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  1. Article ; Online: Using cryoEM and cryoET to visualize membrane penetration of a non-enveloped virus

    Xian Xia / Z. Hong Zhou

    STAR Protocols, Vol 3, Iss 4, Pp 101825- (2022)

    2022  

    Abstract: Summary: Key to cell entry by non-enveloped viruses is virus-cell interactions at the cell or endosomal membrane. Here, we detail our protocols to capture such interactions between non-enveloped virus bluetongue virus (BTV) and vesicular membrane by ... ...

    Abstract Summary: Key to cell entry by non-enveloped viruses is virus-cell interactions at the cell or endosomal membrane. Here, we detail our protocols to capture such interactions between non-enveloped virus bluetongue virus (BTV) and vesicular membrane by cryogenic electron microscopy (cryoEM) and tomography (cryoET). Key steps include virus isolation, liposome preparation, virus-liposome incubation and vitrification, cryoEM and cryoET imaging, data processing for 3D reconstruction, and subtomogram averaging. The protocols can be generally applicable to studies of cell entry by other non-enveloped viruses.For complete details on the use and execution of this protocol, please refer to Xia et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
    Keywords Microbiology ; Microscopy ; Structural biology ; Cryo-EM ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Multiple conformations of trimeric spikes visualized on a non-enveloped virus

    Yinong Zhang / Yanxiang Cui / Jingchen Sun / Z. Hong Zhou

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 9

    Abstract: Zhang and Cui et al. present in situ cryoEM structures of the trimeric spike of cytoplasmic polyhedrosis virus in both open and close conformations, and demonstrate that spike detachment from the capsid is triggered by the presence of SAM and ATP. ...

    Abstract Zhang and Cui et al. present in situ cryoEM structures of the trimeric spike of cytoplasmic polyhedrosis virus in both open and close conformations, and demonstrate that spike detachment from the capsid is triggered by the presence of SAM and ATP.
    Keywords Science ; Q
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150

    Yun-Tao Liu / David Strugatsky / Wei Liu / Z. Hong Zhou

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 9

    Abstract: Here, cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion’s capsid-bound tegument protein, pp150. tRNA recruitment is mediated by the interactions specific for HCMV only, suggesting the explanation ...

    Abstract Here, cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion’s capsid-bound tegument protein, pp150. tRNA recruitment is mediated by the interactions specific for HCMV only, suggesting the explanation for the absence of such tRNA densities in related herpesviruses.
    Keywords Science ; Q
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Hierarchical organization and assembly of the archaeal cell sheath from an amyloid-like protein

    Hui Wang / Jiayan Zhang / Daniel Toso / Shiqing Liao / Farzaneh Sedighian / Robert Gunsalus / Z. Hong Zhou

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 11

    Abstract: Abstract Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, ... ...

    Abstract Abstract Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked β-hoops, each of which is comprised of two to six 400 nm-diameter rings of β-strand arches (β-rings). With both similarities to and differences from amyloid cross-β fibril architecture, each β-ring contains two giant β-sheets contributed by ~ 450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into β-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent β-hoops into the immature sheath cylinder at the junction of two daughter cells.
    Keywords Science ; Q
    Subject code 612
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics

    Jane K.J. Lee / Yun-Tao Liu / Jason J. Hu / Inna Aphasizheva / Ruslan Aphasizhev / Z. Hong Zhou

    Journal of Structural Biology: X, Vol 7, Iss , Pp 100088- (2023)

    2023  

    Abstract: Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly ... ...

    Abstract Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoan Leishmania tarentolae (LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC β-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulae α0β6, α1β6, α2β6, α3β6, α4β6, α5β6, α6β6) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
    Keywords Propionyl-CoA ; Statistical mechanics ; Thermodynamics ; Rate constant ; Conformation ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Isotropic reconstruction for electron tomography with deep learning

    Yun-Tao Liu / Heng Zhang / Hui Wang / Chang-Lu Tao / Guo-Qiang Bi / Z. Hong Zhou

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 17

    Abstract: Cryogenic electron tomography suffers from anisotropic resolution due to the missing-wedge problem. Here, the authors present IsoNet, a neural network that learn the feature representation from similar structures in the tomogram and recover the missing ... ...

    Abstract Cryogenic electron tomography suffers from anisotropic resolution due to the missing-wedge problem. Here, the authors present IsoNet, a neural network that learn the feature representation from similar structures in the tomogram and recover the missing information for isotropic tomogram reconstruction.
    Keywords Science ; Q
    Language English
    Publishing date 2022-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Protein chainmail variants in dsDNA viruses

    Z. Hong Zhou / Joshua Chiou

    AIMS Biophysics, Vol 2, Iss 2, Pp 200-

    2015  Volume 218

    Abstract: First discovered in bacteriophage HK97, biological chainmail is a highly stable system formed by concatenated protein rings. Each subunit of the ring contains the HK97-like fold, which is characterized by its submarine-like shape with a 5-stranded β ... ...

    Abstract First discovered in bacteriophage HK97, biological chainmail is a highly stable system formed by concatenated protein rings. Each subunit of the ring contains the HK97-like fold, which is characterized by its submarine-like shape with a 5-stranded β sheet in the axial (A) domain, spine helix in the peripheral (P) domain, and an extended (E) loop. HK97 capsid consists of covalently-linked copies of just one HK97-like fold protein and represents the most effective strategy to form highly stable chainmail needed for dsDNA genome encapsidation. Recently, near-atomic resolution structures enabled by cryo electron microscopy (cryoEM) have revealed a range of other, more complex variants of this strategy for constructing dsDNA viruses. The first strategy, exemplified by P22-like phages, is the attachment of an insertional (I) domain to the core 5-stranded β sheet of the HK97-like fold. The atomic models of the Bordetella phage BPP-1 showcases an alternative topology of the classic HK97 topology of the HK97-like fold, as well as the second strategy for constructing stable capsids, where an auxiliary jellyroll protein dimer serves to cement the non-covalent chainmail formed by capsid protein subunits. The third strategy, found in lambda-like phages, uses auxiliary protein trimers to stabilize the underlying non-covalent chainmail near the 3-fold axis. Herpesviruses represent highly complex viruses that use a combination of these strategies, resulting in four-level hierarchical organization including a non-covalent chainmail formed by the HK97-like fold domain found in the floor region. A thorough understanding of these structures should help unlock the enigma of the emergence and evolution of dsDNA viruses and inform bioengineering efforts based on these viruses.
    Keywords structural biology ; microbiology ; protein chainmail ; HK97 ; BPP-1 ; P22 ; lambda ; Herpesvirus ; RRV ; HK97-like fold ; virus ; cryoEM ; X-ray crystallography ; Biology (General) ; QH301-705.5 ; Biotechnology ; TP248.13-248.65
    Subject code 500
    Language English
    Publishing date 2015-06-01T00:00:00Z
    Publisher AIMS Press
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Structural basis for capsid recruitment and coat formation during HSV-1 nuclear egress

    Elizabeth B Draganova / Jiayan Zhang / Z Hong Zhou / Ekaterina E Heldwein

    eLife, Vol

    2020  Volume 9

    Abstract: During herpesvirus infection, egress of nascent viral capsids from the nucleus is mediated by the viral nuclear egress complex (NEC). NEC deforms the inner nuclear membrane (INM) around the capsid by forming a hexagonal array. However, how the NEC coat ... ...

    Abstract During herpesvirus infection, egress of nascent viral capsids from the nucleus is mediated by the viral nuclear egress complex (NEC). NEC deforms the inner nuclear membrane (INM) around the capsid by forming a hexagonal array. However, how the NEC coat interacts with the capsid and how curved coats are generated to enable budding is yet unclear. Here, by structure-guided truncations, confocal microscopy, and cryoelectron tomography, we show that binding of the capsid protein UL25 promotes the formation of NEC pentagons rather than hexagons. We hypothesize that during nuclear budding, binding of UL25 situated at the pentagonal capsid vertices to the NEC at the INM promotes formation of NEC pentagons that would anchor the NEC coat to the capsid. Incorporation of NEC pentagons at the points of contact with the vertices would also promote assembly of the curved hexagonal NEC coat around the capsid, leading to productive egress of UL25-decorated capsids.
    Keywords nuclear egress complex ; membrane budding ; capsid budding ; herpes simplex virus type 1 ; herpesvirus ; nuclear egress ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 690
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins

    Muchen Pan / Ana L. Alvarez-Cabrera / Joon S. Kang / Lihua Wang / Chunhai Fan / Z. Hong Zhou

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 16

    Abstract: Mammalian reovirus (MRV) is a double-stranded RNA (dsRNA) virus that affects the gastrointestinal and respiratory tracts. Here, the authors present the 3.3 Å cryo-EM asymmetric reconstruction of transcribing MRV that reveals the organization of the dsRNA ...

    Abstract Mammalian reovirus (MRV) is a double-stranded RNA (dsRNA) virus that affects the gastrointestinal and respiratory tracts. Here, the authors present the 3.3 Å cryo-EM asymmetric reconstruction of transcribing MRV that reveals the organization of the dsRNA genome, RNA interaction with the polymerase complex, and how the polymerase interacts extensively with its co-factor, µ2, to form a transcription enzyme complex, which engages and regulates RNA transcription.
    Keywords Science ; Q
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Nature Portfolio
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    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Exosomes from Von Hippel-Lindau-Null Cancer Cells Promote Metastasis in Renal Cell Carcinoma

    Kailey Flora / Moe Ishihara / Zhicheng Zhang / Elizabeth S. Bowen / Aimee Wu / Tala Ayoub / Julian Huang / Celine Cano-Ruiz / Maia Jackson / Kaveeya Reghu / Yasmeen Ayoub / Yazhen Zhu / Hsian-Rong Tseng / Z. Hong Zhou / Junhui Hu / Lily Wu

    International Journal of Molecular Sciences, Vol 24, Iss 24, p

    2023  Volume 17307

    Abstract: Exosomes are extracellular vesicles that modulate essential physiological and pathological signals. Communication between cancer cells that express the von Hippel-Lindau (VHL) tumor suppressor gene and those that do not is instrumental to distant ... ...

    Abstract Exosomes are extracellular vesicles that modulate essential physiological and pathological signals. Communication between cancer cells that express the von Hippel-Lindau (VHL) tumor suppressor gene and those that do not is instrumental to distant metastasis in renal cell carcinoma (RCC). In a novel metastasis model, VHL(−) cancer cells are the metastatic driver, while VHL(+) cells receive metastatic signals from VHL(−) cells and undergo aggressive transformation. This study investigates whether exosomes could be mediating metastatic crosstalk. Exosomes isolated from paired VHL(+) and VHL(−) cancer cell lines were assessed for physical, biochemical, and biological characteristics. Compared to the VHL(+) cells, VHL(−) cells produce significantly more exosomes that augment epithelial-to-mesenchymal transition (EMT) and migration of VHL(+) cells. Using a Cre- loxP exosome reporter system, the fluorescent color conversion and migration were correlated with dose-dependent delivery of VHL(−) exosomes. VHL(−) exosomes even induced a complete cascade of distant metastasis when added to VHL(+) tumor xenografts in a duck chorioallantoic membrane (dCAM) model, while VHL (+) exosomes did not. Therefore, this study supports that exosomes from VHL(−) cells could mediate critical cell-to-cell crosstalk to promote metastasis in RCC.
    Keywords exosomes ; metastasis ; renal cell carcinoma ; EMT ; cell–cell communication ; CAM model ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 610
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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