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

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

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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Article ; Online: Aspergillus nidulans

Lingo, Dale E / Shukla, Nandini / Osmani, Aysha H / Osmani, Stephen A

Molecular biology of the cell

2021 Volume 32, Issue 12, Page(s) 1181–1192

Abstract: After growing on surfaces, including those of medical and industrial importance, fungal biofilms self-generate internal microenvironments. We previously reported that gaseous microenvironments around ... ...

Abstract	After growing on surfaces, including those of medical and industrial importance, fungal biofilms self-generate internal microenvironments. We previously reported that gaseous microenvironments around founder
MeSH term(s)	Aspergillus nidulans/physiology ; Aspergillus nidulans/ultrastructure ; Autophagy ; Biofilms ; Endocytosis ; Endoplasmic Reticulum/metabolism ; Endoplasmic Reticulum/physiology ; Exocytosis ; Fungal Proteins/metabolism ; Golgi Apparatus/metabolism ; Golgi Apparatus/physiology ; Light ; Microtubules/metabolism ; Transcription Factors/metabolism
Chemical Substances	Fungal Proteins ; Transcription Factors
Language	English
Publishing date	2021-04-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E20-11-0734
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Article: Mutant Prion Protein Endoggresomes are Hubs for Local Axonal Organelle-Cytoskeletal Remodeling.

Chaiamarit, Tai / Verhelle, Adriaan / Chassefeyre, Romain / Shukla, Nandini / Novak, Sammy Weiser / Andrade, Leonardo R / Manor, Uri / Encalada, Sandra E

bioRxiv : the preprint server for biology

2023

Abstract: Dystrophic axons comprising misfolded mutant prion protein (PrP) aggregates are a characteristic pathological feature in the prionopathies. These aggregates form inside endolysosomes -called endoggresomes-, within swellings that line up the length of ... ...

Abstract	Dystrophic axons comprising misfolded mutant prion protein (PrP) aggregates are a characteristic pathological feature in the prionopathies. These aggregates form inside endolysosomes -called endoggresomes-, within swellings that line up the length of axons of degenerating neurons. The pathways impaired by endoggresomes that result in failed axonal and consequently neuronal health, remain undefined. Here, we dissect the local subcellular impairments that occur within individual mutant PrP endoggresome swelling sites in axons. Quantitative high-resolution light and electron microscopy revealed the selective impairment of the acetylated vs tyrosinated microtubule cytoskeleton, while micro-domain image analysis of live organelle dynamics within swelling sites revealed deficits uniquely to the MT-based active transport system that translocates mitochondria and endosomes toward the synapse. Cytoskeletal and defective transport results in the retention of mitochondria, endosomes, and molecular motors at swelling sites, enhancing mitochondria-Rab7 late endosome contacts that induce mitochondrial fission via the activity of Rab7, and render mitochondria dysfunctional. Our findings point to mutant Pr Pendoggresome swelling sites as selective hubs of cytoskeletal deficits and organelle retention that drive the remodeling of organelles along axons. We propose that the dysfunction imparted locally within these axonal micro-domains spreads throughout the axon over time, leading to axonal dysfunction in prionopathies.
Language	English
Publishing date	2023-03-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.19.533383
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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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Article ; Online: Polycystic ovary syndrome and its management: In view of oxidative stress.

Bhattacharya, Koushik / Dey, Rajen / Sen, Debanjana / Paul, Nimisha / Basak, Asim Kumar / Purkait, Mohuya Patra / Shukla, Nandini / Chaudhuri, Gargi Ray / Bhattacharya, Aniruddha / Maiti, Rajkumar / Adhikary, Krishnendu / Chatterjee, Prity / Karak, Prithviraj / Syamal, Alak Kumar

Biomolecular concepts

2024 Volume 15, Issue 1

Abstract: In the past two decades, oxidative stress (OS) has drawn a lot of interest due to the revelation that individuals with many persistent disorders including diabetes, polycystic ovarian syndrome (PCOS), cardiovascular, and other disorders often have ... ...

Abstract	In the past two decades, oxidative stress (OS) has drawn a lot of interest due to the revelation that individuals with many persistent disorders including diabetes, polycystic ovarian syndrome (PCOS), cardiovascular, and other disorders often have aberrant oxidation statuses. OS has a close interplay with PCOS features such as insulin resistance, hyperandrogenism, and chronic inflammation; there is a belief that OS might contribute to the development of PCOS. PCOS is currently recognized as not only one of the most prevalent endocrine disorders but also a significant contributor to female infertility, affecting a considerable proportion of women globally. Therefore, the understanding of the relationship between OS and PCOS is crucial to the development of therapeutic and preventive strategies for PCOS. Moreover, the mechanistic study of intracellular reactive oxygen species/ reactive nitrogen species formation and its possible interaction with women's reproductive health is required, which includes complex enzymatic and non-enzymatic antioxidant systems. Apart from that, our current review includes possible regulation of the pathogenesis of OS. A change in lifestyle, including physical activity, various supplements that boost antioxidant levels, particularly vitamins, and the usage of medicinal herbs, is thought to be the best way to combat this occurrence of OS and improve the pathophysiologic conditions associated with PCOS.
MeSH term(s)	Female ; Humans ; Polycystic Ovary Syndrome/therapy ; Polycystic Ovary Syndrome/complications ; Antioxidants/therapeutic use ; Hyperandrogenism/complications ; Oxidative Stress ; Insulin Resistance
Chemical Substances	Antioxidants
Language	English
Publishing date	2024-01-19
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2557908-3
ISSN	1868-503X ; 1868-5021
ISSN (online)	1868-503X
ISSN	1868-5021
DOI	10.1515/bmc-2022-0038
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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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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

2020 Volume 46, Issue 3, Page(s) 200–212

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.
MeSH term(s)	Homeostasis ; Metabolic Networks and Pathways ; Peroxisomes/metabolism
Language	English
Publishing date	2020-10-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	194216-5
ISSN	1362-4326 ; 0968-0004 ; 0376-5067
ISSN (online)	1362-4326
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2020.09.006
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Article ; Online: Microtubules are reversibly depolymerized in response to changing gaseous microenvironments within

Shukla, Nandini / Osmani, Aysha H / Osmani, Stephen A

Molecular biology of the cell

2017 Volume 28, Issue 5, Page(s) 634–644

Abstract: How microtubules (MTs) are regulated during fungal biofilm formation is unknown. By tracking MT +end-binding proteins (+TIPS) ... ...

Abstract	How microtubules (MTs) are regulated during fungal biofilm formation is unknown. By tracking MT +end-binding proteins (+TIPS) in
MeSH term(s)	Actin Depolymerizing Factors/metabolism ; Aspergillus nidulans/metabolism ; Aspergillus nidulans/physiology ; Biofilms/growth & development ; Cellular Microenvironment/physiology ; Dyneins/metabolism ; Gases ; Microtubule-Associated Proteins/metabolism ; Microtubules/metabolism ; Polymerization
Chemical Substances	Actin Depolymerizing Factors ; Gases ; Microtubule-Associated Proteins ; Dyneins (EC 3.6.4.2)
Language	English
Publishing date	2017-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E16-10-0750
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Zs.MO 410: Show issues

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Article ; Online: PxdA interacts with the DipA phosphatase to regulate peroxisome hitchhiking on early endosomes.

Salogiannis, John / Christensen, Jenna R / Songster, Livia D / Aguilar-Maldonado, Adriana / Shukla, Nandini / Reck-Peterson, Samara L

Molecular biology of the cell

2021 Volume 32, Issue 6, Page(s) 492–503

Abstract: In canonical microtubule-based transport, adaptor proteins link cargoes to dynein and kinesin motors. Recently, an alternative mode of transport known as "hitchhiking" was discovered, where cargoes achieve motility by hitching a ride on already-motile ... ...

Abstract	In canonical microtubule-based transport, adaptor proteins link cargoes to dynein and kinesin motors. Recently, an alternative mode of transport known as "hitchhiking" was discovered, where cargoes achieve motility by hitching a ride on already-motile cargoes, rather than attaching to a motor protein. Hitchhiking has been best studied in two filamentous fungi,
MeSH term(s)	Aspergillus nidulans/metabolism ; Basidiomycota/metabolism ; Biological Transport ; Dyneins/metabolism ; Endoplasmic Reticulum/metabolism ; Endosomes/metabolism ; Fungal Proteins/metabolism ; Kinesins/metabolism ; Metabolic Networks and Pathways ; Microtubules/metabolism ; Mitochondria/metabolism ; Peroxisomes/metabolism ; Peroxisomes/physiology ; Phosphoric Monoester Hydrolases/metabolism ; Protein Transport/genetics ; Protein Transport/physiology ; Transport Vesicles/metabolism
Chemical Substances	Fungal Proteins ; DipA protein, Aspergillus nidulans (EC 3.1.3.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2) ; Dyneins (EC 3.6.4.2) ; Kinesins (EC 3.6.4.4)
Language	English
Publishing date	2021-01-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E20-08-0559
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Zs.MO 410: Show issues

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Article ; Online: Identification of interphase functions for the NIMA kinase involving microtubules and the ESCRT pathway.

Govindaraghavan, Meera / McGuire Anglin, Sarah Lea / Shen, Kuo-Fang / Shukla, Nandini / De Souza, Colin P / Osmani, Stephen A

PLoS genetics

2014 Volume 10, Issue 3, Page(s) e1004248

Abstract: The Never in Mitosis A (NIMA) kinase (the founding member of the Nek family of kinases) has been considered a mitotic specific kinase with nuclear restricted roles in the model fungus Aspergillus nidulans. By extending to A. nidulans the results of a ... ...

Abstract	The Never in Mitosis A (NIMA) kinase (the founding member of the Nek family of kinases) has been considered a mitotic specific kinase with nuclear restricted roles in the model fungus Aspergillus nidulans. By extending to A. nidulans the results of a synthetic lethal screen performed in Saccharomyces cerevisiae using the NIMA ortholog KIN3, we identified a conserved genetic interaction between nimA and genes encoding proteins of the Endosomal Sorting Complex Required for Transport (ESCRT) pathway. Absence of ESCRT pathway functions in combination with partial NIMA function causes enhanced cell growth defects, including an inability to maintain a single polarized dominant cell tip. These genetic insights suggest NIMA potentially has interphase functions in addition to its established mitotic functions at nuclei. We therefore generated endogenously GFP-tagged NIMA (NIMA-GFP) which was fully functional to follow its interphase locations using live cell spinning disc 4D confocal microscopy. During interphase some NIMA-GFP locates to the tips of rapidly growing cells and, when expressed ectopically, also locates to the tips of cytoplasmic microtubules, suggestive of non-nuclear interphase functions. In support of this, perturbation of NIMA function either by ectopic overexpression or through partial inactivation results in marked cell tip growth defects with excess NIMA-GFP promoting multiple growing cell tips. Ectopic NIMA-GFP was found to locate to the plus ends of microtubules in an EB1 dependent manner, while impairing NIMA function altered the dynamic localization of EB1 and the cytoplasmic microtubule network. Together, our genetic and cell biological analyses reveal novel non-nuclear interphase functions for NIMA involving microtubules and the ESCRT pathway for normal polarized fungal cell tip growth. These insights extend the roles of NIMA both spatially and temporally and indicate that this conserved protein kinase could help integrate cell cycle progression with polarized cell growth.
MeSH term(s)	Aspergillus nidulans/genetics ; Cell Cycle/genetics ; Cell Cycle Proteins/genetics ; Cell Nucleus/genetics ; Endosomal Sorting Complexes Required for Transport/genetics ; Endosomal Sorting Complexes Required for Transport/metabolism ; Green Fluorescent Proteins ; Interphase/genetics ; Microtubules/genetics ; Mitosis/genetics ; NIMA-Related Kinase 1 ; Protein-Serine-Threonine Kinases/genetics
Chemical Substances	Cell Cycle Proteins ; Endosomal Sorting Complexes Required for Transport ; Green Fluorescent Proteins (147336-22-9) ; NIMA-Related Kinase 1 (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2014-03-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1004248
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