scholarly journals Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms

Diversity ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 225
Author(s):  
Yuji Tomaru ◽  
Kei Kimura
Keyword(s):  
Culture Method ◽  
Host Cells ◽  
Natural Sediment ◽  
Viral Genomes ◽  
Planktonic Diatoms ◽  
Ecological Relationships ◽  
Ssrna Virus ◽  
Single Host ◽  
Complete Lysis ◽  
Ssdna Viruses

Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated Chaetoceros tenuissimus and C. setoensis cells. A previously unknown ssDNA virus type was detected in inoculated C. tenuissimus cells, but not in C. setoensis cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.

scholarly journals Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox

2021 ◽  
Author(s):  
Avantika Lal ◽  
Mariana Galvao Ferrarini ◽  
Andreas J. Gruber
Keyword(s):  
Host Cell ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Viruses ◽  
Host Cells ◽  
Binding Motifs ◽  
Viral Genomes ◽  
Host Interactions ◽  
Human Host ◽  
Ssrna Virus

AbstractViruses are intracellular parasites that need their host cell to reproduce. Consequently, they have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactome of viral genomes and the consequences of these interactions for infection are still to be mapped for most RNA viruses. To facilitate these efforts we have developed SMEAGOL, a fast and user-friendly toolbox to analyze the enrichment or depletion of RBP binding motifs across RNA sequences (https://github.com/gruber-sciencelab/SMEAGOL). To shed light on the interaction landscape of RNA viruses with human host cell RBPs at a large scale, we applied SMEAGOL to 197 single-stranded RNA (ssRNA) viral genome sequences. We find that the majority of ssRNA virus genomes are significantly enriched or depleted in binding motifs for human RBPs, suggesting selection pressure on these interactions. Our analysis provides an overview of potential virus - RBP interactions, covering the majority of ssRNA viral genomes fully sequenced to date, and represents a rich resource for studying host interactions vital to the virulence of ssRNA viruses. Our resource and the SMEAGOL toolbox will support future studies of virus / host interactions, ultimately feeding into better treatments.

scholarly journals Cyanobiont-bearing Dinoflagellate Ornithocercus in Temperate Coastal Waters: Cyanobiont Genetic Diversity and Host Specificity

2020 ◽  
Author(s):  
Miran Kim ◽  
Dong Choi ◽  
Myung Park
Keyword(s):  
Genetic Diversity ◽  
Coastal Waters ◽  
Host Cells ◽  
Genetic Types ◽  
Four Seasons ◽  
Wide Range ◽  
Single Host ◽  
Unicellular Organisms ◽  
Miseq Platform ◽  
Bacterial Groups

Abstract Cyanobacteria are ubiquitous in marine environments and play an important role as primary producers. Some cyanobacteria, the so called cyanobionts (cyanobacterial symbionts), have a symbiotic relationship with unicellular organisms. Among these relationships, in particular, the nature (e.g., genetic diversity, host or cyanobiont specificity, and cyanobionts seasonality) of the cyanobionts-dinoflagellate host consortia remain poorly understood. In this study, 16S rDNA of cyanobionts in a total of 138 single host cells isolated over four seasons in temperate waters were sequenced using the MiSeq platform. Genetic analysis of cyanobionts from the dinoflagellate host Ornithocercus revealed that three genetic types of Synechococcales cyanobionts occurred at a wide range of water temperatures (11–24°C) and their distribution seems to be closely associated with the variation in salinity. Furthermore, this study showed the presence of some degree of host (or cyanobiont) specificity in cyanobionts (or host) among Ornithocercus species as well as among other dinophysoid species (i.e. Amphisolenia, Citharistes, and Histioneis). In addition to Synechococcales cyanobionts, this study identified some OTU sequences affiliated with the Vampirovibrionales and Chroococcidiopsidales in some Ornithocercus cells, suggesting that Ornithocercus species seem to be an additional new habitat for those bacterial groups.

scholarly journals Bacteriophage self-counting in the presence of viral replication

2021 ◽  
Vol 118 (51) ◽  
pp. e2104163118
Author(s):  
Tianyou Yao ◽  
Seth Coleman ◽  
Thu Vu Phuc Nguyen ◽  
Ido Golding ◽  
Oleg A. Igoshin
Keyword(s):  
Gene Expression ◽  
Viral Replication ◽  
Viral Gene Expression ◽  
Host Cells ◽  
Optimal Decision ◽  
Viral Gene ◽  
Viral Genomes ◽  
Viral Copy Number ◽  
Viral Copy ◽  
Type Phage

When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases because of replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that instead of hindering lambda’s decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wild-type phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision—lysis upon single-phage infection and lysogeny at higher MOI.

scholarly journals Viral Genome Conformations and Contacts across Different Lifecycle Stages

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 109
Author(s):  
Peter G. Stockley ◽  
Nikesh Patel ◽  
Emma L. Wroblewski ◽  
Andrew J. P. Scott ◽  
Carlos P. Mata ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Drug Targets ◽  
Three Dimensional ◽  
Host Cells ◽  
Dimensional Structure ◽  
Viral Genomes ◽  
Starting Point ◽  
B Virus ◽  
Infection Mechanisms ◽  
Conformational Memory

Single-stranded RNA viral genomes (gRNA) are dynamic molecules that permit packaging into virions and their subsequent extrusion during infection. For viruses with such genomes, we discovered a previously unsuspected mechanism that regulates their assembly. This regulation is the result of multiple cognate coat protein (CP)–gRNA contacts distributed across the RNA. Collectively, these interactions make the assembly highly efficient and specific. The regions of the gRNA packaging signals (PSs) driving this assembly are potential drug targets, whilst the manipulation of PS–CP contacts with nonviral RNA cargos is a route towards bespoke virus-like particles. Infectivity depends on the virions being able to transfer their gRNAs into host cells. The starting point for this transfer appears to be an encapsidated RNA with a defined three-dimensional structure, especially around the PSs. A combination of asymmetric cryo-electron microscopy structure determination and X-ray synchrotron footprinting were used to define these contacts and structures in a number of viral examples, including hepatitis B virus and enteroviruses. These tools allow us to look beyond the outer CP layer of the virion shell and to see the functional, asymmetric components that regulate viral infectivity. This revealed yet more unexpected aspects of critical infection mechanisms, such as the RNA conformational changes required for encapsidation, the details of PS–CP contacts regulating the assembly, and the conformational “memory” imposed by encapsidation.

scholarly journals Expression of a Single, Host-Specific, Bacterial Pathogenicity Gene in Plant Cells Elicits Division, Enlargement, and Cell Death

1999 ◽  
Vol 12 (6) ◽  
pp. 556-560 ◽  
Author(s):  
Y. P. Duan ◽  
A. Castañeda ◽  
G. Zhao ◽  
G. Erdos ◽  
D. W. Gabriel
Keyword(s):  
Single Gene ◽  
Plant Cells ◽  
Host Cells ◽  
Microbial Pathogens ◽  
Bacterial Pathogenicity ◽  
Site Of Action ◽  
Single Host ◽  
Protein Secretion System ◽  
Type Iii Protein Secretion ◽  
Specific Symptoms

A fundamental question about microbial pathogens is how they elicit host-specific symptoms. We report here that expression of a single gene from a plant-pathogenic bacterium in plant cells elicits host-specific symptoms diagnostic of the disease caused by the pathogen. Expression of pthA from Xanthomonas citri in citrus cells is sufficient to cause division, enlargement, and death of host cells. Since elicitation of these symptoms depends on a functional type III protein secretion system in X. citri, we deduce that the PthA protein is a specific plant signal, its site of action is inside the plant cell, and it is a major determinant of host range.

scholarly journals Distinct Viral Populations Differentiate and Evolve Independently in a Single Perennial Host Plant

2006 ◽  
Vol 80 (5) ◽  
pp. 2349-2357 ◽  
Author(s):  
Chiraz Jridi ◽  
Jean-François Martin ◽  
Véronique Marie-Jeanne ◽  
Gérard Labonne ◽  
Stéphane Blanc
Keyword(s):  
Complex Structure ◽  
Plum Pox Virus ◽  
Virus Population ◽  
Intensive Study ◽  
Heterogeneous Distribution ◽  
Nested Clade Analysis ◽  
Viral Genomes ◽  
Immunodeficiency Virus ◽  
Single Host ◽  
Exhaustive Study

ABSTRACT The complex structure of virus populations has been the object of intensive study in bacteria, animals, and plants for over a decade. While it is clear that tremendous genetic diversity is rapidly generated during viral replication, the distribution of this diversity within a single host remains an obscure area in this field of science. Among animal viruses, only Human immunodeficiency virus and Hepatitis C virus populations have recently been thoroughly investigated at an intrahost level, where they are structured as metapopulations, demonstrating that the host cannot be considered simply as a “bag” containing a homogeneous or unstructured swarm of mutant viral genomes. In plants, a few reports suggested a possible heterogeneous distribution of virus variants at different locations within the host but provided no clues as to how this heterogeneity is structured. Here, we report the most exhaustive study of the structure and evolution of a virus population ever reported at the intrahost level through the analysis of a Prunus tree infected by Plum pox virus for over 13 years following a single inoculation event and by using analysis of molecular variance at different hierarchical levels combined with nested clade analysis. We demonstrate that, following systemic invasion of the host, the virus population differentiates into several distinct populations that are isolated in different branches, where they evolve independently through contiguous range expansion while colonizing newly formed organs. Moreover, we present and discuss evidence that the tree harbors a huge “bank” of viral clones, each isolated in one of the myriad leaves.

scholarly journals Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination

2017 ◽  
Author(s):  
A.K. Erickson ◽  
P.R. Jesudhasan ◽  
M.J. Mayer ◽  
A. Narbad ◽  
S.E. Winter ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Genetic Recombination ◽  
Enteric Viruses ◽  
Intestinal Bacteria ◽  
Enteric Virus ◽  
Viral Fitness ◽  
Host Cells ◽  
Bacterial Strains ◽  
Viral Recombination ◽  
Viral Genomes

SUMMARYIntestinal bacteria promote infection of several mammalian enteric viruses, but the mechanisms and consequences are unclear. We screened a panel of 41 bacterial strains as a platform to determine how different bacteria impact enteric viruses. We found that most bacterial strains bound poliovirus, a model enteric virus. Given that each bacterium bound multiple virions, we hypothesized that bacteria may deliver multiple viral genomes to a mammalian cell even when very few virions are present, such as during the first replication cycle after inter-host transmission. We found that exposure to certain bacterial strains increased viral co-infection even when the ratio of virus to host cells was low. Bacteria-mediated viral co-infection correlated with bacterial adherence to cells. Importantly, bacterial strains that induced viral co-infection facilitated viral fitness restoration through genetic recombination. Thus, bacteria-virus interactions may increase viral fitness through viral recombination at initial sites of infection, potentially limiting abortive infections.

scholarly journals Division of single host cells after infection with chlamydiae.

1978 ◽  
Vol 19 (1) ◽  
pp. 281-286 ◽  
Author(s):  
K D Horoschak ◽  
J W Moulder
Keyword(s):  
Host Cells ◽  
Single Host

Viral Life History Traits

2016 ◽  
Author(s):  
Joshua S. Weitz
Keyword(s):  
Life History ◽  
Mortality Rate ◽  
Host Cell ◽  
Life History Traits ◽  
Viral Infections ◽  
Burst Size ◽  
Host Cells ◽  
Viral Genomes ◽  
Life History Stages ◽  
Viral Progeny

This chapter discusses a number of key commonalities and differences among viral life history traits. Viruses have two key life history stages: inside and outside a host cell. Viral infections of microbes often lead to the death of host cells and the release of viral progeny. Viral infections can also lead to the integration of viral genomes with those of their hosts; induction of these genomes can result in subsequent lysis and release of viral progeny. Viruses are distinguished not only by the host they infect but also by the quantitative rates and levels at which these interactions take place. Viral life history traits reflect the combined interactions of viruses and hosts; that is, they are not encoded solely by viral genomes. Viral life history traits can also vary by orders of magnitude, whether for time to lysis, burst size, probability of lysogeny, rate of induction, adsorption rate, or mortality rate.

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