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Cited by 42Advanced Proteomics Techniques and ApplicationsMitochondrial Function and PathologyBioinformatics and Genomic Networks

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

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Van Strien, Joeri, Guerrero-Castillo, Sergio, Chatzispyrou, Iliana A, Houtkooper, Riekelt H, Brandt, Ulrich, Huynen, Martijn A·2019·Bioinformatics
DOI 10.1093/bioinformatics/btz025PMC PMC6735710

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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.

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Metadata

Authors
Van Strien, J., Guerrero-Castillo, S., Chatzispyrou, I. A., Houtkooper, R. H., Brandt, U., & Huynen, M. A.
Affiliations
  • Radboud University Nijmegen (NL)
  • Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Department of Pediatrics, , Nijmegen, The Netherlands
  • Amsterdam University Medical Centers (NL)
  • Goethe University Frankfurt (DE)
Corresponding author
Huynen, Martijn A
ORCID
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2019-01-14
Volume
35
Issue
17
Pages
3083-3091
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btz025
PMC
PMC6735710
OpenAlex
W2949088611
Cited by
42
References
2
Citations by year
2026: 3 · 2025: 5 · 2024: 4 · 2023: 7 · 2022: 2 · 2021: 12 · 2020: 6 · 2019: 3
FWCI
2.30
Type
journal article
Language
en
Open access
Licence
Locations
  • Bioinformatics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Radboud Repository (Radboud University) (submittedVersion, other-oa)
  • Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
  • Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) (submittedVersion, cc-by)
  • Pure Amsterdam UMC (submittedVersion, cc-by)
  • Radboud Repository (Radboud University) (submittedVersion)
Funders
Netherlands Organization for Health Research and Development (91217009)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
complexome profiling, Barth syndrome, mitochondrial protein complexes, tafazzin, cardiolipin remodeling, inner mitochondrial membrane, copal, dynamic time warping, prohibitin, large ribosomal subunit
MeSH terms
Humans, Mitochondria, Mutation, Mass Spectrometry, Mitochondrial Proteins, Barth Syndrome

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