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  1. Article ; Online: Convergent and divergent mechanisms of peroxisomal and mitochondrial division.

    Subramani, Suresh / Shukla, Nandini / Farre, Jean-Claude

    The Journal of cell biology

    2023  Volume 222, Issue 9

    Abstract: Organelle division and segregation are important in cellular homeostasis. Peroxisomes (POs) and mitochondria share a core division machinery and mechanism of membrane scission. The division of each organelle is interdependent not only on the other but ... ...

    Abstract Organelle division and segregation are important in cellular homeostasis. Peroxisomes (POs) and mitochondria share a core division machinery and mechanism of membrane scission. The division of each organelle is interdependent not only on the other but also on other organelles, reflecting the dynamic communication between subcellular compartments, even as they coordinate the exchange of metabolites and signals. We highlight common and unique mechanisms involved in the fission of these organelles under the premise that much can be gleaned regarding the division of one organelle based on information available for the other.
    MeSH term(s) Peroxisomes/metabolism ; Mitochondria/metabolism
    Language English
    Publishing date 2023-08-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.202304076
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  2. Article ; Online: BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of

    Farré, Jean-Claude / Li, Paul / Subramani, Suresh

    International journal of molecular sciences

    2021  Volume 22, Issue 9

    Abstract: The maintenance of intracellular ... ...

    Abstract The maintenance of intracellular NAD
    MeSH term(s) Carbon/pharmacology ; Fluorescence ; Fungal Proteins/metabolism ; Green Fluorescent Proteins/metabolism ; Malate Dehydrogenase/metabolism ; Models, Biological ; NAD/metabolism ; Oleic Acid/metabolism ; Peroxisomes/metabolism ; Protein Transport/drug effects ; Reproducibility of Results ; Saccharomycetales/enzymology
    Chemical Substances Fungal Proteins ; NAD (0U46U6E8UK) ; Green Fluorescent Proteins (147336-22-9) ; Oleic Acid (2UMI9U37CP) ; Carbon (7440-44-0) ; Malate Dehydrogenase (EC 1.1.1.37)
    Language English
    Publishing date 2021-05-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22094890
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  3. Article ; Online: BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of Pichia pastoris Malate Dehydrogenase

    Jean-Claude Farré / Paul Li / Suresh Subramani

    International Journal of Molecular Sciences, Vol 22, Iss 4890, p

    2021  Volume 4890

    Abstract: The maintenance of intracellular NAD + /NADH homeostasis across multiple, subcellular compartments requires the presence of NADH-shuttling proteins, which circumvent the lack of permeability of organelle membranes to these cofactors. Very little is known ...

    Abstract The maintenance of intracellular NAD + /NADH homeostasis across multiple, subcellular compartments requires the presence of NADH-shuttling proteins, which circumvent the lack of permeability of organelle membranes to these cofactors. Very little is known regarding these proteins in the methylotrophic yeast, Pichia pastoris . During the study of the subcellular locations of these shuttling proteins, which often have dual subcellular locations, it became necessary to develop new ways to detect the weak peroxisomal locations of some of these proteins. We have developed a novel variation of the traditional Bimolecular Fluorescence Complementation (BiFC), called divergent BiFC, to detect intraorganellar colocalization of two noninteracting proteins based on their proximity-based protein crowding within a small subcellular compartment, rather than on the traditional protein–protein interactions expected for BiFC. This method is used to demonstrate the partially peroxisomal location of one such P. pastoris NADH-shuttling protein, malate dehydrogenase B, only when cells are grown in oleate, but not when grown in methanol or glucose. We discuss the mode of NADH shuttling in P. pastoris and the physiological basis of the medium-dependent compartmentalization of Pp MdhB.
    Keywords redox balance ; NADH shuttle ; peroxisomal malate dehydrogenase ; environment-dependent peroxisomal targeting ; intraorganellar protein crowding ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Automated, image-based quantification of peroxisome characteristics with

    Neal, Maxwell L / Shukla, Nandini / Mast, Fred D / Farré, Jean-Claude / Pacio, Therese M / Raney-Plourde, Katelyn E / Prasad, Sumedh / Subramani, Suresh / Aitchison, John D

    bioRxiv : the preprint server for biology

    2024  

    Abstract: perox-per- ... ...

    Abstract perox-per-cell
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.08.588597
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  5. Article ; Online: Recognition and Chaperoning by Pex19, Followed by Trafficking and Membrane Insertion of the Peroxisome Proliferation Protein, Pex11.

    Zientara-Rytter, Katarzyna M / Mahalingam, Shanmuga S / Farré, Jean-Claude / Carolino, Krypton / Subramani, Suresh

    Cells

    2022  Volume 11, Issue 1

    Abstract: Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how ... ...

    Abstract Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the
    MeSH term(s) Amino Acid Sequence ; Cell Proliferation ; Humans ; Membrane Proteins/metabolism ; Molecular Chaperones/metabolism
    Chemical Substances Membrane Proteins ; Molecular Chaperones ; PEX11A protein, human ; PEX19 protein, human (157153-79-2)
    Language English
    Publishing date 2022-01-04
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11010157
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  6. Article ; Online: OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway

    Jean-Claude Farre / Krypton Carolino / Lou Devanneaux / Suresh Subramani

    eLife, Vol

    2022  Volume 11

    Abstract: How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these ...

    Abstract How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these pathways enter mitochondria for ATP production and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation in Pichia pastoris was abolished in NADH-shuttling- and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by a high AMP/ATP ratio. In OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by the Δgal83 mutant, were rescued by deletion of three transcriptional repressor genes (MIG1, MIG2, and NRG1) controlled by SNF1 signaling. Our results are interpreted in terms of a mechanism by which peroxisomal and mitochondrial proteins and/or metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol, and the nucleus. We discuss the physiological relevance of this work in the context of human OXPHOS deficiencies.
    Keywords peroxisome proliferation ; mitochondria ; OXPHOS ; SNF1 ; interorganelle communication ; feedback loop ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway.

    Farre, Jean-Claude / Carolino, Krypton / Devanneaux, Lou / Subramani, Suresh

    eLife

    2022  Volume 11

    Abstract: How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these ...

    Abstract How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these pathways enter mitochondria for ATP production and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation in Pichia pastoris was abolished in NADH-shuttling- and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by a high AMP/ATP ratio. In OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by the Δgal83 mutant, were rescued by deletion of three transcriptional repressor genes (MIG1, MIG2, and NRG1) controlled by SNF1 signaling. Our results are interpreted in terms of a mechanism by which peroxisomal and mitochondrial proteins and/or metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol, and the nucleus. We discuss the physiological relevance of this work in the context of human OXPHOS deficiencies.
    MeSH term(s) Adenosine Triphosphate/metabolism ; Cell Proliferation ; Genes, Fungal ; Humans ; Methanol/metabolism ; Mitochondrial Diseases/metabolism ; NAD/metabolism ; Oxidative Phosphorylation ; Peroxisomes/metabolism ; Protein Serine-Threonine Kinases/genetics ; Repressor Proteins/metabolism ; Saccharomycetales ; Signal Transduction
    Chemical Substances Repressor Proteins ; NAD (0U46U6E8UK) ; Adenosine Triphosphate (8L70Q75FXE) ; SNF1-related protein kinases (EC 2.7.1.-) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Methanol (Y4S76JWI15)
    Language English
    Publishing date 2022-04-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.75143
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  8. Article ; Online: Recognition and Chaperoning by Pex19, Followed by Trafficking and Membrane Insertion of the Peroxisome Proliferation Protein, Pex11

    Katarzyna M. Zientara-Rytter / Shanmuga S. Mahalingam / Jean-Claude Farré / Krypton Carolino / Suresh Subramani

    Cells, Vol 11, Iss 157, p

    2022  Volume 157

    Abstract: Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the Pichia pastoris Pex11 is recognized and chaperoned by Pex19, ... ...

    Abstract Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the Pichia pastoris Pex11 is recognized and chaperoned by Pex19, targeted to peroxisome membranes and inserted therein. We demonstrate that Pex11 contains one Pex19-binding site (Pex19-BS) that is required for Pex11 insertion into peroxisomal membranes by Pex19, but is non-essential for peroxisomal trafficking. We provide extensive mutational analyses regarding the recognition of Pex19-BS in Pex11 by Pex19. Pex11 also has a second, Pex19-independent membrane peroxisome-targeting signal (mPTS) that is preserved among Pex11-family proteins and anchors the human HsPex11γ to the outer leaflet of the peroxisomal membrane. Thus, unlike most PMPs, Pex11 can use two mechanisms of transport to peroxisomes, where only one of them depends on its direct interaction with Pex19, but the other does not. However, Pex19 is necessary for membrane insertion of Pex11. We show that Pex11 can self-interact, using both homo- and/or heterotypic interactions involving its N-terminal helical domains. We demonstrate that Pex19 acts as a chaperone by interacting with the Pex19-BS in Pex11, thereby protecting Pex11 from spontaneous oligomerization that would otherwise cause its aggregation and subsequent degradation.
    Keywords peroxisomal membrane protein ; peroxisome proliferation protein ; peroxisome division ; Pex11 ; Pex19 ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Mechanistic insights into selective autophagy pathways: lessons from yeast.

    Farré, Jean-Claude / Subramani, Suresh

    Nature reviews. Molecular cell biology

    2016  Volume 17, Issue 9, Page(s) 537–552

    Abstract: Autophagy has burgeoned rapidly as a field of study because of its evolutionary conservation, the diversity of intracellular cargoes degraded and recycled by this machinery, the mechanisms involved, as well as its physiological relevance to human health ... ...

    Abstract Autophagy has burgeoned rapidly as a field of study because of its evolutionary conservation, the diversity of intracellular cargoes degraded and recycled by this machinery, the mechanisms involved, as well as its physiological relevance to human health and disease. This self-eating process was initially viewed as a non-selective mechanism used by eukaryotic cells to degrade and recycle macromolecules in response to stress; we now know that various cellular constituents, as well as pathogens, can also undergo selective autophagy. In contrast to non-selective autophagy, selective autophagy pathways rely on a plethora of selective autophagy receptors (SARs) that recognize and direct intracellular protein aggregates, organelles and pathogens for specific degradation. Although SARs themselves are not highly conserved, their modes of action and the signalling cascades that activate and regulate them are. Recent yeast studies have provided novel mechanistic insights into selective autophagy pathways, revealing principles of how various cargoes can be marked and targeted for selective degradation.
    MeSH term(s) Animals ; Autophagy ; Autophagy-Related Proteins/genetics ; Autophagy-Related Proteins/metabolism ; Eukaryotic Cells/classification ; Eukaryotic Cells/cytology ; Eukaryotic Cells/pathology ; Humans ; Metabolic Networks and Pathways ; Mitochondria/pathology ; Phosphorylation
    Chemical Substances Autophagy-Related Proteins
    Language English
    Publishing date 2016-07-06
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2031313-5
    ISSN 1471-0080 ; 1471-0072
    ISSN (online) 1471-0080
    ISSN 1471-0072
    DOI 10.1038/nrm.2016.74
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    Zs.A 5446: Show issues Location:
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    Zs.MG 26: Show issues

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  10. Article: Balancing the Opposing Principles That Govern Peroxisome Homeostasis

    Mahalingam, Shanmuga S / Shukla, Nandini / Farré, Jean-Claude / Zientara-Rytter, Katarzyna / Subramani, Suresh

    Trends in biochemical sciences. 2021 Mar., v. 46, no. 3

    2021  

    Abstract: Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two ... ...

    Abstract Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two opposing processes that regulate peroxisome homeostasis. The intersection between these processes also provides exciting avenues for future research. This review highlights the links between peroxisome biogenesis and degradation, incorporating an integrative approach that is critical not only for a mechanistic understanding, but also for manipulating the balance between these processes in relevant disease models.
    Keywords biogenesis ; disease models ; homeostasis
    Language English
    Dates of publication 2021-03
    Size p. 200-212.
    Publishing place Elsevier Ltd
    Document type Article
    Note NALT-AP-4-rerunAP2-fuzzy
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2020.09.006
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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