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Article ; Online: Immunolabel-First-Expand-Later Expansion Microscopy Approach Using Stable STED Dyes.

Kong, Dong / Luvsanjav, Delgermaa / Loncarek, Jadranka

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2725, Page(s) 89–101

Abstract: Multiple expansion microscopy approaches have been successfully used in the analysis of centrioles, centrosomes, and cilia, helping to reveal the localization of numerous centrosomal and ciliary proteins at nanoscale resolution. In this chapter, we ... ...

Abstract	Multiple expansion microscopy approaches have been successfully used in the analysis of centrioles, centrosomes, and cilia, helping to reveal the localization of numerous centrosomal and ciliary proteins at nanoscale resolution. In this chapter, we describe the use of two stable STED dyes in combination with expansion microscopy, which allows the robust detection by conventional and STED microscopy of proteins immunolabeled prior to sample expansion. We demonstrate the stability of these dyes during the crosslinking, polymerization, and denaturation steps of an expansion protocol thereby allowing their use in an immunolabel-first-expand-later approach. Our protocol overcomes the frequent technical limitation of poor, unreproducible binding of primary antibodies to proteins after denaturation. We demonstrate the applicability of this approach by analyzing both a centriole appendage protein Cep164 and a ciliary protein ARL13B.
MeSH term(s)	Microscopy/methods ; Coloring Agents/metabolism ; Centrioles/metabolism ; Centrosome/metabolism ; Antibodies/metabolism ; Cilia/metabolism
Chemical Substances	Coloring Agents ; Antibodies
Language	English
Publishing date	2023-10-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3507-0_5
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Article ; Online: Analyzing Centrioles and Cilia by Expansion Microscopy.

Kong, Dong / Loncarek, Jadranka

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2329, Page(s) 249–263

Abstract: Expansion microscopy is an imaging method based on isotropic physical expansion of biological samples, which improves optical resolution and allows imaging of subresolutional cellular components by conventional microscopes. Centrioles are small ... ...

Abstract	Expansion microscopy is an imaging method based on isotropic physical expansion of biological samples, which improves optical resolution and allows imaging of subresolutional cellular components by conventional microscopes. Centrioles are small microtubule-based cylindrical structures that build centrosomes and cilia, two organelles essential for vertebrates. Due to a centriole's small size, electron microscopy has traditionally been used to study centriole length and ultrastructural features. Recently, expansion microscopy has been successfully used as an affordable and accessible alternative to electron microscopy in the analysis of centriole and cilia length and structural features. Here, we describe an expansion microscopy approach for the analysis of centrioles and cilia in large populations of mammalian adherent and nonadherent cells and multiciliated cultures.
MeSH term(s)	Cell Adhesion ; Cell Culture Techniques/methods ; Cell Line ; Centrioles/ultrastructure ; Cilia/ultrastructure ; Humans ; Microscopy
Language	English
Publishing date	2021-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1538-6_18
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Article ; Online: Human centrosome organization and function in interphase and mitosis.

Vasquez-Limeta, Alejandra / Loncarek, Jadranka

Seminars in cell & developmental biology

2021 Volume 117, Page(s) 30–41

Abstract: Centrosomes were first described by Edouard Van Beneden and named and linked to chromosome segregation by Theodor Boveri around 1870. In the 1960-1980s, electron microscopy studies have revealed the remarkable ultrastructure of a centriole -- a nine-fold ...

Abstract	Centrosomes were first described by Edouard Van Beneden and named and linked to chromosome segregation by Theodor Boveri around 1870. In the 1960-1980s, electron microscopy studies have revealed the remarkable ultrastructure of a centriole -- a nine-fold symmetrical microtubular assembly that resides within a centrosome and organizes it. Less than two decades ago, proteomics and genomic screens conducted in multiple species identified hundreds of centriole and centrosome core proteins and revealed the evolutionarily conserved nature of the centriole assembly pathway. And now, super resolution microscopy approaches and improvements in cryo-tomography are bringing an unparalleled nanoscale-detailed picture of the centriole and centrosome architecture. In this chapter, we summarize the current knowledge about the architecture of human centrioles. We discuss the structured organization of centrosome components in interphase, focusing on localization/function relationship. We discuss the process of centrosome maturation and mitotic spindle pole assembly in centriolar and acentriolar cells, emphasizing recent literature.
MeSH term(s)	Centrioles/metabolism ; Centrosome/metabolism ; Humans ; Interphase/genetics
Language	English
Publishing date	2021-04-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2021.03.020
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Article ; Online: Centrosomal organization of Cep152 provides flexibility in Plk4 and procentriole positioning.

Sullenberger, Catherine / Kong, Dong / Avazpour, Pegah / Luvsanjav, Delgermaa / Loncarek, Jadranka

The Journal of cell biology

2023 Volume 222, Issue 12

Abstract: Centriole duplication is a high-fidelity process driven by Polo-like kinase 4 (Plk4) and a few conserved initiators. Dissecting how Plk4 and its receptors organize within centrosomes is critical to understand the centriole duplication process and ... ...

Abstract	Centriole duplication is a high-fidelity process driven by Polo-like kinase 4 (Plk4) and a few conserved initiators. Dissecting how Plk4 and its receptors organize within centrosomes is critical to understand the centriole duplication process and biochemical and architectural differences between centrosomes of different species. Here, at nanoscale resolution, we dissect centrosomal localization of Plk4 in G1 and S phase in its catalytically active and inhibited state during centriole duplication and amplification. We build a precise distribution map of Plk4 and its receptor Cep152, as well as Cep44, Cep192, and Cep152-anchoring factors Cep57 and Cep63. We find that Cep57, Cep63, Cep44, and Cep192 localize in ninefold symmetry. However, during centriole maturation, Cep152, which we suggest is the major Plk4 receptor, develops a more complex pattern. We propose that the molecular arrangement of Cep152 creates flexibility for Plk4 and procentriole placement during centriole initiation. As a result, procentrioles form at variable positions in relation to the mother centriole microtubule triplets.
MeSH term(s)	Cell Cycle/genetics ; Centrioles/genetics ; Centrosome ; Microtubules/genetics ; S Phase ; Humans ; Cell Cycle Proteins/genetics ; Protein Serine-Threonine Kinases/genetics
Chemical Substances	CEP152 protein, human ; PLK4 protein, human (EC 2.7.1.-) ; Cell Cycle Proteins ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2023-09-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.202301092
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Article ; Online: An engineered cell line with a hRpn1-attached handle to isolate proteasomes.

Negi, Hitendra / Osei-Amponsa, Vasty / Ibrahim, Bishoy / Evans, Christine N / Sullenberger, Catherine / Loncarek, Jadranka / Chari, Raj / Walters, Kylie J

The Journal of biological chemistry

2023 Volume 299, Issue 8, Page(s) 104948

Abstract: Regulated protein degradation in eukaryotes is performed by the 26S proteasome, which contains a 19-subunit regulatory particle (RP) that binds, processes, and translocates substrates to a 28-subunit hollow core particle (CP) where proteolysis occurs. In ...

Abstract	Regulated protein degradation in eukaryotes is performed by the 26S proteasome, which contains a 19-subunit regulatory particle (RP) that binds, processes, and translocates substrates to a 28-subunit hollow core particle (CP) where proteolysis occurs. In addition to its intrinsic subunits, myriad proteins interact with the proteasome transiently, including factors that assist and/or regulate its degradative activities. Efforts to identify proteasome-interacting components and/or to solve its structure have relied on over-expression of a tagged plasmid, establishing stable cell lines, or laborious purification protocols to isolate native proteasomes from cells. Here, we describe an engineered human cell line, derived from colon cancer HCT116 cells, with a biotin handle on the RP subunit hRpn1/PSMD2 (proteasome 26S subunit, non-ATPase 2) for purification of 26S proteasomes. A 75-residue sequence from Propionibacterium shermanii that is biotinylated in mammalian cells was added following a tobacco etch virus protease cut site at the C terminus of hRpn1. We tested and found that 26S proteasomes can be isolated from this modified HCT116 cell line by using a simple purification protocol. More specifically, biotinylated proteasomes were purified from the cell lysates by using neutravidin agarose resin and released from the resin following incubation with tobacco etch virus protease. The purified proteasomes had equivalent activity in degrading a model ubiquitinated substrate, namely ubiquitinated p53, compared to commercially available bovine proteasomes that were purified by fractionation. In conclusion, advantages of this approach to obtain 26S proteasomes over others is the simple purification protocol and that all cellular proteins, including the tagged hRpn1 subunit, remain at endogenous stoichiometry.
MeSH term(s)	Animals ; Cattle ; Humans ; Cell Line ; Cytoplasm/metabolism ; Mammals/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Ubiquitin/metabolism ; Cytological Techniques/methods
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ubiquitin
Language	English
Publishing date	2023-06-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.104948
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Article ; Online: Differential sensitivity of the yeast Lon protease Pim1p to impaired mitochondrial respiration.

Metzger, Meredith B / Scales, Jessica L / Grant, Garis A / Molnar, Abigail E / Loncarek, Jadranka / Weissman, Allan M

The Journal of biological chemistry

2023 Volume 299, Issue 8, Page(s) 104937

Abstract: Mitochondria are essential organelles whose proteome is well protected by regulated protein degradation and quality control. While the ubiquitin-proteasome system can monitor mitochondrial proteins that reside at the mitochondrial outer membrane or are ... ...

Abstract	Mitochondria are essential organelles whose proteome is well protected by regulated protein degradation and quality control. While the ubiquitin-proteasome system can monitor mitochondrial proteins that reside at the mitochondrial outer membrane or are not successfully imported, resident proteases generally act on proteins within mitochondria. Herein, we assess the degradative pathways for mutant forms of three mitochondrial matrix proteins (mas1-1HA, mas2-11HA, and tim44-8HA) in Saccharomyces cerevisiae. The degradation of these proteins is strongly impaired by loss of either the matrix AAA-ATPase (m-AAA) (Afg3p/Yta12p) or Lon (Pim1p) protease. We determine that these mutant proteins are all bona fide Pim1p substrates whose degradation is also blocked in respiratory-deficient "petite" yeast cells, such as in cells lacking m-AAA protease subunits. In contrast, matrix proteins that are substrates of the m-AAA protease are not affected by loss of respiration. The failure to efficiently remove Pim1p substrates in petite cells has no evident relationship to Pim1p maturation, localization, or assembly. However, Pim1p's autoproteolysis is intact, and its overexpression restores substrate degradation, indicating that Pim1p retains some functionality in petite cells. Interestingly, chemical perturbation of mitochondria with oligomycin similarly prevents degradation of Pim1p substrates. Our results demonstrate that Pim1p activity is highly sensitive to mitochondrial perturbations such as loss of respiration or drug treatment in a manner that we do not observe with other proteases.
MeSH term(s)	ATP-Dependent Proteases/genetics ; ATP-Dependent Proteases/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Cell Respiration
Chemical Substances	ATP-Dependent Proteases (EC 3.4.21.-) ; Mitochondrial Proteins ; Saccharomyces cerevisiae Proteins ; PIM1 protein, S cerevisiae (EC 3.4.21.-)
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.104937
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Article ; Online: Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription.

Sundara Rajan, Soumya / Ebegboni, Vernon J / Pichling, Patricio / Ludwig, Katelyn R / Jones, Tamara L / Chari, Raj / Tran, Andy / Kruhlak, Michael J / Loncarek, Jadranka / Caplen, Natasha J

Molecular and cellular biology

2024 Volume 44, Issue 3, Page(s) 103–122

Abstract: EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity ...

Abstract	EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
MeSH term(s)	Humans ; Neurodegenerative Diseases ; Nucleic Acids/chemistry ; Nucleic Acids/metabolism ; RNA Polymerase II/metabolism ; RNA-Binding Protein EWS/genetics ; RNA-Binding Protein EWS/metabolism
Chemical Substances	EWSR1 protein, human ; Nucleic Acids ; RNA Polymerase II (EC 2.7.7.-) ; RNA-Binding Protein EWS
Language	English
Publishing date	2024-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1080/10985549.2024.2315425
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Article ; Online: Building the right centriole for each cell type.

Loncarek, Jadranka / Bettencourt-Dias, Mónica

The Journal of cell biology

2017 Volume 217, Issue 3, Page(s) 823–835

Abstract: The centriole is a multifunctional structure that organizes centrosomes and cilia and is important for cell signaling, cell cycle progression, polarity, and motility. Defects in centriole number and structure are associated with human diseases including ... ...

Abstract	The centriole is a multifunctional structure that organizes centrosomes and cilia and is important for cell signaling, cell cycle progression, polarity, and motility. Defects in centriole number and structure are associated with human diseases including cancer and ciliopathies. Discovery of the centriole dates back to the 19th century. However, recent advances in genetic and biochemical tools, development of high-resolution microscopy, and identification of centriole components have accelerated our understanding of its assembly, function, evolution, and its role in human disease. The centriole is an evolutionarily conserved structure built from highly conserved proteins and is present in all branches of the eukaryotic tree of life. However, centriole number, size, and organization varies among different organisms and even cell types within a single organism, reflecting its cell type-specialized functions. In this review, we provide an overview of our current understanding of centriole biogenesis and how variations around the same theme generate alternatives for centriole formation and function.
MeSH term(s)	Animals ; Centrioles/genetics ; Centrioles/metabolism ; Humans
Language	English
Publishing date	2017-12-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201704093
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Article ; Online: With Age Comes Maturity: Biochemical and Structural Transformation of a Human Centriole in the Making.

Sullenberger, Catherine / Vasquez-Limeta, Alejandra / Kong, Dong / Loncarek, Jadranka

Cells

2020 Volume 9, Issue 6

Abstract: Centrioles are microtubule-based cellular structures present in most human cells that build centrosomes and cilia. Proliferating cells have only two centrosomes and this number is stringently maintained through the temporally and spatially controlled ... ...

Abstract	Centrioles are microtubule-based cellular structures present in most human cells that build centrosomes and cilia. Proliferating cells have only two centrosomes and this number is stringently maintained through the temporally and spatially controlled processes of centriole assembly and segregation. The assembly of new centrioles begins in early S phase and ends in the third G1 phase from their initiation. This lengthy process of centriole assembly from their initiation to their maturation is characterized by numerous structural and still poorly understood biochemical changes, which occur in synchrony with the progression of cells through three consecutive cell cycles. As a result, proliferating cells contain three structurally, biochemically, and functionally distinct types of centrioles: procentrioles, daughter centrioles, and mother centrioles. This age difference is critical for proper centrosome and cilia function. Here we discuss the centriole assembly process as it occurs in somatic cycling human cells with a focus on the structural, biochemical, and functional characteristics of centrioles of different ages.
MeSH term(s)	Aging ; Centrioles/chemistry ; Centrioles/ultrastructure ; Centrosome/chemistry ; Centrosome/ultrastructure ; Humans
Language	English
Publishing date	2020-06-09
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells9061429
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Article ; Online: CPAP insufficiency leads to incomplete centrioles that duplicate but fragment.

Vásquez-Limeta, Alejandra / Lukasik, Kimberly / Kong, Dong / Sullenberger, Catherine / Luvsanjav, Delgermaa / Sahabandu, Natalie / Chari, Raj / Loncarek, Jadranka

The Journal of cell biology

2022 Volume 221, Issue 5

Abstract: Centrioles are structures that assemble centrosomes. CPAP is critical for centrosome assembly, and its mutations are found in patients with diseases such as primary microcephaly. CPAP's centrosomal localization, its dynamics, and the consequences of its ... ...

Abstract	Centrioles are structures that assemble centrosomes. CPAP is critical for centrosome assembly, and its mutations are found in patients with diseases such as primary microcephaly. CPAP's centrosomal localization, its dynamics, and the consequences of its insufficiency in human cells are poorly understood. Here we use human cells genetically engineered for fast degradation of CPAP, in combination with superresolution microscopy, to address these uncertainties. We show that three independent centrosomal CPAP populations are dynamically regulated during the cell cycle. We confirm that CPAP is critical for assembly of human centrioles, but not for recruitment of pericentriolar material on already assembled centrioles. Further, we reveal that CPAP insufficiency leads to centrioles with incomplete microtubule triplets that can convert to centrosomes, duplicate, and form mitotic spindle poles, but fragment owing to loss of cohesion between microtubule blades. These findings further our basic understanding of the role of CPAP in centrosome biogenesis and help understand how CPAP aberrations can lead to human diseases.
MeSH term(s)	Cell Division ; Centrioles/genetics ; Centrosome ; Humans ; Microtubule-Associated Proteins/genetics ; Microtubules/genetics ; Spindle Poles
Chemical Substances	CENPJ protein, human ; Microtubule-Associated Proteins
Language	English
Publishing date	2022-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.202108018
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