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1. Peroxisomal Stress Response and Inter-Organelle Communication in Cellular Homeostasis and Aging

   https://doi.org/10.3390/antiox11020192  

   Kim, J; Bai, H (January 2022, Antioxidants)

   Santos, AL (Ed.)

   Peroxisomes are key regulators of cellular and metabolic homeostasis. These organelles play important roles in redox metabolism, the oxidation of very-long-chain fatty acids (VLCFAs), and the biosynthesis of ether phospholipids. Given the essential role of peroxisomes in cellular homeostasis, peroxisomal dysfunction has been linked to various pathological conditions, tissue functional decline, and aging. In the past few decades, a variety of cellular signaling and metabolic changes have been reported to be associated with defective peroxisomes, suggesting that many cellular processes and functions depend on peroxisomes. Peroxisomes communicate with other subcellular organelles, such as the nucleus, mitochondria, endoplasmic reticulum (ER), and lysosomes. These inter-organelle communications are highly linked to the key mechanisms by which cells surveil defective peroxisomes and mount adaptive responses to protect them from damages. In this review, we highlight the major cellular changes that accompany peroxisomal dysfunction and peroxisomal inter-organelle communication through membrane contact sites, metabolic signaling, and retrograde signaling. We also discuss the age-related decline of peroxisomal protein import and its role in animal aging and age-related diseases. Unlike other organelle stress response pathways, such as the unfolded protein response (UPR) in the ER and mitochondria, the cellular signaling pathways that mediate stress responses to malfunctioning peroxisomes have not been systematically studied and investigated. Here, we coin these signaling pathways as “peroxisomal stress response pathways”. Understanding peroxisomal stress response pathways and how peroxisomes communicate with other organelles are important and emerging areas of peroxisome research. 

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2. Glial peroxisome dysfunction induces axonal swelling and neuroinflammation in Drosophila

   https://doi.org/10.1093/g3journal/jkae243  

   Sodders, Maggie; Das, Anurag; Bai, Hua (October 2024, G3: Genes, Genomes, Genetics)

   Tennessen, J (Ed.)

   Abstract Glial cells are known to influence neuronal functions through glia–neuron communication. The present study aims to elucidate the mechanism behind peroxisome-mediated glia–neuron communication using Drosophila neuromuscular junction (NMJ) as a model system. We observe a high abundance of peroxisomes in the abdominal NMJ of adult Drosophila. Interestingly, glia-specific knockdown of peroxisome import receptor protein, Pex5, significantly increases axonal area and volume and leads to axon swelling. The enlarged axonal structure is likely deleterious, as the flies with glia-specific knockdown of Pex5 exhibit age-dependent locomotion defects. In addition, impaired peroxisomal ether lipid biosynthesis in glial cells also induces axon swelling. Consistent with our previous work, defective peroxisomal import function upregulates pro-inflammatory cytokine upd3 in glial cells, while glia-specific overexpression of upd3 induces axonal swelling. Furthermore, motor neuron-specific activation of the JAK-STAT pathway through hop overexpression results in axon swelling. Our findings demonstrated that impairment of glial peroxisomes alters axonal morphology, neuroinflammation, and motor neuron function. 

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3. Plant peroxisome proteostasis—establishing, renovating, and dismantling the peroxisomal proteome

   https://doi.org/10.1042/EBC20210059  

   Muhammad, DurreShahwar; Smith, Kathryn A.; Bartel, Bonnie (May 2022, Essays in Biochemistry)

   Abstract Plant peroxisomes host critical metabolic reactions and insulate the rest of the cell from reactive byproducts. The specialization of peroxisomal reactions is rooted in how the organelle modulates its proteome to be suitable for the tissue, environment, and developmental stage of the organism. The story of plant peroxisomal proteostasis begins with transcriptional regulation of peroxisomal protein genes and the synthesis, trafficking, import, and folding of peroxisomal proteins. The saga continues with assembly and disaggregation by chaperones and degradation via proteases or the proteasome. The story concludes with organelle recycling via autophagy. Some of these processes as well as the proteins that facilitate them are peroxisome-specific, while others are shared among organelles. Our understanding of translational regulation of plant peroxisomal protein transcripts and proteins necessary for pexophagy remain based in findings from other models. Recent strides to elucidate transcriptional control, membrane dynamics, protein trafficking, and conditions that induce peroxisome turnover have expanded our knowledge of plant peroxisomal proteostasis. Here we review our current understanding of the processes and proteins necessary for plant peroxisome proteostasis—the emergence, maintenance, and clearance of the peroxisomal proteome. 

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4. Peroxisomal import stress activates integrated stress response and inhibits ribosome biogenesis

   https://doi.org/10.1093/pnasnexus/pgae429  

   Kim, Jinoh; Huang, Kerui; Vo, Pham_Thuy Tien; Miao, Ting; Correia, Jacinta; Kumar, Ankur; Simons, Mirre_J P; Bai, Hua (October 2024, PNAS Nexus)

   Metallo, Christian (Ed.)

   Abstract Impaired organelle-specific protein import triggers a variety of cellular stress responses, including adaptive pathways to balance protein homeostasis. Most of the previous studies focus on the cellular stress response triggered by misfolded proteins or defective protein import in the endoplasmic reticulum or mitochondria. However, little is known about the cellular stress response to impaired protein import in the peroxisome, an understudied organelle that has recently emerged as a key signaling hub for cellular and metabolic homeostasis. To uncover evolutionarily conserved cellular responses upon defective peroxisomal import, we carried out a comparative transcriptomic analysis on fruit flies with tissue-specific peroxin knockdown and human HEK293 cells expressing dominant-negative PEX5C11A. Our RNA-seq results reveal that defective peroxisomal import upregulates integrated stress response (ISR) and downregulates ribosome biogenesis in both flies and human cells. Functional analyses confirm that impaired peroxisomal import induces eIF2α phosphorylation and ATF4 expression. Loss of ATF4 exaggerates cellular damage upon peroxisomal import defects, suggesting that ATF4 activation serves as a cellular cytoprotective mechanism upon peroxisomal import stress. Intriguingly, we show that peroxisomal import stress decreases the expression of rRNA processing genes and inhibits early pre-rRNA processing, which leads to the accumulation of 47S precursor rRNA and reduction of downstream rRNA intermediates. Taken together, we identify ISR activation and ribosome biogenesis inhibition as conserved adaptive stress responses to defective peroxisomal import and uncover a novel link between peroxisomal dysfunction and rRNA processing. 

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5. A role of villin-dependent F-actin organization in peroxisome motility in Arabidopsis cells

   https://doi.org/10.1101/2025.04.23.650090  

   Huang, Calvin H; Koenig, Amanda; Lee, Yuh-Ru Julie; Shi, Yibo; Hu, Jianping; Liu, Bo (April 2025, bioRxiv)

   ABSTRACT Actin microfilaments (F-actin) serve as the track for directional movement of organelles in plant cells. In actively growing plant cells, F-actin often form robust bundles that trespass the cellular dimension. To test how the F-actin network was employed for peroxisome movement, we wished to disturb actin organization by genetically compromising the function of villin (VLN) proteins that serve as the primary bundling factor inArabidopsis thalianacells. To do so, we isolated T-DNA insertional mutants in threeVLNgenes that were most actively expressed in vegetative tissues. We found that thevln4mutation greatly enhanced the growth defects caused by thevln2 vln3double mutant as thevln2 vln3 vln4triple mutant had a great reduction of organ growth and formed heavily deformed tissues. Both VLN2 and VLN4 proteins were detected on bundled F-actin filaments. Compared to the wild-type cells, the double and triple mutants exhibited progressively reduction of stable F-actin bundles and had fine F-actin filaments undergo rapid remodeling. The defective F-actin network did not prevent peroxisomes from taking on both rapid and slow movements along the F-actin tracks. However, we found that compromised F-actin bundling caused significant reductions in the speed of peroxisome movement and the displacement distance of peroxisome positions. Using a correlation analysis method, we also demonstrated that the complex heterogeneous peroxisome movement may be classified into clusters reflecting the directionality of peroxisome movement. The triple mutant suffered from a significant reduction of peroxisomes exhibiting long-range and linear movement. Our results provided insights into how VLN-dependent F-actin organization was coupled with the complex patterns of peroxisome movement. 

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