Pulse-chase SILAC–based analyses reveal selective oversynthesis and rapid turnover of mitochondrial protein components of respiratory complexes

Mammalian mitochondria assemble four complexes of the respiratory chain (RCI, RCIII, RCIV, and RCV) by combining 13 polypeptides synthesized within mitochondria on mitochondrial ribosomes (mitoribosomes) with over 70 polypeptides encoded in nuclear DNA, translated on cytoplasmic ribosomes, and imported into mitochondria. We have previously observed that mitoribosome assembly is inefficient because some mitoribosomal proteins are produced in excess, but whether this is the case for other mitochondrial assemblies such as the RCs is unclear. We report here that pulse-chase stable isotope labeling with amino acids in cell culture (SILAC) is a valuable technique to study RC assembly because it can reveal considerable differences in the assembly rates and efficiencies of the different complexes. The SILAC analyses of HeLa cells indicated that assembly of RCV, comprising F1/Fo-ATPase, is rapid with little excess subunit synthesis, but that assembly of RCI (i.e. NADH dehydrogenase) is far less efficient, with dramatic oversynthesis of numerous proteins, particularly in the matrix-exposed N and Q domains. Unassembled subunits were generally degraded within 3 h. We also observed differential assembly kinetics for individual complexes that were immunoprecipitated with complex-specific antibodies. Immunoprecipitation with an antibody that recognizes the ND1 subunit of RCI co-precipitated a number of proteins implicated in FeS cluster assembly and newly synthesized ubiquinol-cytochrome c reductase Rieske iron-sulfur polypeptide 1 (UQCRFS1), the Rieske FeS protein in RCIII, reflecting some coordination between RCI and RCIII assemblies. We propose that pulse-chase SILAC labeling is a useful tool for studying rates of protein complex assembly and degradation.

Selective over-synthesis and rapid turnover of mitochondrial protein components of respiratory complexes

Mammalian mitochondria assemble four complexes of the respiratory chain (RCI, III, IV and V) by combining 13 polypeptides synthesized within mitochondria on mitochondrial ribosomes (mitoribosomes) with over 70 polypeptides encoded in nuclear DNA, translated on cytoplasmic ribosomes and imported into mitochondria. We report that pulse-chase SILAC can also serve as a valuable approach to study RC assembly as it reveals considerable differences in the rates and efficiency of assembly of different complexes. While assembly of RCV, ATPase, was rapid with little excess synthesis of subunits, RCI, NADH dehydrogenase, assembly was far less efficient with dramatic over-synthesis of numerous proteins, particularly in the matrix exposed N- and Q- Domains. Subunits that do not engage in assembly are generally degraded within three hours. Differential assembly kinetics were also observed for individual complexes immunoprecipitated with complex-specific antibodies. Immunoprecipitation with an antibody that recognizes the ND1 subunit of RCI co-precipitated a number of proteins implicated in FeS cluster assembly as well as newly-synthesized UQCRFS1, the Rieske FeS protein in RCIII, reflecting a degree of coordination of RCI and RCIII assembly.

Overexpression of the Rieske FeS protein of the Cytochromeb6fcomplex increases C4photosynthesis

C4plants contribute 20% to the global primary productivity despite representing only 4% of higher plant species. Their CO2concentrating mechanism operating between mesophyll and bundle sheath cells increases CO2partial pressure at the site of Rubisco and hence photosynthetic efficiency. Electron transport chains in both cell types supply ATP and NADPH for C4photosynthesis. Since Cytochromeb6fis a key point of control of electron transport in C3plants, we constitutively overexpressed the Rieske FeS subunit inSetaria viridisto study the effects on C4photosynthesis. Rieske FeS overexpression resulted in a higher content of Cytochromeb6fin both mesophyll and bundle sheath cells without marked changes in abundances of other photosynthetic complexes and Rubisco. Plants with higher Cytochromeb6fabundance showed better light conversion efficiency in both Photosystems and could generate higher proton-motive force across the thylakoid membrane. Rieske FeS abundance correlated with CO2assimilation rate and plants with a 10% increase in Rieske FeS content showed a 10% increase in CO2assimilation rate at ambient and saturating CO2and high light. Our results demonstrate that Cytochromeb6fcontrols the rate of electron transport in C4plants and that removing electron transport limitations can increase the rate of C4photosynthesis.

Over-expression of the RieskeFeS protein increases electron transport rates and yield in Arabidopsis

In this study we have generated transgenic Arabidopsis plants over-expressing the Rieske FeS protein (PetC), a component of the cytochrome b6f (cyt b6f) complex. Increasing the levels of this protein, resulted in the concomitant increase in the levels of cyt f (PetA) and cyt b6 (PetB), core proteins of the cyt b6f complex. Interestingly, an increase in the levels of proteins in both the PSI and PSII complexes was also seen in the Rieske FeS ox plants. Although the mechanisms leading to these changes remain to be identified, the transgenic plants presented here provide novel tools to explore this. Importantly, the overexpression of the Rieske FeS protein resulted in a substantial and significant impact on the quantum efficiency of PSI and PSII, electron transport, biomass and seed yield in Arabidopsis plants. These results demonstrate the potential for manipulating electron transport processes to increase crop productivity.One-sentence summaryOver-expression of the Rieske FeS protein results in significant increases in the quantum efficiencies or PSI and PSII, increases in Amax and has the potential to increase crop productivity