Potyviruses and the Digital Revolution

Gibbs, Adrian; Ohshima, Kazusato

doi:10.1146/annurev-phyto-073009-114404

Cited by 248 publications

(180 citation statements)

References 87 publications

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“…Potyviruses are single-stranded positive sense RNA viruses that represent one of the most speciose taxa of plant viruses and infect a broad range of plant species, including most crop plants, causing severe losses in agriculture worldwide (Gibbs and Ohshima, 2010). The potyviral genome possesses a 3# poly(A) tail but lacks a cap structure at the 5# end, which is instead covalently bound to a virus-encoded protein termed VPg.…”

mentioning

confidence: 99%

A Plant Small Polypeptide Is a Novel Component of DNA-Binding Protein Phosphatase 1-Mediated Resistance to Plum pox virus in Arabidopsis

Castelló

Carrasco²,

Navarrete-Gómez³

et al. 2011

Plant Physiology

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DNA-binding protein phosphatases (DBPs) have been identified as a novel class of plant-specific regulatory factors playing a role in plant-virus interactions. NtDBP1 from tobacco (Nicotiana tabacum) was shown to participate in transcriptional regulation of gene expression in response to virus infection in compatible interactions, and AtDBP1, its closest relative in the model plant Arabidopsis (Arabidopsis thaliana), has recently been found to mediate susceptibility to potyvirus, one of the most speciose taxa of plant viruses. Here, we report on the identification of a novel family of highly conserved small polypeptides that interact with DBP1 proteins both in tobacco and Arabidopsis, which we have designated DBP-interacting protein 2 (DIP2). The interaction of AtDIP2 with AtDBP1 was demonstrated in vivo by bimolecular fluorescence complementation, and AtDIP2 was shown to functionally interfere with AtDBP1 in yeast. Furthermore, reducing AtDIP2 gene expression leads to increased susceptibility to the potyvirus Plum pox virus and to a lesser extent also to Turnip mosaic virus, whereas overexpression results in enhanced resistance. Therefore, we describe a novel family of conserved small polypeptides in plants and identify AtDIP2 as a novel host factor contributing to resistance to potyvirus in Arabidopsis.

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mentioning

confidence: 99%

A Plant Small Polypeptide Is a Novel Component of DNA-Binding Protein Phosphatase 1-Mediated Resistance to Plum pox virus in Arabidopsis

Castelló

Carrasco²,

Navarrete-Gómez³

et al. 2011

Plant Physiology

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“…It contains more than 200 definite and tentative species (Berger et al, 2005) which cause significant losses in agricultural, pasture, horticultural and ornamental plants (Ward and Shukla, 1991). They infect a wide range of monocotyledonous and dicotyledonous plant species and have been found in most parts of the world (Gibbs and Ohshima 2010). Potyvirus distribution is worldwide, they are most prevalent in tropical and subtropical countries (Shukla et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Mixed-Infection of Papaya Ring Spot Virus and Tomato Leaf Curl New Delhi Virus in Coccinia grandis in India

Sultana¹,

Roy²,

Sherpa³

2017

Int.J.Curr.Microbiol.App.Sci

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“…Many potyviruses are important pathogens of agricultural crops. They are able to infect a wide range of mono-and dicotyledonous plant species [243], causing symptoms that severely reduce the yield and quality of crops. The economic impact of these viruses on agriculture is well-documented [244].…”

Section: Potyvirus and Its Proteinsmentioning

confidence: 99%

“…Rapid rise of academic interest in this topic followed the complete sequencing of the first two potyviruses: TEV [250] and Tobacco vein mottling virus (TVMV) [251]. Many excellent reviews have been published since then [243,246,[252][253][254][255][256]. …”

Section: Potyvirus and Its Proteinsmentioning

confidence: 99%

Chemometric Approaches for Systems Biology

Fortuny¹

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The present Ph.D. thesis is devoted to study, develop and apply approaches commonly used in chemometrics to the emerging field of systems biology. Existing procedures and new methods are applied to solve research and industrial questions in different multidisciplinary teams. The methodologies developed in this document will enrich the plethora of procedures employed within omic sciences to understand biological organisms and will improve processes in biotechnological industries integrating biological knowledge at different levels and exploiting the software packages derived from the thesis.This dissertation is structured in four parts. The first block describes the framework in which the contributions presented here are based. The objectives of the two research projects related to this thesis are highlighted and the specific topics addressed in this document via conference presentations and research articles are introduced. A comprehensive description of omic sciences and their relationships within the systems biology paradigm is given in this part, jointly with a review of the most applied multivariate methods in chemometrics, on which the novel approaches proposed here are founded.The second part addresses many problems of data understanding within metabolomics, fluxomics, proteomics and genomics. Different alternatives are proposed in this block to understand flux data in steady state conditions. Some are based on applications of multivariate methods previously applied in other chemometrics areas. Others are novel approaches based on a bilinear decomposition using elemental metabolic pathways, from which a GNU licensed toolbox is made freely available for the scientific community. As well, a framework for metabolic data understanding is proposed for non-steady state data, using the same bilinear decomposition proposed for steady state data, but modelling the dynamics of the experiments using novel two and three-way data analysis procedures. Also, the relationships between different omic levels are assessed in this part integrating different sources of information of plant viruses in data fusion models. Finally, an example of interaction between organisms, oranges and fungi, is studied via multivariate image analysis techniques, with future application in food industries.v The third block of this thesis is a thoroughly study of different missing data problems related to chemometrics, systems biology and industrial bioprocesses. In the theoretical chapters of this part, new algorithms to obtain multivariate exploratory and regression models in the presence of missing data are proposed, which serve also as preprocessing steps of any other methodology used by practitioners. Regarding applications, this block explores the reconstruction of networks in omic sciences when missing and faulty measurements appear in databases, and how calibration models between near infrared instruments can be transferred, avoiding costs and time-consuming full recalibrations in bioindustries and research laboratories. Finally,...

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Potyviruses and the Digital Revolution

Cited by 248 publications

References 87 publications

A Plant Small Polypeptide Is a Novel Component of DNA-Binding Protein Phosphatase 1-Mediated Resistance to Plum pox virus in Arabidopsis

A Plant Small Polypeptide Is a Novel Component of DNA-Binding Protein Phosphatase 1-Mediated Resistance to Plum pox virus in Arabidopsis

Mixed-Infection of Papaya Ring Spot Virus and Tomato Leaf Curl New Delhi Virus in Coccinia grandis in India

Chemometric Approaches for Systems Biology

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