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Article ; Online: CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator‐like effectors in two divergent pathogens

Zárate‐Chaves, Carlos Andrés / Audran, Corinne / Medina Culma, César Augusto / Escalon, Aline / Javegny, Stéphanie / Gagnevin, Lionel / Thomas, Emilie / Pimparé, Léa‐Lou / López, Camilo E. / Jacobs, Jonathan M. / Noël, Laurent D. / Koebnik, Ralf / Bernal, Adriana Jimena / Szurek, Boris

New Phytologist. 2023 May, v. 238, no. 4 p.1593-1604

2023

Abstract: Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR–Cas9 for directed mutagenesis in bacteria. Here, we successfully ... ...

Abstract	Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR–Cas9 for directed mutagenesis in bacteria. Here, we successfully applied a CRISPR interference strategy to investigate the cryptic role of the transcription activator‐like effector (tale) multigene family in several plant‐pathogenic Xanthomonas bacterial species, owing to their contribution to pathogen virulence. Single guide RNAs (sgRNAs) designed against Xanthomonas phaseoli pv manihotis tale conserved gene sequences efficiently silenced expression of all tales, with concomitant decrease in virulence and TALE‐induced host gene expression. The system is readily translatable to other Xanthomonas species infecting rice, citrus, Brassica, and cassava, silencing up to 16 tales in a given strain using a single sgRNA. Complementation with plasmid‐borne designer tales lacking the sgRNA‐targeted sequence restored molecular and virulence phenotypes in all pathosystems. Our results evidenced that X. campestris pv campestris CN08 tales are relevant for symptom development in cauliflower. They also show that the MeSWEET10a sugar transporter is surprisingly targeted by the nonvascular cassava pathogen X. cassavae, highlighting a new example of TALE functional convergence between phylogenetically distant Xanthomonas. Overall, this novel technology provides a platform for discovery and rapid functional understanding of highly conserved gene families.
Keywords	Brassica ; CRISPR-Cas systems ; Citrus ; Xanthomonas campestris pv. phaseoli ; cassava ; cauliflower ; gene expression ; insertional mutagenesis ; multigene family ; pathogens ; phylogeny ; rice ; sugars ; technology ; toxicity ; virulence
Language	English
Dates of publication	2023-05
Size	p. 1593-1604.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18808
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator-like effectors in two divergent pathogens.

Zárate-Chaves, Carlos Andrés / Audran, Corinne / Medina Culma, César Augusto / Escalon, Aline / Javegny, Stéphanie / Gagnevin, Lionel / Thomas, Emilie / Pimparé, Léa-Lou / López, Camilo E / Jacobs, Jonathan M / Noël, Laurent D / Koebnik, Ralf / Bernal, Adriana Jimena / Szurek, Boris

The New phytologist

2023 Volume 238, Issue 4, Page(s) 1593–1604

Abstract: Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR-Cas9 for directed mutagenesis in bacteria. Here, we successfully ... ...

Abstract	Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR-Cas9 for directed mutagenesis in bacteria. Here, we successfully applied a CRISPR interference strategy to investigate the cryptic role of the transcription activator-like effector (tale) multigene family in several plant-pathogenic Xanthomonas bacterial species, owing to their contribution to pathogen virulence. Single guide RNAs (sgRNAs) designed against Xanthomonas phaseoli pv manihotis tale conserved gene sequences efficiently silenced expression of all tales, with concomitant decrease in virulence and TALE-induced host gene expression. The system is readily translatable to other Xanthomonas species infecting rice, citrus, Brassica, and cassava, silencing up to 16 tales in a given strain using a single sgRNA. Complementation with plasmid-borne designer tales lacking the sgRNA-targeted sequence restored molecular and virulence phenotypes in all pathosystems. Our results evidenced that X. campestris pv campestris CN08 tales are relevant for symptom development in cauliflower. They also show that the MeSWEET10a sugar transporter is surprisingly targeted by the nonvascular cassava pathogen X. cassavae, highlighting a new example of TALE functional convergence between phylogenetically distant Xanthomonas. Overall, this novel technology provides a platform for discovery and rapid functional understanding of highly conserved gene families.
MeSH term(s)	Transcription Activator-Like Effectors/genetics ; Xanthomonas/genetics ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Virulence/genetics ; Biological Transport ; Plant Diseases/microbiology ; Oryza/genetics
Chemical Substances	Transcription Activator-Like Effectors ; Bacterial Proteins
Language	English
Publishing date	2023-03-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18808
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Article ; Online: Cassava bacterial blight, caused by Xanthomonas axonopodis pv. Manihotis

Verdier, Valerie M. / López Carrascal, Camilo Ernesto / Bernal, Adriana Jimena

2017

Keywords	manihot esculenta ; plant diseases ; xanthomonas manihotis ; symptoms ; aetiology ; epidemiology ; disease resistance ; disease control ; biological control ; enfermedades de las plantas ; síntomas ; etiología ; epidemiología ; resistencia a la enfermedad ; control de enfermedades ; control biológico
Language	English
Publishing date	2017-06-20T08:59:38Z
Publisher	International Center for Tropical Agriculture
Publishing country	fr
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Problemas fitopatológicos en especies de la familia Solanaceae causados por los géneros Phytophthora , Alternaria y Ralstonia en Colombia. Una revisión.

Carreño Natalia / Vargas Ángela / Bernal Adriana Jimena / Restrepo Silvia

Agronomía Colombiana, Vol 25, Iss 2, Pp 320-

2007 Volume 329

Abstract: La familia Solanaceae es considerada el tercer taxa botánico más importante a nivel agronómico, hecho que ha generado que mundialmente se invierta un gran esfuerzo en estudiar la biología, ecología y diversidad de hábitats de muchas de sus especies. En ... ...

Abstract	La familia Solanaceae es considerada el tercer taxa botánico más importante a nivel agronómico, hecho que ha generado que mundialmente se invierta un gran esfuerzo en estudiar la biología, ecología y diversidad de hábitats de muchas de sus especies. En Colombia, las especies más cultivadas son comúnmente atacadas por patógenos que limitan la producción y la calidad final del producto. El presente documento expone la recopilación de los estudios publicados realizados en Colombia, referentes a las enfermedades causadas por tres de los patógenos más importantes que afectan la familia Solanaceae: Phytophthora , Alternaria y Ralstonia .
Keywords	control químico ; control biológico ; papa ; tomate ; uchuva ; lulo ; tomate de árbol ; ají ; pimentón ; tabaco. ; Plant ecology ; QK900-989
Language	English
Publishing date	2007-12-01T00:00:00Z
Publisher	Centro Editorial of Facultad de Ciencias Agrarias, Universidad Nacional de Colombia
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Characterization of cellulases of fungal endophytes isolated from Espeletia spp.

Cabezas, Luisa / Calderon, Carolina / Medina, Luis Miguel / Bahamon, Isabela / Cardenas, Martha / Bernal, Adriana Jimena / Gonzalez, Andrés / Restrepo, Silvia

Journal of microbiology (Seoul, Korea)

2012 Volume 50, Issue 6, Page(s) 1009–1013

Abstract: Endophytes are microorganisms that asymptomatically invade plant tissues. They can stimulate plant growth and/or provide defense against pathogen attacks through the production of secondary metabolites. Most endophyte species are still unknown, and ... ...

Abstract	Endophytes are microorganisms that asymptomatically invade plant tissues. They can stimulate plant growth and/or provide defense against pathogen attacks through the production of secondary metabolites. Most endophyte species are still unknown, and because they may have several applications, the study of their metabolic capabilities is essential. We characterized 100 endophytes isolated from Espeletia spp., a genus unique to the paramo ecosystem, an extreme environment in the Andean mountain range. We evaluated the cellulolytic potential of these endophytes on the saccharification of the oil palm empty fruit bunch (OPEFB). The total cellulolytic activity was measured for each endophyte on filter paper (FPA). In addition, the specific carboxymethyl cellulase (CMCase), exoglucanase, and β-glucosidase activities were determined. We found four fungi positive for cellulases. Of these fungi, Penicillium glabrum had the highest cellulolytic activity after partial purification, with maximal CMCase, exoglucanase and β-glucosidase enzyme activities of 44.5, 48.3, and 0.45 U/ml, respectively. Our data showed that the bioprospection of fungi and the characterization of their enzymes may facilitate the process of biofuel production.
MeSH term(s)	Cellulases/isolation & purification ; Cellulases/metabolism ; Endophytes/enzymology ; Enzyme Activation ; Ferns/microbiology ; Fungi/enzymology ; Fungi/isolation & purification
Chemical Substances	Cellulases (EC 3.2.1.-)
Language	English
Publishing date	2012-12-30
Publishing country	Korea (South)
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2012399-1
ISSN	1976-3794 ; 1225-8873
ISSN (online)	1976-3794
ISSN	1225-8873
DOI	10.1007/s12275-012-2130-5
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Article ; Online: A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes.

Soto, Johana Carolina / Ortiz, Juan Felipe / Perlaza-Jiménez, Laura / Vásquez, Andrea Ximena / Lopez-Lavalle, Luis Augusto Becerra / Mathew, Boby / Léon, Jens / Bernal, Adriana Jimena / Ballvora, Agim / López, Camilo Ernesto

BMC genomics

2015 Volume 16, Page(s) 190

Abstract: Background: Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic ... ...

Abstract	Background: Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. Results: A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. Conclusions: This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.
MeSH term(s)	Chromosome Mapping ; Cluster Analysis ; Genetic Linkage ; Genetic Markers ; Genome, Plant ; Genotype ; Manihot/genetics ; Plant Immunity/genetics ; Plant Proteins/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sequence Analysis, DNA
Chemical Substances	Genetic Markers ; Plant Proteins
Language	English
Publishing date	2015-03-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-015-1397-4
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Article ; Online: A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

Soto, Johana Carolina / Ortiz, Juan Felipe / Perlaza-Jiménez, Laura / Vásquez, Andrea Ximena / Becerra López Lavelle, Luis Augusto / Mathew, Boby / Léon, Jens / Bernal, Adriana Jimena / Ballvora, Agim / López Carrascal, Camilo Ernesto

BMC Genomics

2015

Abstract: CIAT- Outstanding Research Publication Award (ORPA) - 2015 ... Background Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense ... ...

Abstract	CIAT- Outstanding Research Publication Award (ORPA) - 2015 Background Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. Results A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. Conclusions This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity ...
Keywords	chromosome mapping ; genetic maps ; manihot esculenta crantz ; dna ; genes ; genetic markers ; polymorphism ; mapas genéticos ; adn ; marcadores genéticos ; polimorfismo
Language	English
Publishing date	2015-04-07T14:42:21Z
Publisher	Springer
Publishing country	fr
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Disruption of ATCSLD5 results in reduced growth, reduced xylan and homogalacturonan synthase activity and altered xylan occurrence in Arabidopsis

Bernal, Adriana Jimena / Jensen, Jakob Krüger / Harholt, Jesper / Sørensen, Susanne / Moller, Isabel / Blaukopf, Claudia / Johansen, Bo / de Lotto, Robert / Pauly, Markus / Scheller, Henrik Vibe / Willats, William G.T

Plant journal. 2007 Dec., v. 52, no. 5

2007

Abstract: Members of a large family of cellulose synthase-like genes (CSLs) are predicted to encode glycosyl transferases (GTs) involved in the biosynthesis of plant cell walls. The CSLA and CSLF families are known to contain mannan and glucan synthases, ... ...

Abstract	Members of a large family of cellulose synthase-like genes (CSLs) are predicted to encode glycosyl transferases (GTs) involved in the biosynthesis of plant cell walls. The CSLA and CSLF families are known to contain mannan and glucan synthases, respectively, but the products of other CSLs are unknown. Here we report the effects of disrupting ATCSLD5 expression in Arabidopsis. Both stem and root growth were significantly reduced in ATCSLD5 knock-out plants, and these plants also had increased susceptibility to the cellulose synthase inhibitor isoxaben. Antibody and carbohydrate-binding module labelling indicated a reduction in the level of xylan in stems, and in vitro GT assays using microsomes from stems revealed that ATCSLD5 knock-out plants also had reduced xylan and homogalacturonan synthase activity. Expression in Nicotiana benthamiana of ATCSLD5 and ATCSLD3, fluorescently tagged at either the C- or the N-terminal, indicated that these GTs are likely to be localized in the Golgi apparatus. However, the position of the fluorescent tag affected the subcellular localization of both proteins. The work presented provides a comprehensive analysis of the effects of disrupting ATCSLD5 in planta, and the possible role(s) of this gene and other ATCSLDs in cell wall biosynthesis are discussed.
Keywords	xylan
Language	English
Dates of publication	2007-12
Size	p. 791-802.
Publisher	Blackwell Publishing Ltd
Publishing place	Oxford, UK
Document type	Article
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/j.1365-313X.2007.03281.x
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Article: Disruption of ATCSLD5 results in reduced growth, reduced xylan and homogalacturonan synthase activity and altered xylan occurrence in Arabidopsis.

The Plant journal : for cell and molecular biology

2007 Volume 52, Issue 5, Page(s) 791–802

Abstract	Members of a large family of cellulose synthase-like genes (CSLs) are predicted to encode glycosyl transferases (GTs) involved in the biosynthesis of plant cell walls. The CSLA and CSLF families are known to contain mannan and glucan synthases, respectively, but the products of other CSLs are unknown. Here we report the effects of disrupting ATCSLD5 expression in Arabidopsis. Both stem and root growth were significantly reduced in ATCSLD5 knock-out plants, and these plants also had increased susceptibility to the cellulose synthase inhibitor isoxaben. Antibody and carbohydrate-binding module labelling indicated a reduction in the level of xylan in stems, and in vitro GT assays using microsomes from stems revealed that ATCSLD5 knock-out plants also had reduced xylan and homogalacturonan synthase activity. Expression in Nicotiana benthamiana of ATCSLD5 and ATCSLD3, fluorescently tagged at either the C- or the N-terminal, indicated that these GTs are likely to be localized in the Golgi apparatus. However, the position of the fluorescent tag affected the subcellular localization of both proteins. The work presented provides a comprehensive analysis of the effects of disrupting ATCSLD5 in planta, and the possible role(s) of this gene and other ATCSLDs in cell wall biosynthesis are discussed.
MeSH term(s)	Arabidopsis/enzymology ; Arabidopsis/genetics ; Arabidopsis/growth & development ; Arabidopsis Proteins/analysis ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Benzamides/pharmacology ; Glucosyltransferases/analysis ; Glucosyltransferases/genetics ; Glucosyltransferases/metabolism ; Glucuronidase/analysis ; Pectins/biosynthesis ; Pentosyltransferases/metabolism ; Plants, Genetically Modified/metabolism ; Nicotiana/genetics ; Xylans/metabolism
Chemical Substances	Arabidopsis Proteins ; Benzamides ; Xylans ; isoxaben (82558-50-7) ; Pectins (89NA02M4RX) ; CSLD5 protein, Arabidopsis (EC 2.4.1.-) ; Glucosyltransferases (EC 2.4.1.-) ; cellulose synthase (EC 2.4.1.-) ; Pentosyltransferases (EC 2.4.2.-) ; 1,4-beta-D-xylan synthase (EC 2.4.2.24) ; Glucuronidase (EC 3.2.1.31) ; polygalacturonic acid (VV3XD4CL04)
Language	English
Publishing date	2007-09-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/j.1365-313X.2007.03281.x
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