National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35GM122510
United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments. Authors: Fengbin Wang / Diana P Baquero / Leticia C Beltran / Zhangli Su / Tomasz Osinski / Weili Zheng / David Prangishvili / Mart Krupovic / Edward H Egelman / Abstract: Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) ...Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
7: DNA (301-MER) 8: DNA (301-MER) A: Structural protein B: Structural protein C: Structural protein D: Structural protein E: Structural protein F: Structural protein G: Structural protein H: Structural protein I: Structural protein J: Structural protein K: Structural protein L: Structural protein M: Structural protein N: Structural protein O: Structural protein P: Structural protein Q: Structural protein R: Structural protein S: Structural protein T: Structural protein U: Structural protein V: Structural protein W: Structural protein a: Structural protein b: Structural protein c: Structural protein d: Structural protein e: Structural protein f: Structural protein g: Structural protein h: Structural protein i: Structural protein j: Structural protein k: Structural protein l: Structural protein m: Structural protein n: Structural protein o: Structural protein p: Structural protein q: Structural protein r: Structural protein s: Structural protein t: Structural protein u: Structural protein v: Structural protein w: Structural protein
Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
Type
Name
Symmetry operation
Number
identity operation
1_555
1
Buried area
370700 Å2
ΔGint
-2578 kcal/mol
Surface area
185600 Å2
-
Components
#1: DNA chain
DNA (301-MER)
Mass: 92878.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unclassified Rudivirus Plasmid details: It is rod-like virus purified from a S. solfataricus strain
#2: DNA chain
DNA (301-MER)
Mass: 92869.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unclassified Rudivirus
#3: Protein
... Structuralprotein
Mass: 14207.113 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Source: (natural) unclassified Rudivirus
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Experimental details
-
Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction
-
Sample preparation
Component
Name: S. solfataricus rod-shaped virus, SSRV1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)
Organism: unclassified Rudivirus
Details of virus
Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural host
Organism: Saccharolobus solfataricus
Buffer solution
pH: 6
Specimen
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support
Details: unspecified
Vitrification
Cryogen name: ETHANE
-
Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELD
Image recording
Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
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