Wolfe-‐Simon - NAS

Geobiochemistry Microbes and the four basic strategies for Life on Earth: What we can learn from what we know (and how to look for what we don’t know) Dr. Felisa Wolfe-­‐Simon NASA Astrobiology InsFtute U.S. Geological Survey, Menlo Park, CA www.geobiochemistry.org contact: felisawolfesimon@gmail.com QuesFons: 1.  What are the hallmarks of known life? 2.  What must all life accomplish? 3.  Describe the major differences between autotrophy and heterotrophy. 4.  What would you suggest we look for on Mars as an indicator of life as we know it? 5.  How might we look for life or life-­‐like processes elsewhere in the Universe? 6.  How might we look for alterna4ve life here on our own planet, Earth? Acknowledgements Funding NASA Astrobiology InsFtute NASA Exobiology/Astrobiology Intellectual and technical contribu2on USGS: R. Oremland, S. Baseman, J. Switzer Blum, A. Foster, S. Hoe`, T. Kulp, J. MacFarland, L. Miller, T. Schraga, M. Waldrop. SLAC: Sam Webb. LLNL: J. Pec-­‐Ridge and P. Weber. ASU: A. Anbar, P. Davies, G. Gordon, W. Vermaas. Duquesne: J. Stolz. www.geobiochemistry.com Overarching QuesFon Geology  Biology? Biology  Geology? What are the underlying geo-­‐bio-­‐chemical
mechanisms? Overarching QuesFon Geology  Biology? Biology  Geology? What are the underlying geo-­‐bio-­‐chemical
mechanisms? PROTEROZOIC
Paleo-­‐
Meso-­‐ Neo-­‐
CENOZOIC
MESOZOIC
PALEOZOIC
65
248
Mn and Fe: SODs and Diatoms in the modern 543
Higgins, Wolfe-­‐Simon, Robinson, Qin, Saito & Pearson Geochim. Cosmochim. Acta in review.
Nitrogen cycling and primary producers: compound specific δ15N 900
Sulfur and Arsenic: Cyanobacteria and anoxygenic photosynthesis 1600
Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009; Wolfe-­‐Simon, Hoe`, & Oremland for submission to J Bact. Mo: nitrogen assimilaFon and sulfidic oceans Glass, Wolfe-­‐Simon & Anbar 2009 Geobiology; Glass, Wolfe-­‐Simon, Elser & Anbar 2010 L & O ARCHAEAN
2500
Fe vs. Cu: prokaryotes and eukaryotes Wolfe-­‐Simon & Anbar, for submission to Metallomics AlternaFve Early Life? Arsenic? 3800
HADEAN
Wolfe-­‐Simon et al. 2006 Plant Physiology; Wolfe-­‐Simon et al. 2005 J. Phycology 4500
Wolfe-­‐Simon, Davies & Anbar 2009 Int. J. Astrobiology; Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon 2009 Astrobiology; Oremland, SalFkov, Wolfe-­‐Simon, & Stolz 2009 Geomicro. Journal ; Wolfe-­‐Simon, Switzer-­‐Blum, Kulp, Gordon, Hoe`, Pec-­‐Ridge, Stolz, Webb, Davies, Anbar & Oremland, 2010 Science. PROTEROZOIC
Paleo-­‐
Meso-­‐ Neo-­‐
CENOZOIC
MESOZOIC
PALEOZOIC
65 Mn Fe: PaSI o FDe-­‐deficiency nd aFdaptaFon e: SODs atnd iatoms in the modern Chauhan, Fromme, olbeck, BPoekema, Kolber, Wolfe-­‐Simon t al. JB
et al. 2G006 Plant hysiology; Wolfe-­‐Simon et al. ,2 e005 . Piochemistry hycology in press. 248 Wolfe-­‐Simon 543
Higgins, Wolfe-­‐Simon, Robinson, Qin, Saito & Pearson Geochim. Cosmochim. Acta in review.
900
Sulfur and Arsenic: Cyanobacteria and anoxygenic photosynthesis 1600
Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009; Wolfe-­‐Simon, Hoe`, & Oremland for submission to J Bact. Mo: nitrogen assimilaFon and sulfidic oceans Glass, Wolfe-­‐Simon & Anbar 2009 Geobiology; Glass, Wolfe-­‐Simon, Elser & Anbar 2010 L & O ARCHAEAN
2500
Fe vs. Cu: prokaryotes and eukaryotes Wolfe-­‐Simon & Anbar, for submission to Metallomics AlternaFve Early Life? Arsenic? 3800
HADEAN
Nitrogen cycling and primary producers: compound specific δ15N 4500
Wolfe-­‐Simon, Davies & Anbar 2009 Int. J. Astrobiology; Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon 2009 Astrobiology; Oremland, SalFkov, Wolfe-­‐Simon, & Stolz 2009 Geomicro. Journal ; Wolfe-­‐Simon, Switzer-­‐Blum, Kulp, Gordon, Hoe`, Pec-­‐Ridge, Stolz, Webb, Davies, Anbar & Oremland, 2010 Science. CENOZOIC
MESOZOIC
PALEOZOIC
65 Mn Fe: PaSI o FDe-­‐deficiency nd aFdaptaFon e: SODs atnd iatoms in the modern Chauhan, Fromme, olbeck, BPoekema, Kolber, Wolfe-­‐Simon t al. JB
et al. 2G006 Plant hysiology; Wolfe-­‐Simon et al. ,2 e005 . Piochemistry hycology in press. 248 Wolfe-­‐Simon Nitrogen cycling and primary producers: compound specific δ15N ARCHAEAN
PROTEROZOIC
Paleo-­‐
Meso-­‐ Neo-­‐
543
Higgins, Wolfe-­‐Simon, Robinson, Qin, Saito & Pearson Geochim. Cosmochim. Acta in review.
Interdisciplinary methods include: Bacteria c900
ulturing Zooplankton culturing Sulfur and Arsenic: Cyanobacteria and anoxygenic photosynthesis 1-­‐D and 2-­‐D protein gel Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009; Hoe`, & Oremland for submission to J Bact. Immunolabelling techniques 1600 Wolfe-­‐Simon, Molecular techniques (cloning, sequencing, genomics, etc.) Mo: nitrogen assimilaFon and sulfidic oceans Glass, Wolfe-­‐Simon & Anbar 2009 Geobiology; ICP-­‐MS Glass, Wolfe-­‐Simon, Elser & Anbar 2010 L & O ESI-­‐MS 2500
HPLC Fe vs. Cu: prokaryotes and eukaryotes Wolfe-­‐Simon & Anbar, for submission to Metallomics Chromatography Spectroscopy Synchrotron AlternaFve Early Life? Arsenic? 3800
HADEAN
4500
Wolfe-­‐Simon, Davies & Anbar 2009 Int. J. Astrobiology; Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon 2009 Astrobiology; Oremland, SalFkov, Wolfe-­‐Simon, & Stolz 2009 Geomicro. Journal ; Wolfe-­‐Simon, Switzer-­‐Blum, Kulp, Gordon, Hoe`, Pec-­‐Ridge, Stolz, Webb, Davies, Anbar & Oremland, 2010 Science. PROTEROZOIC
Paleo-­‐
Meso-­‐ Neo-­‐
CENOZOIC
MESOZOIC
PALEOZOIC
65 Mn FFe: aFdaptaFon o oFD
e: PCaSI nd haracterizaFon e: SODs atnd f e-­‐deficiency iatoms increased in tDhe OC mbodern y a Fe-­‐limited green alga C
hauhan, F
romme, G
olbeck, B
oekema, K
olber, W
olfe-­‐Simon t al. JB
Wolfe-­‐Simon e, t Daiamond, l. 2006 PAlant nbar Physiology; & Hartnec Wolfe-­‐Simon et al. ,2 e005 . Piochemistry hycology in press. 248 Wolfe-­‐Simon 543
Higgins, Wolfe-­‐Simon, Robinson, Qin, Saito & Pearson Geochim. Cosmochim. Acta in review.
900
Sulfur and Arsenic: Cyanobacteria and anoxygenic photosynthesis 1600
Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009; Wolfe-­‐Simon, Hoe`, & Oremland for submission to J Bact. Mo: nitrogen assimilaFon and sulfidic oceans Glass, Wolfe-­‐Simon & Anbar 2009 Geobiology; Glass, Wolfe-­‐Simon, Elser & Anbar 2010 L & O ARCHAEAN
2500
Fe vs. Cu: prokaryotes and eukaryotes Wolfe-­‐Simon & Anbar, for submission to Metallomics AlternaFve Early Life? Arsenic? 3800
HADEAN
Nitrogen cycling and primary producers: compound specific δ15N 4500
Wolfe-­‐Simon, Davies & Anbar 2009 Int. J. Astrobiology; Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon 2009 Astrobiology; Oremland, SalFkov, Wolfe-­‐Simon, & Stolz 2009 Geomicro. Journal ; Wolfe-­‐Simon, Switzer-­‐Blum, Kulp, Gordon, Hoe`, Pec-­‐Ridge, Stolz, Webb, Davies, Anbar & Oremland, 2010 Science. The structure of today: 1. Thermodynamic basics (of life) 2. Four metabolic strategies of life (on Earth) 3. Unity of biochemistry 4. Cell structure and components The structure of today: 1. Thermodynamic basics (of life) 2. Four metabolic strategies of life (on Earth) 3. Unity of biochemistry 4. Cell structure and components Acid-­‐Base protons (H+) Redox (reducFon-­‐oxidaFon) electrons (H) 4H+ + CO2 + 4e-­‐  CH2O + H2O (reducFon, gain e-­‐) 2H2O  O2 + 4H + + 4e -­‐ (oxidaFon, loss of e-­‐) CO2 + H2O  CH2O + O2 (total, reducFon+oxidaFon) Canfield et al. 2006 Canfield et al. 2006 Canfield et al. 2006 X Canfield et al. 2006 ΔG° = -­‐nFE° lnKeq = nFE°/RT E = (RT/nF) lnKeq The electron tower E = E°+ (RT/nF) ln(prod/reac) Canfield et al. 2006 The electron tower Canfield et al. 2006 Respira2on Biological oxidaFon uFlizing an electron transport system that may operate with either oxygen or another external or reducible inorganic or organic compound as terminal electron acceptor. Aerobic respiraFon Canfield et al. 2006 Electron transport chain (simplified) ETC H+ H+ ADP +Pi ATP H+ H+ Canfield et al. 2006 Konhauser 2007 Anaerobic respiraFon Canfield et al. 2006 Konhauser 2007 Anaerobic respiraFon Canfield et al. 2006 Konhauser 2007 Anaerobic respiraFon The structure of today: 1. Thermodynamic basics (of life) 2. Four metabolic strategies of life (on Earth) 3. Unity of biochemistry 4. Cell structure and components Necessary for life: 1. energy 2. carbon Energy Phototrophy Photoautotroph Lithotrophy Chemoautotroph Photoheterotroph (chemo)Heterotroph Energy + Carbon Phototrophy Autotrophy Photoautotroph Lithotrophy Chemoautotroph Primary produc4on CO2  CH2O Heterotrophy Photoheterotroph (chemo)Heterotroph Secondary produc4on CH2O  CO2 Energy + Carbon Phototrophy Autotrophy Photoautotroph Lithotrophy Chemoautotroph Primary produc4on CO2  CH2O Heterotrophy Photoheterotroph (chemo)Heterotroph Secondary produc4on CH2O  CO2 PhotosyntheFc Bacteria Groups Type Bacterial Group Division e-­‐ source Anoxygenic Filamentous green Chloroflexi Organic, S2-­‐, S2O3 Anoxygenic Green Sulfur Chlorobi H2, S2-­‐, S0, S2O3 Anoxygenic Purple Proteobacteria (α, γ) H2, S2-­‐, S0, S2O3, Organic Anoxygenic Heliobacteria Firmicutes Organic Oxygenic Cyanobacteria H2O Cyanobacteria PhotosyntheFc Bacteria Groups -­‐ NO
2 Division Type Bacterial Group Anoxygenic Filamentous green Chloroflexi 2+
Fe e-­‐ source Organic, S2-­‐, S2O3 Anoxygenic Green Sulfur Chlorobi Anoxygenic Purple Proteobacteria (α, γ) H2, S2-­‐, S0, S2O3, Organic Anoxygenic Heliobacteria Firmicutes Organic Oxygenic Cyanobacteria H2O -­‐
AsO3 Cyanobacteria H2, S2-­‐, S0, S2O3 Arsenic-­‐driven photosynthesis. Arsenite Arsenate 16s Arra Time (h) Kulp et al. Science 2008 Arsenic-­‐driven photosynthesis. Arsenite Arsenate 16s Arra Time (h) Kulp et al. Science 2008 Purple Anoxygenic Photosynthesis Purple Anoxygenic Photosynthesis ArrA As(III) As(V) High Arsenic Soda Lakes (CA) Oremland, SalFkov, Wolfe-­‐Simon, & Stolz. Geomicro. J. 2009 Mono Lake Photo credits: Henry Bortman, Astrobiology Magazine Winogradsky Enrichment Mono Lake Sediments: 10 Mile Beach
OxidaFon under PAR Wolfe-­‐Simon*, Hoe`*, Baesman & Oremland, in prep How do we know the cyanobacterium is behind arsenite oxidaFon? hν
As(III) As(V) hν
H2O As(III) O2 As(V) How do we know the cyanobacterium is behind arsenite oxidaFon? hν
As(III) As(V) Several ways to test: 1.  IsolaFon of cyanobacterium. 2.  Aerobic light/dark experiments. 3.  Chemical inhibiFon of PSII (DCMU). 4.  Biophysical inhibiFon of PSII (p700). 5.  Axenic isolate from culture collecFon. hν
H2O As(III) O2 As(V) Biophysical inhibiFon of PSII. Custom built 700nm LED light box for far red light experiments. >700nm light excites PSI almost exclusively therefore inducing physiological responses related to anoxygenic metabolism. Custom built in house. Arsenite oxidaFon under 700nm Wolfe-­‐Simon*, Hoe`*, Baesman & Oremland, in prep Arsenite oxidaFon under 700nm Wolfe-­‐Simon*, Hoe`*, Baesman & Oremland, in prep S2-­‐ oxidaFon under PAR 3.0
Dark: S2-
[S2-] mM
2.5
2.0
1.5
1.0
0.5
Light: S2-
0.0
6.0
Light
Chl a (mg ml-1)
5.0
4.0
3.0
2.0
1.0
Dark
0.0
0
Wolfe-­‐Simon*, Hoe`*, Baesman & Oremland, in prep 50
100
150
Time (h)
200
250
16s idenFficaFon of Mono Lake cyanobacterium: Order: Oscillatoriales Genus: Oscillatoria 16s ribosomal RNA gene screen showed this Mono Lake isolate 98 to 99% similar to members of the Oscillatoriales, an order of filamentous cyanobacteria known to grow under hypersaline, elevated temperatures and other extreme-­‐type condiFons. Members of this order have also been shown to uFlize facultaFve anoxygenic photosynthesis with sulfide and recently, to also be diazotrophs. Wolfe-­‐Simon*, Hoe`*, Baesman & Oremland, in prep Filamentous cyanobacterium isolated from Mono Lake exhibiQng facultaQve anoxygenic photosynthesis using As(3+), S(2-­‐) and.... Dark field UV Wolfe-­‐Simon, Hoe` and Oremland, in prep Cyanobacterial Oxygenic Photosynthesis Cyanobacterial SULFIDE-­‐driven FacultaFve Anoxygenic Photosynthesis Cyanobacterial ARSENITE-­‐driven FacultaFve Anoxygenic Photosynthesis (proposed) Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009 Summary: The flexibility of the life WE DO KNOW. Cyanobacteria are capable of facultaFve anoxygenic photosynthesis using a variety of electron donors in addiFon to water, in parFcular arsenite. This may suggest alternaFve roles for cyanobacteria in the modern environment as well as help explain past redox status of the oceans. Lastly, in parFcular, the oxidaFon of arsenite to arsenate would have provided an early oxidant to microbial populaFons in an otherwise low redox potenFal environment. The structure of today: 1. Thermodynamic basics (of life) 2. Four metabolic strategies of life (on Earth) 3. Unity of biochemistry 4. Cell structure and components The tree of life. Konhauser 2007; a`er Woese et al. 1990 Cellular composiFon 1. Nucleic acids 2. Proteins 3. Lipid Cellular composiFon 1. Nucleic acids •  InformaFon storage. •  Subject to Darwinian selecFon. Cellular composiFon 1. Nucleic acids •  InformaFon storage. •  Subject to Darwinian selecFon. Zhou et al 1998 Cellular composiFon •  Catalyze metabolic reacFons. •  Structural support. 2. Proteins Klukas et al 1999 Cellular composiFon •  Catalyze metabolic reacFons. •  Structural support. 2. Proteins Klukas et al 1999 Cellular composiFon outside inside 3. Lipids Cellular composiFon -
O
As+
OH
O
O
As+
OH
H
outside inside O
-
OH
O
O
O
O P O
O P O-
-
3. Lipids O
O
O
O
R
R
O O
O
R'
O O
O
R'
Cellular composiFon 1. Nucleic acids= P 2. Proteins= N 3. Lipid = C The tree of life. Konhauser 2007; a`er Woese et al. 1990 Cellular composiFon 1. Nucleic acids 2. Proteins 3. Lipid AlternaFve biochemistry Cellular composiFon 1. Nucleic acids= P As? 2. Proteins= N 3. Lipids = C Periodic Table Atomic
Radius
Electronegativity
N
0.75
3.0
P
1.26
2.18
As
1.33
2.19
Modified aNer da Silva & Williams, Fig. 1.1 SpeciaFon diagrams Reaction
pKa
pKa PO4
H3AsO4 ↔ H2AsO4- + H+
2.22
2.12
H2AsO4- ↔ HAsO42- + H+
6.98
7.21
11.60
12.20
HAsO42- ↔ AsO43- + H+
Wolfe-­‐Simon et al. Int. J. Astrobiology 2009 Mono Lake Growth curves GFAJ-­‐1 isolate PO43-­‐ 0.30
0.25
AsO43-­‐ OD680
0.20
0.15
0.10
Control 0.05
0.00
5 x 108
PO43-­‐ AsO43-­‐ cells ml-1
5 x 107
5 x 106
Control 5 x 105
Wolfe-­‐Simon et al. Science 2010 0
120
240
Time (h)
360
480
S. Hoe`, USGS Electron Microscopy 5µm
+As/-­‐P 5µm
+As/-­‐P 5µm
-­‐As/+P 1µm
5µm
Wolfe-­‐Simon et al. Science 2010 J. Switzer Blum,USGS & J. Stolz, Univ. Duquesne Wolfe-­‐Simon et al. Science 2010 G. Gordon, ASU Whole cell NanoSIMS imaging +As/-P
- 12
: C
-
75
- 12
As : C
+As/-P
-
2 µm
1 µm
1 µm
Ratios
Ratios
1.00
1.00
0.75
0.75
0.50
0.50
0.25
0.25
2 µm
0.00
0.00
SE
1 µm
Wolfe-­‐Simon et al. Science 2010 J. Pec-­‐Ridge & P. Weber, LLNL Whole Cell fracQonaQon: Radiolabeled 73AsO4 distribuQon Chloroform (lipids)
1.5% (±0.8%)
Final aqueous fraction
(DNA/RNA)
11% (±0.1%)
Phenol:Chlorform
(proteins + lipids)
5.1% (±4.1%)
Phenol
(protein + s.m.w. metabolites)
80.3% (±1.7%)
Wolfe-­‐Simon et al. Science 2010 T. Kulp, USGS NanoSIMS +As/-­‐P -­‐As/+P 75As-­‐:12C-­‐ +As/-­‐P -­‐As/+P 13.4 (±2.5) 6.9 (±1.6) (All values mulFplied by 10-­‐6) Wolfe-­‐Simon et al. Science 2010 J. Pec-­‐Ridge & P. Weber, LLNL Arsenic K-­‐edge XANES '"$#
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S. Webb, SSRL EXAFS As DNA fit
Wolfe-­‐Simon et al. Science 2010 "
S. Webb, SSRL EXAFS As DNA fit
Wolfe-­‐Simon et al. Science 2010 "
S. Webb, SSRL What we don’t know. 1.  QuanFtaFvely, how much As is subsFtuFng for P? 5 %? 50 %? 2.  What is, if any, the affect of growth phase? 3.  Crystal structure? 4.  If we add back P, how do the cells parFFon if given +As/+P? 5.  What is the frequency this occurs in situ? 6.  …..And MANY other quesFons! Our current next steps: -­‐  Synchrotron studies on cellular fracFons -­‐  In depth physiological characterizaFon of GFAJ-­‐1 -­‐  Genomic sequencing of GFAJ-­‐1 -­‐  Cryo-­‐NMR Interested? Do you have a useful tool we haven’t thought of? Want to run some samples? felisawolfesimon@gmail.com Big Picture Modified aNer da Silva & Williams, Fig. 1.1 Big Picture Modified aNer da Silva & Williams, Fig. 1.1 PROTEROZOIC
Paleo-­‐
Meso-­‐ Neo-­‐
CENOZOIC
MESOZOIC
PALEOZOIC
65 Mn FFe: aFdaptaFon o oFD
e: PCaSI nd haracterizaFon e: SODs atnd f e-­‐deficiency iatoms increased in tDhe OC mbodern y a Fe-­‐limited green alga C
hauhan, F
romme, G
olbeck, B
oekema, K
olber, W
olfe-­‐Simon t al. JB
Wolfe-­‐Simon e, t Daiamond, l. 2006 PAlant nbar Physiology; & Hartnec Wolfe-­‐Simon et al. ,2 e005 . Piochemistry hycology in press. 248 Wolfe-­‐Simon 543
Higgins, Wolfe-­‐Simon, Robinson, Qin, Saito & Pearson Geochim. Cosmochim. Acta in review.
900
Sulfur and Arsenic: Cyanobacteria and anoxygenic photosynthesis 1600
Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009; Wolfe-­‐Simon, Hoe`, & Oremland for submission to J Bact. Mo: nitrogen assimilaFon and sulfidic oceans Glass, Wolfe-­‐Simon & Anbar 2009 Geobiology; Glass, Wolfe-­‐Simon, Elser & Anbar 2010 L & O ARCHAEAN
2500
Fe vs. Cu: prokaryotes and eukaryotes Wolfe-­‐Simon & Anbar, for submission to Metallomics AlternaFve Early Life? Arsenic? 3800
HADEAN
Nitrogen cycling and primary producers: compound specific δ15N 4500
Wolfe-­‐Simon, Davies & Anbar 2009 Int. J. Astrobiology; Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon 2009 Astrobiology; Oremland, SalFkov, Wolfe-­‐Simon, & Stolz 2009 Geomicro. Journal ; Wolfe-­‐Simon, Switzer-­‐Blum, Kulp, Gordon, Hoe`, Pec-­‐Ridge, Stolz, Webb, Davies, Anbar & Oremland, 2010 Science. PROTEROZOIC
Paleo-­‐
Meso-­‐ Neo-­‐
CENOZOIC
MESOZOIC
PALEOZOIC
65 Mn FFe: aFdaptaFon o oFD
e: PCaSI nd haracterizaFon e: SODs atnd f e-­‐deficiency iatoms increased in tDhe OC mbodern y a Fe-­‐limited green alga C
hauhan, F
romme, G
olbeck, B
oekema, K
olber, W
olfe-­‐Simon t al. JB
Wolfe-­‐Simon e, t Daiamond, l. 2006 PAlant nbar Physiology; & Hartnec Wolfe-­‐Simon et al. ,2 e005 . Piochemistry hycology in press. 248 Wolfe-­‐Simon 543
Higgins, Wolfe-­‐Simon, Robinson, Qin, Saito & Pearson Geochim. Cosmochim. Acta in review.
900
Sulfur and Arsenic: Cyanobacteria and anoxygenic photosynthesis 1600
Johnston*, Wolfe-­‐Simon*, Pearson & Knoll PNAS 2009; Wolfe-­‐Simon, Hoe`, & Oremland for submission to J Bact. Mo: nitrogen assimilaFon and sulfidic oceans Glass, Wolfe-­‐Simon & Anbar 2009 Geobiology; Glass, Wolfe-­‐Simon, Elser & Anbar 2010 L & O ARCHAEAN
2500
Fe vs. Cu: prokaryotes and eukaryotes Wolfe-­‐Simon & Anbar, for submission to Metallomics AlternaFve Early Life? Arsenic? 3800
HADEAN
Nitrogen cycling and primary producers: compound specific δ15N 4500
Wolfe-­‐Simon, Davies & Anbar 2009 Int. J. Astrobiology; Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon 2009 Astrobiology; Oremland, SalFkov, Wolfe-­‐Simon, & Stolz 2009 Geomicro. Journal ; Wolfe-­‐Simon, Switzer-­‐Blum, Kulp, Gordon, Hoe`, Pec-­‐Ridge, Stolz, Webb, Davies, Anbar & Oremland, 2010 Science. Acknowledgements Funding NASA Astrobiology InsFtute NASA Exobiology/Astrobiology Intellectual and technical contribu2on USGS: R. Oremland, S. Baseman, J. Switzer Blum, A. Foster, S. Hoe`, T. Kulp, J. MacFarland, L. Miller, T. Schraga, M. Waldrop. SLAC: Sam Webb. LLNL: J. Pec-­‐Ridge and P. Weber. ASU: A. Anbar, P. Davies, G. Gordon, W. Vermaas. Duquesne: J. Stolz. www.geobiochemistry.com EXTRA SLIDES Relevant references: F. Wolfe-­‐Simon, D. Grzebyk, O. Schofield, and P. G. Falkowski (2005). The role and evoluFon of superoxide dismutase in algae. Journal of Phycology. 41: 453-­‐465. F. Wolfe-­‐Simon, V. Starovoytov, J.R. Reinfelder, O. Schofield, and P. G. Falkowski (2006). LocalizaFon and role of manganese superoxide dismutase in a marine diatom. Plant Physiology. 142: 1701-­‐1709. P.C.W. Davies, S.A. Benner, C.E. Cleland, C.H. Lineweaver, C.P. McKay & F. Wolfe-­‐Simon (2009). Signatures of a Shadow Biosphere. Astrobiology. 9: 241-­‐249. J.B. Glass, F. Wolfe-­‐Simon, and A.D. Anbar (2009), CoevoluFon of marine metal availability and photoautotrophic nitrogen assimilaFon. Geobiology. 7: 100-­‐123. F. Wolfe-­‐Simon, P.C.W. Davies and A.D. Anbar (2009). Did nature also choose Arsenic? Interna4onal Journal of Astrobiology. 8: 69-­‐74. D.T. Johnston*, F. Wolfe-­‐Simon*, A. Pearson, and A.H. Knoll (2009). Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth’s middle age. PNAS. 106: 16925-­‐16929. *Authors contributed equally R.S. Oremland, C. SalFkov, F. Wolfe-­‐Simon, and J.F. Stolz (2009). Arsenic in the evoluFon of Earth and extraterrestrial ecosystems. Geomicrobiology Journal. 26: 522 -­‐ 536. J.B. Glass, F. Wolfe-­‐Simon, J.J. Elser and A.D. Anbar (2010). Molybdenum–nitrogen colimitaFon in heterocystous cyanobacteria. Limnology and Oceanography. 55: 667–676. D. Chauhan, I.M. Folea, C. Jolley, R. Kouřil, C. Lubner, S. Lin, D. Kolber, F. Wolfe-­‐Simon, J.Golbeck, E.J. Boekema & P. Fromme (2010). A novel photosyntheFc strategy for adaptaFon to low iron environments in the world's oceans. Biochemistry. in press. M.B. Higgins, F. Wolfe-­‐Simon, R.S. Robinson, Y. Qin, M.A. Saito and A. Pearson (2010). Paleoenvironmental implicaFons of taxonomic variaFon among δ15N values of chloropigments. Geochimica et Cosmochimica Acta. in review. F. Wolfe-­‐Simon, J. Switzer Blum, T.R. Kulp, G.W. Gordon, S.E. Hoe`, J. Pec-­‐Ridge, J.F. Stolz, S.M. Webb, P.K. Weber, P.C.W. Davies, A.D. Anbar and R.S. Oremland (2010). A bacterium that can grow by using arsenic instead of phosphorus. Science. DOI:
10.1126/science.1197258 www.geobiochemistry.org Helpful books: IntroducQon to Geomicrobiology. K. Konhauser (2007) AquaQc Geomicrobiology. D. Canfield, Thamdrump and Kristensen (2005) Brock Microbiology, 12th ediQon. Madigan, MarFnko, Dunlap, and Clark (2009) The limits of organic life in planetary systems. NAS report/J. Baross and others (2007) Geomicrobiology, 5th ediQon. Erlich and Newman (2009) Biochemistry , 6th ediQon. Berg, Tymoczko and Stryer (2006) Molecular Biology of the Cell, 5th ediQon. Alberts, Johnson, Lewis, Raff, Roberts and Walter (2007) A field guide to Bacteria. Dyer (2003) Whole Cell NanoSIMS imaging -As/+P
+As/-P
Ratios
1.00
0.75
75
-
As :12C
-
0.50
0.25
1 µm
2 µm
31
- 12
P: C
6.00
-
4.00
2.00
1 µm
2 µm
0.00
SE
1 µm
2 µm
Wolfe-­‐Simon et al. Science 2010 0.00
8.00
S. Webb, SSRL Wolfe-­‐Simon et al. Science 2010 XRF Energy Source + light phototroph -­‐ light chemotroph Electron Source organic inorganic lithotroph organotroph Carbon Source CO2 autotroph organic-­‐C heterotroph Phosphate vs. Arsenate -
-
O
-
O
P
O
O
OH
-
O
As
O
OH
Arsenic toxicity Dr. Abul Hussam George Mason University A woman of Alampur village in Bangladesh's KushFa district, one of the worst arsenic-­‐
contaminated areas, collects water from a SONO filter. (Dr. A.K.M. Munir; Pic. Post-­‐Gazece) Regions of high Arsenic Crustal Abundances seawater avg: 1.3nM As P 1Wilkie et al. 1998, 2Von Damm 1990, 3Langner 2001 Regions of high Arsenic seawater avg: 1.3nM 1Wilkie et al. 1998, 2Von Damm 1990, 3Langner 2001 MarFn and Russell 2003 MarFn and Russell 2003 Phosphorus? If P is relaFvely unavailable and insoluble, and is not abundant in hydrothermal sulfide-­‐rich environments, then why choose P? Westheimer revisited •  link together and sFll ionize: 1.  retain molecule in a lipid membrane 2.  stabilize diesters against hydrolysis 3.  linearize molecule O
•  intermediary metabolite •  energy sources O
P
O
Davis 1958; Westheimer 1987; Benner and Hucer 2002 OH
The biochemical importance of phosphate. ATP Acetyl Co-­‐A RNA NADPH Westheimer’s arguments against arsenate • Toxic • Unstable Arsenic analogs form spontaneously adenosine + arsenate kform 5’AMAs + H O khydrol 2
compound
kform
(M-1s-1)
ΔG°′
(kcal mol-1)
5′ AMAs
8.9 x 10-4
-3.6
5′ AMP
<1.0 x 10-9
2.3
glucose-6-arsenate
1.4 x 10-6
3.4
glucose-6-phosphate
~1 x 10-9
3.3
George et al 1970; Long et al 1973; Lagunas et al 1984 O
increases with tAhe si aliterature. ddiFon Toxic? Evidence from 2 uptake + arsenate + arsenate + phosphate + phosphate Crane and Lipmann 1953 Biochemical synthesis of ADP-­‐As Vm
Km (X)
Km (ADP)
nmol min-1 mg-1
mM
µM
Pi
200 ± 20
0.6 ± 0.1
9±2
Asi
170 ± 20
0.8 ± 0.1
13 ± 2
X
As and P are strikingly similar as substrates for the synthesis of ADP-­‐As or ATP respecFvely. Gresser 1981; Moore et al 1983 Glucose-­‐6-­‐arsenate leads to formaFon of NADPH ReacFon condiFons Hexokinase
µg ml-1
Pi
mM
Asi
mM
122
10
0
138
10
0
113
0
10
44
0
10
6.1
122
6.1
Hexokinase NADP reduction rate
nmol min-1 mg-1
Glucose-­‐6-­‐Pi dehydrogenase ADP-­‐As  glucose-­‐6-­‐arsenate  NADPH (in presence of sub. mitochondrial parFcles) Gresser 1981 6.2
RecogniFon of As by known biochemistry Evidence of arsenate substitution for phosphate by modern, extant biochemical processes Reaction or Enzyme Phosphate compound Arseno-­‐analog Reference Adenylate deaminase Adenylate kinase Aspartate aminotransferase Chloroplastic electron transport Glucose-­‐6-­‐phosphate dehydrogenase Hexokinase Human red blood cell sodium pump O2 Mitochondrial consumption Myokinase RNA Polymerase R. rubrum light induced Phosphoenolpyruvate phosphorylation mutase Phosphotransacetylase Protein synthesis Purine nucleoside phosphorylase 5'AMP AMP pyridoxal phosphate ATP glucose-­‐6-­‐phosphate ATP Pi Pi AMP pyrophosphate ADP+Pi phosphonopyruvate Pi ATP hydrolysis Pi (Lagunas et al., 1984) (Adams et al., 1984) (Ali & Dixon, 1992) (Avron & Jagendorf, 1959) (Gresser, 1981) (Gresser, 1981; Moore et al., 1983) (Kenney & Kaplan, 1988) (Crane & Lipmann, 1953) (Lagunas et al., 1984) (Rozovskaya et al., 1984) (Slooten & Nuyten, 1983) (Chawla et al., 1995) (Kyrtopoulos & Satchel, 1972) (Ozawa et al., 1970) (Kline & Schramm, 1993) Wolfe-­‐Simon et al. Int. J. Astrobiology 2009 5'AMAs 5'AM(CH2)As pyridoxal arsenate ADP-­‐As glucose-­‐6-­‐arsenate ADP-­‐As Asi Asi AMAs pyroarsenate ADP+Asi arsenopyruvate Asi ADP-­‐As hydrolysis Asi Rapid hydrolyFc properFes a benefit?
Arsenate molecules have higher hydrolysis rates-­‐ However, this may have been an advantage to be able to access the uFlity of such molecules before the evoluFon of the complex machinery necessary for building and manipulaFng phosphate analogs. Arsenic compound are unstable, but… Equlibrium! keq = [products]/[reactants] [reactants] > [products] Possible ecological relaFonship between the shadow biosphere and the regular biosphere: Ecologically separate Ecologically integrated Biochemically integrated Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-­‐Simon. Astrobiology (2009) Perhaps arsenic could have served two funcFons: 1. Metabolite 2. EnergeFc substrate Wolfe-­‐Simon et al I. J. Astrobiology 2009 Two for one: dissimilatory and assimilatory Wolinella succinogenes strain ATCC 29543
Helicobacter bilis strain Hb1
Sulfurospirillum halorespirans strain PCE-M2
Tindallia californiensis strain APO
Tsukamurella pulmonis strain IMMIB D-1321
Mycobacterium goodii strain M069
Demetria terragena strain HK1 0089
Actinomyces meyeri strain Prevot 2477B
Spirochaeta americana strain ASpG1
Oscillatoria sp. PCC 8927
Thioalkalimicrobium cyclicum strain ALM1
Thioalkalivibrio jannaschii strain ALM2
Escherichia coli strain O157:H7
Halomonas alkaliphila
Halomonas venusta strain NBSL13
GFAJ - 1
0.1
Halomonas sp. GTW
Halomonas sp. G27
Halomonas sp. DH77
Halomonas sp. mp3
Halomonas sp. IB-O18
Halomonas sp. ML-185
Nitrosomonas eutropha C91
Bordetella trematum strain DSM 11334
Burkholderia kururiensis strain KP23
Leptothrix discophora strain SS-1
Comamonas nitrativorans strain 23310
Ehrlichia muris strain AS145
Roseospira navarrensis strain SE3104
Magnetospirillum magnetotacticum strain DSM 3856
Magnetospirillum gryphiswaldense strain MSR-1
Paracoccus alkenifer strain A901/1
Paracoccus pantotrophus strain ATCC 35512
Nitrobacter alkalicus strain AN1
Methylobacterium nodulans strain ORS 2060
Desulfonatronum thiodismutans strain MLF1
Desulfovibrio longreachensis strain 16910a
Geobacter pelophilus strain Dfr2
Desulfobulbus elongatus strain FP
Cellular composiFon 1. Nucleic acids= P 2. Proteins= N 3. Lipid = C Picture of the z shcheme and the proteins The basics of all life Canfield et al. 2006 Exogenous source for P? (See M. Pasek, T. Kee and others) Exogenous source for P? (See M. Pasek, T. Kee and others) Z. Lipanovic Exogenous source for P? (See M. Pasek, T. Kee and others) Center for Meteorite Studies Z. ASU Lipanovic