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Integrative Structural Biology of Biological CO2 Fixation
0:00:05 Introduction: The presentation focuses on the study of biological CO2 fixation in acetogenic bacteria, "alien microbes" with unique metabolisms.
0:00:29 Acetogens: These bacteria can grow on various substrates, including gases (CO2 and hydrogen), and produce acetate.
0:00:58 Biotechnology: Modified acetogens, can produce biofuels, represent a significant green fuel industry.
0:01:42 Research Focus: The lab aims to understand the biochemical basis and enzymatic reactions behind this "exotic mechanism" for both fundamental biochemistry and biotechnological applications.
0:02:10 Methanogens: Another class of anaerobic microbes, methanogens, use CO2 and hydrogen to produce methane. Both, acetogens and methanogens, live in extreme, low-oxygen, high-salt conditions and use variations on the same metabolic pathway.
0:03:03 Wood-Ljungdahl pathway: Both acetogens and methanogens use variants of the Wood–Ljungdahl pathway.
0:03:07 Thermodynamics: The energy yield from CO2 and hydrogen is very low (around -95 kJ/mol under standard conditions, and less than 1/3 ATP under physiological conditions), meaning these organisms live at the thermodynamic limit of life.
0:04:12 The Wood-Ljungdahl Pathway: This pathway involves combining two CO2 molecules to form acetyl-CoA, similar to "Lego bricks." It's a linear pathway with two branches: the methyl branch (CO2 to formate to a methyl group) and the carbonyl branch (CO2 to carbon monoxide).
0:05:10 Acetogen Process: CO2 is reduced to formate, then transferred to tetrahydrofolate (THF) and reduced to a methyl group. This is condensed with carbon monoxide to form acetyl-CoA.
0:06:29 Energy Conservation: Acetogens secrete acetate, and the main energy gain comes from the two NADH molecules produced. CO2 fixation acts as a terminal electron sink.
0:06:56 Respiration in Acetogens: The three main proteins involved are electron bifurcating hydrogenase, a membrane-bound respiratory complex, and a sodium-dependent ATP synthase.
0:08:25 Challenges: Studying these metalloproteins is difficult due to their oxygen sensitivity and the need for fully anaerobic conditions, and also standard protein production methods are not useable.
0:09:48 Structural Biology: The lab developed an anoxic workflow for structural biology, determining structures of key respiration complexes in acetogens.
0:10:21 Hydrogen-Dependent CO2 Reductase (HDCR): A highly efficient enzyme, 10,000 times more efficient than chemical catalysts, forming irregular filaments.
0:11:36 HDCR Structure: Composed of hydrogenases (blue), formate hydrogenases (green), and a polyferredoxin-like protein filament (center) with iron-sulfur clusters for electron transfer.
0:12:04 Filament Formation: Deletion of specific C-terminal helixes disrupts filament formation and reduces enzyme activity.
0:13:15 Enzymatic Nanowire: The elongated HDCR molecule resembles an enzyme-decorated nanowire with a long iron-sulfur chain, similar to light-harvesting complexes in photosynthesis.
0:15:51 Cryo-Electron Tomography: Used to visualize HDCR in vivo, revealing large, ring-shaped superstructures (over 200 nm diameter) within the cells.
0:18:35 Speculation: The superstructures might aid in organizing metabolism, similar to pyrenoids or carboxysomes, possibly concentrating formate.
0:19:19 Other Nanowires: Other examples, like tungsten-containing aldehyde:ferredoxin oxidoreductase, also form filaments, suggesting this might be a broader phenomenon.
0:21:11 Electron-Bifurcating Hydrogenase: Another key enzyme that uses hydrogen to reduce ferredoxin (thermodynamically unfavorable) via electron bifurcation.
0:21:47 Electron Bifurcation: A process coupling endergonic and exergonic reactions, splitting a two-electron pair into one high-potential and one low-potential electron.
0:23:28 Atypical Bifurcation: This enzyme lacks the typical features (stabilized anionic semiquinone, second FAD) of classical bifurcation enzymes.
0:23:57 Structural Analysis: Structure determination reveals a unique mechanism involving redox-dependent affinity modulation and kinetic gating.
0:26:13 Redox-Dependent Switch: The enzyme modulates FMN binding based on redox state.
0:26:55 Conformational Change: Loop movement, triggered by reduction, kicks out a domain, bringing a cluster closer for electron transfer.
0:27:59 Analogy to Complex III/b6f: The enzyme has a mechanism, involving movement of an iron-sulfur protein, vaguely resembling the Q cycle in mitochondria/chloroplasts.
0:28:27 Modularity: The bifurcating module (HndBC) can be combined with different enzymes, such as the Sdh transhydrogenase, showcasing a concept of "molecular Lego."
0:29:48 Anaerobic Metabolism: Anaerobic metabolism is different and involves redox-controlled conformational changes, kinetic gating, and many redox cofactors.
0:31:03 Integrative Approach: Understanding these systems requires integrative structural biology, spectroscopy, biochemistry, and microbiology.
0:31:32 Acknowledgements: The speaker thanks their team and collaborators.