Peroxisome proliferator-activated receptor alpha (PPAR alpha) belongs to the steroid/nuclear receptor superfamily. Two-dimensional (2D) SDS-PAGE analysis of brown adipose tissue (BAT) unexpectedly revealed six spots that were, present only in PPAR alpha-null mice. Proteomic analysis indicated that these proteins were tropomyosin-1 alpha chain, tropomyosin beta chain, myosin regulatory light chain 2, myosin light chain 3, and parvalbumin alpha. Analyses of mRNA have revealed that PPAR alpha suppressed the genes encoding these proteins in a synchronous manner in adult wild-type mice. Histological and physiological analyses of BAT showed in adult wild-type mice, a marked suppression of BAT growth concurrent with a prominent decrease in lipolytic and thermogenesis activities. These results suggest that in adult mice, PPAR alpha functions to suppress the expression of the proteins that may be involved in the architecture of BAT, and thus may function in keeping BAT in a quiescent state. (c) 2005 Elsevier Inc. All rights reserved.