Systematic discovery of DNA-binding tandem repeat proteins.

Area of Science:

• Molecular Biology
• Biotechnology
• Genomics

Background:

• Tandem repeat proteins (TRPs) are diverse and bind various ligands, with DNA-binding TRPs like zinc finger (ZNF) and transcription activator-like effector (TALE) proteins being crucial in biology and biotechnology.
• The vast diversity of TRPs remains largely unexplored, indicating a significant gap in our understanding and potential applications.

Purpose of the Study:

• To identify novel DNA-binding TRPs by exploring their unexplored diversity.
• To develop and apply computational tools for predicting DNA-binding capabilities within TRP families.
• To experimentally validate predicted TRPs and characterize their DNA-binding specificity and functional potential.

Main Methods:

• Extensive analysis of TRPs in public databases.
• Development of a protein language model for DNA-binding protein prediction (PLM-DBPPred).
• Experimental screening of predicted DNA-binding TRPs, including sequence specificity assays and functional characterization.

Main Results:

• Identification of 11 novel DNA-binding TRPs, with six demonstrating sequence specificity.
• Demonstration that Short TALE-like Repeat proteins (STARs) can be programmed to target specific DNA sequences.
• Creation of artificial transcription factors using reprogrammed STAR proteins for targeted gene activation.
• Discovery of novel TRP families (MOON, pTERF) with unique DNA-binding features.

Conclusions:

• The study significantly expands the known diversity of DNA-binding TRPs.
• A systematic, computational approach combined with experimental validation is highly effective for discovering new biological insights and tools.
• Reprogrammable STAR proteins offer a promising platform for developing novel gene-targeting biotechnological tools.