Evolution of giant pandoravirus revealed by CRISPR/Cas9

A Star-Structured Polymer Electrolyte for Low-Temperature Solid-State Lithium Batteries

Solid-state polymer lithium metal batteries (SSLMBs) have attracted considerable attention because of their excellent safety and high energy density. However, the application of SSLMBs is significantly impeded by uneven Li deposition at the interface between solid-state electrolytes and lithium metal anode, especially at a low temperature. Herein, this issue is addressed by designing an agarose-based solid polymer electrolyte containing branched structure. The star-structured polymer is synthesized by grafting poly (ethylene glycol) monomethyl-ether methacrylate and lithium 2-acrylamido-2-methylpropanesulfonate onto tannic acid. The star structure regulates Li-ion flux in the bulk of the electrolyte and at the electrolyte/electrode interfaces. This unique omnidirectional Li-ion transportation effectively improves ionic conductivity, facilitates a uniform Li-ion flux, inhibits Li dendrite growth, and alleviates polarization. As a result, a solid-state LiFePO4||Li battery with the electrolyte exhibits outstanding cyclability with a specific capacity of 134 mAh g-1 at 0.5C after 800 cycles. The battery shows a high discharge capacity of 145 mAh g-1 at 0.1 C after 200 cycles, even at 0 °C. The study offers a promising strategy to address the uneven Li deposition at the solid-state electrolyte/electrode interface, which has potential applications in long-life solid-state lithium metal batteries at a low temperature.

Functional redundancy revealed by the deletion of the mimivirus GMC-oxidoreductase genes

The mimivirus 1.2 Mb genome was shown to be organized into a nucleocapsid-like genomic fiber encased in the nucleoid compartment inside the icosahedral capsid. The genomic fiber protein shell is composed of a mixture of two GMC-oxidoreductase paralogs, one of them being the main component of the glycosylated layer of fibrils at the surface of the virion. In this study, we determined the effect of the deletion of each of the corresponding genes on the genomic fiber and the layer of surface fibrils. First, we deleted the GMC-oxidoreductase, the most abundant in the genomic fiber, and determined its structure and composition in the mutant. As expected, it was composed of the second GMC-oxidoreductase and contained 5- and 6-start helices similar to the wild-type fiber. This result led us to propose a model explaining their coexistence. Then we deleted the GMC-oxidoreductase, the most abundant in the layer of fibrils, to analyze its protein composition in the mutant. Second, we showed that the fitness of single mutants and the double mutant were not decreased compared with the wild-type viruses under laboratory conditions. Third, we determined that deleting the GMC-oxidoreductase genes did not impact the glycosylation or the glycan composition of the layer of surface fibrils, despite modifying their protein composition. Because the glycosylation machinery and glycan composition of members of different clades are different, we expanded the analysis of the protein composition of the layer of fibrils to members of the B and C clades and showed that it was different among the three clades and even among isolates within the same clade. Taken together, the results obtained on two distinct central processes (genome packaging and virion coating) illustrate an unexpected functional redundancy in members of the family Mimiviridae, suggesting this may be the major evolutionary force behind their giant genomes.

The consequences of viral infection on protists

Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.

Genetic manipulation of giant viruses and their host, Acanthamoeba castellanii

Giant viruses (GVs) provide an unprecedented source of genetic innovation in the viral world and are thus, besides their importance in basic and environmental virology, in the spotlight for bioengineering advances. Their host, Acanthamoeba castellanii, is an accidental human pathogen that acts as a natural host and environmental reservoir of other human pathogens. Tools for genetic manipulation of viruses and host were lacking. Here, we provide a detailed method for genetic manipulation of A. castellanii and the GVs it plays host to by using CRISPR-Cas9 or homologous recombination. We detail the steps of vector preparation (4 d), transfection of amoeba cells (1 h), infection (1 h), selection (5 d for viruses, 2 weeks for amoebas) and cloning of recombinant viruses (4 d) or amoebas (2 weeks). This procedure takes ~3 weeks or 1 month for the generation of recombinant viruses or amoebas, respectively. This methodology allows the generation of stable gene modifications, which was not possible by using RNA silencing, the only previously available reverse genetic tool. We also include detailed sample-preparation steps for protein localization by immunofluorescence (4 h), western blotting (4 h), quantification of viral particles by optical density (15 min), calculation of viral lethal dose 50 (7 d) and quantification of DNA replication by quantitative PCR (4 h) to allow efficient broad phenotyping of recombinant organisms. This methodology allows the function of thousands of ORFan genes present in GVs, as well as the complex pathogen-host, pathogen-pathogen or pathogen-symbiont interactions in A. castellanii, to be studied in vivo.

Gene duplication as a major force driving the genome expansion in some giant viruses

IMPORTANCE

Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes.

Giant variations in giant virus genome packaging

Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid protein and the packaging ATPase (pATPase) comprise a highly conserved morphogenesis module in giant viruses, yet some giant viruses dispense with an icosahedral capsid, and others encode multiple versions of pATPases, including conjoined ATPase doublets, or encode none. Some giant viruses have acquired DNA-condensing proteins to compact their genomes, including sheath-like structures encasing folded DNA or densely packed viral nucleosomes that show a resemblance to eukaryotic nucleosomes at the telomeres. Here, we review what is known and unknown about these ATPases and condensing proteins, and place these variations in the context of viral lifecycles.

Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses

Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.

Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses

The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.

Using AlphaFold Predictions in Viral Research

Elucidation of the tertiary structure of proteins is an important task for biological and medical studies. AlphaFold, a modern deep-learning algorithm, enables the prediction of protein structure to a high level of accuracy. It has been applied in numerous studies in various areas of biology and medicine. Viruses are biological entities infecting eukaryotic and procaryotic organisms. They can pose a danger for humans and economically significant animals and plants, but they can also be useful for biological control, suppressing populations of pests and pathogens. AlphaFold can be used for studies of molecular mechanisms of viral infection to facilitate several activities, including drug design. Computational prediction and analysis of the structure of bacteriophage receptor-binding proteins can contribute to more efficient phage therapy. In addition, AlphaFold predictions can be used for the discovery of enzymes of bacteriophage origin that are able to degrade the cell wall of bacterial pathogens. The use of AlphaFold can assist fundamental viral research, including evolutionary studies. The ongoing development and improvement of AlphaFold can ensure that its contribution to the study of viral proteins will be significant in the future.