Extended Data Fig. 4: Phylogenetic distribution of domain architecture for NusG, NusA and RpoB. A.
From: Functionally uncoupled transcription–translation in Bacillus subtilis
Multiple sequence alignments (Methods) for NusA (602 columns), NusG (325 columns), and the β subunit of the RNAP RpoB (1732 columns) for species shown in Fig. 4. The alignments are visualized in a binary fashion to highlight presence/absence of certain domains: white indicates presence of an amino acid in the alignment, and black indicates presence of a gap. The alignments were trimmed by removing columns with >95% gaps. Species with no homologues, partial or pseudogene homologues, or multiple homologues are shown as grey lines. Phylogenetic tree and fraction of terminators with stop-to-stem distances within 12 nt from Fig. 4 are reproduced in linearized form. The position of domains from the E. coli protein are identified by bars above the alignments. For RpoB, conserved bacterial regions identified by70 (βb1 to βb16) are shown. The NusA C-terminal domain11,71 (orange box) is missing in a large fraction of Firmicutes (partly present in Mollicutes, which include Mycoplasma and Spiroplasma; red brace), Campylobacterota, Thermotogota, Fusobacteria, and Actinobacteria. NusG has a largely conserved domain architecture, with Actinobacteria showing N-terminal extension. As previously noted in detail70, the β subunit of the RNAP has multiple insertion domains in diverse bacteria. Insertion domain βSI2, recently implicated10 (green box) in transcription-translation coupling is lineage-specific and absent in many clades of Gram-positive bacteria, as noted in10. Dashed box in tree highlights clade containing Mycoplasma. b. Close-up view of our analysis of the clade containing Mycoplasma (indicated by black dots). Sub-tree includes species with n ≤ 20 identified terminators (marked in light red). Grayscale representation of stop-to-stem distributions and fraction of terminators with d ≤ 12 nt are the same as Fig. 4. M. pneumoniae is highlighted in cyan, and has no identified terminator (0/14) with d ≤ 12 nt. c. Cumulative distribution of stop-to-stem distance for bioinformatically identified terminators in M. pneumoniae.
