Insights Into the Peroxisomal Protein Inventory of Zebrafish

Effects of environmentally relevant concentrations of glyphosate and aminomethylphosphonic acid on biotransformation and stress response proteins in the liver of zebrafish (Danio rerio)

Herbicides pose a threat to various non-target organisms, including fish. A widely used herbicide, glyphosate, and its main breakdown product, aminomethylphosphonic acid (AMPA), are quite ubiquitous in freshwater systems. The aim of this work was to analyze changes in the relative abundance of hepatic proteins participating in the biotransformation and response to chemical stress in adult zebrafish Danio rerio exposed to environmentally relevant concentrations of glyphosate (100 μg/L), AMPA (100 μg/L), and their mixture (50 μg/L + 50 μg/L) for two weeks. Proteomic analysis showed that the tested concentrations caused dysregulation of various biotransformation proteins, the most upregulated of which in all treatment groups was the Phase I enzyme cyp27a7. While glyphosate had a more pronounced impact on the biotransformation pathways, AMPA showed stronger interference with redox homeostasis. When acting together, the parent compound and its metabolite were more potent to disturb fish metabolic processes, including nucleotide metabolism and proteasome pathway, and to downregulate proteins known for their roles in protection from oxidative modifications of cellular constituents and disruption of redox signaling.

Modelling Peroxisomal Disorders in Zebrafish

Peroxisomes are ubiquitous, dynamic, oxidative organelles with key functions in cellular lipid metabolism and redox homeostasis. They have been linked to healthy ageing, neurodegeneration, cancer, the combat of pathogens and viruses, and infection and immune responses. Their biogenesis relies on several peroxins (encoded by PEX genes), which mediate matrix protein import, membrane assembly, and peroxisome multiplication. Defects in peroxins or peroxisomal enzymes can result in severe disorders, including developmental and neurological abnormalities. The drive to understand the role of peroxisomes in human health and disease, as well as their functions in tissues and organs or during development, has led to the establishment of vertebrate models. The zebrafish (Danio rerio) has become an attractive vertebrate model organism to investigate peroxisomal functions. Here, we provide an overview of the visualisation of peroxisomes in zebrafish, as well as the peroxisomal metabolic functions and peroxisomal protein inventory in comparison to human peroxisomes. We then present zebrafish models which have been established to investigate peroxisomal disorders. These include model zebrafish for peroxisome biogenesis disorders/Zellweger Spectrum disorders, and single enzyme deficiencies, particularly adrenoleukodystrophy and fatty acid beta-oxidation abnormalities. Finally, we highlight zebrafish models for deficiencies of dually targeted peroxisomal/mitochondrial proteins. Advantages for the investigation of peroxisomes during development and approaches to the application of zebrafish models for drug screening are discussed.

Discovering predisposing genes for hereditary breast cancer using deep learning

Breast cancer (BC) is the most common malignancy affecting Western women today. It is estimated that as many as 10% of BC cases can be attributed to germline variants. However, the genetic basis of the majority of familial BC cases has yet to be identified. Discovering predisposing genes contributing to familial BC is challenging due to their presumed rarity, low penetrance, and complex biological mechanisms. Here, we focused on an analysis of rare missense variants in a cohort of 12 families of Middle Eastern origins characterized by a high incidence of BC cases. We devised a novel, high-throughput, variant analysis pipeline adapted for family studies, which aims to analyze variants at the protein level by employing state-of-the-art machine learning models and three-dimensional protein structural analysis. Using our pipeline, we analyzed 1218 rare missense variants that are shared between affected family members and classified 80 genes as candidate pathogenic. Among these genes, we found significant functional enrichment in peroxisomal and mitochondrial biological pathways which segregated across seven families in the study and covered diverse ethnic groups. We present multiple evidence that peroxisomal and mitochondrial pathways play an important, yet underappreciated, role in both germline BC predisposition and BC survival.

Navigating sex and sex roles: deciphering sex-biased gene expression in a species with sex-role reversal (Syngnathus typhle)

Sexual dimorphism, the divergence in morphological traits between males and females of the same species, is often accompanied by sex-biased gene expression. However, the majority of research has focused on species with conventional sex roles, where females have the highest energy burden with both egg production and parental care, neglecting the diversity of reproductive roles found in nature. We investigated sex-biased gene expression in Syngnathus typhle, a sex-role reversed species with male pregnancy, allowing us to separate two female traits: egg production and parental care. Using RNA sequencing, we examined gene expression across organs (brain, head kidney and gonads) at various life stages, encompassing differences in age, sex and reproductive status. While some gene groups were more strongly associated with sex roles, such as stress resistance and immune defence, others were driven by biological sex, such as energy and lipid storage regulation in an organ- and age-specific manner. By investigating how genes regulate and are regulated by changing reproductive roles and resource allocation in a model system with an unconventional life-history strategy, we aim to better understand the importance of sex and sex role in regulating gene expression patterns, broadening the scope of this discussion to encompass a wide range of organisms.

The peroxisome: an update on mysteries 3.0

Peroxisomes are highly dynamic, oxidative organelles with key metabolic functions in cellular lipid metabolism, such as the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as the regulation of cellular redox balance. Loss of peroxisomal functions causes severe metabolic disorders in humans. Furthermore, peroxisomes also fulfil protective roles in pathogen and viral defence and immunity, highlighting their wider significance in human health and disease. This has sparked increasing interest in peroxisome biology and their physiological functions. This review presents an update and a continuation of three previous review articles addressing the unsolved mysteries of this remarkable organelle. We continue to highlight recent discoveries, advancements, and trends in peroxisome research, and address novel findings on the metabolic functions of peroxisomes, their biogenesis, protein import, membrane dynamics and division, as well as on peroxisome-organelle membrane contact sites and organelle cooperation. Furthermore, recent insights into peroxisome organisation through super-resolution microscopy are discussed. Finally, we address new roles for peroxisomes in immune and defence mechanisms and in human disorders, and for peroxisomal functions in different cell/tissue types, in particular their contribution to organ-specific pathologies.

The mitochondrial amidoxime reducing component-from prodrug-activation mechanism to drug-metabolizing enzyme and onward to drug target

The mitochondrial amidoxime-reducing component (mARC) is one of five known molybdenum enzymes in eukaryotes. mARC belongs to the MOSC domain superfamily, a large group of so far poorly studied molybdoenzymes. mARC was initially discovered as the enzyme activating N-hydroxylated prodrugs of basic amidines but has since been shown to also reduce a variety of other N-oxygenated compounds, for example, toxic nucleobase analogs. Under certain circumstances, mARC might also be involved in reductive nitric oxide synthesis through reduction of nitrite. Recently, mARC enzymes have received a lot of attention due to their apparent involvement in lipid metabolism and, in particular, because many genome-wide association studies have shown a common variant of human mARC1 to have a protective effect against liver disease. The mechanism linking mARC enzymes with lipid metabolism remains unknown. Here, we give a comprehensive overview of what is currently known about mARC enzymes, their substrates, structure, and apparent involvement in human disease.

Molecular basis of the glycosomal targeting of PEX11 and its mislocalization to mitochondrion in trypanosomes

PEX19 binding sites are essential parts of the targeting signals of peroxisomal membrane proteins (mPTS). In this study, we characterized PEX19 binding sites of PEX11, the most abundant peroxisomal and glycosomal membrane protein from Trypanosoma brucei and Saccharomyces cerevisiae. TbPEX11 contains two PEX19 binding sites, one close to the N-terminus (BS1) and a second in proximity to the first transmembrane domain (BS2). The N-terminal BS1 is highly conserved across different organisms and is required for maintenance of the steady-state concentration and efficient targeting to peroxisomes and glycosomes in both baker's yeast and Trypanosoma brucei. The second PEX19 binding site in TbPEX11 is essential for its glycosomal localization. Deletion or mutations of the PEX19 binding sites in TbPEX11 or ScPEX11 results in mislocalization of the proteins to mitochondria. Bioinformatic analysis indicates that the N-terminal region of TbPEX11 contains an amphiphilic helix and several putative TOM20 recognition motifs. We show that the extreme N-terminal region of TbPEX11 contains a cryptic N-terminal signal that directs PEX11 to the mitochondrion if its glycosomal transport is blocked.

Computational Approaches for Peroxisomal Protein Localization

Computational approaches are practical when investigating putative peroxisomal proteins and for sub-peroxisomal protein localization in unknown protein sequences. Nowadays, advancements in computational methods and Machine Learning (ML) can be used to hasten the discovery of novel peroxisomal proteins and can be combined with more established computational methodologies. Here, we explain and list some of the most used tools and methodologies for novel peroxisomal protein detection and localization.

Computational Evaluation of Peroxisomal Targeting Signals in Metazoa

Most soluble proteins enclosed in peroxisomes encode either type-1 or type-2 peroxisomal targeting signals (PTS1 or PTS2), which act as postal codes and define the proteins' intracellular destination. Thus, various computational programs have been developed to evaluate the probability of specific peptide sequences for being a functional PTS or to scan the primary sequence of proteins for such signals. Among these prediction algorithms the PTS1-predictor ( https://mendel.imp.ac.at/pts1/ ) has been amply used, but the research logic of this and other PTS1 prediction tools is occasionally misjudged giving rise to characteristic pitfalls. Here, a proper utilization of the PTS1-predictor is introduced together with a framework of additional tests to increase the validity of the interpretation of results. Moreover, a list of possible causes for a mismatch between results of such predictions and experimental outcomes is provided. However, the foundational arguments apply to other prediction tools for PTS1 motifs as well.

OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection

We present the OrganelX e-Science Web Server that provides a user-friendly implementation of the In-Pero and In-Mito classifiers for sub-peroxisomal and sub-mitochondrial localization of peroxisomal and mitochondrial proteins and the Is-PTS1 algorithm for detecting and validating potential peroxisomal proteins carrying a PTS1 signal sequence. The OrganelX e-Science Web Server is available at https://organelx.hpc.rug.nl/fasta/.