Two Ancient Classes of MIKC-type MADS-box Genes are Present in the Moss Physcomitrella patens

Abstract

Characterization of seven MADS-box genes, termed PPM1-PPM4 and PpMADS1-PpMADS3, from the moss model species Physcomitrella patens is reported. Phylogeny reconstructions and comparison of exon-intron structures revealed that the genes described here represent two different classes of homologous, yet distinct, MIKC-type MADS-box genes, termed MIKC(c)-type genes-"(c)" stands for "classic"-(PPM1, PPM2, PpMADS1) and MIKC(*)-type genes (PPM3, PPM4, PpMADS2, PpMADS3). The two gene classes deviate from each other in a characteristic way, especially in a sequence stretch termed intervening region. MIKC(c)-type genes are abundantly present in all land plants which have been investigated in this respect, and give rise to well-known gene types such as floral meristem and organ identity genes. In contrast, LAMB1 from the clubmoss Lycopodium annotinum was identified as the only other MIKC(*)-type gene published so far. Our findings strongly suggest that the most recent common ancestor of mosses and vascular plants contained at least one MIKC(c)-type and one MIKC(*)-type gene. Our studies thus reveal an ancient duplication of an MIKC-type gene that occurred before the separation of the lineages that led to extant mosses and vascular plants more than about 450 MYA. The identification of bona fide K-domains in both MIKC(*)-type and MIKC(c)-type proteins suggests that the K-domain is more ancient than is suggested by a recent alternative hypothesis. MIKC(*)-type genes may have escaped identification in ferns and seed plants so far. It seems more likely, however, that they represent a class of genes which has been lost in the lineage which led to extant ferns and seed plants. The high number of P. patens MADS-box genes and the presence of a K-box in the coding region and of some potential binding sites for MADS-domain proteins and other transcription factors in the putative promoter regions of these genes suggest that MADS-box genes in mosses are involved in complex gene regulatory networks similar to those in flowering plants.

Common Functions for Diverse Small RNAs of Land Plants

“…For instance, miR534 directed the cleavage of two mRNAs encoding ankyrin repeat proteins, while miR536 directed the cleavage of an F-box encoding mRNA. The P. patensspecific miR538 was demonstrated to target three MADS box transcription factors: PPM1, Pp MADS1, and a close relative of PPM2, Phypa1_1 109598 (Krogan and Ashton, 2000;Henschel et al, 2002). Among these miR538 targets, PPM1 has been demonstrated to play a role in moss development; antisense knockdown of PPM1 results in delayed gametangia development and aberrant leaf development (Singer et al, 2007).…”

The MADS-domain protein PPM2 preferentially occurs in gametangia and sporophytes of the moss Physcomitrella patens

“…Since alternative splicing events have been reported in the exons encoding the C-terminal domain of PPM2 (Krogan and Ashton, 2000;Henschel et al, 2002), we chose to fuse both reporter genes to exon 7 of PPM2 in order to abolish these events. As a consequence, both fusion proteins should represent all PPM2 expression domains.…”

“…One important finding for the reconstruction of the evolutionary history of the MADS-box gene family was the identification of angiosperm gene orthologs in gymnosperms showing a high degree of functional conservation (Sundström & Engström, 2002). So far MIKC c MADS-box genes have been characterized from different representatives of lycophytes (Svensson & Engström, 2002;Tanabe et al, 2003), pteridophytes (Münster et al, 1997;Hasebe et al, 1998;Münster et al, 2002), bryophytes (Krogan and Ashton, 2000;Henschel et al, 2002;Hohe et al, 2002) and green algae (Tanabe et al, 2005). However, no evidence for the existence of seed plant gene orthologs could be obtained from non-seed plants.…”

“…To take advantage of unique technical approaches for detailed protein expression analysis, as well as for direct functional studies, the characterization of MADS-box genes has been initiated in the moss Physcomitrella patens (Krogan and Ashton, 2000;Henschel et al, 2002;Hohe et al, 2002). Physcomitrella provides the potential to manipulate gene loci directly due to the high frequency of efficient homologous recombination in its genome (overview in: Schaefer, 2002).…”

“…Physcomitrella provides the potential to manipulate gene loci directly due to the high frequency of efficient homologous recombination in its genome (overview in: Schaefer, 2002). Based on cDNA cloning and EST sequencing, four MIKC c MADS-box genes from Physcomitrella have been previously characterized (Krogan and Ashton, 2000;Henschel et al, 2002;Hohe et al, 2002). After sequencing of the entire Physcomitrella genome, a genomewide survey of the raw sequence data led to the identification of a total of six different MIKC c MADS-box gene loci (V.Q.…”