COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome.

Martijn A Huynen,Iliana A Chatzispyrou,Riekelt H Houtkooper,Sergio Guerrero-Castillo,Joeri Van Strien,Ulrich Brandt,Alfonso Valencia

doi:10.1093/bioinformatics/btz025

Abstract

MotivationComplexome profiling combines native gel electrophoresis with mass spectrometry to obtain the inventory, composition and abundance of multiprotein assemblies in an organelle. Applying complexome profiling to determine the effect of a mutation on protein complexes requires separating technical and biological variations from the variations caused by that mutation.ResultsWe have developed the COmplexome Profiling ALignment (COPAL) tool that aligns multiple complexome profiles with each other. It includes the abundance profiles of all proteins on two gels, using a multi-dimensional implementation of the dynamic time warping algorithm to align the gels. Subsequent progressive alignment allows us to align multiple profiles with each other. We tested COPAL on complexome profiles from control mitochondria and from Barth syndrome (BTHS) mitochondria, which have a mutation in tafazzin gene that is involved in remodeling the inner mitochondrial membrane phospholipid cardiolipin. By comparing the variation between BTHS mitochondria and controls with the variation among either, we assessed the effects of BTHS on the abundance profiles of individual proteins. Combining those profiles with gene set enrichment analysis allows detecting significantly affected protein complexes. Most of the significantly affected protein complexes are located in the inner mitochondrial membrane (mitochondrial contact site and cristae organizing system, prohibitins), or are attached to it (the large ribosomal subunit).Availability and implementationCOPAL is written in python and is available from http://github.com/cmbi/copal.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

Complexome profiling combines native gel electrophoresis with protein mass spectrometry to obtain a comprehensive inventory of the proteins and multiprotein complexes in a biological sample
We implemented a combination of bioinformatic approaches in COmplexome Profiling ALignment (COPAL), allowing large-scale comparative analyses of complexome profiles
It is instructive to examine the differences between the results obtained with COPAL and the subsequent gene set enrichment analysis (GSEA) with those obtained using expert, manual curation

Summary

Introduction

Complexome profiling combines native gel electrophoresis with protein mass spectrometry to obtain a comprehensive inventory of the proteins and multiprotein complexes (the complexome) in a biological sample. Blue-native gel electrophoresis separates intact protein complexes from each other (Schagger and von Jagow, 1991; Wittig et al, 2006) After cutting the gel lanes into slices, these are subjected to tryptic digest and mass spectrometry, yielding an abundance profile reflecting the migration pattern in the native gel VC The Author(s) 2019. Similar abundance profiles indicate interaction between proteins. Agglomerative clustering based on profile-similarity can be used to assemble protein complexes from the dataset (Giese et al, 2015; Heide et al, 2012)

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Results

Conclusion