The alternative oxidase (AOX) of plant mitochondria transfers electrons from the ubiquinone pool to oxygen without energy conservation. AOX can use reductant in excess of cytochrome pathway capacity, preventing reactive oxygen species (ROS) formation from an over-reduced ubiquinone pool, and thus may be involved in acclimation to oxidative stresses. The AOX connection with mitochondrial ROS has been investigated only in isolated mitochondria and suspension culture cells. To study ROS and AOX in whole plants, transformed lines of Arabidopsis (Arabidopsis thaliana) were generated: AtAOX1a overexpressors, AtAOX1a anti-sense plants, and overexpressors of a mutated, constitutively active AtAOX1a. In the presence of KCN, leaf tissue of either mutant or wild-type AOX overexpressors showed no increase in oxidative damage, whereas antisense lines had levels of damage greater than those observed for untransformed leaves. Similarly, ROS production increased markedly in anti-sense and untransformed, but not overexpressor, roots with KCN treatment. Thus, AOX functions in leaves and roots, as in suspension cells, to ameliorate ROS production when the cytochrome pathway is chemically inhibited. However, in contrast with suspension culture cells, no changes in leaf transcript levels of selected electron transport components or oxidative stress-related enzymes were detected under nonlimiting growth conditions, regardless of transformation type. Further, a microarray study using an anti-sense line showed AOX influences outside mitochondria, particularly in chloroplasts and on several carbon metabolism pathways. These results illustrate the value of expanding AOX transformant studies to whole tissues.The cyanide-resistant alternative oxidase (AOX) of plant mitochondria accepts electrons from the ubiquinone (UQ) pool and uses them to reduce oxygen to water, with no conservation of energy through proton gradient formation. AOX can compete with the energyconserving cytochrome (Cyt) pathway for reductant (Millenaar and Lambers, 2003;Finnegan et al., 2004), and in vivo studies using oxygen isotope fractionation indicate that AOX is nearly always active (Robinson et al., 1995). This situation raises the question of why an apparently energy-wasteful pathway operates in plant mitochondria.Because AOX can use reductant in excess of either the Cyt pathway capacity or the rate of ATP use, AOX may act to reduce formation of reactive oxygen species (ROS; Purvis and Shewfeldt, 1993;Millar et al., 2001a;Mittler, 2002). Over-reduction of the mitochondrial UQ pool is an important source of cellular ROS (Møller, 2001), and AOX, unrestricted by proton gradient size, can prevent such over-reduction. AOX function in this respect has been demonstrated in culture cells and isolated mitochondria. Tobacco (Nicotiana tabacum) culture cells anti-sense for AOX produce more ROS than wild-type cells, while AOX-overexpressing cells produce less (Maxwell et al., 1999). In isolated mitochondria, ROS production decreases when AOX is activated by a-keto acids (Past...