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Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

Danchin EG, Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso MN, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P - PLoS Pathog. (2013)

Bottom Line: Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species.A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita.Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1355 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; CNRS, UMR 7254 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; Université de Nice Sophia-Antipolis, UMR ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France.

ABSTRACT
Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means.

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Gene Ontology annotation of putative transcription factors.This Venn diagram represents the number of proteins that cumulate transcription-related terms in their Gene Ontology annotation in protein set 1. A total of 315 proteins have been assigned the term ‘Transcription’ in their Biological Process G.O. annotation. A total of 191 proteins have been assigned the term ‘Nucleus’ in their Cellular Component G.O. annotation. A total of 197 proteins have been assigned the term ‘Transcription factor activity” in their Molecular Function G.O. annotation. Overall, a total of 109 proteins in set 1 cumulate these three transcription factor-related G.O. terms.
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ppat-1003745-g004: Gene Ontology annotation of putative transcription factors.This Venn diagram represents the number of proteins that cumulate transcription-related terms in their Gene Ontology annotation in protein set 1. A total of 315 proteins have been assigned the term ‘Transcription’ in their Biological Process G.O. annotation. A total of 191 proteins have been assigned the term ‘Nucleus’ in their Cellular Component G.O. annotation. A total of 197 proteins have been assigned the term ‘Transcription factor activity” in their Molecular Function G.O. annotation. Overall, a total of 109 proteins in set 1 cumulate these three transcription factor-related G.O. terms.

Mentions: Because putative transcription factors specific from RKN and other plant-damaging organisms constitute interesting potential targets, we searched, in set 1, proteins that were annotated with the term “transcription” in the “biological process” ontology, with the term “transcription factor activity” in the “molecular function” ontology and with the term “nucleus” in the “cellular component” ontology. We found a total of 109 RKN proteins that cumulated these three annotations (Figure 4).


Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

Danchin EG, Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso MN, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P - PLoS Pathog. (2013)

Gene Ontology annotation of putative transcription factors.This Venn diagram represents the number of proteins that cumulate transcription-related terms in their Gene Ontology annotation in protein set 1. A total of 315 proteins have been assigned the term ‘Transcription’ in their Biological Process G.O. annotation. A total of 191 proteins have been assigned the term ‘Nucleus’ in their Cellular Component G.O. annotation. A total of 197 proteins have been assigned the term ‘Transcription factor activity” in their Molecular Function G.O. annotation. Overall, a total of 109 proteins in set 1 cumulate these three transcription factor-related G.O. terms.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3814813&req=5

ppat-1003745-g004: Gene Ontology annotation of putative transcription factors.This Venn diagram represents the number of proteins that cumulate transcription-related terms in their Gene Ontology annotation in protein set 1. A total of 315 proteins have been assigned the term ‘Transcription’ in their Biological Process G.O. annotation. A total of 191 proteins have been assigned the term ‘Nucleus’ in their Cellular Component G.O. annotation. A total of 197 proteins have been assigned the term ‘Transcription factor activity” in their Molecular Function G.O. annotation. Overall, a total of 109 proteins in set 1 cumulate these three transcription factor-related G.O. terms.
Mentions: Because putative transcription factors specific from RKN and other plant-damaging organisms constitute interesting potential targets, we searched, in set 1, proteins that were annotated with the term “transcription” in the “biological process” ontology, with the term “transcription factor activity” in the “molecular function” ontology and with the term “nucleus” in the “cellular component” ontology. We found a total of 109 RKN proteins that cumulated these three annotations (Figure 4).

Bottom Line: Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species.A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita.Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1355 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; CNRS, UMR 7254 ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France ; Université de Nice Sophia-Antipolis, UMR ISA, Institut Sophia Agrobiotech, Sophia-Antipolis, France.

ABSTRACT
Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means.

Show MeSH
Related in: MedlinePlus