Leigh syndrome can be caused by mutations in one of over 30 different genes. In humans, most genes are found in DNA in the cell's nucleus, called nuclear DNA. However, some genes are found in DNA in specialized structures in the cell called mitochondria. This type of DNA is known as mitochondrial DNA (mtDNA). While most people with Leigh syndrome have a mutation in nuclear DNA, about 20 to 25 percent have a mutation in mtDNA.  Most genes associated with Leigh syndrome are involved in the process of energy production in mitochondria. Mitochondria use oxygen to convert the energy from food into a form cells can use. Five protein complexes, made up of several proteins each, are involved in this process, called oxidative phosphorylation. The complexes are named complex I, complex II, complex III, complex IV, and complex V. During oxidative phosphorylation, the protein complexes drive the production of ATP, the cell's main energy source, through a step-by-step transfer of negatively charged particles called electrons. Many of the gene mutations associated with Leigh syndrome affect proteins in complexes I, II, IV, or V or disrupt the assembly of these complexes. These mutations reduce or eliminate the activity of one or more of these complexes, which can lead to Leigh syndrome.  Disruption of complex IV, also called cytochrome c oxidase or COX, is the most common cause of Leigh syndrome. The most frequently mutated gene in COX-deficient Leigh syndrome is called SURF1. This gene, which is found in nuclear DNA, provides instructions for making a protein that helps assemble the COX protein complex (complex IV). The COX protein complex, which is involved in the last step of electron transfer in oxidative phosphorylation, provides the energy that will be used in the next step of the process to generate ATP. Mutations in the SURF1 gene typically lead to an abnormally short SURF1 protein that is broken down in cells, resulting in the absence of functional SURF1 protein. The loss of this protein reduces the formation of normal COX complexes, which impairs mitochondrial energy production.  Other nuclear DNA mutations associated with Leigh syndrome decrease the activity of other oxidative phosphorylation protein complexes or affect additional steps related to energy production. For example, Leigh syndrome can be caused by mutations in genes that form the pyruvate dehydrogenase complex. These mutations lead to a shortage of pyruvate dehydrogenase, an enzyme involved in mitochondrial energy production.  The most common mtDNA mutation in Leigh syndrome affects the MT-ATP6 gene, which provides instructions for making a piece of complex V, also known as the ATP synthase protein complex. Using the energy provided by the other protein complexes, the ATP synthase complex generates ATP. MT-ATP6 gene mutations, found in 10 to 20 percent of people with Leigh syndrome, block the generation of ATP. Other mtDNA mutations associated with Leigh syndrome decrease the activity of other oxidative phosphorylation protein complexes or lead to reduced mitochondrial protein synthesis, all of which impair mitochondrial energy production.  Although the exact mechanism is unclear, researchers believe that impaired oxidative phosphorylation can lead to cell death because of decreased energy available in the cell. Certain tissues that require large amounts of energy, such as the brain, muscles, and heart, seem especially sensitive to decreases in cellular energy. Cell death in the brain likely causes the characteristic lesions seen in Leigh syndrome, which contribute to the signs and symptoms of the condition. Cell death in other sensitive tissues may also contribute to the features of Leigh syndrome.