Plant Viruses: From Targets to Tools for CRISPR

Plant viruses cause devastating diseases in many agriculture systems, being a serious threat for the provision of adequate nourishment to a continuous growing population. At the present, there are no chemical products that directly target the viruses, and their control rely mainly on preventive sanitary measures to reduce viral infections that, although important, have proved to be far from enough. The current most effective and sustainable solution is the use of virus-resistant varieties, but which require too much work and time to obtain. In the recent years, the versatile gene editing technology known as CRISPR/Cas has simplified the engineering of crops and has successfully been used for the development of viral resistant plants. CRISPR stands for ‘clustered regularly interspaced short palindromic repeats’ and CRISPR-associated (Cas) proteins, and is based on a natural adaptive immune system that most archaeal and some bacterial species present to defend themselves against invading bacteriophages. Plant viral resistance using CRISPR/Cas technology can been achieved either through manipulation of plant genome (plant-mediated resistance), by mutating host factors required for viral infection; or through manipulation of virus genome (virus-mediated resistance), for which CRISPR/Cas systems must specifically target and cleave viral DNA or RNA. Viruses present an efficient machinery and comprehensive genome structure and, in a different, beneficial perspective, they have been used as biotechnological tools in several areas such as medicine, materials industry, and agriculture with several purposes. Due to all this potential, it is not surprising that viruses have also been used as vectors for CRISPR technology; namely, to deliver CRISPR components into plants, a crucial step for the success of CRISPR technology. Here we discuss the basic principles of CRISPR/Cas technology, with a special focus on the advances of CRISPR/Cas to engineer plant resistance against DNA and RNA viruses. We also describe several strategies for the delivery of these systems into plant cells, focusing on the advantages and disadvantages of the use of plant viruses as vectors. We conclude by discussing some of the constrains faced by the application of CRISPR/Cas technology in agriculture and future prospects.

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CRISPR/Cas9-Based Antiviral Strategy: Current Status and the Potential Challenge

Molecules ◽

10.3390/molecules24071349 ◽

2019 ◽

Vol 24 (7) ◽

pp. 1349 ◽

Cited By ~ 11

Author(s):

Choongho Lee

Keyword(s):

Viral Infections ◽

Adaptive Immune System ◽

Virus Genome ◽

General Concept ◽

Current Status ◽

Adaptive Immune ◽

Chronic Viral Infections ◽

B Virus ◽

Immunodeficiency Virus ◽

Potential Challenge

From its unexpected discovery as a bacterial adaptive immune system to its countless applications as one of the most versatile gene-editing tools, the CRISPR/Cas9 system has revolutionized every field of life science. Virology is no exception to this ever-growing list of CRISPR/Cas9-based applications. Direct manipulation of a virus genome by CRISPR/Cas9 has enabled a systematic study of cis-elements and trans-elements encoded in a virus genome. In addition, this virus genome-specific mutagenesis by CRISPR/Cas9 was further funneled into the development of a novel class of antiviral therapy targeting many incurable chronic viral infections. In this review, a general concept on the CRISPR/Cas9-based antiviral strategy will be described first. To understand the current status of the CRISPR/Cas9-based antiviral approach, a series of recently published antiviral studies involving CRISPR/Cas9-mediated control of several clinically-relevant viruses including human immunodeficiency virus, hepatitis B virus, herpesviruses, human papillomavirus, and other viruses will be presented. Lastly, the potential challenge and future prospect for successful clinical translation of this CRISPR/Cas9-based antiviral method will be discussed.

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Expanding the size limit of RNA viruses: Evidence of a novel divergent nidovirus in California sea hare, with a ~35.9 kb virus genome

10.1101/307678 ◽

2018 ◽

Cited By ~ 2

Author(s):

Humberto J Debat

Keyword(s):

Rna Viruses ◽

Rna Virus ◽

Genome Structure ◽

Aplysia Californica ◽

Domain Architecture ◽

Size Variation ◽

Virus Genome ◽

Rna Sequences ◽

Virus Rna ◽

A Genome

While RNA viruses thrive with massive structural and functional diversity, their genomes size variation is particularly low, ranging only from ~2-to-33 kb. Here, I present the characterization of RNA sequences corresponding to the first virus associated with Aplysia californica . Genome structure and domain architecture suggest that the identified virus is a novel member of Nidovirales . The proposed aplysia californica nido-like virus (AcNV), with a genome sequence of ca.35,906 nt, represents the longest ever recorded RNA virus yet. Phylogenetic insights indicate that AcNV clusters in a major phylloclade of unclassified invertebrate nidoviruses, Roniviridae , and Mesoniviridae . Basal branching in this emerging cluster could indicate that AcNV is a member of a novel divergent clade within Nidovirales . Further, virus RNA detection in multiple independent studies suggests that AcNV is neurotropic with a broad cell/tissue/organ tropism, supported by AcNV occurrence in diverse organs, including the first detection of a Nidovirales in single specific neurons.

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The Role of microRNAs in the Viral Infections

Current Pharmaceutical Design ◽

10.2174/1381612825666190110161034 ◽

2019 ◽

Vol 24 (39) ◽

pp. 4659-4667 ◽

Cited By ~ 4

Author(s):

Mona Fani ◽

Milad Zandi ◽

Majid Rezayi ◽

Nastaran Khodadad ◽

Hadis Langari ◽

...

Keyword(s):

Viral Infections ◽

Rna Viruses ◽

Regulation Of Gene Expression ◽

Molecular Structures ◽

Main Function ◽

Cellular Functions ◽

Viral Genes ◽

Non Coding Rnas ◽

Post Transcriptional Regulation

MicroRNAs (miRNAs) are non-coding RNAs with 19 to 24 nucleotides which are evolutionally conserved. MicroRNAs play a regulatory role in many cellular functions such as immune mechanisms, apoptosis, and tumorigenesis. The main function of miRNAs is the post-transcriptional regulation of gene expression via mRNA degradation or inhibition of translation. In fact, many of them act as an oncogene or tumor suppressor. These molecular structures participate in many physiological and pathological processes of the cell. The virus can also produce them for developing its pathogenic processes. It was initially thought that viruses without nuclear replication cycle such as Poxviridae and RNA viruses can not code miRNA, but recently, it has been proven that RNA viruses can also produce miRNA. The aim of this articles is to describe viral miRNAs biogenesis and their effects on cellular and viral genes.

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Intra-Colonial Viral Infections in Western Honey Bees (Apis mellifera)

Microorganisms ◽

10.3390/microorganisms9051087 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1087

Author(s):

Loreley Castelli ◽

María Laura Genchi García ◽

Anne Dalmon ◽

Daniela Arredondo ◽

Karina Antúnez ◽

...

Keyword(s):

Apis Mellifera ◽

Honey Bee ◽

Viral Infections ◽

Sampling Period ◽

Virus Genome ◽

The Individual ◽

Bee Virus ◽

Insight Into ◽

Bee Viruses

RNA viruses play a significant role in the current high losses of pollinators. Although many studies have focused on the epidemiology of western honey bee (Apis mellifera) viruses at the colony level, the dynamics of virus infection within colonies remains poorly explored. In this study, the two main variants of the ubiquitous honey bee virus DWV as well as three major honey bee viruses (SBV, ABPV and BQCV) were analyzed from Varroa-destructor-parasitized pupae. More precisely, RT-qPCR was used to quantify and compare virus genome copies across honey bee pupae at the individual and subfamily levels (i.e., patrilines, sharing the same mother queen but with different drones as fathers). Additionally, virus genome copies were compared in cells parasitized by reproducing and non-reproducing mite foundresses to assess the role of this vector. Only DWV was detected in the samples, and the two variants of this virus significantly differed when comparing the sampling period, colonies and patrilines. Moreover, DWV-A and DWV-B exhibited different infection patterns, reflecting contrasting dynamics. Altogether, these results provide new insight into honey bee diseases and stress the need for more studies about the mechanisms of intra-colonial disease variation in social insects.

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In Vivo Imaging of Biodegradable Implants and Related Tissue Biomarkers

Polymers ◽

10.3390/polym13142348 ◽

2021 ◽

Vol 13 (14) ◽

pp. 2348

Author(s):

Leon Riehakainen ◽

Chiara Cavallini ◽

Paolo Armanetti ◽

Daniele Panetta ◽

Davide Caramella ◽

...

Keyword(s):

Imaging Modality ◽

Imaging Techniques ◽

Special Focus ◽

Tissue Remodelling ◽

Biodegradable Implant ◽

Advantages And Disadvantages ◽

Non Invasive ◽

Positron Emission ◽

Longitudinal Imaging

Non-invasive longitudinal imaging of osseointegration of bone implants is essential to ensure a comprehensive, physical and biochemical understanding of the processes related to a successful implant integration and its long-term clinical outcome. This study critically reviews the present imaging techniques that may play a role to assess the initial stability, bone quality and quantity, associated tissue remodelling dependent on implanted material, implantation site (surrounding tissues and placement depth), and biomarkers that may be targeted. An updated list of biodegradable implant materials that have been reported in the literature, from metal, polymer and ceramic categories, is provided with reference to the use of specific imaging modalities (computed tomography, positron emission tomography, ultrasound, photoacoustic and magnetic resonance imaging) suitable for longitudinal and non-invasive imaging in humans. The advantages and disadvantages of the single imaging modality are discussed with a special focus on preclinical imaging for biodegradable implant research. Indeed, the investigation of a new implant commonly requires histological examination, which is invasive and does not allow longitudinal studies, thus requiring a large number of animals for preclinical testing. For this reason, an update of the multimodal and multi-parametric imaging capabilities will be here presented with a specific focus on modern biomaterial research.

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Genome-Wide Identification and Expression Analysis of the Histone Deacetylase Gene Family in Wheat (Triticum aestivum L.)

Plants ◽

10.3390/plants10010019 ◽

2020 ◽

Vol 10 (1) ◽

pp. 19

Author(s):

Peng Jin ◽

Shiqi Gao ◽

Long He ◽

Miaoze Xu ◽

Tianye Zhang ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Mosaic Virus ◽

Stress Responses ◽

Viral Infections ◽

Phylogenetic Analyses ◽

Plant Viruses ◽

Gene Family Evolution ◽

Yellow Mosaic Virus ◽

Wheat Yellow Mosaic Virus

Histone acetylation is a dynamic modification process co-regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDACs play vital roles in abiotic or biotic stress responses, their members in Triticumaestivum and their response to plant viruses remain unknown. Here, we identified and characterized 49 T. aestivumHDACs (TaHDACs) at the whole-genome level. Based on phylogenetic analyses, TaHDACs could be divided into 5 clades, and their protein spatial structure was integral and conserved. Chromosomal location and synteny analyses showed that TaHDACs were widely distributed on wheat chromosomes, and gene duplication has accelerated the TaHDAC gene family evolution. The cis-acting element analysis indicated that TaHDACs were involved in hormone response, light response, abiotic stress, growth, and development. Heatmaps analysis of RNA-sequencing data showed that TaHDAC genes were involved in biotic or abiotic stress response. Selected TaHDACs were differentially expressed in diverse tissues or under varying temperature conditions. All selected TaHDACs were significantly upregulated following infection with the barley stripe mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV), and wheat yellow mosaic virus (WYMV), suggesting their involvement in response to viral infections. Furthermore, TaSRT1-silenced contributed to increasing wheat resistance against CWMV infection. In summary, these findings could help deepen the understanding of the structure and characteristics of the HDAC gene family in wheat and lay the foundation for exploring the function of TaHDACs in plants resistant to viral infections.

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VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

10.1101/2021.04.29.442004 ◽

2021 ◽

Author(s):

Rajan Saha Raju ◽

Abdullah Al Nahid ◽

Preonath Shuvo ◽

Rashedul Islam

Keyword(s):

Genome Sequence ◽

Rna Viruses ◽

Hierarchical Classification ◽

Classification Problem ◽

Virus Genome ◽

Taxonomic Classification ◽

Dna Viruses ◽

Dna And Rna ◽

Full Length Genome

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available at https://omics-lab.com/virustaxo/.

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Current and Emerging Themes in the Structural Analysis of Viral RNA Genomes: Applications for the Development of Novel Therapeutic Drugs

Genomics and Computational Biology ◽

10.18547/gcb.2015.vol1.iss1.e15 ◽

2015 ◽

Vol 1 (1) ◽

pp. 15 ◽

Cited By ~ 2

Author(s):

Cristina Romero-López ◽

Alfredo Berzal-Herranz

Keyword(s):

Rna Folding ◽

Viral Infections ◽

Genome Structure ◽

Rna Molecules ◽

Molecular Virology ◽

Viral Genomes ◽

Viral Propagation ◽

Bioinformatic Tools ◽

Rna Domains ◽

Functional Rna

RNA molecules assume different roles in many different biological processes. This functional diversity is intimately related to RNA folding. In recent years, advances in the field of structure analysis by high-throughput methodologies and the development of novel potent bioinformatic tools have enabled the first structural maps of the eukaryotic transcriptome and the further establishment of novel function-structure relationships. This important progress has been of special relevance in the field of molecular virology. Viral genomes are compact entities that require overlapping coding levels to bear all the genetic information required for viral propagation. This is achieved by the acquisition of functional RNA domains, structurally conserved encoding units that perform essential roles for the consecution of the viral cycle. Interfering with the activity of these structural elements offers a potential means of treating viral infections, such as that caused by the hepatitis C virus, HCV. This review summarizes major achievements in the development of emerging methodologies for the analysis of RNA folding and their application to the study of the HCV genome structure. It will also examine the progress toward the design of novel antiviral compounds based in nucleic acids able to interfere with the folding of functional RNA domains.

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PRIVATIZATION OF RUSSIA’S ENERGY ASSETS IN THE INTERNATIONAL CONTEXT

MGIMO Review of International Relations ◽

10.24833/2071-8160-2013-4-31-242-250 ◽

2013 ◽

pp. 242-250

Author(s):

Y. V. Borovsky

Keyword(s):

Oil And Gas ◽

The State ◽

Energy Industry ◽

Special Focus ◽

Russian Government ◽

Advantages And Disadvantages ◽

Russian State ◽

National Power ◽

Widespread Belief ◽

Energy Assets

The article deals with privatization in Russia’s energy sector with a special focus on a recent purchase of the private TNK-BP by the state-owned Rosneft. The author analyses the past, present and future privatization deals related to the Russian oil, gas and power generation industry as compared to accumulated international experience. For instance, the article displays the ways the Norwegian, Brazilian, French and British authorities privatized national strategic energy assets. The study presented in the article also aims to find out key advantages and disadvantages of state or private ownership in the Russian and global energy industry. For example, it sheds light on some considerable achievements of the Russian state-controlled companies in oil production amid a widespread belief that more than a decade-long growth in the Russian oil industry is due only to private firms that were created in the 1990s. Additionally, the state-controlled Norwegian oil and gas firm Statoil that shows strong operational and financial results on the Norwegian Continental Shelf and abroad is also in the spotlight of the current study. In line with the mentioned takeover of TNK-BP the author examines outcomes of the reorganization of RAO UES of Russia (the dismantled Russian electric power monopoly) that was seen as a massive privatization of the national power industry. Moreover, the study presents two groups of interests prevailing in the Russian government and energy business to give an outlook on the Russian energy industry.

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A Four-Partner Plant–Virus Interaction: Enemies Can Also Come from Within

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-05-10-0107 ◽

2010 ◽

Vol 23 (11) ◽

pp. 1394-1402 ◽

Cited By ~ 46

Author(s):

Marie-Line Iskra-Caruana ◽

Franc-Christophe Baurens ◽

Philippe Gayral ◽

Matthieu Chabannes

Keyword(s):

Viral Genome ◽

Plant Viruses ◽

Plant Genome ◽

Interspecific Crosses ◽

Streak Virus ◽

Alternative Source ◽

Remarkable Feature ◽

Tropical Crops ◽

Causative Agents ◽

Partner Interaction

Plant viruses are disseminated by either vertical (vegetative multiplication or sexual reproduction) or horizontal (vector-mediated) propagation. Plant pararetroviruses—members of the Caulimoviridae family—have developed an alternative strategy for vertical propagation via integration within the host plant genome, although integration is not required for viral replication. Integrated endogenous pararetrovirus (EPRV) sequences have undergone extensive viral genome rearrangements and contain more than one copy of the viral genome. Furthermore, EPRV can become infectious upon spontaneous escape of active virus following stresses such as wounding, tissue culture, or interspecific crosses. Such infectious EPRV are of great importance, not only in terms of their ability to precipitate epidemic outbreaks but also because of their effect on breeding of numerous plant genomes in temperate and tropical crops. This is especially true for banana, a crop susceptible to banana streak viruses, the causative agents of banana streak disease. Thus, the classical three-component banana–Banana streak virus (BSV)–mealybug pathosystem can be expanded to include endogenous BSV as an alternative source of active virions. The BSV-banana pathosystem is one of only three pathosystems known to date to harbor this remarkable feature, and the present review focuses exclusively on it to illustrate this four-partner interaction.

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