NK genes

By | May 7, 2021
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Comparison of whole genome sequences from different representatives animals revealed that HOX, PARA HOX and NK were originally close to each other in the genome, forming a big mega cluster / super Hox cluster and later would have followed different evolutionary paths in each lineage.

The expression pattern of these three gene clusters are also interesting. Hox genes are expressed in all three germ layers but predominantly in ectodermal and neuroectoderm , ParaHox genes are expressed primarily in endodermal derivatives, and NK genes are expressed mostly in mesodermal derivatives.

Today we discuss about “NK GENES”.


It was in the year 1989 Yongsok Kim and Marshall Nirenberg discovered four Drosophila melanogaster homeobox genes by screening a genomic DNA library with oligodeoxynucleotides that correspond to a conserved amino acid sequence that is part of homeobox, which was published in PNAS. Named after the discoverers, NK1, NK3 and NK4 mapped to the same cytological location – bands 93D/E on chromosome 3. NK2 is located on chromosome 1. Later three more Nk genes were isolated near 93D/E cluster and tally finally rose to nine NK genes with the discovery of two more genes.

The NK cluster in Drosophila is also in chromosome 3R like Hox complex and clustering is thought to be crucial for the proper execution of their developmental programs.The nomenclature for NK genes is complex( more complex then Hox genes). First they were denoted by Nk and a number but later the
genes were renamed to reflect the known mutational alleles

NK1 : S59 or slouch (slou),
NK2 : ventral nervous system defective (vnd),
NK3 : bagpipe (bap),
NK4 : muscle-specific homeobox 2 (msh2) or tinman (tin)
NK5 : Hmx
Lbx : Ladybird early (lbe ) and Ladybird late (lbl)
Msx : Drop / muscle-specific homeodomain 1
Tlx : C15

Six of the above NK genes are present in a cluster on chromosome 3 and are called 93D/E or NK gene cluster. These six NK or homeobox genes are tin, bap, lbl, lbe, C15 and slou. The other Nk genes are dispersed on other chromosomes.

93 D / E Cluster or NK cluster

The relatively high divergence of homeodomain sequences among NK genes and the presence of clear vertebrate homologs for the majority of them indicate that these homeobox genes did not arise from a recent amplification of a common ancestor. However, Ladybird early and late gene pair may result from a more recent tandem duplication of an lb-like ancestral gene as their homeodoamins show much similarity.Apart from Homeodomain Nk genes share a short motif similar to EH1(Groucho interacting domain– Groucho is well known co repressor) near amino terminus, which displays similarities with the Eh1 repression domain originally found in transcriptional regressors of the Engrailed (En) family.

The expression of NK cluster genes has been very well studied in D. melanogaster. An exciting finding is that all six members of the originally described at 93D/E cluster (tin, bap, lbe, lbl,C15 and slou) take part in early mesodermal patterning and differentiation. The interactions among these genes is complex in mesoderm patterening but tinman serves as common initiator in most cases.The collinear expression pattern among NK genes is not clear but some data suggest temporal colinearity like vertebrate Hox genes. tin is the first gene to be expressed; it appears in all mesodermal cells and is then restricted to the dorsal mesodermal cells at gastrulation. tin is crucial in specifying the dorsal mesoderm derivatives.tin then activates its neighboring bap in the visceral mesoderm primordia. The remaining NK cluster genes function after the cardiac, visceral and somatic primordia have been established.Important targets of tin regulatation are mef2 ,beta tubulin and tin itself.

Like Hox genes, NK genes are also conserved through out evolution. Nk genes are found in Ctenophores (NK-Like) and Sponges also meaning that the common ancestor of Ctenophores and other metazoans possessed at least a single Hox-like gene. In vertebrates the NK cluster is split into three where only two gene pairs are maintained close together: NK3-NK4 and Lbx-Tlx.


Jagla, K., Bellard, M. & Frasch, M.
A cluster of Drosophila homeobox genes involved in mesoderm differentiation programs.
Bioessays 23, 125–133 (2001).

Jordi Garcia-Fernandez