Organization of an echinoderm Hox gene cluster

Abstract

The Strongylocentrotus purpuratus genome contains a single ten-gene Hox complex >0.5 megabase in length. This complex was isolated on overlapping bacterial artificial chromosome and P1 artificial chromosome genomic recombinants by using probes for individual genes and by genomic walking. Echinoderm Hox genes of Paralog Groups (PG) 1 and 2 are reported. The cluster includes genes representing all paralog groups of vertebrate Hox clusters, except that there is a single gene of the PG4-5 types and only three genes of the PG9-12 types. The echinoderm Hox gene cluster is essentially similar to those of the bilaterally organized chordates, despite the radically altered pentameral body plans of these animals.

Figure 1

Phylogenetic tree for Metazoa, including representative protostome phyla and the three phyla that constitute the deuterostomes. Molecular phylogenies divide the protostomes into two great clades, namely the ecdysozoans (here arthropods to priapulids) and the lophotrochozoans (here flatworms to molluscs); deuterostomes consist of hemichordates and echinoderms, which are sister groups, plus chordates (vertebrate and invertebrate) (–44). The only phyla in which Hox gene clusters have been structurally characterized at the genome level are boxed (see text for references). The echinoderm box refers to the present work.

Figure 2

Alignment of vertebrate, amphioxus, Drosophila, and S. purpuratus homeodomain sequences. The S. purpuratus homeodomain sequences are shown flanked by arrows representing the positions of the PCR fragments used in our screens (18). Homeodomain sequences for some genes were obtained by other methods or were from a combination of sources, e.g., clones isolated by genomic walking or cDNA clones, as described in the text. In vertebrate homeodomain consensus sequences (VERT), uppercase letters indicate a residue conserved in all known vertebrate sequences of that paralog group, e.g., all mouse and human PG1 genes (24). Lowercase letters indicate a residue found in the majority but not all vertebrate sequences of each paralog group, i.e., comparing the multiple vertebrate sequences available for each Paralog Group (there is only a single amphioxus gene from each Paralog Group). Dashes indicate amino acid identity at that position between the S. purpuratus genes and all vertebrate genes as well as Drosophila and amphioxus genes of that paralog group. Amphioxus sequences [AMP, from Branchiostoma (3)] are shown below the vertebrate consensus sequences. Drosophila sequences included in the comparison are Labial (LB), Proboscipedia (PB), Deformed (DFD), and Abdominal B (ABD-B). Sequences are compiled from ref. .

Figure 3

Genome blot hybridizations carried out on pulsed-field electrophoretic displays of S. purpuratus genomic DNA. The DNA was obtained from sperm of a single individual. Seven different restriction enzymes were used for the blots in each panel, as indicated. Arrows indicate common bands revealed by probes for more than one gene.

Figure 4

Organization of the S. purpuratus Hox gene cluster. The diagram is not to scale, as the intergenic distances within the cluster have not been determined. The sequence of Hox genes within the cluster was inferred from their locations within PAC and BAC genomic inserts (see text) and the overlaps amongst clones containing each gene. For brevity, only one set of PAC genomic clones is shown, though each genomic region was analyzed on the basis of overlaps of multiple independent PAC and BAC clones. The correct names of the Hox genes with respect to their paralogous affinities with vertebrate Hox genes appear at the top of the diagram, and beneath in parentheses are designations found in earlier literature describing isolations of Hox homeodomains or cDNAs in various laboratories (see text for references). The dashed line indicates the span of the 450-kb fragment indicated in Fig. 3, which includes all the genes from SpHox4/5 to SpHox11/13a.