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Methods in Molecular Biology (Clifton,... 2024Eukaryotic cells are compartmentalized by membrane-bounded organelles to ensure that specific biochemical reactions and cellular functions occur in a spatially...
Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation.
Eukaryotic cells are compartmentalized by membrane-bounded organelles to ensure that specific biochemical reactions and cellular functions occur in a spatially restricted manner. The subcellular localization of proteins is largely determined by their intrinsic targeting signals, which are mainly constituted by short peptides. A complete organelle targeting signal may contain a core signal (CoreS) as well as auxiliary signals (AuxiS). However, the AuxiS is often not as well characterized as the CoreS. Peroxisomes house many key steps in photorespiration, besides other crucial functions in plants. Peroxisome targeting signal type 1 (PTS1), which is carried by most peroxisome matrix proteins, was initially recognized as a C-terminal tripeptide with a "canonical" consensus of [S/A]-[K/R]-[L/M]. Many studies have shown the existence of auxiliary targeting signals upstream of PTS1, but systematic characterizations are lacking. Here, we designed an analytical strategy to characterize the auxiliary targeting signals for plant peroxisomes using large datasets and statistics followed by experimental validations. This method may also be applied to deciphering the auxiliary targeting signals for other organelles, whose organellar targeting depends on a core peptide with assistance from a nearby auxiliary signal.
Topics: Peroxisomes; Computational Biology; Protein Transport; Peroxisomal Targeting Signals; Protein Sorting Signals; Plant Proteins; Databases, Protein; Amino Acid Sequence
PubMed: 38861094
DOI: 10.1007/978-1-0716-3802-6_21 -
Cellular & Molecular Biology Letters Jun 2024The molecular basis for bulk autophagy activation due to a deficiency in essential nutrients such as carbohydrates, amino acids, and nitrogen is well understood. Given...
The molecular basis for bulk autophagy activation due to a deficiency in essential nutrients such as carbohydrates, amino acids, and nitrogen is well understood. Given autophagy functions to reduce surplus to compensate for scarcity, it theoretically possesses the capability to selectively degrade specific substrates to meet distinct metabolic demands. However, direct evidence is still lacking that substantiates the idea that autophagy selectively targets specific substrates (known as selective autophagy) to address particular nutritional needs. Recently, Gross et al. found that during phosphate starvation (P-S), rather than nitrogen starvation (N-S), yeasts selectively eliminate peroxisomes by dynamically altering the composition of the Atg1/ULK kinase complex (AKC) to adapt to P-S. This study elucidates how the metabolite sensor Pho81 flexibly interacts with AKC and guides selective autophagic clearance of peroxisomes during P-S, providing novel insights into the metabolic contribution of autophagy to special nutritional needs.
Topics: Autophagy; Phosphates; Saccharomyces cerevisiae Proteins; Peroxisomes; Saccharomyces cerevisiae; Autophagy-Related Protein-1 Homolog; Autophagy-Related Proteins; Protein Serine-Threonine Kinases; Protein Kinases
PubMed: 38834954
DOI: 10.1186/s11658-024-00597-3 -
Medecine Sciences : M/S May 2024
Topics: Animals; Hepacivirus; Hepatitis C; Peroxisomes
PubMed: 38819270
DOI: 10.1051/medsci/2024043 -
Insect Biochemistry and Molecular... Jul 2024Peroxisomes are ubiquitous cellular organelles participating in a variety of critical metabolic reactions. PEX14 is an essential peroxin responsible for peroxisome...
Peroxisomes are ubiquitous cellular organelles participating in a variety of critical metabolic reactions. PEX14 is an essential peroxin responsible for peroxisome biogenesis. In this study, we identified the human PEX14 homolog in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae). N. lugens PEX14 (NlPEX14) showed significant topological similarity to its human counterpart. It is expressed throughout all developmental stages, with the highest expression observed in adult insects. Down-regulation of NlPEX14 through injection of NlPEX14-specific double-strand RNA impaired nymphal development. Moreover, females subjected to dsNlPEX14 treatment exhibited a significantly reduced lifespan. Additionally, we found abnormal ovarian development and a significant decrease in the number of eggs laid in NlPEX14-downregulated females. Further experiments support that the shortening of lifespan and the decrease in female fecundity can be attributed, at least partially, to the accumulation of fatty acids and reduced expression of vitellogenin. Together, our study reveals an indispensable function of NlPEX14 for insect reproduction and establishes a causal connection between the phenotypes and peroxisome biogenesis, shedding light on the importance of peroxisomes in female fecundity.
Topics: Animals; Hemiptera; Female; Fertility; Insect Proteins; Peroxisomes; Longevity; Nymph; Peroxins; Membrane Proteins; Vitellogenins
PubMed: 38815735
DOI: 10.1016/j.ibmb.2024.104139 -
Nature Communications May 2024Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of...
Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of ether lipids. Consequently, peroxisome dysfunction leads to pediatric-onset neurodegenerative conditions, including Peroxisome Biogenesis Disorders (PBD). Due to the dynamic, tissue-specific, and context-dependent nature of their biogenesis and function, live cell imaging of peroxisomes is essential for studying peroxisome regulation, as well as for the diagnosis of PBD-linked abnormalities. However, the peroxisomal imaging toolkit is lacking in many respects, with no reporters for substrate import, nor cell-permeable probes that could stain dysfunctional peroxisomes. Here we report that the BODIPY-C12 fluorescent fatty acid probe stains functional and dysfunctional peroxisomes in live mammalian cells. We then go on to improve BODIPY-C12, generating peroxisome-specific reagents, PeroxiSPY650 and PeroxiSPY555. These probes combine high peroxisome specificity, bright fluorescence in the red and far-red spectrum, and fast non-cytotoxic staining, making them ideal tools for live cell, whole organism, or tissue imaging of peroxisomes. Finally, we demonstrate that PeroxiSPY enables diagnosis of peroxisome abnormalities in the PBD CRISPR/Cas9 cell models and patient-derived cell lines.
Topics: Peroxisomes; Humans; Fatty Acids; Fluorescent Dyes; Boron Compounds; Peroxisomal Disorders; Animals
PubMed: 38773129
DOI: 10.1038/s41467-024-48679-2 -
Biochimica Et Biophysica Acta.... Aug 2024Peroxisome biogenesis disorders are caused by pathogenic variants in genes involved in biogenesis and maintenance of peroxisomes. However, mitochondria are also often...
Peroxisome biogenesis disorders are caused by pathogenic variants in genes involved in biogenesis and maintenance of peroxisomes. However, mitochondria are also often affected in these diseases. Peroxisomal membrane proteins, including PEX14, have been found to mislocalise to mitochondria in cells lacking peroxisomes. Recent studies indicated that this mislocalisation contributes to mitochondrial abnormalities in PEX3-deficient patient fibroblasts cells. Here, we studied whether mitochondrial morphology is also affected in PEX3-deficient HEK293 cells and whether PEX14 mislocalises to mitochondria in these cells. Using high-resolution imaging techniques, we show that although endogenous PEX14 mislocalises to mitochondria, mitochondrial morphology was normal in PEX3-KO HEK293 cells. However, we discovered that overexpression of tagged PEX14 in wild-type HEK293 cells resulted in its mitochondrial localisation, accompanied by altered mitochondrial morphology. Our data indicate that overexpression of tagged PEX14 alone directly or indirectly cause mitochondrial abnormalities in cells containing peroxisomes.
Topics: Humans; Mitochondria; Membrane Proteins; HEK293 Cells; Peroxisomes; Peroxins; Protein Transport; Lipoproteins; Repressor Proteins
PubMed: 38762172
DOI: 10.1016/j.bbamcr.2024.119754 -
Free Radical Biology & Medicine Aug 2024Androgen receptor (AR)-targeting therapy induces oxidative stress in prostate cancer. However, the mechanism of oxidative stress induction by AR-targeting therapy...
Oxidative stress in peroxisomes induced by androgen receptor inhibition through peroxisome proliferator-activated receptor promotes enzalutamide resistance in prostate cancer.
Androgen receptor (AR)-targeting therapy induces oxidative stress in prostate cancer. However, the mechanism of oxidative stress induction by AR-targeting therapy remains unclear. This study investigated the mechanism of oxidative stress induction by AR-targeting therapy, with the aim to develop novel therapeutics targeting oxidative stress induced by AR-targeting therapy. Intracellular reactive oxygen species (ROS) was examined by fluorescence microscopy and flow cytometry analysis. The effects of silencing gene expression and small molecule inhibitors on gene expression and cytotoxic effects were examined by quantitative real-time PCR and cell proliferation assay. ROS induced by androgen depletion co-localized with peroxisomes in prostate cancer cells. Among peroxisome-related genes, PPARA was commonly induced by AR inhibition and involved in ROS production via PKC signaling. Inhibition of PPARα by specific siRNA and a small molecule inhibitor suppressed cell proliferation and increased cellular sensitivity to the antiandrogen enzalutamide in prostate cancer cells. This study revealed a novel pathway by which AR inhibition induced intracellular ROS mainly in peroxisomes through PPARα activation in prostate cancer. This pathway is a promising target for the development of novel therapeutics for prostate cancer in combination with AR-targeting therapy such as antiandrogen enzalutamide.
Topics: Male; Humans; Phenylthiohydantoin; Nitriles; Peroxisomes; Oxidative Stress; Drug Resistance, Neoplasm; Benzamides; Receptors, Androgen; Reactive Oxygen Species; PPAR alpha; Cell Proliferation; Prostatic Neoplasms; Cell Line, Tumor; Gene Expression Regulation, Neoplastic; Signal Transduction; Androgen Receptor Antagonists; RNA, Small Interfering
PubMed: 38762061
DOI: 10.1016/j.freeradbiomed.2024.05.030 -
PloS One 2024The membrane peroxisomal proteins PEX11, play a crucial role in peroxisome proliferation by regulating elongation, membrane constriction, and fission of pre-existing...
The membrane peroxisomal proteins PEX11, play a crucial role in peroxisome proliferation by regulating elongation, membrane constriction, and fission of pre-existing peroxisomes. In this study, we evaluated the function of PEX11B gene in neural differentiation of human embryonic stem cell (hESC) by inducing shRNAi-mediated knockdown of PEX11B expression. Our results demonstrate that loss of PEX11B expression led to a significant decrease in the expression of peroxisomal-related genes including ACOX1, PMP70, PEX1, and PEX7, as well as neural tube-like structures and neuronal markers. Inhibition of SIRT1 using pharmacological agents counteracted the effects of PEX11B knockdown, resulting in a relative increase in PEX11B expression and an increase in differentiated neural tube-like structures. However, the neuroprotective effects of SIRT1 were eliminated by PPAR inhibition, indicating that PPARɣ may mediate the interaction between PEX11B and SIRT1. Our findings suggest that both SIRT1 and PPARɣ have neuroprotective effects, and also this study provides the first indication for a potential interaction between PEX11B, SIRT1, and PPARɣ during hESC neural differentiation.
Topics: Humans; Sirtuin 1; PPAR gamma; Cell Differentiation; Human Embryonic Stem Cells; Membrane Proteins; Neurons; Cell Line; Peroxisomes
PubMed: 38753762
DOI: 10.1371/journal.pone.0298274 -
Journal of Cell Science May 2024Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis.... (Review)
Review
Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis. Their abundance and activity are dynamically regulated in response to nutrient availability and cellular stress. Damaged or superfluous peroxisomes are removed mainly by pexophagy, the selective autophagy of peroxisomes induced by ubiquitylation of peroxisomal membrane proteins or ubiquitin-independent processes. Dysregulated pexophagy impairs peroxisome homeostasis and has been linked to the development of various human diseases. Despite many recent insights into mammalian pexophagy, our understanding of this process is still limited compared to our understanding of pexophagy in yeast. In this Cell Science at a Glance article and the accompanying poster, we summarize current knowledge on the control of mammalian pexophagy and highlight which aspects require further attention. We also discuss the role of ubiquitylation in pexophagy and describe the ubiquitin machinery involved in regulating signals for the recruitment of phagophores to peroxisomes.
Topics: Peroxisomes; Humans; Animals; Ubiquitination; Autophagy; Macroautophagy; Mammals; Membrane Proteins
PubMed: 38752931
DOI: 10.1242/jcs.259775 -
International Journal of Biological... Jun 2024Fusarium crown rot, caused by Fusarium pseudograminearum, is a devastating disease affecting the yield and quality of cereal crops. Peroxisomes are single-membrane...
Fusarium crown rot, caused by Fusarium pseudograminearum, is a devastating disease affecting the yield and quality of cereal crops. Peroxisomes are single-membrane organelles that play a critical role in various biological processes in eukaryotic cells. To functionally characterise peroxisome biosynthetic receptor proteins FpPEX5 and FpPEX7 in F. pseudograminearum, we constructed deletion mutants, ΔFpPEX5 and ΔFpPEX7, and complementary strains, ΔFpPEX5-C and ΔFpPEX7-C, and analysed the functions of FpPEX5 and FpPEX7 proteins using various phenotypic observations. The deletion of FpPEX5 and FpPEX7 resulted in a significant deficiency in mycelial growth and conidiation and blocked the peroxisomal targeting signal 1 and peroxisomal targeting signal 2 pathways, which are involved in peroxisomal matrix protein transport, increasing the accumulation of lipid droplets and reactive oxygen species. The deletion of FpPEX5 and FpPEX7 may reduce the formation of toxigenic bodies and decrease the pathogenicity of F. pseudograminearum. These results indicate that FpPEX5 and FpPEX7 play vital roles in the growth, asexual reproduction, virulence, and fatty acid utilisation of F. pseudograminearum. This study provides a theoretical basis for controlling stem rot in wheat.
Topics: Fusarium; Fungal Proteins; Virulence; Peroxisomes; Trichothecenes; Plant Diseases; Spores, Fungal; Triticum; Reactive Oxygen Species; Peroxisome-Targeting Signal 1 Receptor; Gene Deletion; Gene Expression Regulation, Fungal; Peroxisomal Targeting Signal 2 Receptor; Mycelium
PubMed: 38734339
DOI: 10.1016/j.ijbiomac.2024.132227