scholarly journals Viral genome-capsid core senses host environments to prime RNA release

2021 ◽  
Author(s):  
Ranita Ramesh ◽  
Sean M. Braet ◽  
Varun Venkatakrishnan ◽  
Palur Venkata Raghuvamsi ◽  
Jonathan Chua Wei Bao ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Environmental Changes ◽  
Structure Refinement ◽  
Coat Proteins ◽  
Fold Axis ◽  
Turnip Crinkle Virus ◽  
Plant Host ◽  
Conformational Switching ◽  
Macromolecular Assemblies ◽  
Viral Coat

Viruses are metastable macromolecular assemblies containing a nucleic acid core packaged by capsid proteins that are primed to disassemble in host-specific environments leading to genome release and replication. The mechanism of how viruses sense environmental changes associated with host entry to prime them for disassembly is unknown. We have applied a combination of mass spectrometry, cryo-EM, and simulation-assisted structure refinement to Turnip crinkle virus (TCV), which serves as a model non-enveloped icosahedral virus (Triangulation number = 3, 180 copies/icosahedron). Our results reveal genomic RNA tightly binds a subset of viral coat proteins to form a stable RNA-capsid core which undergoes conformational switching in response to host-specific environmental changes. These changes include: i) Depletion of Ca 2+ which triggers viral particle expansion ii) Increase in osmolytes further disrupt interactions of outer coat proteins from the RNA-capsid core to promote complete viral disassembly. A cryo-EM structure of the expanded particle shows that RNA is asymmetrically extruded from a single 5-fold axis during disassembly. The genomic RNA:capsid protein interactions confer metastability to the TCV capsid and drive release of RNA from the disassembling virion within the plant host cell.

scholarly journals Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher R. Horne ◽  
Hariprasad Venugopal ◽  
Santosh Panjikar ◽  
David M. Wood ◽  
Amy Henrickson ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Dna Binding ◽  
Protein Interactions ◽  
Acid Metabolism ◽  
Environmental Changes ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Nutrient Source ◽  
Cryo Electron Microscopy ◽  
Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

scholarly journals POT1-TPP1 differentially regulates telomerase via POT1 His266 and as a function of single-stranded telomere DNA length

2019 ◽  
Vol 116 (47) ◽  
pp. 23527-23533 ◽  
Author(s):  
Mengyuan Xu ◽  
Janna Kiselar ◽  
Tawna L. Whited ◽  
Wilnelly Hernandez-Sanchez ◽  
Derek J. Taylor
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Environmental Changes ◽  
Lymphocytic Leukemia ◽  
Protein Protein Interactions ◽  
Cellular Environment ◽  
Multiple Protein ◽  
Linear Chromosomes ◽  
Hydroxyl Radical Footprinting ◽  
Regulate Telomere Length

Telomeres cap the ends of linear chromosomes and terminate in a single-stranded DNA (ssDNA) overhang recognized by POT1-TPP1 heterodimers to help regulate telomere length homeostasis. Here hydroxyl radical footprinting coupled with mass spectrometry was employed to probe protein–protein interactions and conformational changes involved in the assembly of telomere ssDNA substrates of differing lengths bound by POT1-TPP1 heterodimers. Our data identified environmental changes surrounding residue histidine 266 of POT1 that were dependent on telomere ssDNA substrate length. We further determined that the chronic lymphocytic leukemia-associated H266L substitution significantly reduced POT1-TPP1 binding to short ssDNA substrates; however, it only moderately impaired the heterodimer binding to long ssDNA substrates containing multiple protein binding sites. Additionally, we identified a telomerase inhibitory role when several native POT1-TPP1 proteins coat physiologically relevant lengths of telomere ssDNA. This POT1-TPP1 complex-mediated inhibition of telomerase is abrogated in the context of the POT1 H266L mutation, which leads to telomere overextension in a malignant cellular environment.

scholarly journals Regulation of Clathrin-Mediated Endocytosis

2018 ◽  
Vol 87 (1) ◽  
pp. 871-896 ◽  
Author(s):  
Marcel Mettlen ◽  
Ping-Hung Chen ◽  
Saipraveen Srinivasan ◽  
Gaudenz Danuser ◽  
Sandra L. Schmid
Keyword(s):  
Conformational Changes ◽  
Posttranslational Modifications ◽  
Mammalian Cells ◽  
Environmental Changes ◽  
Protein Complexes ◽  
Adaptor Protein ◽  
Endocytic Pathway ◽  
Coat Proteins ◽  
Membrane Composition ◽  
Coated Pits

Clathrin-mediated endocytosis (CME) is the major endocytic pathway in mammalian cells. It is responsible for the uptake of transmembrane receptors and transporters, for remodeling plasma membrane composition in response to environmental changes, and for regulating cell surface signaling. CME occurs via the assembly and maturation of clathrin-coated pits that concentrate cargo as they invaginate and pinch off to form clathrin-coated vesicles. In addition to the major coat proteins, clathrin triskelia and adaptor protein complexes, CME requires a myriad of endocytic accessory proteins and phosphatidylinositol lipids. CME is regulated at multiple steps—initiation, cargo selection, maturation, and fission—and is monitored by an endocytic checkpoint that induces disassembly of defective pits. Regulation occurs via posttranslational modifications, allosteric conformational changes, and isoform and splice-variant differences among components of the CME machinery, including the GTPase dynamin. This review summarizes recent findings on the regulation of CME and the evolution of this complex process.

scholarly journals Finally, a Role Befitting Astar: Strongly Conserved, Unessential Microvirus A* Proteins Ensure the Product Fidelity of Packaging Reactions

2019 ◽  
Vol 94 (2) ◽  
Author(s):  
Aaron P. Roznowski ◽  
Sarah M. Doore ◽  
Sundance Z. Kemp ◽  
Bentley A. Fane
Keyword(s):  
Dna Replication ◽  
Genome Size ◽  
Protein Interactions ◽  
Protein A ◽  
Coat Proteins ◽  
Single Stranded Dna ◽  
Rolling Circle ◽  
A Charge ◽  
Ssdna Viruses ◽  
J Protein

ABSTRACT In microviruses, 60 copies of the positively charged DNA binding protein J guide the single-stranded DNA genome into the icosahedral capsid. Consequently, ∼12% of the genome is icosahedrally ordered within virions. Although the internal volume of the ϕX174, G4, and α3 capsids are nearly identical, their genome lengths vary widely from 5,386 (ϕX174) to 6,067 (α3) nucleotides. As the genome size increases, the J protein’s length and charge decreases. The ϕX174 J protein is 37 amino acids long and has a charge of +12, whereas the 23-residue G4 and α3 proteins have respective +6 and +8 charges. While the large ϕX174 J protein can substitute for the smaller ones, the converse is not true. Thus, the smallest genome, ϕX174, requires the more stringent J protein packaging guide. To investigate this further, a chimeric virus (ϕXG4J) was generated by replacing the indigenous ϕX174 J gene with that of G4. The resulting mutant, ϕXG4J, was not viable on the level of plaque formation without ϕX174 J gene complementation. During uncomplemented infections, capsids dissociated during packaging or quickly thereafter. Those that survived were significantly less stable and infectious than the wild type. Complementation-independent ϕXG4J variants were isolated. They contained duplications that increased genome size by as much as 3.8%. Each duplication started at nucleotide 991, creating an additional DNA substrate for the unessential but highly conserved A* protein. Accordingly, ϕXG4J viability and infectivity was also restored by the exogenous expression of a cloned A* gene. IMPORTANCE Double-stranded DNA viruses typically package their genomes into a preformed capsid. In contrast, single-stranded RNA viruses assemble their coat proteins around their genomes via extensive nucleotide-protein interactions. Single-stranded DNA (ssDNA) viruses appear to blend both strategies, using nucleotide-protein interactions to organize their genomes into preformed shells, likely by a controlled process. Chaotic genome-capsid associations could inhibit packaging or genome release during the subsequent infection. This process appears to be partially controlled by the unessential A* protein, a shorter version of the essential A protein that mediates rolling-circle DNA replication. Protein A* may elevate fitness by ensuring the product fidelity of packaging reactions. This phenomenon may be widespread in ssDNA viruses that simultaneously synthesize and package DNA with rolling circle and rolling circle-like DNA replication proteins. Many of these viruses encode smaller, unessential, and/or functionally undefined in-frame versions of A/A*-like proteins.

Interaction of plant viruses and viral coat proteins with mixed model membranes

Biochemistry ◽  
1987 ◽  
Vol 26 (19) ◽  
pp. 6217-6223 ◽  
Author(s):  
Klaas P. Datema ◽  
Ruud B. Spruijt ◽  
Benedictus J. M. Verduin ◽  
Marcus A. Hemminga
Keyword(s):  
Mixed Model ◽  
Plant Viruses ◽  
Model Membranes ◽  
Coat Proteins ◽  
Viral Coat ◽  
Viral Coat Proteins

scholarly journals The cutting edge: membrane-anchored serine protease activities in the pericellular microenvironment

2010 ◽  
Vol 428 (3) ◽  
pp. 325-346 ◽  
Author(s):  
Toni M. Antalis ◽  
Marguerite S. Buzza ◽  
Kathryn M. Hodge ◽  
John D. Hooper ◽  
Sarah Netzel-Arnett
Keyword(s):  
Serine Protease ◽  
Serine Proteases ◽  
Catalytic Domain ◽  
Proteolytic Processing ◽  
Coat Proteins ◽  
Vital Functions ◽  
Human Pathology ◽  
Functional Consequences ◽  
Viral Coat ◽  
Precursor Molecules

The serine proteases of the trypsin-like (S1) family play critical roles in many key biological processes including digestion, blood coagulation, and immunity. Members of this family contain N- or C-terminal domains that serve to tether the serine protease catalytic domain directly to the plasma membrane. These membrane-anchored serine proteases are proving to be key components of the cell machinery for activation of precursor molecules in the pericellular microenvironment, playing vital functions in the maintenance of homoeostasis. Substrates activated by membrane-anchored serine proteases include peptide hormones, growth and differentiation factors, receptors, enzymes, adhesion molecules and viral coat proteins. In addition, new insights into our understanding of the physiological functions of these proteases and their involvement in human pathology have come from animal models and patient studies. The present review discusses emerging evidence for the diversity of this fascinating group of membrane serine proteases as potent modifiers of the pericellular microenvironment through proteolytic processing of diverse substrates. We also discuss the functional consequences of the activities of these proteases on mammalian physiology and disease.

scholarly journals Front Cover: Template‐Free Self‐Assembly of Artificial De Novo Viral Coat Proteins into Nanorods: Effects of Sequence, Concentration, and Temperature (Chem. Eur. J. 47/2019)

2019 ◽  
Vol 25 (47) ◽  
pp. 10971-10971
Author(s):  
Ernesto Cazares Vargas ◽  
Martien A. Cohen Stuart ◽  
Renko de Vries ◽  
Armando Hernandez‐Garcia
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Coat Proteins ◽  
Front Cover ◽  
Viral Coat ◽  
Template Free ◽  
Viral Coat Proteins

Golgi processed foot-and-mouth disease virus proteins

1983 ◽  
Vol 41 ◽  
pp. 642-643
Author(s):  
S. H. Wool ◽  
J. Polatnick
Keyword(s):  
Guinea Pig ◽  
Rna Polymerase ◽  
Nonstructural Protein ◽  
Foot And Mouth Disease ◽  
Viral Rna ◽  
Coat Proteins ◽  
Mouth Disease Virus ◽  
Viral Coat ◽  
Membrane Bound

The Golgi apparatus was isolated from infected baby hamster kidney cells by centrifugation through discontinuous sucrose gradients. Tritium-labeled protein samples were analyzed by polyacrylamide gel electrophoretic autoradiograms. Pulse-chase studies showed that the viral-induced RNA polymerase passed through the Golgi as infection progressed. Some viral coat proteins were also associated with the Golgi as were other as yet unidentified viral proteins (Fig. 1). Immune labeling of isolated and in situ Golgi confirmed the presence of viral RNA polymerase. The isolated (Fig. 2) and in situ Golgi were labeled with guinea pig antipolymerase antibody and ferritin-labeled goat anti-guinea pig sera to show the presence of viral RNA polymerase.Earlier work in this laboratory established that the RNA polymerase was bound to membranes of newly formed smooth vacuoles during infection with FMDV. The smaller protein on the gel in Fig. 1 (arrow) corresponds in size to VPg (a nonstructural protein bound to the 5' end of viral RNA) has also been shown to be membrane bound.

Phytochrome Signaling Networks

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Mei-Chun Cheng ◽  
Praveen Kumar Kathare ◽  
Inyup Paik ◽  
Enamul Huq
Keyword(s):  
Protein Interactions ◽  
Translational Regulation ◽  
Regulatory Networks ◽  
Annual Review ◽  
Publication Date ◽  
Protein Protein Interactions ◽  
Conformational Switching ◽  
E3 Ligases ◽  
Almost All

The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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