shuttle craft: Biological Overview | Evolutionary Homologs | Developmental Biology | Effects of Mutation | References

Gene name - shuttle craft

Synonyms -

Cytological map position - 35C1--35C1

Function - transcription factor

Keywords - segmentation, CNS

Symbol - stc

FlyBase ID:FBgn0001978

Genetic map position - 2-[51]

Classification - zinc finger, C4HC3 type (PHD finger),
and RD-domain protein

Cellular location - nuclear and cytoplasmic

NCBI links: Precomputed BLAST | Entrez Gene

shuttle craft (stc) was identified in a cDNA expression cloning screen for single-stranded nucleic acid binding proteins expressed during Drosophila oogenesis. stc is a dual personality gene: stc maternal and zygotic transcripts control two distinct traits. Maternal mutants exhibit defects in segmentation, while zygotic mutants show defects in axon guidance. Possessing a novel double stranded DNA-binding domain, and a separate single-stranded nucleic acid binding domain that binds nucleic acids non-specifically, Stc, along with its mammalian homolog NF-X1, define a new class of transcription factors (Stroumbakis, 1996).

Embryos lacking the stc maternal function display defects in segment polarity gene expression (these segmentation defects are detected by examination of cuticle preparations), and die during early embryogenesis. Although wild-type embryos exhibit a dynamic cell-cycle-dependent STC nuclear distribution pattern during cellularization (see stc Developmental Biology ), stc maternal mutants show no defects in pre-cellularization mitosis. Examination of cuticle preparations from late embryos derived from stc maternal mutants shows poor cuticle development and variable segmentation defects consisting of either the loss or the fusion of abdominal denticle belts. In extreme cases, embryos are missing as many as five segments. In addition, most of the maternally mutant embryos appear to arrest development by stage 16 of embryogenesis (Stroumbakis, 1998).

In wild type flies, during germband extension, Engrailed protein is expressed as a position-specific series of three oral, three thoracic, and nine abdominal stripes. During this same developmental period, virtually all embryos derived from maternally mutant oocytes fertilized with wild-type sperm display severe segmentation defects evident in distinct regions of the embryo. The defects are most obvious in thoracic segments T1-T3 as well as in abdominal segments. The T1-T3 regions contain a deletion of one or two segments as judged by the reduction in the number of Engrailed stripes. A more variable phenotype is associated in A4-A8 where Engrailed stripes appear disrupted, fused or deleted. Compared with wild-type embryos, three segments are missing (Stroumbakis. 1998).

shuttle craft zygotic mutants show defects in neural projections that are independent of the segmentation defects observed in maternal mutations. Wild-type flies project nerves (the segmental nerve [SNB] and the intersegmental nerve [ISN]) that follow routes from specific motoneurons and initiate their journey laterally from the ventral nerve cord. These nerves begin their migration at the end of germband retraction, which, coincidentally, is the same period when Stc protein is first detected in the CNS. As they exit the CNS and join together, the SNB and the ISN normally project in a characteristically direct path along specific guideposts, initially provided by the segmental branches of the trachea and later by axons derived from the dorsal sensory neurons. However, this is not the case in stc mutant embryos: in these mutants, the nerves appear to either navigate in a misguided manner or fail to maintain their precise positions after migration. Unlike previously described mutations in genes that appear to block migration of growth cones at specific locations (e.g., short stop, stranded, and beaten path), the projection of these nerves in the stc mutant embryo is not blocked. Instead, these nerves appear disarrayed, possibly because they are either partially misrouted during their migration or their exact position is not maintained after migration, as they continue to extend to their ultimate muscle field targets. Toward the end of embryogenesis, stc mutant embryos also display a slight failure in their ability to completely condense their CNS (Stroumbakis, 1996).

Maternal stc mutants exhibit their own axon guidance phenotypes. An additional phenotype distinct from either the early maternal effect segmentation or the late zygotic loss-of-function defects affects the migrating ISN and SNB nerves, which often fail to join when exiting the CNS and continue traveling in a misguided manner. These motoneuronal axon guidance defects are fully penetrant and occur in neuromeric segments that do not otherwise display severe maternal effect segmentation abnormalities (Stroumbakis, 1998).

It is concluded that the maternal and zygotic sources of Stc protein are functionally independent and play different roles during embryonic development. The presence of a maternally associated axon guidance phenotype, in addition to the segmentation defect, implies that there are at least two distinct independently-acting activities associated with maternally derived Stc protein in the embryo. The stc maternal effect phenotype is similar to that associated with disruptions in hopscotch and marelle, which encode two important components of the Drosophila embryonic JAK/STAT signaling pathway. It is also interesting to note that the human Stc homolog, NF-X1, is a transcription factor activated by the cytokine IFN-gamma (Song, 1994), one of many ligands that are know to function in JAK/STAT signaling. These observations raise the possibility that the stc maternal function may participate in or may be a target of the JAK/STAT signaling pathway (Stroumbakis, 1998).


Two of the three cDNAs sequenced have a small 21-bp deletion that results in a transcript containing a predicted in-frame deletion of seven amino acids. There are at least two alternatively spliced isoforms of STC mRNA. In this region stc genomic DNA contains two putative donor splice junction sequences separated by 21 bp that appear to splice to a single splice acceptor site (Stroumbakis, 1996).

cDNA length - 3963 base pairs

Bases in 5' UTR - 223

Bases in 3' UTR - 422


Amino Acids - 1106

Structural Domains

NF-X1 is a novel cytokine-inducible transcription factor that has been implicated in the control of immune responses in humans, presumably by regulating expression of class II major histocompatibility genes. The first reported NF-X1 homolog is Drosophila shuttle craft. STC and NF-Xi are highly conserved throughout three-quarters of their length (amino acids 275 to 1095 of the STC sequence), in which 40% of the amino acids are identical. This conservation increases to 56% when conservative amino acid substitutions are included. The deduced sequence of the fly and human proteins defines a new family of molecules distinguished by a novel cysteine-rich DNA-binding motif (consisting of seven copies of the consensus sequence Cx3Cx3LxCGx0-5HxCx3CHxGxCx2Cx7-9CxC, termed STC/NF-X1 repeats). This motif has been shown to confer a sequence-specific double-stranded DNA-binding activity to NF-X1 (Song, 1994). The motif is somewhat reminiscent but distinct from both the cystein-rich LIM and Ring domains of metal-binding proteins. In addition, both Stc and NF-X1 are highly conserved outside of the STC/NF-X1 repeats, at their extreme C-termini. The STC C terminus includes a 222-amino-acid region encoded by the original partial stc cDNA clone that has been shown to bind single stranded DNA in a sequence-independent manner (the basis of its original identification) but that does not bind double-stranded DNA or RNA. There is a region of 35 amino acids near the N-terminus of the protein composed entirely of tandem repeats of Arg-Asp (or Glu) dipeptides. The function of this alternating series of basic and acidic residues has yet to be determined, but it has also been reported in a limited number of putative RNA-binding proteins, where it is known as the RD domain. Other regions of interest include a bipartite nuclear localization signal and 13 potential N-linked glycosylation sites. Two possible tyrosine kinase phosphorylation sites are also present (Stroumbakis, 1996).


The class II major histocompatibility complex (MHC) molecules function in the presentation of processed peptides to helper T cells. As most mammalian cells can endocytose and process foreign antigen, the critical determinant of an antigen-presenting cell is its ability to express class II MHC molecules. Expression of these molecules is usually restricted to cells of the immune system and dysregulated expression is hypothesized to contribute to the pathogenesis of a severe combined immunodeficiency syndrome and certain autoimmune diseases. Human complementary DNA clones encoding a newly identified, cysteine-rich transcription factor, NF-X1, which binds to the conserved X-box motif of class II MHC genes, have been obtained, and the primary amino acid sequence deduced. The major open reading frame encodes a polypeptide of 1,104 amino acids with a symmetrical organization. A central cysteine-rich portion encodes the DNA-binding domain, and is subdivided into seven repeated motifs. This motif is similar to but distinct from the LIM domain and the RING finger family, and is reminiscent of known metal-binding regions. The unique arrangement of cysteines indicates that the consensus sequence CX3CXL-XCGX1-5HXCX3CHXGXC represents a novel cysteine-rich motif. Two lines of evidence indicate that the polypeptide encodes a potent and biologically relevant repressor of HLA-DRA transcription: (1) overexpression of NF-X1 from a retroviral construct strongly decreases transcription from the HLA-DRA promoter, and (2) the NF-X1 transcript is markedly induced late after induction with interferon gamma (IFN-gamma), coinciding with postinduction attenuation of HLA-DRA transcription. The NF-X1 protein may therefore play an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma (Song, 1994).

shuttle craft:
Biological Overview | Developmental Biology | Effects of Mutation | References

date revised: 20 November 98

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