Peptides as signals - Intercellular Communication in Plants - page 43

A systemic analysis of small ORFs in Arabidopsis that encode putative secreted
peptides has identified a family of 34 genes, many of which contain the RALF-
like sequence (Olsen et al. , 2002). Biological functions of RALFs have not been
well understood. The existence of the larger number of putative secreted RALF-
like molecules suggests that many of them may be signals involved in a vari-
ety of biological pathways. Another search for CLV3 homologues has identified
42 CLV3 -related ( CLE ) sequences in plants (Cock & McCormick, 2001). Among
them, 24 are in the Arabidopsis genome. Speculatively, these CLE genes could en-
code the ligands for many RLKs. A similar search has identified a large number
of putative genes that encode peptides homologous to SCR (Vanoosthuyse et al. ,
2001).
One of the challenges of this approach is to determine that these in silico genes
do encode polypeptides. The peptidomics approach may offer a way to aid the sys-
tematic discovery of peptides (Schulz-Knappe et al. , 2001). The approach takes
advantage of high sensitivity of mass spectrometry technology in identification of
proteins and improvements in separating and isolating peptides to systematically
identify a complement of peptide molecules produced by particular tissues, organs,
or whole organisms. Such an approach has recently led to the discovery of a large
number of new animal neuropeptides and peptide hormones that had eluded iden-
tification through classical methods (Takahashi et al. , 1997; Sweedler et al. , 2000;
Clynen et al. , 2001; Schrader & Schulz-Knappe, 2001; Svensson et al. , 2003). For
instance, Svensson et al . (2003) simultaneously detected more than 550 endogenous
neuropeptides from hypothalamic extracts, which include previously described and
many novel neuropeptides. These structural peptidomics approaches can be explored
to identify the major complement of peptides produced by plant cells.
A more challenging task is to determine whether a peptide really functions as a
signal because many small proteins have other regulatory or nonregulatory functions.
A method to address this question is to determine if a peptide binds to a receptor.
Binding of a peptide to a cell surface receptor will provide strong evidence of
function as a signal molecule. Several high-throughput protein-protein interaction
technologies have been developed in recent years (Drewes & Bouwmeester, 2003).
It should be feasible to apply them in generating interaction maps between peptide
molecules and the putative receptor kinases encoded by the plant genomes. Such
information will not only provide important clues as to whether a peptide functions
as a signal but also facilitate identification of its receptors and downstream signaling
components.

2.5 Concluding remarks

Intercellular communication mechanisms are believed to have evolved after plants
and animals diverged from their common unicellular ancestor (Meyerowitz, 1999).
The striking similarity in plant's and animal's signal perception and transduction
pathways mediated by peptide signals indicates that those organisms have used a