Reconstruction of Nitrogenase Predecessors Suggests Origin from Maturase-Like Proteins

Garcia, Amanda K.; Kolaczkowski, Bryan; Kaçar, Betül

doi:10.1093/gbe/evac031

Cited by 17 publications

(16 citation statements)

References 79 publications

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“…We demonstrate that there currently exists no candidate, evolutionary predecessor of the Gsubunit family, whether another protein, protein fragment, or segment of non-genic DNA. This finding sets the origin of the G-subunit apart from other major evolutionary events in the history of nitrogen fixation that are explainable by gene duplication, including the divergence between other catalytic subunits, between nitrogenases and their maturation protein scaffolds, and between nitrogenase isozymes 32,60 . The addition of such a small and evolutionarily enigmatic protein domain appears to be an anomaly across biogeochemical enzymes.…”

Section: Discussionmentioning

confidence: 91%

An orphan protein drove the ecological expansion of nitrogen fixation

Cuevas-Zuviría

Garcia

Carruthers

et al. 2023

Preprint

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Nitrogenases have catalyzed biological nitrogen fixation for billions of years and revolutionized planet Earth by supplying essential nitrogen to the biosphere. How these molecular machines were built and distributed by microbial processes and a shifting geochemical landscape remains an open question. Here, we probe the birth and functional evolution of the G-subunit, an integral, Precambrian component of certain nitrogenases that makes its appearance midway through the history of nitrogen fixation. Our results establish the G-subunit as an unprecedented molecular novelty that was integrated into preexisting interaction pathways for nitrogenase metallocluster incorporation. In the wake of Earth oxygenation, the G-subunit primed nitrogenases and their microbial hosts to exploit newly diversified geochemical environments. The history of the nitrogenase G-subunit showcases the elaborate tango between contingent evolutionary events and environmental conditions that together open an adaptive frontier for molecular innovations with global consequences.

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Section: Discussionmentioning

confidence: 91%

An orphan protein drove the ecological expansion of nitrogen fixation

Cuevas-Zuviría

Garcia

Carruthers

et al. 2023

Preprint

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“…Finally, the results provide new insight into the origins and evolution of nitrogenase, including the biogenesis of the complex metalloclusters. NifB likely originated in methanogens (4, 41), and recent evidence suggests nitrogenase likely evolved from ancestors that resemble maturases, the proteins that today function in nitrogenase cofactor assembly (e.g., NifEN) (42). These predecessor proteins evolved into modern enzymes harboring diverse metallocofactors and activities, such as nitrogenases and CfbCD, but there are likely others yet to be discovered.…”

Section: Discussionmentioning

confidence: 99%

The nitrogenase cofactor biogenesis enzyme NifB is essential for the viability of methanogens

Saini,

Dhamad,

Muniyasamy

et al. 2023

Preprint

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Dinitrogen (N2) is only bioavailable to select bacteria and archaea that possess the metalloenzyme nitrogenase, which reduces N2 to NH3 in a process called nitrogen fixation or diazotrophy. A long-term goal is to engineer diazotrophy into plants to decrease the use of nitrogen fertilizers, saving billions of dollars annually and greatly reducing nutrient pollution. This goal has not been realized, in part due to the inability to produce the nitrogenase metallocofactor within plants. Biogenesis of the cofactor requires NifB, a radical S-adenosy-L-methionine (SAM) enzyme that generates a precursor [8Fe-9S-C] cluster that matures into the final metallocofactor. Although maturation of nitrogenase is the only known function of NifB in bacteria, bioinformatic analyses reveal that NifB is conserved across methanogens, including those lacking nitrogenase, which suggests NifB functions outside of nitrogenase maturation. Indeed, several lines of evidence show that NifB is essential for viability of the model diazotroph, Methanosarcina acetivorans. First, CRISPRi repression was unable to abolish NifB production, whereas CRISPRi repression abolishes non-essential nitrogenase production. Second, unlike nitrogenase production, NifB production is not controlled by fixed nitrogen availability. Finally, nifB could not be deleted from M. acetivorans unless complemented in trans with nifB from other methanogens, including Methanothrix thermoacetophila, a species that lacks nitrogenase. Notably, M. thermoacetophila NifB supported diazotrophy in M. acetivorans, demonstrating that NifB from a non-diazotrophic methanogen produces the [8Fe-9S-C] cluster. Overall, these results link the metallocofactor biogenesis function of NifB to nitrogen fixation and methanogenesis, two processes of global importance.

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“…To minimize bias of the method, different alignment algorithms were used to generate alternative trees following Garcia et al 79 The combined phylogeny of IF2 and EF‐Tu was constructed using the same 408 IF2 and 408 EF‐Tu sequences. In total, 816 sequences were aligned together using MAFFT L‐INS‐i 35 and MUSCLE v3.8 alignment.…”

Section: Methodsmentioning

confidence: 99%

Early divergence of translation initiation and elongation factors

et al. 2022

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Protein translation is a foundational attribute of all living cells. The translation function carried out by the ribosome critically depends on an assortment of protein interaction partners, collectively referred to as the translation machinery. Various studies suggest that the diversification of the translation machinery occurred prior to the last universal common ancestor, yet it is unclear whether the predecessors of the extant translation machinery factors were functionally distinct from their modern counterparts. Here we reconstructed the shared ancestral trajectory and subsequent evolution of essential translation factor GTPases, elongation factor EF-Tu (aEF-1A/eEF-1A), and initiation factor IF2 (aIF5B/eIF5B). Based upon their similar functions and structural homologies, it has been proposed that EF-Tu and IF2 emerged from an ancient common ancestor. We generated the phylogenetic tree of IF2 and EF-Tu proteins and reconstructed ancestral sequences corresponding to the deepest nodes in their shared evolutionary history, including the last common IF2 and EF-Tu ancestor. By identifying the residue and domain substitutions, as well as structural changes along the phylogenetic history, we developed an evolutionary scenario for the origins, divergence and functional refinement of EF-Tu and IF2 proteins. Our analyses suggest that the common ancestor of IF2 and EF-Tu was an IF2-like GTPase protein. Given the central importance of the translation machinery to all cellular life, its earliest evolutionary constraints and trajectories are key to characterizing the universal constraints and capabilities of cellular evolution.

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Reconstruction of Nitrogenase Predecessors Suggests Origin from Maturase-Like Proteins

Cited by 17 publications

References 79 publications

An orphan protein drove the ecological expansion of nitrogen fixation

An orphan protein drove the ecological expansion of nitrogen fixation

The nitrogenase cofactor biogenesis enzyme NifB is essential for the viability of methanogens

Early divergence of translation initiation and elongation factors

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