Abstract
The peroxisome is a key organelle of low abundance that fulfils various functions essential for human cell metabolism. Severe genetic diseases in humans are caused by defects in peroxisome biogenesis or deficiencies in the function of single peroxisomal proteins. To improve our knowledge of this important cellular structure, we studied for the first time human liver peroxisomes by quantitative proteomics. Peroxisomes were isolated by differential and Nycodenz density gradient centrifugation. A label-free quantitative study of 314 proteins across the density gradient was accomplished using high resolution mass spectrometry. By pairing statistical data evaluation, cDNA cloning and in vivo colocalization studies, we report the association of five new proteins with human liver peroxisomes. Among these, isochorismatase domain containing 1 protein points to the existence of a new metabolic pathway and hydroxysteroid dehydrogenase like 2 protein is likely involved in the transport or β-oxidation of fatty acids in human peroxisomes. The detection of alcohol dehydrogenase 1A suggests the presence of an alternative alcohol-oxidizing system in hepatic peroxisomes. In addition, lactate dehydrogenase A and malate dehydrogenase 1 partially associate with human liver peroxisomes and enzyme activity profiles support the idea that NAD+ becomes regenerated during fatty acid β-oxidation by alternative shuttling processes in human peroxisomes involving lactate dehydrogenase and/or malate dehydrogenase. Taken together, our data represent a valuable resource for future studies of peroxisome biochemistry that will advance research of human peroxisomes in health and disease.
Highlights
The peroxisome is a single membrane-surrounded organelle present in virtually all eukaryotic cells
To provide an estimate for the enrichment of peroxisomes in fraction 6, relative protein quantification based on spectral counts (SC) [30] was performed that resulted in an abundance ratio of 51% (884 SC) for the total of peroxisomal proteins to non-peroxisomal proteins (Fig. 1B and Table S1)
Concluding Remarks Our label-free quantitative proteomics survey held the great promise of identifying new proteins associated with human liver peroxisomes
Summary
The peroxisome is a single membrane-surrounded organelle present in virtually all eukaryotic cells. Despite its simple architecture peroxisomes play an essential role in various metabolic pathways including fatty acid (FA) a- and b-oxidation, ether-phospholipid biosynthesis, reactive oxygen metabolism and glyoxylate detoxification [1]. The involvement of peroxisomes in such an array of metabolic functions renders it essential in human beings. Its importance is underscored by the existence of a large variety of inherited diseases directly linked to the absence or impaired functions of human peroxisomes [2,3]. Despite the fact that much progress has been made with respect to a better understanding of peroxisome biochemistry and related diseases [1], it can be anticipated that additional peroxisomal disorders exist. Detailed knowledge of the proteome of peroxisomes may pave the way for discovering so far unknown disorders caused by the malfunctioning of peroxisomal proteins
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