The CRF domain defines Cytokinin Response Factor proteins in plants

Department of Biological Sciences, Auburn University, Auburn, AL 36849-5407, USA.
BMC Plant Biology (Impact Factor: 3.94). 04/2010; 10:74. DOI: 10.1186/1471-2229-10-74
Source: PubMed

ABSTRACT 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. 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.
We 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.
CRF 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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Greenhouse and field culture systems were used to study the effect of drought conditions on the storage root (SR) formation in ‘Beauregard’ sweetpotato (Ipomoea batatas). In the greenhouse culture system, drought was simulated by withholding water for 5 and 10 days after transplanting (DAT) cuttings in dry sand. Control plants received water at planting and every 3 days thereafter. In the field studies, natural drought conditions and selective irrigation were used to impose water deprivation during the critical SR formation period. Greenhouse drought for 5 and 10 DAT reduced the number of SRs by 42% and 66%, respectively, compared with the controls. Field drought resulted in a 49% reduction in U.S. #1 SR yield compared with the irrigated condition. Quantitative real-time polymerase chain reaction (PCR) analysis showed differential expression of a set of sweetpotato transcription factors and protein kinases among greenhouse-grown plants subjected to well-watered conditions and water deficit during 5 DAT. A significant enhancement of expression was observed for known drought stress-associated genes such as an abscisic acid-responsive elements-binding factor, dehydration-responsive element-binding factor, and homeodomain- zip proteins. Members of calcium-binding proteins showed differential expression under drought stress. For the first time it is reported that knotted1-like homeobox and BEL1-like genes showed altered expression in response to drought stress under a greenhouse condition. In summary, the results suggest that water deprivation during the SR formation period influences root development and expression patterns of stress-responsive genes and those previously found associated with SR formation in sweetpotato.
    Journal of the American Society for Horticultural Science. American Society for Horticultural Science 01/2014; 139:317-324. · 1.05 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In plants, the ERF/EREBP family of transcriptional regulators plays a key role in adaptation to various biotic and abiotic stresses. These proteins contain a conserved AP2 DNA-binding domain and several uncharacterized motifs. Here, we describe a short motif, termed 'EDLL', that is present in AtERF98/TDR1 and other clade members from the same AP2 sub-family. We show that the EDLL motif, which has a unique arrangement of acidic amino acids and hydrophobic leucines, functions as a strong activation domain. The motif is transferable to other proteins, and is active at both proximal and distal positions of target promoters. As such, the EDLL motif is able to partly overcome the repression conferred by the AtHB2 transcription factor, which contains an ERF-associated amphiphilic repression (EAR) motif. We further examined the activation potential of EDLL by analysis of the regulation of flowering time by NF-Y (nuclear factor Y) proteins. Genetic evidence indicates that NF-Y protein complexes potentiate the action of CONSTANS in regulation of flowering in Arabidopsis; we show that the transcriptional activation function of CONSTANS can be substituted by direct fusion of the EDLL activation motif to NF-YB subunits. The EDLL motif represents a potent plant activation domain that can be used as a tool to confer transcriptional activation potential to heterologous DNA-binding proteins.
    The Plant Journal 02/2012; 70(5):855-65. DOI:10.1111/j.1365-313X.2012.04935.x · 6.82 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We developed a custom 4x44K sweetpotato oligonucleotide microarray (SPOArrav1) based on the Agilent platform. The array included probes for 14K transcripts selected from a de novo sweetpotato transcriptome assembly that was built integrating next generation sequencing (NGS) data from root, leaf and stem tissues and expressed sequence tags (ESTs) from GenBank. SPOArrav1 was used to analyze gene expression profile of both storage and fibrous roots, each with six biological replicates. In total, 1,111 unique transcripts involved in regulatory role, transport, molecular signaling and cell wall organogenesis were differentially expressed in early developing storage roots vs. fibrous root, in which 783 and 328 transcripts were upregulated and downregulated, respectively, in storage roots. Expression profiling of selected genes through quantitative RT-PCR validated the microarray results. Comparison of the expression of 54 selected genes in storage root showed a significantly high positive correlation of microarray and digital gene expression analysis for 32 genes in the sweetpotato root transcriptome. The novel finding of this study was the association of seven BEL1-like genes and six calcium binding proteins with the sweetpotato storage root development. In addition, 68 transcripts with no functional annotation also showed enhanced expression in young storage roots from both microarray and digital expression analyses; these may represent putative genes specific to the onset of storage root formation in sweetpotato. This research demonstrated, for the first time, the utility of global transcriptome analysis through combination of NGS and custom oligonucleotide microarray in the genome-wide gene expression profiling of sweetpotato root development.
    International Plant and Animal Genome Conference XXI 2013;

Preview (3 Sources)

Available from