Plant transcription factors - being in the right place with the right company

Abstract

Transcriptional regulation underlies many of the growth and developmental processes that shape plants as well as their adaptation to their environment. Key to transcriptional control are transcription factors, DNA-binding proteins that serve two essential functions: to find the appropriate DNA contact sites in their target genes; and to recruit other proteins to execute transcriptional transactions. In recent years, protein structural, genomic, bioinformatic, and proteomic analyses have led to new insights into how these central functions are regulated. Here, we review new findings relating to plant transcription factor function and to their role in shaping transcription in the context of chromatin.

Keywords: Binding specificity; Chromatin; DNA binding; Pioneer transcription factor; Protein condensation; Transcription.

Figure 1. Architecture of a transcription factor.

a. Transcription factors consist of multiple modular domains. Structured domains are used for DNA binding and are frequently used for protein interactions. Activation domains, repressive domains, and regions that recruit chromatin remodelers typically reside in intrinsically disordered regions. Protein cartoons created with Illustrate [56] of the LFY DBD (PDB 2VY1) [4], ARF1 DBD (PDB 4LDX) [1], LFY SAM (PDB 4UDE) [57], and ARF7 PB1 (PDB 4NJ7) [58] domains. b. Analysis of percentage of protein comprised of intrinsically disordered regions from Arabidopsis transcription factors and non-transcription factors on a proteome-wide scale using Metapredict [59] reveals enrichment of intrinsically disordered regions in transcription factors.

Figure 2. LFY pioneer transcription factor licenses cell fate reprogramming and subsequent activation of transcription at the APETALA1 locus.

a. The LFY dimer (red shapes) binds it cis motif near the dyad (midpoint) of the nucleosome and triggers local chromatin opening via eviction of histone H1 (green circles) and recruitment of SWI/SNF chromatin remodelers (blue shape). b. Subsequently other transcription factors can access the locus. Their accumulation is either directly activated by LFY (LMI2, yellow) or in response to altered hormone levels and plant age (DELLA proteins plus SQUAMOSA PROTEIN BINDING PROTEINS; purple shape) or photoperiod FLOWERING LOCUS T (together with FD, pink) [23,24,60-63]. c. The assembled transcription factors likely engage with additional chromatin regulators (blue shape) to cooperatively open the AP1 locus. d. Finally, the general transcriptional machinery (white large shape) is recruited. e. Shallow DNA contacts with one face of the DNA by the LFY dimer allow co-binding with the histone octamer. Previously published structure of LFY displayed as a dimer (one of the monomers is semi-transparent) binding the pseudo-palindromic recognition site within AP1 (pdb: 2vy1 [4]). DNA is in grey and semi-transparent except for the half-site bound by the opaque monomer on the left. LFY residues which interact with DNA are in pink and displayed in stick style over the cartoon in helix-tube mode in the rotated view below. Visualization using chimera [64].