Ancestry and diversity of BEL1 -like homeobox genes revealed by gymnosperm ( Gnetum gnemon ) homologs

Abstract

BEL1-like homeobox genes encode plant-specific transcription factors, at least some of which are important for ovule development. Here we report MELBEL1-MELBEL4,the first BEL1-like genes from a non-flowering plant, the gymnosperm Gnetum gnemon. Our analyses suggest that there was already at least one BEL1-like gene present in the most recent common ancestor of extant seed plants about 300 million years ago. Multiple sequence alignments revealed that since this time, not only the DNA-binding homeodomain, but also a protein-protein interaction domain upstream of the homeodomain, termed the BEL domain, has been highly conserved. Sequence comparison of the BEL domain with upstream domains that have been conserved in other TALE homeodomain proteins, i.e. MEIS, KNOX, and PBC, revealed only weak sequence similarity. However, since homology has been shown for MEIS, KNOX, and PBC domains and since KNOX and BEL domains directly interact in vivo, it appears likely that the BEL domain was also derived from an ancestral upstream (MEINOX) domain.

Identification and characterization of homeobox genes in Eucalyptus

“…Although these two homeodomain families harbor specific structural similarities, our phylogenetics reconstruction revealed only weak statistical support for the TALE super class (Figure 2). This uncertain evolutionary relationship between TALE members has already been observed in the literature (Bürglin, 1997;Becker et al, 2002).…”

“…This class is characterized by three extra amino acids between homeodomain helix 1 and helix 2 (Chan et al, 1998;Bellaoui et al, 2001;Becker et al, 2002). However this characteristic three amino acid insertion was not found in two Eucalyptus EST-contigs classified as Bell (EGQHLV3278D04 and EGABST2040C11) and in one classified as Knox (EGCEST6032A06), probably due to incomplete sequencing (Figure 1).…”

“…They are thus classified in the TALE (Three Amino acid Loop Extension) super-class (Chan et al, 1998;Bellaoui et al, 2001;Becker et al, 2002).…”

TheArabidopsisBEL1-LIKE HOMEODOMAIN Proteins SAW1 and SAW2 Act Redundantly to RegulateKNOXExpression Spatially in Leaf Margins

“…In Arabidopsis, there are 12 TALE homeobox genes closely related in sequence to BEL1 that have been identified, including BLH1-7, BLH10, BLH11 (for BEL1-LIKE HOMEODOMAIN), BLR, PNF, and ATH1 (Quaedvlieg et al, 1995;Reiser et al, 1995;Bellaoui et al, 2001;Becker et al, 2002;Byrne et al, 2003;Roeder et al, 2003;Smith and Hake, 2003;Smith et al, 2004;Hackbusch et al, 2005; this study). These deduced BLH proteins share at least three regions of sequence similarity: the DNA binding homeodomain and the BELL and SKY domains involved in BEL1 interactions with KNOX TALE homeodomain proteins (Bellaoui et al, 2001;Becker et al, 2002). Phylogenetic analysis of this gene family ( Figure 1A; Becker et al, 2002) indicates that the genes most closely related in sequence to BEL1 are two genes formerly referred to as BLH2 and BLH4 (Becker et al, 2002) that we designate SAW1 and SAW2, respectively, based on their loss-of-function leaf phenotype (see below).…”

“…These deduced BLH proteins share at least three regions of sequence similarity: the DNA binding homeodomain and the BELL and SKY domains involved in BEL1 interactions with KNOX TALE homeodomain proteins (Bellaoui et al, 2001;Becker et al, 2002). Phylogenetic analysis of this gene family ( Figure 1A; Becker et al, 2002) indicates that the genes most closely related in sequence to BEL1 are two genes formerly referred to as BLH2 and BLH4 (Becker et al, 2002) that we designate SAW1 and SAW2, respectively, based on their loss-of-function leaf phenotype (see below). We focused on these two genes as the ones most likely to have overlapping functions with BEL1, similar to the situation observed with Arabidopsis MADS domain proteins (Pelaz et al, 2000).…”