Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life

Abstract

Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S0)-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S0 reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.

Structure ofEscherichia colirespiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation

“…In membrane-bound hydrogenase (MBH), an equivalent M Glu141 is separated from the closest ionizable H Lys409 by distance of 20 Å, which in a hydrophobic environment with a dielectric constant of 10, allow them to mutually modulate the pKa of each other by approximately 1 pH unit, similar to the free energy conserved upon ferredoxin oxidation by the protein complex. This distance is reduced to around 13 Å in membrane-bound sulfane sulfur reductase (MBS) and to around 6 Å in complex I, consistent with the proportionally higher free energy of catalyzed reactions (Yu et al, 2020;2018).…”

“…The peripheral arm-NuoH complex is undoubtably one of the stand-alone evolutionary modules. This is supported by the differences in its position between complex I and membrane-bound hydrogenases (Yu et al, 2020;2018), and its susceptibility to dissociation from the membrane arm in E. coli (Baranova et al, 2007;Efremov and Sazanov, 2011) as expected for a late evolutionary addition (Levy et al, 2008). The initial association of the hydrogen-evolving module with an antiporter may have had an evolutionary advantage with the proton-translocating module serving as a source of protons (Yu et al, 2018), biasing H2 evolution towards the reaction product or to enhance Na + extraction from the cells (Boyd et al, 2014).…”

“…The proposed mechanism is applicable to all the complexes that are evolutionary related to complex I (Efremov and Sazanov, 2012;Yu et al, 2020;2018). In all of these, the cavity formed between the peripheral arm and NuoH subunit is sealed.…”

“…The interface between peripheral and membrane arms is primarily formed through interaction between subunits NuoB and NuoD of the peripheral arm with the cytoplasmic surface of NuoH and the TMH1-TMH2 loop of subunit NuoA in the membrane domain. The residues involved in the direct interaction between the arms and the interface structure are highly conserved (Figure -figure supplement 1) between all complex I and related membrane-bound hydrogenases (Baradaran et al, 2013;Grba and Hirst, 2020;Kampjut and Sazanov, 2020;Yu et al, 2020;2018).…”

“…Multiple proton pathways have been suggested (Baradaran et al, 2013;Efremov and Sazanov, 2012;Kampjut and Sazanov, 2020;Verkhovskaya and Bloch, 2012;Yu et al, 2020;2018). However, they all end up on intracellular/matrix side of the membrane, which makes it difficult to explain the energy conversion mechanism.…”