Functional and structural study of the transcription factor PBF-2

The sessile nature of plants prevents them from escaping harsh environmental conditions and imposes a requirement for adaptation to the stresses which they encounter. This places much importance on signalling pathways that will sense potentially harmful conditions and the transcription factors that will respond by modifying gene expression appropriately to deal with forthcoming danger. Plants devote a relatively large portion of their genome to encoding transcription factors, about 50% of which are specific to plants. Potential pathogens are continuously interacting with plants however, very few will successfully invade a plant and cause disease. In response to pathogen infection, plants undergo massive changes in gene expression. In potato, the pathogenesis-related gene PR-10a is induced in response to infection by the late blight pathogen Phytophthora infestans or treatment of tissues with elicitors of the defence response. This induction requires a 35-bp promoter element termed the Elicitor Response Element (ERE) which on its own can confer pathogen inducibility. The ERE is recognized by the nuclear factor PBF-2 whose DNA-binding activity is induced during the defence response. Interestingly, PBF-2 preferentially binds the single-stranded forms of the ERE with sequence specificity. This study defines the functional ERE as the sequence GTCAAAAA/T, which we have termed the PB (PBF-2 Binding) element. This sequence is found in the promoters of numerous defence genes and is enriched in the promoters of Arabidopsis genes coregulated during pathogen infection. PBF-2 is capable of transactivating gene expression in a PB element dependent manner and mutations of an Arabidopsis PBF-2 homolog result in increased disease susceptibility. The crystal structure of PBF-2 reveals that it is a homotetramer of 24 kD proteins which associate with cyclic C ₄ symmetry to produce a whirligig-like quaternary structure novel for single-stranded DNA binding proteins. The novel quaternary structure has inspired the name ‘Whirly’ for this ubiquitous class of plant proteins. Nevertheless, the structure of the protomers shares the basic structural properties of other single-stranded DNA binding proteins demonstrating the convergent evolution of single-stranded DNA binding modules. The three-dimensional structure also provides insight into the mechanisms of DNA binding which supports hypotheses proposed from biochemical assays. Overall, PBF-2 represents a novel class of plant transcription factors which could potentially exploit melted promoter regions to regulate plant defence gene expression.