MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
* Author for correspondence (e-mail: cvogel{at}mrc-lmb.cam.ac.uk)
Hobert et al. (Hobert et al.,
2004) have made a number of criticisms on our paper
(Vogel et al., 2003
). In the
following paragraphs we give our replies to these criticisms. In a number of
cases, the comments do provide useful corrections to the paper. Nevertheless,
the major conclusions of our paper are not affected by these corrections and
they remain both novel and valid.
Previous work on the immunoglobulin superfamily repertoire
Prior to our work, Hynes and Zhao (Hynes
and Zhao, 2000) stated that the number of IgSF proteins in
Drosophila was about 150, and for about 130 of these they listed some
or all of the domains by which they are formed. This information should have
been cited in our paper and we regret not having done so. Their results for
C. elegans are similar to those we published
(Teichmann and Chothia, 2000
)
prior to their paper. The work by Hutter et al.
(Hutter et al., 2000
) is
acknowledged as a whole in our paper, but we are not able to make more
detailed comparisons with our current work because their web database is
inaccessible at present. The paper by Aurelio et al.
(Aurelio et al., 2002
) is
discussed below.
Experimental characterisation of IgSF proteins
The most useful part of the correspondence by Hobert et al.
(Hobert et al., 2004) is that
which draws our attention to experimental work of which we were unaware. These
correct the classification of two IgSF proteins: UNC-73 is an intracellular
signalling molecule (Kubiseski et al.,
2003
) and not a secreted protein; and UNC-89 is a muscle protein
and not an extracellular matrix protein
(Flaherty et al., 2002
). In
addition, there are experimental papers on C. elegans IgSF proteins
that we should have cited:
Hobert et al. (Hobert et al.,
2004) correctly note that two Ig domains are missing from the
Perlecan structure in figure 1 of our paper
(Vogel et al., 2003
). They
also point out that whilst Zig-2 to Zig-8 are correctly described as secreted
proteins in figure 3 of our paper, they are carelessly placed with Zig-1 in
the cell surface category in table 2.
Classification of IgSF proteins
The classification of the IgSF proteins in our paper is based on their
structural features, their subcellular location and sequence similarities. We
give some rough descriptions of the more common functions of the proteins in
the different classes. Hobert et al. strongly object to this
(Hobert et al., 2004). They
claim that we imply that all proteins in Class I are cell adhesion
molecules. We actually say that the experimentally characterised proteins in
this class are "mainly cell adhesion molecules". We and
most readers are well aware of the multiple roles of, for example, Roundabout.
Similarly, Hobert et al. (Hobert et al.,
2004
) claim that we imply that all Class III proteins are
signalling molecules, whereas we state that "those characterised so
far are signalling molecules".
Only a wilful literalist would take rough descriptions of the more common
known functions to be precise descriptions of the functions for all the
proteins in a class. Proteins with similar domain structures and related
sequences do tend to have related functions (e.g.
Hegyi and Gerstein, 2001). But,
as we say in the paper (p. 6327), any
type of function suggested for new proteins by their structural and sequence
similarties to characterised proteins will need to be refined or corrected by
experiments.
Conclusions
Many of the criticisms above are concerned with work by others that should have been cited. The criticisms of the results are in some cases correct but their overall effect is small. The more serious criticisms require that two proteins, UNC-73 and UNC-89, are placed in different classes, and that the secreted proteins Zig-2 to Zig-8 are placed in the correct part of table 3.
Because of the improvements in predictions of protein sequences made by the
curators of the genome sequences, and because of improvements in sequence
comparison procedures (Karplus et al.,
1998; Gough et al.,
2001
; Madera and Gough,
2002
), our descriptions of the IgSF proteins in
Drosophila and C. elegans go beyond those published
previously. The matches made by the sequence comparison programs are
accompanied by a score that is an estimate of the match being in error. We
have used conservative scores and would expect a very large proprotion of our
assignments to be correct. However, given that we deal with over two hundred
sequences, which together have about a thousand domains, we might also expect
that a few assignments will be incorrect, and that some assignments will be
missed because of the limitations of some of the hidden Markov models.
The criticisms made by Hobert et al.
(Hobert et al., 2004) do not
affect the novel and significant parts of our paper. We show that about half
of the IgSF proteins in C. elegans and three-quarters of those in
Drosophila have evolved since the divergence of the two organisms.
The larger size of the Drosophila IgSF repertoire involves mainly
cell surface and secreted proteins, and many of these have arisen through gene
duplications. We believe that this overall expansion of the IgSF must be one
of the factors that contributed to the formation of the more complex
physiology of Drosophila. It is difficult to understand the assertion
made by Hobert et al. (Hobert et al.,
2004
) that this view is invalidated by the increases in the
repertoire produced by the alternative splicing of genes. Both factors are
clearly important. In fact, the protein they take to illustrate the importance
of splicing, DSCAM, is also a good example of repertoire expansion: there are
probably four DSCAM sequences in Drosophila and none in C.
elegans.
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