Redox biochemistry of energy conservation in methanogens and their syntrophic partners
C. S. Raman (Principal Investigator)
University of Maryland, Baltimore
Very little is known about how microbes harvest energy for long term survival in their native niches. Laboratory-based assessments of extreme energy stress in organisms, such as methane producing Archaea, are unimpressive when compared to deep-sea sediment microbes, which support cellular respiration rates of 1 e¯ cell-1 sec-1. Surprisingly, recent studies have shown that oxygen (O2) penetrates up to 75 m below the sea floor, suggesting that achieving anaerobiosis in the biosphere is rather difficult. That is, even the “strict” anaerobes cannot escape O2 and must find ways to deal with it. Until recently, the consensus has been that oxidative stress response systems protect these organisms from exposure to O2. This paradigm was overturned by the finding that methanogens thriving in highly oxic conditions do not express O2 detoxification genes. So, the question arises about why obligately anaerobic methanogens and their syntrophic partners (sulfate-reducing bacteria, SRB) encode cytochrome oxidases (COX), which are well known to be essential for the survival of O2-respiring organisms. Consequently, the long-term goal of this project is to uncover extraordinary energy conservation mechanisms in the microbial world. The short-term objective is to understand the molecular mechanisms by which methanogen and SRB COX function.
In 1978, the classical view that SRB are obligate anaerobes was challenged by the discovery of these organisms in oxic environments. Although sulfate reduction is inhibited by O2, several SRB were subsequently found to thrive in air. Over two decades ago, it was shown that SRB can mediate O2 respiration and couple it to ATP production, but the ability of these organisms to reproducibly grow aerobically with O2 as the terminal electron acceptor was only demonstrated in 2016 and again in 2018. Several SRB encode at least two COX systems. Whether these O2 reductases conserve energy remains unknown. Meanwhile, we have discovered a third unusual COX in SRB. Therefore, one of our research goals is to determine its function. Independent of SRB, a longstanding dogma posits that O2 is
detrimental to methanogenic archaea. Whereas the final step of methanogenesis is blocked by O2, methanogens from at least three different Orders persist in aerobic habitats – some forming syntrophic consortia with O2-evolving cyanobacteria. Taking clues from SRB physiology, we probed for methanogen COX. We found two or more in some methanogens. Our second goal is to investigate these novel systems.
Methodologies utilized in this project: Systems Biochemistry, Large integral membrane metalloenzyme assemblies, Hemoproteins, Aerobic and Anaerobic Microbiology (sulfate-reducing bacteria, methanogens, hyperthermophilic archaea, and other novel organisms), Syntrophy, Physiology, Fermentation, Genetics, Molecular Biology, Structural Biology (Cryo-EM and X-ray Crystallography), Mass Spectrometry Proteomics, Membrane Proteins, Protein Chemistry, Bioelectrochemistry, Electronic Spectroscopy, Electron Paramagnetic Spectroscopy, Oxygen Electrode Measurements, Whole cell studies, and Proton Motive Force measurements.
Relevance to DOE-Physical Biosciences Program This proposal is aimed at new energy-relevant redox biochemical mechanisms in bacteria, archaea, and syntrophic mutualisms thereof. It is focused on delineating structure-function relationships in integral-membrane supramolecular energy-transducing machines and rationalizing how these metalloprotein assemblies control electron flow in biological
systems. Our work is likely to inform the design of bio-inspired catalysts as well. Collectively, the proposed research is of clear and present interest to the core programmatic research activities of BES.
