Homeobox

A homeobox is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development (morphogenesis) in animals, fungi and plants.

Discovery
They were discovered independently in 1983 by Ernst Hafen, Michael Levine and William McGinnis working in the lab of Walter Jakob Gehring at the University of Basel, Switzerland; and by Matthew P. Scott and Amy Weiner, who were then working with Thomas Kaufman at Indiana University in Bloomington.

Homeodomain
A homeobox is about 180 base pairs long. It encodes a protein domain (the homeodomain) which when expressed (i.e. as protein) can bind DNA. The following shows the consensus 60-polypeptide chain corresponding to homeobox domain, with typical intron positions noted with dashes:

RRRKRTA-YTRYQLLE-LEKEFLF-NRYLTRRRRIELAHSL-NLTERHIKIWFQN-RRMK-WKKEN

Homeobox genes encode transcription factors that typically switch on cascades of other genes. The homeodomain binds DNA in a sequence-specific manner. However, the specificity of a single homeodomain protein is usually not enough to recognize only its desired target genes. Most of the time, homeodomain proteins act in the promoter region of their target genes as complexes with other transcription factors. Such complexes have a much higher target specificity than a single homeodomain protein. Homeodomains are encoded both by genes of the Hox gene clusters and by other genes throughout the genome.

The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure.

The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.

Hox genes


They are essential metazoan genes as they determine the identity of embryonic regions along the anterio-posterior axis. The first vertebrate Hox gene was isolated in Xenopus by Eddy De Robertis and colleagues in 1984, marking the beginning of the young science of Evo-devo.

In vertebrates, the four paralog clusters are partially redundant in function, but have also acquired several derived functions. In particular, HoxA and HoxD specify segment identity along the limb axis.

The main interest in this set of genes stems from their unique behaviour. They are typically found in an organized cluster. The linear order of the genes within a cluster is directly correlated to the order of the regions they affect as well as the timing in which they are affected. This phenomenon is called colinearity. Due to this linear relationship, changes in the gene cluster due to mutations generally result in similar changes in the affected regions.

For example, when one gene is lost the segment develops into a more anterior one, while a mutation that leads to a gain of function causes a segment to develop into a more posterior one. This is called ectopia. Famous examples are Antennapedia and bithorax in Drosophila, which can cause the development of legs instead of antennae and the development of a duplicated thorax, respectively.

Molecular evidence shows that some limited number of Hox genes have existed in the Cnidaria since before the earliest true Bilatera, making these genes pre-Paleozoic.

Diversity
The homeobox genes were first found in the fruit fly Drosophila melanogaster and have subsequently been identified in many other species, from insects to reptiles and mammals.

Homeobox genes were previously only identified in bilateria but more recently cnidaria have also been found to contain homeobox domains and the "missing link" in the evolution between the two has been identified.

Homeobox genes have even been found in fungi, for example the unicellular yeasts, and in plants.

Plants
The well known homeotic genes in plants (MADS-box genes) are not homologous to Hox genes in animals. Plants and animals do not share the same homeotic genes, and this suggests that homeotic genes arose independently in the early evolution of animals and plants.

Human genes
Humans generally contain Hox genes in four clusters:

There is also a "distal-less homeobox" family: DLX1, DLX2, DLX3, DLX4, DLX, and DLX6.

"HESX homeobox 1" is also known as HESX1.

Short stature homeobox gene is also known as SHOX.

Additional human proteins containing this domain per UniProt annotation:
 * ADNP; ALX3; ALX4; ARGFX; ARX
 * BAPX1; BARHL1; BARHL2; BARX1; BARX2; CART1
 * CDX1; CDX2; CDX4; CRX; CUTL1; CUTL2
 * DBX1; DBX2; DLX1; DLX2; DLX3; DLX4; DLX5; DLX6; DMBX1; DPRX; DRGX; DUX1; DUX2; DUX3; DUX4; DUX4c; DUX5; DUXA
 * EMX1; EMX2; EN1; EN2; ESX1L; EVX1; EVX2
 * GBX1; GBX2; GSC; GSC2; GSX1; GSX2
 * HDX; HESX1; HHEX; HLX1; HMBOX1; HMX1; HMX2; HMX3; HOMEZ; HOPX
 * IRX1; IRX2; IRX3; IRX4; IRX5; IRX6; ISL1; ISL2; ISX
 * LASS3; LASS5; LASS6; LBX1; LBX2; LHX1; LHX2; LHX3; LHX4; LHX5; LHX6; LHX8; LHX9; LMX1A; LMX1B; LOC340260
 * MEIS1; MEIS2; MEIS3; MEOX1; MEOX2; MIXL1; MKX; MNX1; MSX1; MSX2
 * NANOG; NANOGP1; NANOGP8; NKX2-2; NKX2-3; NKX2-4; NKX2-5; NKX2-8; NKX3-1; NKX6-1; NKX6-2; NKX6-3; NOBOX
 * ONECUT1; ONECUT2; ONECUT3; OTP; OTX1; OTX2
 * PAX3; PAX4; PAX6; PAX7; PAX7B; PBX1; PBX2; PBX3; PBX4; PDX1; PHOX2A; PHOX2B; PITX1; PITX2; PITX3; PKNOX1; PKNOX2; POU1F1; POU2F1; POU2F2; POU2F3; POU3F1; POU3F2; POU3F3; POU3F4; POU4F1; POU4F2; POU4F3; POU5F1; POU5F1P1; POU5F1P4; POU5F2; POU6F2; PROP1; PRRX1; PRRX2
 * RAX; RAXL1; RHOXF1; RHOXF2
 * SATB1; SATB2; SEBOX; SHOX; SHOX2; SIX1; SIX2; SIX3; SIX4; SIX5; SIX6
 * TCF1; TCF2; TGIF1; TGIF2; TGIF2LX; TGIF2LY; TITF1; TLX1; TLX2; TLX3; TSHZ1; TSHZ2; TSHZ3
 * VAX1; VAX2; VENTX; VSX1; VSX2
 * ZFHX2; ZFHX3; ZFHX4; ZHX1

Mutations
Mutations to homeobox genes can produce easily visible phenotypic changes.

Two examples of homeobox mutations in the above-mentioned fruit fly are legs where the antennae should be (antennapedia), and a second pair of wings.

Duplication of homeobox genes can produce new body segments, and such duplications are likely to have been important in the evolution of segmented animals. However, Hox genes typically determine the identity of body segments.

Interestingly, there is one insect family, the xyelid sawflies, in which both the antennae and mouthparts are remarkably leg-like in structure. This is not uncommon in arthropods as all arthropod appendages are homologous.

Regulation
The regulation of Hox genes is highly complex and involves reciprocal interactions, mostly inhibitory. Drosophila is known to use the Polycomb and Trithorax Complexes to maintain the expression of Hox genes after the down-regulation of the pair-rule and gap genes that occurs during larval development. Polycomb-group proteins can silence the HOX genes by modulation of chromatin structure.