scholarly journals Why genes overlap in viruses

2010 ◽  
Vol 277 (1701) ◽  
pp. 3809-3817 ◽  
Author(s):  
Nicola Chirico ◽  
Alberto Vianelli ◽  
Robert Belshaw
Keyword(s):  
Rna Viruses ◽  
Harmful Effect ◽  
Negative Relationship ◽  
Mutation Rates ◽  
Virus Species ◽  
Overlapping Genes ◽  
Genome Length ◽  
Dna Viruses ◽  
The Relationship ◽  
Gene Overlap

The genomes of most virus species have overlapping genes—two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length.

I'll manage myself: the moderator effect of positive framing on the relationship between organisational politics and engagement

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Robinson James
Keyword(s):  
Work Engagement ◽  
Structural Equation ◽  
Harmful Effect ◽  
Negative Relationship ◽  
Partial Least Square ◽  
Least Square ◽  
Moderator Effect ◽  
Content Type ◽  
The Relationship ◽  
Organisational Politics

PurposeThis study aims to investigate the influence of organisational politics on work engagement and the moderator effect of positive framing on this relationshipDesign/methodology/approachData were collected from 241 public sector employees in Sri Lanka through a structured questionnaire and analysed with partial least square structural equation modelling (PLS_SEM).FindingsThe results indicated that organisational politics negatively influenced employees' work engagement, positive framing positively influenced engagement and weakened the negative relationship between politics and engagement.Practical implicationsThis study suggests that organisation and individuals must take the necessary steps to enhance work engagement. Organisations must be transparent in all activities to avoid employees' negative perception. Also, organisations need to take steps to recruit employees with positive framing or develop this competency through training and development. Individuals also need to take necessary steps to frame the work environment positively to enhance their engagement in work.Originality/valueThis study extends the literature by being the first to examine the positive framing as a moderator in the relationship between politics and engagement. This study found that positive framing as a resource reduced the harmful effect of organisational politics on engagement and suggested positive framing can be considered as a resource in the future investigation of the job demand–resource model.

scholarly journals Viral Mutation Rates

2010 ◽  
Vol 84 (19) ◽  
pp. 9733-9748 ◽  
Author(s):  
Rafael Sanjuán ◽  
Miguel R. Nebot ◽  
Nicola Chirico ◽  
Louis M. Mansky ◽  
Robert Belshaw
Keyword(s):  
Mutation Rate ◽  
Rna Viruses ◽  
Experimental Testing ◽  
Mutation Rates ◽  
Cell Infection ◽  
Nucleotide Substitutions ◽  
Data Set ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Viral Mutation

ABSTRACT Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10−8 to10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut .

scholarly journals Properties and abundance of overlapping genes in viruses

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Timothy E Schlub ◽  
Edward C Holmes
Keyword(s):  
Genome Structure ◽  
Virus Genome ◽  
Overlapping Genes ◽  
Genome Database ◽  
Dna Viruses ◽  
Virus Family ◽  
Flexible Genome ◽  
Gene Overlap ◽  
Reference Genomes ◽  
Rna And Dna

Abstract Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering <10 nt, and 84 per cent are <50 nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families.

scholarly journals Episodic diversifying selection and intragenomic interactions shape the evolution of DNA and RNA viruses

2019 ◽  
Author(s):  
Stéphane Aris-Brosou ◽  
Louis Parent ◽  
Neke Ibeh
Keyword(s):  
Rna Viruses ◽  
Viral Evolution ◽  
Amino Acid Level ◽  
Mutation Rates ◽  
Correlated Evolution ◽  
Dna Viruses ◽  
Diversifying Selection ◽  
Dna And Rna ◽  
Show Evidence ◽  
Key Aspects

AbstractViruses are known to have some of the highest and most diverse mutation rates found in any biological replicator, topped by single-stranded (ss) RNA viruses, while double-stranded (ds) DNA viruses have rates approaching those of bacteria. As mutation rates are tightly and negatively correlated with genome size, selection is a clear driver of viral evolution. However, the role of intragenomic interactions as drivers of viral evolution is less well documented. To understand how these two processes affect viral evolution, we systematically surveyed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus type and which functions show evidence for episodic diversifying selection and correlated evolution. We show that while evidence for selection is mostly found in single stranded viruses, and correlated evolution is more prevalent in DNA viruses, the genes that are affected by both processes are involved in key aspects of their life cycle, favoring viral stability over proliferation. We further show that both evolutionary processes are intimately linked at the amino acid level, which suggests that selection alone does not explain the whole evolutionary —and epidemiological— potential of viruses.

scholarly journals Nucleoside Analogue Mutagenesis of a Single-Stranded DNA Virus: Evolution and Resistance

2012 ◽  
Vol 86 (18) ◽  
pp. 9640-9646 ◽  
Author(s):  
Pilar Domingo-Calap ◽  
Marianoel Pereira-Gómez ◽  
Rafael Sanjuán
Keyword(s):  
Nucleoside Analogue ◽  
Rna Viruses ◽  
Spontaneous Mutation ◽  
Chemical Mutagenesis ◽  
Mutation Rates ◽  
Nucleotide Substitutions ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Population Extinction ◽  
Nucleotide Mutation

It has been well established that chemical mutagenesis has adverse fitness effects in RNA viruses, often leading to population extinction. This is mainly a consequence of the high RNA virus spontaneous mutation rates, which situate them close to the extinction threshold. Single-stranded DNA viruses are the fastest-mutating DNA-based systems, with per-nucleotide mutation rates close to those of some RNA viruses, but chemical mutagenesis has been much less studied in this type of viruses. Here, we serially passaged bacteriophage ϕX174 in the presence of the nucleoside analogue 5-fluorouracil (5-FU). We found that 5-FU was unable to trigger population extinction for the range of concentrations tested, but it negatively affected viral adaptability. The phage evolved partial drug resistance, and parallel nucleotide substitutions appearing in independently evolved lines were identified as candidate resistance mutations. Using site-directed mutagenesis, two single-nucleotide substitutions in the lysis protein E (T572C and A781G) were shown to be selectively advantageous in the presence of 5-FU. In RNA viruses, base analogue resistance is often mediated by changes in the viral polymerase, but this mechanism is not possible for ϕX174 and other single-stranded DNA viruses because they do not encode their own polymerase. In addition to increasing mutation rates, 5-FU produces a wide variety of cytotoxic effects at the levels of replication, transcription, and translation. We found that substitutions T572C and A781G lost their ability to confer 5-FU resistance after cells were supplemented with deoxythymidine, suggesting that their mechanism of action is at the DNA level. We hypothesize that regulation of lysis time may allow the virus to optimize progeny size in cells showing defects in DNA synthesis.

scholarly journals Temperature effects on virion volume and genome length in dsDNA viruses

2016 ◽  
Vol 12 (3) ◽  
pp. 20160023 ◽  
Author(s):  
Rachel L. Nifong ◽  
James F. Gillooly
Keyword(s):  
Environmental Temperature ◽  
Size Variation ◽  
Genome Length ◽  
Dsdna Virus ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Virus Size ◽  
Dsdna Viruses ◽  
Gene Overlap ◽  
Growth And Reproduction

Heterogeneity in rates of survival, growth and reproduction among viruses is related to virus particle (i.e. virion) size, but we have little understanding of the factors that govern the four to five orders of magnitude in virus size variation. Here, we analyse variation in virion size in 67 double-stranded DNA viruses (i.e. dsDNA) that span all major biomes, and infect organisms ranging from single-celled prokaryotes to multicellular eukaryotes. We find that two metrics of virion size (i.e. virion volume and genome length) decrease by about 55-fold as the temperature of occurrence increases from 0 to 40°C. We also find that gene overlap increases exponentially with temperature, such that smaller viruses have proportionally greater gene overlap at higher temperatures. These results indicate dsDNA virus size increases with environmental temperature in much the same way as the cell or genome size of many host species.

scholarly journals Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1092 ◽  
Author(s):  
Ashleigh F. Porter ◽  
Mang Shi ◽  
John-Sebastian Eden ◽  
Yong-Zhen Zhang ◽  
Edward C. Holmes
Keyword(s):  
Phylogenetic Diversity ◽  
Rna Viruses ◽  
Virus Species ◽  
Dna Virus ◽  
Dna Viruses ◽  
Experimental Control ◽  
Transcriptomic Data ◽  
Invertebrate Species ◽  
Double Stranded Dna ◽  
Disease Associations

DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. By incorporating the sequence of a “blank” experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.

Oncogenesis and the Lucké Virus

1968 ◽  
Vol 26 ◽  
pp. 200-201
Author(s):  
A. E. Vatter ◽  
J. Zambernard
Keyword(s):  
Rna Viruses ◽  
Vegetative State ◽  
Temperature Sensitive ◽  
Structural Level ◽  
Oncogenic Viruses ◽  
Dna Viruses ◽  
Leopard Frogs ◽  
Renal Adenocarcinoma ◽  
Induced Tumors ◽  
Northern Leopard Frogs

Oncogenic viruses, like viruses in general, can be divided into two classes, those that contain deoxyribonucleic acid (DNA) and those that contain ribonucleic acid (RNA). The RNA viruses have been recovered readily from the tumors which they cause whereas, the DNA-virus induced tumors have not yielded the virus. Since DNA viruses cannot be recovered, the bulk of present day investigations have been concerned with RNA viruses.The Lucké renal adenocarcinoma is a spontaneous tumor which occurs in northern leopard frogs (Rana pipiens) and has received increased attention in recent years because of its probable viral etiology. This hypothesis was first advanced by Lucké after he observed intranuclear inclusions in some of the tumor cells. Tumors with inclusions were examined at the fine structural level by Fawcett who showed that they contained immature and mature virus˗like particles.The use of this system in the study of oncogenic tumors offers several unique features, the virus has been shown to contain DNA and it can be recovered from the tumor, also, it is temperature sensitive. This latter feature is of importance because the virus can be transformed from a latent to a vegetative state by lowering or elevating the environmental temperature.

Risk Attitude and Corporate Investment under Output Market Uncertainty: Evidence from The Mekong River Delta, Vietnam

2016 ◽  
pp. 59-70
Author(s):  
Ninh Le Khuong ◽  
Nghiem Le Tan ◽  
Tho Huynh Huu
Keyword(s):  
Negative Relationship ◽  
Risk Attitude ◽  
Business Strategies ◽  
Risk Averse ◽  
Market Uncertainty ◽  
Firm Investment ◽  
Output Market ◽  
The Impact ◽  
The Relationship

This paper aims to detect the impact of firm managers’ risk attitude on the relationship between the degree of output market uncertainty and firm investment. The findings show that there is a negative relationship between these two aspects for risk-averse managers while there is a positive relationship for risk-loving ones, since they have different utility functions. Based on the findings, this paper proposes recommendations for firm managers to take into account when making investment decisions and long-term business strategies as well.

Relationship of Organizational Citizenship Behavior and Production Deviance: Role of Perceived Organizational Politics

2019 ◽  
Vol 34 (2) ◽  
pp. 367-382
Author(s):  
Irsa Fatima Makhdoom ◽  
Mohsin Atta ◽  
Najma Iqbal Malik
Keyword(s):  
Organizational Citizenship ◽  
Organizational Citizenship Behavior ◽  
Negative Relationship ◽  
Civic Virtue ◽  
Organizational Politics ◽  
Work Behavior ◽  
Citizenship Behavior ◽  
Production Deviance ◽  
Relationship Of ◽  
The Relationship

The present study was an endeavor to extend the literature of perceived organizational politics by examining its moderating role between the relationship of organizational citizenship behavior and production deviance. Organizational Citizenship Behavior Scale (Mackenzie, Podsakoff, & Paine, 1999), Production Deviance sub-scale of Counterproductive Work Behavior Checklist-32 (Spector et al., 2006), and Perception of Organizational Politics Scale (Kacmar & Carlson, 1997) were used in present study. Hierarchical regression analyses revealed that low levels of perceived organizational politics moderated the relationship between courtesy and production deviance by strengthening the negative relationship of these behaviors while perceived organizational politics did not act as a moderator for the relationship of civic virtue and conscientiousness with production deviance. High level of go-along-to-get-ahead as a moderator strengthened the relationship of civic virtue and conscientiousness with production deviance and its low level was found to be moderating the relationship between courtesy and production deviance. Future implications of the study were also discussed.

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