Intracellular protein sorting plays a key role in the regulation of cellular metabolism, gene expression, signal transduction and a number of other cellular processes. Proteins targeted to specific cellular compartments contain organelle-specific targeting sequences which interact with various components of the import machinery that are often evolutionarily conserved. For example, proteins targeted to peroxisomes interact with specific receptor proteins through unique peroxisomal targeting signals (PTS) which results in their import into peroxisomal matrix or insertion into peroxisomal membrane. Peroxisomal protein import has been studied in a number of species and several conserved PTS and receptor proteins have been identified. In our study, we report the unexpected finding that cytochrome c (cyt c), which lacks a canonical PTS, is targeted to peroxisomes of the methylotrophic yeast, Pichia pastoris. This is a unique feature of P. pastoris and is not observed in other yeast species such as the conventional yeast, Saccharomyces cerevisiae or other methylotrophic yeasts such as Hansenula polymorpha. Using S. cerevisiae cyc1 null mutant strain as a surrogate model, we demonstrate that P. pastoris cytochrome c (PpCyt c) is targeted to S. cerevisiae peroxisomes indicating that peroxisomal targeting is a unique and inherent property of PpCyt c and the machinery required for this is conserved in S. cerevisiae as well. We further demonstrate that Ppcyt c targeted to the fatty acid-induced peroxisomes of S. cerevisiae is a hemoprotein with covalently attached heme suggesting that PpCyt c synthesized in cytosol is first targeted to mitochondria where heme is added to the apoprotein by cytochrome c heme lyase and the holoprotein is then re-targeted to peroxisomes through an unknown mechanism. Proteins imported into peroxisomes carry specific peroxisomal targeting signals (PTS) known as PTS1 and PTS2. PTS1 is a tripeptide sequence (SKL) at the carboxy terminus of peroxisomal matrix proteins. To investigate whether the carboxy terminus of PpCyt c contain PTS1 or PTS1-like sequences, we made GFP fusion proteins with PpCyt c carboxy terminal amino acids (GFP-ATK, GFP-LAKATK) and examined their ability to localize to peroxisomes. Neither of these two proteins is targeted to peroxisomes indicating that PTS1-like sequences are not involved in peroxisomal targeting of Ppcyt c. Two receptors known as Pex5 and Pex7 are known to be involved in peroxisomal protein import and we therefore examined PpCyt c import into peroxisomes of P. pastoris strains lacking pex5 and pex7. Peroxisomal import of PpCyt c is abolished in pex5 but not pex7 mutant strain indicating that PpCyt c is imported into peroxisomes by a pex5-dependent but PTS1independent pathway. Since we observed significant amino acid differences between PpCyt c and S. cerevisiae cytochrome c (ScCyt c) in their carboxy-and amino-termini, we interchanged these amino acids between PpCyt c and ScCyt c and examined their subcellular localization. Such studies revealed that swapping the N-terminal or C-terminal amino acids of PpCyt c with those of S. cerevisaie cytochrome c (ScCyt c) abolishes peroxisomal localization of PpCyt c. Thus, both N-and C-terminal amino acids of PpCyt c are essential for its import into peroxisomes. Interestingly, in a number of fungal species, the N-and C-terminal amino acid sequences of cytochrome c are identical to those of PpCyt c indicating that peroxisomal targeting of cytochrome c may be observed in other yeast species as well. S. cerevisiae cells expressing PpCyt c exhibit several unique biochemical properties. S. cerevisiae cells expressing PpCyt c grow more rapidly than those expressing ScCyt c when cultured on media containing oleic acid as the sole carbon source and uptake of C-oleic acid from the medium as well as its assimilation into neutral lipids is quantitatively higher in the former. Surprisingly, the phenotype of S. cerevisiae cells expressing PpCyt c is dramatically altered such that the kinetics of growth on fatty acid containing media as well as lipid profile appear to be identical to those of P. pastoris rather than S. cerevisiae. Thus peroxisomal targeting of cytochrome c dramatically alters the kinetics of growth of S. cerevisiae cells in fatty acid containing media as well as the lipid metabolism raising several interesting questions on the molecular mechanisms involved in the alteration of phenotype of S. cerevisiae. It is likely that peroxisomal targeting of cytochrome c results in quantitative as well as qualitative changes in fatty acid metabolism and this opens up new vistas for the bioconversion of fatty acids into value-added lipid products by metabolic engineering. Based on these studies, we propose a new role for cytochrome c in peroxisomal fatty acid metabolism. Our study demonstrates that evolutionarily conserved proteins such as cytochrome c can acquire unique, species-specific functions that may be of great physiological significance to that organism.