scholarly journals The Closest Relatives of Icosahedral Viruses of Thermophilic Bacteria Are among Viruses and Plasmids of the Halophilic Archaea

2009 ◽  
Vol 83 (18) ◽  
pp. 9388-9397 ◽  
Author(s):  
Matti Jalasvuori ◽  
Silja T. Jaatinen ◽  
Simonas Laurinavičius ◽  
Elina Ahola-Iivarinen ◽  
Nisse Kalkkinen ◽  
...  
Keyword(s):  
Thermophilic Bacteria ◽  
Thermus Thermophilus ◽  
Halophilic Archaea ◽  
Structural Proteins ◽  
The Novel ◽  
Viral Membrane ◽  
Double Stranded Dna ◽  
Icosahedral Virus ◽  
Bacteriophage Genome ◽  
Icosahedral Viruses

ABSTRACT We have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus P23-77 of Thermus thermophilus. P23-77 has an ∼17-kb circular double-stranded DNA genome, which was annotated to contain 37 putative genes. Virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. Analysis of the bacteriophage genome revealed it to be evolutionarily related to another Thermus phage (IN93), archaeal Halobacterium plasmid (pHH205), a genetic element integrated into Haloarcula genome (designated here as IHP for integrated Haloarcula provirus), and the Haloarcula virus SH1. These genetic elements share two major capsid proteins and a putative packaging ATPase. The ATPase is similar with the ATPases found in the PRD1-type viruses, thus providing an evolutionary link to these viruses and furthering our knowledge on the origin of viruses.

scholarly journals Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae

2014 ◽  
Vol 159 (6) ◽  
pp. 1541-1554 ◽  
Author(s):  
Alice Pawlowski ◽  
Ilona Rissanen ◽  
Jaana K. H. Bamford ◽  
Mart Krupovic ◽  
Matti Jalasvuori
Keyword(s):  
Thermophilic Bacteria ◽  
Halophilic Archaea ◽  
The Novel

scholarly journals Nuclear cGAS: sequestration and beyond

2021 ◽  
Author(s):  
Juli Bai ◽  
Feng Liu
Keyword(s):  
Innate Immune ◽  
Complex Nature ◽  
Type I ◽  
Replication Forks ◽  
The Novel ◽  
Nuclear Function ◽  
Double Stranded Dna ◽  
Open Questions ◽  
Established Role ◽  
Dependent Signaling Pathway

AbstractThe cyclic GMP-AMP (cGAMP) synthase (cGAS) has been identified as a cytosolic double stranded DNA sensor that plays a pivotal role in the type I interferon and inflammation responses via the STING-dependent signaling pathway. In the past several years, a growing body of evidence has revealed that cGAS is also localized in the nucleus where it is associated with distinct nuclear substructures such as nucleosomes, DNA replication forks, the double-stranded breaks, and centromeres, suggesting that cGAS may have other functions in addition to its role in DNA sensing. However, while the innate immune function of cGAS is well established, the non-canonical nuclear function of cGAS remains poorly understood. Here, we review our current understanding of the complex nature of nuclear cGAS and point to open questions on the novel roles and the mechanisms of action of this protein as a key regulator of cell nuclear function, beyond its well-established role in dsDNA sensing and innate immune response.

DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning

2021 ◽  
pp. 2150018
Author(s):  
Omar Barukab ◽  
Farman Ali ◽  
Sher Afzal Khan
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Biological Activities ◽  
Dna Binding Proteins ◽  
Support Vector ◽  
The Novel ◽  
Double Stranded Dna ◽  
Difference Formula ◽  
Ensemble Strategy ◽  
Inflammatory Drugs

DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e. lung, breast, and liver cancer) and chronic diseases (i.e. AIDS/HIV, asthma), while other kinds are involved in antibiotics, steroids, and anti-inflammatory drugs designing. These crucial processes are closely related to DBPs types. DBPs are categorized into single-stranded DNA-binding proteins (ssDBPs) and double-stranded DNA-binding proteins (dsDBPs). Few computational predictors have been reported for discriminating ssDBPs and dsDBPs. However, due to the limitations of the existing methods, an intelligent computational system is still highly desirable. In this work, features from protein sequences are discovered by extending the notion of dipeptide composition (DPC), evolutionary difference formula (EDF), and K-separated bigram (KSB) into the position-specific scoring matrix (PSSM). The highly intrinsic information was encoded by a compression approach named discrete cosine transform (DCT) and the model was trained with support vector machine (SVM). The prediction performance was further boosted by the genetic algorithm (GA) ensemble strategy. The novel predictor (DBP-GAPred) acquired 1.89%, 0.28%, and 6.63% higher accuracies on jackknife, 10-fold, and independent dataset tests, respectively than the best predictor. These outcomes confirm the superiority of our method over the existing predictors.

scholarly journals Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers

Archaea ◽  
2006 ◽  
Vol 2 (2) ◽  
pp. 83-93 ◽  
Author(s):  
Céline Brochier-Armanet ◽  
Patrick Forterre
Keyword(s):  
Ribosomal Proteins ◽  
Thermophilic Bacteria ◽  
Thermus Thermophilus ◽  
Optimal Growth ◽  
Selective Advantage ◽  
Hyperthermophilic Archaea ◽  
Reverse Gyrase ◽  
Depth Analysis ◽  
History Of ◽  
Evolutionary Step

Reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT) to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. Here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. We found genes coding for reverse gyrase in the genomes of several thermophilic bacteria that belong to phyla other than Aquificales and Thermotogales. Several of these bacteria are not, strictly speaking, hyperthermophiles because their reported optimal growth temperatures are below 80 °C. Furthermore, we detected a reverse gyrase gene in the sequence of the large plasmid ofThermus thermophilusstrain HB8, suggesting a possible mechanism of transfer to theT. thermophilusstrain HB8 involving plasmids and transposases. The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. Although poorly resolved, the complete reverse gyrase phylogeny suggests an ancient acquisition of the gene by bacteria via one or two LGT events, followed by its secondary distribution by LGT within bacteria. Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co-transferred with the reverse gyrase gene. Our new analysis of the reverse gyrase history strengthens the hypothesis that the acquisition of reverse gyrase may have been a crucial evolutionary step in the adaptation of bacteria to high-temperature environments. However, it also questions the role of this enzyme in thermophilic bacteria and the selective advantage its presence could provide.

scholarly journals Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Hiromi Nishida ◽  
Reina Abe ◽  
Taishi Nagayama ◽  
Kentaro Yano
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Common Ancestor ◽  
Deinococcus Radiodurans ◽  
Thermophilic Bacteria ◽  
Thermus Thermophilus ◽  
Genomic Signatures ◽  
Genome Signature ◽  
Gc Contents

The extremely radioresistant bacteria of the genus Deinococcus and the extremely thermophilic bacteria of the genus Thermus belong to a common taxonomic group. Considering the distinct living environments of Deinococcus and Thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. Their guanine-cytosine (GC) contents are similar; however, we hypothesized that their genomic signatures would be different. Our findings indicated that the genomes of Deinococcus radiodurans and Thermus thermophilus have different tetranucleotide frequencies. This analysis showed that the genome signature of D. radiodurans is most similar to that of Pseudomonas aeruginosa, whereas the genome signature of T. thermophilus is most similar to that of Thermanaerovibrio acidaminovorans. This difference in genome signatures may be related to the different evolutionary backgrounds of the 2 genera after their divergence from a common ancestor.

Deltahedral views of fullerene polymorphism

1993 ◽  
Vol 343 (1667) ◽  
pp. 133-144 ◽  
Keyword(s):  
Virus Particles ◽  
Lattice Symmetry ◽  
Surface Lattice ◽  
Lower Symmetry ◽  
Icosahedral Virus ◽  
Buckminster Fuller ◽  
Icosahedral Viruses ◽  
Underlying Geometry ◽  
Triangulation Number ◽  
Geodesic Dome

Fullerenes and icosahedral virus particles share the underlying geometry applied by Buckminster Fuller in his geodesic dome designs. The basic plan involves the construction of polyhedra from 12 pentagons together with some number of hexagons, or the symmetrically equivalent construction of triangular faceted surface lattices (deltahedra) with 12 five-fold vertices and some number of six-fold vertices. All the possible designs for icosahedral viruses built according to this plan were enumerated according to the triangulation number T = ( h 2 + hk + k 2 of icosadelta-hedra formed by folding equilateral triangular nets with lattice vectors of indices h, k connecting neighbouring five-fold vertices. Lower symmetry deltahedra can be constructed in which the vectors connecting five-fold vertices are not all identical. Applying the pentagon isolation rule, the possible designs for fullerenes with more than 20 hexagonal facets can be defined by the set of vectors in the surface lattice net of the corresponding deltahedra. Surface lattice symmetry and geometrical relations among fullerene isomers can be displayed more directly in unfolded deltahedral nets than in projected views of the deltahedra or their hexagonally and pentagonally facted dual polyhedra.

scholarly journals Supramolecular Architecture of Severe Acute Respiratory Syndrome Coronavirus Revealed by Electron Cryomicroscopy

2006 ◽  
Vol 80 (16) ◽  
pp. 7918-7928 ◽  
Author(s):  
Benjamin W. Neuman ◽  
Brian D. Adair ◽  
Craig Yoshioka ◽  
Joel D. Quispe ◽  
Gretchen Orca ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Particle Image ◽  
Structural Proteins ◽  
Supramolecular Architecture ◽  
Oligomeric State ◽  
Electron Cryomicroscopy ◽  
Detailed Model ◽  
Viral Membrane ◽  
Assembly Pathway ◽  
Lattice Formation

ABSTRACT Coronavirus particles are enveloped and pleomorphic and are thus refractory to crystallization and symmetry-assisted reconstruction. A novel methodology of single-particle image analysis was applied to selected virus features to obtain a detailed model of the oligomeric state and spatial relationships among viral structural proteins. Two-dimensional images of the S, M, and N structural proteins of severe acute respiratory syndrome coronavirus and two other coronaviruses were refined to a resolution of ∼4 nm. Proteins near the viral membrane were arranged in overlapping lattices surrounding a disordered core. Trimeric glycoprotein spikes were in register with four underlying ribonucleoprotein densities. However, the spikes were dispensable for ribonucleoprotein lattice formation. The ribonucleoprotein particles displayed coiled shapes when released from the viral membrane. Our results contribute to the understanding of the assembly pathway used by coronaviruses and other pleomorphic viruses and provide the first detailed view of coronavirus ultrastructure.

scholarly journals Penetration of Membrane-Containing Double-Stranded-DNA Bacteriophage PM2 into Pseudoalteromonas Hosts

2004 ◽  
Vol 186 (16) ◽  
pp. 5342-5354 ◽  
Author(s):  
Hanna M. Kivelä ◽  
Rimantas Daugelavičius ◽  
Riina H. Hankkio ◽  
Jaana K. H. Bamford ◽  
Dennis H. Bamford
Keyword(s):  
Lipid Membrane ◽  
Cell Envelope ◽  
Integral Membrane Protein ◽  
Infection Process ◽  
Cell Surface Receptor ◽  
Viral Membrane ◽  
Bacteriophage Prd1 ◽  
Double Stranded Dna ◽  
Surface Receptor ◽  
A Cell

ABSTRACT The icosahedral bacteriophage PM2 has a circular double-stranded DNA (dsDNA) genome and an internal lipid membrane. It is the only representative of the Corticoviridae family. How the circular supercoiled genome residing inside the viral membrane is translocated into the gram-negative marine Pseudoalteromonas host has been an intriguing question. Here we demonstrate that after binding of the virus to an abundant cell surface receptor, the protein coat is most probably dissociated. During the infection process, the host cell outer membrane becomes transiently permeable to lipophilic gramicidin D molecules proposing fusion with the viral membrane. One of the components of the internal viral lipid core particle is the integral membrane protein P7, with muralytic activity that apparently aids the process of peptidoglycan penetration. Entry of the virion also causes a limited depolarization of the cytoplasmic membrane. These phenomena differ considerably from those observed in the entry process of bacteriophage PRD1, a dsDNA virus, which uses its internal membrane to make a cell envelope-penetrating tubular structure.

scholarly journals LLOVIU VIRUS - A NOVEL FILOVIRUS, ENDEMIC IN EUROPE

2018 ◽  
Vol 63 (2) ◽  
pp. 58-61
Author(s):  
T. E. Sizikova ◽  
V. N. Lebedev ◽  
N. V. Karulina ◽  
S. V. Borisevich
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Biological Properties ◽  
Human Cells ◽  
Structural Proteins ◽  
The Novel ◽  
Virus Family ◽  
Vesicular Stomatitis ◽  
Novel Agent ◽  
Recombinant Vectors

The data on a recently revealed novel filovirus (Lloviu virus, family Filoviridae, genera Cuevavirus) in Europe are viewed in this issue. The molecular-biological properties of genome fragments of Lloviu virus were isolated from perished bats (Miniopterus sсhreibersii). Because infectious Lloviu virus has not been isolated yet, the capacity of virus to infect cells of different species and its potential to cause disease in humans is unclear. The recombinant vectors (vesicular stomatitis virus and plasmids) expressing structural proteins of Lloviu virus were used to study different elements of the virus. The question of interaction of structural proteins of Lloviu virus expressed by recombinant vectors with receptors of bat and human cells is considered. The possibility of pathogenicity of the novel agent for humans is considered. The conclusion is made about the necessity of continuous epidemical and epizootical monitoring of the new filovirus infection.

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