The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions, and rearrangements

Abstract

Some plants like Arabidopsis thaliana increase in freezing tolerance when exposed to low nonfreezing temperatures, a process known as cold acclimation. Other plants including tomato, Solanum lycopersicum, are chilling sensitive and incur injury during prolonged low temperature exposure. A key initial event that occurs upon low temperature exposure is the induction of genes encoding the CBF transcription factors. In Arabidopsis three CBF genes, present in a tandemly-linked cluster, are induced by low temperatures. Tomato also harbors three tandemly-linked CBF genes, Sl-CBF3-CBF1-CBF2, but only one of these, Sl-CBF1, is low-temperature responsive. Here we report that Solanum species that are closely-allied to cultivated tomato essentially share this structural organization, but the locus is in a dynamic state of flux. Additional paralogs and in-frame deletions between adjacent genes occur, and the genomic regions flanking the CBF genes are dissimilar across Solanum species. Nevertheless, the CBF1 upstream region remains intact and highly conserved. This feature differed for CBF2 and CBF3, whose upstream regions were far less conserved. CBF1 was also the only low-temperature responsive gene in the cluster and its expression was greatly affected by a circadian clock. The tuber-bearing S. tuberosum and S. commersonii also harbored a fourth gene, CBF4, which was also low temperature responsive. CBF4 was physically linked to CBF5 in S. tuberosum, but CBF5 was absent from S. commersonii. Phylogenic analyses suggest that CBF5-CBF4 resulted from the duplication of the CBF3-CBF1-CBF2 cluster. DNA sequence motifs shared between the Solanum CBF1 and CBF4 upstream regions were identified, portions of which were also present in the Arabidopsis CBF1-3 upstream regions. These results suggest that much greater functional constraints are placed upon the Solanum CBF1 upstream regions over the other CBF upstream regions and that CBF4 has retained the capacity for low temperature responsiveness following the duplication event that gave rise to CBF4.

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

“…Phylogenetic analysis highlighted a common origin of CBFs in Solanum species with respect to other plants from temperate regions that can cold acclimate, such as Arabidopsis, wheat (Triticum aestivum) and Brassica napus (Jaglo et al, 2001). This suggests homogenization mechanisms exist in Solanum, as previously reported (Pennycooke et al, 2008). Despite observed orthology for most of the CBF1 gene family, S. commersonii CBF1 clustered apart from other CBF1 sequences.…”

“…By contrast, low conservation of CBF2 and CBF4 upstream regions was observed ( Figure 5B). The S. commersonii cCBF2 possessed only portions of a coding sequence with numerous nonsense codons in all reading frames (Supplemental Figure 13A) (Pennycooke et al, 2008). The duplicated S. commersonii CBF3 encoded the amino acid block ASP-ALA-SER-TRY-ARG (hereafter DASWR) positioned immediately downstream from the 60-amino-acid AP2/ERF DNA binding domain in the CBF protein.…”

Plant Abiotic Stress: Insights from the Genomics Era

“…This suggests nonidentical, though potentially overlapping, signaling pathways. Similar results in wheat (Badawi et al, 2007) and tomato (Pennycooke et al, 2008) suggest circadian regulation under homeostatic conditions concurring with dawn and dusk periods, maybe overlapping with stomatal aperture changes. Light is also implicated in regulating the CBF pathway, for instance a low red to far-red ratio of light is sufficient to increase CBF gene expression and confer freezing tolerance at temperatures higher than those required for cold acclimation (Franklin et al, 2007), providing evidence for a second temperature-regulated step in this pathway.…”

“…DREB1/CBF expression may be important for avoiding plant growth retardation by the accumulation of DREB1/CBF proteins under unstressed conditions (Kidokoro et al, 2009). Downregulation occurs through a complex network of transcription factors, such as ZAT12 downregulating CBF2 (Vogel et al, 2005), and MYB15 interacting with ICE1, subsequently binding to the MYB recognition sequences in the CBF promoters The CBF pathway is not only present in dicots such as Arabidopsis, but is widespread through monocots and multiple plant genera, including those native to warm regions and not inherently cold tolerant, with variation in CBF gene copy numbers (Qin et al, 2004, Skinner et al, 2006, Badawi et al, 2007, Stockinger et al, 2007, Tamura et al, 2007, , Pennycooke et al, 2008, Knox et al, 2010. A recent paper by one of the pioneers of the field presents a detailed overview of the status of CBF research today (Thomashow, 2010)., and readers wishing for further detail are directed to this review Alternative cold tolerance pathways also initiate transcription of cold-responsive genes, for example Arabidopsis SFR2 encodes a novel β-glycosidase, contributing to freezing tolerance and distinct from the CBF pathway (Thorlby et al, 2004).…”

Functionality of soybean CBF/DREB1 transcription factors

“…In potato (S. tuberosum and S. commersonii), an additional set of tandem-linked CBF genes (CBF4-5) were found as orthologs to S. tuberosum and S. commersonii CBF1-3 [43]. Unlike the Arabidopsis, tomato, and potato CBF genes, the soybean GmCBF genes are distributed on distinct chromosomes.…”