From single proteins to supercomplexes : a proteomic view on plant mitochondria

Abstract

The primary function of plant mitochondria is respiration, which is why they are often referred to as “powerhouses of the cell”. Besides their central role in energy metabolism, plant mitochondria are also involved in the photorespiratory C2 cycle and in the provision of carbon skeletons to support efficient nitrogen assimilation. All these functions are catalyzed by mitochondrial proteins. Their composition, abundance and interactions in plant mitochondria are the subject of this thesis. In yeast, Trypanosomes, and several mammalian cell types, mitochondria are organized as extensive mitochondrial networks, resulting in a situation where a cell only hosts few but large mitochondria. In plants, hundreds of small mitochondria are only connected by fusion and fission over time but not physically. Hence, the organelles form individual, functional units. Paradoxically, their biochemical and physiological characterization focuses on large organelle populations and thereby disregards the properties of the individual mitochondrion. This partially is based on the fact that cell biological approaches capturing structural features of plant mitochondria often are of limited value for understanding their physiological properties. Chapter 2.1 of this thesis models the protein content of a single mitochondrion by combining proteomics with classical cell biology. Besides other insights into the function of a single plant mitochondrion, it could be shown that proteins involved in ATP synthesis and transport make up nearly half of the plant mitochondrial proteome. The five protein complexes of the OXPHOS system contribute most to this segment of the mitochondrial proteome, underlining the overall importance of mitochondrial ATP synthesis for the entire plant cell. Despite the central function of OXHPOS components in plants, certain unicellular parasites and yeasts apparently do not need a complete OXPHOS system. Intriguingly, it recently has been reported that the mitochondrial genome of the multicellular parasitic flowering plant Viscum album (European mistletoe) is reduced and lacks the genes encoding the mitochondrially encoded subunits of complex I. This implies that the corresponding genes either have been lost or, alternatively, were transferred to the nuclear genome. The consequences for the mitochondrial respiratory chain were so far unknown. Chapter 2.2 presents data suggesting that V. album indeed lacks mitochondrial complex I. The absence of complex I is accompanied by a rearrangement of the respiratory chain including (i) stable supercomplexes composed of complexes III2 and IV, and (ii) the occurrence of numerous alternative oxidoreductases. Mitochondria of V. album also possess less cristae than mitochondria from non-parasitic plants, which can be explained by low amounts of ATP synthase dimers. The mitochondrial proteome consists of proteins encoded in the nucleus or in the rudimentary mitochondrial genome. The few proteins encoded on the mitochondrial genome are translated by mitochondrial ribosomes. While structure and composition of these mitoribosomes are well established in yeast and mammals, the current knowledge of plant mitoribosomes is negligible. Isolation of plant mitoribosomes is difficult due to their sedimentation coefficient, which is very close to that of cytosolic ribosomes, their interaction with the inner mitochondrial membrane, and the attachment of cytosolic ribosomes to the mitochondrial surface. As part of this dissertation, plant mitoribosomes were analyzed via a novel complexome profiling strategy (chapter 2.3). This revealed an unconventional molecular mass of the small ribosomal subunit of plants. In addition, several pentatricopeptide repeat (PPR) proteins were discovered to form part of both, the large and the small mitoribosomal subunit.