Fig. 1: Schematic overview of interactions of TBP, RefMSA, and the spatio-temporal analyses.

a The interaction overview of TBP (shown in dark brown) depicting the structure of TBP and its interactions with various components of the transcription initiation complexes in eukaryotes. The bottom inset highlights the structural view of TBP associations with DNA (gray) and RNA polymerase II (beige) mediated by TFIIB (green). b A comprehensive common TBP reference multiple sequence alignment (RefMSA) at the level of TBP-lobes (N-terminal and C-terminal lobes indicated in “blue” and “red”, respectively) was constructed based on an initial structural alignment of TBP-lobes (see “Methods” section, Supplementary Fig. 2a and Supplementary Data 16 for details). The initial structural alignment of TBP lobes was used to develop a common TBP numbering (CTN) scheme for any residue in the RefMSA. This is illustrated in the example just below the cartoon as three elements for every residue position. The first element of a CTN defines the lobes (N or C), the second refers to the secondary structure element (e.g. L1 for loop 1, H2 for helix 2, etc.) and the third position represents the position in the specified secondary structure element. Thus in the given example an alignment position N.H2.13 would refer to the 13th position in helix H2 of the N-terminal lobe (see Supplementary Fig. 2a). c The approach employed in the study involves traversing multiple phylogenetic ranges (temporal), as well as considering different sets of TBP-lobe sequences (spatial) to uncover conserved molecular signatures.