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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

MscI partial digestion of talC-BamHI fragment cloned in pUC19.2 μg plasmid DNA was digested with 5 u MscI enzyme. The digestion times are given in minutes above the gel. M, 100 bp DNA ladder makers.
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f2: MscI partial digestion of talC-BamHI fragment cloned in pUC19.2 μg plasmid DNA was digested with 5 u MscI enzyme. The digestion times are given in minutes above the gel. M, 100 bp DNA ladder makers.

Mentions: To test if the partial digestion is functional, the BamHI fragment of talC23 was cloned into pUC19 and partially digested with MscI. The digestion time varied from 10 minutes to 150 minutes while the initial quantity of plasmid DNA (2 μg) and MscI (5 units) was maintained at the same level in all digestions. Agarose gel electrophoresis revealed ladder-like banding patterns as expected. As shown in Fig. 2, apart from the bands around 3 kb, which correspond to the vector and its derivatives, a total of 21 cascading bands were visible, which are consistent with the number of repeat units of talC. The intensity of the 100-bp band increased along the digestion course, which is consistent with the fact that the final digestion products of the repeat region are the fragments with only one repeat unit. Similarly, partial MscI digestion of the 18 unique pTALBamHI clones all yielded expected ladder-like banding patterns after agarose gel electrophoresis (data not shown).


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

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

MscI partial digestion of talC-BamHI fragment cloned in pUC19.2 μg plasmid DNA was digested with 5 u MscI enzyme. The digestion times are given in minutes above the gel. M, 100 bp DNA ladder makers.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: MscI partial digestion of talC-BamHI fragment cloned in pUC19.2 μg plasmid DNA was digested with 5 u MscI enzyme. The digestion times are given in minutes above the gel. M, 100 bp DNA ladder makers.
Mentions: To test if the partial digestion is functional, the BamHI fragment of talC23 was cloned into pUC19 and partially digested with MscI. The digestion time varied from 10 minutes to 150 minutes while the initial quantity of plasmid DNA (2 μg) and MscI (5 units) was maintained at the same level in all digestions. Agarose gel electrophoresis revealed ladder-like banding patterns as expected. As shown in Fig. 2, apart from the bands around 3 kb, which correspond to the vector and its derivatives, a total of 21 cascading bands were visible, which are consistent with the number of repeat units of talC. The intensity of the 100-bp band increased along the digestion course, which is consistent with the fact that the final digestion products of the repeat region are the fragments with only one repeat unit. Similarly, partial MscI digestion of the 18 unique pTALBamHI clones all yielded expected ladder-like banding patterns after agarose gel electrophoresis (data not shown).

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