Pan-metabolic profiling of Archaea

The Archaea are a goldmine of discoveries, with fundamentally new forms regularly being discovered through metagenomics. We are beginning to realize the vast diversity of archaeal ecological adaptions, and how much we do not know regarding their metabolism. Uncharacterized genes of Archaea present a plethora of opportunities to, at the cutting edge of the field, identify new metabolic traits. Yet, to detect which gene innovations form the base for the ecological success of specific groups we have to look to the entire genomics space.

This project aims at using genomic data to forge robust links between physiological phenotypes among modern Archaea and their genomics adaptations and how those are evolving.

By performing large-scale whole-genomics comparisons complemented with thorough phylogenetic analysis of all single gene trees, we will be able to define archaeal metabolic profiles, clusters of genes conserved among organisms with similar phenotypic traits, and identify what makes them so special. The metabolic profiles, defined at a pan-phenotypic level, will serve not only to develop a classification-tool aiming at an automatic metabolic classification of newly sequenced genomes, but also to pinpoint unknown archaeal conserved genes, potentially linked to metabolism, to be functional characterized.

Duration: 01.06.2016-30.09.2025

Funding agency: WWTF

Project leader: Dr. Filipa Sousa

Participants: Filipa Sousa, Chloe Ellis, Anwar Hiralal, Marta Medic, Govind Nair, Sinje Neukirchen, Anastasiia Padalko, Edith Pichlhöfer, Chris Pruckner, Christa Schleper, Johanna Spiegelhofer, Joost van Ham, Jordi Zamarreno Beas

Website: https://www.wwtf.at/programmes/vienna_research_groups/VRG15-007

Peer-reviewed publications related to or funded through this project

• Padalko A, Nair G, Sousa FL.0.Fusion/fission protein family identification in Archaea. mSystems0:e00948-23.https://doi.org/10.1128/msystems.00948-23
• Neukirchen S, Sousa FL. (2021) DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. Microb Genom. 2021 Jul;7(7):000603. doi: 10.1099/mgen.0.000603. PMID: 34241589; PMCID: PMC8477390.
• Preiner M, Asche S, Becker S, Betts HC, Boniface A, Camprubi E, Chandru K, Erastova V, Garg SG, Khawaja N, Kostyrka G, Machné R, Moggioli G, Muchowska KB, Neukirchen S, Peter B, Pichlhöfer E, Radványi Á, Rossetto D, Salditt A, Schmelling NM, Sousa FL, Tria FDK, Vörös D, Xavier JC. (2020) The Future of Origin of Life Research: Bridging Decades-Old Divisions. Life (Basel). 2020 Feb 26;10(3):20. doi: 10.3390/life10030020. PMID: 32110893; PMCID: PMC7151616.
• Chernyh NA, Neukirchen S, Frolov EN, Sousa FL, Miroshnichenko ML, Merkel AY, Pimenov NV, Sorokin DY, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Lebedinsky AV, Cardoso Pereira IA, Bonch-Osmolovskaya EA. (2020) Dissimilatory sulfate reduction in the archaeon 'Candidatus Vulcanisaeta moutnovskia' sheds light on the evolution of sulfur metabolism. Nat Microbiol. 2020 Nov;5(11):1428-1438. doi: 10.1038/s41564-020-0776-z. Epub 2020 Aug 17. PMID: 32807893.
• Manoharan L, Kozlowski JA, Murdoch RW, Löffler FE, Sousa FL, Schleper C. (2019) Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota. mBio. 2019 Sep 10;10(5):e02039-19. doi: 10.1128/mBio.02039-19. Erratum in: MBio. 2019 Oct 29;10(5): PMID: 31506313; PMCID: PMC6737245.
• Wu HY, Nöllenburg M, Sousa FL, Viola I. (2019) Metabopolis: scalable network layout for biological pathway diagrams in urban map style. BMC Bioinformatics. 2019 Apr 15;20(1):187. doi: 10.1186/s12859-019-2779-4. PMID: 30991966; PMCID: PMC6466808.
• Degli Esposti M, Mentel M, Martin W, Sousa FL. (2019) Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments. Front Microbiol. 2019 Mar 18;10:499. doi: 10.3389/fmicb.2019.00499. PMID: 30936856; PMCID: PMC6431628.
• Duarte AG, Catarino T, White GF, Lousa D, Neukirchen S, Soares CM, Sousa FL, Clarke TA, Pereira IAC. (2018) An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation. Nat Commun. 2018 Dec 21;9(1):5448. doi: 10.1038/s41467-018-07839-x. PMID: 30575735; PMCID: PMC6303296.
• Sousa F, Preiner M, Martin WF. (2018) Native metals, electron bifurcation, and CO2 reduction in early biochemical Evolution. Current Opinion in Microbiology. 2018 Jun; 43:77-83. doi: 10.1016/j.mib.2017.12.010
• Videira MAM, Lobo SAL, Silva LSO, Palmer DJ, Warren MJ, Prieto M, Coutinho A, Sousa FL, Fernandes F, Saraiva LM. (2018) Staphylococcus aureus haem biosynthesis and acquisition pathways are linked through haem monooxygenase IsdG. Mol Microbiol. 2018 Aug;109(3):385-400. doi: 10.1111/mmi.14060. Epub 2018 Aug 2. PMID: 29989674.
• Abdel Azim A, Pruckner C, Kolar P, Taubner RS, Fino D, Saracco G, Sousa FL, Rittmann SKR. (2017) The physiology of trace elements in biological methane production. Bioresour Technol. 2017 Oct;241:775-786. doi: 10.1016/j.biortech.2017.05.211. Epub 2017 Jun 2. PMID: 28628982.