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2009 Annual Science Report

Montana State University Reporting  |  JUL 2008 – AUG 2009

Executive Summary

Iron-sulfur clusters are ubiquitous in biology and possess features that are reminiscent of the features of iron-sulfur minerals. The structure/reactivity relationships between iron-sulfur metalloenzymes and iron-sulfur minerals has been noted by a number of investigators and is the basis for aspects of a “Metabolism First” origin of life scenario and more specifically for the “Iron Sulfur World”. These provide a framework for the research being conducted at the Astrobiology Biogeocatalysis Research Center with a focus on revealing the connection between iron-sulfur minerals and iron-sulfur metalloenzymes. The adaptation of iron-sulfur motifs from the abiotic world to the biological world may have been an early event in the generation of the building blocks of life on Earth and possibly a common feature of life elsewhere in the universe. ABRC research is aimed at providing the structural and chemical determinants that define the catalytic properties of iron-sulfur-based ... Continue reading.

Field Sites
5 Institutions
9 Project Reports
17 Publications
9 Field Sites
Roadmap
Objectives

Project Reports

  • Subglacial Methanogenesis and Its Role in Planetary Carbon Cycling

    Methanogens are thought to be among the earliest emerging life forms. Today, the distribution of methanogens is narrowly constrained, due in part to the energetics of the reactions which support this functional class of organism (namely carbon dioxide reduction with hydrogen and acetate fermentation). Methanogens utilize a number of metalloenzymes that have active site clusters comprised of a unique array of metals. The goals of this project are 1) identifying a suite of biomarkers indicative of biological CH4 production 2). quantifying the flux of CH~4~ from sub-ice systems and 3). developing an understanding how life thrives at the thermodynamic limits of life. This project represents a unique extension of the ABRC and bridges the research goals of several nodes, namely the JPL-Icy Worlds team and the ASU-Follow the Elements team.

    ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 6.1 6.2 7.1 7.2
  • Viral Ecology and Evolution

    This project is aimed at probing the occurrence and evolution of archaeal viruses in the extreme environments in the thermal areas in Yellowstone National Park. Viruses are the most abundant life-like entities on the planet and are likely a major reservoir of genetic diversity for all life on the planet and these studies are aimed at providing insights into the role of viruses in the evolution of early life on Earth.

    ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1 6.2 7.1 7.2
  • Computational Chemical Modeling the Link Between Structure and Reactivity of Iron-Sulfur Motifs

    Traditionally, the iron-sulfur mineral catalysis, iron-sulfur enzyme catalysis, and biomimetic thrust areas of ABRC have their own unique ways to probe the structure/function relationships at the surface defect sites, at the enzymatic active sites, or at the interface of biomacromolecular and iron-sulfur particle layers, respectively. Computation chemistry can provide a cohesive link among these thrust areas through bridging the enzymatic/mineral catalysis and molecular structure/chemical reactivity via fundamental physico-chemical properties at the molecule level.

    ROADMAP OBJECTIVES: 3.1 3.2 3.3 3.4 7.1 7.2
  • Evolution of Nitrogen Fixation, Photosynthesis, Hydrogen Metabolism, and Methanogenesis

    We have developed a new line of investigation to complement our work on the biochemistry of complex iron-sulfur cluster enzyme structure, function and biosynthesis with the aim of probing complex iron-sulfur enzyme evolution. We are studying the phylogenetic trajectory of multiple genes involved in complex iron-sulfur cluster function and biosynthesis to probe the evolutionary origin of aspect of hydrogen metabolism and modes of biological nitrogen fixation.

    ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1 6.2 7.1 7.2
  • Origin of Life and Catalysis – Philosophical Considerations

    The philosophy origins of life focus group at the ABRC is interested in exploring the known physical constraints of the origins of life as well as examining the epistemic foundations on which origins of life thought are founded upon. To address these goals, the group consists of persons from divergent studies areas including chemistry and biochemistry, physics, philosophy, and history of science. Synergy resulting from a sustained group interaction of this multi-disciplinary team has resulted in the creation of a number of lines of inquiry that the group is pursuing.

    ROADMAP OBJECTIVES: 3.1 3.2 3.3 3.4 4.2
  • Molecular Beam Studies of Nitrogen Reactions on Iron-Sulfur Surfaces

    It is generally accepted that surface-mediated reactions occur on defect sites. The role of defects in the formation of ammonia is being systematically evaluated using molecular beam-surface scattering experiments in which a hydrogen atom plasma source (deuterium due to easier detection) is used to hydrogenate a pyrite surface. The hydrogenated surface is subsequently bombarded with a molecular beam of energetic nitrogen molecules and the conversion of nitrogen to products, such as ammonia is probed through mass spectrometry.

    ROADMAP OBJECTIVES: 3.1 3.2 3.3 7.1 7.2
  • Probing the Structure and Nitrogen Reduction Activity of Iron-Sulfur Minerals

    Iron-sulfur compounds are common in both biological and geological systems. The adaptation of Fe-S clusters from the abiotic world to the biological world may have been an early event in the development of life on Earth and possibly a common feature of life elsewhere in the universe. The iron-sulfur mineral thrust of the ABRC is focused on examining the structure and reactivity of FeS minerals using nitrogen fixation as a model reaction.

    ROADMAP OBJECTIVES: 3.1 3.2 3.3 7.1 7.2
  • Biomimetic Cluster Synthesis: Bridging the Structure and Reactivity of Biotic and Abiotic Iron-Sulfur Motifs

    Synthetic approaches are being utilized to bridge the gap between Fe-S minerals and highly evolved biological Fe-S metalloenzymes. These studies are focusing on organic template (protein) mediated cluster assembly (biomineralization), probing properties of synthetic clusters, both as homogeneous and heterogeneous catalysts, investigating the impact of size scale on the properties of synthetic Fe-S clusters, and computational modeling of the structure and catalytic properties of synthetic Fe-S nanoparticles in the 5-50 nm range.

    ROADMAP OBJECTIVES: 3.1 3.2 3.3 3.4 7.1 7.2
  • Structure, Function, and Biosynthesis of the Complex Iron-Sulfur Clusters at the Active Sites of Nitrogenases and Hydrogenases

    Iron-sulfur clusters are thought to be among the most ancient cofactors in living systems. The iron-sulfur enzyme thrust is focused on examining the structure, mechanism, and biosynthesis of the complex Fe-S enzymes nitrogenase and hydrogenase. Biochemical, biophysical, and structure biology approaches are being employed to provide insights into complex iron-sulfur biosynthesis to establish paradigms for complex iron-sulfur cluster biosynthesis that can be placed in the context of the evolution of iron-sulfur motifs from the abiotic to biotic systems.

    ROADMAP OBJECTIVES: 3.1 3.2 3.3 6.1 6.2 7.1 7.2

Education & Public Outreach

Publications

  • Banfield, J. F., & Young, M. (2009). Variety—the Splice of Life—in Microbial Communities. Science, 326(5957), 1198–1199. doi:10.1126/science.1181501

  • Boyd, E. S., Spear, J. R., & Peters, J. W. (2009). [FeFe] Hydrogenase Genetic Diversity Provides Insight into Molecular Adaptation in a Saline Microbial Mat Community. Applied and Environmental Microbiology, 75(13), 4620–4623. doi:10.1128/aem.00582-09

  • Chandra, T., Silver, S. C., Zilinskas, E., Shepard, E. M., Broderick, W. E., & Broderick, J. B. (2009). Spore Photoproduct Lyase Catalyzes Specific Repair of the 5 R but Not the 5 S Spore Photoproduct. Journal of the American Chemical Society, 131(7), 2420–2421. doi:10.1021/ja807375c

  • Fu, C-Y., Wang, K., Gan, L., Lanman, J., Khayat, R., Young, M. J., … Johnson, J. E. (2010). In Vivo Assembly of an Archaeal Virus Studied with Whole-Cell Electron Cryotomography. Structure, 18(12), 1579–1586. doi:10.1016/j.str.2010.10.005

  • Inskeep, W. P., Rusch, D. B., Jay, Z. J., Herrgard, M. J., Kozubal, M. A., Richardson, T. H., … Frazier, M. (2010). Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function. PLoS ONE, 5(3), e9773. doi:10.1371/journal.pone.0009773

  • Klem, M. T., Young, M., & Douglas, T. (2010). Biomimetic synthesis of photoactive α-Fe 2 O 3 templated by the hyperthermophilic ferritin from Pyrococus furiosus. J. Mater. Chem., 20(1), 65–67. doi:10.1039/b918620d

  • McGlynn, S. E., Boyd, E. S., Shepard, E. M., Lange, R. K., Gerlach, R., Broderick, J. B., & Peters, J. W. (2009). Identification and Characterization of a Novel Member of the Radical AdoMet Enzyme Superfamily and Implications for the Biosynthesis of the Hmd Hydrogenase Active Site Cofactor. Journal of Bacteriology, 192(2), 595–598. doi:10.1128/jb.01125-09

  • McGlynn, S. E., Mulder, D. W., Shepard, E. M., Broderick, J. B., & Peters, J. W. (2009). Hydrogenase cluster biosynthesis: organometallic chemistry nature’s way. Dalton Trans., None(22), 4274. doi:10.1039/b821432h

  • McGlynn, S. E., Shepard, E. M., Winslow, M. A., Naumov, A. V., Duschene, K. S., Posewitz, M. C., … Peters, J. W. (2008). HydF as a scaffold protein in [FeFe] hydrogenase H-cluster biosynthesis. FEBS Letters, 582(15), 2183–2187. doi:10.1016/j.febslet.2008.04.063

  • Mulder, D. W., Boyd, E. S., Sarma, R., Lange, R. K., Endrizzi, J. A., Broderick, J. B., & Peters, J. W. (2010). Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydAΔEFG. Nature, 465(7295), 248–251. doi:10.1038/nature08993

  • Mulder, D. W., Ortillo, D. O., Gardenghi, D. J., Naumov, A. V., Ruebush, S. S., Szilagyi, R. K., … Peters, J. W. (2009). Activation of HydA ΔEFG Requires a Preformed [4Fe-4S] Cluster. Biochemistry, 48(26), 6240–6248. doi:10.1021/bi9000563

  • Murphy, R., & Strongin, D. (2009). Surface reactivity of pyrite and related sulfides. Surface Science Reports, 64(1), 1–45. doi:10.1016/j.surfrep.2008.09.002

  • Sarma, R., Barney, B. M., Hamilton, T. L., Jones, A., Seefeldt, L. C., & Peters, J. W. (2008). Crystal Structure of the L Protein of Rhodobacter sphaeroides Light-Independent Protochlorophyllide Reductase with MgADP Bound: A Homologue of the Nitrogenase Fe Protein † ‡. Biochemistry, 47(49), 13004–13015. doi:10.1021/bi801058r

  • Boyd, E.S., Anbar, A.D., Miller, S., Hamilton, T.L., Lavin, M. & Peters, J.W.  (Submitted).  An early origin for Molybdenum-nitrogenase.  Science.
  • Haydon, N., McGlynn, S.E. & Robus, O.  (Submitted).  Quantum mechanics and the emergence of life giving catalysts.  Origin of Life and Evolution of Biospheres.
  • Klem, M., Young, M. & Douglas, T.  (2008).  Biomimetic synthesis of b -TiO 2 inside a viral capsid.  J. Materials Chem, 18: 3821-3823.
  • Shepard, E.M. & Broderick, J.B.  (2009).  S-Adenosylmethionine and iron-sulfur clusters in biological radical reactions: The radical SAM superfamily [Book Chapter].  Comprehensive Natural Products Chemistry II.  Vol. In press.

2009 Teams