Functional analysis of plastid-encoded genes

Plastid chromosomes from the variety of plant species contain several conserved open reading frames of unknown function, which most probably represent functional genes. The primary aim of this thesis was the analysis of the role of two such ORFs, designated ycfs or hypothetical chloroplast reading frames, namely ycf9 (ORF62) and ycf10 (ORF229, cemA). Both were analyzed in Nicotiana tabacum (tobacco) via their inactivation using biolistic plastid transformation. A new experimental protocol, based on pulsed-field gel electrophoresis (PFGE), was established to reliably assess the homoplastomic state of transformed plants. 1. Functional analysis of the ycf9 gene product: The inactivation of ycf9 in N. tabacum as well as in Chlamydomonas reinhardtii yielded a homoplastomic mutant phenotype after several rounds of regeneration under selective pressure. The mutant plants grew photoautotrophically, but displayed two clear phenotypes, a light-sensitive one, increasing with the light intensity, and a dwarf phenotype under low-light combined with temperatures below 20°C. The ycf9 gene product was exclusively located in PSII core complexes. This localization was based on the isolation of protein complexes released from thylakoids by controlled, partial lysis, followed by sucrose density gradient centrifugation or 2D gel electrophoresis. This finding revised data of the literature. Biochemical analysis indicated an involvement of the protein in the interaction of the light harvesting antenna II complex (LHCII) with PSII cores. In particular, PSII-LHCII supercomplexes could no longer be isolated from transplastomic tobacco plants. Furthermore, the minor chlorophyll a/b-binding proteins CP26, and to a lesser extent CP29, were substantially reduced under most growth conditions analyzed, in both, tobacco and photoautotrophically grown Chlamydomonas mutants (Swiatek et al. 2001). The gene was therefore renamed psbZ. The ∆psbZ-related alterations in the supramolecular organization of PSII complexes were accompanied by considerable modification in (i) the phosphorylation pattern of PSII subunits, (ii) the rate of deepoxydation of xanthophylls, and (iii) the kinetics and amplitude of non-photochemical quenching. The proposed position of PsbZ in close proximity to CP43 enables the protein to interact with PSII cores to elicit an adaptation process in response to excess light excitation. The molecular mechanism underlying this energy dissipation process remains to be investigated. 2. Functional analysis of the ycf10 gene product: Biolistic plastid transformation was also used to inactivate the ycf10 reading frame in tobacco. After several rounds of regeneration under selective pressure, homoplastomic plants were obtained. Northern analysis uncovered co-transcription of ycf10 within the psaI-ycf4-ycf10-petA gene cluster, with at least two promotor regions upstream of the psaI gene. The mutant plants grew photoautotrophically and developed dark green leaves with numerous pale green to white regions, the latter devoid of photosynthetic activity. The loss of ycf10 did not affect photosynthetic activity, as indicated by unaltered chlorophyll fluorescence. The tobacco ycf10 gene product was localized in the chloroplast inner envelope membrane. Neither protein composition of stroma or thylakoid fractions, nor the stability of the photosynthetic protein complexes were affected in the mutant plants. In contrast, CO2- dependent oxygen evolution was strongly reduced, with a maximum rate of Ci-dependent photosynthesis being approximately 50% lower than in wild-type plants. Two explanations can account for the observed phenomenon: (i) de-regulation of carbonconcentrating mechanisms in transformed cells, or (ii) an indirect effect on CO2-uptake in ∆ycf10 plants. 3. Pulsed-field gel electrophoresis is an ideal tool to verify the homoplastomic state of transformed plants: To enhance the sensitivity of detection of heteroplastomic states, and to distinguish between plastome-located wild-type segments in transplastomic material and promiscuous DNA, a new approach was developed. Customary Southern and PCR techniques are not sensitive enough or not discriminating the latter alternatives, respectively. Pulsed-field gel electrophoresis allows to isolate virtually contamination-free plastid DNA. Plastid DNA isolated this way lacked traces of nuclear and mitochondrial DNA at a detection level of 50 DNA molecules. This excludes that gene-specific PCR amplification products originate from promiscuous nuclear or mitochondrial gene copies. Therefore, PFGE appears to be an ideal tool to investigate the homoplastomic state of transformed plants, especially when combined with radiolabeled probes and Southern techniques