TABLE 3.

Comparative proteome analysis with the phosphoproteome of C. reinhardtii

Gene model (JGI, version 2)aFunction and/or homologies of depicted proteins to proteins of other organisms, their conserved domains, and their NCBI accession no.b
Flagella (24)
    C_20170 gi|23128981 |ref|ZP_00110817.1 | COG2319: FOG: WD40 repeat (Nostoc punctiforme PCC 73102)
    C_20337 (C)* gi|1353876 |gb|AAB01817.1 | glutamine synthetase (Chlamydomonas reinhardtii); u.a., GS1, glutamine synthetase, cytosolic isozyme, CO2-responsive gene
    C_50072 gi|23128003| ref|ZP_00109860.1| COG2453: predicted protein, tyrosine phosphatase (N. punctiforme PCC73102); KOG: protein tyrosine phosphatase (CDC14)
    C_50129 gi|12620209| gb|AAG60619.1 | adenylate cyclase (Cryptococcus neoformans var. grubii); gnl|CDD|37 smart00044, CYCc, Adenylyl/guanylyl cyclase, catalytic domain
    C_60100 gi|23479871| gb|EAA16587.1| R27-2 protein (Plasmodium yoelii yoelii); gnl|CDD|10914 COG1196, Smc, chromosome segregation ATPases
    C_90101 gi|21039486| gb|AAM33652.1| mastigoneme-like protein (C. reinhardtii); KOG: fibrillins and related proteins containing Ca2+-binding EGF-like domains
    C_110095u.a., coiled-coil protein
    C_150121 gi|50906913| ref|XP_464945.1| putative PKG-lb (Oryza sativa japonica cultivar group); gnl|CDD|17776 cd00180, S_TKc, serine/threonine protein kinases, catalytic domain; gnl|CDD|16536 cd00143, PP2Cc, serine/threonine phosphatases, family 2C, catalytic domain; gnl|CDD|14778 cd00038, CAP_ED, effector domain of the CAP family of transcription factors
    C_270111 gi|62650163| ref|XP_575971.1| similar to hypothetical protein A530045M11 (Rattus norvegicus); u.a., FAP74, conserved uncharacterized flagellum-associated protein
    C_290071 gi|68353830| ref|XP_690098.1| similar to cold autoinflammatory syndrome 1 protein (cryopyrin) (NACHT-, LRR-, and PYD-containing protein 3) (PYRIN-containing APAF1-like protein 1) (Angiotensin/vasopressin receptor AII/AVP-like) (Danio rerio); c.d., leucine-rich repeats, ribonuclease inhibitor-like subfamily
    C_360006 gi|27529748| dbj|BAA76788.2| KIAA0944 protein (Homo sapiens); u.a., DHC6, dynein heavy chain 6 (putative flagellar inner-arm dynein heavy chain)
    C_410060 gi|57087161| ref|XP_536793.1| similar to hydrocephalus-inducing protein (Canis familiaris); u.a., similar to mouse hydrocephaly protein hydin HY3
    C_420012 gi|29135339| ref|NP_619615.2| polycystic kidney and hepatic disease 1-like 1 (Mus musculus); gnl|CDD|27705 cd00603, IPT_PCSR, IPT domain of plexins and cell surface receptors (PCSR) and related proteins
    C_550085No significant similarity found; u.a., FAP1
    C_570035 gi|50057451| emb|CAH03435.1| hypothetical transmembrane protein (Paramecium tetraurelia); u.a., FAP113
    C_590094No significant similarity found
    C_590099 gi|68371158| ref|XP_695404.1| similar to SI:PACKTRZ.2 (novel protein similar to human polycystic kidney disease 2-like 1 [PKD2L1]), partial (Danio rerio); u.a., PKD2, weakly similar to polycystin-2; KOG: Ca2+-modulated nonselective cation channel polycystin
    C_700061 gi|67475672| ref|XP_653525.1| plasma membrane calcium-transporting ATPase, putative (Entamoeba histolytica HM-1:IMSS)
    C_750005 (C)* gi|10441431| gb|AAG17036.1|S-adenosylmethionine synthetase (Pinus contorta)
    C_750038 gi|71755035| ref|XP_828432.1| hypothetical protein Tb11.02.0990 (Trypanosoma brucei); u.a., FAP75, flagellum-associated P-loop-containing protein
    C_760066No significant similarity found
    C_850039No significant similarity found
    C_870044No significant similarity found
    C_910056 gi|29827935| ref|NP_822569.1| putative ABC transporter solute-binding protein (Streptomyces avermitilis MA-4680)
    C_970003 gi|50750584| ref|XP_422048.1| similar to tubulin alpha-5 chain, chicken (Gallus gallus); u.a., FAP248
    C_1120028 (B)* gi|16974385| gb|AAL31118.1| gene info AT5g19940/F28l16_90 (Arabidopsis thaliana); gnl|CDD|16052 pfam04755, PAP_fibrillin
    C_1150005 gi|7441384| pir||T08164 dynein α heavy chain (C. reinhardtii) (fragment); u.a., DHC1, flagellar inner-arm dynein 1 heavy chain α
    C_1340006 gi|18164| emb|CAA32061.1| OEE3 precursor protein (C. reinhardtii); u.a., oxygen-evolving enhancer protein 3 (PsbQ)
    C_1460023 (C)* gi|619932| gb|AAB61446.1| isocitrate lyase (C. reinhardtii)
    C_1580045 gi|130264| sp|P18068| PLAS_CHLRE plastocyanin, chloroplast precursor (PC6-2); c.d., gnl|CDD|15127 pfam00127, copper-binding proteins, plastocyanin/azurin family
    C_1710010 gi|2494209| sp|Q39575|DYHG_CHLRE dynein γ chain, flagellar outer arm; u.a., ODA2 flagellar outer dynein arm heavy chain γ (PF28); gnl|CDD|26007 pfam03028 dynein heavy chain
    C_2350009u.a., FAP157, conserved uncharacterized flagellum-associated protein
Centriole (13)
    C_20130 gi|62860034| ref|NP_001016608.1| hypothetical protein LOC549362 (Xenopus tropicalis); u.a., novel protein (WD repeat domain), described as protocilium-class FABP protein in human centrosome
    C_200025c.d., coiled-coil protein
    C_200196 gi|70879596| gb|EAN92756.1| hypothetical protein, conserved (Trypanosoma cruzi); u.a., coiled-coil protein with homology to a putative transcript, CG15792-PC, isoform C (Drosophila melanogaster), a hypothetical protein CE2713 (Corynebacterium efficiens YS-314), and to ciliary rootlet coiled-coil rootletin NP_055490.2 (H. sapiens)
    C_1120028 (A)* gi|16974385| gb|AAL31118.1| AT5g19940/F28l16_90 (A. thaliana); gnl|CDD|16052 pfam04755, PAP_fibrillin, PAP_fibrillin
Thioredoxin-interacting partners (18)
    C_20337 (A)* gi|1353876| gb|AAB01817.1| glutamine synthetase (C. reinhardtii); u.a., GS1, cytosolic glutamine synthetase, CO2-responsive gene
    C_30202 gi|515618| emb|CAA52439.1| sedoheptulose-bisphosphatase (C. reinhardtii)
    C_120103 gi|24030434| gb|AAN41372.1| dihydroxy-acid dehydratase (A. thaliana); CDD|25654 pfam00920, ILVD_EDD, dehydratase family
    C_200083 gi|39936346| ref|NP_948622.1| elongation factor Tu (Rhodopseudomonas palustris CGA009); u.a., EEF1, putative mitochondrial translation factor Tu; gnl|CDD|9925 COG0050, TufB, GTPases, translation elongation factors
    C_750005 (A)* gi|10441431| gb|AAG17036.1|S-adenosylmethionine synthetase (Pinus contorta)
    C_1460023 (A)* gi|619932| gb|AAB61446.1| isocitrate lyase
    C_1600004 gi|50660327| gb|AAT80888.1| chloroplast chaperonin 21 (Vitis vinifera)
Chloroplast 70S ribosome (33, 34)
    C_150160 gi|34398358| gbAAO22241.1| 41-kDa ribosome-associated protein precursor (C. reinhardtii); u.a., chloroplast RNA-binding protein, chloroplast ribosome-associated RAP41 stem-loop binding protein
  • a *, proteins that appear in different subproteomes (A, flagella; B, centriole; C, thioredoxin target).

  • b u.a., user annotation notes, which can be found on the JGI website under the gene model number; c.d., conserved domains.