Evolution of Plant Homeobox Genes

Abstract

Plant homeobox genes can be classified into 14 evolutionary classes, each characterised by fusion of the homeodomain with class‐specific codomains. Among these classes only BEL and KNOX are found in red algae, whereas unicellular green algae also include members of the classes WOX, DDT and PINTOX. All 14 classes are found only in land plants, including moss and vascular plants, suggesting that homeobox genes have proliferated within each class particularly in flowering plants, indicating that all classes had already differentiated in the common ancestor of moss and vascular plants. In different land plants, including moss and flowering plant, multiple gene copies are observed for most classes, suggesting that proliferation and functional differentiation of gene paralogues within the original classes reflects the increasing complexity of plant development and architecture.

Key Concepts:

  • Homeobox genes in plant can be classified into 14 distinct classes all of which had appeared in the common ancestor of Bryophyta and Tracheophyta.

  • Functional differentiation of plant homeodomain protein classes relates to acquisition of a class‐specific codomain architecture.

  • Proliferation of paralogous genes within each class in land plants concomitantly with increasing organismal complexity.

Keywords: homeobox; homeodomain; transcription factor; plant

Figure 1.

Multiple sequence alignment of homeodomain sequence representatives from Arabidopsis thaliana (At), rice Oryza sativa (Os), moss Physcomitrella patens (Pp) and spikemoss Selaginella moellendorffii (Sm). Canonical homeodomain sequence numbering (excluding loops), the TALE class three‐residue insertion (abc) and the position of the three homeodomain helices (bottom line) are indicated. Conserved amino acids of different physicochemical properties are highlighted in different colours. Adapted from Mukherjee et al., with permission of Oxford University Press.

Figure 2.

Schematic overview of the domain architecture of all 14 classes of plant homeodomain proteins with associated codomains: HD, homeodomain; LZ, Leucine Zipper motif; HD‐SAD, homeodomain‐START‐associated domain. For the DDT class, only D‐TOX A is indicated with its full symbol, whereas D‐TOX B, C, D, E, F, G and H are indicated by the respective letters. D‐TOX E=WSD and D‐TOX F=D‐TOX ZF. Adapted from Mukherjee et al., with permission of Oxford University Press.

Figure 3.

Schematic representation of the evolutionary history of plant homeobox gene classes and codomains following. A class or motif represented in a parental branch indicates that the same class/motif is also present in all of its child‐branches except for the losses of the START domain from the genomes of unicellular green algae and red algae, represented by the domain crossed in red. The HDZIP I–IV classes are represented by the single domain architecture HDLZ‐CPSC‐START‐HD‐SAD‐MEKHLA. In this representation, arrows separate motif groups whose addition defines, in the order, HD‐ZIP classes I, II, IV and III. Acquisition of the MEKHLA domain from a cyanobacterial/chloroplast genome is indicated by an arrow. Adapted from Mukherjee et al., with permission of Oxford University Press.

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Mukherjee, Krishanu, and Brocchieri, Luciano(Sep 2010) Evolution of Plant Homeobox Genes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022865]