporter +++++ .++++. 1.661.92.522.571.421.122.613.051.81.471.15
    ′894026D104026Plastid ATP/ADP transporter −−..− −−.−−− 0.730.791.050.980.810.350.380.530.490.60.33
    ′894092F042863Plastid ATP/ADP transporter ..... −....− 0.730.851.041.081.150.420.80.560.540.70.42
    ′894063B073927Plasma membrane proton ATPase −−−−− −.−−.− 0.320.30.380.480.530.790.410.550.680.730.7
    ′894040E11592Vacuolar ATP synthase, subunit A ..... .....+ 1.21.771.081.121.190.761.351.141.251.51.78
    ′894018B074771 ATPvE Vacuolar ATPase chain E .+.++ .+++++ 1.051.151.051.181.441.031.721.421.241.311.44
    ′894022G07′[4453] ATPvL1 Vacuolar ATPase proteolipid subunit ..+++ .+++++ 1.261.401.421.702.011.151.381.551.511.681.60
    ′963017F05′[4552]Proton-translocating, vacuolar pyrophosphatase −−..− −−−−−− 0.840.730.990.910.450.610.520.430.560.650.34
    ′894054D08′[7558]Putative transporter/GTP binding ++.++ ...... 1.281.371.151.461.321.181.311.281.121.231.24
    ′894071E08′[4402]Similar to mitochondrial substrate carrier +++−− +++... 3.632.921.660.430.173.742.364.481.40.46NA
    ′894099G11′3494PTB4, phosphate transporter ..... −−−−−− 1.071.041.041.070.960.740.550.470.430.620.35
Oxidative stress, chaperones, proteolysis
    ′894081G123424 FSD1 Iron chloroplast superoxide dismutase +++++ −+++++ 1.581.61.781.982.830.871.41.891.922.193.11
    ′963046E045826 GPX1 Glutathionine peroxidase +++++ .+++++ 3.143.323.172.62.71.22.533.724.153.142.2
    ′894082E096986Thioredoxin peroxidase/hydroperoxide reductase +.+++ +++.+. 1.951.492.432.071.961.181.922.141.781.951.16
    ′963032D035314Putative vanadium chloroperoxidase +++++ .+.... 15.1512.7646.9940.925.640.921.560.570.831.160.58
    ′963025C054324Putative peroxiredoxin Q +++++ ...−−+ 2.333.714.752.244.350.96NA0.970.230.253.9
    ′894062A078645PDX1, pyridoxin biosynthesis protein ++++. .+++++ 1.711.711.71.631.000.862.642.351.91.982.49
    ′894024F095909 HSP90A Heat shock protein 90, cytosolic −−−−− −−−−−− 0.20.320.360.460.730.450.210.520.590.570.58
    ′963036F104194 HSP70C Mitochondrial HSP70 chaperone ..−−+ .....+ 0.880.900.690.790.911.061.161.131.071.121.20
    ′894078G054517 HSP70B Chloroplast HSP70 chaperone +++++ −.++++ 1.231.621.341.491.380.840.961.531.641.491.77
    ′963026B057505 CGE1 Cochaperone of chloroplast HSP70 ....+ .....+ 1.350.790.790.911.811.020.871.671.131.272.97
    ′963041D041067 VIPP1 Membrane-associated 30-kDa chloroplast protein +++++ .+++++ 1.962.062.131.872.801.104.465.103.948.753.37
    ′894038F088733 HCF136 PS II stability/assembly factor +++++ −++.+. 4.463.894.114.763.680.765.581.73.32.781.4
    ′894044H012747 ALB3.1Required for LHC integration ++.−− ...... 1.811.440.860.820.810.841.330.740.810.820.62
    ′963035G03′[4315] CPN60A Alpha subunit Rubisco-binding protein, GroEL −−−−− −−−−.. 0.290.260.170.270.420.70.310.530.680.70.72
    ′894062E015669 CPN60B Beta subunit Rubisco-binding protein, GroEL −−−−− ...... 0.350.230.220.30.440.640.210.730.760.91.15
    ′894039G091845GROES-like protein ..−−− ...... 0.90.960.630.860.851.191.391.361.321.421.46
    ′894076H02′[4562]Rubisco activase +++.+ +−−+.− 1.901.771.421.071.391.770.490.681.361.060.44
    ′963050F023862 HSP22C Chloroplast 22-kDa heat shock protein .−... .+...+ 0.770.731.130.881.171.102.211.251.522.092.96
    ′963068F015588 HSP22E Chloroplast 22-kDa heat shock protein ++++. −+++++ 1.742.682.392.141.10.371.333.554.065.3918.74
    ′894096A07′[7754] HSP22F Chloroplast 22-kDa heat shock protein ++++. −+++++ 1.613.231.832.420.890.491.85.115.698.2242.22
    ′894008D032231Cytosolic peptidyl-prolyl cis-trans isomerase −−−−− .−.−−− 0.330.390.430.420.341.030.530.680.670.70.37
    ′894086F07344Chloroplast peptidyl-prolyl cis-trans isomerase −−−−− ..−−−− 0.310.430.340.410.321.080.720.630.720.80.46
    ′963042H09344Chloroplast peptidyl-prolyl cis-trans isomerase −−−−− .−−−−− 0.420.510.370.440.301.040.540.570.770.710.50
    ′894005A06′[2563]Chloroplast peptidyl-prolyl cis-trans isomerase −−−−− −−−−−− 0.590.460.360.360.260.720.270.330.310.330.18
    ′894037G118546AAA-type ATPase, possibly mitochondrial +++++ .+++++ 3.623.053.033.791.911.112.262.272.192.531.79
    ′894006G025487PAF1 (proteasome alpha-6 subunit) ..... .....+ 0.911.030.870.960.770.752.031.381.482.543.00
    ′894014B045527UBC2, ubiquitin-conjugating enzyme E2 ..... ..++++ 0.911.210.881.030.980.681.342.041.631.72.22
    ′894080E104988UBC2, ubiquitin-conjugating enzyme E2 −−−+. ..++++ 0.660.880.901.210.921.071.071.071.961.852.48
    ′894008E117585SKP1 E3 ubiquitin ligase; similar to Skp1 −−... .+++++ 0.780.890.830.920.91.12.232.372.11.962.83
    ′963033H105803 DEGPd Chloroplast serine endoprotease ++++. .+++++ 1.771.991.761.641.050.892.293.142.071.681.72
    ′963014H048642Cysteine protease +++++ ...+++ 2.212.262.923.033.120.971.331.41.721.882.07
    ′963078B033753Cathepsin Z precursor −−−−. ++++++ 0.830.630.540.840.971.472.142.082.382.925.47
    ′894024A086171Aspartic proteinase, delta subunit +++++ .+++++ 3.474.575.874.974.260.661.622.182.312.432.46
    ′963065A087713Aspartyl aminopeptidase +++++ −+.... 7.0710.313.3415.819.270.711.821.181.280.880.67
    ′894082D094868LCI5 +++++ .−−... 4.523.383.311.731.571.280.580.570.981.030.79
Other metabolic and/or biosynthetic processes
    ′894007D09NoneCYB5-1 .+−−− .+.... 1.061.270.80.810.691.361.961.481.111.391.2
    ′894042G02′[1451]ASSD, aspartate-semialdehyde dehydrogenase ++−−− .+++++ 1.281.180.680.520.311.121.772.321.571.381.75
    ′894082E036330CPX1 −−−−− −−−−−− 0.390.270.260.220.430.540.360.310.390.360.3
    ′894102G04′[3236]Putative Mg chelatase subunit +++++ .+...+ 2.181.831.361.361.561.061.731.321.421.531.72
    ′894024D10150CHLH1 +++++ −+.... 3.333.003.321.851.620.861.511.261.11.180.59
    ′894093F092392 CHL27A CTH1, Mg-ProtoIX monomethyl ester cyclase +++++ +++++. 17.9617.4417.2811.544.973.078.64.758.528.512.77
    ′894066E112088 CHL27B CRD1, Mg-ProtoIX monomethyl ester cyclase −−−−− −−−−−− 0.090.120.10.080.080.20.110.180.130.120.02
    ′894038E112279 CUTA1 Copper-binding protein, chloroplast −−−−− .+++++ 0.660.70.620.60.50.833.83.083.033.432.41
    ′894086H065963GLN1, glutamine synthetase +.+++ ...... 1.571.382.021.541.80.681.21.491.751.921.77
    ′894006D026255GLN2, chloroplast glutamine synthetase ..++. ...... 1.011.231.541.531.241.160.81.331.71.371.47
    ′894044E117939ASNS, asparagine synthase ++.+− −...++ 1.391.711.121.60.60.791.731.541.371.492.21
    ′963047G059088NADB, l-aspartate oxidase ++++. −+++++ 1.661.391.321.331.180.657.153.172.313.11.83
    ′894039C12651HDH, histidinol dehydrogenase ...++ ...... 1.281.10.981.461.531.251.151.161.141.281.3
    ′894014G02976Putative lumenal 17.4-kDa protein −−..− −−−−−− 0.790.810.860.880.80.880.40.320.520.580.33
    ′963046C035100Putative lumenal polypeptide +++.− −−−−−− 1.331.361.451.090.830.820.530.530.590.380.1
    ′894083E11′[8722]ACS3, putative acetyl-CoA synthetase +++++ ++++++ 4.197.4616.3426.0929.733.137.2515.0411.0013.888.88
    ′894086H03′[7647]SMT1, similar to sterol-C24-methyltransferase −−−−− −−−−−− 0.580.340.260.270.480.550.550.50.370.360.18
    ′894006B03′[9318]DES6, omega-6 desaturase ++++. −−−−−− 2.112.513.472.850.860.670.320.610.660.470.26
    ′894055F12′[9376]LOX1-like lipoxygenase −−−−− −−−−−− 0.140.190.190.20.210.420.080.070.20.120.08
    ′894081C10′[174]NNT, NAD transhydrogenase −−−−− −−−−−− 0.420.480.80.810.480.260.060.240.290.140.03
    ′963047D024325SAS1, S-adenosylmethionine synthetase −−−−− −.−−−− 0.840.530.330.280.30.510.640.410.590.640.42
    ′894062A096078THIH, thiazole biosynthesis protein −−−−− −−−−−− 0.080.080.130.20.180.250.050.160.240.130.06
    ′963041C092889THI4, putative thiamine biosynthesis protein −−−−− −−−−−− 0.420.440.390.290.150.310.050.120.180.120.01
    ′894057E11′[6582]HCP, hydroxylamine reductase −−−−− −−−−−− 0.180.230.190.270.370.640.290.390.440.540.43
    ′894018F096945Putative HCP-like hydroxylamine reductase −−−−− −−−−−− 0.150.170.290.390.420.380.050.080.170.180.14
    ′963036C07959DS2, 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase +++++ .+..++ 2.263.015.333.41.571.211.771.981.861.591.86
    ′963035C07955Putative carbamoyl phosphate synthetase .−... −..... 0.920.791.021.010.930.760.891.431.71.590.96
    ′894097B092841IGPD (imidazoleglycerol-phosphate dehydratase) .+... −.+..+ 1.041.170.911.151.030.71.761.311.541.961.84
    ′894103C12′[2773]SAH1, S-adenosyl homocysteine hydrolase −−−−− −−−−−− 0.460.30.280.120.060.250.690.390.640.690.27
    ′894056F03′[6078]THIH-like protein, thiazole biolsynthesis −−−−− ...... 0.170.250.160.420.381.031.030.940.790.831.07
    ′894096H021312HISC2, putative histidinol-phosphate transaminase −.−.−. −+++++ 0.820.960.891.220.880.732.262.252.282.532.88
    ′963030A072652 FER1 FER1, ferritin −−−−− −−−−−− 0.770.610.680.580.290.560.540.420.40.430.17
    ′963042H066157ACH, aconitate hydratase ++.−− ...−−− 1.651.20.90.740.630.940.940.930.630.630.27
    ′963044D082010APOC, apospory-associated protein ...−− .−−−−− 1.011.071.130.730.540.80.570.560.340.330.25
    ′894037G088636ALS, acetolactate synthase +++++ ...... 1.391.291.471.551.331.141.231.231.251.351.38
    ′894064A10468ILV3, dihydroxy-acid dehydratase −−−.− ..++++ 0.490.550.430.80.570.831.411.982.002.073.88
    ′894080E01773Putative acetyl-CoA carboxylase subunit .−−−+ −.−−−− 0.960.780.750.691.330.830.490.330.50.540.38
    ′894062A078645PDX1, pyridoxine biosynthesis protein ++++. .+++++ 1.711.711.71.631.000.862.642.351.91.982.49
    ′894102B02′[2302]Putative Igr3p cargo protein −−−−− +....− 0.280.290.320.330.323.95NANANANA0.72
    ′894019G084767Adenylosuccinate synthetase (AMP biosynthesis) −−−−− −−.−.. 0.30.330.320.450.40.760.620.840.870.921.01
    ′894068F05415dTDP-glucose 4-6-dehydratase −−−−− −−.−−− 0.50.460.60.60.430.90.390.50.620.660.28
Signal transduction, transcription, translation
    ′894096C06467Sensory opsin A −−−−− −−−−−− 0.630.560.740.790.670.590.380.590.690.630.07
    ′963038D057033RABF1, RabH/Rab5 type of small GTPase +++++ .+++++ 1.491.731.872.22.070.992.22.231.91.741.64
    ′963048H07′[6103]GBLP, guanine nucleotide binding protein ....+ ...++. 0.931.071.091.011.441.421.31.531.631.471.46
    ′894006F01′[9232]SKS1-like protein kinase −−−−− .−−−−− 0.540.530.580.430.370.770.20.40.420.360.18
    ′963045F12′[2130]PP1, serine/threonine protein phosphatase −−−−− −−−−−− 0.450.420.440.540.550.530.310.40.450.450.31
    ′894006C117297XPO1, exportin- −.−.. −−−−.− 0.720.90.830.810.840.450.490.120.360.250.36
    ′894006C087660GBP1p, G-strand-binding protein −−−−− −−−−−− 0.240.170.130.20.150.590.220.250.260.290.3
    ′963046C028379Putative nucleosome assembly protein 1-like protein +++++ ....++ 2.242.472.863.964.340.981.081.191.261.321.37
    ′894027A08NoneATP dependent helicase −−−−− .−.... 0.280.190.270.410.370.740.630.730.730.750.84
    ′963047C115558Putative transcription factor IIB −−−−− +...+. 0.220.280.30.370.32.691.22NA1.153.12NA
    ′963087F057852Probably DNA-binding protein −−−−− −−.... 0.40.310.260.320.350.750.50.831.051.011.14
    ′894081G038592Potential RNA-binding protein ++.−− .−.−−− 1.561.291.080.80.680.990.730.760.550.530.26
    ′894010G038151Similar to Arabidopsis SC35-like splicing factor SCL35 −−−−− −−−−−− 0.390.470.550.540.390.480.270.30.320.410.31
    ′963079B086042EFIA1, putative eukaryotic translation initiation factor ..−−− ...+++ 0.940.880.550.610.630.921.251.431.651.531.72
    ′894081B087498EFIA2, putative elongation factor 1 a 2 +.+++ ++++++ 1.241.231.61.441.131.862.322.672.42.452.38
    ′963077H031273Protein translation factor, similar to SUI1 ..... −+.+++ 1.181.251.120.970.91.191.721.441.932.295.69
    ′894080F075613NOP56-like, nucleolar rRNA processing protein −−−−− ...... 0.390.490.280.480.41.230.741.361.061.271.24
    ′963030C088384Fibrillarin-related nucleolar RNA-binding protein −−−−− .−...+ 0.220.250.210.520.340.890.270.750.841.071.33
    ′894069A016666HMGB1, high-mobility-group DNA-binding protein −−−−− −−−−−− 0.480.570.670.640.250.450.440.560.520.470.37
    ′963047E09115NHP2, high-mobility-group nucleolar protein −−−−− .−...+ 0.380.390.360.570.461.140.411.231.091.251.61
Cytoplasmic and chloroplast ribosomal proteinsg
    ′894081C016021RPS3a-like .++++ ++++++ 1.021.211.421.631.72.691.792.662.492.634.00
    ′963045C05448RPS5 .+.++ +−.... 0.981.151.021.311.311.280.510.840.770.720.73
    ′894070B042212RPL22 ....+ ++++.+ 0.971.020.911.141.371.961.542.171.741.421.94
    ′963038E052202RPS20 ..... +..... 1.110.961.060.971.292.030.971.231.421.221.19
    ′894011F03′[8867]RPS16 −.−++ .++.++ 0.721.060.41.982.771.263.914.881.262.812.85
    ′894006G10′[9571]RPS17 ...++ +....+ 1.001.091.11.241.352.420.961.571.811.662.24
    ′894064E105820RPS19 ....+ +.++++ 0.871.071.011.211.542.081.621.971.861.831.79
    ′894037B078122RPS25 ..... +..... 1.170.951.191.051.132.000.71.251.231.091.00
    ′894014F124106RPS30 .++++ ++++++ 1.011.271.221.651.74.071.682.42.482.042.22
    ′894017F085393RPS27 ....+ +.++++ 0.921.331.281.221.251.891.311.762.11.972.36
    ′963036H096746RPL6 ..+.. +..++. 1.241.091.361.041.071.461.681.82.232.11.93
    ′894027B042452RPL9 ...+. +..+.. 1.001.021.021.241.072.721.161.491.691.491.6
    ′963038C05′[3133]RPL10 ....+ ..++++ 0.920.940.990.931.151.651.281.811.751.582.19
    ′894065B099108RPL11 ....+ +..++. 1.110.791.141.131.292.560.931.251.731.591.57
    ′894064D043624RPL12 ...++ +..+++ 0.951.030.971.231.322.351.161.571.671.541.99
    ′894019C087238RPL15 ..+.+ +...+. 1.21.21.451.291.463.481.261.761.961.851.5
    ′963063C083RPL17 ..... +..... 1.070.860.990.961.172.050.70.931.291.111.22
    ′894039B072305RPL23 ....+ +..... 1.070.941.111.161.252.090.661.071.631.221.1
    ′963048E032072RPL24 ....+ +..... 1.110.860.981.131.332.270.841.391.631.31.31
    ′963017B08′[8598]RPL27 ...++ +..... 1.060.961.001.121.111.850.91.271.281.21.21
    ′894006A06111RPL30 ....+ +..... 1.10.981.061.121.673.350.971.391.91.521.5
    ′894066H096057RPL35 −−−−− .−.... 0.480.410.310.30.550.90.490.70.770.81.22
    ′894026G082805RPSCL1 −−−−− −−−−−− 0.250.20.210.190.210.320.10.110.130.120.05
    ′894044G055258RPSCL3 −−−−− .−−−.+ 0.380.410.190.290.520.950.760.740.830.951.27
    ′894037C039418RPSCL13 −−−−− ...... 0.460.330.320.340.621.020.610.710.871.011.4
    ′894002G05825RPSCL20 −−−−− .−−−.. 0.370.270.190.280.491.140.380.510.770.780.88
    ′963039A058056RPLCL1 −−−−− .−.−.+ 0.350.290.20.270.590.960.590.820.820.991.94
    ′894037B112083RPLCL6 −−−−− .−.... 0.470.380.250.270.541.30.470.640.850.991.26
    ′894089F044407RPLCL9 −−−−− +...−+ 0.480.480.260.30.541.251.010.881.000.881.2
    ′963032C103366RPLCL12 −−−−− −−−−.. 0.340.230.140.180.40.930.490.540.690.861.15
    ′894055G04′[2967]RPLCL18 −−−−− +−−−.+ 0.40.360.20.240.51.30.530.740.80.931.48
    ′894050B05′[6564]RPLCL28 −−−−− +−−..+ 0.340.310.20.30.681.140.570.741.021.062.01
    ′894073D04′9202RPLCL31 −−−−− +....+ 0.460.450.240.290.541.140.740.820.941.021.2
Putative structural, surface, and matrix proteins
    ′894017B127239VFL2, centrin (caltractin) −−−−− +−.−−− 0.650.540.660.610.741.510.420.60.590.540.34
    ′894032G127345TUA2, a tubulin 2 −−−−− ..−−.− 0.380.340.280.360.331.290.480.50.580.680.57
    ′894006H0782CHLRE_650068, microtubule-associated protein +++++ ++++++ 2.733.082.933.083.31.315.635.275.435.598.45
    ′963046E088405TUA1, alpha tubulin 1 −−−−− −−−−−. 0.460.320.30.290.260.770.060.080.120.07NA
    ′894056C11′[7442]TUB1, beta tubulin 1 −−−−− +−−−−− 0.270.190.210.270.161.180.10.220.230.240.02
    ′894093H02′[3445]TUB2, beta tubulin G1 −−−−− +..−−. 0.540.360.290.230.124.160.810.560.350.16NA
    ′894056E01′[1531]FAP15, flagellar proteome −−−−− −−−−−. 0.240.240.370.390.390.490.030.070.20.06NA
    ′894083H05′[285]SYP71, syntaxin ++.++ .++++. 1.371.271.31.651.821.191.92.572.422.441.32
    ′963026C08568FLA14, dynein light chain −−−−− +−..−− 0.360.330.350.360.311.850.670.740.860.590.32
    ′963077B032780FMG1b, flagellar membrane glycoprotein 1b −−−−− −−−−−− 0.190.170.170.180.120.160.070.020.020.040.01
    ′963046G04835Putative cell adhesion protein +++++ ...... 3.342.13.964.015.511.131.251.271.181.281.36
    ′963024H078951KATA, kinesin-like motor protein +.++. ...... 1.951.143.242.111.410.840.680.881.141.050.95
    ′963046H097877Putative sulfated surface glycoprotein .++.− −−−−−− 1.191.321.120.890.830.340.340.320.360.440.09
    ′894078A071239Similar to pherphorin of Volvox ....− −−−−−− 0.911.041.230.860.20.370.170.190.240.30.17
    ′963029B121971GAS31, hydroxyproline-rich glycoprotein −−−−− −−.−−. 0.40.360.370.310.20.620.35NA0.260.25NA
    ′894068G03′[6102]Putative prolyl 4-hydroxylase, a subunit −−−−− +−.−−− 0.150.180.190.230.311.270.370.990.780.310.14
    ′894068C014654Putative prolyl 4-hydroxylase, a subunit −−−−− −−−−−− 0.040.050.040.050.080.210.040.080.110.050.01
    ′894042G047452Putative prolyl 4-hydroxylase, a subunit −−−−− ...−.. 0.070.190.070.10.10.151.020.560.840.790.88
    ′894101C02[428]Putative prolyl 4-hydroxylase, a subunit −−−−− −−.−−− 0.170.240.190.160.190.480.130.280.250.20.05
Unknownh
    ′963016B041549Unknown +++++ ..++++ 8.9510.9418.5722.7212.481.04NA4.173.293.721.4
    ′963033D03NoneUnknown +++++ −+++++ 13.4615.0122.7423.5122.30.394.55.344.583.852.16
    ′963032A086781Unknown +++++ .+++++ 35.6930.8359.2350.0634.640.6822.6916.0517.9921.919.76
    ′963047F052729Unknown +++++ .++++. 2.074.4216.0018.9115.011.051.745.64.763.561.21
    ′963096E101549Unknown +++++ .+++++ 16.9821.8832.6735.4223.930.953.613.893.324.621.47
    ′894063D103295Unknown, starch-binding domain of glycoside hydrolase +++++ .+.+++ 5.184.3316.5414.5913.150.921.541.161.531.711.63
    ′963027G016569Unknown +++++ ..−−.+ 1.564.3516.0023.0118.731.011.40.350.311.365.06
    ′963063B085533Unknown +++++ −+++++ 10.0517.4923.7321.9918.270.412.964.273.853.252.39
    ′963068A11NoneUnknown +++++ .+++++ 6.978.9717.4918.0812.561.244.322.151.72.86.36
    ′963032A01′9229Unknown proline-rich protein +++++ ++++++ 5.46.8518.0123.0324.961.264.617.676.5710.678.17
  • a The ≥3-fold change is for at least two points in either CC425 and/or the sac1 mutant. Some genes that did not satisfy these criteria but were discussed in the text are also included. This table also has a finer partitioning of the genes into categories than Table S1 in the supplemental material, but the genes can be tracked by the clone ID numbers.

  • b The identifier of the array element, based on the cDNA clone used as a template for PCR amplification. Clone numbers followed by a letter in parentheses belong to a category used to generate Fig. 3A through E, as indicated.

  • c The identification number in the 20021010 assembly of ESTs for a predicted unique gene (ACE) in which this clone is a member. The bracketed numbers are for clones not used in the ACE assembly but that match a specific ACE as determined by BLAST analysis.

  • d Difference in transcript abundance (+ or −; a dot indicates no statistically significant change) relative to RNA from CC425 at time zero. The five symbols represent 2, 4, 8, 12, and 24 h after initiation of sulfur starvation of CC425; the data for the sac1 mutant include a comparison of the sac1 zero time point (initial symbol) with the wild-type zero time point.

  • e NA, not enough high-quality data for statistical tests.

  • f The read did not match any of the ACEs and thus was not included in the assembly of reads.

  • g RP, ribosomal protein; L, large subunit; S, small subunit; CL, chloroplast; the number represents the molecular mass of the subunit.

  • h A selection of 10 of the 187 “unknowns” that satisfied the ≥3-fold selection criterion. The abundance of the transcripts from these genes within the unknown category exhibited the greatest increase following S deprivation.

  • i SQ, sulfoquinovose.

  • j SQ, sulfoquinovosyl.