The Obvious and the Hidden: Prediction and Function of Fungal Peroxisomal Matrix Proteins
- 31 October 2018
- book chapter
- Published by Springer Nature
- Vol. 89, 139-155
Abstract
Fungal peroxisomes are characterized by a number of specific biological functions. To understand the physiology and biochemistry of these organelles knowledge of the proteome content is crucial. Here, we address different strategies to predict peroxisomal proteins by bioinformatics approaches. These tools range from simple text searches to network based learning strategies. A complication of this analysis is the existence of cryptic peroxisomal proteins, which are overlooked in conventional bioinformatics queries. These include proteins where targeting information results from transcriptional and posttranscriptional alterations. But also proteins with low efficiency targeting motifs that are predominantly localized in the cytosol, and proteins lacking any canonical targeting information, can play important roles within peroxisomes. Many of these proteins are so far unpredictable. Detection and characterization of these cryptic peroxisomal proteins revealed the presence of novel peroxisomal enzymatic reaction networks in fungi.Keywords
This publication has 87 references indexed in Scilit:
- Alternative splicing affects the targeting sequence of peroxisome proteins in ArabidopsisPlant Cell Reports, 2017
- Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutesGenome Biology, 2015
- Dual targeting of peroxisomal proteinsFrontiers in Physiology, 2013
- Transfer of metabolites across the peroxisomal membraneBiochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2012
- The significance of peroxisomes in secondary metabolite biosynthesis in filamentous fungiBiotechnology Letters, 2011
- MEME SUITE: tools for motif discovery and searchingNucleic Acids Research, 2009
- Atg26-Mediated Pexophagy Is Required for Host Invasion by the Plant Pathogenic Fungus Colletotrichum orbiculareThe Plant Cell, 2009
- The rat liver peroxisomal membrane forms a permeability barrier for cofactors but not for small metabolites in vitroJournal of Cell Science, 2004
- Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiaeNature, 2003
- L-Lactate Dehydrogenase A4- and A3B Isoforms Are Bona Fide Peroxisomal Enzymes in Rat LiverJournal of Biological Chemistry, 1996