AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.
Gene model reviewed during 5.49
There is only one protein coding transcript and one polypeptide associated with this gene
586 (aa); 64 (kD predicted)
Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Dfd using the Feature Mapper tool.
The distribution of transcripts appears to be unaffected by mutations in the tsh gene.
During the cellular blastoderm stage, Dfd transcripts are located in a 6-7 cell-wide band at 65-75% egg length which includes parasegment 1. In stages 9,10, before the gnathal buds form, Dfd is expressed in parasegment 1 and the region anterior to it and is found in both ecotodermal and mesodermal cells. By stage 11, Dfd is expressed in the mandibular and maxillary buds. Expression anterior to PS1 has declined and Dfd expression defines parasegment 1. Neural derivatives of PS1 also express Dfd transcripts. The Dfd pattern established by stage 11 persists until hatching. In larvae, transcripts are observed in the eye-antennal disc in the region corresponding to the primordium of the maxillary palp and in the peripodial membrane.
Dfd protein is first detected in cellular blastoderm embryos in a 6 cell wide stripe encircling the embryo. Early in gastrulation, some of these Dfd-expressing cells invaginate to form the cephalic furrow. Before full germ band extension, a differential posterior border of Dfd expression occurs. The lateral expression boundary extends 2-3 cells farther posteriorly than the ventral boundary. The lateral boundary appears to mark the future outlines of the maxillary segment while the ventral expression boundary corresponds to the parasegment 1 boundary. By stage 11, Dfd protein expression is mainly confined to the maxillary and mandibular segments laterally and to parasegments 0 and 1 ventrally. There is also some ventral expression in the hypopharyngeal lobe. As the germ band retracts, only cells in the lateral half of the mandibular segment and at the posterior border of the maxillary segment continue to express Dfd protein. At this stage some Dfd protein is observed on the dorsal surface in one or two rows at the anterior portion of the dorsal ridge.
GBrowse - Visual display of RNA-Seq signalsView Dmel\Dfd in GBrowse 2
Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.
Source for identity of: Dfd CG2189
Dfd maintains the boundary between the maxillary and mandibular head lobes by activating localised apoptosis in the embryo.
In vitro DNA-binding studies reveal pros enhances Dfd regulatory region binding to DNA by more than 10-fold. pros protein modulates the DNA binding activity of Dfd by pros-mediated conformational changes.
Effects of overexpression of ANTP-C genes on tarsal segmentation in ss mutants is studied.
Water activity differentially affects Dfd homeodomain and Ubx homeodomain DNA binding activity: formation of the Ubx HD-DNA complex is associated with significantly greater water release than that of the Dfd HD-DNA complex. No influence of pH in water release was detected for either homeodomain. Chimeric Ubx-Dfd homeodomains demonstrates the C terminal region of the Ubx HD is the primary determinant for the greater water release associated with DNA binding for the protein.
Module E, a 120bp fragment of the Dfd epidermal autoregulatory element, contains a 51bp region, called 5-6, that is required to generate a functional Dfd response element, Dfd RE. Deaf1 acts through Module E in embryos and may function on other Dfd REs also.
A phylogenetic analysis of the Antp-class of homeodomains in nematode, Drosophila, amphioxus, mouse and human indicates that the 13 cognate group genes of this family can be divided into two major groups. Genes that are phylogenetically close are also closely located on the chromosome, suggesting that the colinearity between gene expression and gene arrangement was generated by successive tandem gene duplications and that the gene arrangement has been maintained by some sort of selection.
Transcriptional activity of the N domain of Dfd can be modulated by the acidic and C-tail domains.
It has been previously reported that Scr embryos display partial transformation of the labial segment to a more anterior maxillary identity. This transformation seems unusual because the Dfd protein does not accumulate in the labial cells of an Scr mutant. It is proposed that the putative ectopic maxillary sense organ in Scr mutants may instead be the labial sensory organ which is now visible because of incomplete head involution.
Analysis of Dfd-Ecol\lacZ constructs indicates that the large intron of Dfd contains an enhancer that directs expression in the central nervous system. This 'Neural autoregulatory enhancer' (NAE) requires Dfd protein function for its full activity.
The 1.28 gene is directly activated by Dfd in the maxillary segment but not in the mandibular segment. Four Dfd-product binding sites have been identified within a 664bp fragment of the 1.28 regulatory region, in addition to a Dfd epidermal autoactivation element (DEAE).
ImpE1 and Dfd have been examined for their positions relative to the Broad complex genes in the hormone-regulated pathway of CNS metamorphosis. Dfd mutants manifest a defect in subesophageal ganglion metamorphosis, but expression of Dfd in the CNS is indifferent to 20HE levels.
Systematic characterisation of DNA sequence recognition properties reveals that Antp, Ubx and Dfd protein homeodomain regions binds preferentially to a core sequence which differs from the binding sequence of Abd-B. Antp and Ubx homeodomains display indistinguishable preferences outside the core, while Ubx differs.
Suboesophageal ganglion (SEG) maturation during metamorphosis has a significant postembryonic requirement for Dfd.
The 2.7kb Dfd epidermal autoregulatory element (Dfd EAE) contains multiple modules that can function independently. Module E is a 120bp autoregulatory sequence, in vitro footprinting experiments detect a single Dfd binding site that is likely to be directly bound by Dfd protein in the developing embryo. A nearby block of DNA sequence contains functionally important cofactor binding sites.
trx exerts its effects by positively regulating homeotic gene expression, but Ubx, Antp, abd-A, Abd-B, Scr and Dfd all have different tissue-specific, parasegment-specific and promoter-specific reductions in expression in a trx mutant background.
Dfd is required to activate the 1.28 gene in the maxillary segment, but ectopic expression of Dfd is incapable of activating 1.28 elsewhere.
Dfd and Ba are both persistently expressed in ventral maxillary cells, and combinatorially specify a subsegmental code required for a group of cells to differentiate maxillary cirri. The regulatory effect of Dfd on Ba is mediated by a ventral maxillary-specific enhancer located 3' to the Ba transcription unit.
The homologs of Antp, ftz, Scr, Dfd, Ama, bcd, zen, pb and lab, but not zen2 are all present in D.pseudoobscura.pseudoobscura, in the same linear order and similarly spaced along the chromosome as in D.melanogaster.
Comparative analysis of the homeobox sequences reveals the subdivision of the Antp-type homeobox genes into three classes early in metazoan evolution, one includes Abd-B, the second includes abd-A, Ubx, Antp, Scr, Dfd and ftz, and the third includes zen, zen2, pb and lab.
The Dfd autoregulatory enhancer provides spatio-temporally restricted gene expression in the CNS of mid-gestation mouse embryos. The Dfd autoregulatory feed back loop has been conserved in the vertebrate and arthropod lineages.
Immunoprecipitation and filter elution assays identified a 900 bp autoregulatory element that specifically binds Dfd protein in embryos. Homeodomain exchange experiments demonstrated that the Dfd homeodomain interacts with the Antp transcription unit.
Ectopic expression of Dfd activates Dfd expression in a subset of cells in different segments. These cells belong to the anterior compartments of the three thoracic and A1 to A8 abdominal segments, and the Dfd expression requires wild type wg and en expression. Indeed wg product can activate Dfd in many embryonic cells. Scr, Antp, Ubx and Abd-B repress Dfd both transcriptionally and at the phenotypic level, as does abd-A when supplied at high levels with a heat shock construct.
The effect of ectopic expression of Dfd was investigated on the normal development of sensory organs in the embryonic PNS.
Analysis of Dfd-Ubx chimeric coding regions identifies specific amino acid residues at the amino end of the Ubx homeo domain that are required to specifically regulate Antp transcription. In the context of Dfd protein, these amino-end residues are sufficient to switch from Dfd- to Ubx-like targeting specificity.
Ecol\lacZ reporter gene constructs demonstrate that human Hox4B upstream element can provide expression in a posterior head segment. One possible mechanism that would allow this is the conservation of the Dfd specific autoregulatory circuit in both the arthropod and chordate lineages.
Dfd gene product is not required for salivary gland development, at least up until the cuticle forms.
ae expression is not modulated by Dfd.
The roles of Dfd and lab have been studied through an analysis of their expression patterns in embryonic and imaginal tissues of mutant individuals.
DNA binding assays demonstrate that there is a direct interaction between Dfd protein and the Dfd autoregulatory element.
Deletion analysis of the Dfd autoregulatory element, using a Ecol\lacZ reporter gene, demonstrates that the element contains compartment specific sub-elements similar to those of other homeotic loci.
Ectopic Dfd expression in the eye-antennal disc can disrupt the normal development of the head but has no detectable effect on the thoracic or abdominal segments.
Mutant analysis demonstrates that activation of Dfd is dependent on combinatorial input from at least three levels of early hierarchy.
Dfd- flies have defects in embryonic and larval heads: development of ectopic structures. Temperature shift studies demonstrate Dfd is required during segmentation and head involution, and during late larval and pupal stages.
The substitution of the Abd-B homeodomain for that of Dfd results in a protein that differs from the Dfd protein at only 30 residues so providing a different spectrum of regulatory targets. Dfd expression domain was normal in heat shocked embryos expressing the chimeric gene but transcript levels were low resulting in weak, patchy patterns.
A modification and reduction in en and Dfd protein distribution is seen in mutant cad embryos.
The role of the homeodomain in determining target specificity has been tested by replacing the homeobox of Dfd with that of Ubx. The resulting chimeric protein cannot activate transcription from Dfd but can activate ectopic transcription of Antp, a gene normally regulated by Ubx.
Dfd expression is dependent on pair rule genes and at least two other factors that are differentially distributed along both the anterior posterior and dorsal ventral axis.
The DNA sequences of the homeobox region of 11 Drosophila genes, including Dfd, have been compared.
The Dfd mutant maxillary palp phenotype can be attributed to cell death and subsequent duplication of bristles, but the mandibular and premandibular defects of the embryonic head cannot. Temperature shift experiments demonstrate that Dfd is required throughout the larval and pupal stages.
Null mutations act as recessive lethals. Homozygous or hemizygous animals die at the end of embryogenesis and show a spectrum of defects in the head. There are no discernible defects in the trunk. The head defects are associated with missing structures normally derived from the mandibular and maxillary segments, the dorsal lateral papillae of the maxillary sense organ, the mouth hooks, and the maxillary cirri. The remaining gnathal structures are present albeit disarranged likely due to abnormalities in the movements associated with head involution. A weak homeotic transformation (30-50% penetrance) has also been noted in animals hemizygous for a breakpoint-associated revertant of the single dominant gain-of-function allele (Dfdrv1). The phenotype is an apparent transformation of the H piece and lateral-graten which appear to be replaced by cephalopharyngeal plates. This phenotype has not been observed in any other mutant genotype and the reason for its low-penetrance production by this particular allele is not known. X-ray-induced somatic clones of Dfd- cells have shown that the locus is also required for adult head development. These cells develop normally in the thorax and abdomen but do not form structures in the ventral anterior aspect of the head; specifically the vibrissae and maxillary palps. Clones in the dorsal posterior part of the head form ectopic bristles which have been interpreted as a head to thoracic transformation. A temperature-conditional allele has been used to define two temperature-critical periods for Dfd+ activity. The first is during embryogenesis during segmentation and head involution, while the second occurs in the late third instar larval through mid-pupal stages. These times correlate nicely with the observed cuticular defects in mutant animals and the times of peak gene product accumulation. There is a single dominant gain-of-function allele which causes defects in the ventral aspects of the adult head similar to those seen in the Dfd- head clones mentioned above. There are no defects seen in the posterior of the head nor does this allele cause any embryonic or larval defects as a heterozygote, homozygote, or hemizygote. This allele is associated with a group of roo insertion elements (ca. 50 kb of inserted DNA) as well as a duplication of the 3' exons of the Dfd transcription unit. The mutant causes an extended spatial domain of expression of the locus into the eye portion of the eye-antennal disc as compared to the pattern seen in normal animals. The precise cause-effect relationship between the observed molecular defect and the mutant phenotype is not known except that partial deletion of the roo elements but not the 3' end duplication causes a reversion of the dominant phenotype and has no apparent effect on the wild type function of the resident Dfd gene. This dominant allele has been reverted and these revertants act as a simple recessive loss-of-function alleles with the one exception noted above. The Dfd transcript is initially detected at the blastoderm stage in a band of cells at the position of the future cephalic furrow. This RNA shows maximal accumulation from 6-12 hours of embryogenesis when it is found in the mandibular and maxillary lobes, as well as in the subesophageal region of the CNS. The amount of Dfd RNA diminishes through the first and second larval instars and peaks again during the third instar. At this point, it is found in the peripodial membrane cells of the eye-antennal discs. The cells which accumulate the RNA are those which have been fate mapped to give rise to the adult-head-capsule structures which are defective in Dfd- clones. Antibodies raised to Dfd protein have shown a similar pattern of accumulation to that seen for the RNA. The protein is first detected in cellular blastoderm stage in a stripe of six cells which circumscribes the embryo. As germ-band elongation proceeds and segmentation becomes evident Dfd protein is detected in the mandibular and maxillary lobes and a portion of the dorsal ridge. During germ-band shortening protein is no longer detectable in the mandibular lobe or in the anterior lateral aspect of the maxillary lobe. The process of head involution carries the Dfd-expressing cells interiorly where they are found in portions of the pharynx at the end of embryogenesis. Dfd-positive cells are also found in the subesophageal region of the CNS in the maxillary ganglion. This expression pattern has been shown to be dependent on the prior expression of the gap and pair-rule segmentation genes for its inception and on an autogenous regulatory element upstream of the Dfd transcription initiation site for the maintenance of Dfd expression into the later stages of embryogenesis. Immunostaining of imaginal discs shows Dfd-positive cells in the peripodial membrane of the eye-antennal discs with no detectable accumulation in the disc proper. There are also a few cells in the stalk of the labial discs which appear to accumulate Dfd protein. The Dfd cDNA driven by a heat shock promoter has been returned to flies and used to ectopi