Evolutionary relationships among Rel domains indicate functional diversification by recombination

Abstract

The recent sequencing of several complete genomes has made it possible to track the evolution of large gene families by their genomic structure. Following the large-scale association of exons encoding domains with well defined functions in invertebrates could be useful in predicting the function of complex multidomain proteins in mammals produced by accretion of domains. With this objective, we have determined the genomic structure of the 14 genes in invertebrates and vertebrates that contain rel domains. The sequence encoding the rel domain is defined by intronic boundaries and has been recombined with at least three structurally and functionally distinct genomic sequences to generate coding sequences for: (i) the rel/Dorsal/NFkappaB proteins that are retained in the cytoplasm by IkB-like proteins; (ii) the NFATc proteins that sense calcium signals and undergo cytoplasmic-to-nuclear translocation in response to dephosphorylation by calcineurin; and (iii) the TonEBP tonicity-responsive proteins. Remarkably, a single exon in each NFATc family member encodes the entire Ca(2+)/calcineurin sensing region, including nuclear import/export, calcineurin-binding, and substrate regions. The Rel/Dorsal proteins and the TonEBP proteins are present in Drosophila but not Caenorhabditis elegans. On the other hand, the calcium-responsive NFATc proteins are present only in vertebrates, suggesting that the NFATc family is dedicated to functions specific to vertebrates such as a recombinational immune response, cardiovascular development, and vertebrate-specific aspects of the development and function of the nervous system.

Figure 1

Placement of introns within the aligned rel domain protein sequences. Only the rel domain is shown. Intron positions in the protein sequence are indicated by a black bar. No attempt has been made to assign the positions of the introns in codons. The alignment shown is that of Brocchieri and Karlin (50). The recognition, dimerization, and specificity regions are indicated above the aligned sequences. For the relish protein, a gap was shifted 18 amino acids to produce the alignment shown, allowing the common intron insertion site to align. The realignment resulted in the loss of only one amino acid identity. NLS, nuclear localization sequence.

Figure 2

Intronic boundaries predict functional domains within the proteins containing rel domains. (A) Genomic structure of the NFATc family of proteins; Roman numerals designate exons. The exon encoding the cytoplasmic-to-nuclear shuttling motifs or the “translocation exon” contains the serine-rich region and SP repeats (33) that are phosphorylation sites by GSK3 and perhaps other kinases, as well as substrates for calcineurin (32). In addition, this domain contains the nuclear localization signal and nuclear export sequence in NFATc1 required for cytoplasmic-to-nuclear shuttling (31). The rel domains are shown according to Muller et al., with the yellow exons indicating the specificity domain and pink exons containing the dimerization domain (23). (B) Genomic structures of four genes encoding rel proteins that are mechanistically distinct from the NFATc proteins by virtue of being retained in the cytoplasm by IkB-like proteins. The specificity and dimerization regions of the rel domain of the Dorsal protein are encoded by a common exon shown in pink and yellow.

Figure 3

Evolutionary diversification of the function of the rel domain by recombination.