Abstract
BACKGROUND: Plant-pathogen interactions at early stages of infection are important to the fate of interaction. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, which is a devastating disease in rice. Although in vivo and in vitro systems have been developed to study rice-Xoo interactions, both systems have limitations. The resistance mechanisms in rice can be better studied by the in vivo approach, whereas the in vitro systems are suitable for pathogenicity studies on Xoo. The current in vitro system uses minimal medium to activate the pathogenic signal (expression of pathogenicity-related genes) of Xoo, but lacks rice-derived factors needed for Xoo activation. This fact emphasizes the need of developing a new in vitro system that allow for an easy control of both pathogenic activation and for the experiment itself. RESULTS: We employed an in vitro system that can activate pathogenicity-related genes in Xoo using rice leaf extract (RLX) and combined the in vitro assay with RNA-Seq to analyze the time-resolved genome-wide gene expression of Xoo. RNA-Seq was performed with samples from seven different time points within 1 h post-RLX treatment and the expression of up- or downregulated genes in RNA-Seq was validated by qRT-PCR. Global analysis of gene expression and regulation revealed the most dramatic changes in functional categories of genes related to inorganic ion transport and metabolism, and cell motility. Expression of many pathogenicity-related genes was induced within 15 min upon contact with RLX. hrpG and hrpX expression reached the maximum level within 10 and 15 min, respectively. Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genes were downregulated for 10 min and were then upregulated. Genes related to inorganic ion uptake were upregulated within 5 min. We introduced a non-linear regression fit to generate continuous time-resolved gene expression levels and tested the essentiality of the transcriptionally upregulated genes by a pathogenicity assay of lesion length using single-gene knock-out Xoo strains. CONCLUSIONS: The in vitro system combined with RNA-Seq generated a genome-wide time-resolved pathogenic gene expression profile within 1 h of initial rice-Xoo interactions, demonstrating the expression order and interaction dependency of pathogenic genes. This combined system can be used as a novel tool to study the initial interactions between rice and Xoo during bacterial blight progression.
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Claims 10
Claim · model-written summary
Rice leaf extract activated pathogenicity related genes in Xoo in vitro.
- Taxon
- rice
Oryza sativae0 - Interactor
- Xooe0pathogen
- Outcome
- activate pathogenicity-related genes in Xooe0
Not reportedValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“an in vitro system that can activate pathogenicity-related genes in Xoo using rice leaf extract (RLX)”
Claim · model-written summary
The strongest gene expression changes concerned inorganic ion transport and metabolism and cell motility.
- Taxon
- riceOryza sativae1
- Outcome
- the most dramatic changes in functional categories of genes related to inorganic ion transport and metabolism, and cell motilitye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Global analysis of gene expression and regulation revealed the most dramatic changes in functional categories of genes related to inorganic ion transport and metabolism, and cell motility”
e1“rice leaf extract (RLX)”
Claim · model-written summary
Rice leaf extract induced many pathogenicity related genes within 15 minutes.
- Taxon
- riceOryza sativae1
- Treatment
- RLXe0
- Interactor
- Xooe2pathogen
- Outcome
- Expression of many pathogenicity-related genese0
- Direction
- inducede0
- Value
- 15 mine0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Expression of many pathogenicity-related genes was induced within 15 min upon contact with RLX”
e1“rice leaf extract (RLX)”
e2“pathogenicity-related genes in Xoo”
Claim · model-written summary
Xoo hrpG expression peaked within 10 minutes of rice leaf extract exposure.
- Taxon
- riceOryza sativae1
- Interactor
- Xooe2pathogen
- Gene
- hrpGe0
- Outcome
- hrpG and hrpX expressione0
- Direction
- maximume0
- Value
- 10e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“hrpG and hrpX expression reached the maximum level within 10 and 15 min, respectively”
e1“rice leaf extract (RLX)”
e2“pathogenicity-related genes in Xoo”
Claim · model-written summary
Xoo hrpX expression peaked within 15 minutes of rice leaf extract exposure.
- Taxon
- riceOryza sativae1
- Interactor
- Xooe2pathogen
- Gene
- hrpXe0
- Outcome
- hrpG and hrpX expressione0
- Direction
- maximume0
- Value
- 15 mine0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“hrpG and hrpX expression reached the maximum level within 10 and 15 min, respectively”
e1“rice leaf extract (RLX)”
e2“pathogenicity-related genes in Xoo”
Claim · model-written summary
Chemotaxis, flagella biosynthesis and cyclic-di-GMP controlling genes were initially downregulated for 10 minutes.
- Taxon
- riceOryza sativae1
- Treatment
- RLXe1
- Outcome
- Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genese0
- Direction
- downregulatede0
- Value
- 10 mine0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genes were downregulated for 10 min and were then upregulated”
e1“rice leaf extract (RLX)”
Claim · model-written summary
Those chemotaxis, flagella and cyclic-di-GMP genes were subsequently upregulated.
- Taxon
- riceOryza sativae1
- Treatment
- RLXe1
- Outcome
- Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genese0
- Direction
- upregulatede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genes were downregulated for 10 min and were then upregulated”
e1“rice leaf extract (RLX)”
Claim · model-written summary
Inorganic ion uptake genes were upregulated within five minutes.
- Taxon
- riceOryza sativae1
- Treatment
- RLXe1
- Outcome
- Genes related to inorganic ion uptakee0
- Direction
- upregulatede0
- Value
- 5 mine0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Genes related to inorganic ion uptake were upregulated within 5 min”
e1“rice leaf extract (RLX)”
Claim · model-written summary
The combined in vitro and RNA Seq system produced a genome wide expression profile across the first hour of rice Xoo interaction.
- Taxon
- riceOryza sativae0
- Interactor
- Xooe0pathogen
- Outcome
- genome-wide time-resolved pathogenic gene expression profilee0
- Value
- 1 he0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The in vitro system combined with RNA-Seq generated a genome-wide time-resolved pathogenic gene expression profile within 1 h of initial rice-Xoo interactions”
Claim · model-written summary
The combined system showed gene expression order and dependence on interaction with rice.
- Taxon
- riceOryza sativae1
- Interactor
- Xooe1pathogen
- Outcome
- expression order and interaction dependency of pathogenic genese0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“demonstrating the expression order and interaction dependency of pathogenic genes”
e1“initial rice-Xoo interactions”
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