Functional Evolution of a Cold-induced Gene, CBF3, in Arabidopsis thaliana Ecotypes
Date Issued
2006
Date
2006
Author(s)
Lin, Yen-Heng
DOI
zh-TW
Abstract
We are interested in functional evolution of CBF3, one of the “master switches” in cold-regulated pathways, in 28 ecotypes of Arabidopsis thaliana. We analyzed sequence polymorphism of 1297-bp promoter and 909-bp transcriptional unit (TU) regions with the aids of different software. After 1.5h chilling treatment (4oC), the CBF3 expression levels were measured by real-time PCR, and the expression variations were mapped to the phylogeny tree constructed according to promoter sequences polymorphisms. The promoter and TU evolution are compatible with neutral evolution while heterogeneity of natural selection was also detected by the sliding window method of Tajima’s D test. A region in promoter was possibly subject to balancing selection, however, the meaning of this is not clear at present. We also found selection against low frequency alleles in C-terminal transcriptional activation domain. In protein sequence evolution, the CBF3 is under strong purifying selection which is against deleterious substitution. However, in contrast to highly conserved AP2 domain, the Ka/Ks ratio fluctuated in transcriptional activation domain in paired comparisons among CBF paralogs. A region with ω more than one was found. The amino acid residue within this region, 151E, was identified by codeml (PAML package) as positively selected site. 151E was substituted by 151A in seven ecotypes we have studied. According to a previous report of trans-activation assay in the transcriptional activation domain, this substitution led to stronger trans-activity. We believe this substitution was favored by positive selection to acquire better cold-tolerance for Arabidopsis in the wild. Using the allele-specific expression approach, we identified two nucleotide sites that are related to low expression of CBF3 after chilling treatment. Kas-2, a CBF3 natural knockout line, was found in this study and will be useful to evaluate the roles of CBF3 in freezing tolerance in Arabidopsis.
Subjects
阿拉伯芥
冷誘導基因
功能性演化
中性演化
天擇
CBF3
Arabidopsis thaliana
real-time PCR
functional evolution
neutral evolution
natural selection
positive selection
SDGs
Type
other
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