The Proteome of Human Liver Peroxisomes: Identification of Five New Peroxisomal Constituents by a Label-Free Quantitative Proteomics Survey

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.

Proteome Analysis of Peroxisomes from Etiolated Arabidopsis Seedlings Identifies a Peroxisomal Protease Involved in β-Oxidation and Development

“…2, A and B). Notably, subcellular distribution as well as spectral count-based quantification of peroxisomal proteins in this study are comparable to the data reported for peroxisomes isolated from human liver tissue (Gronemeyer et al, 2013a). ZOOM fractionation before 1-DE allowed us to detect 26 additional peroxisomal proteins that were undetected in T1 and T2, including two new peroxisomal proteins later verified in this study (see below), and therefore significantly improved the coverage of the peroxisomal proteome (Fig.…”

The conserved AAA-ATPase Msp1 confers organelle specificity to tail-anchored proteins

“…In support of a similar role in metazoans, ATAD1 has recently been found on peroxisomes (23,24) and mitochondria (25). In contrast to these similarities, ATAD1 in mouse brains has been suggested to regulate synaptic plasticity and learning by downregulating postsynaptic AMPA receptors (26), indicating that Msp1 homologs may also have been coopted in evolution for other specialized functions.…”

Plasmalogens and fatty alcohols in rhizomelic chondrodysplasia punctata and Sjögren‐Larsson syndrome

“…Several lines of evidence point to the presence of a FAO-like complex within peroxisomes. The activity of an alcohol:NAD + oxidoreductase has been detected in peroxisomes (Sakuraba and Noguchi 1995) but more recently, proteomic analyses of peroxisomes from human and rat tissues identified alcohol dehydrogenase 1A (ADH1A) as a FADH with a PTS1-containing signal (Islinger et al 2007;Gronemeyer et al 2013). These observations suggest that peroxisomes possess the capability to metabolize fatty alcohols back to fatty acids, but further functional studies need to be performed.…”