Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana.
BACKGROUND
CBF/DREB duplicate genes are widely distributed in higher plants and encode transcriptional factors, or CBFs, which bind a DNA regulatory element and impart responsiveness to low temperatures and dehydration.


RESULTS
We explored patterns of genetic variations of CBF1, -2, and -3 from 34 accessions of Arabidopsis thaliana. Molecular population genetic analyses of these genes indicated that CBF2 has much reduced nucleotide diversity in the transcriptional unit and promoter, suggesting that CBF2 has been subjected to a recent adaptive sweep, which agrees with reports of a regulatory protein of CBF2. Investigating the ratios of Ka/Ks between all paired CBF paralogus genes, high conservation of the AP2 domain was observed, and the major divergence of proteins was the result of relaxation in two regions within the transcriptional activation domain which was under positive selection after CBF duplication. With respect to the level of CBF gene expression, several mutated nucleotides in the promoters of CBF3 and -1 of specific ecotypes might be responsible for its consistently low expression.


CONCLUSIONS
We concluded from our data that important evolutionary changes in CBF1, -2, and -3 may have primarily occurred at the level of gene regulation as well as in protein function.
Lin
Yen-Heng
YH
Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan. b89206032@ntu.edu.tw
Hwang
Shih-Ying
SY
Hsu
Po-Yen
PY
Chiang
Yu-Chung
YC
Huang
Chun-Lin
CL
Wang
Chun-Neng
CN
Lin
Tsan-Piao
TP
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D055785:Gene Knockdown Techniques; D055786:Gene Knockout Techniques; D020131:Genes, Duplicate / Q000235:genetics*; D005828:Genetics, Population; D018745:Genome, Plant / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000737:chemistry / Q000235:genetics; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic; D015533:Transcriptional Activation / Q000235:genetics
D029681:Arabidopsis Proteins; C104387:CBF1 protein, Arabidopsis; C118228:CBF2 protein, Arabidopsis; C114578:DREB1A protein, Arabidopsis; D015534:Trans-Activators; D014157:Transcription Factors