Efficient enrichment cloning of TAL effector genes from Xanthomonas

Many plant-pathogenic xanthomonads use a type III secretion system to translocate Transcription Activator-Like (TAL) effectors into eukaryotic host cells where they act as transcription factors. Target genes are induced upon binding of a TAL effector to double-stranded DNA in a sequence-specific man...

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Main Authors: T.T. Tran, H. Doucouré, M. Hutin, L.M. Jaimes Niño, B. Szurek, S. Cunnac, R. Koebnik
Format: Article
Language:English
Published: Elsevier 2018-01-01
Series:MethodsX
Online Access:http://www.sciencedirect.com/science/article/pii/S2215016118301420
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spelling doaj-e1718830c6e84eeb95dde6579401cd402020-11-25T01:46:19ZengElsevierMethodsX2215-01612018-01-01510271032Efficient enrichment cloning of TAL effector genes from XanthomonasT.T. Tran0H. Doucouré1M. Hutin2L.M. Jaimes Niño3B. Szurek4S. Cunnac5R. Koebnik6IRD, Cirad, Univ. Montpellier, IPME, Montpellier, FranceIRD, Cirad, Univ. Montpellier, IPME, Montpellier, FranceIRD, Cirad, Univ. Montpellier, IPME, Montpellier, FranceUniversidad de los Andes, Bogotá, ColombiaIRD, Cirad, Univ. Montpellier, IPME, Montpellier, FranceIRD, Cirad, Univ. Montpellier, IPME, Montpellier, FranceIRD, Cirad, Univ. Montpellier, IPME, Montpellier, France; Corresponding author.Many plant-pathogenic xanthomonads use a type III secretion system to translocate Transcription Activator-Like (TAL) effectors into eukaryotic host cells where they act as transcription factors. Target genes are induced upon binding of a TAL effector to double-stranded DNA in a sequence-specific manner. DNA binding is governed by a highly repetitive protein domain, which consists of an array of nearly identical repeats of ca. 102 base pairs. Many species and pathovars of Xanthomonas, including pathogens of rice, cereals, cassava, citrus and cotton, encode multiple TAL effectors in their genomes. Some of the TAL effectors have been shown to act as key pathogenicity factors, which induce the expression of susceptibility genes to the benefit of the pathogen. However, due to the repetitive character and the presence of multiple gene copies, high-throughput cloning of TAL effector genes remains a challenge. In order to isolate complete TAL effector gene repertoires, we developed an enrichment cloning strategy based on • genome-informed in silico optimization of restriction digestions, • selective restriction digestion of genomic DNA, and • size fractionation of DNA fragments.Our rapid, cheap and powerful method allows efficient cloning of TAL effector genes from xanthomonads, as demonstrated for two rice-pathogenic strains of Xanthomonas oryzae from Africa. Method name: TAL fishing, Keywords: Enrichment cloning, Type III secretion, Type III effector, TAL effector, TALome, Xanthomonas, Bacterial leaf blight, Bacterial leaf streak, Ricehttp://www.sciencedirect.com/science/article/pii/S2215016118301420
collection DOAJ
language English
format Article
sources DOAJ
author T.T. Tran
H. Doucouré
M. Hutin
L.M. Jaimes Niño
B. Szurek
S. Cunnac
R. Koebnik
spellingShingle T.T. Tran
H. Doucouré
M. Hutin
L.M. Jaimes Niño
B. Szurek
S. Cunnac
R. Koebnik
Efficient enrichment cloning of TAL effector genes from Xanthomonas
MethodsX
author_facet T.T. Tran
H. Doucouré
M. Hutin
L.M. Jaimes Niño
B. Szurek
S. Cunnac
R. Koebnik
author_sort T.T. Tran
title Efficient enrichment cloning of TAL effector genes from Xanthomonas
title_short Efficient enrichment cloning of TAL effector genes from Xanthomonas
title_full Efficient enrichment cloning of TAL effector genes from Xanthomonas
title_fullStr Efficient enrichment cloning of TAL effector genes from Xanthomonas
title_full_unstemmed Efficient enrichment cloning of TAL effector genes from Xanthomonas
title_sort efficient enrichment cloning of tal effector genes from xanthomonas
publisher Elsevier
series MethodsX
issn 2215-0161
publishDate 2018-01-01
description Many plant-pathogenic xanthomonads use a type III secretion system to translocate Transcription Activator-Like (TAL) effectors into eukaryotic host cells where they act as transcription factors. Target genes are induced upon binding of a TAL effector to double-stranded DNA in a sequence-specific manner. DNA binding is governed by a highly repetitive protein domain, which consists of an array of nearly identical repeats of ca. 102 base pairs. Many species and pathovars of Xanthomonas, including pathogens of rice, cereals, cassava, citrus and cotton, encode multiple TAL effectors in their genomes. Some of the TAL effectors have been shown to act as key pathogenicity factors, which induce the expression of susceptibility genes to the benefit of the pathogen. However, due to the repetitive character and the presence of multiple gene copies, high-throughput cloning of TAL effector genes remains a challenge. In order to isolate complete TAL effector gene repertoires, we developed an enrichment cloning strategy based on • genome-informed in silico optimization of restriction digestions, • selective restriction digestion of genomic DNA, and • size fractionation of DNA fragments.Our rapid, cheap and powerful method allows efficient cloning of TAL effector genes from xanthomonads, as demonstrated for two rice-pathogenic strains of Xanthomonas oryzae from Africa. Method name: TAL fishing, Keywords: Enrichment cloning, Type III secretion, Type III effector, TAL effector, TALome, Xanthomonas, Bacterial leaf blight, Bacterial leaf streak, Rice
url http://www.sciencedirect.com/science/article/pii/S2215016118301420
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