- Award ID(s):
- 1907069
- NSF-PAR ID:
- 10387014
- Date Published:
- Journal Name:
- Essays in Biochemistry
- ISSN:
- 0071-1365
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Synopsis The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by Liquid chromatography/Tandem mass spectrometry data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. Non-directional stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a non-directional response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine, and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. Non-directional stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient non-directional stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.more » « less
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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.more » « less
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Abstract The sorting of eukaryotic proteins to various organellar destinations requires receptors that recognize cargo protein targeting signals and facilitate transport into the organelle. One such receptor is the peroxin
PEX 5, which recruits cytosolic cargo carrying a peroxisome‐targeting signal (PTS ) type 1 (PTS 1) for delivery into the peroxisomal lumen (matrix). In plants and mammals,PEX 5 is also indirectly required for peroxisomal import of proteins carrying aPTS 2 signal becausePEX 5 binds thePTS 2 receptor, bringing the associatedPTS 2 cargo to the peroxisome along withPTS 1 cargo. DespitePEX 5 being thePTS 1 cargo receptor, previously identified Arabidopsispex5 mutants display either impairment of bothPTS 1 andPTS 2 import or defects only inPTS 2 import. Here, we report the first Arabidopsispex5 mutant with an exclusivePTS 1 import defect. In addition to markedly diminishedGFP ‐PTS 1 import and decreased pex5‐2 protein accumulation, thispex5‐2 mutant shows typical peroxisome‐related defects, including inefficient β‐oxidation and reduced growth. Growth at reduced or elevated temperatures ameliorated or exacerbatedpex5‐2 peroxisome‐related defects, respectively, without markedly changing pex5‐2 protein levels. In contrast to the diminishedPTS 1 import,PTS 2 processing was only slightly impaired andPTS 2‐GFP import appeared normal inpex5‐2 . This finding suggests that even minor peroxisomal localization of thePTS 1 proteinDEG 15, thePTS 2‐processing protease, is sufficient to maintain robustPTS 2 processing. -
Summary Catabolism of fatty acids stored in oil bodies is essential for seed germination and seedling development in Arabidopsis. This fatty acid breakdown occurs in peroxisomes, organelles that sequester oxidative reactions. Import of peroxisomal enzymes is facilitated by peroxins including
PEX 5, a receptor that delivers cargo proteins from the cytosol to the peroxisomal matrix. After cargo delivery, a complex of thePEX 1 andPEX 6ATP ases and thePEX 26 tail‐anchored membrane protein removes ubiquitinatedPEX 5 from the peroxisomal membrane. We identified Arabidopsispex6 andpex26 mutants by screening for inefficient seedling β‐oxidation phenotypes. The mutants displayed distinct defects in growth, response to a peroxisomally metabolized auxin precursor, and peroxisomal protein import. The lowPEX 5 levels in these mutants were increased by treatment with a proteasome inhibitor or by combiningpex26 with peroxisome‐associated ubiquitination machinery mutants, suggesting that ubiquitinatedPEX 5 is degraded by the proteasome when the function ofPEX 6 orPEX 26 is reduced. Combiningpex26 with mutations that increasePEX 5 levels either worsened or improvedpex26 physiological and molecular defects, depending on the introduced lesion. Moreover, elevatingPEX 5 levels via a35S: transgene exacerbatedPEX 5pex26 defects and ameliorated the defects of only a subset ofpex6 alleles, implying that decreasedPEX 5 is not the sole molecular deficiency in these mutants. We found peroxisomes clustered around persisting oil bodies inpex6 andpex26 seedlings, suggesting a role for peroxisomal retrotranslocation machinery in oil body utilization. The disparate phenotypes of thesepex alleles may reflect unanticipated functions of the peroxisomalATP ase complex. -
SUMMARY Peroxisomes are universal eukaryotic organelles essential to plants and animals. Most peroxisomal matrix proteins carry peroxisome targeting signal type 1 (PTS1), a C‐terminal tripeptide. Studies from various kingdoms have revealed influences from sequence upstream of the tripeptide on peroxisome targeting, supporting the view that positive charges in the upstream region are the major enhancing elements. However, a systematic approach to better define the upstream elements influencing PTS1 targeting capability is needed. Here, we used protein sequences from 177 plant genomes to perform large‐scale and in‐depth analysis of the PTS1 domain, which includes the PTS1 tripeptide and upstream sequence elements. We identified and verified 12 low‐frequency PTS1 tripeptides and revealed upstream enhancing and inhibiting sequence patterns for peroxisome targeting, which were subsequently validated
in vivo . Follow‐up analysis revealed that nonpolar and acidic residues have relatively strong enhancing and inhibiting effects, respectively, on peroxisome targeting. However, in contrast to the previous understanding, positive charges alone do not show the anticipated enhancing effect and that both the position and property of the residues within these patterns are important for peroxisome targeting. We further demonstrated that the three residues immediately upstream of the tripeptide are the core influencers, with a ‘basic‐nonpolar‐basic’ pattern serving as a strong and universal enhancing pattern for peroxisome targeting. These findings have significantly advanced our knowledge of the PTS1 domain in plants and likely other eukaryotic species as well. The principles and strategies employed in the present study may also be applied to deciphering auxiliary targeting signals for other organelles.