Extended Data Fig. 9: Mitochondrial β-signal versus bacterial β-signal interactions with the β-barrel assembly machineries.

a, Alignment of mitochondrial and bacterial β-barrel protein sequences (left) containing the C-terminal β-signal strand (green lettering)^{19,26,33,36,64}. The β-signal consensus of mitochondria and bacteria is highlighted¹⁹. Alignment of Sam50 and BamA sequences (right) containing β1 (underlined in blue). The consensus with the highly conserved glycine on the C-terminal side of β1 allows a direct comparison between bacteria and mitochondria. C.c., Caulobacter crescentus; C.g., Candida glabrata; D.m., Drosophila melanogaster; E.c., Escherichia coli; H.s., Homo sapiens; N.c., Neurospora crassa; N.m., Neisseria meningitidis; R.p., Rickettsia prowazekii; S.c. Saccharomyces cerevisiae; V.c., Vibrio cholerae. b, Cartoon representation of the hybrid interaction between the C-terminal β-signal (green lettering)-containing strand according to structural or crosslinking data (shaded green) of the β-barrel substrates with β1 of Sam50 or BamA, respectively (shaded blue). For the bacterial BAM machinery, the β-signal-strand of several substrates was found to associate with its N-terminl part with BamA β1 to form an asymmetric intermediate (register shift) creating a C-terminal overhang (shaded red) of the β-signal of the substrate (lower panel)^33,35. It was proposed that β1 of these substrates can begin to form hydrogen bonds with the overhang of its own C-terminal β-signal-strand to start the barrel closure followed by sequential disruption of the hydrogen bonds between the β-signal-strand and BamA³³. In contrast for the mitochondrial SAM machinery, the β-signal-strands of the Tom40 and Por1 substrates are specifically associated with Sam50 β1 without a register shift (upper panel)²³, as also observed for the bacterial substrate EspP^34,36. Thus, all analyzed mitochondrial β-signals (and one bacterial substrate) associate with Sam50/BamA β1 without a C-terminal overhang, implying a direct β-strand exchange mechanism for barrel closure and release²³. c, Interactions between BamA (PDB ID: 6V05) and its substrate (second BamA) with its close-up view with C-terminal overhang. Hydrophilic and hydrophobic interactions are shown with brown dotted lines and black broken lines, respectively. Residues facing the barrel lumen and lipid phase are shown in black and gray, respectively.