Structural and Functional Genomics in Semi-Autonomous Organelles: Composition and Origin of Proteomes of Chloroplasts and Mitochondria and Related Transcriptomics

Mitochondria and chloroplasts are semi-autonomous organelles that have arisen through an endosymbiotic event and, over evolutionary time, have donated most of their genome to the nucleus of the host cell. Due to this transfer of genetic material, the expression of many proteins of the organellar proteomes, now synthesized in the cytosol and re-targeted to the organelles, came under control of the nucleus. Subsequently, means of communication between organelles and nucleus must exist, enabling the organelles to take influence on the nuclear gene expression. This thesis focused on structural and functional genomics in mitochondria and chloroplasts, addressing questions related to the composition, origin and evolution of the organelles, as well as, chloroplast-to-nucleus signaling. The accuracy of five different predictors for the detection of N-terminal targeting peptides was evaluated employing test sets consisting of proteins with experimentally proven subcellular localization, and found to be substantially lower than reported before. Combinations of the predictors showed to be more accurate than any of the predictors alone and were subsequently used to estimate the size and composition of the organellar proteomes. A prediction of the mitochondrial proteomes for ten species was performed and revealed that functional mitochondria harbor from a few hundred to more than 3,000 gene products. A core set of conserved mitochondrial proteins could be identified whose functions are mostly related to transport and metabolism, and -- if mutated -- are frequently associated with disease in humans. In collaboration with W. Martin (Universität Düsseldorf) and co-workers, the cyanobacterial heritage of the Arabidopsis genome was estimated by phylogenetic inferrence and about 4,800 genes (or 18% of the genome) were shown to have been acquired from the prokaryotic ancestor. In both flowering plants, A. thaliana and O. sativa, about 7% of the whole proteome were predicted to be targeted to the chloroplast, with close to 600 of those proteins shared by both species and most likely to be derived from cyanobacteria. The functions of this subset are mainly related to metabolism and energy. In both organelles, species-specific proteins were detected indicating a functional diversification. Even though in A. thaliana the cTP-featuring proteins are predominantly of prokaryotic origin (more than 50%), this indicates that post-endosymbiotic relocations of proteins from/to the chloroplast occurred by altered targeting. These findings were also confirmed for mitochondria. A differential-expression analysis of the nuclear chloroplast transcriptome under 35 environmental and genetic conditions was performed. It revealed, that most of those conditions elicit only three main classes of transcriptome response. Two of these classes, probably involving GUN-type plastid signaling, are characterized by alterations, in opposite directions, in the expression of largely overlapping sets of genes. Thus these findings, suggest the existence of a regulatory, binary master-switch