TGA transcription factors-Structural characteristics as basis for functional variability

Abstract

TGA transcription factors are essential regulators of various cellular processes, their activity connected to different hormonal pathways, interacting proteins and regulatory elements. Belonging to the basic region leucine zipper (bZIP) family, TGAs operate by binding to their target DNA sequence as dimers through a conserved bZIP domain. Despite sharing the core DNA-binding sequence, the TGA paralogues exert somewhat different DNA-binding preferences. Sequence variability of their N- and C-terminal protein parts indicates their importance in defining TGA functional specificity through interactions with diverse proteins, affecting their DNA-binding properties. In this review, we provide a short and concise summary on plant TGA transcription factors from a structural point of view, including the relation of their structural characteristics to their functional roles in transcription regulation.

Keywords: DOG1 domain; TGA transcription factors; functional variability; intrinsically disordered regions; plant transcription regulation; post-translational modifications; structural characteristics.

FIGURE 1

Unrooted phylogenetic tree of Arabidopsis and tobacco TGAs. Phylogenetic analysis of TGA factors shows an earlier separation of clades into two branches, one dividing into clades II, IV, and V, the other into clades I and III, indicating a closer evolutionary relationship between clade members in the same branch. TGA involvement in regulation of different processes, based on literature search, is represented for each clade. Sequence alignment by MUSCLE (Edgar, 2004) and phylogenetic analysis by the Maximum Likelihood method, based on the JTT matrix-based model (Jones et al., 1992), were conducted in MEGA7 (Kumar et al., 2016). The branch length scale represents the number of substitutions per site. Protein sequences with listed protein identification numbers were retrieved from UniProtKB (https://www.uniprot.org/): AtTGA1 (Q39237), AtTGA2 (P43273), AtTGA3 (Q39234), AtTGA4 (Q39162), AtTGA5 (Q39163), AtTGA6 (Q39140), AtTGA7 (Q93ZE2), AtPAN (Q9SX27), AtTGA9 (Q93XM6), AtTGA10 (E3VNM4), NtTGA1A (P14232), NtPG13 (Q05699), NtTGA2.1 (O24160), NtTGA2.2 (Q9SQK1), and NtTGA10 (Q52MZ2).

FIGURE 2

Among the three main TGA protein parts, the bZIP domain is the most highly conserved. (A) The AlphaFold generated 3D model of AtTGA1 (Jumper et al., 2021; Varadi et al., 2022) (pLDDT, AlphaFold per-residue confidence score) and (B) a schematic representation of TGA domain organization, showing the flexible N-terminus, the bZIP domain and the C-terminus, encompassing a putative Delay of Germination 1 (DOG1) domain. The nuclear localization signal (NLS) and glutamine rich regions Q1 and Q2 are indicated. (C) Multiple sequence alignment of ten Arabidopsis and five tobacco TGAs, with segments of high similarity or identity colored darkest and lowest similarity lightest, shows the bZIP domain retains the highest sequence identity throughout the whole protein sequence. In cases where sequence segments at N-terminal or C-terminal ends are not aligned to any of the other sequences, they are considered identical and are colored black. (D) A closer examination of the bZIP domain shows few variations in the basic region, while the three zipper heptads, with conserved leucine residue positions marked, show higher variability. The alignment and sequence logo were prepared and visualized with Geneious Prime 2020 (Kearse et al., 2012), using default parameters. (E) Structural model of the human FosB-JunD bZIP dimer in complex with DNA (5VPE entry in RCSB PDB) (Yin et al., 2017). The models in (A,E) were visualized in UCSF ChimeraX (Pettersen et al., 2021).

FIGURE 3

The N-termini of TGAs are intrinsically disordered. Representation of intrinsic disorder regions of full-length TGA amino acid sequences from Arabidopsis and tobacco, created based on IUPred2 prediction algorithm results (Mészáros et al., 2018). The N-termini of analyzed TGAs show generally high (>0.5), yet clade-specific pattern of intrinsic disorder probability, while the disorder probability is considerably lower in their C-termini. Charts representing TGAs from the same clade were aligned based on the conserved bZIP domain, which is shown as grey area.

FIGURE 4

Schematic representation of TGA protein parts contribution to TGA function. All three protein parts of TGAs are multifunctional, each involved in several tasks connected to their interaction with target DNA motifs, dimerization and/or oligomerization and protein-protein interactions with transcription factors, cofactors or other proteins, resulting in a specific shift in gene expression activity.