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Article ; Online: Molecular structures and function of the autophagosome-lysosome fusion machinery.

Diao, Jiajie / Yip, Calvin K / Zhong, Qing

Autophagy reports

2024 Volume 3, Issue 1

Abstract: Macroautophagy (also known as autophagy) plays a pivotal role in maintaining cellular homeostasis. The terminal step of the multi-step autophagy degradation pathway involves fusion between the cargo-laden, double-membraned autophagosome and the lytic ... ...

Abstract	Macroautophagy (also known as autophagy) plays a pivotal role in maintaining cellular homeostasis. The terminal step of the multi-step autophagy degradation pathway involves fusion between the cargo-laden, double-membraned autophagosome and the lytic organelle lysosome/vacuole. Over the past decade, various core components of the molecular machinery that execute this critical terminal autophagy event have been identified. This review highlights recent advances in understanding the molecular structures, biochemical functions, and regulatory mechanisms of key components of this highly sophisticated machinery including the SNARE fusogens, tethering factors, Rab GTPases and associated guanine nucleotide exchange factors, and other accessory factors.
Language	English
Publishing date	2024-02-04
Publishing country	United States
Document type	Journal Article
ISSN	2769-4127
ISSN (online)	2769-4127
DOI	10.1080/27694127.2024.2305594
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Article ; Online: Biochemical and Structural Characterization of Human Core Elongator and Its Subassemblies.

Dalwadi, Udit / Mannar, Dhiraj / Zierhut, Felix / Yip, Calvin K

ACS omega

2022 Volume 7, Issue 4, Page(s) 3424–3433

Abstract: Conserved from yeast to humans and composed of six core subunits (Elp1-Elp6), Elongator is a multiprotein complex that catalyzes the modification of the anticodon loop of transfer RNAs (tRNAs) and in turn regulates messenger RNA decoding efficiency. ... ...

Abstract	Conserved from yeast to humans and composed of six core subunits (Elp1-Elp6), Elongator is a multiprotein complex that catalyzes the modification of the anticodon loop of transfer RNAs (tRNAs) and in turn regulates messenger RNA decoding efficiency. Previous studies showed that yeast Elongator consists of two subassemblies (yElp1/2/3 and yElp4/5/6) and adopts an asymmetric overall architecture. Yet, much less is known about the structural properties of the orthologous human Elongator. Furthermore, the order in which the different Elongator subunits come together to form the full assembly as well as how they coordinate with one another to catalyze tRNA modification is not fully understood. Here, we purified recombinant human Elongator subunits and subassemblies and examined them by single-particle electron microscopy. We found that the human Elongator complex is assembled from two subcomplexes that share similar overall morphologies as their yeast counterparts. Complementary co-purification and pulldown assays revealed that the scaffolding subunit human ELP1 (hELP1) has stabilizing effects on the human ELP3 catalytic subunit. Furthermore, the peripheral hELP2 subunit appears to enhance the integrity and substrate-binding ability of the dimeric hELP1/2/3. Lastly, we found that hELP4/5/6 is recruited to hELP1/2/3 via hELP3. Collectively, our work generated insights into the assembly process of core human Elongator and the coordination of different subunits within this complex.
Language	English
Publishing date	2022-01-18
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.1c05719
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Article ; Online: Structural insights into the function of Elongator.

Dalwadi, Udit / Yip, Calvin K

Cellular and molecular life sciences : CMLS

2018 Volume 75, Issue 9, Page(s) 1613–1622

Abstract: Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial ... ...

Abstract	Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial dysautonomia. Elongator consists of two copies of six core subunits (Elp1, Elp2, Elp3, Elp4, Elp5, and Elp6) that are organized into two subcomplexes: Elp1/2/3 and Elp4/5/6 and form a stable assembly of ~ 850 kDa in size. Although the catalytic subunit of Elongator is Elp3, which contains a radical S-adenosyl-L-methionine (SAM) domain and a putative histone acetyltransferase domain, the Elp4/5/6 subcomplex also possesses ATP-modulated tRNA binding activity. How at the molecular level, Elongator performs its multiple functions and how the different subunits regulate Elongator's activities remains poorly understood. Here, we provide an overview of the proposed functions of Elongator and describe how recent structural studies provide new insights into the mechanism of action of this multifunctional complex.
MeSH term(s)	Animals ; Histone Acetyltransferases/metabolism ; Humans ; Peptide Elongation Factors/metabolism ; Protein Binding/physiology ; Protein Subunits/metabolism ; RNA, Transfer/metabolism ; Transcription, Genetic/physiology
Chemical Substances	Peptide Elongation Factors ; Protein Subunits ; RNA, Transfer (9014-25-9) ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2018-01-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-018-2747-6
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Article ; Online: Recent Advances in Single-Particle Electron Microscopic Analysis of Autophagy Degradation Machinery.

Cheung, Yiu Wing Sunny / Nam, Sung-Eun / Yip, Calvin K

International journal of molecular sciences

2020 Volume 21, Issue 21

Abstract: Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient ... ...

Abstract	Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient deprivation. The multi-step degradation process, from sequestering cytoplasmic cargo into the double-membrane vesicle termed autophagosome to the delivery of the autophagosome to the lysosome or lytic vacuole for breakdown, is mediated by the core autophagy machinery composed of multiple Atg proteins, as well as the divergent sequence family of selective autophagy receptors. Single-particle electron microscopy (EM) is a molecular imaging approach that has become an increasingly important tool in the structural characterization of proteins and macromolecular complexes. This article summarizes the contributions single-particle EM have made in advancing our understanding of the core autophagy machinery and selective autophagy receptors. We also discuss current technical challenges and roadblocks, as well as look into the future of single-particle EM in autophagy research.
MeSH term(s)	Animals ; Autophagosomes ; Autophagy ; Humans ; Microscopy, Electron/methods ; Single Molecule Imaging/methods ; Vacuoles
Language	English
Publishing date	2020-10-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21218051
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Article ; Online: Conformational landscape of the yeast SAGA complex as revealed by cryo-EM.

Vasyliuk, Diana / Felt, Joeseph / Zhong, Ellen D / Berger, Bonnie / Davis, Joseph H / Yip, Calvin K

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12306

Abstract: Spt-Ada-Gcn5-Acetyltransferase (SAGA) is a conserved multi-subunit complex that activates RNA polymerase II-mediated transcription by acetylating and deubiquitinating nucleosomal histones and by recruiting TATA box binding protein (TBP) to DNA. The ... ...

Abstract	Spt-Ada-Gcn5-Acetyltransferase (SAGA) is a conserved multi-subunit complex that activates RNA polymerase II-mediated transcription by acetylating and deubiquitinating nucleosomal histones and by recruiting TATA box binding protein (TBP) to DNA. The prototypical yeast Saccharomyces cerevisiae SAGA contains 19 subunits that are organized into Tra1, core, histone acetyltransferase, and deubiquitination modules. Recent cryo-electron microscopy studies have generated high-resolution structural information on the Tra1 and core modules of yeast SAGA. However, the two catalytical modules were poorly resolved due to conformational flexibility of the full assembly. Furthermore, the high sample requirement created a formidable barrier to further structural investigations of SAGA. Here, we report a workflow for isolating/stabilizing yeast SAGA and preparing cryo-EM specimens at low protein concentration using a graphene oxide support layer. With this procedure, we were able to determine a cryo-EM reconstruction of yeast SAGA at 3.1 Å resolution and examine its conformational landscape with the neural network-based algorithm cryoDRGN. Our analysis revealed that SAGA adopts a range of conformations with its HAT module and central core in different orientations relative to Tra1.
MeSH term(s)	Cryoelectron Microscopy ; Histone Acetyltransferases/metabolism ; Histones/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Histones ; Saccharomyces cerevisiae Proteins ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2022-07-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16391-0
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Article: Characterizing the molecular architectures of chromatin-modifying complexes.

Setiaputra, Dheva T / Yip, Calvin K

Biochimica et biophysica acta. Proteins and proteomics

2017 Volume 1865, Issue 11 Pt B, Page(s) 1613–1622

Abstract: Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to ...

Abstract	Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors. These chromatin modifications are often catalyzed by multi-subunit enzyme complexes, whose large size, sophisticated composition, and inherent conformational flexibility pose significant technical challenges to their biochemical and structural characterization. Multiple structural approaches including nuclear magnetic resonance spectroscopy, X-ray crystallography, single-particle electron microscopy, and crosslinking coupled to mass spectrometry are often used synergistically to probe the overall architecture, subunit organization, and catalytic mechanisms of these macromolecular assemblies. In this review, we highlight several recent chromatin-modifying complexes studies that embodies this multipronged structural approach, and explore common themes amongst them. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
MeSH term(s)	Animals ; Chromatin/chemistry ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Crystallography, X-Ray ; DNA/chemistry ; DNA/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Humans ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/metabolism ; Nuclear Magnetic Resonance, Biomolecular
Chemical Substances	Chromatin ; DNA-Binding Proteins ; Multiprotein Complexes ; DNA (9007-49-2)
Language	English
Publishing date	2017-06-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 1570-9639 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	1570-9639 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbapap.2017.06.018
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Article: Structural biology of the macroautophagy machinery.

Chew, Leon H / Yip, Calvin K

Frontiers in biology

2016 Volume 9, Issue 1, Page(s) 18–34

Abstract: Macroautophagy is a conserved degradative process mediated through formation of a unique double-membrane structure, the autophagosome. The discovery of autophagy-related (Atg) genes required for autophagosome formation has led to the characterization of ... ...

Abstract	Macroautophagy is a conserved degradative process mediated through formation of a unique double-membrane structure, the autophagosome. The discovery of autophagy-related (Atg) genes required for autophagosome formation has led to the characterization of approximately 20 genes mediating this process. Recent structural studies of the Atg proteins have provided the molecular basis for their function. Here we summarize the recent progress in elucidating the structural basis for autophagosome formation.
Language	English
Publishing date	2016-09-21
Publishing country	China
Document type	Journal Article
ZDB-ID	2658772-5
ISSN	1674-7992 ; 1674-7984
ISSN (online)	1674-7992
ISSN	1674-7984
DOI	10.1007/s11515-014-1293-3
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Article ; Online: Biochemical Characterization of the TINTIN Module of the NuA4 Complex Reveals Allosteric Regulation of Nucleosome Interaction.

Dalwadi, Udit / Corrado, Elaina / Fleming, Kaelin D / Moeller, Brandon E / Nam, Sung-Eun / Burke, John E / Yip, Calvin K

Molecular and cellular biology

2022 Volume 42, Issue 11, Page(s) e0017022

Abstract: ... ...

Abstract	T
MeSH term(s)	Nucleosomes/metabolism ; Allosteric Regulation ; Saccharomyces cerevisiae Proteins/metabolism ; Histones/metabolism ; Acetyltransferases/chemistry ; Saccharomyces cerevisiae/metabolism ; Chromatin/metabolism ; Histone Acetyltransferases/metabolism
Chemical Substances	Nucleosomes ; Saccharomyces cerevisiae Proteins ; Histones ; Acetyltransferases (EC 2.3.1.-) ; Chromatin ; Histone Acetyltransferases (EC 2.3.1.48) ; Eaf3 protein, S cerevisiae (EC 2.3.1.-) ; NuA4 protein, S cerevisiae (EC 2.3.1.48)
Language	English
Publishing date	2022-10-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/mcb.00170-22
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Article ; Online: Biochemical Characterization of the TINTIN Module of the NuA4 Complex Reveals Allosteric Regulation of Nucleosome Interaction

Dalwadi, Udit / Corrado, Elaina / Fleming, Kaelin D. / Moeller, Brandon E. / Nam, Sung-Eun / Burke, John E. / Yip, Calvin K.

Molecular and Cellular Biology. 2022 Nov. 1, v. 42, no. 11 p.e00170-22-

2022

Abstract: Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) is an integral module of the essential yeast lysine acetyltransferase complex NuA4 that plays key roles in transcription regulation and DNA repair. Composed of ... ...

Abstract	Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) is an integral module of the essential yeast lysine acetyltransferase complex NuA4 that plays key roles in transcription regulation and DNA repair. Composed of Eaf3, Eaf5, and Eaf7, TINTIN mediates targeting of NuA4 to chromatin through the chromodomain-containing subunit Eaf3 that is shared with the Rpd3S histone deacetylase complex. How Eaf3 mediates chromatin interaction in the context of TINTIN and how is it different from what has been observed in Rpd3S is unclear. Here, we reconstituted recombinant TINTIN and its subassemblies and characterized their biochemical and structural properties. Our coimmunoprecipitation, AlphaFold2 modeling, and hydrogen deuterium exchange mass spectrometry (HDX-MS) analyses revealed that the Eaf3 MRG domain contacts Eaf7 and this binding induces conformational changes throughout Eaf3. Nucleosome-binding assays showed that Eaf3 and TINTIN interact non-specifically with the DNA on nucleosomes. Furthermore, integration into TINTIN enhances the affinity of Eaf3 toward nucleosomes and this improvement is a result of allosteric activation of the Eaf3 chromodomain. Negative stain electron microscopy (EM) analysis revealed that TINTIN binds to the edge of nucleosomes with increased specificity in the presence of H3K36me3. Collectively, our work provides insights into the dynamics of TINTIN and the mechanism by which its interactions with chromatin are regulated.
Keywords	DNA ; DNA repair ; deuterium ; electron microscopy ; histone deacetylase ; lysine N-acetyltransferase ; mass spectrometry ; nucleosomes ; precipitin tests ; transcription (genetics) ; yeasts ; chromatin ; transcription ; NuA4 ; lysine acetyltransferase ; Eaf3 ; TINTIN ; hydrogen deuterium exchange mass spectrometry ; single-particle analysis
Language	English
Dates of publication	2022-1101
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/mcb.00170-22
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 1666: Show issues

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Article ; Online: Novel Genetic and Phenotypic Expansion in

Hentrich, Lea / Parnes, Mered / Lotze, Timothy Edward / Coorg, Rohini / de Koning, Tom J / Nguyen, Kha M / Yip, Calvin K / Jungbluth, Heinz / Koy, Anne / Dafsari, Hormos Salimi

Genes

2023 Volume 14, Issue 10

Abstract: Biallelic variants in the Golgi SNAP receptor complex member 2 gene ( ...

Abstract	Biallelic variants in the Golgi SNAP receptor complex member 2 gene (
MeSH term(s)	Adolescent ; Child ; Child, Preschool ; Female ; Humans ; Male ; Ataxia/genetics ; Dystonia ; Dystonic Disorders ; Mutation ; Myoclonic Epilepsies, Progressive/genetics ; Myoclonus ; Qb-SNARE Proteins/genetics ; Seizures
Chemical Substances	GOSR2 protein, human ; Qb-SNARE Proteins
Language	English
Publishing date	2023-09-25
Publishing country	Switzerland
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14101860
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