Semaphorin K1

Details Semaphorin K1 Semaphorin K1

2001-01-26

2003-06-24

Smith, Lynette R. F. (Department: 1645)

Organic compounds -- part of the class 532-570 series

Organic compounds

Carbohydrates or derivatives

C536S023100, C530S300000, C530S327000, C530S324000, C530S350000, C435S069100

Reexamination Certificate

active

06583277

ABSTRACT:

FIELD OF THE INVENTION
The field of this invention is polypeptides involved in cell guidance.
BACKGROUND
The semaphorins constitute a large family of evolutionally conserved glycoproteins that are defined by a characteristic semaphorin domain of approximately 500 amino acids (1-3). The first vertebrate semaphorin, collapsin-1 in chick, was identified by its ability to induce growth cone collapse (4). Consistent with this function, its mammalian homologue, sema III, has been shown to repel specific subsets of sensory axons (5). As a result of these and other studies, Coll-1/sema III/D has been implicated in the patterning of sensory axon projections into the ventral spinal cord and cranial nerve projections into the periphery (6-11).
Several other semaphorins have also been implicated as repulsive and/or attractive cues in axon guidance, axon fasciculation, and synapse formation (1, 12-17). In addition, members of semaphorin family have been implicated in functions outside the nervous system, including bone skeleton and heart formation (9), immune function (18, 19), tumor suppression (20-22), and conferring drug resistance to cells (23).
Recent studies have identified the first semaphorin receptor as a member of the neuropilin family. Neuropilin-1 is a high affinity receptor for sema III, E and IV, whereas neuropilin-2 binds differentially to the subfamily of secreted semaphorins (24-27).
The vertebrate semaphorin family can be classified into several phylogenetically distinct subfamilies (15). Each subfamily has a unique structural arrangement of protein domains. The secreted members of the semaphorin family contain a characteristic semaphorin domain at the N-terminus, followed by an immunoglobulin (Ig) domain and a stretch of basic amino acids in the carboxyl-terminal region. Between the N-terminal semaphorin domain and the transmembrane spanning region, the transmembrane semaphorins contain several alternative structural motifs including either an Ig domain, a stretch of thrombospondin repeats, or a sequence with no obvious domain homology. Interestingly, semaphorin-like sequences have been identified in the genomes of poxviruses (1) and alcelaphine herpesvirus-1 (28), occupying unique branches of the semaphorin phylogenetic tree. Here we report the identification of a GPI-linked human semaphorin—semaphorin K1—which is homologous to the semaphorin encoded by alcelaphine herpesvirus-1 and show that semaphrin K1 polypeptides and nucleic acids are bioactive in modulating nervous and immune system function.
CITED LITERATURE
Cited Literature
1.
Kolodkin, A.-L., Matthes, D.-J. & Goodman, C.-S. (1993) Cell, 75,
1389-1399
2.
Puschel, A.-W., Adams, R.-H. & Betz, H. (1995) Neuron, 14,
941-948.
3.
Luo, Y., et al. (1995) Neuron 14, 1131-1140.
4.
Luo, Y., Raible, D. & Raper, J.-A. (1993) Cell, 75, 217-227.
5.
Messersmith, E.-K., et al. (1995) Neuron 14, 949-959.
6.
Fan, J. & Raper, J.-A. (1995) Neuron, 14, 263-274.
7.
Kobayashi, H., et al. (1997) J. Neurosci. 17, 8339-8352.
8.
Puschel, A.-W., Adams, R.-H. & Betz, H. (1996) Mol. Cell.
Neurosci. 7, 419-431.
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Behar, O., et al. (1996) Nature, 383, 525-528.
10.
Shepherd, I.-T., et al. (1997) Development, 124, 1377-1385.
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Taniguchi, M., et al. (1997) Neuron 19, 519-530.
12.
Kolodkin, A. L., et al. (1992). Neuron 9, 831-845.
13.
Matthes, D.-J., et al. (1995) Cell 81, 631-639.
14.
Wong, J. T., Yu, W. T., O'Connor, T. P. (1997) Development 124,
3597-3607.
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Adams, R.-H., Betz, H., & Puschel, A.-W. (1996) Mech Dev. 57,
33-45.
16.
Feiner, L., et al. (1997) Neuron 19, 539-545.
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Yu, H-H., Araj, H.-H., Ralls, S.-A. & Kolodkin A.-L. (1998) Neuron
20, 207-220.
18.
Bougeret, C., et al. (1992) J. Immunol. 148, 318-323.
19.
Hall, K.-T., et al. (1995) Proc. Natl. Acad. Sci. 93, 11780-11785.
20.
Xiang, R.-H., et al. (1996) Genomics, 32, 39-48.
21.
Roche, J., et al. (1996) Oncogene 12, 1289-1297.
22.
Sekido, Y., et al. (1996) Proc. Natl. Acad. Sci. 93, 4120-4125.
23.
Yamada, T., et al. (1997) Proc. Natl. Acad. Sci. 94, 14713-14718.
24.
He, Z. & Tessier-Lavigne, M. (1997) Cell 90, 739-751.
25.
Kolodkin, A.-L., et al. (1997) Cell, 90, 753-762.
26.
Chen, H., et al. (1997) Neuron 19, 547-559.
27.
Kitsukawa, T., et al. (1997) Neuron 19, 995-1005.
28.
Ensser. A. & Fleckenstein, B. (1995) J. Gen. Virol. 76, 1063-1067.
29.
Frohman, M. A. (1993) Methods Enzymol. 218, 340-356.
30.
Koppel, A.-M., et al. (1997) Neuron 19, 531-537.
31.
Eickholt, B. J., et al. (1997) Mol. Cell Neurosci, 9, 358-371.
32.
Schaeren-Wiemers, N. & Gerfin-Moser, A. (1993) Histochemistry
100, 431-440.
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Altschul, S.-F., et al. (1990) J. Mol. Biol. 215, 403-410.
34.
Kyte, J & Doolittle, R. F. (1982) J. Mol. Biol. 157, 105-132.
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von Heijne, G. (1985) J. Mol. Biol. 184, 99-105.
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SUMMARY OF THE INVENTION
The invention provides methods and compositions relating to semaphorin K1 (sema K1) polypeptides, related nucleic acids, polypeptide domains thereof having sema K1-specific structure and activity and modulators of sema K1 function. The polypeptides may be produced recombinantly from transformed host cells from the subject sema K1 polypeptide encoding nucleic acids or purified from mammalian cells. The invention provides isolated sema K1 gene hybridization probes and primers capable of specifically hybridizing with the disclosed sema K1-encoding genes, sema K1-specific binding agents such as specific antibodies, and methods of making and using the subject compositions in diagnosis (e.g. nucleic acid hybridization screens for sema K1 transcripts), modulating cellular physiology (e.g. by contacting with exogenous sema K1) and in the biopharmaceutical industry (e.g. as immunogens, reagents for isolating other semaphorins, reagents for screening chemical libraries for lead pharmacological agents, etc.).
DETAILED DESCRIPTION OF THE INVENTION
The nucleotide sequence of a natural cDNA encoding a human sema K1 polypeptide is shown as SEQ ID NO:1, and the full conceptual translate is shown as SEQ ID NO:2. The sema K1 polypeptides of the invention include one or more functional domains of SEQ ID NO:2, which domains comprise at least one of (a) SEQ ID NO:2, (b) at least 100 contiguous residues of SEQ ID NO:2, (c) at least 60 contiguous residues of SEQ ID NO:2, residues 340-634, and (d) at least 12 contiguous residues of SEQ ID NO:2, residues 481-634. A cDNA encoding an alcelaphine herpesvirus semaphorin having sequence similarity to the subject sema K1 polypeptides, and its translate are shown as SEQ ID NO:3 and 4, respectively. Sema K1 specific polynucleotides and polypeptides having human sema K1-specific sequences are readily discernable from alignments of the sequences. Preferred sema K1 polypeptides have one or more human sema K1-specific activities, such as cell surface receptor binding and/or binding inhibitory activity and sema K1-specific immunogenicity and/or antigenicity.
Sema K1-specific activity or function may be determined by convenient in vitro, cell-based, or in vivo assays: e.g. in vitro binding assays, cell culture assays, in animals (e.g. gene therapy, transgenics, etc.), etc. Binding assays encompass any assay where the molecular interaction of an sema K1 polypeptide with a binding, target is evaluated. The binding target may be a natural extracellular binding target such as a nerve or immune cell surface protein; or non-natural binding target such a specific immune protein such as an antibody, or an sema K1 specific agent such as those identified in screening assays such as described below. Sema K1-binding specificity may be assayed by binding equilibrium constants (usually at least about 10
7
M
−1
, preferably at least about 10
8
M
−1
, more preferably at least about 10
9
M
−1
), by growth cone collapse assays, by the ability to elicit sema K1 specific antibody in a heterologous host (e.g. a rodent or rabbit), etc.
For example, deletion mutagenesis is used to define functional sema K1 domains which specifically bi

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