Identification of susceptibility targets of bacterial leaf blight and development of genome edited rice lines with increased resistance

Research output: Thesis › Doctoral thesis

Authors

  • Stefanie Mücke

Research Organisations

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Details

Original languageEnglish
QualificationDoctor rerum naturalium
Awarding Institution
Supervised by
  • Jens Boch, Supervisor
Date of Award14 Sept 2020
Place of PublicationHannover
Publication statusPublished - 2020

Abstract

Phytopathogenic Xanthomonas oryzae bacteria infect rice and cause severe harvest loss, which challenges the stable food supply. Transcription activator-like effectors (TALEs) are major virulence factors of these pathogens and manipulate the host gene expression to benefit infection. With the help of the AnnoTALE tool, TALEs can be assigned into classes, which represent closely related TALEs that likely activate the same gene. Analyzing the TALome diversity of 34 Asian Xanthomonas oryzae pv. oryzae (Xoo) strains revealed a total of 45 TALE classes and a common core set of 10 TALE classes present in more than 80% of strains. Combining computational TALE target gene predictions and transcriptomics data of infected rice produced 61 likely TALE target genes for three selected Xoo strains. Representative TALEs of these strains were reconstructed and introduced into a naturally TALE-free Xoo strain to verify the correlation between individual TALEs and specific induced genes. 13 genes were shown to be TALE-dependently induced upon infection in rice. Using reporter assays, direct interaction between TALEs and their corresponding target promoters could be demonstrated. These newly identified target genes unveiled convergent evolution between Xoo and rice-pathogenic Xanthomonas oryzae pv. oryzicola, which share more common target genes addressed by different TALE classes than previously believed. Individual TALEs did not have a strong influence on virulence in gain-of-function assays but several TALE classes might be linked to salicylic acid manipulation, which controls Xoo resistance reactions. Rice plants were edited using CRISPR/Cas9 to knockout target genes or mutate multiple TALE binding sites in target promoters. Initial results indicate reduced virulence of wild type Xoo strains on rice plants with 7 mutated TALE binding sites in TALE target promoters identified in this thesis. Taken together, a detailed picture of TALE-induced plant processes could be established that significantly expands understanding of Xanthomonas oryzae virulence strategies. Additionally, the groundwork was laid to facilitate the development of novel resistances to overcome this important rice disease.

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@phdthesis{a40bde4cc7e446999a0caac4dc95f297,
title = "Identification of susceptibility targets of bacterial leaf blight and development of genome edited rice lines with increased resistance",
abstract = "Phytopathogenic Xanthomonas oryzae bacteria infect rice and cause severe harvest loss, which challenges the stable food supply. Transcription activator-like effectors (TALEs) are major virulence factors of these pathogens and manipulate the host gene expression to benefit infection. With the help of the AnnoTALE tool, TALEs can be assigned into classes, which represent closely related TALEs that likely activate the same gene. Analyzing the TALome diversity of 34 Asian Xanthomonas oryzae pv. oryzae (Xoo) strains revealed a total of 45 TALE classes and a common core set of 10 TALE classes present in more than 80% of strains. Combining computational TALE target gene predictions and transcriptomics data of infected rice produced 61 likely TALE target genes for three selected Xoo strains. Representative TALEs of these strains were reconstructed and introduced into a naturally TALE-free Xoo strain to verify the correlation between individual TALEs and specific induced genes. 13 genes were shown to be TALE-dependently induced upon infection in rice. Using reporter assays, direct interaction between TALEs and their corresponding target promoters could be demonstrated. These newly identified target genes unveiled convergent evolution between Xoo and rice-pathogenic Xanthomonas oryzae pv. oryzicola, which share more common target genes addressed by different TALE classes than previously believed. Individual TALEs did not have a strong influence on virulence in gain-of-function assays but several TALE classes might be linked to salicylic acid manipulation, which controls Xoo resistance reactions. Rice plants were edited using CRISPR/Cas9 to knockout target genes or mutate multiple TALE binding sites in target promoters. Initial results indicate reduced virulence of wild type Xoo strains on rice plants with 7 mutated TALE binding sites in TALE target promoters identified in this thesis. Taken together, a detailed picture of TALE-induced plant processes could be established that significantly expands understanding of Xanthomonas oryzae virulence strategies. Additionally, the groundwork was laid to facilitate the development of novel resistances to overcome this important rice disease.",
author = "Stefanie M{\"u}cke",
note = "Doctoral thesis",
year = "2020",
doi = "10.15488/10076",
language = "English",
school = "Leibniz University Hannover",

}

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TY - BOOK

T1 - Identification of susceptibility targets of bacterial leaf blight and development of genome edited rice lines with increased resistance

AU - Mücke, Stefanie

N1 - Doctoral thesis

PY - 2020

Y1 - 2020

N2 - Phytopathogenic Xanthomonas oryzae bacteria infect rice and cause severe harvest loss, which challenges the stable food supply. Transcription activator-like effectors (TALEs) are major virulence factors of these pathogens and manipulate the host gene expression to benefit infection. With the help of the AnnoTALE tool, TALEs can be assigned into classes, which represent closely related TALEs that likely activate the same gene. Analyzing the TALome diversity of 34 Asian Xanthomonas oryzae pv. oryzae (Xoo) strains revealed a total of 45 TALE classes and a common core set of 10 TALE classes present in more than 80% of strains. Combining computational TALE target gene predictions and transcriptomics data of infected rice produced 61 likely TALE target genes for three selected Xoo strains. Representative TALEs of these strains were reconstructed and introduced into a naturally TALE-free Xoo strain to verify the correlation between individual TALEs and specific induced genes. 13 genes were shown to be TALE-dependently induced upon infection in rice. Using reporter assays, direct interaction between TALEs and their corresponding target promoters could be demonstrated. These newly identified target genes unveiled convergent evolution between Xoo and rice-pathogenic Xanthomonas oryzae pv. oryzicola, which share more common target genes addressed by different TALE classes than previously believed. Individual TALEs did not have a strong influence on virulence in gain-of-function assays but several TALE classes might be linked to salicylic acid manipulation, which controls Xoo resistance reactions. Rice plants were edited using CRISPR/Cas9 to knockout target genes or mutate multiple TALE binding sites in target promoters. Initial results indicate reduced virulence of wild type Xoo strains on rice plants with 7 mutated TALE binding sites in TALE target promoters identified in this thesis. Taken together, a detailed picture of TALE-induced plant processes could be established that significantly expands understanding of Xanthomonas oryzae virulence strategies. Additionally, the groundwork was laid to facilitate the development of novel resistances to overcome this important rice disease.

AB - Phytopathogenic Xanthomonas oryzae bacteria infect rice and cause severe harvest loss, which challenges the stable food supply. Transcription activator-like effectors (TALEs) are major virulence factors of these pathogens and manipulate the host gene expression to benefit infection. With the help of the AnnoTALE tool, TALEs can be assigned into classes, which represent closely related TALEs that likely activate the same gene. Analyzing the TALome diversity of 34 Asian Xanthomonas oryzae pv. oryzae (Xoo) strains revealed a total of 45 TALE classes and a common core set of 10 TALE classes present in more than 80% of strains. Combining computational TALE target gene predictions and transcriptomics data of infected rice produced 61 likely TALE target genes for three selected Xoo strains. Representative TALEs of these strains were reconstructed and introduced into a naturally TALE-free Xoo strain to verify the correlation between individual TALEs and specific induced genes. 13 genes were shown to be TALE-dependently induced upon infection in rice. Using reporter assays, direct interaction between TALEs and their corresponding target promoters could be demonstrated. These newly identified target genes unveiled convergent evolution between Xoo and rice-pathogenic Xanthomonas oryzae pv. oryzicola, which share more common target genes addressed by different TALE classes than previously believed. Individual TALEs did not have a strong influence on virulence in gain-of-function assays but several TALE classes might be linked to salicylic acid manipulation, which controls Xoo resistance reactions. Rice plants were edited using CRISPR/Cas9 to knockout target genes or mutate multiple TALE binding sites in target promoters. Initial results indicate reduced virulence of wild type Xoo strains on rice plants with 7 mutated TALE binding sites in TALE target promoters identified in this thesis. Taken together, a detailed picture of TALE-induced plant processes could be established that significantly expands understanding of Xanthomonas oryzae virulence strategies. Additionally, the groundwork was laid to facilitate the development of novel resistances to overcome this important rice disease.

U2 - 10.15488/10076

DO - 10.15488/10076

M3 - Doctoral thesis

CY - Hannover

ER -