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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Article
  • Peer Reviewed
UC Santa Barbara Previously Published Works (2022)
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
    Cover page: Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2015)
    Pex1 and Pex6 are Type-2 AAA+ ATPases required for the de novo biogenesis of peroxisomes. Mutations in Pex1 and Pex6 account for the majority of the most severe forms of peroxisome biogenesis disorders in humans. Here, we show that the ATP-dependent complex of Pex1 and Pex6 from Saccharomyces cerevisiae is a heterohexamer with alternating subunits. Within the Pex1/Pex6 complex, only the D2 ATPase ring hydrolyzes ATP, while nucleotide binding in the D1 ring promotes complex assembly. ATP hydrolysis by Pex1 is highly coordinated with that of Pex6. Furthermore, Pex15, the membrane anchor required for Pex1/Pex6 recruitment to peroxisomes, inhibits the ATP-hydrolysis activity of Pex1/Pex6.
      Cover page: The Pex1/Pex6 Complex Is a Heterohexameric AAA+ Motor with Alternating and Highly Coordinated Subunits
      • Thesis
      • Peer Reviewed
      UC Santa Barbara Electronic Theses and Dissertations (2024)

      Peroxisomes are compartmentalized membrane-bound organelles evolved to enable cells to metabolically adapt to their environment, that are themselves near omnipresent throughout eukarya. In humans, peroxisomes are essential for normal development, insofar that peroxisome dysfunction causes both pre- and post-natal mortal insufficiencies that would disbar one from addressing the vicissitudes of life; and yet there is a dearth of data detailing the genes governing peroxisome function and homeostasis. To this end, we executed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We uncovered various genes that hold potential as novel regulators of peroxisomes, such as suppressor of cytokine signaling-3 (SOCS3), C2orf15, Insulin Degrading Enzyme (IDE), and Ring finger protein 146 (RNF146). Through rigorous inspection, we were able to classify SOCS3 as a spurious hit generated by off-target effects, while potentially developing a novel way to find Cas9 related off-targets. Contemporaneously, we found through study of C2orf15 that there were computational aberrations embedded in the sgRNA generation processes of our colleagues’ CRISPRi library, leading us to the discovery that Mitochondrial Ribosomal Protein L30 (MRPL30) modulates peroxisome abundance. Our dual-screen experiments then showed that IDE resembled a profligate peroxisome cargo regulator where its suppression strongly bolstered peroxisome matrix import, an antipodal effect relative to most peroxisome biogenesis gene knockdowns. We chose to focus our efforts on RNF146, an E3 ligase with a predilection for poly(ADP-ribose), where its suppression caused an ebbing in the import function of peroxisomes. Loss of RNF146 caused peroxisome import malfunction by unfettered oversaturation of the poly(ADP-ribose) polymerases TNKS and TNKS2, which then bind, PARsylate, and impair peroxisomal proteins, chiefly PEX14. Because RNF146/TNKS/2 are more renowned for their connection to Wnt-signaling, mainly the degradation of AXIN1, a component of the destruction complex, we hypothesized that the peroxisome, via PEX14, would participate in the homeostatic equilibrium of RNF146/TNKS/2’s proteasomal facilitations. We discovered that both loss of PEX14 and PEX19 destabilized AXIN1, as predicted, which subsequently compromised the steady-state levels of beta-catenin induced transcription. We then extrapolated these findings to other realms of developmental biology, mainly the Wnt-signaling influenced stem cell fate of neural progenitor cells (NPCs) and neural crest stem cells (NCSCs). Interestingly, our early results suggest that loss of PEX14 and PEX19 may bias the differentiation decision of stem cells similar to a loss in AXIN1, in line with our model. In totality, the consequences of our genome-wide screen, the collective observations, and various data paint a larger picture in which peroxisomes are interlinked to, and participate in, multifarious regulatory pathways of the cell.

      • 8 supplemental ZIPs
      Cover page: The Genome-wide Elucidation of Genes Involved in Peroxisome Homeostasis and its Consequences on Interlinked Cell Regulation Pathways
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2013)
      Secretory and transmembrane proteins enter the endoplasmic reticulum (ER) as unfolded proteins and exit as either folded proteins in transit to their target organelles or as misfolded proteins targeted for degradation. The unfolded protein response (UPR) maintains the protein-folding homeostasis within the ER, ensuring that the protein-folding capacity of the ER meets the load of client proteins. Activation of the UPR depends on three ER stress sensor proteins, Ire1, PERK, and ATF6. Although the consequences of activation are well understood, how these sensors detect ER stress remains unclear. Recent evidence suggests that yeast Ire1 directly binds to unfolded proteins, which induces its oligomerization and activation. BiP dissociation from Ire1 regulates this oligomeric equilibrium, ultimately modulating Ire1's sensitivity and duration of activation. The mechanistic principles of ER stress sensing are the focus of this review.
        Cover page: Endoplasmic Reticulum Stress Sensing in the Unfolded Protein Response
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2018)
        Pex1 and Pex6 form a heterohexameric motor essential for peroxisome biogenesis and function, and mutations in these AAA-ATPases cause most peroxisome-biogenesis disorders in humans. The tail-anchored protein Pex15 recruits Pex1/Pex6 to the peroxisomal membrane, where it performs an unknown function required for matrix-protein import. Here we determine that Pex1/Pex6 from S. cerevisiae is a protein translocase that unfolds Pex15 in a pore-loop-dependent and ATP-hydrolysis-dependent manner. Our structural studies of Pex15 in isolation and in complex with Pex1/Pex6 illustrate that Pex15 binds the N-terminal domains of Pex6, before its C-terminal disordered region engages with the pore loops of the motor, which then processively threads Pex15 through the central pore. Furthermore, Pex15 directly binds the cargo receptor Pex5, linking Pex1/Pex6 to other components of the peroxisomal import machinery. Our results thus support a role of Pex1/Pex6 in mechanical unfolding of peroxins or their extraction from the peroxisomal membrane during matrix-protein import.
          • Article
          • Peer Reviewed
          UC Santa Barbara Previously Published Works (2024)
          Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
            Cover page: Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types
            • Article
            • Peer Reviewed
            UC Santa Barbara Previously Published Works (2024)
            The heterohexameric ATPases associated with diverse cellular activities (AAA)-ATPase Pex1/Pex6 is essential for the formation and maintenance of peroxisomes. Pex1/Pex6, similar to other AAA-ATPases, uses the energy from ATP hydrolysis to mechanically thread substrate proteins through its central pore, thereby unfolding them. In related AAA-ATPase motors, substrates are recruited through binding to the motor's N-terminal domains or N terminally bound cofactors. Here, we use structural and biochemical techniques to characterize the function of the N1 domain in Pex6 from budding yeast, Saccharomyces cerevisiae. We found that although Pex1/ΔN1-Pex6 is an active ATPase in vitro, it does not support Pex1/Pex6 function at the peroxisome in vivo. An X-ray crystal structure of the isolated Pex6 N1 domain shows that the Pex6 N1 domain shares the same fold as the N-terminal domains of PEX1, CDC48, and NSF, despite poor sequence conservation. Integrating this structure with a cryo-EM reconstruction of Pex1/Pex6, AlphaFold2 predictions, and biochemical assays shows that Pex6 N1 mediates binding to both the peroxisomal membrane tether Pex15 and an extended loop from the D2 ATPase domain of Pex1 that influences Pex1/Pex6 heterohexamer stability. Given the direct interactions with both Pex15 and the D2 ATPase domains, the Pex6 N1 domain is poised to coordinate binding of cofactors and substrates with Pex1/Pex6 ATPase activity.
              Cover page: The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1
              • Article
              • Peer Reviewed
              UC Santa Barbara Previously Published Works (2024)
              Peroxisomes are membrane-bound organelles harboring metabolic enzymes. In humans, peroxisomes are required for normal development, yet the genes regulating peroxisome function remain unclear. We performed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We found that inhibition of RNF146, an E3 ligase activated by poly(ADP-ribose), reduced the import of proteins into peroxisomes. RNF146-mediated loss of peroxisome import depended on the stabilization and activity of the poly(ADP-ribose) polymerase tankyrase, which binds the peroxisomal membrane protein PEX14. We propose that RNF146 and tankyrase regulate peroxisome import efficiency by PARsylation of proteins at the peroxisome membrane. Interestingly, we found that the loss of peroxisomes increased tankyrase and RNF146-dependent degradation of non-peroxisomal substrates, including the beta-catenin destruction complex component AXIN1, which was sufficient to alter the amplitude of beta-catenin transcription. Together, these observations not only suggest previously undescribed roles for RNF146 in peroxisomal regulation, but also a novel role in bridging peroxisome function with Wnt/beta-catenin signaling during development.
                Creative Commons 'BY-NC' version 4.0 license
                • Article
                • Peer Reviewed
                UC Santa Barbara Previously Published Works (2024)
                Peroxisomes are membrane-bound organelles harboring metabolic enzymes. In humans, peroxisomes are required for normal development, yet the genes regulating peroxisome function remain unclear. We performed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We found that inhibition of RNF146, an E3 ligase activated by poly(ADP-ribose), reduced the import of proteins into peroxisomes. RNF146-mediated loss of peroxisome import depended on the stabilization and activity of the poly(ADP-ribose) polymerases TNKS and TNKS2, which bind the peroxisomal membrane protein PEX14. We propose that RNF146 and TNKS/2 regulate peroxisome import efficiency by PARsylation of proteins at the peroxisome membrane. Interestingly, we found that the loss of peroxisomes increased TNKS/2 and RNF146-dependent degradation of non-peroxisomal substrates, including the β-catenin destruction complex component AXIN1, which was sufficient to alter the amplitude of β-catenin transcription. Together, these observations not only suggest previously undescribed roles for RNF146 in peroxisomal regulation but also a novel role in bridging peroxisome function with Wnt/β-catenin signaling during development.
                  Cover page: A genome-wide screen links peroxisome regulation with Wnt signaling through RNF146 and TNKS/2Creative Commons 'BY-NC-ND' version 4.0 license
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