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VII. CONTEXT: THE ORGANISM

VII. CONTEXT: THE ORGANISM. CONTEXT: THE ORGANISM. Isolated from a neutral volcanic hot spring Thermophilic, gram negative bacterium (optimal temp 77ºC) Chemolithoautotroph. Huber et al., 1992.

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VII. CONTEXT: THE ORGANISM

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  1. VII. CONTEXT: THE ORGANISM

  2. CONTEXT: THE ORGANISM • Isolated from a neutral volcanic hot spring • Thermophilic, gram negative bacterium (optimal temp 77ºC) • Chemolithoautotroph Huber et al., 1992

  3. Connections to other parts of the curriculum (autotrophy, redox/electron transport, evolution, phylogeny, etc.) Context as Bridge

  4. Extremophiles Chemolithoautotrophy A. degensii isolation and characterization Horizontal gene transfer CONTEXT: Contents

  5. -20 to 121 C P < 120 Mpo -0.2 to 11 pH salinities up to 6 M Basically our idea of normal is pretty narrow Extremophiles

  6. Thermophile 45° C - 117° C Psychrophile -10° C - 10° C Barophile Acidophile Halophile alkaphile Extremophiles

  7. Singer and Hickey (2003) compare three characteristics of genomes: nucleotide content, codon usage and amino acid composition: 2-fold decrease in the amount of Q in thermophiles (thermolabile)? Investigated in: Das and Gerstein. 2000. The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct. Integr. Genomics 1:76-88 Comparing the genomes of thermophiles and mesophiles

  8. To learn limits of life on earth To learn what conditions (& planets/moons) to look for life in solar system To obtain biocatalysts (enzymes) which work under extreme conditions Why study extremophiles?

  9. Important extremophile enzyme applications 1. Washing machine: Protease at alkaline pH, bleach and high temperature 2. Starch hydrolysis industrial process: α-amylase active and stable at 104° C 3. Biomining: Bacteria which reduce or oxidize metals at pH 1.0 during mining operations To obtain extremophilic enzymes, look in extreme environments Extreme Applications

  10. The Context is the goal Scott et al., 2006

  11. CO2  biomass carbon Carbohydrates, amino acids, nucleic acids, etc. Many pathways for carbon fixation Calvin Benson Bassham cycle Rev. TCA cycle Acetyl CoA pathway Hydroxypropionate cycle All have in common: Energetically expensive High demand for ATP, NAD(P)H Autotrophy

  12. Chemolithoautotrophs by Comparison EnergyElectronsCarbonPractitioners photo litho auto trophs plants, algae chemo organo hetero trophs humans, E. coli chemo litho auto trophs protagonists of this presentation Courtesy of KM Scott

  13. “…something from almost nothing…”--J. Shively Ammonifex degensii (and other chemolithoautotrophs) can generate all their lipids, proteins, nucleic acids, cofactors, cell wall components from CO2, NO3, PO4 (!!) Chemolithoautotrophy Courtesy of KM Scott

  14. How do cells obtain energy from lithotrophic electron transport? • Electrons are fed into electron transport chains • As the electrons travel down the electron transport chain, protons are pumped out of the cell at “coupling sites” • The proton motive force that is generated is used for ATP synthesis etc.

  15. Formation of Ammonium from Nitrate During Chemolithoautotrophic Growth of the Extremely Thermophilic Bacterium Ammonifex degensii System. Appl. Microbiol. 19, 40-49 (1996) R. Huber, P. Rossnagel, C. R. Woese, R. Rachel, T. A. Langworthy, and K. O. Stetter

  16. From Karl Stetter’s notebook, used by permission

  17. Courtesy of Karl Stetter

  18. Ammonifex: Ammonium maker (Ammon, ammonium salt; L. facere) degensii: named after Egon T. Degens Ammonifex degensii

  19. Egon T. Degens Courtesy of Karl Stetter

  20. April 15, 1928- February 19, 1989 Aries Geologist and geochemist at Hamburg University Established first organic geochemistry labs Worked also at PSU and CalTech Cycles of elements, SCOPE/UNEP (the scientific committee on problems of the environment/United nations Environment Program Egon T. Degens

  21. 300 articles and 19 books (Co-)Author of Biogeochmistry of Major World Rivers (1991) Perspectives on Biogeochemistry (1989) Structural Molecular Biology of Phosphates (1971) Egon T. Degens

  22. Courtesy of Karl Stetter

  23. Courtesy of Karl Stetter

  24. “At a nitrate-containing volcanic hot spring in Java, • 10ml of anaerobic modified medium was inoculated • with 1ml of original sample material….” Courtesy of Karl Stetter

  25. Courtesy of Karl Stetter

  26. University of Regensberg, photo by Cheryl Kerfeld

  27. University of Regensberg, photo by Cheryl Kerfeld

  28. University of Regensberg, photo by Cheryl Kerfeld

  29. Courtesy of Karl Stetter

  30. Presenting the paper….Isolation After 3 days… sample KC4 showed growth of rod-shaped cells. Huber et al., 1996

  31. Phylogenetic analysis 16s rRNA (1996) A. degensii is related to Desulfotomaculum, a sulfate reducing species ref A. degensii has a distant relationship with thermophilic clostridia Huber et al., 1996

  32. * Melting point analysis → 53% GC Chromatographic base analysis → 55.5% GC Results from sequencing? DNA base composition

  33. * Glycerol diethers---------------85% * Glycerol monoethers-----------9% * Fatty acid methyl esters-------8% Lipids

  34. Lipids Huber et al., 1996

  35. “New” biospheres • Mid-ocean crust (300 meter deep borehole) • Small subunit rRNA from organisms collected on filters sequenced • The most abundant class of clones is most closely related to A. degensii • Science, 299: 120-123 (2003)

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