A homeobox is a DNA sequence, around 180 long, that regulates large-scale anatomical features in the early stages of embryonic development. Mutations in a homeobox may change large-scale anatomical features of the full-grown organism.
Homeoboxes are found within that are involved in the regulation of patterns of anatomical development (morphogenesis) in , fungus, , and numerous single cell .
Homeosis is a term coined by William Bateson to describe the outright replacement of a discrete body part with another body part, e.g. antennapedia—replacement of the antenna on the head of a fruit fly with legs.[Materials for the study of variation, treated with especial regard to discontinuity in the origin of species William Bateson 1861–1926. London : Macmillan 1894 xv, 598 p] The "homeo-" prefix in the words "homeobox" and "homeodomain" stems from this mutation, which is observed when some of these genes are mutated in animals. The homeobox domain was first identified in a number of Drosophila Homeosis and segmentation proteins, but is now known to be well-conserved in many other animals, including .
Discovery
The existence of homeobox genes was first discovered in
Drosophila by isolating the gene responsible for a homeotic transformation where legs grow from the head instead of the expected antennae. Walter Gehring identified a gene called
antennapedia that caused this homeotic phenotype.
Analysis of
antennapedia revealed that this gene contained a 180 base pair sequence that encoded a DNA binding domain, which William McGinnis termed the "homeobox".
The existence of additional
Drosophila genes containing the
antennapedia homeobox sequence was independently reported by Ernst Hafen, Michael Levine,
William McGinnis, and Walter Jakob Gehring of the University of Basel in
Switzerland and Matthew P. Scott and Amy Weiner of Indiana University in Bloomington in 1984.
Isolation of homologous genes by Edward de Robertis and William McGinnis revealed that numerous genes from a variety of species contained the homeobox.
Subsequent
Phylogenetics studies detailing the evolutionary relationship between homeobox-containing genes showed that these genes are present in all
Bilateria animals.
Homeodomain structure
The characteristic homeodomain
protein fold consists of a 60-
amino acid long domain composed of three
alpha helix. The following shows the consensus homeodomain (~60 amino acid chain):
Helix 1 Helix 2 Helix 3/4
______________ __________ _________________
RRRKRTAYTRYQLLELEKEFHFNRYLTRRRRIELAHSLNLTERHIKIWFQNRRMKWKKEN
....|....|....|....|....|....|....|....|....|....|....|....|
10 20 30 40 50 60
Helix 2 and helix 3 form a so-called
helix-turn-helix (HTH) structure, where the two alpha helices are connected by a short loop region. The
N-terminus two helices of the homeodomain are antiparallel and the longer
C-terminus helix is roughly perpendicular to the axes of the first two. It is this third helix that interacts directly with
DNA via a number of hydrogen bonds and hydrophobic interactions, as well as indirect interactions via water molecules, which occur between specific
and the exposed
nucleotide within the
major groove of the DNA.
Homeodomain proteins are found in .
Sequence specificity
Homeodomains can bind both specifically and nonspecifically to
B-DNA with the C-terminal recognition helix aligning in the DNA's major groove and the unstructured peptide "tail" at the N-terminus aligning in the minor groove. The recognition helix and the inter-helix loops are rich in
arginine and
lysine residues, which form
to the DNA backbone. Conserved
hydrophobic residues in the center of the recognition helix aid in stabilizing the helix packing. Homeodomain proteins show a preference for the DNA sequence 5'-TAAT-3'; sequence-independent binding occurs with significantly lower affinity. The specificity of a single homeodomain protein is usually not enough to recognize specific target gene promoters, making cofactor binding an important mechanism for controlling binding sequence specificity and target gene expression. To achieve higher target specificity, homeodomain proteins form complexes with other transcription factors to recognize the promoter region of a specific target gene.
Biological function
Homeodomain proteins function as transcription factors due to the DNA binding properties of the conserved HTH motif. Homeodomain proteins are considered to be master control genes, meaning that a single protein can regulate expression of many target genes. Homeodomain proteins direct the formation of the body axes and body structures during
Embryogenesis.
Many homeodomain proteins induce cellular differentiation by initiating the cascades of coregulated genes required to produce individual tissues and organs. Other proteins in the family, such as NANOG are involved in maintaining
pluripotency and preventing cell differentiation.
Regulation
Hox gene and their associated
are highly conserved developmental master regulators with tight tissue-specific, spatiotemporal control. These genes are known to be dysregulated in several cancers and are often controlled by DNA methylation.
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.
Mutations
Mutations to homeobox genes can produce easily visible
phenotype changes in body segment identity, such as the Antennapedia and Bithorax mutant phenotypes in
Drosophila. Duplication of homeobox genes can produce new body segments, and such duplications are likely to have been important in the
evolution of segmented animals.
Evolution
Phylogenetic analysis of homeobox gene sequences and homeodomain protein structures suggests that the last common ancestor of plants, fungi, and animals had at least two homeobox genes.
Molecular evidence shows that some limited number of Hox genes have existed in the
Cnidaria since before the earliest true
Bilateria, making these genes pre-
Paleozoic.
It is accepted that the three major animal ANTP-class clusters, Hox, ParaHox, and NK (MetaHox), are the result of segmental duplications. A first duplication created MetaHox and ProtoHox, the latter of which later duplicated into Hox and ParaHox. The clusters themselves were created by tandem duplications of a single ANTP-class homeobox gene.
Gene duplication followed by neofunctionalization is responsible for the many homeobox genes found in eukaryotes.
Comparison of homeobox genes and gene clusters has been used to understand the evolution of genome structure and body morphology throughout metazoans.
Types of homeobox genes
Hox genes
Hox genes are the most commonly known subset of homeobox genes. They are essential
Metazoa genes that determine the identity of embryonic regions along the anterior-posterior axis.
The first vertebrate Hox gene was isolated in
Xenopus by Edward De Robertis and colleagues in 1984.
The main interest in this set of genes stems from their unique behavior and arrangement in the genome. Hox genes are typically found in an organized cluster. The linear order of Hox genes within a cluster is directly correlated to the order in which they are expressed in both time and space during development. This phenomenon is called colinearity.
Mutations in these Homeotic gene cause displacement of body segments during embryonic development. This is called ectopia. 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. Famous examples are Antennapedia and Bithorax complex in Drosophila, which can cause the development of legs instead of antennae and the development of a duplicated thorax, respectively.
In vertebrates, the four paralog clusters are partially redundant in function, but have also acquired several derived functions. For example, HoxA and HoxD specify segment identity along the limb axis.
LIM genes
LIM genes (named after the initial letters of the names of three proteins where the characteristic domain was first identified) encode two 60 amino acid cysteine and histidine-rich LIM domains and a homeodomain. The LIM domains function in protein-protein interactions and can bind zinc molecules. LIM domain proteins are found in both the cytosol and the nucleus. They function in cytoskeletal remodeling, at focal adhesion sites, as scaffolds for protein complexes, and as transcription factors.
Pax genes
Most Pax genes contain a homeobox and a paired domain that also binds DNA to increase binding specificity, though some Pax genes have lost all or part of the homeobox sequence.
Pax genes function in embryo segmentation,
nervous system development, generation of the frontal eye fields,
Skeleton development, and formation of face structures. Pax 6 is a master regulator of eye development, such that the gene is necessary for development of the optic vesicle and subsequent eye structures.
POU genes
Proteins containing a POU region consist of a homeodomain and a separate, structurally homologous POU domain that contains two
helix-turn-helix motifs and also binds DNA. The two domains are linked by a flexible loop that is long enough to stretch around the DNA helix, allowing the two domains to bind on opposite sides of the target DNA, collectively covering an eight-base segment with consensus sequence 5'-ATGCAAAT-3'. The individual domains of POU proteins bind DNA only weakly, but have strong sequence-specific affinity when linked. The POU domain itself has significant structural similarity with repressors expressed in
, particularly
lambda phage.
Plant homeobox genes
As in animals, the plant homeobox genes code for the typical 60 amino acid long DNA-binding homeodomain or in case of the TALE (three amino acid loop extension) homeobox genes for an atypical homeodomain consisting of 63 amino acids. According to their conserved intron–exon structure and to unique codomain architectures they have been grouped into 14 distinct classes: HD-ZIP I to IV, BEL, KNOX, PLINC, WOX, PHD, DDT, NDX, LD, SAWADEE and PINTOX.
Conservation of codomains suggests a common eukaryotic ancestry for TALE
and non-TALE homeodomain proteins.
Human homeobox genes
The Hox genes in humans are organized in four chromosomal clusters:
| gene |
| HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, HOXA11, HOXA13 |
| HOXB1, HOXB2, HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, HOXB8, HOXB9, HOXB13 |
| HOXC4, HOXC5, HOXC6, HOXC8, HOXC9, HOXC10, HOXC11, HOXC12, HOXC13 |
| HOXD1, HOXD3, HOXD4, HOXD8, HOXD9, HOXD10, HOXD11, HOXD12, HOXD13 |
ParaHox genes are analogously found in four areas. They include CDX1, CDX2, CDX4; GSX1, GSX2; and PDX1. Other genes considered Hox-like include EVX1, EVX2; GBX1, GBX2; MEOX1, MEOX2; and MNX1. The NK-like (NKL) genes, some of which are considered "MetaHox", are grouped with Hox-like genes into a large ANTP-like group.
Humans have a "distal-less homeobox" family: DLX1, DLX2, DLX3, DLX4, DLX5, and DLX6. Dlx genes are involved in the development of the nervous system and of limbs.
Human TALE (Three Amino acid Loop Extension) homeobox genes for an "atypical" homeodomain consist of 63 rather than 60 amino acids:
IRX1, IRX2, IRX3, IRX4, IRX5, IRX6; MEIS1, MEIS2, MEIS3; MKX; PBX1, PBX2, PBX3, PBX4; PKNOX1, PKNOX2; TGIF1, TGIF2, TGIF2LX, TGIF2LY.
In addition, humans have the following homeobox genes and proteins:
-
LIM-class: ISL1, ISL2; LHX1, LHX2, LHX3, LHX4, LHX5, LHX6, LHX8, LHX9; LMX1A, LMX1B
-
POU-class: HDX; POU1F1; POU2F1; POU2F2; POU2F3; POU3F1; POU3F2; POU3F3; POU3F4; POU4F1; POU4F2; POU4F3; POU5F1; POU5F1P1; POU5F1P4; POU5F2; POU6F1; and POU6F2
-
CERS-class: LASS2, LASS3, LASS4, LASS5, LASS6;
-
HNF-class: HMBOX1; HNF1A, HNF1B;
-
SINE-class: SIX1, SIX2, SIX3, SIX4, SIX5, SIX6
-
CUT-class: ONECUT1, ONECUT2, ONECUT3; CUX1, CUX2; SATB1, SATB2;
-
ZF-class: ADNP, ADNP2; TSHZ1, TSHZ2, TSHZ3; ZEB1, ZEB2; ZFHX2, ZFHX3, ZFHX4; ZHX1, HOMEZ;
-
PRD-class: ALX1 (CART1), ALX3, ALX4; ARGFX; ARX; DMBX1; DPRX; DRGX; DUXA, DUXB, DUX (1, 2, 3, 4, 4c, 5); ESX1; GSC, GSC2; HESX1; HOPX; ISX; LEUTX; MIXL1; NOBOX; OTP; OTX1, OTX2, CRX; PAX2, PAX3, PAX4, PAX5, PAX6, PAX7, PAX8; PHOX2A, PHOX2B; PITX1, PITX2, PITX3; PROP1; PRRX1, PRRX2; RAX, RAX2; RHOXF1, RHOXF2/2B; SEBOX; SHOX, SHOX2; TPRX1; UNCX; VSX1, VSX2
-
NKL-class: BARHL1, BARHL2; BARX1, BARX2; BSX; DBX1, DBX2; EMX1, EMX2; EN1, EN2; HHEX; HLX1; LBX1, LBX2; MSX1, MSX2; NANOG; NOTO; TLX1, TLX2, TLX3; TSHZ1, TSHZ2, TSHZ3; VAX1, VAX2, VENTX;
-
Nkx: NKX2-1, NKX2-4; NKX2-2, NKX2-8; NKX3-1, NKX3-2; NKX2-3, NKX2-5, NKX2-6; HMX1, HMX2, HMX3; NKX6-1; NKX6-2; NKX6-3;
See also
Further reading
External links
