NK homeobox genes with choanocyte-specific expression in homoscleromorph sponges

Data on nonbilaterian animals (sponges, cnidarians, and ctenophores) have suggested that Antennapedia (ANTP) class homeobox genes played a crucial role in the early diversification of animal body plans. Estimates of ancestral gene diversity within this important class of developmental regulators have been mostly based on recent analyses of the complete genome of a demosponge species, leading to the proposal that all ANTP families found in nonsponges animals (eumetazoans) derived from an ancestral "proto-NK" six-gene cluster. However, a single sponge species cannot reveal ancestral metazoan traits, in particular because lineage-specific gene duplications or losses are likely to have occurred during the long history of the Porifera. We thus looked for ANTP genes by degenerate polymerase chain reaction search in five species belonging to the Homoscleromorpha, a sponge lineage recently phylogenetically classified outside demosponges and characterized by unique histological features. We identified new genes of the ANTP class called HomoNK. Our phylogenetic analyses placed HomoNK (without significant support) close to the NK6 and NK7 families of cnidarian and bilaterian ANTP genes and did not recover the monophyly of the proposed "proto-NK" cluster. Our expression analyses of the HomoNK gene OlobNK in adult Oscarella lobularis showed that this gene is a strict marker of choanocytes, the most typical sponge cell type characterized by an apical flagellum surrounded by a collar of microvilli. These results are discussed in the light of the predominant neurosensory expression of NK6 and NK7 genes in bilaterians and of the recent proposal that choanocytes could be the sponge homologs of sensory cells.     

Ancient linkage of a POU class 6 and an anterior Hox-like gene in cnidaria: implications for the evolution of homeobox genes

Linkage analyses in metazoan genomes suggest two ancestral arrays for the majority of homeobox genes. The related homeobox genes and chromosomal regions that are dispersed in extant species derived possibly from only two single common ancestor regions. One proposed ancestral array, designated as ANTP mega-array, contains most of the ANTP class homeobox genes; the second, named the contraHox super-paralogon, would consist of the classes PRD, POU, LIM, CUT, prospero, TALE and SIX. Here, we report the tight linkage of a POU class 6 gene to an anterior Hox-like gene in the hydrozoan Eleutheria dichotoma and discuss its possible significance for the evolution of homeobox genes. POU class 6 genes also seem to be ancestrally linked to the HoxC and A clusters in vertebrates, despite POU homeobox genes belonging to the contraHox paralogon. Hence, the much tighter linkage of a POU class 6 gene to an anterior Hox-like gene in a cnidarian is possibly the evolutionary echo of an ancestral genomic region from which most metazoan homeobox classes emerged.     

An orphan PRD class homeobox gene expressed in mouse brain and limb development

We report the cDNA sequence and expression of a mouse homeobox gene, Dmbx1, from the PRD class and comparison to its human orthologue. The gene defines a new homeobox gene family, Dmbx, phylogenetically distinct from the Ptx, Alx, Prx Otx, Gsc, Otp and Pax gene families. The Dmbx1 gene is expressed in the developing mouse diencephalon, midbrain and hindbrain, and has dynamic expression during forelimb and hindlimb development. Unusually for homeobox genes, there is no orthologue in the Drosophila or Caenorhabditis genomes; we argue this reflects secondary loss.     

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.     

The homeobox genes of <Emphasis Type="Italic">Encephalitozoon cuniculi</Emphasis> (Microsporidia) reveal a putative mating-type locus

Homeobox genes have been found in animals, fungi, and plants. Recently, the complete genomic sequence of Encephalitozoon cuniculi has become available and it was shown that this Microsporida species is related to fungi. Given this close relatedness to fungi, I have searched the genome of E. cuniculifor homeobox genes. There are 12 homeobox genes as well as one STE12 orthologue. The large number of homeobox genes when compared to the annotations, which only list one, suggests that possibly other smaller genes may have been overlooked in the published analysis and E. cuniculi may have more than 1,997 genes. Sequence and phylogenetic analyses show that the E. cuniculi homeobox genes also fall into two distinct groups, with two TALE and ten typical homeobox genes being present. Like in the mating-type locus of yeast and other fungi, one TALE and one typical homeobox are found in close proximity of each other on the chromosome, suggesting that Microsporidia also contain a mating-type locus.     

Homeobox Genes in the Rodent Pineal Gland: Roles in Development and Phenotype Maintenance

The pineal gland is a neuroendocrine gland responsible for nocturnal synthesis of melatonin. During early development of the rodent pineal gland from the roof of the diencephalon, homeobox genes of the orthodenticle homeobox (Otx)- and paired box (Pax)-families are expressed and are essential for normal pineal development consistent with the well-established role that homeobox genes play in developmental processes. However, the pineal gland appears to be unusual because strong homeobox gene expression persists in the pineal gland of the adult brain. Accordingly, in addition to developmental functions, homeobox genes appear to be key regulators in postnatal phenotype maintenance in this tissue. In this paper, we review ontogenetic and phylogenetic aspects of pineal development and recent progress in understanding the involvement of homebox genes in rodent pineal development and adult function. A working model is proposed for understanding the sequential action of homeobox genes in controlling development and mature circadian function of the mammalian pinealocyte based on knowledge from detailed developmental and daily gene expression analyses in rats, the pineal phenotypes of homebox gene-deficient mice and studies on development of the retinal photoreceptor; the pinealocyte and retinal photoreceptor share features not seen in other tissues and are likely to have evolved from the same ancestral photodetector cell.     

A low diversity of ANTP class homeobox genes in Placozoa

Homeobox genes of the ANTP and PRD classes play important roles in body patterning of metazoans, and a large diversity of these genes have been described in bilaterian animals and cnidarians. Trichoplax adhaerens (Phylum Placozoa) is a small multicellular marine animal with one of the simplest body organizations of all metazoans, showing no symmetry and a small number of distinct cell types. Only two ANTP class genes have been described from Trichoplax: the Hox/ParaHox gene Trox-2 and a gene related to the Not family. Here we report an extensive screen for ANTP class genes in Trichoplax, leading to isolation of three additional ANTP class genes. These can be assigned to the Dlx, Mnx and Hmx gene families. Sequencing approximately 12-20 kb around each gene indicates that none are part of tight gene clusters, and in situ hybridization reveals that at least two have spatially restricted expression around the periphery of the animal. The low diversity of ANTP class genes isolated in Trichoplax can be reconciled with the low anatomical complexity of this animal, although the finding that these genes are assignable to recognized gene families is intriguing.     

LIM同源框基因家族与神经系统

同源框基因是指一类含有同源序列的基因,它编码的蛋白质作为转录调节因子调节细胞的发育和分化,控制基因的表达形式。ＬＩＭ同源框基因不仅含有同源框基因也含有编码ＬＩＭ结构域的保守序列。     

SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize

The expression of class 1 knotted1-like homeobox (knox) genes affects numerous plant developmental processes, including cell-fate acquisition, lateral organ initiation, and maintenance of shoot apical meristems. The SEMAPHORE1 gene product is required for the negative regulation of a subset of maize knox genes, the duplicated loci rough sheath 1 and gnarley1 (knox4). Recessive mutations in semaphore1 result in the ectopic expression of knox genes in leaf and endosperm tissue. Genetic analyses suggest that SEMAPHORE1 may regulate knox gene expression in a different developmental pathway than ROUGH SHEATH2, the first-identified regulator of knox gene expression in maize. Mutations at semaphore1 are pleiotropic, disrupting specific domains of the shoot. However, unlike previously described mutations that cause ectopic knox gene expression, semaphore1 mutations affect development of the embryo, endosperm, lateral roots, and pollen. Moreover, polar transport of the phytohormone auxin is significantly reduced in semaphore1 mutant shoots. The data suggest that many of the pleiotropic semaphore1 phenotypes result from defective polar auxin transport (PAT) in sem1 mutant shoots, and support models correlating down-regulated knox gene expression and PAT in maize shoots.