scholarly journals Viral gain-of-function experiments uncover residues under diversifying selection in nature

2018 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Daniel T. Johnson ◽  
Stephanie J. Spielman ◽  
Katherine L. Petrie ◽  
Debora S. Marks ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Host Shift ◽  
Host Recognition ◽  
Proof Of Concept ◽  
Bacteriophage Λ ◽  
Gain Of Function ◽  
Diversifying Selection ◽  
Genomic Epidemiology ◽  
Recognition Protein ◽  
Key Residues

Viral gain-of-function mutations are commonly observed in the laboratory; however, it is unknown whether those mutations also evolve in nature. We identify two key residues in the host recognition protein of bacteriophage λ that are necessary to exploit a new receptor; both residues repeatedly evolved among homologs from environmental samples. Our results provide evidence for widespread host-shift evolution in nature and a proof of concept for integrating experiments with genomic epidemiology.

scholarly journals Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Hemanth KN Reddy ◽  
Marta Carroni ◽  
Janos Hajdu ◽  
Martin Svenda
Keyword(s):  
Lipid Membrane ◽  
3D Structure ◽  
Vital Role ◽  
Host Recognition ◽  
Protein Conformations ◽  
Wild Type ◽  
Viral Membrane ◽  
Recognition Protein ◽  
New Protein ◽  
Wild Type Virion

Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

scholarly journals Electron cryo-microscopy of Bacteriophage PR772 reveals the composition and structure of the elusive vertex complex and the capsid architecture

2019 ◽  
Author(s):  
Hemanth. K. N. Reddy ◽  
Janos Hajdu ◽  
Marta Carroni ◽  
Martin Svenda
Keyword(s):  
Lipid Membrane ◽  
3D Structure ◽  
Vital Role ◽  
Host Recognition ◽  
Protein Conformations ◽  
Wild Type ◽  
Composition And Structure ◽  
Recognition Protein ◽  
New Protein ◽  
Wild Type Virion

AbstractBacteriophage PR772, a member of theTectiviridaefamily, has a 70-nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveals the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T=25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

scholarly journals Gain-of-function mutations in beet DODA2 identify key residues for betalain pigment evolution

2018 ◽  
Vol 219 (1) ◽  
pp. 287-296 ◽  
Author(s):  
Alexander Bean ◽  
Rasika Sunnadeniya ◽  
Neda Akhavan ◽  
Annabelle Campbell ◽  
Matthew Brown ◽  
...  
Keyword(s):  
Gain Of Function ◽  
Key Residues ◽  
Betalain Pigment

scholarly journals Disruption of the Interaction between ORF33 and the Conserved Carboxyl-Terminus of ORF45 Abolishes Progeny Virion Production of Kaposi Sarcoma-Associated Herpesvirus

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1828
Author(s):  
Joseph Gillen ◽  
Fanxiu Zhu
Keyword(s):  
Kaposi Sarcoma ◽  
Tegument Protein ◽  
Carboxyl Terminus ◽  
Proof Of Concept ◽  
Cell Penetration ◽  
Viral Production ◽  
Reading Frame ◽  
Virion Production ◽  
Key Residues ◽  
Efficient Viral Replication

The Open Reading Frame 45 (ORF45) of Kaposi sarcoma-associated herpesvirus (KSHV) is a gammaherpesvirus-specific, immediate-early, tegument protein required for efficient viral replication and virion production. We have previously shown that ORF45 interacts with the conserved herpesviral protein ORF33 through the highly conserved C-terminal 19 amino acids (C19) of ORF45. Because the deletion of C19 abolished ORF33 accumulation and viral production, we reasoned that this interaction could be critical for viral production and explored as an antiviral target for gammaherpesviruses. In work described in this article, we characterize this interaction in further detail, first by revealing that this interaction is conserved among gammaherpesviruses, then by identifying residues in C19 critical for its interaction with and stabilization of ORF33. More importantly, we show that disruption of the interaction, either by mutating key residues (W403A or W405A) in C19 or by using competing cell penetration peptide TAT-C19, dramatically reduce the yield of KSHV progeny viruses. Our results not only reveal critical roles of this interaction to viral production but also provide a proof of concept for targeting the ORF33-ORF45 interaction as a novel antiviral strategy against KSHV and other gammaherpesviruses.

scholarly journals Hydrophobicity–water/air–based enrichment cell for microplastics analysis within environmental samples: A proof of concept

MethodsX ◽  
2020 ◽  
Vol 7 ◽  
pp. 100732 ◽  
Author(s):  
Gerrit Renner ◽  
Alexander Nellessen ◽  
Alexander Schwiers ◽  
Mike Wenzel ◽  
Torsten C. Schmidt ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Proof Of Concept

Capsid transformation during packaging of bacteriophage λ DNA

1976 ◽  
Vol 276 (943) ◽  
pp. 51-61 ◽  
Keyword(s):  
Tertiary Structure ◽  
Unit Length ◽  
Protein A ◽  
Chemical Properties ◽  
Subunit Structure ◽  
Bacteriophage Λ ◽  
Protein Mass ◽  
Recognition Protein ◽  
Protein Components

Assembly pathways of complex viruses might not be simple additions of one protein after another with rigid tertiary structure. It might in fact involve shifts in subunit structure, movement of subunits relative to each other to form new arrangements, transient action of proteins and protein segments, involvement of structure forming ‘microenvironments’ of the host. Thus morphogenesis of the bacteriophage λ head starts with the formation of a core-containing DNA-free petit λ particle. In a first transition, and dependent on a host function, the core is released, minor protein components of the capsid are processed and the particle’s structure is altered, as shown by a change of its hydrodynamic properties. The resulting ‘prehead’ undergoes a second transition triggered by a complex of DNA and recognition protein (A-protein). This transition is more drastic than the first one. The particle doubles its volume without increasing in protein mass, the shell becomes thinner, and the surface structure is changed. Concomitantly with this process, the DNA becomes packaged and the particle becomes able to bind the small ‘ D -protein’ in amounts equimolar to the capsid protein, which it could not do before. The D -protein addition probably causes another shift of the capsid structure. DNA packaging is completed, and the DNA is cut from concatemeric precursors to unit length molecules. Binding sites are created for the tail connector molecules which in turn allow the independently assembled tail to attach. Research on these processes proceeds along several lines: comparison of physical and chemical properties of particles accumulating in mutants; pulse-chase experiments on assembly precursors; morphogenesis in vitro ’, and model transitions of aberrant λ polyheads.

scholarly journals Genomic epidemiology of rifampicin ADP-ribosyltransferase (Arr) in the Bacteria domain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sergio Morgado ◽  
Érica Fonseca ◽  
Ana Carolina Vicente
Keyword(s):  
Phylogenetic Reconstruction ◽  
In Silico Analysis ◽  
Resistance Phenotype ◽  
Genomic Epidemiology ◽  
Rifampin Resistance ◽  
Vitro Analysis ◽  
Key Residues ◽  
Adp Ribosyltransferase ◽  
In Vitro Analysis

AbstractArr is an ADP-ribosyltransferase enzyme primarily reported in association with rifamycin resistance, which has been used to treat tuberculosis in addition to Gram-positive infections and, recently, pan-resistant Gram-negative bacteria. The arr gene was initially identified on the Mycolicibacterium smegmatis chromosome and later on Proteobacteria plasmids. This scenario raised concerns on the distribution and spread of arr, considering the Bacteria domain. Based on 198,082 bacterial genomes/metagenomes, we performed in silico analysis, including phylogenetic reconstruction of Arr in different genomic contexts. Besides, new arr alleles were evaluated by in vitro analysis to assess their association with rifampin resistance phenotype. The arr gene was prevalent in thousands of chromosomes and in hundreds of plasmids from environmental and clinical bacteria, mainly from the phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Furthermore, this gene was identified in other and new genomic contexts. Interestingly, Arr sequences associated with rifampin resistance were distributed across all phylogeny, indicating that, despite the diversity, their association with rifampin resistance phenotype were maintained. In fact, we found that the key residues were highly conserved. In addition, other analyzes have raised evidence of another Arr function, which is related to guanidine metabolism. Finally, this scenario as a whole also suggested the Actinobacteria phylum as a potential ancestral source of arr within the Bacteria domain.

scholarly journals High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria

2020 ◽  
Vol 117 (31) ◽  
pp. 18670-18679 ◽  
Author(s):  
Kaitlyn E. Kortright ◽  
Benjamin K. Chan ◽  
Paul E. Turner
Keyword(s):  
Escherichia Coli ◽  
High Throughput ◽  
Environmental Samples ◽  
Proof Of Concept ◽  
Cellular Receptors ◽  
Transposon Insertion ◽  
Genes Encoding ◽  
Phage Receptor ◽  
Bacterial Genes ◽  
Transposon Insertion Sequencing

As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage–bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses ofEscherichia coli(phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere.

scholarly journals Gain‐of‐function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

Evolution ◽  
2018 ◽  
Vol 72 (10) ◽  
pp. 2234-2243 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Daniel T. Johnson ◽  
Stephanie J. Spielman ◽  
Katherine L. Petrie ◽  
Debora S. Marks ◽  
...  
Keyword(s):  
Bacteriophage Lambda ◽  
Gain Of Function ◽  
Diversifying Selection

scholarly journals Human peptidoglycan recognition protein S is an effector of neutrophil-mediated innate immunity

Blood ◽  
2005 ◽  
Vol 106 (7) ◽  
pp. 2551-2558 ◽  
Author(s):  
Ju Hyun Cho ◽  
Iain P. Fraser ◽  
Koichi Fukase ◽  
Shoichi Kusumoto ◽  
Yukari Fujimoto ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Antimicrobial Effect ◽  
Protein S ◽  
Host Recognition ◽  
Human Neutrophils ◽  
Peptidoglycan Recognition Protein ◽  
Acid Type ◽  
Potential Synergy ◽  
Recognition Protein ◽  
Bacterial Peptidoglycan

AbstractInnate immune responses to bacteria require cooperative interactions between host recognition molecules and phagocytes. The peptidoglycan recognition proteins (PGRPs) are a large group of proteins found in insects and mammals that bind to bacterial peptidoglycan (PGN). PGRP-S is located with other antimicrobial proteins, such as lysozyme, in the granules of human neutrophils. Whereas both PGRP-S and lysozyme recognize PGN, the exact binding specificity of human PGRP-S, its functional activity, and its potential synergy with other neutrophil-derived bactericidal proteins such as lysozyme have not been determined. Here we show that human PGRP-S binds to and inhibits the growth of Staphylococcus aureus (containing lysine-type PGN) and Escherichia coli (containing mesodiaminopimelic acid-type PGN). The binding affinity and thus antimicrobial activity of PGRP-S is determined by the third amino acid in the PGN stem peptide. Furthermore, the antimicrobial effect of PGRP-S against E coli is synergistic with lysozyme, and lysozyme and PGRP-S colocalize in neutrophil extracellular traps (NETs), suggesting that these granule-derived proteins act together to kill bacteria trapped in the NETs. Taken together, these results indicate that human PGRP-S plays a role in innate immunity in the context of neutrophils by contributing to the killing of intracellular and extracellular bacteria. (Blood. 2005;106:2551-2558)

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