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Chlamydomonas Gene, Locus and Allele Names
This page presents guidelines for naming Chlamydomonas genes, incorporating annotation usage to May 2006. Many issues still need to be resolved, however, and your suggestions are welcome.
The list gives names for traditional mutants and mapped loci, as well as names proposed for genes identified in the genome sequence.
In some cases the locus names have been carried over to annotation, but for many old loci identified only by phenotype, more specific gene names have now been adopted. Nevertheless, we believe that to avoid confusion the old names should be reserved from further use for unrelated genes. Please scroll to the bottom of the page for a more detailed explanation of the distinction between loci and genes.
Please send additions and corrections to Elizabeth Harris
For more information on the annotation process, and to register as an annotator, please see the chlamydomonas.info page
The preferred format for gene names in C. reinhardtii is a 3-letter symbol, in uppercase for nuclear genes, or lower case for organelle genes; this is followed by either an uppercase number (preferred in most cases) or one or more letters:
RPS3, a nuclear gene, encoding radial spoke protein 3
ARG4, a nuclear gene, encoding an enzyme in the arginine biosynthesis pathway; named initially as the fourth arginine-requiring mutant discovered, so this number does not correspond to the sequence of this enzyme in the biosynthetic pathway
COX2a or COX3, nuclear genes, or cox1, a mitochondrial gene
PETC, a nuclear gene, or petB, a chloroplast gene; historically genes for components of photosynthesis have been named with letters, corresponding to the names used for cyanobacteria as proposed by Hallick and Bottomley in 1984
The following designations are currently in use for
nuclear genes and genetic loci. If you are looking for a name for
a newly identified gene, please check first to see if it falls into an existing category of phenotype or gene family, and if so, use the appropriate name. You should also check with the genome annotators to establish the appropriate number for a new gene with this prefix. If this is a novel gene or phenotype and you
want to choose a new name altogether, choose a letter combination that
isn't represented here yet. Again, we would appreciate your checking with us to be sure this name hasn't been requested by someone else.
If you're naming a molecular marker for which no gene or mutant phenotype
has been identified, we suggest that you use a combination of one or two
letters with two or more numbers, to create a name that doesn't look like
a traditional locus name - e.g. GP201, S641. Check the Locus class in
ChlamyDB
for marker names that have already been used.
Most journals render locus, allele and gene names in italics. We don't italicize them in the databases on the web, however, in order to simplify coding and to keep the file sizes as small as possible.
Alphabetical List of Locus/Gene and Allele Names
UPPERCASE letters indicate names that have been used for mapped loci in the nuclear genome, or for sequenced genes
lowercase letters indicate names that have been used for mutants, or in a few specific cases for organelle genes.
The descriptions give mutant phenotypes and/or gene products
-----
-A-
AAO - aldehyde oxidase
AAT - aspartate aminotransferase; has also been used in the genome annotation for acetyl-CoA acyltransferase
AC, ac - acetate requiring, an old designation; many loci
ACC - acetyl coA carboxylase
ACE - has been used to refer to contig assemblies, do not use as a gene name
ACH - aconitate hydratase
ACK - acetate kinase
ACL - ATP citrate lyase
ACP - acyl carrier protein
ACS - acetyl-coenzyme A synthase
ACT, act - used historically as the locus name indicating cycloheximide (Actidione) resistance; the genes corresponding to these loci have now been identified as proteins of the 60S ribosomal subunit
ACTIN - the locus representing the primary gene encoding actin; ACT can probably be substituted in future
ACYLC - mapped locus corresponding to an EST whose gene product is probably an acyl carrier protein; see ACP
ACV - serine/threonine kinase
ADF, adf - altered acid-activated deflagellation
ADH - aldehyde-alcohol dehydrogenase
ADI - arginine deiminase
ADK - adenylate kinase-
AGG, agg - modified phototactic aggregation, an old mutant
AGL, agl - sexual agglutination defective; also see the SAD locus
AGO - argonaut-like protein
ALAD - ALA dehydratase
ALB3 - albino-3 like protein
ALD - ALD1 is aldehyde dehydrogenase, ALD2 and ALD3 are fructose-1,6-bisphosphate aldolase; FBA is an alternative root for the latter
ALK - aurora Ipl1-like protein kinase; if additional genes of this type are found, should number ALK1, ALK2 etc.
ALS - acetolactate synthase; see also SMR
AMI - acetamidase
AMT - ammonium transport protein
AMX - amine oxidase
ANI, ani - anisomycin resistant; the ANI1 locus is also known as PDR1
ANT - mitochondrial ADP/ATP translocator
AOX - alternative oxidase
AP - aspartic proteinase; a three-letter name would be preferable
AP1 - has been used in genome annotation for clathrin adaptor complex subunits
APC - anaphase promoting complex
APM, apm - as a genetic locus, amiprophos methyl resistant
APO - apospory associated protein
APR - adenylylsulfate reductase; APS has also been used
APX - ascorbate peroxidase
ARF - ADP ribosylation factor
ARG, arg - arginine-requiring; note that for historical reasons the enzymes in the arginine biosynthesis pathway are not numbered sequentially, and the numbers assigned to the loci do not necessarily correspond to the equivalent genes in other organisms
ARL - class of small GTPases; qualified as ARLA, ARLB, ARLC
ARO - AROK has been used for shikimate kinase; probably should keep ARO as a general root for other genes in the same pathway, but change the nomenclature to the three-letter plus number system
ARP - actin-related protein; also see NAP, novel actin-related protein
ARS - arylsulfatase. ARS was also used early on as a name for some chloroplast autonomously replicating sequences
ASA - ATP synthase, mitochondrial associated protein
ASB - anthranilate synthase beta subunit
ASC - activating signal cointegrator
ATP, atp - genes for components of the photosynthetic and mitochondrial ATP synthase complexes. Genes for components of the chloroplast CF0/CF1 ATP synthase are designated with letters (atpA, atpB, ATPC etc.), the mitochondrial F0/F1 equivalents with numbers (ATP1, ATP2, etc.)
ATPv - genes for vacuolar ATPase subunits
ATS - ATP sulfurylase
ATX - copper chaperone protein
-----
-B-
BBS - used to designate proteins related to those identified in the human genome as Bardet-Biedl Syndrome proteins
BCS - BCS1 has been proposed in the genome annotation as the name for a specific gene encoding an AAA family ATPase, by analogy to a yeast mitochondrial protein
BET - BET1 has been proposed in the genome annotation as the name for gene encoding a protein similar to Arabidopsis BET1
BIO - biotin synthase
BIP - proposed in the genome annotation as the name for genes encoding isoforms of heat shock protein 70 specific for the endoplasmic reticulum
BKT - beta-carotene ketolase
BLD, bld - formerly BALD; mutant strains lack flagella. BLD1 encodes intraflagellar transport protein IFT52, also known as Osm-6 protein
BOP, bop - bypass of paralysis, a class of suppressors of motility mutations
BPL - biotin-protein ligase
BRC, brc and BRS, brs - brown conditional and brown stringent, mutants affecting porphyrin biosynthesis
BRD - used in ChromDB for a bromodomain containing protein
BSAS - beta-substituted alanine synthase
BTA - betaine lipid synthase
BUB - used in genome annotation for a mitotic spindle checkpoint protein
-----
-C-
CA, ca - used for a class of carbonic anhydrase mutants; should be replaced by CAH
CAA, CAB, CAC - reserved for nuclear genes involved in expression of chloroplast psa genes (see below)
CAB - genes encoding chlorophyll a/b binding proteins, also called LHC proteins. LHC is the preferred gene designation for these genes, with CAB to be reserved for genes involved in psaA cofactor assembly
CAD, cad - cadmium resistant
CAH - carbonic anhydrase
CALK - provisional name used for a specific Chlamydomonas protein kinase, now replaced with ALK
CAM - calmodulin; cam has also been used previously to designate chloramphenicol resistant mutants in the chloroplast genome
CAN, can - canavanine resistant, an old locus
CAO - chlorophyll a oxidase (= chlorophyll b synthase)
cap - chloramphenicol resistant, chloroplast mutants
CAR, car - carotenoid deficient; car was also used by Sager for a chloroplast carbomycin resistant mutant
CAS - calcium sensing receptor
CAT - catalase
CAX - cation exchanger
CB, cb - cell cycle blocked; a prefix used by Howell and Naliboff for a group of temperature-sensitive cell-cycle mutants; CDC is preferred for cell division cycle proteins
CBA, CBB, CBC, CBD, CBE, CBH - reserved for nuclear genes involved in expression of chloroplast psbgenes (see below)
CBLP - G-protein beta subunit
CBN, cbn - chlorophyll b deficient
CBP - ubiquinol-cytochrome c chaperone
CBR - NADH:cytochrome b5 reductase
CCB - nuclear genes involved in expression of chloroplast petB gene (see below)
CCD - coiled-coil domain protein
CCM - protein(s) of carbon-concentrating system
CCP - CCP1 and CCP2 have been used as gene names for two low CO2 inducible chloroplast envelope proteins; see also LCI
CCS - loci affecting chloroplast c-type cytochrome assembly; CCS1 through CCS5 are nuclear gene loci identified by mutation, ccsA is a chloroplast locus
CCT - T-complex protein 1
CD, cd - an old prefix designating some chlorophyll-b deficient mutants. CBN is preferred
cdb - used for a mutant with a temperature-sensitive block in cell division
CDC - cell division cycle protein; by analogy to yeast and other organisms, this is preferred to CB or CDB
CDF - a family of manganese transporters
CDI - cholesterol delta isomerase; has been used as a gene name for a sterol isomerase in Chlamydomonas
CDK - ccyclin-dependent kinase; four-letter roots have been used in the genome annotation - CDKA1, CDKA2, CDKB1, CDKB2 etc.
CDO - cysteine dioxygenase
CDS, cds - as a mutant phenotype, cadmium sensitive; CDS has also been used in the genome annotation to designate both an ATP-binding cassette half-transporter and a CDP-DAG synthetase
cen - name given to a mutant with pleiotropic defects in expression of nuclear genes involved in photosynthesis
CFA - cyclopropane fatty acid synthase
CGE - chloroplast GrpE homolog; = co-chaperone CGE1
CGS - cystathionine synthetase
CHC - clathrin heavy chain
che - altered chemotactic responses; see SUC
CHL - subunits of protochlorophyllide reductase and magnesium chelatase; chl has been used as an allele name for chlorophyll-deficient mutants; see also BRC and BRS
Chltex1 - see TCTEX1
CHOP - see COP (chlamyopsin)
CHR - chromatin remodeling complex proteins
CHS - chlorophyll synthase; see also CAO
CHY - carotene hydroxylase
cia - used as the designation for a group of mutants that require high concentrations of CO2
CIS - citrate synthase
CK - casein kinase; a three-letter name would be preferable
CKS - cyclin dependent kinase
CLC - clathrin light chain
CLP - Clp protease; 4-letter names have been used here, e.g. CLPP, CLPR, CLPY
CLPK - cyclic nucleotide dependent protein kinase
CMK - diphosphocytidyl methyl erythritol kinase
CMS - methyl-D-erythritol phosphate cytidylyltransferase
cmu - mutant with defect in organization of cytoplasmic microtubules
CNA, CNB, CNC - prefixes used for a group of molecular markers
CNK - NIMA-related kinase
CNX - molybdopterin biosynthesis protein
cob - cytochrome b (mitochondrial gene)
col - colchicine resistant; defined as a mutant phenotype, some of these mutants have been shown to be in the tubulin genes
COP - chlamyopsins, the rhodopsin-like photoreceptor proteins
COQ - flavin-dependent monoxygenase
cor - used for a colchicine-resistant mutant; col is preferred
COX - cytochrome oxidase subunits; cox1 is encoded in the mitochondrial DNA; COX2a, COX2b and COX3 are nuclear genes
CP12 - Calvin cycle CP12 protein; a three-letter name would be preferable
CPC, cpc - motility impaired, defect in central pair microtubules
CPD, CPE - condensin complex subunits; perhaps it would be better to use a single 3-letter root for all subunits of this complex
CPH - DNA photolyase protein
CPI - cycloeucalenol cycloisomerase
CPK - calcium-dependent protein kinase
CPN - chaperonin
CPSF - mRNA cleavage and polyadenylation specificity factor subunit; PSF is a better alternative
CPX - coproporphyrinogen oxidase
CPY - carboxypeptidase, serine-type protease
CR, cr - chloroplast ribosome deficient; an old group of loci.
There are a series of sequences in GenBank identified as CR004, CR008, etc. where CR appears to stand for Chlamydomonas reinhardtii; these are predicted but as yet unidentified proteins. As their functions are determined, they should be given new names. There are also many proteins listed in GenBank and elsewhere as Cr...., where the rest of the name is a valid gene name. Although this is a useful convention when comparing similar proteins from several organisms, within the Chlamydomonas context it should not be used.
CRD, crd - copper response defect
CRP - dispersed repetitive DNA sequences
CRR - copper response regulator
CRT - calreticulin
CRY, cry - cryptopleurine resistant; has also been used as an alternative name for the CPH1 gene. Historically use of CRY as the cryptopleurine resistance locus has precedence, but since this locus was eventually identified as RPS14, the gene for a 40S ribosomal protein, it might be reasonable to discard this use.
CSN - COP9 signalosome subunits
CSP - ribosome-associated protein; RAP is an alternative
CSR, csr - chlorsulfuron resistant
CSTF - mRNA cleavage stimulation factor, similar to a human protein of that name
CTH - copper target homolog
CTP - copper transporting ATPase
CTR - copper transporter, transmembrane
CUL - cullin; E3 ubiquitin ligase SCF complex subunit
CUT - as CUTA, a copper binding protein
CW, cw - cell wall deficient
CYB - cytochrome b, specifically CYB5 for cytochrome b5; see also cob, the mitochondrial cytochrome b apoprotein
CYC - cycochrome c; sometimes appears as CYTC
CYG - guanylate cyclase
CYN - peptidyl-prolyl cis-trans isomerase, cyclophilin type
CYP - has been used both for cysteine protease and for cyclophilin
cyr - cycloheximide-resistant, found to be an allele at the ACT2 locus
CYT, cyt - cytokinesis deficient
CYTC - see CYC
----- -D-
DAL - allantoinase
DCL - dicer-like protein
DEG - serine protease, trypsin family
DES - fatty acid desaturase, used specifically to date for omega-6 desaturase; also see FAD
DGD - digalactosyldiacylglycerol synthase
DGK - diacylglycerol kinase; KDG is alternative
DHC - dynein heavy chain
DIC - dynein intermediate chain; see also IC
DID - vacuolar assembly/sorting protein, named based on similarity to yeast proteins
dif - mutants affecting gametic differentiation
DIM - dimethyladenosine transferase
DIP - deflagellation inducible protein
DK, dk - dark-dier, an old group of mutants with mitochondrial defects
DLAT - dihydrolipoamide acetyltransferase. A 3-letter name would be preferable
DLC - dynein light chain; see also LC
DMT - DNA methyltransferase
DR, dr, dr-u - DCMU-resistant
ds - DCMU sensitive
DPN - diphosphate nucleotidase
DRP - dynamin-type GTPase
DSP - dual specificity protein phosphatase
dum - mitochondrial mutants deficient in cytochrome b or other respiratory functions
DUR - enzymes related to urea metabolism
DVR - divinyl protochlorophyllide reductase
DXR - deoxyxylulose-5-phosphate reductoisomerase
DXS - deoxyxylulose-5-phosphate synthase
----- -E-
EB1 - microtubule-associated protein Eb1
ECP - extracellular polypeptide
ECT - CTP:ethanolamine cytidylyltransferase
EEF, EF - (eukaryotic) elongation factors; EEF is preferred. However, note that EEF1 has been used in genome annotation for the mitochondrial translation factor Tu. Is this an inconsistent usage, if EE indicates "eukaryotic elongation"
EFG - elongation factor, GTP-binding-like protein
EFP - elongation factor P (used in genome annotation for chloroplast and mitochondrial EF-P proteins)
EFT - elongation factor Ts (chloroplast and mitochondria)
EIF - (eukaryotic) initiation factor
ELI - early light-inducible protein
ENH, enh - for "enhancer", a class of mutants that modify expression of UNI1 mutations
EPT - CTP:ethanolamine cytidylyltransferase
ERD - used in genome annotation for conserved proteins similar to KDEL receptor invovled in ER retention
ERF - eukaryotic release factor
ERO - conserved protein involved in redox reactions in the ER lumen
ERV - used in genome annotation for "ERV1 protein", also called Augmenter of liver regeneration in mammals
ERY, ery, er-u - erythromycin resistant
ES, es - suppressors of erythromycin resistance
ETF - electron transport flavoprotein; appears in genome annotation as ETFA and ETFB
ETK - ethanolamine kinase
ETR - ethanolamine phosphotransferase
EYE, ey or eye - eyespot-deficient mutants; EYE is now the preferred gene name
EZY, ezy - zygote-specific gene
----- -F-
F - used to designate a group of non-photosynthetic mutants selected after treatment with 5-fluorodeoxyuridine; mostly being renamed now to correspond to the genes affected as these are identified
FA, fa - impaired flagellar autotomy
FAB - FAB1 has been used in the genome annotation for FAB1-type 1-phosphatidylinositol-4-phosphate 5-kinase, FAB2 for delta-9-ACP desaturase
fac - fluoroacetate resistant
FAD - fatty acid desaturase; also see DES
FAM, fam or famr - fluoroacetamide resistant
FAP - genes encoding proteins of the flagellar proteome
FAR, far - the FAR1 locus corresponds to a regulatory gene involved in expression of nitrate reductase
FAS - used in the genome annotation for a series of proteins resembling cyanobacterial secreted and surface proteins with FAS1 domains
FBA - fructose-1,6-bisphosphate aldolase; also see ALD
FBP - fructose bisphosphatase
FDH - formaldehyde dehydrogenase
FDX - ferredoxin-NADP+ reductase; FNR is alternative
FEA - iron assimilating protein
FER - apoferritin
FES - mitochondrial Rieske iron-sulfur protein
FG - ferredoxin-dependent glutamate synthase; a three-letter name would be preferable
FIP - FIP37 is a protein required for chromosome maintenance in Arabidopsis and yeast; a putative homolog has been identified in the Chlamy genome
FKB - FKBP-type peptidyl-prolyl cis-trans isomerase
FLA, fla - flagellar assembly impaired; mostly temperature-conditional mutants
FLP - ferroxidase-like protein
FMG - flagella membrane glycoprotein
FNR - ferredoxin-NADP+ reductase; the gene encoding the chloroplast enzyme is also identified as PETH
FOX - multicopper ferroxidase
FPS - farnesyl pyrophosphate synthase; also appears in annotation as FPPS
FRDA - frataxin; a 3-letter name would be preferable
FSA - fructose-1,6-bisphosphate aldolase; ALD has also been used as a root name for this enzyme
FSD - superoxide dismutase, Fe; alternative to SOD2
FSR, fsr - fusidic acid resistant
FTR - ferredoxin-thioredoxin reductase; FTRC has been used in annotation to indicate the catalytic chain of this enzyme, and FTRV has been used for the variable chain
FTSH - "FtsH protease
FTSZ - plastid division protein FtsZ
FTT - 14-3-3 protein; GRF and ERB have also been used as gene names for 14-4-4 and related proteins, based on similarity to other organisms
FUD - used as a prefix for a group of non-photosynthetic mutants isolated using 5-fluorodeoxyuridine. Most are chloroplast mutants, but a few are in the nuclear genome.
FUM - fumarate hydratase; FUMA has also been used in annotation, but FUM will probably suffice
FUO - flavoprotein ubiquinone oxidoreductase
FUS, fus - mutant defective in sexual fusion, maps to the mating type locus; affected gene is a sex recognition glycoprotein. SFU is an alternative name
FUT - fucosyltransferase
----- -G-
G6PD - used to indicate glucose-6-phosphate dehydrogenase; a 3-letter name would be preferable, but GPD has already been used for glycerol-3-phosphate dehydrogenase
GAE - UDP-glucose epimerase
GAK - kinase associated with gliding motility
GAL - galactose kinase
GAM, gam - defects in gametogenesis and/or mating
gag - O-glycosylation and sexual aglutination, see SAD
GAP - glyceraldehyde-3-phosphate dehydrogenase; GAPA and GAPC have been used as locus names, but GAP1, GAP2 etc. would be preferable
GAR - gamete activation regulated
GAS - genes expressed during sexual differentiation
GAT - glutamyl-tRNA amidotransferase
GBA - used in annotation for GTP-binding protein TypA
GBLP - G protein beta subunit; has been used specifically for a gene product alternatively called RACK1 protein.
GBP - G-strand binding protein
GBSS - has been used for starch synthase, granule bound; probably we should continue with STA for the enzymes of starch biosynthesis
GCP - gamma tubulin ring complex protein
GCS - glycine cleavage system
GDH - glutamate dehydrogenase; has also been used in annotation for glycolate dehydrogenase
GDI - GDP dissociation inhibitor protein
GGH - gamma-glutamyl hydrolase
GGPS - geranylgeranyl pyrophosphate synthase
GGR - geranylgeranyl reductase
GID - glucose-inhibited division protein
GLE - gamete lytic enzyme, see also MMP
GLK - glucokinase
GLN, gln - used for an old mutant unable to use glutamine as sole nitrogen source; now preferred as the root for enzymes of the glutamine synthesis pathway. Old locus GS1 becomes GLN1, old GS2 (plastid glutamine synthetase) becomes GLN2.
GLYK - glycerate 3-kinase
GLYM - serine hydroxymethyl transferase
GME - GDP-D-mannose-3,5-epimerase
GMP1 - GDP-mannose pyrophosphorylase
GND - 6-phosphogluconate dehydrogenase
GOR - glutathione reductase-related protein
GOS - membrane-anchored golgi SNARE protein
GP - used for the genes encoding two proteins of the vegetative cell wall; a three-letter name would be preferable
GPD - glycerol-3-phosphate dehydrogenase
GPM - phosphoglucomutase
GPPS - geranyl pyrophosphate synthase
GPT - glutamic-pyruvic transaminase
GPX - glutathione peroxidase
GR - used for glutathione reductase; a 3-letter name would be preferred. See GOR, also GSHR
GRF - 14-3-3 protein; see also ERB and FTT
GRP - glycine-rich protein; may be replaced with more specific names when functions are identified
GRX - glutaredoxin
GS - glutamine synthetase; see GLN
GSA - glutamate-1-semialdehyde aminotransferase
GSH - GSH1 has been used to designate glutamate-cysteine ligase, GSH2 for glutathione synthetase; GSHR has been suggested for glutathione reductase
GSHR, - glutathione reductase; see also GOR, GR
GSK - glycogen synthase kinase
GSP - gamete-specific protein
GTA - global transcription factor, group A
GTE - global transcription factor, group E
GTF - global transcription factor, TFIID type
GTR - glutamyl-tRNA reductase; HEMA is alternative
GTS - glutamyl-tRNA synthetase
GUA - GMP synthetase
Gul or GUL - the Gulliver transposon
GUN4 - "genomes uncoupled", used to annotate a tetrapyrrole-binding protein similar to Arabidopsis GUN4
----- -H-
HAC - CREB-binding protein, as used in ChromDB
HAG - histone acetyltransferase
HCF - used in annotation for photosystem II stability/assembly factor HCF136
HCP - has been used both for hybrid-cluster protein and for histone deacetylase, Sin3 complex component' since the latter usage refers to ChromDB, it should probably be adopted, and a different name given to the hybrid-cluster protein genes
HCS - holocytochrome-c synthase
HDA - histone deacetylase
HDS - 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
HEM - used for enzymes of heme biosynthesis; also see HEMA, HEMC, HEMD, HEME, HEMH. We should adopt gene-specific names with 3-letter root plus number, but we need to form a consensus on whether to use HEM1, HEM2, HEM3 etc. or separate root names for each enzyme, e.t. UMT1, UPD1, etc.
HEMA - glutamyl-tRNA reductase
HEMC, HEM3 - porphobilinogen deaminase; also see PBG
HEMD - uroporphyrinogen III methylase or uroporphyrinogen III synthase; see UMT, UPS
HEME - uroporphyrinogen decarboxylase; see UPD
HEMH - ferrochelatase; also annotated as HEM15
hf - high chlorophyll fluorescence
HFO - histone H4
HIS - histones; see also HFO, HON, HTA, HTB, HTR
HKR, hkr - gene required for low-affinity potassium transport, and the mutant that defines this locus; see also TRK; HKR has also been used in genome annotation for histidine kinase response regulator
HLA - high light inducible; used so far for only one gene, could be changed
HLIP - from higher plant terminology, a single helix LHC family protein
HLP - histone-like DNA binding protein
HMA - heavy metal transporting ATPase
HMT - homocysteine S-methyltransferase
HON - histone H1
HPD - hydroxyphenylpyruvate dioxygenase
HPR - hydroxypyruvate reductase
HPT - hexose phosphate transporter
HRP - hydroxyproline-rich glycoprotein
HSP - heat shock proteins (HSP22, HSP70A, HSP70B, HSP70C
HST - homogentisate solanesyltransferase
HTA - histone H2A
HTB - histone H2B
HTR - histone H3
HTV - histone H3 variant
HXA - histone acetyltransferase complex component
HXK - hexokinase
HY3 - hydin
HYD - hydrogenase, several enzymes and assembly factors
HYP - used in genome annotation for 'hypothetical protein'; presumably these will eventually be given more precise names
----- -I-
IAT - inositol acyltransferase
IC - dynein intermediate chain; see DIC
ICL - isocitrate lyase
IDA, ida - inner dynein arm mutations
IDH - isocitrate dehydrogenase, NAD-dependent
IDHP - isocitrate dehydrogenase, NADP-dependent; unless there is a strong precedent from other organisms, perhaps the isocitrate dehydrogenase genes should be IDH1, IDH2 etc. instead
IDI - used for isopentenyl-diphosphate delta-isomerase; IPI is preferred (isopentenyl pyrophosphate isomerase)
IDS - isopentenyl diphosphate/dimethylallyl diphosphate synthase
IF1 - eukaryotic initiation factor, as IF1, IF2, IF3 etc., usually then followed by a letter (e.g. IF4E). EIF is probably preferable
IFM - mitochondrial initiation factor
IFT - intraflagellar transport proteins; see also BLD
ILV - genes involved in soleucine/valine synthesis
IMP, imp - impotent, a group of mutants impaired in the sexual
cycle
IMR, imr - imazaquin resistant
INFA - used for a putative organellar initiation factor; this could probably be renamed
IPA - importin alpha
IPB - importin beta
IPI - isopentenyl pyrophosphate isomerase
IPY - inorganic pyrophosphatase; IPYR has also been used in annotation
IRK - inward rectifier potassium channel protein
ISA - isoamylase
ISC - iron-sulfur cluster assembly protein; also appears in annotation as ISCA
ISO, iso - non-mating, gene involved in sex determination
ISU - iron-sulfur cluster assembly protein
----- -J-
----- -K-
KAP - kinesin associated protein
KAS - ketoacyl ACP synthase
KAT - katanin
KC - casein kinase
kd - nystatin resistant
KDG - diacylglycerol kinase; KDG4 is annotated as ceramide kinase
KHP - kinesin-like protein; used specifically for tbe gene encoding the 87kDa protein Khp1, first identified by the fla10 mutant
KH-P1 - used in genome annotation for an RNA-binding protein with one KH-domain; this needs to be changed, since it can be confused with KHP1, and is not a valid C. reinhardtii format
kir-u - kirromycin resistant (chloroplast mutants)
KLP - kinesin-like protein; used specifically for tbe gene encoding the 83kDa protein Klp1
kr-u - kanamycin resistant (chloroplast mutants)
KUP - potassium transporter
----- -L-
LAO - L-amino acid oxidase
LC - dynein light chains, see DLC
LCI - low CO2 inducible protein
LCR - low CO2 stress response regulator
LCYE - used for lycopene epsilon cyclase; LEC is preferred
LDE - used in annotation for "light-dependent expression"; such genes are being given other names as they have been further identified
LEC - lycopene epsilon cyclase
LEU - enzymes in the leucine biosynthesis pathway. LEU1 has been used for isopropylmalate dehydratase, LEU3 for isopropylmalate dehydrogenase. LEU2 hasn't been used yet.
LF, lf - long flagella, see also ULF
LGD - L-galactose dehydrogenase
LHC - genes encoding chlorophyll a/b binding proteins, separated as LHCA and LHCB series, plus some others; see also CAB
LI818 - widely used name for a particular light-inducible chlorophyll a/b binding protein
LIG - DNA ligase
LIL - used in annotation for Lhc-like protein Lhl3; this could be changed
LIP - chloroplast envelope carrier protein
LIS, lis - light-regulated motility suppressors
lit - lithium sensitive
LON - used in annotation for ATP-dependent protease PIM1/LON; this could be changed
lor - used for a pale green mutant; also see PG
LPB - low photochemical bleaching protein
LRG, lrg - light regulation of gametogenesis
LSD - used for a specific zinc-finger protein, in reference to an Arabidopsis gene
LSM - a family of small nuclear riboproteins; also see SMP
LTS, lts - light-sensitive
LUT, lut - lutescent
----- -M-
MAA, maa - methylanthranilic acid resistant; MAA7 corresponds to the gene encoding trytophan synthase
MAB, MAC, MAJ - reserved for nuclear genes involved in expression of chloroplast psa genes (see below)
MAD - mitotic spindle assembly checkpoint protein
MAK - mitogen-activated protein kinase; MAPK has been used more frequently
MAL - altered chemotactic response to maltose (che mutations)
MAM - used in genome annotation for a genes encoding proteins similar to yeast Mam3p, involved in mitochondrial biogenesis
MAP - methionyl aminopeptidase
MAPK - mitogen-activated protein kinase; MAPKK is MAP kinase kinase
MAS - malate synthase
MAT, mat - old mutants showing altered maternal (chloroplast) inheritance; this name survives currently as MAT3, a homolog of human retinoblastoma protein
MBA, MBC, MBD, MBE, MBF, MBH, MB(, MBJ, MBK, MBL, MBM, MBN, MBT, MBZ - reserved for nuclear genes involved in expression of chloroplast psb genes (see below)
MBB - genes involved in mRNA processing or stability of the chloroplast psbB genes; see below; e.g. MBB1 encodes a tetratricopeptide-like repeat protein
MBO, mbo - moves backwards only
MCA, MCB, MCD, MCG, MCL - genes involved in mRNA processing or stability of the chloroplast pet genes; see below; e.g. MCA1 encodes an RNA stability factor; see below
MCCB - used in annotation for methylcrotonyl-CoA carboxylase; should be replaced with a 3-letter root
MCM - minichromosome maintenance protein, a family of eukaryotic DNA replication proteins
MCP - molybdenum cofactor carrier protein
MCS - used in annotation for a methyl-D-erythritol cyclodiphosphate synthase
MDA, MDB, MDE, MDF, MDH, MDI - reserved for nuclear genes involved in expression of chloroplast atpgenes (see below)
MDH - malate dehydrogenase; both numerical (MDH1, MDH2) and letter (MDHC, MDHG, MDHM) gene names have been used in annotation; the former conform better to our preferred naming patterns
ME, me - altered methylation of chloroplast DNA
MEMB - Qb-SNARE protein, Bos1/Membrin family. Could we change this to MEM1, MEM etc.?
MEN - menaquinone biosynthesis; MEN2 has been used in genome annotation for naphthoate synthase, equivalent to the bacterial menB gene product
MES - methionine sensitive
MET, met - MET1 was used to designate a gene encoding a chloroplast DNA methyltransferase; met has been used as the name for a mutant showing temperature-sensitive metaphase arrest. MET14 and MET16have been used in genome annotation for adenylylsulfate kinases
mf - low chlorophyll fluorescence
MFDX - used in annotation for an adrenodoxin-like ferredoxin,
MFT - MATE family transporter
MGD - enzymes in the biosynthetic pathway for the chloroplast membrane lipid monogalactosyldiacylglycerol
MGE - mitochondrial grpE homolog
MGO - mago nashi-like protein
MGTE - used for Mg/Co/Ni transporter MgtE; could we change this to MGT plus a number?
mia - "modifiers of inner arms", a class of phototaxis mutants
MID, mid - minus dominance, a gene in the mating type locus
MIN, min - eyespots reduced in size
MIND - cell division inhibitor MinDn
MINE - protein similar to bacterial cell division site determinant MinE
MIOX - by similarity to Arabidopsis Miox4, encoding myo-inositol oxygenase
MIP - aquaporin, major intrinsic protein
MKP - MAP kinase phosphatase
MLT, mlt - used to describe a mutant with multiple eyespots; MLT1 is also known as PTX4
MMC - mitochondrial matrix protein
MMP - matrix metalloproteinase
MND - MND1 has been used in genome annotation for a protein involved in homologous chromosome pairing and meiotic double-strand break repair, similar to human GAJ
MNT - manganese transport protein; also see RET
MOC - mitochondrial transcription termination factor
MOG - used once in annotation for a molybdopterin biosynthesis protein; CNX has been used more recently for proteins in this pathway, and is preferred
MON - a gene involved in cytokinesis
MPC - mitochondrial phosphate carrier protein
MPK - mitogen-activated protein kinase
MPP - mitochondrial processing peptidase; MPPA has been used for the alpha subunit of this enzyme
MRE - specifically (to date), MRE11, encoding a DNA repair protein named in other organisms
MRP - a subfamily of ABC transporters
MSCP - used in annotation for a mitochondrial substrate carrier protein; could be simplified to MSC
MSD - Mn superoxide dismutase; the first member of this family, now MSD1, was previously identified as SOD1
MSH - used in genome annotation for a DNA mismatch repair protein, MutS type
MSR, msr - methionine sulfoximine resistant
MSRA - methionine-S-sulfoxide reductase
MST - mastigoneme or mastigoneme-like protein
MT, MTA - MT is the locus name for the mating type region; MTA has been used for some mating-type specific genes found within this locus
MT4 - previously used for heat shock protein 33, which should probably be given a name in the HSP series
MTD - minus-gamete-specific protein
MTF - by analogy to yeast, a mitochondrial targeted RNA methyltransferase; also see DIM
MTP - manganese transporter
mud - myxothiazol resistant (a mitochondrial mutant)
MUT - used for a series of loci related to gene silencing; MUT6 encodes a DEAH-box RNA helicase, MUT9 a serine/threonine protein kinase, MUT11 a protein containing WD40 repeats
MYO - myosin
----- -N-
NAB - nucleic acid binding protein
NAC, nac - nuclear genes involved in expression of the chloroplast psbD gene
NAD - mitochondrial NADH dehydrogenase
NAH - Na+/H+ antiporter
NAP - novel actin-like protein
NAR, nar - genes involved in nitrate assimilation; we need to resolve alternative numbering systems within this group, however
NAT - N-acetyltransferase
ncc - nuclear mutation that destabilizes chloroplast atpA mRNA
nd, nd-u - neamine dependent
NDA - NADH dehydrogenase
NEK - used for NIMA-related kinase, but replaced by CNK in recent genome annotation
NEP - nucleolar essential protein, by similarity to a yeast protein involved in biogenesis of the 40S ribosomal subunit
NFA - nucleosome assembly factor
NFC - nucleosome/chromatin assembly factor, also known as nucleosome remodeling factor
NFD - chromatin-associated HMGB protein
NIA - see NIT
NIC, nic - nicotinamide-requiring
NifU - used in annotation of proteins containing a NifU domain; not properly a gene name for Chlamydomonas yet. Should we use NIF for this class of proteins?
NII - nitrite reductase
NIT, nit - loci involved in nitrate reductase expression; the gene
represented by the NIT1 locus is properly designated Nia1
NMA - alternative name for NIMA-related kinase. Since these genes are now designated CNK, NMA could potentially be used for something else.
NMT - used in annotation for an N-terminal myristoyl transferase. MYR or MYT might be better
NP, np - non-phototactic or negatively phototactic
NPH - nephrocystin
npq - xanthophyll mutants, altered photochemical quenching
NPSN - a family of Qb-SNARE proteins; hasn't been used systematically as a gene name in Chlamy yet
NR, nr, nr-u - neamine resistant
NRAMP - used for NRAMP metal ion transporters; a 3-letter root would be preferable
NRG - NRG1 was used as a gene designation for a putative gag protein; NRG2 has also been reported, but no protein product was given
NRT - nitrate transport protein
NSF - N-ethylmaleimide sensitive fusion protein
NTR - NADPH-dependent thioredoxin reductase; also see TRR
NUK - NADH:ubiquinone oxidoreductase
NUO - NADH:ubiquinone oxidoreductase (mitochondrial Complex I)
NUP - nucleoporin
----- -O-
OASTL - O-acetylserine(thiol)lyase; should be simplified to a 3-letter root
OAT - ornithine aminotransferase
ODA, oda - outer dynein arms
ODC - ornithine decarboxylase
OEE - oxygen-evolving enhancer protein; the Oee proteins are products of the PSBO, PSBP and PSBQ genes
OEP80 - similar to chloroplast outer envelope protein Oep80. OEP hasn't been used generally as a gene root in C. reinhardtii yet, but could be if needed
OFD - used in annotation for a flagellar protein similar to mammalian oral-facial-digital 1
OGT - O-linked N-acetylglucosamine transferase
OMT - oxoglutarate/malate translocator
ORC - origin recognition complex
ORY, ory - oryzalin resistant
osm - requires hyperosmotic medium for growth
OSM6 - named for a C. elegans protein; in Chlamy this is intraflagellar transport particle protein 52 or IFT52 gene, also known as the BLD1 locus
OTC - ornithine carbamoyltransferase; ARG4 is the equivalent C. reinhardtii locus
OXA - see ALB3
----- -P-
PAA - phospholipase A2 activating protein
PAB, pab - two mapped loci for mutants requiring p-amino benzoic acid; NOT the beta subunit of the 20S proteasome, for which we are using the root PSMB
PABP - RNA-binding protein RB47
PACRG - parkin co-regulated gene homolog; appears in the basal body proteome as BUG21
PAF - polyadenylation specificity factor; also appears as CPSF and PASF
PAL - phenylalanine ammonia lyase
PAO - pheophorbide a oxygenase
PAP - lipid phosphate phosphatase
PASF - see PAF
PBG - porphobilinogen deaminase; HEM3 is alternative
PBT - used to designate several mapped molecular markers
PC - protochlorophyllide reductase; gene PorA
PCMA - a molecular marker
PCK - phosphoenolpyruvate carboxykinase
PCN - proliferating cell nuclear antigen homolog
PCS - phytochelatin synthase
PCY, pcy - plastocyanin; PETE is the preferred name for this gene
PCYA - phycocyanobilin:ferredoxin oxidoreductase
PD, pd - phosphatase deficient
PDE - cyclic nucleotide phosphodiesterase
PDF - peptide deformylase
PDH - pyruvate dehydrogenase
PDI - protein disulfide isomerase
PDR, pdr - pleiotropic drug resistance, a genetic locus whose product has not yet been identified
PDK - pyruvate dehydrogenase kinase
PDS - phytoene desaturase
PDX - peroxiredoxin; also see PRX and TPX
PER, per - altered circadian rhythm
PET, pet - genes involved in the photosynthetic cytochrome b6/f complex; PET indicates nuclear-encoded, pet chloroplast-encoded genes
PEX - peroxisomal biogenesis protein
PF, pf - paralyzed flagella
PFL - pyruvate formate lyase
PFD - prefoldin
PFK - phosphofructokinase
PFP - pyrophosphate fructose-6-phosphate 1-phosphotransferase
PFR - pyruvate ferredoxin oxidoreductase
pg, pgr - pale green; see also CBN
PGH - enolase (phosphoenolpyruvate hydratase)
PGI - phosphoglucose isomerase (glucose-6-phosphate isomerase)
PGK - phosphoglycerate kinase
PGLS - phosphogluconolactonase; should we simplify this to PGL?
PGM - phosphoglycerate mutase
PGP - phosphoglycolate phosphatase
PGR - a thylakoid membrane protein for which there is an Arabidopsis mutant called pgr5
PGYRP - acronym for 'proline-, glycine-, and tyrosine-rich protein'. We need a simpler gene name.
pho - phosphatase deficient
PHOA, PHOD, PHOX - alkaline phosphatase, by analogy to bacterial genes. Perhaps we should replace these with a numbered series with the PHO root.
PHOT - used as a locus name for phototropin, a blue light receptor protein
PHR, phr - photoreactivation deficient; photolyase genes
PIC - cystatin
PIN - peptidylprolyl isomerase, parvulin type
PIS - phosphatidylinositol synthase
PKA - protein kinase A
PKC - protein kinase C
PKG - cGMP-dependent protein kinase
PKHD - used in annotation for the gene encoding a fibrocystin-like protein, by similarity to human "polycystic kidney and hepatic disease" protein
PKS - polyketide synthase
PLA - phospholipase A
PLC - phospholipase C
PLP - plastid lumenal peptide
PMA - plasma membrane-type proton ATPase
PMAST - mastigoneme protein gene; use MST instead
PMP, pmp - defective inorganic carbon transport
PMH - plasma membrane H+-transporting ATPase
PNP - polynucleotide phosphorylase
POL - DNA polymerase; there are several 4-letter subcategories including POLA, POLD, POLE etc.
POR, PORA - NADPH:protochlorophyllide oxidoreducta; see also PC
PP - protein phosphatase
PPA - inorganic pyrophosphatase; has also been used for protein phosphatases
PPCK - phosphoenolpyruvate carboxykinase
PPDK - pyruvate, phosphate dikinase
PPE - pentose-5-phosphate 3-epimerase
PPMT - magnesium protoporphyrin methyltransferase; CHLM is an alternative
PPO - protoporphyrinogen oxidase
ppr - gene name for mutants with defective photophobic response
PPR, PPRC - used in annotation for proteins containing PPR repeats
PPT - phosphate/phosphoenolpyruvate translocator
PPX - protoporphyrinogen oxidase
pr, PR - paromomycin resistant mutant and its corresponding mapped locus; gene product not yet identified
PRA - prenylated Rab acceptor
PRAB - name used for a molecular marker on linkage group V
PRF - peptide chain release factor
PRIS - prismane protein
PRK - phosphoribulokinase
PRL - used in genome annotation for a series of genes whose products are similar to plant pathogenesis-related proteins; PRY has also been used for such proteins
PRO - enzymes of proline biosynthesis; in particular, PROB has been used in annotation for genes encoding glutamate 5-kinase
PRP - proline-rich protein; however, see also PRPL and PRPS
PRPL - plastid ribosomal protein, large subunit; preferable to RPL, in order to avoid confusion with cytosolic ribosomal proteins
PRPS - plastid ribosomal protein, small subunit; preferable to RPS, in order to avoid confusion with cytosolic ribosomal proteins
PRX - peroxiredoxin; PDX is an alternative. See also TPX
PRY - see PRL
PSA, psa, PSB, psb, etc. - nuclear and chloroplast loci respectively for genes encoding components of the photosystem I (A) and II (B) reaction centers
PSD - phosphatidylserine decarboxylase
PSI - pseudouridine synthase
PSM - multicatalytic endopeptidase (20S proteasome); PSMA is the root for proteins of the alpha subunit, PSMB for those of the beta subunit
PSR - phosphate starvation regulator
PSRP - plastid-specific ribosomal protein; see also PRPL and PRPS
PSY - phytoene synthase
PTA, PTB - phosphate transporters
ptm - mutants affecting phototaxis and motility
PTOX - quinol-to-oxygen oxidoreductase
PTP - protein tyrosine phosphatase
PTX, ptx - mutants with altered phototaxis and their corresponding loci
PUR - enzymes of purine metabolism, in particular PURA for the gene encoding adenylosuccinate synthetase
PYB - aspartate carbamoyltransferase
PYC - pyruvate carboxylase
PYK - pyruvate kinase
PYR, pyr - as a mutant and mapped locus, pyrathiamine resistant; also used in annotation for genes encoding enzymes of pyrimidine biosynthesis
----- -Q-
QCR - ubiquinol-cytochrome c oxidoreductase
----- -R-
RAA - genes involved in expression of the chloroplast psaA gene, e.g. RAA1, RAA2; see below
RAB - Ras small GTPase, Rab type; many subfamilies
RACK - "Receptor of activated protein kinase C" a component of 40S small ribosomal subunit; also see G protein beta subunit, GBLP
RAD - DNA repair proteins
RAE - mRNA export protein
RAN - GTPase, Ran type; RANBP has been used for RAN binding protein
RAP - ribosome-associated protein
RBCS - small subunit of ribulose bisphosphate carboxylase (nuclear)
rbcL, rcl - large subunit of ribulose bisphosphate carboxylase (chloroplast)
RBD - rubredoxin
RBL - alternative name for the gene encoding roadblock protein; see RDB
RBO - respiratory burst oxidase
RBP - RNA polymerase II
RBX - ring-box protein
RCA - Rubisco activase
RDB - roadblock protein
RDP - rhodanese domain phosphatase
RECA - recombination protein RecA
REGA - homolog of the Volvox somatic regenerator
RER - ER retrieval protein
RET - manganese transport protein; MNT is alternative
REX - DNA repair protein
RFC - replication factor C
RGN, rgn - "rogaine", a suppresor of bld2 mutants
RHP - Rhesus proteins, CO2 gas channel proteins
RIB - ribbon protein: RIB43a is a flagellar protofilament ribbon protein, RIB72 an axonemal protein.
RIBP1 was previously used for the gene for the 60S ribosomal protein P1, but RPP is now preferred
RME - receptor mediated endocytosis protein
RNB - RNase II RNA-binding protein
RNC - used in annotation for an RNAse III-like protein
RNP - small nucleolar ribonucleoprotein
RNT - "regulator of nonsense transcripts" protein
RPA - DNA-directed RNA polymerase I, subunit A; also described in annotation as replication factor-A protein
RPB - DNA-directed RNA polymerase II
RPE - ribulose-5-phosphate 3-epimerase or pentose phosphate epimerase
rpo - chloroplast-encoded RNA polymerase subunits
RPO - DNA-directed RNA polymerase; RPO has primarily been used for the chloroplast RNA polymerase components, but these annotations need to be reviewed carefully for consistency. Also see RPA and RPB.
RPL, RPS - ribosomal proteins; RPL and RPS following by a number denote the 60S and 40S proteins of the cytosolic ribosome. Lower case rpl and rps have traditionally been used to name chloroplast genes encoding chloroplast ribosomal proteins. Nuclear genes encoding plastid ribosomal proteins are now being designated PRPL and PRPS for proteins of the large and small subunits, respectively. Similarly, genes encoding mitochondrial ribosomal proteins are now MRPL and MRPS. (The mitochondrial genome in C. reinhardtii encodes no ribosomal proteins.)
RPN - 26S proteasome regulatory complex
RPP - RPP0, RPP1 and RPP3 are genes encoding the P0, P1 and P2 proteins of the 60S ribosomal protein.
RPPK - ribose-phosphate pyrophosphokinase
RPS - 40S ribosomal proteins; see RPL
RPT - has been used both for a subset of 26S proteasome regulatory complex proteins and for a raptor homolog protein; resolution of this conflict is needed
RRA - ribonuclease activity regulator
RRN - ribosomal RNAs
RRP - ribosomal RNA processing protein
rsn - radiation sensitive mutants
RSP - radial spoke protein
RUB - rubredoxin
RUV - DNA helicase
RTE - retrotransposable element
RWP - RWPxRK type transcription factor
----- -S-
S926 - a mapped locus on linkage group XIX, corresponding to flagellar protein Fap131
SAC, sac - sulfur deprivation response
SAD - sexual adhesion defective
SAG - sexual agglutination defective
SAH - S-adenosyl-L-homocysteine hydrolase
SAMS - S-adenosyl methionine synthetase; SAS is an alternative
SAR - Sar-type GTPase, COP-II complex
SAS - S-adenosyl methionine synthetase
SAT - serine acetyl transferase
SBDP - selenium binding protein; a 3-letter root would be better
SBP - sedoheptulose-1,7-bisphosphatase
SC5D - a specific sterol desaturase; SUR has also been used as the root name for this gene family, as well as for surfeit1 protein, which is unrelated
SCL - has been used for selenocysteine lyase and also for succinate-CoA ligase; this needs to be resolved
SCO - cytochrome c oxidase assembly factor
SDC - serine decarboxylase
SDH - succinate dehydrogenase, mitochondrial
sd-u - streptomycin dependent (chloroplast mutations)
SEC - protein transport protein; more specifically a large group of translocases, components of COP-II and other complexes
SEL - selenoproteins; SelK1, SelM1 and SelM2, and SelW1 have been identified to date. SEL has also been used in annotation of some proteins similar to ones sequenced from the cyanobacterium Synechococcus elongatus; this is not a good use of this root.
SER - serpin, an inhibitor of serine-type protease
SET - used in annotation for proteins, especially histone methyltransferases, containing SET domains; nomenclature is disorganized, with some annotators using letters - SETa, SETh, etc. - and others using numbers
SFA - SF-assemblin
SFU - sexual fusion defective
SFT - used in one annotation for "SNARE protein, SFT1-like"; there are other SNARE proteins with totally different gene names.
SGA - used in ChromDB for silencing group A protein, so we should keep this usage; within the Chlamy context, SGA has also been used for serine glyoxylate aminotransferase, which should be given a different name
SHF, shf - mutants with short flagella
SHMT - serine hydroxymethyltransferase
SHY - alternative name for surfeit1 protein; see SUR
SIG - sigma factor associated with chloroplast RNA polymerase; RPOD is an alternative gene name
sim - nuclear mutant that suppresses initiation codon defects in chloroplast genes
SIR - sulfite reductase
SKP - see UBL; SKP1 was used in annotation for ubiquitin ligase E3, which is also known as SKP1 in other organisms.
SKS - sexual signalling kinase
SLY - SM/Sec1 family protein
SMC - condensin complex subunit
SMP - a class of small nuclear ribonucleoproteins
SMR - sulfmeturon methyl resistant
SMT - used in annotation both for ubiquitin-like protein SMT1 and for sterol-C24-methyltransferase
SNAP - SNAP adaptor protein
SNF - used in annotation for an ESCRT-III complex component; also see VPS
SNT - histone deacetylase complex, SIN3 component; used in ChromDB so should be kept in Chlamy annotation
SOC - solute carrier protein
SOD - superoxide dismutase; also see MSD as an alternative for the manganese enzyme family
SOUL - heme-binding protein
SOX - sulfite oxidase
SPF - suppressors of pf mutations; presumably these loci will receive other names as their gene products are identified
SPL - splicing factor
SPO - meiosis-specific topoisomerase
SPP - signal peptide peptidase
SPPS - solanesyl diphosphate synthase (polyprenyl diphosphate synthase)
SPR, spr - spectinomycin resistant; one nuclear gene locus, and several mutations in chloroplast 16S rRNA
SPS - spermine synthase
SPT - serine palmitoyltransferase
SQD - sulfolipid biosynthetic pathway; SQD1 is UDP-sulfoquinovose synthase, SQD2 is sulfolipid synthase
SQE - squalene epoxidase
SQS - squalene synthase
SR, sr, sr-u - streptomycin resistant
SRK - serine/threonine protein kinase; also see MUT
SRP - signal recognition particle
SRT - histone deacetylase, SIR2 family; used in ChromDB
SRX - cysteine sulfinic acid reductase
SSD - sterol sensing domain protein
ST, STA, STB - genes involved in starch metabolism
STL - protein kinase Stl
SUC - two loci identified by mutants che that show no chemotactic response to sucrose
SULP - sulfate transport system permease
SUN - a suppressor of uni mutations
SYN - syntaxin
STT - STT7 is a chloroplast protein kinase required state transition; a mutant has been isolated
SUF - genes involved in biogenesis of the chloroplast FeS cluster; have been named in annotation according to the cyanobacterial system
SULP - sulfate transport system permease
SULTR - sulfate transporter
SUOX - sulfite oxidase; SOX is preferred
SUR - used in annotation both for sterol desaturase and for surfeit1 protein
SUV - mitochondrial DNA/RNA helicase, similar to yeast SUV3
SYP - syntaxin
----- -T-
TAA, TAC, TAJ - reserved for nuclear genes involved in expression of chloroplast psagenes (see below)
TAB - required for translation of psaB (see below); TAB2 encodes a chloroplast RNA-binding protein
TAL - transaldolase
TBA, TBB, TBC, TBD, TBE, TBF, TBH, TBI, TBJ, TBK, TBL, TBN, TBT, TBZ - reserved for nuclear genes involved in expression of chloroplast psb genes (see below)
TBC - required for translation of psbC (see below)
TBG - alternate name for gamma tubulin; TUG is preferred
TBY - -tubby-like protein
TCA, TCB, TCD, TCG, TCL - required for translation of chloroplast pet genes
TCR - used for a series of molecular markers
TCTEX - Tctex proteins
TDA, TDB, TDE, TDF, TDH, TDI - reserved for nuclear genes involved in expression of chloroplast atp genes (see below)
TEK - tektin
TGD - used in annotation of a lipid transfer protein, based on similarity to plants, but probably not a good choice since it seems to have more than one meaning even within higher plants: tri-galactosyl diacyl glycerol, or dTDP-glucose 4,6-dehydratase
THI, thi - thiamine-requiring
thm - altered thylakoid membrane protein; two mutants, no mapped loci
TIC - chloroplast inner membrane translocation protein
TIG - trigger factor, involved in protein folding
TIM - mitochondrial import inner membrane translocase
TIP - as a locus/mutant name, thylakoid insertion protein; also used once in genome annotation for a translational inhibitor protein
TLA - chlorophyll antenna size regulatory protein
TNR, tnr - a temperature-conditional flagellar assembly mutant
TOC - used first as the name for a Chlamydomonas transposon; more recently used in genome annotation for a group of chloroplast outer envelope proteins
TOM - mitochondrial import receptor subunit
TOP - DNA topoisomerase and gyrase proteins
TPX - thioredoxin peroxidase
TPI - triose phosphate isomerase
TPP, TPPB - trehalose-6-phosphate phosphatase
TPR - proteins containing TPR repeats
TPX - alternative name for peroxiredoxin
TRK, trk - mutants with altered potassium transport; KDP is synonymous
TRN - transportin
TRP - TRP ion channel protein
TRR - alternate name for thioredoxin reductase; TXR is probably better. NTR has been used for NADPH-dependent thioredoxin reductase
TRS - transport protein particle (TRAPP)
TRX - thioredoxin; separated into families TRXH, TRXM, etc.
TS - temperature-sensitive, usually referring to growth or cell division
TSA - tryptophan synthase, alpha chain
TSB - tryptophan synthase beta subunit
TSF, tsf - historical use for temperature-conditional flagellar assembly, not a gene name
TSP, tsp - thiostrepton resistant mutant; probably an alteration in chloroplast ribosomal protein L11
TSR - two-component hybrid sensor and regulator
TUA - alpha tubulin
TUB - beta tubulin
TUD - delta tubulin
TUE - epsilon tubulin
tufA - chloroplast elongation factor EF-Tu (chloroplast-encoded)
TUG - gamma tubulin
TUH - eta tubulin
TUN, tun - tunicamycin-resistant mutant
TWF - used for a series of fluoroacetate-resistant mutants; re-use as a phenotypic name could cause confusion
TWI - a protein similar to that encoded by the D. rerio cystic kidney disease gene twister
TXR - thioredoxin reductase; also see TRR and NTR
----- -U-
UBC - ubiquitin-conjugating enzyme
UBI - ubiquitin extension protein
UBL - ubiquitin ligase; also see SKP
UCH - ubiquitin carboxyl-terminal hydrolase
UCP - mitochondrial uncoupling protein
UGD - UDP-glucose dehydrogenase
UGE - UDP glucose epimerase
UGS - soluble starch synthase
UGT - UDP-galactose transporter
UMT - alternative name for uroporphyrinogen III methylase; see HEMD
UNC119 - used in annotation for a signal transduction protein similar to C. elegans UNC119
UNI, uni - uniflagellate; uni3 is a mutation in the gene encoding delta tubulin
UOX - urate oxidase
UPD - uroporphyrinogen decarboxylase; also see HEME
UPS - uroporphyrinogen III synthase; also see HEMD
UROD - see UPD
UVR, uvr - UV-resistant
UVS, uvs - UV-sensitive
----- -V-
VAMP - VAMP7 type R-SNARE proteins; perhaps VMP would be a suitable gene root name for Chlamy?
VFL, vfl - mutants with variable numbers of flagella
VIP - vesicle-inducing protein
VPP - proton-translocating inorganic pyrophosphatase
VPS - a large group of vacuolar assembly and transport proteins, and components of retromer coat complex and ESCRT complexes.
VSP - series of cell wall structural proteins
VSR - vacuolar sorting receptor
VTC - vacuolar transport chaperone
VTE - vitamin E biosynthesis pathway; four genes have been annotated to date in the Chlamy genome
VTI - a family of vesicle transport proteins
----- -W-
W, w - a mutant that is white in the dark, subsequently found to be an allele at the LTS1 locus
WD40 - used in annotation for proteins containing WD40 repeats; presumably these will be given more specific enzyme names eventually
WEE - WEE1 is a cyclin dependent kinase with homologs in many organisms, including Chlamy
----- -X-
XAB - XAB2 has been used in annotation for a transcription-coupled DNA repair protein
XBP - used in annotation for a protein similar to fructose- and sedoheptulose 1,6-bisphosphatases
XDH - xanthine dehydrogenase
XRN - exoribonuclease
XUV - xanthine / uracil / vitamin C permease
----- -Y-
Y, y - yellow in the dark; several loci, which will be given specific gene names as their products are identified
YEL, yel - yellow in the dark; same phenotype as Y, but Y has historically been used to designate mapped loci
YPT - GTP binding proteins
----- -Z-
ZDS - zeta-carotene desaturase
ZEP - zeaxanthin epoxidase
ZIP - zinc transporter
ZRT - zinc transporter, alternative name; see ZIP
ZSP - zygote-specific hydroxyproline-rich or lectin-like proteins
ZYA, ZYB - used to designate some molecular markers
ZYMC - see ZYS; ZYMC16 has been used for a zygote-specific gene in C. reinhardtii; ZYM has been used in Chlamydomonas monoica for a series of mutants blocked in zygote formation and/or maturation
ZYS, zys - zygote-specific proteins
-----
Loci, Alleles, and Genes - some historical distinctions
A locus is a mappable entity. While many
loci are also genes, molecular markers such as RFLPs can also qualify as
loci. An allele is a genetic variant form
of a locus. The preferred system now is to use a three-letter name plus
a number, in upper case for the locus name and in lower case for the allele
name, followed by a hyphen and a second number to denote different alleles
at the same locus. Some older two-letter locus designations and some other
non-standard names have been preserved for historical reasons. As annotation progresses, many previously described loci are becoming identified as genes, and names may therefore be changed to conform with conventions in other organisms. The lists below give the traditional names for mapped loci in C. reinhardtii.
For example, the ADF1 locus has alleles adf1-1, adf1-2, adf1-3,
etc. The gene represented by this locus might be named ADF1, or
might receive a name that corresponds to a homologous protein in another
organism.
Sometimes names for loci describe the phenotypes of mutants at those
loci (e.g. ERY = erythromycin resistant, MBO = move backwards
only, UNI = uniflagellate). In cases where the gene has been identified
first and then mapped, the locus name is usually based on the gene or
gene product name (e.g. ARS, arylsulfatase; COP, chlamyopsin;
DHC, dynein heavy chain). Where the locus was first identified
based on a mutation, identity of the gene affected may be achieved only
years later, and the gene name may therefore have no obvious relationship
to the locus name.
Although loci and alleles are named by conventions specific to Chlamydomonas,
we try wherever possible to follow the conventions for genes and gene
products specified by the Commission
on Plant Gene Nomenclature . However, sometimes a gene is identified
in Chlamydomonas that hasn't been covered by the CPGN, or that hasn't
been found in land plants. In those cases, a provisional gene name is
created based on similarity to yeast, mammals, Drosophila, Caenorhabditis,
or bacteria, as seems appropriate for the particular instance.
Note on nuclear genes involved in expression of chloroplast genes (thanks to Olivier Vallon for this concise summary):
first letter is M for mRNA processing/stability, T for translation, C for cofactor assembly
second letter is A for psa genes, B for psb genes, C for pet genes, D for atp genes
third letter is for the last letter in the target gene name: A for psaA, psbA, petA or atpA, etc...
followed by a figure.
Example: TCA1 codes for a factor involved in translation of petA
Exceptions: CCS is used instead of CCA for factors involved in formation of holo-cytochrome f. RAA rather than MAA is used for genes affecting processing/stability of the psaA mRNA; MAA has been used for methylanthranilic acid resistance.
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