Abstract
BackgroundCytokinin Response Factors (CRFs) are a small subset of AP2/ERF transcription factor genes shown in Arabidopsis to regulate leaf development as part of the cytokinin signal transduction pathway. This study examines the phylogenetic distribution of CRF genes in other plant species, and attempts to identify the extent of sequence conservation and potential gene function among all CRF genes.ResultsWe identified CRF genes in representatives of all major land plant lineages, including numerous flowering plant taxa in addition to the model systems in which ERF genes have been catalogued. Comparative analysis across this broader sampling has identified strongly conserved amino acid motifs other than the AP2/ERF domain for all CRF proteins as well as signature sequences unique to specific clades of CRF genes. One of these motifs, here designated as the CRF domain, is conserved in and unique to CRF proteins distinguishing them from related genes. We show that this novel domain of approximately 65 amino acids is found in CRF proteins from all groups of land plants and only in CRF genes. Phylogenetic analyses suggest that the evolution of CRF genes has included numerous duplication events. In this phylogenetic context we examine protein evolution including the gain and loss of accessory domains, correlate these molecular evolutionary events with experimental data on cytokinin regulation and speculate on the function and evolution of the CRF domain within AP2/ERF transcription factor proteins. We also tested a prediction drawn from the phylogenetic analyses that four CRF domain containing genes from Tomato, previously unexamined for cytokinin response, are transcriptionally inducible by cytokinin, supporting the link between CRF genes, CRF-specific domains and cytokinin regulation.ConclusionCRF genes can be identified in all lineages of land plants, as a distinct subset of AP2/ERF proteins containing a specific and unique CRF domain. The CRF domain can be used to identify previously unclassified predicted genes or genes identified only as members of the AP2/ERF protein family. CRF domain presence and phylogenetic relatedness to known Arabidopsis CRF genes predicts gene function to some extent.
Highlights
Cytokinin Response Factors (CRFs) are a small subset of AP2/Ethylene Response Factors (ERFs) transcription factor genes shown in Arabidopsis to regulate leaf development as part of the cytokinin signal transduction pathway
We have identified a large number of AP2/ERF genes from diverse land plant lineages that are orthologous to a set of genes from Arabidopsis known as Cytokinin Response Factors or CRFs
Sequences are identified by their generic name followed by a number if more than one was identified per genus, unless previously designated a name or for the Solanum lycopersicum or SlCRFs (SlCRF1 previously designated as PTI6 is from SGN-U314347, SlCRF2 is from SGN-U329134, SlCRF3 is from SGNU344182, and SlCRF4 is from SGN-U331355), with full gene names included see Additional File 1
Summary
Cytokinin Response Factors (CRFs) are a small subset of AP2/ERF transcription factor genes shown in Arabidopsis to regulate leaf development as part of the cytokinin signal transduction pathway. AP2/ERF proteins comprise one of the largest families of transcription factors in plants and are defined by the presence of an AP2 DNA binding domain of around 68 amino acids. This protein family can be broadly divided into those proteins with two AP2 domains, e.g. the eponymous floral patterning gene APETELA2, and those with a single AP2 domain such as the Ethylene Response Factors (ERFs) [1,2,3,4,5]. CRF genes have been examined in a preliminary way in Arabidopsis and homologs have been identified in rice there has been little done to establish their presence at a broader phylogenetic scale or to examine basic aspects of molecular evolution such as potentially conserved motifs within these proteins
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