Supplementary Information for the work on
'Immunoglobulin Proteins in Drosophila melanogaster and Caenorhabditis elegans'
C. Vogel, S. A. Teichmann, C. Chothia
MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
Correspondence to: C. Vogel cvogel [at] mrc-lmb . cam . ac . uk
Files
Please read the Notes for any updates.
Pre-print. (Dec 03)
Figure 1. (Dec 03)
Figure 2. (Dec 03)
Figure 3. (Dec 03)
Figure 4. (Dec 03)
Notes (Corrections and Clarifications)
- Lachesin has a GPI anchor, but no predicted transmembrane helix (as might be concluded from the figure).
- Prior to our work, Hynes & Zhao (2000) stated that the number of the IgSF proteins in Drosophila is about 150, and for about130 of these they give descriptions of all or some of their domains. This information should have been cited in our paper. Their results for C. elegans are similar to those of Teichmann & Chothia (2000) published prior to their paper.
- UNC-73 is an intracellular signalling molecule (Kubiseski et al., 2003) and not a secreted protein.
- UNC-89 is a muscle protein and not an extracellular matrix protein (Flaherty et al., 2002).
- Popovici et al. (2002) noted the homology of F59F3.1, F59F3.5, T17A3.1 and T17A3.8 and called them VER proteins.
- Aurelio et al. (2002) characterised the expression of C09E7.3, Y38F1A.9 and Y50E8A.3 and gave the three proteins the names Oig-1, Oig-2 and Oig-3. They also noted that proteins CO9E7.3 and Y42H9B.2 belong to the IgSF. Y54G2A.25 is a replacement for the incomplete prediction Y94H6A_148.d that was used by Teichmann and Chothia (Teichmann and Chothia, 2000).
- The C. elegans Semaphorin-2a is an experimentally characterised sequence (Roy et al., 2000).
- Two Ig domains are missing from the Perlecan structure in Figure 1.
- Whilst Zig 2-8 are correctly described as secreted proteins in Figure 3 in our paper, they are placed with Zig 1 in the Cell surface category in Table 2.
- For C63B7.1, its similar domain architecture and mention next to Klingon/Wrapper in the figures might suggest that C53B7.1 is a homologue of the two fly proteins. This is not the case: see Table 3 in our paper where the probable Drosophila-C. elegans homologues are listed.
- Beat Ia has a slightly different domain architecture than the other Beaten Path proteins in that is has an additional Cysteine knot domain (Pipes et al., 2001).
- K07E12.1/DIG-1 protein has domains characteristic of extracellular proteins and could be classified as an extracellular protein (Hobert et al., 2004).
- In the most recent version of the SUPERFAMILY database (1.63, Jan 2004) showed that
(i) E04F6.8 and E04F6.9 are not recognised as immunoglobulin proteins anymore,
(ii) Y38B5A.1 is not recognised as immunoglobulin protein by SUPERFAMILY, but by Pfam,
(iii) all other IgSF matches in fly and worm could be confirmed (Martin Madera, private communication; Madera and Gough, 2004).
We thank Maura Strigini, Oliver Hobert, Harald Hutter, Richard Hynes and Martin Madera for pointing out the updates, clarifications, corrections listed above.
The comments above affect nine out of the 220 proteins discussed in our paper and do not change the overall results and conclusions.
References
Aurelio, O., Hall, D. H. and Hobert, O. (2002). Immunoglobulin-domain proteins required for maintenance of ventral nerve cord organization. Science 295, 686-690.
Flaherty, D. B., Gernert, K. M., Shmeleva, N., Tang, X., Mercer, K. B., Borodovsky, M. and Benian, G. M. (2002). Titins in C.elegans with unusual features: coiled-coil domains, novel regulation of kinase activity and two new possible elastic regions. J Mol Biol 323, 533-49.
Hobert, O., Hutter, H. and Hynes, R. (2004). Commentary on "The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity" by Vogel C, Teichmann SA and Chothia C. Development.
Hutter, H., Vogel, B. E., Plenefisch, J. D., Norris, C. R., Proenca, R. B., Spieth, J., Guo, C. B., Mastwal, S., Zhu, X. P., Scheel, J. et al. (2000). Cell biology: Conservation and novelty in the evolution of cell adhesion and extracellular matrix genes. Science 287, 989-994.
Hynes, R. O. and Zhao, Q. (2000). The evolution of cell adhesion. J Cell Biol 150, F89-96.
Kubiseski, T. J., Culotti, J. and Pawson, T. (2003). Functional analysis of the Caenorhabditis elegans UNC-73B PH domain demonstrates a role in activation of the Rac GTPase in vitro and axon guidance in vivo. Mol Cell Biol 23, 6823-35.
Letunic, I., Copley, R. R., Schmidt, S., Ciccarelli, F. D., Doerks, T., Schultz, J., Ponting, C. P. and Bork, P. (2004). SMART 4.0: towards genomic data integration. Nucleic Acids Res 32, D142-4.
Madera, M. and Gough, J. (2002). A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Research 19, 30.
Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J. The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 2004 Jan 1;32 Database issue:D235-9.
Pipes, G. C., Lin, Q., Riley, S. E. and Goodman, C. S. (2001). The Beat generation: a multigene family encoding IgSF proteins related to the Beat axon guidance molecule in Drosophila. Development 128, 4545-52.
Popovici, C., Isnardon, D., Birnbaum, D. and Roubin, R. (2002). Caenorhabditis elegans receptors related to mammalian vascular endothelial growth factor receptors are expressed in neural cells. Neurosci Lett 329, 116-20.
Roy, P. J., Zheng, H., Warren, C. E. and Culotti, J. G. (2000). mab-20 encodes Semaphorin-2a and is required to prevent ectopic cell contacts during epidermal morphogenesis in Caenorhabditis elegans. Development 127, 755-767.
Teichmann, S. A. and Chothia, C. (2000). Immunoglobulin superfamily proteins in Caenorhabditis elegans. Journal of Molecular Biology 296, 1367-1383.
Vogel, C., Teichmann, S. A. and Chothia, C. (2003). The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development 130, 6317-28.
Questions and feedback are most welcome. C. Vogel, cvogel {at} mrc-lmb . cam . ac . uk
Home.
Feb 2004