scholarly journals The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

2017 ◽  
Author(s):  
Christoph M. Deeg ◽  
Cheryl-Emiliane T. Chow ◽  
Curtis A. Suttle
Keyword(s):  
Aquatic Ecosystems ◽  
Homing Endonuclease ◽  
Rapid Evolution ◽  
Host Factors ◽  
Metagenomic Data ◽  
Genomic Plasticity ◽  
Translational Machinery ◽  
Independent Replication ◽  
Giant Viruses ◽  
Self Splicing

AbstractGiant viruses are ecologically important players in aquatic ecosystems that have challenged concepts of what constitutes a virus. Herein, we present the giant Bodo saltans virus (BsV), the first characterized representative of the most abundant giant viruses in the oceans, and the first klosneuvirus isolate, a subgroup of theMimiviridaeproposed from metagenomic data. BsV infects an ecologically important microzooplankton, the kinetoplastidBodo saltans. Its 1.39 Mb genome is the largest described for theMimiviridaeand encodes 1227 predicted ORFs, including pathways for host-independent replication. Yet, much of its translational machinery has been lost, including all tRNAs. Essential genes are invaded by homing endonuclease-encoding self-splicing introns that may defend against competing viruses. Putative anti-host factors show extensive gene duplication via a genomic accordion indicating an ongoing evolutionary arms race and highlighting the rapid evolution and genomic plasticity that has led to genome gigantism and the enigma that is giant viruses.

scholarly journals The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Christoph M Deeg ◽  
Cheryl-Emiliane T Chow ◽  
Curtis A Suttle
Keyword(s):  
Aquatic Ecosystems ◽  
Homing Endonuclease ◽  
Rapid Evolution ◽  
Host Factors ◽  
Metagenomic Data ◽  
Replication Machinery ◽  
Genomic Plasticity ◽  
Giant Viruses ◽  
Translational Apparatus ◽  
Self Splicing

Giant viruses are ecologically important players in aquatic ecosystems that have challenged concepts of what constitutes a virus. Herein, we present the giant Bodo saltans virus (BsV), the first characterized representative of the most abundant group of giant viruses in ocean metagenomes, and the first isolate of a klosneuvirus, a subgroup of the Mimiviridae proposed from metagenomic data. BsV infects an ecologically important microzooplankton, the kinetoplastid Bodo saltans. Its 1.39 Mb genome encodes 1227 predicted ORFs, including a complex replication machinery. Yet, much of its translational apparatus has been lost, including all tRNAs. Essential genes are invaded by homing endonuclease-encoding self-splicing introns that may defend against competing viruses. Putative anti-host factors show extensive gene duplication via a genomic accordion indicating an ongoing evolutionary arms race and highlighting the rapid evolution and genomic plasticity that has led to genome gigantism and the enigma that is giant viruses.

scholarly journals Isolation of Yasminevirus, the First Member of Klosneuvirinae Isolated in Coculture with Vermamoeba vermiformis, Demonstrates an Extended Arsenal of Translational Apparatus Components

2019 ◽  
Vol 94 (1) ◽  
Author(s):  
Leena Hussein Bajrai ◽  
Saïd Mougari ◽  
Julien Andreani ◽  
Emeline Baptiste ◽  
Jeremy Delerce ◽  
...  
Keyword(s):  
Gc Content ◽  
Sewage Water ◽  
Giant Virus ◽  
Content Type ◽  
Translational Machinery ◽  
Trna Synthetases ◽  
Double Stranded Dna ◽  
Vermamoeba Vermiformis ◽  
Giant Viruses ◽  
Translational Apparatus

ABSTRACT The family of giant viruses is still expanding, and evidence of a translational machinery is emerging in the virosphere. The Klosneuvirinae group of giant viruses was first reconstructed from in silico studies, and then a unique member was isolated, Bodo saltans virus. Here we describe the isolation of a new member in this group using coculture with the free-living amoeba Vermamoeba vermiformis. This giant virus, called Yasminevirus, has a 2.1-Mb linear double-stranded DNA genome encoding 1,541 candidate proteins, with a GC content estimated at 40.2%. Yasminevirus possesses a nearly complete translational machinery, with a set of 70 tRNAs associated with 45 codons and recognizing 20 amino acids (aa), 20 aminoacyl-tRNA synthetases (aaRSs) recognizing 20 aa, as well as several translation factors and elongation factors. At the genome scale, evolutionary analyses placed this virus in the Klosneuvirinae group of giant viruses. Rhizome analysis demonstrated that the genome of Yasminevirus is mosaic, with ∼34% of genes having their closest homologues in other viruses, followed by ∼13.2% in Eukaryota, ∼7.2% in Bacteria, and less than 1% in Archaea. Among giant virus sequences, Yasminevirus shared 87% of viral hits with Klosneuvirinae. This description of Yasminevirus sheds light on the Klosneuvirinae group in a captivating quest to understand the evolution and diversity of giant viruses. IMPORTANCE Yasminevirus is an icosahedral double-stranded DNA virus isolated from sewage water by amoeba coculture. Here its structure and replicative cycle in the amoeba Vermamoeba vermiformis are described and genomic and evolutionary studies are reported. This virus belongs to the Klosneuvirinae group of giant viruses, representing the second isolated and cultivated giant virus in this group, and is the first isolated using a coculture procedure. Extended translational machinery pointed to Yasminevirus among the quasiautonomous giant viruses with the most complete translational apparatus of the known virosphere.

scholarly journals Bile Facilitates Human Norovirus Interactions with Diverse Histoblood Group Antigens, Compensating for Capsid Microvariation Observed in 2016–2017 GII.2 Strains

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 989
Author(s):  
Michael L. Mallory ◽  
Lisa C. Lindesmith ◽  
Paul D. Brewer-Jensen ◽  
Rachel L. Graham ◽  
Ralph S. Baric
Keyword(s):  
Mucosal Immunity ◽  
Bile Salts ◽  
Rapid Evolution ◽  
Blood Group Antigen ◽  
Host Factors ◽  
Viral Capsid ◽  
Human Populations ◽  
Human Norovirus ◽  
Sudden Rise ◽  
Limited Sequence

Human norovirus (HuNoV) is the leading cause of global infectious acute gastroenteritis, causing ~20% of reported diarrheal episodes. Typically, GII.4 strains cause 50–70% of yearly outbreaks, and pandemic waves of disease approximately every 2–7 years due to rapid evolution. Importantly, GII.4 dominance is occasionally challenged by the sudden emergence of other GII strains, most recently by GII.2 strains which peaked in 2016–2017, dramatically increasing from 1% to 20% of total HuNoV outbreaks. To determine if viral capsid evolution may account for the sudden rise in GII.2 outbreaks, Virus Like Particles (VLPs) of two 2016–2017 GII.2 strains were compared by antigenic and histo blood group antigen (HBGA) binding profiles to the prototypic 1976 GII.2 Snow Mountain Virus (SMV) strain. Despite >50 years of GII.2 strain persistence in human populations, limited sequence diversity and antigenic differences were identified between strains. However, capsid microvariation did affect HBGA binding patterns, with contemporary strains demonstrating decreased avidity for type A saliva. Furthermore, bile salts increased GII.2 VLP avidity for HBGAs, but did not alter antigenicity. These data indicate that large changes in antigenicity or receptor binding are unlikely to explain GII.2 emergence, in contrast to the pandemic GII.4 strains, and indicate that host factors such as waning or remodeling of serum or mucosal immunity likely contributed to the surge in GII.2 prevalence.

scholarly journals A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron

2007 ◽  
Vol 189 (14) ◽  
pp. 5293-5301 ◽  
Author(s):  
David Nord ◽  
Eduard Torrents ◽  
Britt-Marie Sjöberg
Keyword(s):  
Bacillus Anthracis ◽  
Homing Endonuclease ◽  
Insertion Site ◽  
Group I Intron ◽  
Coding Region ◽  
Recognition Sequence ◽  
Intron Insertion ◽  
Group I ◽  
Serovar Typhimurium ◽  
Self Splicing

ABSTRACT The essential Bacillus anthracis nrdE gene carries a self-splicing group I intron with a putative homing endonuclease belonging to the GIY-YIG family. Here, we show that the nrdE pre-mRNA is spliced and that the homing endonuclease cleaves an intronless nrdE gene 5 nucleotides (nt) upstream of the intron insertion site, producing 2-nt 3′ extensions. We also show that the sequence required for efficient cleavage spans at least 4 bp upstream and 31 bp downstream of the cleaved coding strand. The position of the recognition sequence in relation to the cleavage position is as expected for a GIY-YIG homing endonuclease. Interestingly, nrdE genes from several other Bacillaceae were also susceptible to cleavage, with those of Bacillus cereus, Staphylococcus epidermidis (nrdE1), B. anthracis, and Bacillus thuringiensis serovar konkukian being better substrates than those of Bacillus subtilis, Bacillus lichenformis, and S. epidermidis (nrdE2). On the other hand, nrdE genes from Lactococcus lactis, Escherichia coli, Salmonella enterica serovar Typhimurium, and Corynebacterium ammoniagenes were not cleaved. Intervening sequences (IVSs) residing in protein-coding genes are often found in enzymes involved in DNA metabolism, and the ribonucleotide reductase nrdE gene is a frequent target for self-splicing IVSs. A comparison of nrdE genes from seven gram-positive low-G+C bacteria, two bacteriophages, and Nocardia farcinica showed five different insertion sites for self-splicing IVSs within the coding region of the nrdE gene.

scholarly journals Impact of a homing intein on recombination frequency and organismal fitness

2016 ◽  
Vol 113 (32) ◽  
pp. E4654-E4661 ◽  
Author(s):  
Adit Naor ◽  
Neta Altman-Price ◽  
Shannon M. Soucy ◽  
Anna G. Green ◽  
Yulia Mitiagin ◽  
...  
Keyword(s):  
Homing Endonuclease ◽  
Insertion Site ◽  
Population Level ◽  
Laboratory Culture ◽  
Gene Encoding ◽  
Self Splicing ◽  
Fusion Ability ◽  
Organismal Fitness ◽  
Natural Cell

Inteins are parasitic genetic elements that excise themselves at the protein level by self-splicing, allowing the formation of functional, nondisrupted proteins. Many inteins contain a homing endonuclease (HEN) domain and rely on its activity for horizontal propagation. However, successful invasion of an entire population will make this activity redundant, and the HEN domain is expected to degenerate quickly under these conditions. Several theories have been proposed for the continued existence of the both active HEN and noninvaded alleles within a population. However, to date, these models were not directly tested experimentally. Using the natural cell fusion ability of the halophilic archaeon Haloferax volcanii we were able to examine this question in vivo, by mating polB intein-positive [insertion site c in the gene encoding DNA polymerase B (polB-c)] and intein-negative cells and examining the dispersal efficiency of this intein in a natural, polyploid population. Through competition between otherwise isogenic intein-positive and intein-negative strains we determined a surprisingly high fitness cost of over 7% for the polB-c intein. Our laboratory culture experiments and samples taken from Israel’s Mediterranean coastline show that the polB-c inteins do not efficiently take over an inteinless population through mating, even under ideal conditions. The presence of the HEN/intein promoted recombination when intein-positive and intein-negative cells were mated. Increased recombination due to HEN activity contributes not only to intein dissemination but also to variation at the population level because recombination tracts during repair extend substantially from the homing site.

scholarly journals SIBR-Cas enables host-independent and universal CRISPR genome engineering in bacteria

2021 ◽  
Author(s):  
Constantinos Patinios ◽  
Sjoerd Creutzburg ◽  
Adini Arifah ◽  
Belen Perez ◽  
Colin Ingham ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Genome Engineering ◽  
Control Mechanism ◽  
Host Factors ◽  
Mutant Library ◽  
Editing Event ◽  
Knock Out ◽  
Exogenous Expression ◽  
Self Splicing ◽  
Control Delays

CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) and/or exogenous expression of recombinases. In this study, we mitigated these constraints by developing a simple and universal genome engineering tool for bacteria which we termed SIBR-Cas (Self-splicing Intron-Based Riboswitch-Cas). SIBR-Cas was generated from a mutant library of the theophylline-dependent self-splicing T4 td intron that allows for universal and inducible control over CRISPR-Cas counterselection. This control delays CRISPR-Cas counterselection, granting more time for the editing event (e.g., by homologous recombination) to occur. Without the use of exogenous recombinases, SIBR-Cas was successfully applied to knock-out several genes in three bacteria with poor homologous recombination systems. Compared to other genome engineering tools, SIBR-Cas is simple, tightly regulated and widely applicable for most (non-model) bacteria. Furthermore, we propose that SIBR can have a wider application as a universal gene expression and gene regulation control mechanism for any gene or RNA of interest in bacteria.

scholarly journals Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Huaihai Chen ◽  
Kayan Ma ◽  
Yu Huang ◽  
Yuchun Yang ◽  
Zilong Ma ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Comprehensive Evaluation ◽  
Saline Water ◽  
Taxonomic Diversity ◽  
Functional Redundancy ◽  
Global Scale ◽  
Metagenomic Data ◽  
Functional Prediction ◽  
Functional Profiles ◽  
Global Water

A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Here, we examined 938 functionally and taxonomically annotated water metagenomes obtained worldwide to scrutinize the connection between function and taxonomy, and to identify the key driver of water metagenomes function or taxonomic composition at a global scale. We found that pairwise similarity of function was significantly associated with taxonomy, though taxonomy had higher global dissimilarity than function. Classification into six water biomes resulted in greater variation in taxonomic compositions than functional profiles, as the key regulating factor was salinity. Fresh water microbes harbored distinct functional and taxonomic structures from microbes in saline water biomes, despite that taxonomy was more susceptible to gradient of geography and climate than function. In summary, our results find a significant relationship between taxonomic diversity and microbial functioning in global water metagenomes, although microbial taxonomic compositions vary to a larger extent than functional profiles in aquatic ecosystems, suggesting the possibility and necessity for functional prediction of microorganisms based on taxonomy in global aquatic ecosystems.

scholarly journals Insights into genomic evolution from the chromosomal and mitochondrial genomes of Ustilaginoidea virens

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Kang Zhang ◽  
Zaixu Zhao ◽  
Ziding Zhang ◽  
Yuejiao Li ◽  
Shaojie Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Homing Endonuclease ◽  
Rapid Evolution ◽  
Sequence Divergence ◽  
Mitochondrial Genomes ◽  
Structural Variations ◽  
High Quality ◽  
Ustilaginoidea Virens ◽  
Gain Loss

AbstractUstilaginoidea virens, the causal agent of rice false smut, is an economically important filamentous fungal pathogen. A high-quality reference genome of U. virens promotes understanding of molecular mechanisms underlying its virulence and pathogenicity. Here, we report the first chromosome-level assembly of U. virens genome consisting of seven chromosomes ranging from 2.4 to 7.5 Mb. The assembly has dramatic improvements over previous assemblies, including considerably longer contigs, higher proportion of repetitive elements and more functionally annotated genes. Phylogenetic analyses revealed an extremely low intraspecific sequence divergence in U. virens. By contrast, intraspecific genome comparisons uncovered dynamic genomic alterations including massive structural variations and widespread lineage-specific regions (LSRs) among U. virens strains, which were mainly generated by recent burst of retrotransposons. Genomic plasticity created by structural variations and LSRs might drive rapid evolution of U. virens. High-quality mitochondrial genomes of eight U. virens strains exhibit size variations from 94 to 102 kb. Consistently, U. virens contains conserved lengths of exons and highly dynamic mobile introns, which contribute to intraspecific size variations due to gain/loss of homing endonuclease genes. This study highlights unique characteristics in nuclear and mitochondrial genomic divergence and provides new insights into genomic and mitochondrial evolution of U. virens.

scholarly journals Evolutionary selection of pestivirus variants with altered or no microRNA dependency

2020 ◽  
Vol 48 (10) ◽  
pp. 5555-5571
Author(s):  
Konstantinos G Kokkonos ◽  
Nicolas Fossat ◽  
Louise Nielsen ◽  
Christina Holm ◽  
Wytske M Hepkema ◽  
...  
Keyword(s):  
Host Factors ◽  
Translational Efficiency ◽  
Diarrhea Virus ◽  
Evolutionary Selection ◽  
Argonaute 2 ◽  
Selection Experiments ◽  
Independent Replication ◽  
Compensatory Mutations ◽  
Viral Diarrhea Virus ◽  
Selection Of

Abstract Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was also described for the related pestiviruses, which are important livestock pathogens. The liver-specific miR-122 binds within the HCV 5′ untranslated region (UTR), whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2, respectively) in the pestiviral 3′ UTR. Here, we dissected the mechanism of miRNA dependency of the pestivirus bovine viral diarrhea virus (BVDV). Argonaute 2 (AGO2) and miR-17 binding were essential for viral replication, whereas let-7 binding was mainly required for full translational efficiency. Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found that tropism could be redirected to different miRNAs. AGO cross-linking and immunoprecipitation (CLIP) experiments and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Interestingly, we also identified miRNA-independent variants that were obtained through acquisition of compensatory mutations near the genomic 3′ terminus. Rescue experiments demonstrated that miRNA binding and 3′ mutagenesis contribute to replication through mutually exclusive mechanisms. Altogether, our findings suggest that pestiviruses, although capable of miRNA-independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.

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