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Fungal Peroxisomes Proteomics

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Proteomics of Peroxisomes

Part of the book series: Subcellular Biochemistry ((SCBI,volume 89))

Abstract

Peroxisomes in fungi are involved in a huge number of different metabolic processes. In addition, non-metabolic functions have also been identified. The proteins that are present in a particular peroxisome determine its metabolic function, whether they are the matrix localized enzymes of the different metabolic pathways or the membrane proteins involved in transport of metabolites across the peroxisomal membrane. Other peroxisomal proteins play a role in organelle biogenesis and dynamics, such as fission, transport and inheritance. Hence, obtaining a complete overview of which proteins are present in peroxisomes at a given time or under a given growth condition provides invaluable insights into peroxisome biology. Bottom up approaches are ideal to follow one or a few proteins at a time but they are not able to give a global view of the content of peroxisomes. To gain such information, top down approaches are required and one that has provided valuable insights into peroxisome function is mass spectrometry based organellar proteomics. Here, we discuss the findings of several such studies in yeast and filamentous fungi and outline new insights into peroxisomal function that were gained from these studies.

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Abbreviations

APEX:

Ascorbate peroxidase

DDA:

Data-dependent Acquisition

DIA:

Data-independent Acquisition

ESI:

Electro-spray Ionization

GFP:

Green fluorescent protein

GPF:

Gas Phase Fractionation

ICAT:

Isotope-coded affinity tags

MALDI:

Matrix Assisted Laser Desorption Ionization

MS:

Mass Spectrometry

MS/MS:

Tandem Mass Spectrometry

µLC:

Micro Liquid chromatography

nHPLC:

High performance liquid chromatography

nLC:

Nano Liquid chromatography

PMP:

Peroxisomal membrane protein

PNS:

Post nuclear supernatant

PTS:

Peroxisomal targeting signal

ROS:

Reactive oxygen species

SDS-PAGE:

Sodium dodecyl sulphate polyacrylamide gel electrophoresis

SGD:

Saccharomyces cerevisiae Genome Database

SILAC:

Stable Isotope Labelling by Amino acids in Cell culture

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Acknowledgements

C.W. is supported by a VIDI Grant (723.013.004) from the Netherlands Organization for Scientific Research (NWO).

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Authors and Affiliations

  1. Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands

    Xin Chen & Chris Williams

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  1. Xin Chen
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  2. Chris Williams
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Correspondence to Chris Williams .

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Editors and Affiliations

  1. Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain

    Luis A. del Río

  2. Department of Biosciences, University of Exeter, Exeter, UK

    Michael Schrader

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Chen, X., Williams, C. (2018). Fungal Peroxisomes Proteomics. In: del Río, L., Schrader, M. (eds) Proteomics of Peroxisomes. Subcellular Biochemistry, vol 89. Springer, Singapore. https://doi.org/10.1007/978-981-13-2233-4_3

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