Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition

HOXA11 is a transcription factor implicated in paired appendage development . To identify signatures of evolutionary change in the structural, and puta tive functional, domains of HOXA11, we studied its evolution in tetrapod an d nontetrapod lineages that represent approximately 1.5 billion years of ev olutionary time. Here, Hoxa-11 gene proper sequences were determined for fr og (Xenopus tropicalis), coelacanth (Latimeria chalumnae), common zebrafish (Danio rerio; Hoxa-11a and Hoxa-11b paralogs), and giant zebrafish (D. aeq uipinnatus; Hoxa-11b) and aligned against previously published Hoxa-11 sequ ences of human, mouse, chick, and newt. Based on aligned Hoxa-11 amino acid sequences, the protein was demarcated into three segments: Domains I (N-te rminal) and III (homeobox + C-terminal), which varied slightly in rates and patterns of evolution, and a variable, overall hydrophilic region (HyD), w hich partially overlaps with Domain I. As judged by character reconstructio ns of HOXA11 Domains I and III, no significant changes in rates of coding s equence evolution occurred in tetrapods (frog and chick), relative to coela canth (a lobe-finned fish), i.e., across the fin-limb transition. Accelerat ed rates of Hoxa-11 coding sequence evolution were observed for the mammali an and newt lineages. This was shown to be a gene-specific phenomenon. The duplicated Hoxa-11a and Hoxa-11b genes of zebrafish exhibited accelerated r ates of evolution and accumulated substitutions at sites that are conserved among coelacanth and all tetrapods examined. Amino acid sequence compariso ns of the HyD of HOXA11 suggested that a putative repressor subdomain, cont aining stretches of consecutive alanine residues, emerged within the tetrap ods. A high degree of nucleotide conservation in the 5' half of the Hoxa-11 intron was observed for tetrapod and nontetrapod lineages. Using electroph oretic mobility shift assays, a 35-bp intron sequence, which is 100% conser ved in all Hoxa-11 loci except for the zebrafish Hoxa-11a paralog, was foun d to bind protein(s) in HeLa and chick whole-cell extracts. (C) 2000 Academ ic Press.