Table I.
Genes induced under low-CO2 conditions and/or CCM1-dependent genes revealed by cDNA array analyses
| Array IDa | Clone IDb | WT-LC/ WT-HC | WT-LC/ C16-LC | Genec | Putative Functionc | Organismc | GenBank Hitd | Motif(pfam)e |
|---|---|---|---|---|---|---|---|---|
| 135h02 (28) | AV620271 | 110(±55) | 150(±99) | Mca | Mitochondrial carbonic anhydrase | C. reinhardtii | U41190 | – |
| 002b01 (6) | AV388733 | 57(±27) | 77(±49) | Cah1 | Periplasmic carbonic anhydrase | C. reinhardtii | P20507 | – |
| 019d11 (3) | AV619824 | 57(±38) | 79(±57) | Lci1 | Low-CO2 inducible membrane protein | C. reinhardtii | U31976 | – |
| 018h08 (4) | AV619223 | 56(±18) | 52(±15) | LciA | Nitrite transporter homolog (this study) | C. reinhardtii | AF149737 | – |
| 022b07 | AV623489 | 39(±14) | 50(±25) | Ccp1 | Chloroplast envelope protein LIP-36 | C. reinhardtii | U75345 | – |
| 012g07 | AV637344 | 25(±7.1) | 17(±6.8) | LciB | Putative chloroplast protein (this study) | – | – | Dynamin family (pfam00350) |
| 150h12 | AV629279 | 22(±10) | 12(±5.7) | – | – | – | – | No hit |
| 013d05 | AV638622 | 20(±0.6) | 11(±3.3) | – | Unknown (AT3g61320) | Arabidopsis | NP_191691 | No hit |
| 028e01 (4) | AV630016 | 18(±5.5) | 18(±3.4) | LciC | Putative chloroplast protein (this study) | – | – | Dynamin family (pfam00350) |
| 019b05 (7) | AV619622 | 13(±7.1) | 15(±9.5) | LI818 | Chlorophyll a/b-binding protein-like | C. reinhardtii | X95326 | – |
| 146f04 | AV627166 | 12(±4.5) | 16(±3.7) | – | – | – | – | No hit |
| 019g12 | AV620297 | 12(±5.6) | 14(±2.2) | – | – | – | – | No hit |
| 142b11 | AV624994 | 11(±4.8) | 3.6(±1.7) | Sag29 | Senescence-associated membrane protein | Arabidopsis | NP_196821 | – |
| 024b04 (2) | AV626358 | 11(±2.8) | 13(±3.8) | – | – | – | – | CBM_20, Starch binding domain (pfam00686) |
| 149b12 | AV628400 | 9.7(±3.0) | 7.2(±4.1) | – | – | – | – | Interferon induced GTPase(pfam05049) |
| 154c05 | AV630876 | 9.0(±1.2) | 21(±14) | – | – | – | – | No hit |
| 028f03 (2) | AV630146 | 8.9(±4.2) | 14 (±7.0) | – | Unknown (At2g45870) | Arabidopsis | NP_182111 | No hit |
| 164b10 | BP087144 | 7.7(±1.2) | 6.5(±2.8) | – | – | – | – | No hit |
| 135f03 | AV620059 | 7.6(±4.8) | 7.8(±4.4) | – | – | – | – | No hit |
| 025f01 (3) | AV627578 | 7.5(±3.3) | 8.4(±3.9) | Mmp | Putative mitochondrial matrix protein | C. reinhardtii | Y11586 | – |
| 021c08 | AV622166 | 6.3(±1.2) | 3.3(±0.4) | Sgat | Serine-glyoxylate aminotransferase | Methylobacterium extorquens | P55819 | – |
| 137c09 | AV386723 | 5.7(±1.4) | 14 (±0.8) | Ggps | Geranylgeranyl pyrophosphate synthase | Tagetes erecta | AAG10424 | – |
| 134g10 (3) | AV619535 | 5.2(±1.5) | 8.3(±2.0) | – | – | – | – | No hit |
| 102f05 | AV627999 | 4.9(±1.4) | 3.4(±1.3) | – | – | – | – | No hit |
| 169e06 | BP097010 | 4.8(±1.4) | 6.3(±1.9) | Fhs | 10-Formyltetrahydrofolate synthetase | Arabidopsis | NP_564571 | – |
| 022g04 (2) | AV624187 | 4.8(±1.6) | 3.2(±0.6) | – | Unknown (At5g57040) | Arabidopsis | NC_003076 | Glyoxalase (pfam00903) |
| 151c11 | AV629419 | 4.4(±1.3) | 5.9(±1.8) | Mcp | Mitochondrial carrier protein | Schizosaccharomyces pombe | NP_593701 | – |
| 024a11 (3) | AV626334 | 4.4(±0.6) | 3.7(±0.5) | Gdh1 | Putative glycolate dehydrogenase | Vibrio cholerae | NP_233369 | – |
| 020c02 | AV620842 | 4.2(±1.1) | 4.6(±0.7) | – | – | – | – | No hit |
| 138e10 | AV622332 | 3.8(±0.6) | 4.4(±0.7) | – | – | – | – | No hit |
| 138c12 | AV622214 | 3.8(±0.4) | 4.4(±1.0) | – | – | – | – | No hit |
| 021d10 (2) | AV635342 | 3.6(±1.1) | 3.9(±1.4) | Pgp1 | Phosphoglycolate phosphatase | C. reinhardtii | AB052169 | – |
| 145g10 | AV626859 | 3.4(±0.6) | 6.0(±1.7) | Aat1 | Alanine aminotransferase | C. reinhardtii | U31975 | – |
| 011e02 (2) | AV634930 | 3.4(±1.0) | 4.0(±1.5) | Lci5 | Low-CO2 inducible protein | C. reinhardtii | AAK77552 | No hit |
| 022f03 (2) | AV624023 | 3.4(±0.7) | 2.8(±0.1) | Shmt | Serine hydroxymethyltransferase | C. reinhardtii | AF442558 | – |
| 029g12 (3) | AV631115 | 3.3(±1.1) | 3.7(±0.7) | Sta2 | Granule-bound starch synthase I | C. reinhardtii | AF026420 | – |
| 123h02 | BP098683 | 3.3(±0.8) | 3.6(±0.9) | Sta3 | Soluble starch synthase | C. reinhardtii | AF026422 | – |
| 030h09 | BP086273 | 3.3(±1.0) | 2.8(±0.6) | – | – | – | – | No hit |
| 005c07 | AV387887 | 3.2(±0.8) | 3.5(±0.9) | – | – | – | – | No hit |
| 022b10 | AV623502 | 3.0(±0.5) | 4.7(±0.6) | – | Unknown (At4g36720) | Arabidopsis | NP_195390 | TB2/DP1, HVA22 family (pfam03134) |
| 023d09 | AV624492 | 2.9(±0.3) | 3.0(±0.4) | – | – | – | – | No hit |
| 148a10 | AV627826 | 2.9(±0.5) | 2.8(±0.8) | – | – | – | – | Chromate transporter (pfam02417) |
| 022h10 (2) | AV624435 | 2.8(±0.4) | 2.7(±0.3) | – | – | – | – | No hit |
| 170b12 | BP097305 | 2.8(±0.2) | 2.6(±0.3) | Ndh | Mitochondrial type 2 NADH dehydrogenase | Arabidopsis | NP_193880 | – |
| 167b10 | BP095941 | 2.7(±0.5) | 2.9(±0.3) | CarB | Carbamoyl phosphate synthetase | Arabidopsis | BAB90007 | – |
| 011d04 | AV634814 | 2.6(±0.7) | 2.6(±0.2) | Trxf1 | Thioredoxin f1 | C. reinhardtii | AY184800 | – |
| 003b05 (2) | AV396054 | 2.5(±0.3) | 4.1(±0.9) | GcsP | Glycine cleavage system P-protein | Arabidopsis | O49850 | – |
| 171b12 | BP097792 | 4.7(±2.7) | 2.1 (±0.9) | – | – | – | – | No hit |
| 021d12 | AV622387 | 2.9(±0.3) | 2.4 (±0.2) | – | – | – | – | No hit |
| 010b02 | AV632213 | 2.8(±0.5) | 2.3 (±0.3) | – | Unknown (At1g65230) | Arabidopsis | NP_176702 | No hit |
| 160c11 | BP088539 | 2.6(±0.2) | 2.0 (±0.1) | – | – | – | – | No hit |
| 021e03 | AV622398 | 1.8 (±0.4) | 7.3(±2.4) | – | – | – | – | No hit |
| 023c07 | AV624911 | 1.9 (±0.2) | 4.6(±0.9) | Hspg | Putative heparan sulfate proteoglycan | Ovis aries | AAD01973 | – |
| 139e12 | AV623221 | 2.4 (±0.6) | 4.0(±0.5) | – | – | – | – | Reverse transcriptase (pfam00078) |
| 019h09 (2) | AV620492 | 1.9 (±0.5) | 3.4(±0.4) | Ptp | Putative tyrosine phosphatase | O. sativa | AAF81798 | – |
| 022a05 | AV392559 | 2.1 (±0.6) | 3.2(±0.6) | Vdac | Voltage-dependent anion channel | O. sativa | CAB82853 | – |
| 142e05 | AU301246 | 2.2 (±0.4) | 3.1(±0.3) | – | – | – | – | No hit |
| 024c01 | AV626401 | 2.1 (±0.4) | 3.1(±0.8) | Cah3 | Chloroplast carbonic anhydrase | C. reinhardtii | U40871 | – |
| 022c08 | AV623614 | 2.4 (±0.4) | 2.9(±0.2) | – | Unknown (PA0315) | Pseudomonas aeruginosa | NP_249006 | No hit |
| 148c05 | AV627926 | 2.3 (±0.1) | 2.8(±0.4) | Mdh1 | NADP-malate dehydrogenase | C. reinhardtii | AJ277281 | – |
| 138h02 | AV622607 | 1.8 (±0.1) | 2.7(±0.2) | Cry | Crystallin J1C | T. cystophora | C46745 | – |
| 150d03 | AV628957 | 2.2 (±0.2) | 2.5(±0.4) | – | Unknown (At2g42750) | Arabidopsis | AAM19907 | DnaJ domain (pfam00226) |
Genes whose expression ratios were in excess of 2.5-fold are underlined. Dashes indicate not applicable.
a
Representative array IDs are shown in the first column. Numbers in parentheses indicate numbers of array IDs grouped into the same contigs, after sequencing the 3′ end of the cDNA.
b
GenBank accession numbers for the EST clones.
c
Genes with e-values <e−10 were annotated.
d
Best or most informative GenBank sequence alignments.
e
Motifs were annotated by the conserved domain database using RPS-BLAST (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi).