Advances in bacterial transcription factor research methods and applications
Studies of transcriptional regulation in bacteria facilitate the unraveling of patterns governing processes essential to bacterial life,and control of their metabolic pathways,thereby unlocking their potential for applications in both foundational and practical aspects of life sciences.Bacterial transcription factors(TFs)are critical elements that regulate gene transcription in bacteria,and the technologies used in their study are advancing rapidly toward higher sensitivity and throughput.This review systematically examines the current state of bacterial TF research,outlines the spectrum of methodologies utilized,and discusses progress achieved.We provide an in-depth analysis of an array of techniques employed for screening and verifying bacterial TFs,such as DNA pull-down,bacterial one-hybrid systems,and gel electrophoretic mobility shift assays.We also discuss methods for identifying TF-binding sites,including chromatin immunoprecipitation assays,DNase Ⅰ footprinting,DNA affinity purification sequencing,and systematic evolution of ligands by exponential enrichment.Techniques for investigating protein interactions with TFs are also discussed,including the yeast two-hybrid system,GST pull-down assays,bimolecular fluorescence complementation,fluorescence resonance energy transfer,and surface plasmon resonance.This review also provides an overview of methods for verification of TF function,including gene mutation and gene overexpression technologies,and explores the application of bacterial TFs in basic life science research,synthetic biology,and biosensing technologies.This review critically evaluates the strengths and limitations of these research methods via comparative analyses,highlighting a significant methodological gap in bacterial TF research,namely the lack of universally applicable methods for screening and validating bacterial TFs across diverse bacterial species.This suggests that the development and adoption of emerging technologies including single-cell transcriptomics,spatial transcriptomics,and multimodal structured embedding methods,and their application to bacterial cells have the potential to drive significant breakthroughs in bacterial TFs research.
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