Who came first: NK or HOX??? insights from Homeobox genes of Sponges

By | May 7, 2021
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In this blog post we take a look into homeobox repertoire of “Sponges-The pore bearers”. Homeobox genes in most primitive organism on earth “Ctenophores”  gave some valuable insights and now we go a bit ahead in tree of life to gain further insights from demosponge Amphimedon queenslandica genome sequence.

The first conclusive evidence for presence of antennapedia like Homeobox genes in one of earliest metazoans like sponges came from information on whole genome sequence of demosponge Amphimedon. Like the Nk cluster of bilaterians 6 out of 8 Nk genes found are clustered in 71kb region of Amphimedon, indicating regulatory constraints inherent to the organization of this ancient cluster. Amphimedon does not have any Hox or Para Hox gene and present study till now indicates origin of Hox genes for the first time in Cnidarians(In simple terms Cnidaria occupies a branch higher than sponges in tree of life).These details indicate that Hox like gene might have evolved when sponges split from other eumetazoans.

Homeobox genes in Sponges :

Claire Larroux et al, identified 31 homeobox genes in Amphimedon queenslandica genome which includes eight ANTP, nine Prd, four POU, three LIM-HD, one Six,and six TALE.The number of these Homeoboxes in sponges are considerably smaller when compared to Cnidarians and Bilaterians which can to attributed to excessive gene loss in Sponges.The authors, based on the assignment of Amphimedon genes to metazoan orthology groups predict that last common ancestor of Sponges ,Cnidarians and bilaterians had at least 17 Homeobox genes comprising of LIM-Homeodomain , ANTP, Prd, POU,and Six classes (specific to animals only). The 17 homeobox genes predicted by authors inculde 2 TALE class of Homeodomains ,which are most primitive of all homeobox classes found also in Fungi.

It could be also possible that sponges might have lost HOX and Para Hox genes(as gene loss is excessive in present day Sponges) but authors think it is not the case based on some evidences:
1) Many attempts in various sponges never identified Hox like genes.
2) Size of Homeobox genes is similar to other transcription factors(which are in small number) in Sponges.
3) Evidence from Cnidarians suggest low diversity of of Hox related genes in the cnidarian and bilaterian ancestor.

Based upon phylogenic analysis Degnan’s group also suggest that Hox genes in Bilaterians and Cnidarians arose from an expansion of NK cluster in the common ancestor they share with sponges. According to these authors of all Aphimedon genes, Nk gene MSX is clearly the closest relative of Hox genes.

Amphimedon genome data revealed presence of Eight NK genes indicating the last common ansector might have had atleast 6-7 Nk like genes. Phylogenetic analyses place 8 Homeobox genes into NK-related group of Antp genes.Authors placed the NK genes of Amhimedon tentatively with MSX,NK2/3/4,HEX,TLX (Prox2 in sponges) as eumetazoan orthologs.The other NK genes share similarities with NK5,NK6,NK7 and BAR H.Cnidarians have significantly high number of Antp class of genes indicating increase in diversity of this class between metazoans and Eumetazoans last common ancestors.

In Bilaterians ,apart from other functions of NK genes one of the important function is to specify and pattern mesoderm but as Sponges lack this germ layer it may not be ancestral function of these genes.All animals need to pattern cells along body axis so Nk genes might be performing this function in sponges and other organisms where Hox genes are missing.


Larroux C, Fahey B, Degnan SM, Adamski M, Rokhsar DS, Degnan BM.
The NK homeobox gene cluster predates the origin of Hox genes.
Curr Biol. 2007 Apr 17;17(8):706-10

Recently Degnan’s group had come out with their recent article on NK genes in Sponges dealing in more detail about their organization and regulation of Nk genes,concentrating more on upstream intergenic regions of the homeobox genes in the cluster.The autors show that The upstream intergenic regions of the homeobox genes are significantly smaller in Amphimedon than in eumetazoan orthologs, suggesting that the sponge genes house less cis-regulatory information.They also show expression pattern of Nk genes in their recent paper in Biological Bulletin which is rather simple going well with the data of smaller cis regulation information.Finally they suggest that the size of the intergenic regions upstream of the transcription start site may act as a proxy for estimating regulatory complexity and reflect the limitations of the sponge genome to direct complex and varied morphogenetic processes.

The reference for this article of Biological Bulletin :

Fahey B, Larroux C, Woodcroft BJ, Degnan BM.

Does the high gene density in the sponge NK homeobox gene cluster reflect limited regulatory capacity?
Biol Bull. 2008 Jun;214(3):205-17.