Biochemical characterization and positional cloning of the var2 variegation mutant of Arabidopsis thaliana

Chloroplasts differentiation and development are highly coordinated with their host cells. To better elucidate the mechanisms involved in nuclear-chloroplast interactions, we characterized a nuclear encoded leaf variegation mutation called var2. While cotyledons appear normal, true leaves of var2 emerge as yellow, then turn into green-white sectors. The green sectors contain cells with normal chloroplasts, whereas the white sectors contain cells with abnormal plastid lacking of internal membrane structures. The phenotypes suggested that VAR2 might be involved in thylakoid biogenesis in early chloroplast differentiation. We cloned the VAR2 gene by a map-based method. Five original and two potential alleles were sequenced. Deduced amino acid sequence of VAR2 revealed that it belonged to a gene super family called AAA-ATPase and especially shared high homology with a subfamily of AAA-ATPases called FtsH-like metallopeptidase. VAR2 protein contains three domains including two transmembrane segments on the N-terminus, an AAA-ATPase cassette, and a Zinc binding site for metallopeptidase. Chloroplast import experiments using in vitro translated VAR2 protein indicated that VAR2 is localized on the thylakoid membrane with its C-terminus facing the stroma. Northern and Western blots suggested that VAR2 was only expressed in photosynthetic tissues. Both genetic and biochemical analyses suggested that VAR2 forms homo-multimeric complex. The var2 variegation mechanism is discussed