Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome

Wang, Fengbin; Cvirkaitė-Krupovič, Virginija; Vos, Matthijn; Beltrán, Leticia C.; Li, Jun; Krupovìč, Mart

doi:10.1016/j.bpj.2021.11.1983

Cited by 5 publications

(6 citation statements)

References 67 publications

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“…The difference in helical symmetries results in very small differences in intermolecular interfaces, much like what is observed for pED208 and pKpQIL, which have C5 and C1 symmetries, respectively 47 . This is similar to the quasi-equivalence phenomenon reported in other helical tubes made of helix-turn-helix subunits, such as in archaeal virus SMV1 60 , where very similar interfaces can be preserved even Article https://doi.org/10.1038/s41467-023-36349-8 though there are large apparent changes in symmetry (between C7 and C1 in SMV1).…”

Section: Different Helical Symmetries Still Allow Quasi-equivalent In...supporting

confidence: 83%

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

et al. 2023

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Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been ‘domesticated’, that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

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Section: Different Helical Symmetries Still Allow Quasi-equivalent In...supporting

confidence: 83%

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

et al. 2023

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“…In principle, a massive data set might be collected to obtain a few relatively homogeneous subsets, as was previously done for a spindle-shaped viral tube. 58 Nevertheless, the C8S3-Br width histogram in Figure 5d shows an interesting feature with discrete steps rather than a continuous distribution that could be related to the nanoscale packing. A Fourier transform of the C8S3-Br histogram is shown in the inset of Figure 5d with peaks at 2.70 Å and 5.39 Å, corresponding to the step size for the discretized widths.…”

Section: Impact Of Chemical Modifications On the Self-assemblymentioning

confidence: 93%

Near-Atomic Resolution Structure of J-aggregated Helical Light Harvesting Nanotubes

Deshmukh

Zheng

Chuang

et al. 2022

Preprint

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Function-oriented design of supramolecular self-assemblies represents a foundational goal in chemistry. Especially, chromophore self-assemblies display extreme photophysical changes from their monomers that are sensitive to the nanoscale molecular arrangements. Slip-stacked arrangements in J-aggregates lead to red shifts (>200 nm) and enhanced quantum yields. Actively introducing specific molecular arrangements using supramolecular chemistry provides a platform to tune the excitonic couplings and avail exotic photophysical properties. However, the nanoscale molecular arrangements have not yet been directly observed in these solution-state assemblies. Here, we present a high-resolution structure of the prototypical biomimetic light harvesting nanotubes (LHNs) of an amphiphilic cyanine dye (C8S3-Cl). We achieve a 3.3 Å resolution with helical reconstruction of cryo-EM images, directly visualizing the atomic scale parameters and packing arrangements that control the excitonic properties. Our structure clearly shows a brick layer arrangement of the molecules as opposed to the previously thought herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif – interlocking sulfonates, that may be responsible for the slip-stacked packing and ultimately the J-aggregate nature of LHNs. This motif may be relevant towards other amphiphilic self-assemblies, in general and provides a new chemical handle on predictable self-assemblies.

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“…Both rod-shaped and oval-shaped WSSV capsids are composed of stacked rings, which are distinct from the helical assemblies of many filamentous or spindle-shaped viruses ( 35 – 37 , 39 , 45 ). The base, the body, and the head have their own peculiar structural features.…”

Section: Discussionmentioning

confidence: 99%

Ring-stacked capsids of white spot syndrome virus and structural transitions with genome ejection

et al. 2023

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White spot syndrome virus (WSSV) is one of the largest DNA viruses and the major pathogen responsible for white spot syndrome in crustaceans. The WSSV capsid is critical for genome encapsulation and ejection and exhibits the rod-shaped and oval-shaped structures during the viral life cycle. However, the detailed architecture of the capsid and the structural transition mechanism remain unclear. Here, using cryo–electron microscopy (cryo-EM), we obtained a cryo-EM model of the rod-shaped WSSV capsid and were able to characterize its ring-stacked assembly mechanism. Furthermore, we identified an oval-shaped WSSV capsid from intact WSSV virions and analyzed the structural transition mechanism from the oval-shaped to rod-shaped capsids induced by high salinity. These transitions, which decrease internal capsid pressure, always accompany DNA release and mostly eliminate the infection of the host cells. Our results demonstrate an unusual assembly mechanism of the WSSV capsid and offer structural insights into the pressure-driven genome release.

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Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome

Cited by 5 publications

References 67 publications

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Near-Atomic Resolution Structure of J-aggregated Helical Light Harvesting Nanotubes

Ring-stacked capsids of white spot syndrome virus and structural transitions with genome ejection

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