Homeobox Genes, Retinoic Acid and the Development and Evolution of Dual Body Plans in the Ascidian Herdmania curvata

Ascidians, along with other urochordates, are the most evolutionarydistant group from vertebrates to display definitive chordate-specificcharacters, such as a notochord, dorsal hollow nerve cord, pharynxand endostyle. Most solitary ascidians have a biphasic lifehistory that has partitioned the development of these charactersbetween a planktonic microscopic tadpole larva (notochord anddorsal nerve cord) and a larger sessile adult (pharynx and endostyle).Very little is known of the molecular axial patterning processesoperating during ascidian postlarval development. Two axialpatterning homeobox genes Otx and Cdx are expressed in a spatiallyrestricted manner along the ascidian anteroposterior axis duringembryogenesis and postlarval development (i.e., metamorphosis).Comparisons of these patterns with those of homologous cephalochordateand vertebrate genes suggest that the novel ascidian biphasicbody plan was not accompanied by a deployment of these genesinto new pathways but by a heterochronic shift in tissue-specificexpression. Studies examining the role of all-trans retinoicacid (RA) in axial patterning in chordates also contribute toour understanding of the role of homeobox genes in the developmentof larval and adult ascidian body plans. Our studies demonstratethat RA does not regulate axial patterning in the developingascidian larval neuroaxis in a manner homologous to that foundin vertebrates. Although RA may regulate the expression of someascidian homeobox genes, ectopic application of RA does notappear to alter the morphology of the larval CNS. However, treatmentwith similar or lower concentrations of RA, have a profoundeffect on postlarval development and the juvenile body plan.These changes are correlated to a dramatic reduction of Otxexpression. Through these RA-induced effects we infer that whileRA may regulate the expression of some homeobox genes duringembryogenesis it has a far more dramatic impact on postlarvaldevelopment where regulative processes predominate.     

Developmental Gene Expression in Amphioxus: New Insights into the Evolutionary Origin of Vertebrate Brain Regions, Neural Crest, and Rostrocaudal Segmentation

SYNOPSIS. Amphioxus is widely held to be the closest invertebraterelative of the vertebrates and the best available stand-infor the proximate ancestor of the vertebrates. The spatiotemporalexpression patterns of developmental genes can help suggestbody part homologies between vertebrates and amphioxus. Thisapproach is illustrated using five homeobox genes (AmphiHoxl,AmphiHox2, AmphiOtx, AmphiDll, and AmphiEri) to provide insightsinto the evolutionary origins of three important vertebratefeatures: the major brain regions, the neural crest, and rostrocaudalsegmentation. During amphioxus development, the neural expressionpatterns of these genes are consistent with the presence ofa forebrain (detailed neuroanatomy indicates that the forebrainis all diencephalon without any telencephalon) and an extensivehindbrain; the possible presence of a midbrain requires additionalstudy. Further, during neurulation, the expression pattern ofAmphiDll as well as migratory cell behavior suggest that theepidermal cells bordering the neural plate may represent a phylogeneticprecursor of the vertebrate neural crest. Finally, when theparaxial mesoderm begins to segment, the earliest expressionof AmphiEn is detected in the posterior part of each nascentand newly formed somite. This pattern recalls the expressionof the segment-polarity gene engrailed during establishmentof the segments of metameric protostomes. Thus, during animalevolution, the role of engrailed in establishing and maintainingmetameric body plans may have arisen in a common segmented ancestorof both the protostomes and deuterostomes.     

Classification and nomenclature of all human homeobox genes

Background

The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.

Results

We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.

Conclusion

We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.     

家蚕Hox基因研究进展

Hox基因（homeobox genes）在昆虫躯体模式（body plan）的发育调控机制中扮演着重要角色,其表达具有严格的组织特异性和胚胎发育的程序性。家蚕Bombyx mori作为鳞翅目昆虫的代表,其Hox基因也陆续得到鉴定。在家蚕中存在一个拟复等位基因群--E群基因,其突变表型均与过剩斑纹和过剩附肢有关,这可能与Hox基因有着密切联系。家蚕全基因组测序完成后,发现其Hox基因簇中存在12个特有的homeobox基因（Bmshx1~Bmshx12）, 说明家蚕Hox基因可能具有独特的生物学意义。我们还利用家蚕基因芯片数据分析了Bmlab与Bmpb基因的组织表达特征。通过对家蚕Hox基因的研究,探索家蚕躯体模式建立机制,可望为解析其他鳞翅目昆虫的躯体模式的建立机制提供理论依据。本文就家蚕Hox基因的表达、功能及其与E群突变的关系等方面进行了综述。     

Hox C6 expression during development and regeneration of forelimbs in larval Notophthalmus viridescens

 A central theme concerning the epimorphic regenerative potential of urodele amphibian appendages is that limb regeneration in the adult parallels larval limb development. Results of previous research have led to the suggestion that homeobox containing genes are ”re-expressed” during the epimorphic regeneration of forelimbs of adult Notophthalmus viridescens in patterns which retrace larval limb development. However, to date no literature exists concerning expression patterns of any homeobox containing genes during larval development of this species. The lack of such information has been a hindrance in exploring the similarities as well as differences which exist between limb regeneration in adults and limb development in larvae. Here we report the first such results of the localization of Hox C6 (formerly, NvHBox-1) in developing and regenerating forelimbs of N. viridescens larvae as demonstrated by whole-mount in situ hybridization. Inasmuch as the pattern of Hox C6 expression is similar in developing forelimb buds of larvae and epimorphically regenerating forelimb blastemata of both adults and larvae, our results support the paradigm that epimorphic regeneration in adult newts parallels larval forelimb development. However, in contrast with observations which document the presence of Hox C6 in both intact, as well as regenerating hindlimbs and tails of adult newts, our results reveal no such Hox C6 expression during larval development of hindlimbs or the tail. As such, our findings indicate that critical differences in larval hindlimb and tail development versus adult expression patterns of this gene in these two appendages may be due primarily to differences in gene regulation as opposed to gene function. Thus, the apparent ability of urodeles to regulate genes in such a highly co-ordinated fashion so as to replace lost, differentiated, appendicular structures in adult animals may assist, at least in part, in better elucidating the phenomenon of epimorphic regeneration. Received: 6 November 1998 / Accepted: 12 December 1998     

cDNA cloning and partial sequencing of homeobox genes in Dugesia japonica

In the freshwater planarian Dugesia japonica, four types of cDNAs of homeobox-containing genes have been isolated by screening a cDNA library using a homeobox guessmer. Partial sequencing analysis of two types of cDNAs revealed that one was a homolog of Dth2 which is a homeobox gene in Dugesia tigrina and another was similar to Distal-less gene in Drosophila. This suggests that planarians have many homeobox genes.     

Nucleotide Sequence and Features of the Bacillus licheniformis gnt Operon

Bacillus licheniformis was able to utilize gluconate as thesole carbon source as efficiently as Bacillus subtilis did.Southern analysis indicated that B. licheniformis likely possessesonly one gnt determinant. The nucleotide sequence (6278 bp)of the B. licheniformis DNA containing the gnt operon was determined,revealing the five complete open reading frames (ORF; genes).The putative product of the first gene, oug, did not show anysignificant homology to known proteins, but those of the secondto fifth genes exhibited striking homology to the gntRKPZ genesof B. subtilis, respectively, indicating that they are the correspondinggnt genes of B. licheniformis. Not only is the organizationof the gnt genes of these two Bacilli highly conserved, butso are the cis regulatory elements of their gnt operon. Sequenceanalysis of the upstream regions of these two gnt operons impliedthat a chromosome rearrangement in B. subtilis might have occurredimmediately upstream of the gnt operon during evolution, causingit to diverge from a common ancestor into B. licheniformis andB. subtilis.