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In sunflower, the patterns of mitochondrially encoded proteins were compared in five cytoplasmic male sterile lines and the corresponding maintainer lines. The line RHA265 with the original fertile cytoplasm (N) showed a unique protein of 53 kDa that was not present in the male sterile isonuclear lines with the CMS-inducing cytoplasms GIG1, MAX1 and PET2. GIG1 and PET2 expressed an additional 12.4 kDa protein. In dependence of the nuclear background i.e. RHA265 or HA89, respectively, a nuclear encoded 24 kDa protein was present or absent in the mitochondrial protein patterns of GIG1, MAX1 and PET2.Nuclear and cytoplasmic differences in the total respiration of isolated mitochondria were detected using NADH, malate and succinate as substrates. For succinate oxidation in dependence of the nuclear background ANL1 and its maintainer RHA266 showed higher respiration rates than RHA265, ANL2, GIG1, MAX1 and PET2. For NADH total respiration of ANL2, GIG1 and PET2 was more than twice as high than for the isonuclear maintainer line RHA265. Also MAX1 showed an increased oxygen uptake even though not as high. The results demonstrated that considerable differences in the total respiration are possible without obvious relevance to the production of vital pollen. Regarding the engagement of the cytochrome oxidase and alternative pathway no differences were observed between CMS and maintainer lines.[PUBLICATION ABSTRACT]