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.
Highlights
Xanthomonas TAL effector (TALE) transcriptional activators act as virulence or avirulence factors by activating host disease susceptibility or resistance genes
A few algorithms have been developed for in silico TALE target predictions[14,15,16]. Even though such predictions are not flawless and the targets predicted for a given TALE could vary from script to script, the candidate targets obtained are of great value to the in-depth functional analysis of TALEs17
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, which include entire target DNA-binding repeat regions
Summary
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. Target prediction revealed a number of potential rice targets including several notable genes such as genes encoding SWEET, WRKY, Hen[1], and BAK1 proteins, which provide candidates for further experimental functional analysis of the TALEs. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant hosts, including many economically important crops[1]. The DNA-binding region comprises variable numbers (from 1.5 up to over 30) of tandem 33–34 amino acid repeats that specify target nucleotide sequence. 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, which include entire target DNA-binding repeat regions. Subsequent in silico target prediction revealed a number of potential TALE targets in rice genome, which provide candidates for further experimentally functional analysis of the TALEs
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