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Abstract
Mitochondria are functionally specialized in different tissues, and a detailed understanding
of this specialization is important to elucidate mitochondrial involvement in normal
physiology and disease. In adaptive thermogenesis, brown fat converts mitochondrial
energy to heat, whereas tissue-specific functions of mitochondria in white fat are
less characterized. Here we apply high-resolution quantitative mass spectrometry to
directly and accurately compare the in vivo mouse mitochondrial proteomes of brown
and white adipocytes. Their proteomes are substantially different qualitatively and
quantitatively and are furthermore characterized by tissue-specific protein isoforms,
which are modulated by cold exposure. At transcript and proteome levels, brown fat
mitochondria are more similar to their counterparts in muscle. Conversely, white fat
mitochondria not only selectively express proteins that support anabolic functions
but also degrade xenobiotics, revealing a protective function of this tissue. In vivo
comparison of organellar proteomes can thus directly address functional questions
in metabolism.