Regulatory role of the transcription factor BcMr1 in efflux-mediated multidrug resistance in Botrytis cinerea via pre-adaptation to plant secondary metabolites

Botrytis cinerea causes grey mold of many crops and is one of the top ten diseases in agriculture. Its wide host range and high genetic variability make it highly prone to developing fungicide resistance, particularly multidrug resistance (MDR), which is a resistance to various fungicides with different modes of action. We have recently found that B. cinerea adapts to plant secondary metabolites (PSMs) through the up-regulation of efflux protein ATP-binding cassette (ABC) to develop MDR (which is termed e-MDR) in the interaction with host plants. However, how PSM stimulation is transmitted to ABC expression and how MDR is regulated remain unknown. In this study, the transcription factor (TF) BcMr1, which is related to MDR, was screened and identified from various B. cinerea strains having different sensitivities to fungicides through bioinformatic and transcriptomic analyses, accompanied by chromatin immunoprecipitation-sequencing (ChIP-seq), electrophoretic mobility shift assay (EMSA), yeast one-hybrid (Y1H), and quantitative polymerase chain reaction (qPCR). The results revealed that BcMr1 binds to the promoters of ABC transporter genes and positively regulates the expression of BcatrA, BcatrD, BcatrO, Bmr3, BCIN_03g02050 and BCIN_16g02970, which are ABC efflux proteins, resulting in B. cinerea's e-MDR. Furthermore, PSMs and interacting proteins were shown to be possible activators of this TF. This study provides new insights into the regulatory role of the TF BcMr1 and other downstream candidate genes involved in e-MDR in B. cinerea, which helps to understand the development of MDR in the field through pre-adaption mechanism.