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Comparative Study
. 2013 May 29;8(5):e64267.
doi: 10.1371/journal.pone.0064267. Print 2013.

Comparative transcriptome profiling reveals different expression patterns in Xanthomonas oryzae pv. oryzae strains with putative virulence-relevant genes

Fan Zhang  1 , Zhenglin Du, Liyu Huang, Casiana Vera Cruz, Yongli Zhou, Zhikang Li
Affiliations
Comparative Study

Comparative transcriptome profiling reveals different expression patterns in Xanthomonas oryzae pv. oryzae strains with putative virulence-relevant genes

Fan Zhang et al. PLoS One. .

Abstract

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice bacterial blight, which is a major rice disease in tropical Asian countries. An attempt has been made to investigate gene expression patterns of three Xoo strains on the minimal medium XOM2, PXO99 (P6) and PXO86 (P2) from the Philippines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4,781 transcripts were identified in this study, and 1,151 and 3,076 genes were differentially expressed when P6 was compared with P2 and with C5, respectively. Our results indicated that Xoo strains from different regions exhibited distinctly different expression patterns of putative virulence-relevant genes. Interestingly, 40 and 44 genes involved in chemotaxis and motility exhibited higher transcript alterations in C5 compared with P6 and P2, respectively. Most other genes associated with virulence, including exopolysaccharide (EPS) synthesis, Hrp genes and type III effectors, including Xanthomonas outer protein (Xop) effectors and transcription activator-like (TAL) effectors, were down-regulated in C5 compared with P6 and P2. The data were confirmed by real-time quantitative RT-PCR, tests of bacterial motility, and enzyme activity analysis of EPS and xylanase. These results highlight the complexity of Xoo and offer new avenues for improving our understanding of Xoo-rice interactions and the evolution of Xoo virulence.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Lesion length of rice varieties inoculated by Xanthomonas oryzae pv. oryzae (Xoo) strains and growth curve of Xoo.
(A) Lesion length of 30 rice varieties inoculated by three Xoo strains. * and ** represent significant difference at P<0.05 and 0.001, respectively. (B) Left: Hanyou715 exhibited different lesion lengths after infection with Xoo strains PXO99 (P6) and PXO86 (P2) from the Philippines and GD1358 (C5) from China. Right: growth of P2, P6 and C5 in Hanyou715. (C) Left: Hanyou53 exhibited different lesion lengths after infection with P2, P6 and C5. Right: growth of P2, P6 and C5 in Hanyou715. CFUs indicates the colony-forming units.
Figure 2
Figure 2. Overview of mRNA-seq data and mapping to the Xanthomonas oryzae pv. oryzae (Xoo) PXO99A genome.
(A) Total number of mRNA-seq reads mapped in each Xoo strain library. (B) Histogram presentation of gene ontology classifications. The results are summarized in three categories: cellular components, molecular functions and biology processes. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in that main category. (C) Comparison of transcription measurements by Illumina sequencing and qRT-PCR assays. The correlation coefficient (R2) between the two datasets is 0.8927.
Figure 3
Figure 3. Differentially expressed genes (DEGs) between three Xanthomonas oryzae pv. oryzae strains, PXO99 (P6) and PXO86 (P2) from the Philippines and GD1358 (C5) from China.
(A) Genes related to the two-component systems. (B) Genes related to chemotaxis and motility.
Figure 4
Figure 4. The expression patterns of genes associated with motility and swarming motility of Xanthomonas oryzae pv. oryzae (Xoo) strains PXO99 (P6) and PXO86 (P2) from the Philippines and GD1358 (C5) from China.
(A) The expression patterns of cheA. (B) The expression patterns of cheD. (C) The expression patterns of motC. (D) The expression patterns of motD. The gene expression level (arbitrary units) was normalized using 16sRNA as an internal reference. The gene expression level was quantified by real-time RT-PCR. (E) Swarming motility of Xoo on plates. * and ** represent significant difference at P<0.05 and 0.001, respectively.
Figure 5
Figure 5. The activity of exopolysaccharides (EPS) and xylanase, and the expression patterns of hrp genes and Xop genes of Xanthomonas oryzae pv. oryzae strains PXO99 (P6) and PXO86 (P2) from the Philippines and GD1358 (C5) from China.
(A) EPS activity. (B) Xylanase activity. * and ** represent significance difference at P<0.05 and 0.001, respectively. (C) The expression patterns of hrpG. (D) The expression patterns of hrpX. (E) The expression patterns of hrpB2. (F) The expression patterns of hrpF. (G) The expression patterns of xopN. (H) The expression patterns of xopW. The gene expression level (arbitrary units) was normalized using 16sRNA as an internal reference. The gene expression level was quantified by real-time RT-PCR.
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