TABLE 1.
Induction and repression ratios of 166 C. reinhardtii genes that showed at least a twofold change in transcript abundance in one or more time points (T1 to T5) before and during hydrogen productiona
| Gene function and GenBank accession no. or contig (no. of genes) | GAL file ID | Gene annotation description (closest match) | Peak O2 | Mid O2 | Zero O2 | Mid H2 | Peak H2 |
|---|---|---|---|---|---|---|---|
| Photosynthesis (22) | |||||||
| AB122117.1 | 257.A | LhcI-4 gene for light-harvesting chlorophyll a/b protein of PSI | 0.39 | 0.20 | 0.19 | 0.22 | NA |
| AY171231 | 262.A | Light-harvesting complex I protein | 0.36 | NA | 0.29 | 0.25 | NA |
| X15166 | 250.A | PsaK mRNA for 8.4-kDa subunit of PSI | 0.31 | NA | 0.28 | 0.32 | NA |
| XM_001691032 | 8094.D | PSI reaction center subunit XI, chloroplast precursor | 0.47 | NA | NA | 0.45 | NA |
| AB050007 | 217.A | CP26 | NA | NA | NA | 0.43 | NA |
| AF244524 | 158.A | Chlorophyll a/b binding protein | NA | NA | 0.20 | 0.56 | NA |
| AB051211 | 159.A | Light-harvesting chlorophyll a/b binding protein Lhcb4 | 0.52 | 0.50 | 0.27 | 0.14 | 0.46 |
| AF170026.1 | 426.A | PSII reaction center W protein, chloroplast precursor | NA | NA | 0.50 | 0.34 | 0.50 |
| XM_001701652 | 4465.C | 4.1-kDa PSII subunit (PSBX) | NA | NA | 0.30 | 0.34 | NA |
| J05524 | 463.A | Plastocyanin, chloroplast precursor | 0.27 | NA | 0.11 | 0.22 | 0.29 |
| X04472.1 | 45.A | RbcS2 for ribulose bisphosphate carboxylase/oxygenase | NA | NA | 0.12 | 0.13 | NA |
| D32003 | 155.A | Cytochrome B6-F complex iron-sulfur subunit, chloroplast precursor | 0.53 | NA | 0.30 | 0.36 | NA |
| X92488 | 84.A | Cytochrome B6-F complex 4-kDa subunit, chloroplast precursor | NA | NA | NA | 0.90 | 0.27 |
| L10349 | 243.A | Ferredoxin, chloroplast precursor | 0.21 | 0.44 | 0.11 | 0.12 | 0.27 |
| X13826 | 54.A | Oxygen-evolving enhancer protein 1, chloroplast precursor | 0.56 | 0.77 | 0.42 | 0.42 | NA |
| M15187 | 96.A | Oxygen-evolving enhancer protein 2, chloroplast precursor | 0.44 | NA | NA | 0.31 | NA |
| X13832 | 83.A | Oxygen-evolving enhancer protein 3, chloroplast precursor | NA | NA | 0.39 | 0.39 | NA |
| M36123 | 352.A | Phosphoribulokinase, chloroplast precursor (PRK) | NA | NA | 1.68 | 3.37 | NA |
| AF107303 | 458.A | Open reading frame of intron 2 from chloroplast psbA gene | NA | NA | 1.48 | 1.91 | 2.84 |
| XM_001696073 | 251.A | Chlorophyll a/b binding protein homolog LHCSR1 precursor | 1.93 | 1.30 | NA | 4.55 | 3.07 |
| XM_001696086 | 8770.D | Chlorophyll a/b binding protein homolog LHCSR3 precursor | 4.89 | NA | NA | 1.29 | NA |
| AF479778 | 350.A | Major light-harvesting complex II protein m9 (LHCBM9) | NA | 11.26 | 17.41 | 109.03 | 22.30 |
| Sulfur assimilation (8) | |||||||
| X52304 | 73.A | Arylsulfatase 2 precursor (ARS2) | 15.39 | NA | 7.62 | 18.10 | 5.63 |
| XM_001697170 | 7778.D | Sulfate transporter (SULTR2) | 3.61 | 2.90 | 2.68 | 3.16 | NA |
| XM_001699252 | 8577.D | Sulfite reductase | NA | NA | NA | 0.93 | 3.96 |
| X16179.1 | 382.A | Arylsulfatase 2 precursor | NA | NA | NA | NA | 7.25 |
| U57088 | 468.A | Probable sulfate adenylyl transferase ATS1 | NA | NA | NA | 2.86 | 2.22 |
| AF359251 | 432.A | Extracellular polypeptide Ecp76 | 2.19 | NA | NA | 4.27 | NA |
| 199.8.2.31 | 7885.D | Extracellular polypeptide Ecp88 | 2.96 | 1.31 | 2.75 | 2.15 | NA |
| AF359252 | 167.A | Extracellular polypeptide Ecp88 | 3.25 | NA | 2.40 | 18.90 | 2.33 |
| Carbon metabolism (4) | |||||||
| AF394513 | 337.A | 6-Phosphogluconate dehydrogenase | 2.65 | NA | 1.66 | 2.73 | NA |
| U18765 | 40.A | Probable isocitrate lyase | 0.14 | 0.11 | 0.17 | 0.14 | NA |
| X66410 | 254.A | Pyruvate formate lyase | NA | NA | 3.54 | 1.82 | NA |
| U42979.1 | 252.A | Malate dehydrogenase, sodium acetate induced | 0.64 | NA | NA | 0.42 | 0.6 |
| Proteolysis (5) | |||||||
| X60826 | 67.A | UBI3 mRNA for ubiquitin fusion protein | NA | NA | 1.47 | 3.18 | NA |
| XM_001696123 | 3750.C | 26S proteasome regulatory complex, lid subcomplex, non-ATPase subunit RPN3 (subunit 3) (PSD3) (PSMD3) | NA | 3.63 | 2.77 | 0.76 | NA |
| 72.37.1.5 | 7281.C | F15M7.13, ubiquitin carboxyl-terminal hydrolase, Arabidopsis | NA | 4.01 | NA | NA | NA |
| AY062935 | 348.A | Ubiquitin-conjugating enzyme E2 isoform | 2.98 | 2.09 | NA | 6.00 | NA |
| XM_001695251 | 4464.C | Putative serine carboxypeptidase precursor | NA | NA | NA | 2.48 | |
| Amino acid synthesis (4) | |||||||
| U36197 | 135.A | 5-Methyltetrahydropteroyltriglutamate-homocysteine methyltransferase | NA | NA | 0.38 | 0.29 | NA |
| AF078693 | 447.A | Putative O-acetylserine lyase precursor | NA | 1.89 | 3.00 | 2.89 | 10.93 |
| U46207 | 112.A | Glutamine synthetase, cytosolic isozyme | NA | NA | 0.37 | 0.56 | NA |
| XM_001695007 | 9339.E | Aspartate-semialdehyde dehydrogenase (ASSD1) | NA | 0.80 | 0.74 | 0.40 | 1.17 |
| Transcription and translation (10) | |||||||
| XM_001696696 | 5869.C | PRP3, pre-mRNA processing factor 3 | NA | NA | NA | 2.53 | NA |
| XM_001691400 | 9120.E | Eukaryotic initiation factor 4A-10-like protein | NA | NA | NA | 2.84 | 1.45 |
| XM_001691255 | 4469.C | SF3A3 splicing factor 3a, subunit 3 (SPL3) | NA | NA | 2.78 | 4.11 | NA |
| AY337612 | 4147.C | Chloroplast 30S ribosomal protein S11 (rps11) | NA | NA | NA | NA | 2.49 |
| X95313 | 110.A | 60S ribosomal protein L11 | NA | NA | NA | 2.55 | 0.67 |
| 2019.1.1.5 | 8710.D | 60S ribosomal protein L22 [Drosophila melanogaster], 54.2% identity | NA | 5.31 | NA | 0.56 | NA |
| XM_001696564 | 819.C | 60S ribosomal protein L37A | 0.55 | NA | NA | 0.33 | 0.82 |
| XM_001692618 | 3219.C | 60S ribosomal protein L13 | NA | NA | NA | 0.43 | 0.53 |
| XM_001689821 | 9565.E | 60S ribosomal protein L6 | NA | NA | NA | 0.35 | NA |
| AY177616 | 312.A | 41-kDa ribosome-associated protein precursor | 0.60 | NA | 0.42 | 0.48 | 0.7 |
| Redox cycling (3) | |||||||
| XM_001693558 | 9401.E | Similar to vanadium chloroperoxidase | 2.72 | 1.28 | NA | 3.22 | 7.71 |
| 15.82.2.11 | 9635.E | Putative oxidoreductase [Oryza sativa subsp. japonica], 82.3% identity | 0.67 | NA | 3.11 | 1.90 | NA |
| X78822 | 17.A | Thioredoxin H-type | NA | NA | NA | 0.46 | NA |
| Other pathways and processes (27) | |||||||
| U36196 | 161.A | Protein kinase, 48K | 0.45 | NA | NA | 0.46 | NA |
| XM_001691558 | 4567.C | WNK protein kinase (WNK1) | NA | NA | 2.86 | 1.37 | 0.74 |
| XM_001702027 | 516.B | CDK inhibitor kinase (WEE1) | NA | NA | NA | 3.98 | NA |
| XM_001692562 | 506.B | Rhodanese domain phosphatase (RDP3) | 5.99 | NA | 2.96 | 1.94 | 2.32 |
| XM_001696853 | 645.C | G protein-coupled seven transmembrane receptor | NA | 3.31 | NA | 0.64 | NA |
| XM_001703235 | 9249.E | PWR motif protein (PWR1) | NA | 3.15 | 2.85 | 6.72 | NA |
| XM_001703306 | 3414.C | Selenium binding protein (SBD1) | 5.17 | NA | 2.48 | 2.39 | 4.54 |
| XM_001698919 | 4207.C | Conserved protein similar to EMP70/nonaspanin | NA | 3.51 | NA | 0.55 | NA |
| AF399653.1 | 389.A | Ezy2 | NA | 2.91 | NA | 0.60 | NA |
| L29029 | 186.A | VSP-3 | NA | 3.33 | NA | 0.39 | 0.58 |
| U31975 | 188.A | Alanine aminotransferase | NA | 3.46 | NA | 0.67 | NA |
| XM_001694402 | 9383.E | Hydroxylamine reductase, hybrid cluster protein HCP4 | 2.18 | 3.42 | NA | 1.32 | NA |
| XM_001690300 | 6995.C | NOP58 structural component of C/D snoRNPs | NA | 4.38 | NA | 0.46 | NA |
| XM_001703004 | 8375.D | Type II NADH dehydrogenase (NDA7) | 2.42 | NA | NA | NA | NA |
| XM_001702995 | 8352.D | Dehydrogenase with pyrroloquinoline quinone as a cofactor | NA | NA | 3.84 | 1.34 | NA |
| XM_001690491 | 4875.C | Endoplasmic reticulum-located HSP110/SSE-like protein | NA | NA | 2.67 | 1.46 | NA |
| XM_001701229 | 2968.C | Flagellar-associated protein | NA | NA | 3.04 | NA | NA |
| AF133672 | 311.A | Coproporphyrinogen III oxidase precursor | NA | NA | NA | 3.53 | 2.40 |
| XM_001696259 | 2161.C | Mu1-adaptin (AP1M1) | NA | NA | 1.85 | 2.44 | NA |
| XM_001693906 | 1657.C | 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR1) | NA | NA | NA | 2.98 | NA |
| X76117 | 212.A | Zygote-specific protein | 0.40 | 0.55 | 0.46 | 0.55 | NA |
| XM_001698620 | 9223.E | THI4 regulatory protein | 0.38 | 0.37 | NA | 0.28 | NA |
| XM_001693730 | 166.A | Acyl carrier protein (ACP2) | 0.25 | NA | 0.47 | 0.44 | NA |
| AF295371 | 63.A | Chlamyopsin 2 | 0.53 | NA | 0.48 | 0.28 | NA |
| XM_001690256 | 9591.E | Cell wall protein pherophorin C2 (PHC2) | NA | NA | 0.25 | 0.36 | NA |
| XM_001697461 | 6272.C | Flagellar-associated protein (FAP218) | NA | NA | NA | 0.43 | 1.58 |
| XM_001697963 | 4463.C | Cell wall protein pherophorin C3 (PHC3) | NA | NA | 0.52 | 0.35 | NA |
| Unknown (83) | |||||||
| XM_001690783 | 1650.C | Low-CO2-inducible protein (LCI30) | NA | 2.31 | NA | 1.35 | 0.39 |
| AF015661 | 477.A | Low-CO2-inducible protein (LCI3) | 0.71 | NA | NA | 0.35 | 0.20 |
| 141.1.1.0 | 5077.C | Phenylcoumaran benzylic ether reductase homolog TH6 | NA | NA | NA | NA | 6.82 |
| 25.9.2.51 | 6103.C | CAMK4, calcium/calmodulin-dependent kinase IV [Homo sapiens], 62.2% identity | NA | NA | 3.21 | NA | 0.68 |
| 44.35.1.5 | 6796.C | Fibroin heavy chain precursor [Bombyx mori], 6.8% identity | NA | NA | 3.75 | NA | NA |
| 688.1.1.0 | 9070.E | Large tegument protein [Herpes simplex virus], 10.7% identity | 2.49 | NA | NA | 1.19 | NA |
| 13.36.2.11 | 7462.C | SRP40, suppressor protein SRP40 [Saccharomyces cerevisiae], 68.7% identity | NA | 4.62 | NA | 0.56 | NA |
| 26.39.1.0 | 2318.C | EBNA-1 nuclear protein [Human herpesvirus 4], 27.0% identity | NA | NA | NA | 0.38 | NA |
| X96877 | 483.A | Hypothetical luminal protein precursor, chloroplast | 0.57 | 0.54 | 0.34 | 0.40 | 0.72 |
| XM_001695499 | 1422.C | Predicted protein (SSA15) with TPR, ANK, and zf-MYND domains | NA | NA | 3.72 | 1.38 | NA |
| XM_001700193 | 668.C | Predicted protein CAP_ED, effector domain of CAP transcription factor | NA | NA | 2.56 | 1.44 | 0.63 |
| 3.43.1.0 | 4962.C | Putative glucan synthase [Arabidopsis thaliana], 72.8% identity | NA | NA | 2.76 | 1.49 | NA |
| 16.97.1.5 | 6593.C | Y25C1A.3 protein [Caenorhabditis elegans], 57.9% identity | NA | NA | 3.96 | 1.68 | NA |
| 121.14.1.5 | 6312.C | Vegetative cell wall protein gp1 precursor [C. reinhardtii], 30% identity | NA | NA | NA | 2.27 | NA |
| XM_001694590 | 3153.C | Hypothetical protein | NA | 2.30 | NA | NA | NA |
| 111.18.4.11 | 724.C | Cullin 1B (Nicotiana tabacum), 99.7% identity | NA | 2.87 | NA | NA | NA |
| 7.42.1.5 | 3362.C | Nucleolin (protein C23) [Mesocricetus auratus], 67.8% identity | NA | 6.30 | NA | 0.14 | 0.50 |
| XM_001697504 | 9998.E | Hypothetical protein | NA | NA | 0.49 | 0.39 | 0.33 |
| 152.14.1.5 | 1904.C | CreA protein (Shigella flexneri), 55.4% identity | NA | NA | 2.74 | 1.29 | NA |
| 58.41.1.5 | 1097.C | Fibroin heavy chain precursor (Fib-H) (H-fibroin) [B. mori], 10.5% identity | NA | NA | 2.20 | 0.89 | |
| 576.2.1.0 | 9678.E | 0.61 | NA | 0.52 | 0.33 | 1.81 | |
| 356.1.3.11 | 9243.E | Hypothetical protein | 0.56 | NA | 0.52 | 0.12 | NA |
| 46.52.2.11 | 2626.C | CG2839 protein | NA | 3.73 | 0.86 | 0.79 | NA |
| XM_001689556 | 3709.C | Hypothetical protein, homology to Phytophthora infestans CRN1 | NA | NA | 1.35 | 2.16 | NA |
| XM_001696388 | 9338.E | Hypothetical protein | NA | NA | 1.39 | 2.23 | 1.57 |
| 116.19.1.5 | 8373.D | C_1160006 [158018:161045] | 2.53 | 2.55 | 1.56 | 0.44 | NA |
| XM_001700674 | 4539.C | Hypothetical protein 45% identity to A. thaliana UDP glucosyl transferase | NA | NA | 1.62 | 2.68 | NA |
| XM_001694976 | 6697.C | Hypothetical protein | NA | NA | 2.14 | 3.64 | 2.48 |
| Contig 85.6.1.0 | 2154.C | 0.85 | 6.61 | 2.42 | 0.10 | NA | |
| XM_001693665 | 9725.E | CAS_like, clavaminic acid synthetase-like | 5.31 | NA | 2.64 | 3.94 | 3.02 |
| XM_001689728 | 5855.C | Hypothetical protein with ring finger domain | NA | 3.79 | 2.39 | 1.31 | NA |
| 1.8.3.11 | 8427.D | HC_10364 [926397:929841] | 1.73 | NA | 5.22 | 4.16 | NA |
| 400.2.1.5 | 7404.C | NA | NA | 0.47 | 0.69 | NA | |
| 8.83.1.5 | 4854.C | Tax_Id=9606 splice isoform 1 of Q15149 plectin 1 | NA | NA | 2.39 | 0.70 | NA |
| XM_001698598 | 8873.D | Hypothetical protein | NA | NA | 2.85 | 1.10 | NA |
| XM_001699124 | 5272.C | Hypothetical protein | NA | NA | 2.63 | 1.11 | NA |
| 117.7.1.0 | 3343.C | NA | NA | 3.64 | 1.25 | NA | |
| 30.47.1.5 | 3534.C | Y25C1A.3 protein | NA | NA | 3.26 | 1.32 | NA |
| 205.4.1.5 | 1902.C | NA | NA | 4.02 | 1.41 | 1.40 | |
| XM_001691394 | 4410.C | Hypothetical protein | NA | NA | 3.46 | 1.73 | 1.33 |
| 103.28.2.31 | 8178.D | Hypothetical protein | NA | 6.32 | NA | 0.47 | NA |
| 667.1.1.0 | 4037.C | NA | 4.04 | NA | 0.51 | NA | |
| 17.108.1.0 | 6106.C | C_1740018 [20231:20880] | NA | 4.90 | NA | 0.61 | NA |
| XM_001699240 | 1640.C | TPR repeat protein | NA | 4.17 | NA | 0.78 | NA |
| 26.58.1.5 | 7656.D | NA | 4.40 | NA | 0.81 | NA | |
| 26.55.1.5 | 4842.C | NA | 6.04 | NA | 0.12 | NA | |
| 3.101.2.11 | 6615.C | MGC33630, hypothetical protein MGC33630 | NA | 4.03 | NA | 0.38 | NA |
| XM_001698756 | 5644.C | Hypothetical protein | NA | 3.91 | NA | 0.33 | NA |
| 8.45.1.0 | 2919.C | NA | 4.64 | NA | 0.20 | NA | |
| XM_001692849 | 4703.C | Hypothetical protein, 26% identity to DNA-dependent RNA polymerase E′ (ISS) [Ostreococcus tauri] | NA | 3.88 | NA | 0.45 | 0.74 |
| XM_001695799 | 2172.C | Hypothetical protein | 1.76 | NA | NA | 2.64 | 1.37 |
| XM_001692679 | 1212.C | Hypothetical protein | NA | NA | NA | 2.18 | NA |
| 1.59.2.11 | 3917.C | NA | NA | NA | 2.70 | 1.28 | |
| 10.23.2.11 | 4728.C | NA | NA | NA | 2.68 | NA | |
| 12.107.1.5 | 8247.D | Tax_Id=10090 Ensembl_locations:None RAD54-like | NA | NA | NA | 0.42 | NA |
| XM_001702460 | 8328.D | 44% identity to molecular cochaperone STI1 (ISS) [O. tauri] | NA | NA | NA | 2.24 | NA |
| XM_001694296 | 5751.C | 45% identity to PBCV-1 prolyl 4-hydroxylase (ISS) [O. tauri] | NA | NA | NA | 0.17 | NA |
| 145.2.2.11 | 5700.C | NA | NA | NA | 2.40 | 1.38 | |
| XM_001695405 | 4344.C | 37% identity to PEX22 (peroxin 22), protein binding [A. thaliana] | NA | NA | NA | 2.51 | NA |
| XM_001702135 | 1572.C | Hypothetical protein | NA | NA | NA | 2.18 | NA |
| XM_001691387 | 2256.C | Tax_Id=9606 | NA | NA | NA | 2.33 | NA |
| XM_001701095 | 5542.C | LETM1-like protein | NA | NA | NA | 3.31 | 1.40 |
| XM_001699679 | 2712.C | CG10555 protein | NA | NA | NA | 3.12 | NA |
| XM_001702888 | 6018.C | CG1517 protein | NA | NA | NA | 2.24 | NA |
| 53.15.3.11 | 8244.D | NA | NA | NA | 2.16 | NA | |
| 59.52.1.0 | 1456.C | Tax_Id=10090, Ensembl_locations:7-33233606 | NA | NA | NA | 0.47 | NA |
| 6.97.1.0 | 9930.E | C_60084 [691340:694926] | NA | NA | NA | 3.75 | 1.74 |
| XM_001703534 | 4240.C | Hypothetical protein, 31% identity to ERD4-related membrane protein | NA | NA | NA | 0.38 | NA |
| 93.32.2.31 | 3081.C | NA | NA | NA | 2.20 | NA | |
| 117.16.2.11 | 9185.E | C_1170030 [93583:99018] | NA | NA | 3.75 | 1.51 | 0.77 |
| XM_001696892 | 5915.C | SPRY superfamily | NA | NA | 2.46 | 1.56 | NA |
| XM_001696875 | 8243.D | Hypothetical protein | NA | NA | 2.43 | 1.62 | NA |
| 69.8.2.31 | 632.C | Hypothetical protein | NA | NA | 4.76 | 1.63 | NA |
| 3.168.1.0 | 5052.C | Hypothetical 38.7-kDa protein, 65.6% identity | NA | NA | 2.51 | 1.65 | NA |
| XM_001701276 | 9373.E | Hypothetical protein | NA | NA | 6.36 | 5.95 | 6.53 |
| XM_001701229 | 2968.C | Flagellar-associated protein [Chlamydomonas reinhardtii] | NA | NA | 3.04 | NA | NA |
| 5.123.2.31 | 5749.C | 2.94 | 1.21 | NA | NA | NA | |
| 329.4.1.5 | 4269.C | C_3290004 [33926:36211] | NA | 1.63 | NA | 0.33 | NA |
| XM_001699578 | 4127.C | Hypothetical protein | NA | 1.77 | NA | 2.16 | 1.17 |
| XM_001699290 | 5393.C | 0.79 | NA | NA | 2.03 | 3.39 | |
| 341.1.1.5 | 6015.C | NA | NA | 1.22 | 2.08 | 3.40 | |
| XM_001703283 | 2353.C | 31% identity to 2OG-Fe(II) oxygenase [Frankia sp. strain EAN1pec] | 1.92 | 2.79 | NA | NA | NA |
| 81.50.2.11 | 9274.E | Hypothetical protein containing the TPR domain | NA | NA | 1.48 | 2.70 | 2.44 |
a
Shown are averages obtained from microarray data using two to three independent biological replicates. Ratios of at least twofold induction or repression that passed all stringent criteria for data analysis, including Student's t test (P < 0.05), are bold. Student's t test was carried out on normalized microarray signals against control signals to establish significant differences. A complete list, including results for all genes used for microarray analysis, is shown in Table S1 in the supplemental material. NA, data points that did not pass the background cutoff or other stringent analysis criteria; GAL file ID, GenePix array list file identification number.