biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_vk... ·...
TRANSCRIPT
![Page 1: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/1.jpg)
Biogeochemical cycles
of elements (nitrogen, sulfur, metals)
1
L.P. Wackett, A. G. Dodge, L. B. Ellis, 2004
Microbial Genomics and the Periodic Table,
Appl. Environ. Microbiol., 70, 647 - 655
![Page 2: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/2.jpg)
The elements/metals of life www.webelements.com
Ca: 1.2 kg
K: 150 g
Na: 70 g
Mg: 20-30 g
Essential
Transition Metals
Fe: 4.5 g
Zn: 2.3 g
Cu: 0.072 g
Mo: 0.009 g
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
C: 17250 g
N: 1950 g
O: 45750 g
P: 825 g
S: 150 g
Se: 0.00375 g
2
![Page 3: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/3.jpg)
References - Biogeochemical cycles of elements
A. Butler, 1998 Acquisition and Utilization of Transition Metal Ions by Marine Organisms, Science, 281, 207- 210
F. M. M. Morel and N. M. Price , 2003
Science , 300, 944-947, The Biogeochemical Cycles of Trace Metals in the Oceans
L.P. Wackett, A. G. Dodge, L. B. Ellis, 2004
Microbial Genomics and the Periodic Table, Appl. Environ. Microbiol., 70, 647 - 655
M. Rudolf, P.M.H. Kroneck, 2005 The nitrogen cycle: Its biology. Metal Ions in Biological Systems, 43, 75-103
B.B. Ward, D.G. Capone, J.P. Zehr, 2007 Oceanography 20,101–109, What's New in the Nitrogen Cycle ?
S.M. Sievert, R.P. Kiene, H.N. Schulz-Vogt, 2007 Oceanography 20, 117–123, The Sulfur Cycle
SCOR Working Group , 2007 GEOTRACES – An international study of the global marine biogeochemical cycles of trace elements
and their isotopes, Chemie der Erde, 67, 85–131
G. M. Gadd, 2010 Metals, minerals and microbes: geomicrobiology, and bioremediation, Microbiology, 156, 609–643
3
![Page 4: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/4.jpg)
http://en.wikipedia.org/wiki/Sulfur_cycle
http://www.britannica.com/EBchecked/topic/65875/biogeochemical-cycle
S.M. Sievert, R.P. Kiene, and H.N. Schulz-Vogt, 2007
Oceanography 20, 117–123, The Sulfur Cycle
E.M. Cameron, 1982
Nature 296, 145-148, Sulfate and sulfate reduction in the early Precambrian oceans
G. Wächtershäuser, 1988
Syst Appl Microbiol, 10 , 207-210, Pyrite formation, the first energy source for life: a
hypothesis
R.K. Thauer, A. K. Kaster, et al., 2010
Annu Rev Biochem, 79, 507-36, Hydrogenases from methanogenic archaea, nickel, a novel
cofactor, and H2 storage
T. Urich et al., 2006
Science 311, 996 – 999, X-ray Structure of a Self-Compartmentalizing Sulfur Cycle
4
![Page 5: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/5.jpg)
5
Citation Muhumuza Moses (Lead Author);C Michael Hogan (Topic Editor) "Biogeochemical cycles". In: Encyclopedia of Earth. Eds. Cutler J. Cleveland (Washington, D.C.: Environmental Information Coalition, National Council for Science and the Environment). Last revised Date December 24, 2011. <http://www.eoearth.org/article/Biogeochemical_cycles?topic=49553>
As the Earth is essentially a closed system
with respect to matter, we can say that all
matter on Earth cycles .
![Page 6: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/6.jpg)
Estimated evolution of atmospheric O2
The red and green lines represent the range of the estimates: stage1: 3.85–2.45 Gyr (Ga),
stage2: 2.45–1.85Ga, stage3: 1.85–0.85Ga, stage4: 0.85–0.54Ga, stage5: 0.54Ga–present www.globalchange.umich.edu/globalchange1/current/lectures/Perry_Samson_lectures/evolution_atm/index.html
H.D. Holland, Phil. Trans. R. Soc. B (2006) 361, 903-915
Forms of Life – From Anaerobic to Aerobic
anoxic conditions (-O2) vs oxic conditions (+O2)
6
![Page 7: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/7.jpg)
Today’s Energy Conservation: Reduction of O2 to H2O
Humans are Aerobes
7
![Page 8: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/8.jpg)
G. Wächtershäuser
Munich/Chapel Hill
8
“The deep past of the Earth is
unobservable. Therefore, the
problem of the origin of life can
only be approached by a theory.”
Quote from Origin of Life: RNA World versus Autocatalytic Anabolist
See lecture by T. Cech, Nobel Prize in Chemistry, 1989
T. R. Cech
University of Colorado, Boulder
![Page 9: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/9.jpg)
Emergence of life on the ocean floor hydrothermal vent, Russel and Hall, 1997
9
![Page 10: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/10.jpg)
Basic Redox Couples Thauer et al., Bacteriol. Rev., 41, 100-180 (1977)
10
![Page 11: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/11.jpg)
Biogeochemical Cycles
• Metabolism: All organisms transform (different) compounds
• Metabolic pathways constitute closed global cycles, otherwise intermediates
will accumulate. The larger the amount of the accumulated intermediate, the better
substrate it will be for organisms. On a geological time scale, a new metabolic
pathway will develop which will convert the intermediate.
A B
• Metabolic pathways can be organized and classified according to different
aspects, such as with regard to the ELEMENTS.
11
![Page 12: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/12.jpg)
Elements in the Ocean
12
A. Butler, 1998
Acquisition and Utilization of Transition Metal Ions by
Marine Organisms, Science, 281, 207- 210
![Page 13: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/13.jpg)
Essential Metal Sites (V, Fe, Cu, Mo)
13
A. Butler, 1998
Acquisition and Utilization of
Transition Metal Ions by Marine
Organisms, Science, 281,
207- 210
![Page 14: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/14.jpg)
Vertical profiles of dissolved zinc and iron concentrations in the
north Pacific Ocean.
F M M Morel, N M Price Science 2003, 300 ,944-947 14
![Page 15: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/15.jpg)
(A) Release of complexing agents and metal ligand complexes from marine plankton: CdX,
phytochelatin-Cd complex released by diatoms; CuY, peptide complexes of Cu released by
coccolithophorids; CuZ, unidentified Cu ligand complex released by Synechococcus; sid,
siderophore released by heterotrophic bacteria and cyanobacteria; L, unidentified Co
complexing agent released by Prochlorococcus; C, Cys; E, Glu; G, Gly; Q, Gln; and R, Arg.
F M M Morel, N M Price Science 2003,
300,44-947
15
![Page 16: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/16.jpg)
The N cycle, illustrating the metal cofactors in each enzymatically
catalyzed step. (B) Primary metal requirements for C, N, and P
acquisition and assimilation by phytoplankton
F M M Morel, N M Price Science 2003,
300, 944-947 16
![Page 17: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/17.jpg)
A Cadmium enzyme from a marine organism Lane et al., NATURE, 435, 42 (2005)
Active Cd-Carbonic Anhydrase
(purified by chromatography;
metal analysis by X-ray
spectroscopy)
Note: Until most recently, this
enzyme has been regarded as a
classical Zn-dependent enzyme.
And indeed, usually Cd is highly
toxic, replacing Zn in many
important proteins.
17
![Page 18: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/18.jpg)
The Nitrogen Cycle: Note Activities of Microorganisms http://en.wikipedia.org/wiki/Nitrogen_cycle
18
![Page 19: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/19.jpg)
Important Reactions and Metal Enzymes of the Nitrogen Cycle
19
![Page 20: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/20.jpg)
Oxidation states of N
+5 +3 +2 +1 0 -1 -3
NO3- NO2
- NO N2O N2 H2NOH NH3
20
New intermediate: hydrazine, H2NNH2 Kuypers et al. (2003) „Anaerobic ammonium oxidation by anammox bacteria in the Black Sea”,
Nature 422, 608-611
![Page 21: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/21.jpg)
Essential Metals of the N Cycle
Fe Cu Mo/V
- Nitrate Reductase - Nitrate Reductase
- Nitrite Reductase - Nitrite Reductase
- NO Reductase
- N2O Reductase
- Nitrogenase - Nitrogenase
- Ammonia Mono-
oxygenase
- Hydroxylamine
Oxidoreductase
21
![Page 22: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/22.jpg)
22
![Page 23: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/23.jpg)
Nitrate Reductase
NO3- + 2H+ + 2e- NO2
- + H2O
23
![Page 24: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/24.jpg)
Mo bound to Molybdopterin (a dithiolene – coordinates both Mo and W)
JOURNAL of BIOLOGICAL CHEMISTRY (2009) 284, p. e10, N Kresge, R D Simoni, R L Hill:
The Discovery and Characterization of Molybdopterin - the Work of K. V. Rajagopalan)
24
PDB code: 2NAP
Numerous different forms of
nitrate reductase depending on
the organism
http://www.ebi.ac.uk/thornton-
srv/databases/cgi-
bin/enzymes/GetPage.pl?ec_nu
mber=1.7.99.4
![Page 25: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/25.jpg)
25
![Page 26: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/26.jpg)
Dissimilatory Nitrite Reductase
NO2- + 8H+ + 6e- NH4
+ + 2H2O
26
![Page 27: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/27.jpg)
Cytochrome c Nitrite Reductase
Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, Kroneck
PMH (1999) Nature, 400 , 476–80
27
![Page 28: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/28.jpg)
Nitrogen Uptake
• Nitrogen is an important constituent of biopolymers and numerous essential
biomolecules. The only N compound which can be taken up by higher organisms
is Ammonium, NH4+.
Amino acid synthesis: Amination of α-Ketoglutarate
(assimilatory process vs dissimilatory process)
28
![Page 29: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/29.jpg)
Biological N2 Fixation
Microorganisms can do the job under „normal conditions“ (T, P)
• free living soil bacteria, e.g. Azotobacter vinelandii
• Cyanobacteria with specialized cells, e.g. Anabaena sp., Nostoc sp.)
• Rhizobia which live in special plant organelles (root noudles)
The process, however, is costly. Plants have to deliver up to 25% of their
photosynthetically produced ATP to N2 fixing bacteria in the root nodules.
Note: N2 Fixation is
an anaerobic process
29
![Page 30: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/30.jpg)
N2 Fixation http://en.wikipedia.org/wiki/Nitrogenase
N2 + 8H+ + 16 Mg2+ATP + 8e-
2NH3 + H2 + 16 Mg2+ADP + 16 Pi 30
![Page 31: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/31.jpg)
The chemical speciation of arsenic in the stratified water column of Mono Lake, California
(left) as explained by the metabolism of arsenic by microbial populations present in the
water column (right).
R S Oremland, J F Stolz Science 2003, 300:939-944 31
![Page 32: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/32.jpg)
Phylogenetic diversity of representative arsenic-metabolizing prokaryotics.
R S Oremland, J F Stolz Science 2003, 300,939-944 32
![Page 33: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/33.jpg)
33
The Biogeochemical Cycle of Sulfur
![Page 34: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/34.jpg)
Life without Dioxygen – Respiration with S-Oxides
Reduction of SO42- to H2S
34 http://www.scienceclarified.com/Oi-Ph/Oxygen-Family.html
![Page 35: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/35.jpg)
Reactions of the Biogeochemical Sulfur Cycle SO4
-2
Sulfate Reduction
(Assimilatory)
Organic Sulfur
H2S
Mineralization
Sulfur Oxidation
Sulfate Reduction
(Dissimilatory) Elemental Sulfur
Sulfur Oxidation
Sulfur Reduction
35
![Page 36: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/36.jpg)
Oxidation/Reduction of Sulfur Compounds Coupled to
Energy Conservation Evolved Early in Prokaryotic Evolution
Bacteria Eucarya
Archaea
A. fulgidus
D.desulfuricans
D. vulgaris
T.denitrificans
36
![Page 37: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/37.jpg)
S. Shima et al., Science (2008), 321, 572 - 575
Tracking Footprints of Early Life Nature’s Toolbox to handle Dihydrogen
H2 ⇄ 2H+ + 2e-
37
![Page 38: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/38.jpg)
Overall structure of a Fe-only H2ase from (Handbook of Metalloproteins)
uni- vs bidirectional/
Ni,Fe vs Fe-only
H2 ⇄ 2H+ + 2e-
38
![Page 39: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/39.jpg)
Presence of Toxic Ligands at Active Site
Analysis of CO and CN- by FT IR
39
![Page 40: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/40.jpg)
Fe-only vs Ni,Fe Hydrogenase
Fe2
S
Fe1
S
(Cys)S
H2O
[4Fe4S]
O
C
N
C
O
CN
C
H-Cluster derFe-only Hydrogenase
(Cys)S Ni
(Cys)S(Cys)S
Fe(Cys)S
X
O
CN
C
N
C
[NiFe] Cluster derNi,Fe Hydrogenase
40
![Page 41: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/41.jpg)
Life without O2 - Sulfur Respiration Reduction of SO4
2- to H2S, a multi-electron, multi-proton transfer
process coupled to energy conservation
41
![Page 42: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/42.jpg)
SO42- must be first activated,
then microorganisms can eat it
APS ⇄ AMP + SO32-
Activation of sulfate (E°’ = -516 mV) to
adenosine-5’-phosphosulfate = APS (E°’ = -60 mV)
42
![Page 43: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/43.jpg)
APS Reductase from thermophilic Archaeoglobus fulgidus Fritz et al., PNAS (2002), 99, 1836-41; Schiffer et al., Biochemistry (2006), 45, 2960-67
43
![Page 44: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/44.jpg)
APSR has two [4Fe-4S] – Clusters which interact
9.8 A
310 320 330 340 350 360 370 380
Magnetic field [mT]
2.078 1.941 1.902 2.066 2.045 1.976 1.938 1.890
310 320 330 340 350 360 370 380
Magnetic field [mT]
I II I II
Eo‘ = - 60 mV Eo‘ = - 520 mV >>>
[+] [2+] [+] [+]
44
![Page 45: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/45.jpg)
Chemistry of Sulfite Reduction
Sulfite reduced to
sulfide (directly or via
trithionate/thiosulfate)
by sulfite reductase in
a six-electron transfer
process
Dissimilatory (dSIR) Assimilatory (aSIR)
Sulfite Reduction
ATP PPi
APS
ATP ADP
2 [H]
6 [H]
2 [H]
6 [H]
AMP
3 H2O
PAPS
PAPS
3 H2O
SO32 SO3
2
S3O62
S2O32
S2
S2
ATP-Sulfurylase APS-Kinase
SO32
S2
SO42
45
![Page 46: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/46.jpg)
SIR contains Siroheme
Siroheme = heme-type prosthetic group
catalyzes the six-electron reduction of sulfite to sulfide, and of nitrite to ammonia
formed by methylation, oxidation, and Fe insertion into uroporphyrinogen III
Siroheme
(green)
Heme b
(red)
46
![Page 47: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/47.jpg)
Sulfite Reductase (36 Fe) from Archaeoglobus fulgidus
SO32- + 6e- + 8H+ → H2S + 3 H2O
Schiffer et al. (2008) J. Mol. Biol., 379, 1063-74; Parey et al. (2010) Biochemistry, 49, 8912-21
Unique cofactor: Siroheme coupled to [4Fe-4S]
40 60 80 100 120 140 160 180
g- Value
Magnetic Field [mT]
15.6 8.27 5.63 4.26 3.43 2.87 2.47 2.16 1.93 1.74
30 40 50 60 70 80 90
A B
Magnetic Field [mT]
g- Value
20.1 17.1 14.9 13.3 11.9 10.8 9.9 9.13 8.47 7.9
EPR (X-Band), resonances between g 18 and g 1.9
47
![Page 48: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/48.jpg)
Overall structure of A. fulgidus dSIR 22 complex
• Final model contains four siroheme
and eight [4Fe-4S] centers = 36 Fe
• N- and C-terminal ends involved in
intradimer and interdimer
formation
• Tetrameric state may help to
survive in hot environments
• One -unit contains the catalytic
siroheme center
-subunit -subunit
β-subunit β-subunit
γ-subunit DrsC, interacts with
weakly with 22 complex in A.
Fulgidus, however strongly in D.
vulgaris 48
![Page 49: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/49.jpg)
Cofactors of A. fulgidus dSIR
Functional and structural siroheme-[4Fe-4S] centers in one dimer; both sirohemes are
arranged towards each other.
Minimal distance between the acetate carboxylates 9.6 Å; distance 3.9-4.3 Å from the siroheme
to next [4Fe-4S] cluster.
49
![Page 50: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/50.jpg)
Cofactors of Sulfite Reductase Schiffer et al., J. Mol. Biol. (2008), 379, 1063-74
• Catalytic (left) and structural siroheme-[4Fe-4S] center (right) in one
dimer: note the blocking tryptophan in the structural center
50
![Page 51: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/51.jpg)
SO32- Adduct and the Substrate Channel
Positively charged residues guide the substrate Parey et al. (2010) Biochemistry 49, 8912-21
51
![Page 52: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/52.jpg)
Reactivity in solution & in crystallo of A. fulgidus dSIR Parey et al. (2010) Biochemistry (2010) 49, 8912
52
![Page 53: Biogeochemical cycles of elementswebserver.umbr.cas.cz/~kupper/biogeochemical_cycles_VK... · 2012-06-25 · References - Biogeochemical cycles of elements A. Butler, 1998 Acquisition](https://reader034.vdocument.in/reader034/viewer/2022050105/5f43daa60526f9664f06953a/html5/thumbnails/53.jpg)
Structure of a Self-Compartmentalizing Sulfur Cycle T. Urich et al. (2006) Science 311, 996 – 999
53