Ancestry of KNOX genes revealed by bryophyte (Physcomitrella patens) homologs

Abstract

Summary• Structural and phylogenetic studies of KNOX genes identified in the bryophyte Physcomitrella patens are reported here, to provide insights into the evolution of class 1 and class 2 KNOX genes.• Three KNOTTED1 -like homeobox ( KNOX ) genomic clones were isolated and sequenced from P. patens . Corresponding cDNAs from a library, prepared from mRNA transcripts isolated from gametophytic tissues, were also sequenced.• Conceptual translation and analysis of the bryophyte coding sequences revealed a domain pattern and secondary structures typical of higher plant KNOX proteins. Intron number and positions within the genes were also highly conserved between moss and angiosperm loci, providing further support for their homology. Structural and phylogenetic analyses indicated that moss clones ( MKN2 and MKN4 ) represent class 1 KNOX genes and the remaining clone ( MKN1-3 ) is a class 2 KNOX gene.• We conclude that the observed protein domain pattern is encoded by homeobox genes that evolved after separation of the plant lineage from that of fungi and animals, and must have been present in the common ancestor to mosses and seed plants. It is proposed that gene duplication and diversification, which created class 1 and 2 KNOX gene subfamilies, occurred after separation of this common ancestor from its algal progenitor (since a characterized algal KNOX gene cannot be assigned to class 1 or 2), but before the moss and higher plant lineages diverged.

Gene expression patterns in seed plant shoot meristems and leaves: homoplasy or homology?

“…Thus, both CUC and Class I KNOX gene expression is associated with low levels of auxin. Class I KNOX genes are found in all land plants, and their role in the development of moss sporophytes suggest an ancestral role in preventing premature differentiation in the sporophyte apex of land plants (Champagne and Ashton 2001;Sakakibara et al 2008;Singer and Ashton 2007).…”

A NEWMOSSGENETICS: Targeted Mutagenesis inPhyscomitrella patens

“…Preliminary analysis of genes and ESTs strongly indicate that these sequences are highly similar to those of the corresponding higher plant genes. These similarities extend to codon usage (68,96), intron-exon structure (18,61,67), and multigene family complexity (18,61,95). It is clear that the number of Physcomitrella genes and EST sequences accessible in the database will increase rapidly, and each entry directly enables the generation of the corresponding moss mutant by targeted transgenesis.…”

“…The phylogenetic basal position of Bryophytes among land plants places them in an ideal situation to address fundamental questions such as how have plants evolved from simple to complex forms (29). In this respect, functional analysis of the recently identified Physcomitrella gene homolog to key players in plant development such as the MADS (61) and homeobox genes (18,102) of higher plants may give us valuable information about the ancestral mechanisms that govern the development of land plants (121). One can predict that this is only the beginning.…”

The organization of Physcomitrella patens RAD51 genes is unique among eukaryotic organisms

“…The question arises as to whether this gene duplication ref lects a genome duplication event or is restricted to RAD51. There is little information on the Physcomitrella genome, and data available from other genes (28,29) are too premature to address the question of gene duplication. However, polyploidization in the ancestry of Physcomitrella is discussed (reviewed in ref.…”

“…Organisms with intronless RAD51 genes are unicellular eukaryotes such as budding and fission yeasts, and organisms possessing intronless genomes. Physcomitrella does not belong to the latter group, because introns are found frequently in Physcomitrella genes, and the positions are largely conserved between Physcomitrella and Arabidopsis (28,29). Introns in RAD51 and other RAD51-like genes may serve important functions.…”