Submitted to: Plant Growth Regulation
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/8/2011
Publication Date: 3/23/2011
Citation: Nicholson, S.J., Hoecker, U., Srivastava, V. 2011. A novel Phytochrome B allele in Arabidopsis thaliana exhibits partial mutant phenotype: a short deletion in N-terminal extension reduces Phytochrome B activity. Plant Growth Regulation. 65:207-212. Interpretive Summary: This manuscript is a description of the discovery and characteristics of a new variation of the gene Phytochrome B gene in the Rockcress plant (Arabidopsis thaliana). This new variation of the gene results in an increased stem length in seedlings grown in either white or red light. The gene, called PHYB delta 9-12, is missing a stretch of bases at the beginning of the gene, causing a deletion of amino acids 9 though 12 of the resulting protein. Five other bases are also altered within the gene, but only two of those alteration result in an amino acid change. The deletion of the bases in question does not, beyond eliminating the said amino acids, otherwise inactivate the gene or interfere with protein synthesis. The manuscript describes the genetic characteristics of the gene, noting a slight decrease in gene expression and a slight increase in gene methylation. The manuscript concludes that the effect noted is likely due to the large deletion at the beginning of the gene, and the other noted characteristic of the gene are likely functions of that deletion.
Technical Abstract: During analysis of a line possessing a Phytochrome A epiallele (phyA'), a partial Phytochrome B-deficient phenotype was observed, consisting of lengthened hypocotyls in seedlings grown under constant white light or red light (660 nm). The observed hypocotyls were twice the length (8 mm) of wild-type (4 mm), but approximately half the length of a null phyB-9 mutant (14 mm). Several analyses were performed to characterize this apparent partial phyB mutant. Sequencing of the entire exonic region revealed three point mutations that altered codon usage, and one in-frame 12 bp deletion. Each of the point mutations has been described in other lines that display wild-type phenotype, and therefore their effect is thought to be minimal, if any. The N-terminal deletion of amino acids 9 through 12 (GGGR) is a unique mutation found in this line. This deletion most likely contributes to the phyB mutant phenotype by lowering the binding affinity of the active form of Phytochrome B (Pfr) with Phytochrome Interacting Factor 3 (PIF3).