We are interested in several aspects of microbial evolution, in particular in the diversity of biological systems with focus on energy and carbon microbial metabolic strategies and how they evolved from one to the other.
- Bioenergetic evolution with focus on- “lego” nature of protein complexes, fusions, large scale single gene phylogenetic investigations (tens of thousand genes at a time), large scale comparative genomics, pathway distributions across prokaryotic domains.
- Physiology and ecology of Archaeawith a focus on- metabolism of the different groups of archaea, archaeal innovations and inventions, archaeal diversity.
Leader: Genomic Evolution and Ecology Group
Team: Sinje Neukirchen
Funded Project: Pan-metabolic profiling of Archaea: The ecology of genomics
Vienna Science and Technology Fund Vienna Research Groups 2015 (WWTF) "Computational Biosciences"
- Weiss MC$, Sousa FL$, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. The physiology and habitat of the last universal common ancestor. Nature Microbiology 1: 16116 (2016)
- Martin WF, Neukirchen S, Zimorski V, Gould SB, Sousa FL. Energy for two: New archaeal lineages and the origin of mitochondria. Bioessays 38: 850-856 (2016)
- Sousa FL, Nelson-Sathi S, Martin WF. One step beyond a ribosome: The ancient anaerobic core. Biochim Biophys Act - Bioenerg 1857: 1027-1038 (2016)
- Sousa FL, Neukirchen S, Allen JF, Martin WF. Lokiarchaeon is hydrogen dependent. Nature Microbiology 1: 16034 (2016)
- Martin WF, Sousa FL, Early microbial evolution: The age of anaerobes. Cold Spring Harbor Perspectives in Biology 18: (2016)
- Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann SA, Swint-Kruse L. AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators. Journal of Molecular Biology 428: 671-678 (2016)
- Sousa FL, Parente DJ, Hessman JA, Chazelle A, Teichmann SA, Swint-Kruse L. Data on publications, structural analyses, and queries used to build and utilize the AlloRep database. Data in Brief 8: 948-957 (2016)
- Sousa FL, Hordijk W, Steel M, Martin WF. Autocatalytic sets in metabolism. Journal of Systems Chemistry 6:4 (2015)
- Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524: 427-432 (2015)
- de Vries J, Sousa FL, Bolter B, Soll J, Gould SB (2015) YCF1: A Green TIC? Plant Cell 27: 1827-1833 (2015)
- Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chavez N, Thiergart T, Janssen A, Bryant D, Landan G, Schoenheit P, Siebers B, McInerney JO, Martin WF: Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:77-80 (2015).
- * Martin WF, Sousa FL, Lane N: Energy at life's origin. Science 344:1092-1093 (2014).
- Sousa FL, Martin WF: Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. Biochem Biophys Acta - Bionenerg 1837: 964-981 (2014)
- * Ku C, Roettger M, Zimorski V, Nelson-Sathi S, Sousa FL, Martin WF: Plastid origin: Who, when and why? Acta Soc Bot Pol 83: 281-289 (2014)
- Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IA, Allen JF, Lane N, Martin WF: Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci 368: 20130088 (2013)
- Sousa FL, Shavit-Grievink L, Allen JF, Martin WF: Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome Biol Evol 5: 200-216 (2013)
- Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA: The emergence of protein complexes: Quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochem Soc Trans 40: 475-491 (2012)
- Sousa FL, Alves RJ, Ribeiro MA, Pereira-Leal JB, Teixeira M, Pereira MM: The superfamily of heme-copper oxygen reductases: Types and evolutionary considerations. Biochim Biophys Act 1817: 629-637 (2012)
- Sousa FL, Alves RJ, Pereira-Leal JB, Teixeira M, Pereira MM: A bioinformatics classifier and database for heme-copper oxygen reductases. PLoS One 6: e19117 (2011)
- Refojo PN, Sousa FL, Teixeira M, Pereira MM: The alternative complex III: a different architecture using known building modules. Biochim Biophys Acta 1797: 1869-1876 (2010)
- Sousa FL, Brito JA, Stelter M, Bandeiras TM, Vonrhein C, Teixeira M, Pereira MM, Archer M: Structural and functional insights into sulfide:quinone oxidoreductase. Biochemistry 48: 5613-5622 (2009)
- Verissimo AF, Sousa FL, Baptista AM, Teixeira M, Pereira MM: Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies. Biophys J 95: 4448-4455 (2008)
- Sousa FL, Verissimo AF, Baptista AM, Soulimane T, Teixeira M, Pereira MM: Redox properties of thermophilus ba: Different electron-proton coupling in oxygen reductases? Biophys J 94: 2434-2441 (2008)
- Pereira MM, Sousa FL, Verissimo AF, Teixeira M: Looking for the minimum common denominator in haem-copper oxygen reductases: Towards a unified catalytic mechanism. Biochim Biophys Acta 1777: 929-934 (2008)
- Fernandes AS, Sousa FL, Teixeira M, Pereira MM: Electron paramagnetic resonance studies of the iron-sulfur centers from complex I of Rhodothermus marinus. Biochemistry 45: 1002-1008 (2006)
- Pereira MM, Sousa FL, Teixeira M, Nyquist RM, Heberle J: A tyrosine residue deprotonates during oxygen reduction by the reductase from Rhodothermus marinus. FEBS Lett 580: 1350-1354 (2006)
- Srinivasan V, Rajendran C, Sousa FL, Melo AM, Saraiva LM, Pereira MM, Santana M, Teixeira M, Michel M: Structure at 1.3 A resolution of Rhodothermus marinus caa3 cytochrome domain. J Mol Biol 345: 1047-1057 (2005)
- Melo AM, Lobo SA, Sousa FL, Fernandes AS, Pereira MM, Hreggvidsson GO, Kristjansoon JK, Saraiva LM, Teixeira M: A nhaD Na/H antiporter and a homologues are among the Rhodothermus marinus complex I genes. Biochim Biophys Acta 1709: 95-103 (2005)
$ - equally contributing authors *- invited
Martin WF, Neukirchen S, Sousa FL: Early life. In: Bakermans C (ed.) Microbial Evolution under Extreme Conditions. de Gryter, Boston, pp. 171-184 (2015)
We are always looking for motivated bachelors and masters students that want to learn more about the power of computational analysis to disentangle microbial physiology. If you are interested in a BSc/MSc thesis, just come by.
- PhD and Post Doc positions
From time to time we have open positions for PhD students and PostDocs. If you are interested in working with us, please send an email to firstname.lastname@example.org