@article{0e662ef809d045ebb7c982634c7d224b,
title = "Minimal and hybrid hydrogenases are active from archaea",
abstract = "Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.",
keywords = "anaerobic, archaea, eukaryogenesis, hydrogen, hydrogenase",
author = "Chris Greening and Cabotaje, {Princess R.} and {Valentin Alvarado}, {Luis E.} and Leung, {Pok Man} and Henrik Land and Thiago Rodrigues-Oliveira and Ponce-Toledo, {Rafael I.} and Moritz Senger and Klamke, {Max A.} and Michael Milton and Rachael Lappan and Susan Mullen and Jacob West-Roberts and Jie Mao and Jiangning Song and Marie Schoelmerich and Stairs, {Courtney W.} and Christa Schleper and Rhys Grinter and Anja Spang and Banfield, {Jillian F.} and Gustav Berggren",
note = "Funding Information: This work was supported by two National Health & Medical Research Council Emerging Leader Fellowships (APP1178715 to C.G.; APP1197376 to R.G.), two Australian Research Council Discovery Project grants (DP200103074 and DP230103080, both awarded to C.G. and R.G.), the Swedish Energy Agency (STEM 48574-1 to G.B.), the National Science Foundation Partnerships for International Research and Education grant (OISE-2230766 to C.G. and J.F.B.), the Olle Engkvists stiftelse (220-0226 to G.B. and M. Senger), the Swedish Research Council (Vetenskapsr\u00E5det Starting Grant 2020-05071 to C.W.S.), the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement ERC Starting grant 947317 to A.S. and 101078476 to C.W.S.), the Bill & Melinda Gates Foundation (to J.F.B. and L.E.V.A.), a University of California Dissertation-Year Fellowship (to L.E.V.A.), an Australian Government Research Training Stipend Scholarship (to P.M.L.), a Monash International Tuition Scholarship (to P.M.L.), and a Monash FMNHS Early Career Postdoctoral Fellowship (ECPF23-1113137961 to P.M.L.). Work on \u201CCa. L. ossiferum\u201D was funded by the European Research Council (AdG TACKLE: 695192, StG EVOLPHYSIOL: 803768) and the Austrian Science Fund (FWF: Z437). We thank Alexander L. Jaffe, Yuki Amano, Madalena Alves, Jos\u00E9 Leal, Ricardo Leite, Nelson Sim\u00F5es, and Duarte Toubarro for providing access to genomes. Ping Huang is gratefully acknowledged for support during spectroscopy data acquisition and analysis, and Tristan Wagner, Gerrit Schut, Masaru Nobu, and C.S. Raman are thanked for helpful comments. We thank the MonARCH HPC Cluster and the M3 MASSIVE HPC facility for providing computation platforms. Proteomics analyses were performed by the Mass Spectrometry Facility at Max Perutz Labs, Vienna, Austria, using the VBCF instrument pool. C.G. conceived and oversaw this study. C.G. discovered the archaeal and hybrid [FeFe] hydrogenases. J.F.B. L.E.V.A. S.M. and J.W.-R. contributed original metagenomic datasets and metagenome-assembled genomes. P.M.L. M.M. C.G. L.E.V.A. J.M. J.S. and R.L. conducted homology-based searches. P.M.L. H.L. C.G. and G.B. analyzed domain and genetic organization. R.G. performed structural modeling. T.R.-O. R.I.P.-T. and C.S. conducted transcriptomic and proteomic analysis. P.R.C. H.L. and G.B. conducted heterologous expression and activity assays. P.R.C. M.A.K. M. Senger, and G.B. performed spectroscopic analysis. P.R.C. and M.A.K. performed enzyme isolation and analysis. P.R.C. and G.B. performed protein film electrochemistry analysis. L.E.V.A. P.M.L. C.G. M. Schoelmerich, and J.F.B. conducted genome-wide metabolic analysis. L.E.V.A. A.S. C.G. C.W.S. J.F.B. and P.M.L. performed phylogenetic analysis. C.G. P.M.L. P.R.C. G.B. and R.G. wrote the manuscript with input from all authors. J.F.B. is a co-founder of Metagenomi. A patent on this discovery and application of ultraminimal hydrogenases was submitted. Funding Information: This work was supported by two National Health & Medical Research Council Emerging Leader Fellowships ( APP1178715 to C.G.; APP1197376 to R.G.), two Australian Research Council Discovery Project grants ( DP200103074 and DP230103080 , both awarded to C.G. and R.G.), the Swedish Energy Agency (STEM 48574-1 to G.B.), the National Science Foundation Partnerships for International Research and Education grant ( OISE-2230766 to C.G. and J.F.B.), the Olle Engkvists stiftelse ( 220-0226 to G.B. and M. Senger), the Swedish Research Council (Vetenskapsr\u00E5det Starting Grant 2020-05071 to C.S.), the European Research Council (ERC) under the European Union\u2019s Horizon 2020 research and innovation programme (grant agreement ERC Starting grant 947317 to A.S. and 101078476 to C.S.), the Bill & Melinda Gates Foundation (to J.F.B. and L.E.V.A.), a University of California Dissertation-Year Fellowship (to L.E.V.A.), an Australian Government Research Training Stipend Scholarship (to P.M.L.), a Monash International Tuition Scholarship (to P.M.L.), and a Monash FMNHS Early Career Postdoctoral Fellowship ( ECPF23-1113137961 to P.M.L.). Work on \u201CCa. L. ossiferum\u201D was funded by the Austrian Science Fund FWF Z0437 and ERC starting grant 803768 . We thank Alexander L. Jaffe, Yuki Amano, Madalena Alves, Jos\u00E9 Leal, Ricardo Leite, Nelson Sim\u00F5es, and Duarte Toubarro for providing access to genomes. Ping Huang is gratefully acknowledged for support during spectroscopy data acquisition and analysis, and Tristan Wagner, Gerrit Schut, and C.S. Raman are thanked for helpful comments. We thank the MonARCH HPC Cluster and the M3 MASSIVE HPC facility for providing computation platforms. Proteomics analyses were performed by the Mass Spectrometry Facility at Max Perutz Labs using the VBCF instrument pool. Publisher Copyright: {\textcopyright} 2024 The Authors",
year = "2024",
month = jun,
day = "20",
doi = "10.1016/j.cell.2024.05.032",
language = "English",
volume = "187",
pages = "3357--3372.e19",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "13",
}