Review
Microbiology
Ellen Goncalves de Oliveira, Joao Victor Rodrigues Pessoa Carvalho, Bruna Barbosa Botelho, Clecio Alonso da Costa Filho, Lethicia Ribeiro Henriques, Bruna Luiza de Azevedo, Rodrigo Araujo Lima Rodrigues
Summary: This review presents the peculiarities of giant viruses that infect protists and discusses why they should be considered an outstanding source of new enzymes. By revisiting the genomes and studying the enzymatic machinery of different groups of giant viruses, this review highlights several genes involved in carbohydrate metabolism, DNA replication, and RNA processing that can be explored in biotechnology. Additionally, structural biology evidence using chitinase as a model reinforces the importance of giant viruses as a source of novel enzymes for biotechnological applications.
Article
Virology
Romain Blanc-Mathieu, Hakon Dahle, Antje Hofgaard, David Brandt, Hiroki Ban, Joern Kalinowski, Hiroyuki Ogata, Ruth-Anne Sandaa
Summary: Recent studies challenging the traditional view of viruses as entities with limited metabolic capabilities have identified metabolic genes in viruses with large genomes, such as Prymnesium kappa virus RF01 (PkV RF01). This virus encodes numerous proteins involved in energy metabolism and exhibits unique phenotypic features compared to other viruses in the Mimiviridae family. The presence of these metabolic genes suggests that viruses may actively regulate host energy metabolism and have complex evolutionary histories.
JOURNAL OF VIROLOGY
(2021)
Article
Virology
Yijian Sheng, Zhenqi Wu, Shengzhong Xu, Yongjie Wang
Summary: In this study, a novel tripartite interaction system consisting of micro-green alga (Chlorella sp.), Mimiviridae large green alga virus, and virophage was successfully discovered and identified at the coculture level, with Chlorella sp. as the eukaryotic host. The large green alga virus CV-XW01 is closely related to the Mimiviridae giant virus Cafeteria roenbergensis virus, host virus of the virophage Mavirus, as well as a novel large virus of Mimiviridae that infects a non-protozoan protist host. The virophage CVv-SW01 highly resembles Mavirus in its codon usage frequency and preference, although they are phylogenetically distantly related. These findings provide novel insights into the diversity of large/giant viruses and their virophages.
JOURNAL OF VIROLOGY
(2022)
Article
Limnology
Kyle Michael James Mayers, Janice Lawrence, Katrine Sandnes Skaar, Joachim Paul Topper, Elzbieta Petelenz, Marius Rydningen Saltvedt, Ruth-Anne Sandaa, Aud Larsen, Gunnar Bratbak, Jessica Louise Ray
Summary: Experimental studies show that the appendicularian Oikopleura dioica can efficiently remove viruses from natural virus assemblages, while maintaining viral infectivity in fecal pellets. This interaction has broader implications for the marine virus community, raising questions about virus redistribution and impacts on host dynamics.
LIMNOLOGY AND OCEANOGRAPHY
(2021)
Article
Microbiology
Hiroyuki Hikida, Yusuke Okazaki, Ruixuan Zhang, Thi Tuyen Nguyen, Hiroyuki Ogata
Summary: By re-sequencing a prototype marseillevirus, we evaluated the accuracy of MinION-only genome assemblies for giant viruses. The results showed that MinION provides highly accurate genome assemblies for giant viruses. We also discovered several new species of marseillevirus, pithovirus, and mimivirus using MinION sequencing.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Virology
Haruna Takahashi, Sho Fukaya, Chihong Song, Kazuyoshi Murata, Masaharu Takemura
Summary: A new giant virus, Cotonvirus japonicus, belonging to the Mimiviridae family has been identified, showing unique features compared to other viruses in the Megavirinae subfamily. This discovery sheds light on the diversity of icosahedral mimiviruses and their mechanisms of formation.
JOURNAL OF VIROLOGY
(2021)
Article
Biology
Ruth-Anne Sandaa, Marius R. Saltvedt, Hakon Dahle, Haina Wang, Selina Vage, Romain Blanc-Mathieu, Ida H. Steen, Nigel Grimsley, Bente Edvardsen, Hiroyuki Ogata, Janice Lawrence
Summary: Haptophytes are an important part of the marine phytoplankton community, acting as both primary producers and mixotrophs that graze on bacteria and protists. Viruses play a significant role in influencing the ecology and diversity of phytoplankton, with most interactions described as 'boom and bust'. However, haptophytes are often part of diverse communities with low densities, decreasing their susceptibility to highly specific viruses.
BIOLOGICAL REVIEWS
(2022)
Article
Virology
Briallen Lobb, Anson Shapter, Andrew C. Doxey, Jozef I. Nissimov
Summary: A study found that 30% of the genes in the Coccolithovirus genome are shared by all 14 strains, and core genes are more likely to be similar to host proteins and involved in critical functions, providing a solid foundation for functional predictions of this genome.
Article
Microbiology
Sheng Kao, Chi-Fei Kao, Wen Chang, Chuan Ku
Summary: This study reveals the existence of EFC protein homologs in giant viruses other than poxviruses and speculates that these EFC proteins are present in different subfamilies and phyla of the Nucleocytoviricota. The presence of these EFC protein families suggests a mechanism for virus entry.
MICROBIOLOGY SPECTRUM
(2023)
Review
Biochemical Research Methods
Fangchen Liu, Andrea Giometto, Mingming Wu
Summary: Aquatic microbial communities play a fundamental role in biogeochemical transformations in natural ecosystems, with their composition and function tightly controlled by environmental factors. Microfluidic platforms provide a unique opportunity for quantitative studies and theoretical modeling of microbial communities, which can be applied beyond aquatic ecosystems.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Remote Sensing
Majid Nazeer, Mohammad M. M. Alsahli, Janet Elizabeth Nichol, Jiayi Pan, Weicheng Wu, Muhammad Bilal, Urooj Saeed
Summary: The overgrowth of algae in aquatic ecosystems is a serious threat, and it has been increasing due to human activities. To protect and sustain these ecosystems, it is crucial to understand how the aquatic environment promotes algae growth through comprehensive monitoring. We propose a novel Three band Macroalgae Index (TMI) using Landsat-8 Operational Land Imager (OLI) to detect and monitor algae overgrowth in aquatic ecosystems.
INTERNATIONAL JOURNAL OF REMOTE SENSING
(2023)
Article
Multidisciplinary Sciences
Qianqian Shao, Irina Agarkova, Eric A. Noel, David D. Dunigan, Yunshu Liu, Aohan Wang, Mingcheng Guo, Linlin Xie, Xinyue Zhao, Michael G. Rossmann, James L. Van Etten, Thomas Klose, Qianglin Fang
Summary: This study presents a near-atomic resolution analysis of the capsid of a giant virus, revealing multiple protein variants that do not follow overall symmetry and providing insights into the assembly mechanism of giant virus capsids.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Mahasweta Saha, Patrick Fink
Summary: This review discusses the ecological roles of volatile compounds from freshwater and marine microalgae and macroalgae. The functions of these compounds range from intraspecific communication to defence against competitors and predators. Despite current understanding, there are still knowledge gaps and emerging questions in algal volatile research.
BIOLOGICAL REVIEWS
(2022)
Article
Environmental Sciences
Jing Pu, Kaishan Song, Yunfeng Lv, Ge Liu, Chong Fang, Junbin Hou, Zhidan Wen
Summary: This study developed a method to effectively extract algal blooms and aquatic vegetation from turbid water bodies using high spatial resolution Sentinel 2 images. By combining the extraction results from multiple indices and utilizing image time series information, the study successfully distinguished algal blooms and aquatic vegetation in five typical lakes in China and mapped their spatial distributions.
Article
Microbiology
Julien Andreani, Frederik Schulz, Fabrizio Di Pinto, Anthony Levasseur, Tanja Woyke, Bernard La Scola
Summary: The discovery of a novel giant virus called Fadolivirus, with a genome size of over 1.5Mb encoding a large number of proteins and translation system genes, provides insights into the biology of the Klosneuvirinae viral subfamily.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Arshan Nasir, Ethan Romero-Severson, Jean-Michel Claverie
TRENDS IN MICROBIOLOGY
(2020)
Letter
Medicine, General & Internal
Jacques van Helden, Colin D. Butler, Guillaume Achaz, Bruno Canard, Didier Casane, Jean-Michel Claverie, Fabien Colombo, Virginie Courtier, Richard H. Ebright, Francois Graner, Milton Leitenberg, Serge Morand, Nikolai Petrovsky, Rossana Segreto, Etienne Decroly, Jose Halloy
Editorial Material
Virology
Etienne Decroly, Jean-Michel Claverie, Bruno Canard
Editorial Material
Virology
Etienne Decroly, Jean-Michel Claverie, Bruno Canard
Review
Microbiology
Frederik Schulz, Chantal Abergel, Tanja Woyke
Summary: The discovery of giant viruses with similar characteristics as bacteria and cellular organisms has been a significant breakthrough in biology. Previously, our knowledge of giant viruses was limited to a small number of species-level isolates obtained through laboratory-based co-cultivation. However, advances in sequencing technologies and bioinformatics have expanded our understanding of giant viruses, their diversity, and their impact on global nutrient cycles.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Biology
Alejandro Villalta, Alain Schmitt, Leandro F. Estrozi, Emmanuelle R. J. Quemin, Jean-Marie Alempic, Audrey Lartigue, Vojtech Prazak, Lucid Belmudes, Daven Vasishtanm, Agathe M. G. Colmant, Flora A. Honore, Yohann Coute, Kay Grunewald, Chantal Abergel
Summary: Mimivirus, the prototype of Mimiviridae family of giant dsDNA viruses, has a unique organizational structure with a protein shell composed of two GMC-type oxidoreductases. The genome is arranged in left-handed super-helices with a central channel for transcription. This supramolecular organization is an efficient evolutionary strategy for packaging and protecting the genome.
Article
Multidisciplinary Sciences
Sofia Rigou, Sebastien Santini, Chantal Abergel, Jean-Michel Claverie, Matthieu Legendre
Summary: This study reveals the abundance and diversity of giant viruses in soil through permafrost metagenomics, showing a unique diversity pattern and a high proportion of sequence coverage. Additionally, gene transfers between different viral families were also discovered.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Alejandro Villalta, Batoul Srour, Audrey Lartigue, Martin Clemancey, Deborah Byrne, Florence Chaspoul, Antoine Loquet, Bruno Guigliarelli, Genevieve Blondin, Chantal Abergel, Benedicte Burlat
Summary: Scientists have discovered a protein in the giant virus mimivirus that is rich in the amino acids glycine and cysteine. This protein, called GciS, is one of the most abundant proteins in the viral particles and is likely essential for infection. It has unique binding properties with iron and inorganic sulfide.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Hugo Bisio, Matthieu Legendre, Claire Giry, Nadege Philippe, Jean-Marie Alempic, Sandra Jeudy, Chantal Abergel
Summary: In this study, the researchers used CRISPR/Cas9 technology to genetically modify amoebal giant viruses, and found evidence suggesting that their giant size evolved gradually, possibly as an adaptation to uncertain environments.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Sebastien Santini, Quentin Schenkelaars, Cyril Jourda, Marc Duchesne, Hassiba Belahbib, Caroline Rocher, Marjorie Selva, Ana Riesgo, Michel Vervoort, Sally P. Leys, Laurent Kodjabachian, Andre Le Bivic, Carole Borchiellini, Jean-Michel Claverie, Emmanuelle Renard
Summary: This study analyzed the genome of the glass sponge Oopsacas minuta and found that its genome is small and lacks several key genes for metazoan development. The study also provided the complete genome of a new archaea species in the sponge's symbiotic microbial community.
Article
Virology
Jean-Marie Alempic, Audrey Lartigue, Artemiy E. E. Goncharov, Guido Grosse, Jens Strauss, Alexey N. N. Tikhonov, Alexander N. N. Fedorov, Olivier Poirot, Matthieu Legendre, Sebastien Santini, Chantal Abergel, Jean-Michel Claverie
Summary: A quarter of the Northern hemisphere is covered by permafrost, releasing organic matter and reviving ancient viruses and microbial cells as it thaws due to climate warming, contributing to greenhouse gas emissions. While previous studies mainly focused on bacteria in permafrost, this study reports the preliminary characterization of 13 new viruses isolated from ancient Siberian permafrost samples, suggesting that zombie viruses are not as rare as previously believed. This highlights the potential public health threat of these revived viruses.
Editorial Material
Microbiology
Arshan Nasir, Gustavo Caetano-Anolles, Jean-Michel Claverie
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Gustavo Caetano-Anolles, Jean-Michel Claverie, Arshan Nasir
Summary: Taxonomy, driven by knowledge gaps, technical limitations, and a priorism, has become a battleground. This article assesses the current state of viral classification, highlighting common fallacies. Viruses, as contributors to the genomic makeup of organismal communities, challenge the concept of taxonomic units. They should instead be viewed as processes integrating virions and hosts. Phylogenetic networks and structural phylogenomic analysis can help overcome this impasse and reevaluate the validity of taxonomic units and principles.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sofia Rigou, Alain Schmitt, Jean-Marie Alempic, Audrey Lartigue, Peter Vendloczki, Chantal Abergel, Jean-Michel Claverie, Matthieu Legendre
Summary: This study reports the isolation and genome sequencing of two Pithoviridae viruses from soil samples, as well as three other recent isolates. A comparative genomic study of the Pithoviridae family using twelve available genome sequences reveals a nonuniform genome organization, with core genes concentrated in one region and gene duplications in another. The study also shows that Pithoviridae genomes are more conservative than other families of giant viruses, with a low proportion of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates and massive invasion by inverted repeats.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Nadege Philippe, Avi Shukla, Chantal Abergel, Hugo Bisio
Summary: This article provides a detailed method for genetic manipulation of Acanthamoeba castellanii and the giant viruses it hosts using CRISPR-Cas9 or homologous recombination. It allows the study of gene function in giant viruses and the interactions between pathogens and the host organism A.castellanii.