Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology

Mario Mietzsch; Robert McKenna; Elina Väisänen; Jennifer C. Yu; Maria Ilyas; Joshua A. Hull; Justin Kurian; J. Kennon Smith; Paul Chipman; Yi Lasanajak; David Smith; Maria Söderlund-Venermo; Mavis Agbandje-McKenna

doi:10.3390/v12060653

Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology

Viruses ◽

10.3390/v12060653 ◽

2020 ◽

Vol 12 (6) ◽

pp. 653

Author(s):

Mario Mietzsch ◽

Robert McKenna ◽

Elina Väisänen ◽

Jennifer C. Yu ◽

Maria Ilyas ◽

...

Keyword(s):

Sialic Acid ◽

Structure Evolution ◽

Cellular Interactions ◽

Human Pathogens ◽

Cryo Electron Microscopy ◽

Cellular Entry ◽

Surface Loops ◽

Antigenic Reactivity ◽

Insight Into

Several members of the Protoparvovirus genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.

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Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798321009025 ◽

2021 ◽

Vol 77 (10) ◽

Author(s):

Gabriela C. Schröder ◽

Flora Meilleur

Keyword(s):

Radiation Damage ◽

Reaction Mechanisms ◽

Protein Crystallography ◽

Computational Techniques ◽

Cryo Electron Microscopy ◽

Structural Probe ◽

Metal Cofactor ◽

Neutron Protein Crystallography ◽

Insight Into

Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

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A Vesiculovirus Showing a Steepened Transcription Gradient and Dominanttrans-Repression of Virus Transcription

Journal of Virology ◽

10.1128/jvi.00358-12 ◽

2012 ◽

Vol 86 (16) ◽

pp. 8884-8889 ◽

Cited By ~ 2

Author(s):

Erin N. Hodges ◽

Bianca S. Heinrich ◽

John H. Connor

Keyword(s):

Rapid Decline ◽

Human Pathogens ◽

Wild Type ◽

Virus Transcription ◽

Plaque Phenotype ◽

Vesicular Stomatitis ◽

Viral Attenuation ◽

Negative Sense ◽

Insight Into

Vesicular stomatitis virus (VSV) is a prototype nonsegmented, negative-sense virus used to examine viral functions of a broad family of viruses, including human pathogens. Here we demonstrate that S2VSV, an isolate with a small plaque phenotype compared to other Indiana strain viruses, has a transcription defect resulting in an altered pattern and rapid decline of transcription. The S2VSV transcription gradient is dominant over the wild-type transcription in a coinfection. This is the first characterization of an altered gradient of transcription not dependent on RNA template sequence or host response and may provide insight into new approaches to viral attenuation.

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Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074768 ◽

1983 ◽

Vol 41 ◽

pp. 194-195

Author(s):

D. F. Blake ◽

L. F. Allard ◽

D. R. Peacor

Keyword(s):

High Resolution ◽

Marine Invertebrates ◽

Sea Urchins ◽

Structural Features ◽

Sea Stars ◽

High Resolution Tem ◽

Relationship Of ◽

The Relationship ◽

Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

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Molecular Pathogenesis of Hodgkin Lymphoma: Past, Present, Future

International Journal of Molecular Sciences ◽

10.3390/ijms21186623 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6623 ◽

Cited By ~ 1

Author(s):

Marc Bienz ◽

Salima Ramdani ◽

Hans Knecht

Keyword(s):

Immune System ◽

Targeted Therapy ◽

Signaling Pathways ◽

Hodgkin Lymphoma ◽

Genetic Instability ◽

Host Immune System ◽

Cellular Interactions ◽

Classical Hodgkin Lymphoma ◽

The Past

Our understanding of the tumorigenesis of classical Hodgkin lymphoma (cHL) and the formation of Reed–Sternberg cells (RS-cells) has evolved drastically in the last decades. More recently, a better characterization of the signaling pathways and the cellular interactions at play have paved the way for new targeted therapy in the hopes of improving outcomes. However, important gaps in knowledge remain that may hold the key for significant changes of paradigm in this lymphoma. Here, we discuss the past, present, and future of cHL, and review in detail the more recent discoveries pertaining to genetic instability, anti-apoptotic signaling pathways, the tumoral microenvironment, and host-immune system evasion in cHL.

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First Insight into Nutraceutical Properties of Local Salento Cichorium intybus Varieties: NMR-Based Metabolomic Approach

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18084057 ◽

2021 ◽

Vol 18 (8) ◽

pp. 4057

Author(s):

Chiara Roberta Girelli ◽

Francesca Serio ◽

Rita Accogli ◽

Federica Angilè ◽

Antonella De Donno ◽

...

Keyword(s):

1H Nmr ◽

Cichorium Intybus ◽

Resonance Spectroscopy ◽

Metabolic Profiles ◽

Whole Plant ◽

Different Content ◽

Insight Into ◽

Nutraceutical Properties ◽

Metabolomic Approach

Background: Plants of genus Cichorium are known for their therapeutic and nutraceutical properties determined by a wealth of phytochemical substances contained in the whole plant. The aim of this paper was to characterize the metabolic profiles of local Salento chicory (Cichorium intybus L.) varieties (“Bianca”, “Galatina”, “Leccese”, and “Otranto”) in order to describe their metabolites composition together with possible bioactivity and health beneficial properties. Methods: The investigation was performed by 1H-NMR spectroscopy and Multivariate Analysis (MVA), by which the metabolic profiles of the samples were easily obtained and compared. Results: The supervised Partial Least Squares Discriminant Analysis (PLS-DA) analysis showed as “Bianca” and “Galatina” samples grouped together separated by “Leccese” and “Otranto” varieties. A different content of free amino acids and organic acids was observed among the varieties. In particular a high content of cichoric and monocaffeoyl tartaric acid was observed for the “Leccese” variety. The presence of secondary metabolites adds significant interest in the investigation of Cichorium inthybus, as this vegetable may benefit human health when incorporated into the diet. Conclusions: The 1H-NMR (Nuclear Magnetic Resonance Spectroscopy) based characterization of Salento chicory varieties allowed us to determine the potential usefulness and nutraceutical properties of the product, also providing a method to guarantee its authenticity on a molecular scale.

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

Nature Communications ◽

10.1038/s41467-021-22253-6 ◽

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.

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“Real-World” Microscopy: Understanding Environment-Sensitive Behavior of Ni-Base Welds

Microscopy and Microanalysis ◽

10.1017/s1431927600022765 ◽

1998 ◽

Vol 4 (S2) ◽

pp. 528-529

Author(s):

M. G. Burke ◽

R. J. Wehrer ◽

C.M. Brown

Keyword(s):

Nuclear Power ◽

Base Alloy ◽

Analytical Electron Microscopy ◽

Furnace Cool ◽

Environmental Embrittlement ◽

Reported Study ◽

Compositional Changes ◽

Insight Into ◽

Sensitive Behavior

Ni-base alloy welds such as EN82H weld metal are frequently employed in nuclear power applications where resistance to corrosion is required. Results of a recently reported study of the mechanical properties of EN82H welds show that this alloy is susceptible to low-temperature (∼100°C) environmental embrittlement (LTEE) in hydrogenated water. LTEE is a manifestation of hydrogen embrittlement in these alloys.1 Recent LTEE tests have demonstrated a beneficial effect of a high-temperature (∼1100°C) anneal and furnace-cool in alleviating the material's susceptibility to LTEE. Understanding the reason for the reduction in LTEE susceptibility requires detailed characterization of the microstructure so that the specific structural and compositional changes that have been induced by the solution-anneal can be identified. This study reports the results of light optical and analytical electron microscopy (AEM) characterization of the microstructures of as-fabricated and as-solution-annealed EN82H welds with the objective of providing insight into the observed LTEE behavior.

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Isolation and Molecular Characterization of the Romaine Lettuce Phylloplane Mycobiome

Journal of Fungi ◽

10.3390/jof7040277 ◽

2021 ◽

Vol 7 (4) ◽

pp. 277

Author(s):

Danny Haelewaters ◽

Hector Urbina ◽

Samuel Brown ◽

Shannon Newerth-Henson ◽

M. Catherine Aime

Keyword(s):

Lactuca Sativa ◽

New Combinations ◽

Food Spoilage ◽

Human Pathogens ◽

Plant Leaves ◽

Romaine Lettuce ◽

Future Studies ◽

The Core ◽

American Agriculture

Romaine lettuce (Lactuca sativa) is an important staple of American agriculture. Unlike many vegetables, romaine lettuce is typically consumed raw. Phylloplane microbes occur naturally on plant leaves; consumption of uncooked leaves includes consumption of phylloplane microbes. Despite this fact, the microbes that naturally occur on produce such as romaine lettuce are for the most part uncharacterized. In this study, we conducted culture-based studies of the fungal romaine lettuce phylloplane community from organic and conventionally grown samples. In addition to an enumeration of all such microbes, we define and provide a discussion of the genera that form the “core” romaine lettuce mycobiome, which represent 85.5% of all obtained isolates: Alternaria, Aureobasidium, Cladosporium, Filobasidium, Naganishia, Papiliotrema, Rhodotorula, Sampaiozyma, Sporobolomyces, Symmetrospora and Vishniacozyma. We highlight the need for additional mycological expertise in that 23% of species in these core genera appear to be new to science and resolve some taxonomic issues we encountered during our work with new combinations for Aureobasidiumbupleuri and Curvibasidium nothofagi. Finally, our work lays the ground for future studies that seek to understand the effect these communities may have on preventing or facilitating establishment of exogenous microbes, such as food spoilage microbes and plant or human pathogens.

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Specificities and Synergistic Actions of Novel PL8 and PL7 Alginate Lyases from the Marine Fungus Paradendryphiella salina

Journal of Fungi ◽

10.3390/jof7020080 ◽

2021 ◽

Vol 7 (2) ◽

pp. 80

Author(s):

Bo Pilgaard ◽

Marlene Vuillemin ◽

Jesper Holck ◽

Casper Wilkens ◽

Anne S. Meyer

Keyword(s):

Alginate Lyase ◽

Marine Fungus ◽

Brown Macroalgae ◽

Polysaccharide Lyases ◽

Alginate Lyases ◽

Encoding Genes ◽

Substrate Affinities ◽

Alginate Degradation ◽

Insight Into

Alginate is an anionic polysaccharide abundantly present in the cell walls of brown macroalgae. The enzymatic depolymerization is performed solely by alginate lyases (EC 4.2.2.x), categorized as polysaccharide lyases (PLs) belonging to 12 different PL families. Until now, the vast majority of the alginate lyases have been found in bacteria. We report here the first extensive characterization of four alginate lyases from a marine fungus, the ascomycete Paradendryphiella salina, a known saprophyte of seaweeds. We have identified four polysaccharide lyase encoding genes bioinformatically in P. salina, one PL8 (PsMan8A), and three PL7 alginate lyases (PsAlg7A, -B, and -C). PsMan8A was demonstrated to exert exo-action on polymannuronic acid, and no action on alginate, indicating that this enzyme is most likely an exo-acting polymannuronic acid specific lyase. This enzyme is the first alginate lyase assigned to PL8 and polymannuronic acid thus represents a new substrate specificity in this family. The PL7 lyases (PsAlg7A, -B, and -C) were found to be endo-acting alginate lyases with different activity optima, substrate affinities, and product profiles. PsAlg7A and PsMan8A showed a clear synergistic action for the complete depolymerization of polyM at pH 5. PsAlg7A depolymerized polyM to mainly DP5 and DP3 oligomers and PsMan8A to dimers and monosaccharides. PsAlg7B and PsAlg7C showed substrate affinities towards both polyM and polyG at pH 8, depolymerizing both substrates to DP9-DP2 oligomers. The findings elucidate how P. salina accomplishes alginate depolymerization and provide insight into an efficient synergistic cooperation that may provide a new foundation for enzyme selection for alginate degradation in seaweed bioprocessing.

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