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: 3.81). 04/2010; 10(1):74. DOI: 10.1186/1471-2229-10-74
Source: PubMed


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.

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Available from: Aaron Rashotte, Jul 16, 2015
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    • "Furthermore, gradual reduction of expression of the cotton (Gossypium hirsutum) HD-Zip gene (GhHB1) with development of roots and its induction in response to abscisic acid and salt (Ni et al., 2008) indicated that HD-Zip genes play important roles in both morphogenic processes as well as stress responses of plants. The sweetpotato gene IbCRF1 that showed the second highest increase in expression (fold change of 6) under drought stress is similar to AP2/EREBP genes (Riechmann and Meyerowitz, 1998) and cytokinin response genes (Rashotte and Goertzen, 2010). Expression of many members of the AP2/EREBP gene family is altered in response to abiotic (Chen et al., 2007; Kim et al., 2008; Kizis et al., 2001; Xiong et al., 2002) and biotic stresses (Lin et al., 2007). "
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    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 05/2014; 139(3):317-324. · 1.28 Impact Factor
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    • "These genes were originally identified in arabidopsis microarray experiments of cytokinin response as transcription factor family members that were highly induced at multiple time points after exogenous application of cytokinin (Rashotte et al., 2003). Recent works have revealed the presence of 12 CRFs in Arabidopsis thaliana (AtCRFs) and also similar numbers in other plant genomes including 11 Solanum lycopersicum (SlCRFs) (Rashotte and Goertzen, 2010; Cutcliffe et al., 2011; Shi et al., 2012). Much of the study of CRFs has focused on the arabidopsis system (Rashotte et al., 2006; Cutcliffe et al., 2011), although initial examinations of CRFs in tomato has shown that some SlCRFs are induced by cytokinin in leaves and that one SlCRF gene is expressed in the vasculature of various organs similar to Abbreviations: ABA, abscissic acid; AP2/ERF, APETALA2/ERF; BA, benzyladenine; CRF, cytokinin response factor; SlCRF3, Solanum lycopersicum Cytokinin Response Factor 3; SlCRF5, Solanum lycopersicum Cytokinin Response Factor 5. * Corresponding author at: 101 Rouse Life Sciences, Department of Biological Sciences , Auburn University, Auburn, AL 36849, USA. "
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    ABSTRACT: Cytokinin is an influential hormone involved in numerous aspects of plant growth and development. A group of transcription factors-cytokinin response factors (CRFs) has been included as a side branch to cytokinin signaling pathway which also constitute a subset of the AP2/ERF family of transcription factor proteins. This study examined the expression patterns of two transcription factor genes SlCRF3 and SlCRF5 in tomato (Solanum lycopersicum) to determine their regulation in response to cytokinin and a variety of abiotic stress conditions. Analyses conducted during different developmental stages by RT-PCR or GUS reporter gene expression revealed that these genes are differentially expressed in vegetative and reproductive organs. qRT-PCR experiments were also performed to study regulation by the hormone cytokinin and abiotic stress conditions such as flooding, drought, osmotic, oxidative, and temperature. These showed that SlCRF3 and SlCRF5 have different patterns of regulation in leaf, stem, and roots with SlCRF5 showing greater induction in leaf or root tissue compared to SlCRF3 in most cases. Additionally, knockdown analysis for SlCRF5 revealed defects across development including leaf morphology, primary root growth, and lateral root formation. Together, these findings indicate that SlCRF3 and SlCRF5 are potential regulators of tomato developmental processes associated with cytokinin or abiotic stresses.
    Journal of plant physiology 10/2013; 171(3). DOI:10.1016/j.jplph.2013.09.003 · 2.56 Impact Factor
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    • "Transcription induction of CRFs by cytokinin appears to occur only in specific CRF clades, which include Clades I and IV containing SlCRF1 and SlCRF2 (Zwack et al. 2012). Previous findings of SlCRF cytokinin induction have been limited to leaf tissues in young plants, while here we present a broader examination of cytokinin responsiveness for SlCRF1 and SlCRF2 in different tissues and developmental stages using a range of cytokinin concentrations and treatment durations (Rashotte and Goertzen 2010; Shi et al. 2012). While both SlCRFs were found to be induced (2? fold) in leaves and stems under different cytokinin concentrations at different ages after different treatment times, each has a unique induction pattern (Fig. 4). "
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    ABSTRACT: Key message: SlCRF1 and SlCRF2 are expressed throughout the plant, prominently in vascular tissue. Each SlCRF has a distinct pattern of cytokinin induction and regulation by abiotic stresses in different organs. Cytokinin is an essential plant hormone involved in the regulation of many growth and developmental processes. While many cytokinin signaling pathway components have been well characterized, the cytokinin response factors (CRFs) that form a branch of this pathway are less well understood. This study examines the tomato (Solanum lycopersicum (L.)) CRF genes, SlCRF1 and SlCRF2 presenting a detailed and novel characterization of their developmental expression patterns, transcriptional regulation by hormones particularly cytokinin, and response to abiotic stresses. Both SlCRF1 and SlCRF2 were predominantly expressed in vasculature in tissues throughout the plant, with an overall trend for greater SlCRF2 expression in younger organs. Hormone regulation of SlCRF1 and SlCRF2 transcripts is primarily by cytokinin, which induced both SlCRFs in different organs over a range of developmental stages. The strongest cytokinin induction was found in leaves, with SlCRF2 induced to a higher level than SlCRF1. Examination of SlCRF transcripts during abiotic stress responses revealed that SlCRF1 and SlCRF2 have distinct patterns of regulation from each other and between leaves and roots. Novel connections between SlCRFs and stresses were found in particular including a strong induction of SlCRF1 by cold stress and a strong induction of SlCRF2 by oxidative stress in roots and unique patterns of induction/repression linking both SlCRFs to drought stress and response during recovery. Overall, this study provides a clear picture of SlCRF1 and SlCRF2 expression patterns across tissues during development and in response to cytokinin and specific stresses, indicating their importance in plant growth and environmental responses.
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