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

Abstract

Motivation Complexome 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. Results We 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 implementation COPAL is written in python and is available from http://github.com/cmbi/copal. Supplementary information Supplementary data are available at Bioinformatics online.

A dual function of TMEM70 in OXPHOS: assembly of complexes I and V

“…In the six complexome profiles, four controls and two TMEM70 knockouts, we detected in total 3766 proteins, of which 814 are annotated as mitochondrial in MitoCarta 2.0 33 . The profiles were normalized such that the sum of the intensities of the mitochondrial proteins between the samples were equal, and the profiles were aligned with COPAL 34 to allow comparison between the replicates (see Supplementary Table S4 for the complete results).…”

“…Profiles were corrected so that the sum of intensities of proteins annotated as mitochondrial in MitoCarta 2.0 33 are equal between samples. After normalisation, the profiles were aligned in silico with COPAL 34 to correct for technical variation caused by shifts in protein migration across the gel. Gaps introduced in the alignment were filled by linear interpolation based on its adjacent values.…”

“…Normalized iBAQ values were taken from the profiles after aligning them with COPAL 34 (Supplementary Table S4). In the case of fully assembled complexes, subunits belonging to CI (NDUFB3, NDUFC2, NDUFB1, NDUFA5, NDUFA6, NDUFS4, NDUFB10, NDUFB2, NDUFB5, NDUFS1, NDUFS8, NDUFAB1, NDUFA2, NDUFS2, NDUFS3, NDUFB6, NDUFB4, NDUFB8, NDUFA7, NDUFB7, NDUFV1, NDUFA8, NDUFV3, NDUFA3, NDUFC1, NDUFS5, NDUFA1, NDUFS6, NDUFV2, NDUFS7, NDUFA11, NDUFA9, NDUFB11, NDUFA13, NDUFA12, NDUFB9, ND1, ND2, ND3, ND4, ND5, ND6), CII (SDHA, SDHB, SDHC, SDHD), CIII (CYTB, UQCRQ, UQCR11, UQCRH, UQCRB, UQCRC2, UQCRC1, UQCRFS1, CYC1, UQCR10), CIV (COX6C, COX3, COX2, COX5B, COX4I1, COX6B1, COX7C, COX5A, COX7B, COX7A2, COX8A, COX1), CV (ATP8, ATP6, ATP5G1, ATP5H, ATP5L, ATP5J, ATP5D, ATP5O, ATP5J2, C14orf2, ATP5I, ATP5F1, ATP5C1, USMG5, ATPIF1, ATP5A1, ATP5B) were considered.…”

Protein Interaction Patterns inArabidopsis thalianaLeaf Mitochondria Change in Response to Illumination

“…It is therefore even more surprising that a comprehensive overview of the plant mitochondrial PPIs is still missing and that the role of these PPIs in regulation plant mitochondrial metabolism remains unexplored. Recently, differential complexome profiling analysis of human mitochondria from patients suffering from Barth and Leigh syndrome has revealed altered abundance of inner membrane or inner membrane associated protein complexes (van Strien et al 2019) and complex I assembly intermediates (Alston et al 2020), respectively, indicating that dynamic PPIs have an impact on mitochondrial metabolism.…”

CEDAR, an online resource for the reporting and exploration of complexome profiling data

“…Thus, it has been used to discover new protein complexes or identify new members of known complexes [1,5,8,10,[28][29][30][31][32], to elucidate complex stoichiometry [33,34], to study protein complex assembly [6,7,16,[35][36][37][38][39], to investigate evolutionary conservation of protein complexes [40], to better understand disease mechanisms [41][42][43][44] and to study dynamic reorganization of protein interactions [45]. Furthermore, several computational tools have been developed for the processing, analysis, visualization, interpretation, and comparative analysis of complexome profiling data [5,24,26,27,36,46,47].…”