Structural determinants for NF‐Y subunit organization and NF‐Y/DNA association in plants. (27th November 2020)

• Record Type: Journal Article
• Authors: Chaves‐Sanjuan, Antonio; Gnesutta, Nerina; Gobbini, Andrea; Martignago, Damiano; Bernardini, Andrea; Fornara, Fabio; Mantovani, Roberto; Nardini, Marco
• Is Part Of: Plant journal. Volume 105:Number 1(2021)
• Page Start: 49
• Page End: 61
• Publication Date: 2020-11-27
• Subjects: transcription factor -- histone fold -- CCAAT box -- NF‐Y -- CCT -- CONSTANS -- Ghd8 -- flowering -- Arabidopsis thaliana -- Oryza sativa; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.15038
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: NF‐Y transcription factor comprises three subunits: NF‐YA, NF‐YB and NF‐YC. NF‐YB and NF‐YC dimerize through their histone fold domain (HFD), which can bind DNA in a non‐sequence‐specific fashion while serving as a scaffold for NF‐YA trimerization. Upon trimerization, NF‐YA specifically recognizes the CCAAT box sequence on promoters and enhancers. In plants, each NF‐Y subunit is encoded by several genes giving rise to hundreds of potential heterotrimeric combinations. In addition, plant NF‐YBs and NF‐YCs interact with other protein partners to recognize a plethora of genomic motifs, as the CCT protein family that binds CORE sites. The NF‐Y subunit organization and its DNA‐binding properties, together with the NF‐Y HFD capacity to adapt different protein modules, represent plant‐specific features that play a key role in development, growth and reproduction. Despite their relevance, these features are still poorly understood at the molecular level. Here, we present the structures of Arabidopsis and rice NF‐YB/NF‐YC dimers, and of an Arabidopsis NF‐Y trimer in complex with the FT CCAAT box, together with biochemical data on NF‐Y mutants. The dimeric structures identify the key residues for NF‐Y HFD stabilization. The NF‐Y/DNA structure and the mutation experiments shed light on HFD trimerization interface properties and the NF‐YA sequence appetite for the bases flanking the CCAAT motif. These data explain the logic of plant NF‐Y gene expansion: the trimerization adaptability and the flexible DNA‐binding rules serve the scopes of accommodating the large number of NF‐YAs, CCTs and possibly other NF‐Y HFD binding partners and a diverse audience of genomic motifs. Significance Statement: Plant NF‐Y requires flexible heterotrimerization and DNA‐binding rules to induce the appropriate transcriptional response in a multitude of plant decisions. Here we present the crystallographic structure of a plant NF‐Y/DNA complex and two NF‐YB/NF‐YC dimers, complemented with biochemical mutation experiments, showing the molecular bases for the plant subunit organization and DNA recognition.