Nitrogenase resurrection and the evolution of a singular enzymatic mechanism

• Published in: eLife 2023-02, Vol.12
• Main Authors: Garcia, Amanda K, Harris, Derek F, Rivier, Alex J, Carruthers, Brooke M, Pinochet-Barros, Azul, Seefeldt, Lance C, Kaçar, Betül
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; ancestral sequence reconstruction; Azotobacter vinelandii; Azotobacter vinelandii - genetics; Azotobacter vinelandii - metabolism; Biochemistry and Chemical Biology; early life; evolution; evolutionary biochemistry; Evolutionary Biology; metabolic engineering; Nitrogen - metabolism; Nitrogen Fixation; Nitrogenase - chemistry; Nitrogenase - genetics; Nitrogenase - metabolism
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.85003

The planetary biosphere is powered by a suite of key metabolic innovations that emerged early in the history of life. However, it is unknown whether life has always followed the same set of strategies for performing these critical tasks. Today, microbes access atmospheric sources of bioessential nitrogen through the activities of just one family of enzymes, nitrogenases. Here, we show that the only dinitrogen reduction mechanism known to date is an ancient feature conserved from nitrogenase ancestors. We designed a paleomolecular engineering approach wherein ancestral nitrogenase genes were phylogenetically reconstructed and inserted into the genome of the diazotrophic bacterial model, enabling an integrated assessment of both in vivo functionality and purified nitrogenase biochemistry. Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. Further, we find that all ancestors exhibit the reversible enzymatic mechanism for dinitrogen reduction, specifically evidenced by hydrogen inhibition, which is also exhibited by extant nitrogenase isozymes. Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. The experimental framework established here is essential for probing how nitrogenase functionality has been shaped within a dynamic, cellular context to sustain a globally consequential metabolism.