Evolution and protein interactions of AP2 proteins in Brassicaceae: Evidence linking development and environmental responses

Abstract

Plants have evolved a large number of transcription factors (TF), which are enriched among duplicate genes, highlighting their roles in complex regulatory networks. The APETALA2/EREBP-like genes constitute a large plant TF family and participate in development and stress responses. To probe the conservation and divergence of AP2/EREBP genes, we analyzed the duplication patterns of this family in Brassicaceae and identified interacting proteins of representative Arabidopsis AP2/EREBP proteins. We found that many AP2/EREBP duplicates generated early in Brassicaceae history were quickly lost, but many others were retained in all tested Brassicaceae species, suggesting early functional divergence followed by persistent conservation. In addition, the sequences of the AP2 domain and exon numbers were highly conserved in rosids. Furthermore, we used 16 A. thaliana AP2/EREBP proteins as baits in yeast screens and identified 1,970 potential AP2/EREBP-interacting proteins, with a small subset of interactions verified in planta. Many AP2 genes also exhibit reduced expression in an antherdefective mutant, providing a possible link to developmental regulation. The putative AP2-interacting proteins participate in many functions in development and stress responses, including photomorphogenesis, flower development, pathogenesis, drought and cold responses, abscisic acid and auxin signaling. Our results present the AP2/EREBP evolution patterns in Brassicaceae, and support a proposed interaction network of AP2/EREBP proteins and their putative interacting proteins for further study.

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets

“…Our rationales for the initial selection of marker genes were: genes should have good representation among taxa to reduce the amount of missing data, contain sufficient phylogenetic information, be relatively conserved for reliable alignment and be putative orthologs to yield the correct topology; the gene set is relatively small to avoid very long computational time and high costs for hundreds of taxa in subsequent analyses; and for the supermatrix strategy, a moderate number of genes is used to avoid systematic errors because of greater likelihood for such errors when using large numbers of genes (Jeffroy et al, 2006). In particular, short genes tend to yield largely unresolved trees, even for previously resolved organismal relationships, and thus are not desirable; genes with relatively low sequence similarity are hard to align, or have phylogenetic noises (homoplasy, such as the rapidly evolving resistance genes) (Michelmore & Meyers, 1998); and genes with multiple copies or belonging to large gene families (Zeng et al, 2015) include many paralogs and often introduce uncertainty when identifying orthologs in hundreds of taxa. Therefore, such genes were not selected.…”

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus

“…In that its pivotal importance to plant tolerance, the AP2/ERF superfamily has been identified and investigated in many plants, including Arabidopsis thaliana, Oryza sativa (Nakano et al, 2006 ), Brassica rapa (Song et al, 2013 ), Brassica oleracea (Thamilarasan et al, 2014 ), Populus trichocarpa (Zhuang et al, 2008 ), Vitis vinifera (Licausi et al, 2010 ), Cucumis sativus (Hu and Liu, 2011 ), Triticum aestivum (Zhuang et al, 2011a ), Glycine max (Zhang et al, 2008 ), and Hordeum vulgare (Gil-Humanes et al, 2009 ), Hevea brasiliensis (Duan et al, 2013 ), Arabidopsis lyrata, Capsella rubella, Eutrema salsugineum , and Carica papaya (Zeng et al, 2016 ).…”

New different origins and evolutionary processes of AP2/EREBP transcription factors in Taxus chinensis

“…RAV has a B3 domain in addition to the AP2 domain. Soloists have only one AP2 domain with an HLG-motif instead of YLG- and WLG-motifs and are the smallest group in AP2/EREBP proteins, whereas DREB and ERF constitute the largest groups in nearly all plants [8, 11, 30, 35, 39]. These domain structures of AP2/EREBP proteins have evolved conservatively in many plant species, although most of them are angiosperms.…”

“…AP2/EREBP superfamily proteins are divided into six subgroups, namely, APETELA2 (AP2), AINTEGUMENTA (ANT), related to ABI3/VP1 (RAV), dehydration-responsive element-binding protein (DREB), ethylene-responsive factor (ERF), and soloist in most plants [6, 7]. AP2 and ANT proteins mainly function as key developmental regulators in reproductive and vegetative organs and lateral organ development [8, 9]. As negative regulators, RAV proteins mediate plant defense during abiotic and biotic stress [10–12].…”