Biochemical characterization of modular DNA-binding domains of novel TALE-like proteins

Abstract

Members of the plant pathogenic bacterial genus Xanthomonas inject TALEs (Transcription Activator Like Effector) by a type III secretion system into host plant cells. Inside the plant cells TALEs bind and activate host genes thereby promoting bacterial disease. The DNA binding domain of TALEs is modular and consists of imperfect 33-35 long tandem-arranged amino acid repeats. Each repeat binds to a single nucleotide with position 13, determining base specificity. The base specificity of distinct residues in position 13 is known as the TALE code. This TALE code provides the possibility to create custom TALEs with desired DNA target specificity or to predict DNA targets of native TALEs. This work characterizes two new members of the TALEs, called TALE-likes: (1) Bats, which derive from the bacterium Burkholderia rhizoxinica and (2) MOrTLs, whose DNA sequences were found in a marine metagenomics database. We demonstrate that DNA binding preferences of these two classes of TALE-likes can be predicted with the TALE-code. Yet, some of the repeats have a lower base specificity than TALEs. Additionally the TALE-likes have a different affinity to DNA and higher protein stability compared to TALEs. Analysis of protein chimeras showed that repeats of TALEs and TALE-like proteins are compatible and can be used to create protein chimeras. The TALE-likes have different DNA affinities and protein stabilities as compared to the TALEs. They can be adapted to create new proteins and protein chimeras with new useful properties.