A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\bcd

General Information
SymbolDmel\bcdSpeciesD. melanogaster
NamebicoidAnnotation symbolCG1034
Feature typeprotein_coding_geneFlyBase IDFBgn0000166
Created / Updated2003-12-01/2008-06-23
Genomic Location
Chromosome (arm)3RRecombination map3-48
Cytogenetic map84A5-84A5Sequence location3R:2,581,564..2,585,199 [-]
Map ( GBrowse ) detailed view
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Automatically generated summary

See sections below for more information
The gene bicoid is referred to in FlyBase by the symbol bcd (CG1034, FBgn0000166). It has the cytological map location 84A5. Its sequence location is 3R:2581564..2585199. Its molecular function is described as: specific RNA polymerase II transcription factor activity; morphogen activity; protein binding; translation regulator activity; sequence-specific DNA binding; transcription factor activity. It is involved in the biological processes: anterior region determination; segment polarity determination; determination of anterior/posterior axis, embryo; regulation of transcription, DNA-dependent; maternal determination of anterior/posterior axis, embryo; regulation of transcription from RNA polymerase II promoter; anterior/posterior axis specification; negative regulation of translation; oogenesis; regulation of translation. 413 alleles are reported. The phenotypes of these alleles are annotated with 61 unique terms, many of which group under: embryonic abdomen; embryonic segment; organ system; abdominal ventral denticle belt; cephalopharyngeal skeleton; thoracic segment; larval abdominal segment; embryonic tagma; spiracle; embryonic head. It has 5 annotated transcripts and 5 annotated polypeptides.

External Summaries
hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
bcd: bicoid
Maternal-effect lethal mutations showing defective head and thorax development. Females homozygous for strong alleles produce embryos in which head and thorax are replaced by duplicated telson, including anal plates, tuft, spiracles, and filzkorper; however, no pole cells formed at the anterior end. Deletions and fusions of anterior abdominal segments and occasionally anterior abdominal segments in reversed polarity are also observed. Strong alleles amorphic based on phenotypic similarities of embryos produced by homozygous and hemizygous females. Weak alleles result in pattern defects in heads of embryos; lack only labral derivatives (median tooth, dorsal bridge); intermediate weak genotypes produce reduced head but retain normal thoracic development; intermediate strong produce further reduction of head, deletion of second and third and reduction of first thoracic dentical belts; thoracic segments fused. Partial rescue of embryonic phenotype effected by injection of cytoplasm (5% of volume) from the anterior ends of unfertilized wild-type eggs into the anterior pole of newly fertilized eggs of bcd mothers; injection into ectopic sites stimulates differentiation of anterior structures at site of injection; efficiency proportional to number of bcd+ alleles carried by cytoplasm donor. Phenocopies result from leakage of 5% of egg volume from anterior perforation of normal embryos. The distance of the head fold at gastrulation is proportional to the number of bcd+ alleles in the maternal genotype. bcd mRNA appears as a flattened disc plastered to the anterior extremity of early embryos; by the time of pole cell migration it has become localized to the clear cytoplasm at the periphery, forming a cap over the anterior end of the egg and is distributed in a steeply decreasing gradient such that 90% of the RNA is in the anterior 18% of egg length; by nuclear cycle 14 the RNA begins to disappear and becomes undetectable by midway through cellularization. bcd protein on the other hand forms a shallower gradient in which 57% of protein is in the anterior 18% of egg length, and the gradient doesn't reach baseline until the posterior 30% of egg length; the gradient forms from two to four hours after oviposition in both fertilized and unfertilized eggs, and except during mitosis is concentrated in nuclei; diffusion postulated to account for the establishment of the protein gradient following translation from anteriorly anchored RNA. Protein levels decrease during cellularization, although some nuclear staining persists until the end of germ-band elongation. bcd transcript first detectable in the ovaries of bcd females; forms a ring around the anterior margin of the developing oocyte in stages 5 and 6; in stages 9 and 10 nurse-cell accumulation observed to be localized toward the periphery of the cyst; by stage 12 the nurse cells have emptied their contents into the oocyte and the bcd transcript appears as an anterior cap (St. Johnston, Driever, Berleth, Richstein, and Nusslein-Volhard, 1989, Development Supplement: 13-19). No evidence of translation of bcd protein during oogenesis. Formation of the bcd gradient is regulated by three maternally active genes exu, sww, and stau; exu appears necessary for nurse cell accumulation; sww is required for anterior localization of bcd mRNA in the oocyte; and stau appears to be involved in RNA localization in the embryo. A defect in any of these functions results in little or no gradient of bcd activity. bcd in turn appears to control the activity of anterior gene activity; specifically the anterior pattern of hb expression is not observed and is replaced by a mirror-image posterior hb stripe in bcd- embryos (Tautz, 1988, Nature 332: 281-84; Schroder, Tautz, Seifertz, and Jackle, 1988, EMBO J. 7: 2881-87).
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
84A5-84A5  
Limits computationally determined from genome sequence between P{PZ}pb04498 and P{lacW}l(3)L2100L2100  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
84A1-84A1
(determined by in situ hybridisation)  
84A-84A
(determined by in situ hybridisation)  
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
In direction of increasing cytology: bcd- anon-84Aa+
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\bcd for information on other features
detailed view FBtr0081670 FBtr0081669 FBtr0290294 FBtr0081666 FBtr0081668 FBtr0081665 FBtr0081667 FBtr0081664 FBpp0081170 FBpp0288733 FBpp0081169 FBpp0081166 FBpp0081167 FBpp0081164 FBpp0081165 FBpp0081168
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
FBtr0081664
  1490
  149
FBtr0081665
  2510
  489
FBtr0081666
  2547
  418
FBtr0081667
  2532
  413
FBtr0081668
  2525
  494
Additional Transcript Data & Comments
Reported size (kB)
2.4 (unknown)
2.6, 1.6 (northern blot, sequence analsyis)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
bcd-PA  
FBpp0081164  
16.4  
149  
7.29  
bcd-PD  
FBpp0081165  
54.0  
489  
7.42  
bcd-PE  
FBpp0081166  
45.4  
418  
7.15  
bcd-PF  
FBpp0081167  
44.9  
413  
7.31  
bcd-PG  
FBpp0081168  
54.5  
494  
7.31  
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
The author compared the sequences of several Drosophila melanogater genes and one human gene with consensus RNA Recognition Motifs (RRM) to bcd protein sequence and identified a putative RRM.
bcd protein is translated from in vitro transcribed bcd mRNA in wheat germ extract and rabit reticulocyte lysate and is expressed in Drosophila Scheider cells to yeild a 58 kD protein. Exchange of the bcd 5\\'\\' UTR for Xenopus beta-globin 5\\'\\' UTR yeilds higher protein levels in these translation systems.
One of several products generated by alternative splicing.
bcd protein regulates the expression of cad through translational repression by binding to the cad 3\\'\\'UTR at specific "bicoid binding regions" (BBR). Expression pattern analysis, UV crosslink assays and Schnieder cell co-transfection assays all conclude that the homeodomain of bcd protein is necessary and suffiecient for binding to the BBR of cad transcripts. bcd protein will supress translation of "BBR-containing"mRNAs.
Antibodies recognize a doublet of proteins of 55kD and 57kD. The appearance of two bands is thought to be due to posttranslational modification because the 5aa difference between the two bcd proteins is not enough to account for the 2-3kD size difference.
Both the cad protein gradient and the hb transcript expression pattern are dependant upon the homeodomain and the PEST domain of bcd protein. Deletions and mutations of PEST sequences in the bcd coding region resulted in an inability to repress cad expression in the anterior region of the embryo. Similar deltions result is a loss of hb expression between 20 and 50% egg length in the anterior expression domain. Thus, the deletional analysis of bcd protein domains shows that the domain that is required for translational represssion of cad is also required for transcriptional activation of hb.
The bcd protein was expressed and purified from embryos, Drosophila Schneider cells, and E. coli. The bcd protein produced by embryos and Schneider cells was 58kD, while the protein from E. coli was 53kD,indicating that the protein produced in Drosophila was highly phosphorylated. Indeed, when bcd protein isolated from Drosophila embryos or cells was incubated with phosphatase prior to elecrtophoresis, the protein was resolved at 53kD.
Both the cad protein gradient and the hb transcript expression pattern are dependant upon the homeodomain and the PEST domain of bcd protein. Deletions and mutations of PEST sequences in the bcd coding region resulted in an inability to repress cad expression in the anterior region of the embryo. Similar deltions result is a loss of hb expression between 20 and 50% egg length in the anterior expression domain. Thus, the deletional analysis of bcd protein domains shows that the domain that is required for translational represssion of cad is also required for transcriptional activation of hb.
bcd protein is expressed in yeast under the control of βestradiol in order to control the amount of bcd protein produced. Cooperative binding to bcd response regions on various lacZ reporter constructs was studied with transcription assays, in vitro gel shift assays and foot print analysis. The bcd responsive region of kni was used both in vitro and in vivo to ascertain the strength of bcd binding sites.
CAT assays with bcd protein expressed in Schneider cells show that bcd activates a promoter containing three copies of a bcd consensus sequence. Through studies both in vivo and in vitro it has been shown that the activation of transcription due to bcd is dependant upon the phosphorylation state of bcd protein. Phosphorylated bcd will not activate transcription, and the phosphorylation of bcd is dependant upon tor and phl.
The expression pattern of genes downstream of bcd were analysed after egg ligation at various egg lengths. It was observed that the bcd protein gradient, as well as the cad protein gradient were blocked by egg ligation, and thus, the expression of downstream gap genes were altered. The authors suggest that alteration of the bcd protein gradient, alters the hb expression profile and in turn, through regulation by hb, Kr and kni expression domains are altered, consequently altering the domains of pair-rule gene expression.
bcd protein binds to the BRE (bcd response element) of the cad 3\\'\\'UTR. Binding of bcd protein to cad transcript facilitates proper cad localization, presumably due to translational repression of cad by bcd.
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
Homeobox (IPR001356)
Homeodomain-like (IPR009057)
Homeodomain-related (IPR012287)
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
  • T00063
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    complex substitution
    comment=A deletion of 169 bases and insertion of the bases TA. The net result is that bcd amino acids 156-494 are replaced by 55 out-of-frame amino acids.
    evidence=experimental
    deletion
    comment=A deletion which removes the first 53 amino acids including the PRD domain. Exact boundaries including the location of the 5' end of the deletion unspecified in FBrf0049337.
    evidence=experimental
    deletion
    comment=Approximate location of bcd[7] deletion. bcd[7] is a small deletion of approximately 260bp. The 3' end of deletion was determined by SI nuclease mapping. The size of the deletion was determined by genomic southern analysis of HindIII digests.
    evidence=experimental
    linked_to=HindIII-HindIII_rfrag
    deletion
    comment=In-frame deletion of amino acids 125-135.
    evidence=experimental
    point mutation
    evidence=experimental
    na_change=C2584016T
    pr_change=L122F|bcd-PD,L51F|bcd-PE,L46F|bcd-PF,L127F|bcd -PG
    reported_na_change=C2393T
    reported_pr_change=L127F
    point mutation
    evidence=experimental
    na_change=C2584003T
    pr_change=S126L|bcd-PD,S55L|bcd-PE,S50L|bcd-PF,S131L|bcd -PG
    reported_na_change=C2406T
    reported_pr_change=S131L
    point mutation
    evidence=experimental
    na_change=C2583923T
    pr_change=Q153|bcd-PD,Q82|bcd-PE,Q77|bcd-PF,Q158|bcd -PG
    reported_na_change=C2486T
    reported_pr_change=Q158@
    point mutation
    evidence=experimental
    na_change=C2583845T
    pr_change=Q179|bcd-PD,Q108|bcd-PE,Q103|bcd-PF,Q184|b cd-PG
    reported_na_change=C2564T
    reported_pr_change=Q184@
    point mutation
    evidence=experimental
    na_change=C2583611T
    pr_change=Q257|bcd-PD,Q186|bcd-PE,Q181|bcd-PF,Q262|b cd-PG
    reported_na_change=C2798T
    reported_pr_change=Q262@
    point mutation
    evidence=experimental
    na_change=C2583605T
    pr_change=Q259|bcd-PD,Q188|bcd-PE,Q183|bcd-PF,Q264|b cd-PG
    reported_na_change=C2804T
    reported_pr_change=Q264@
    point mutation
    evidence=experimental
    na_change=T2582525A
    pr_change=L108H|bcd-PA,L448H|bcd-PD,L377H|bcd-PE,L372H|b cd-PF,L453H|bcd-PG
    reported_na_change=T3885A
    reported_pr_change=L453H
    protein binding site
    bcd-protein_bind-5
    3R:2,585,015..2,585,027
    bound_moiety=Sry-deltaXP
    comment=sdbsB
    evidence=experimental
    protein binding site
    bcd-protein_bind-6
    3R:2,584,994..2,585,006
    bound_moiety=Sry-deltaXP
    comment=sdbsA
    evidence=experimental
    protein binding site
    bcd-protein_bind-22
    3R:2,581,738..2,582,217
    bound_moiety=stau-XP
    comment=Region of the bcd 3' UTR required for normal stau protein recruitment.
    evidence=experimental
    protein binding site
    bcd-protein_bind-1
    3R:2,581,894..2,581,946
    bound_moiety=exu-XP
    comment=exu protein binds to the BLE sequence.
    evidence=experimental
    protein binding site
    bcd-protein_bind-2
    3R:2,581,894..2,581,946
    bound_moiety=exl-XP
    comment=exl protein binds to the BLE sequence.
    evidence=experimental
    regulatory region
    bcd-reg_element-1
    3R:2,582,338..2,582,346
    comment=nonamer RNA localization signal
    evidence=experimental
    regulatory region
    bcd-reg_element-2
    3R:2,581,894..2,581,946
    comment=BLE (bicoid localization element) in the bcd mRNA 3'UTR.
    evidence=experimental
    rescue fragment
    comment=Position of restriction fragment on reference sequence inferred by FlyBase curator
    evidence=experimental
    linked_to=EcoRI-EcoRI_rfrag
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data
    Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
     oogenesis stage,adult stage | stage S5-S7
     oocyte | anterior
     oogenesis stage,adult stage
     oogenesis stage,adult stage
     embryonic stage | stage 4
     embryonic stage | stage 4
     embryonic stage | stage 1-2
     oogenesis stage,adult stage
     oocyte | anterior
     oogenesis stage
     oogenesis stage,adult stage
     nurse cell
     embryonic stage | stage 1-2
     oogenesis stage | stage S10
     embryonic stage
     oogenesis stage,adult stage
     oocyte | anterior
     embryonic stage | 0-3.25 hr
     whole organism
     embryonic stage | early
     embryonic stage | stage 3-4
     embryonic stage
     oogenesis stage | stage S10B
     ovary
    (