A widespread module in the bacterial respiratory redox kit

Prokaryotes have huge metabolic diversity, including in the substrates they explore for respiration

Go to the profile of Inês Cardoso Pereira
Jan 03, 2019
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Prokaryotes have huge metabolic diversity, including in the substrates they explore for respiration. This allows them to live in the most extreme environments and breathe various compounds like sulfate, nitrate, CO2 or FeIII. This metabolic diversity is reflected in a varied range of pathways and respiratory proteins. Intriguingly, these proteins are composed by a defined set of redox modules (subunits or domains) that are “mixed and matched” to originate new functions, and which likely reflect the evolutionary processes starting from redox repertoire of the primordial forms of life.

In our lab at ITQB NOVA, we study microorganisms that reduce sulfate as terminal electron acceptor for the respiratory chain. Dissimilatory sulfate reduction is a main process in the biogeochemical sulfur cycle and was present on Earth at 3.55 Bya. We are interested in how these organisms obtain energy from respiring sulfate, and have unravelled several membrane complexes that are involved in the process.

One of the membrane complexes in Deltaproteobacteria sulfate reducers, the QrcABCD complex, has a striking composition, with three subunits related to molybdo-oxidoreductases subunits and the forth a multiheme cytochrome. This complex transfers electrons from the tetraheme cytochrome c3 to the menaquinone pool (Fig. 1). The QrcCD subunits (a quinone-binding integral membrane protein and a soluble iron-sulfur protein), form a particularly interesting dimeric redox module that is found in a wide range of bacterial respiratory systems, but whose role in energy conservation was not known. Its wide distribution, suggests an ancient origin for this redox module.

A Post-Doc in our lab, Américo Duarte, worked hard at stopped-flow experiments inside the anaerobic chamber, to understand the directionality of proton vs. electron uptake by the Qrc complex. We were able to show that Qrc takes up protons from the cytoplasm for reduction of menaquinone at the periplasmic side of the membrane, with electrons coming from the cytochrome c3. This means that Qrc is electrogenic and it has a H+/e- ratio of 1, as expected for a redox loop. This work involved a collaboration with Tom Clarke’s group at University East Anglia.

A structural model, built by Cláudio M. Soares group, enabled us to identify a putative quinone pocket in QrcD, near the periplasmic side of the membrane, and a wire of protonable residues linking the cytoplasm to the quinone site. The model also showed that the quinone site is shielded by direct contact with the periplasm by the FeS QrcC subunit, providing a rationale for why the two proteins always work together. Filipa Sousa group, at the University of Vienna, studied the phylogeny of QrcD and related bacterial proteins, revealing the evolution of this key membrane protein in bacterial bioenergetics, which has a likely ancient origin.

This work provides the first evidence for an energy-conserving membrane complex in sulfate reducers. Furthermore, it also shows how bacterial membrane complexes with the QrcCD/NrfCD/PsrBC module, which have quinone and substrate-binding sites on the same side of the membrane, can in fact be electrogenic (or driven by the pmf). The QrcCD module is an ingenious device to avoid transmembrane electron transfer against the membrane potential, as performed by membrane cytochromes b, as it reduces quinone at the periplasmic side with protons from the cytoplasm. Thus, Qrc defines a new type of bacterial respiratory complex where the quinone and substrate sites are on the same side of the membrane.

References

Américo G. Duarte, Teresa Catarino, Gaye F. White, Diana Lousa, Sinje Neukirchen, Cláudio M. Soares, Filipa L. Sousa, Thomas A. Clarke & Inês A. C. Pereira. An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation (2018) Nature Communications, volume 9, Article number: 5448

Links:

Inês Cardoso Pereira lab: http://www.itqb.unl.pt/research/biological-chemistry/bacterial-energy-metabolism

Cláudio M. Soares lab: http://www.itqb.unl.pt/research/biological-chemistry/protein-modelling

Tom Clarke lab: https://people.uea.ac.uk/en/persons/tom-clarke

Filipa Sousa lab: https://archaea.univie.ac.at/research/filipa-sousa-lab/

Go to the profile of Inês Cardoso Pereira

Inês Cardoso Pereira

Principal Investigator, ITQB NOVA, Universidade Nova de Lisboa

Anaerobic Microbiology

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