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Rapid and efficient genome-wide characterization of Xanthomonas TAL effector genes.

Yu YH, Lu Y, He YQ, Huang S, Tang JL - Sci Rep (2015)

Bottom Line: Their specificity is determined by a tandem repeat domain.Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling.Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.

ABSTRACT
Xanthomonas TALE transcriptional activators act as virulence or avirulence factors by activating host disease susceptibility or resistance genes. Their specificity is determined by a tandem repeat domain. Some Xanthomonas pathogens contain 10-30 TALEs per strain. Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling. To facilitate TALE studies, we developed an efficient and rapid pipeline for genome-wide cloning of tal genes as many as possible from a strain. Here, we report the pipeline and its use to identify all 18 tal genes from a newly isolated strain of the rice pathogen Xathomonas oryzae. Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

No MeSH data available.


Related in: MedlinePlus

A Venn diagram illustrating the number of TALEs sharing identical RVD strings among Xoo strains K74, PXO99A and MAFF311018.
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f4: A Venn diagram illustrating the number of TALEs sharing identical RVD strings among Xoo strains K74, PXO99A and MAFF311018.

Mentions: As described above, DNA-binding specificity of TALEs to plant genes is determined by their RVD strings in the repeat motifs. To gain some general knowledge on the composition features and potential functions of the RVDs in the TalXooK74 effectors, we compared them with those in the TALEs identified from the Philippine strain PXO99A and the Japanese strain MAFF3110182526. The result showed that the RVDs of TalXooK74-1 and TalXooK74-15 are similar to each other, and the RVDs of one (TalXooK74-12) and four (TalXooK74-3, TalXooK74-11, TalXooK74-13, and TalXooK74-17) K74 TALEs are identical to those of PXO99A and MAFF311018 TALEs, respectively, and no TALE is identical among the three strains (Fig. 4; Supplementary Table 7). In total, there are 13 TALEs which are similar among the three strains and may compose a set of core TALEs of the Xoo strains (Supplementary Table 7). Interestingly, the RVD strings of TalXooK74-4 and TalXooK74-16 are very similar to those of the TALEs AvrXa23 and AvrXa27 identified in PXO99A, respectively (Supplementary Table 7), which are avirulence determinants conferring incompatibility on rice cultivars harboring the R genes Xa23 and Xa27, respectively22.


Rapid and efficient genome-wide characterization of Xanthomonas TAL effector genes.

Yu YH, Lu Y, He YQ, Huang S, Tang JL - Sci Rep (2015)

A Venn diagram illustrating the number of TALEs sharing identical RVD strings among Xoo strains K74, PXO99A and MAFF311018.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4536657&req=5

f4: A Venn diagram illustrating the number of TALEs sharing identical RVD strings among Xoo strains K74, PXO99A and MAFF311018.
Mentions: As described above, DNA-binding specificity of TALEs to plant genes is determined by their RVD strings in the repeat motifs. To gain some general knowledge on the composition features and potential functions of the RVDs in the TalXooK74 effectors, we compared them with those in the TALEs identified from the Philippine strain PXO99A and the Japanese strain MAFF3110182526. The result showed that the RVDs of TalXooK74-1 and TalXooK74-15 are similar to each other, and the RVDs of one (TalXooK74-12) and four (TalXooK74-3, TalXooK74-11, TalXooK74-13, and TalXooK74-17) K74 TALEs are identical to those of PXO99A and MAFF311018 TALEs, respectively, and no TALE is identical among the three strains (Fig. 4; Supplementary Table 7). In total, there are 13 TALEs which are similar among the three strains and may compose a set of core TALEs of the Xoo strains (Supplementary Table 7). Interestingly, the RVD strings of TalXooK74-4 and TalXooK74-16 are very similar to those of the TALEs AvrXa23 and AvrXa27 identified in PXO99A, respectively (Supplementary Table 7), which are avirulence determinants conferring incompatibility on rice cultivars harboring the R genes Xa23 and Xa27, respectively22.

Bottom Line: Their specificity is determined by a tandem repeat domain.Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling.Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.

ABSTRACT
Xanthomonas TALE transcriptional activators act as virulence or avirulence factors by activating host disease susceptibility or resistance genes. Their specificity is determined by a tandem repeat domain. Some Xanthomonas pathogens contain 10-30 TALEs per strain. Although TALEs play critical roles in pathogenesis, their studies have so far been limited to a few examples, due to their highly repetitive gene structure and extreme similarity among different members, which constrict sequencing and assembling. To facilitate TALE studies, we developed an efficient and rapid pipeline for genome-wide cloning of tal genes as many as possible from a strain. Here, we report the pipeline and its use to identify all 18 tal genes from a newly isolated strain of the rice pathogen Xathomonas oryzae. Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen1, and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs.

No MeSH data available.


Related in: MedlinePlus