Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation

By Hasan Demirci1, Bradley B. Tolar, Tzanko Doukov, Aldis Petriceks, Akshaye Pal, Yasuo Yoshikuni, Aharon Gomez, David A. Saez, Esteban Vöhringer-Martinez, Thomas Schwander, Tobias J. Erb, Christopher A. Francis, Soichi Wakatsuki

1. Biosciences Division at SLAC National Accelerator Laboratory

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posted-content

Author

Hasan DeMirci and Bradley B. Tolar and Tzanko Doukov and Aldis Petriceks and Akshaye Pal and Yasuo Yoshikuni and Aharon Gomez and David A. Saez and Esteban Vöhringer-Martinez and Thomas Schwander and Tobias J. Erb and Christopher A. Francis and Soichi Wakatsuki

Citation

DeMirci, H. et al., 2020. Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation. Available at: http://dx.doi.org/10.1101/2020.02.05.935528.

Abstract

AbstractAutotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing oxygen-sensitive metal clusters (e.g., Fe-S). Here we investigated how 4-hydroxybutyryl-CoA dehydratase (4HBD) - the key enzyme of the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle for CO2-fixation - adapted as conditions shifted from anoxic to oxic. 4HBD is found in both anaerobic bacteria and aerobic ammonia-oxidizing archaea (AOA). The oxygen-sensitive bacterial 4HBD and oxygen-tolerant archaeal 4HBD share 59 % amino acid identity. To examine the structural basis of oxygen tolerance in archaeal 4HBD, we determined the atomic resolution structure of the enzyme. Two tunnels providing access to the canonical [4Fe-4S] cluster in oxygen-sensitive bacterial 4HBD were closed with four conserved mutations found in all aerobic AOA and other archaea. Further biochemical experiments and molecular dynamics simulations support our findings that restricting access to the active site is the key to oxygen tolerance, explaining how active site evolution drove a major evolutionary transition.Significance statementAutotrophy (primary production) was the first life strategy on Earth. Before photosynthesis (using solar energy to fix carbon dioxide), life relied on chemical reactions for energy. These chemosynthetic reactions are present in all domains of life, including archaea possessing the most energy-efficient carbon fixation pathway - the 3-hydroxypropionate/4-hydroxybutyrate cycle. This efficiency results from enzyme modifications, including enhanced enzyme stability and catalysis of multiple reactions. We reveal the first structure of aerobic 4-hydroxybutyryl-CoA dehydratase (4HBD) from ammonia-oxidizing archaea. These archaea are among the most abundant organisms on the planet, and their 4HBD active site evolved oxygen tolerance to support aerobic metabolism. This modification can provide further insight into enzyme evolution on early earth, as photosynthesis developed and began oxygenating the atmosphere.

DOI

Funding

NSF-STC Biology with X-ray Lasers (NSF-1231306)