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Molecular Biogeochemistry, Lecture 3 12.158 Lecture 3 • Polyisoprenoid lipids – Structural diversity and biosynthesis – Hydrocarbons – Complex lipids in archaea – Isoprenoids of plants and algae – Polyisoprenoids as environment and process indicators • Lacustrine environments – botryococcenes etc • Methanogenesis • Anaerobic oxidation of methane – Fossil record of Archaea 1 2- carbon molecule be the major building block for the complex 27- carbon, 4- ringed structure of the cholesterol molecule? BLOCH, LYNEN, AND THE CORNFORTH / POPJAK TEAM In the late 1930s, another young Jewish émigré from Germany, Konrad Bloch, joined Clarke‟s department as a graduate student. Bloch had already completed most of his thesis research at the University of Basel and had published two papers on that research. Still, the Basel faculty rejected it as “insufficient” (10). Bloch many years later learned that only one examiner on his committee had objected and that was on the grounds that the thesis failed to cite some important references – papers authored by that examiner! Looking back, Bloch realized that this may have been providential. Had he passes he decided to stay on in Germany. At any rate, when Bloch came to New York in 1936, Clarke, a guardian angel to refugee scientists, admitted him to his program and the Ph.D. was awarded about 2 years later. At that point, Schoenheimer offered a Bloch position in his 2 3 Courtesy of the National Library of Medicine. 4 5 Courtesy of the National Library of Medicine. Common Acyclic Isoprenoids isoprene head-to-tail tail-to-tail head-to-head 1 phytol phytane 1 OH crocetane pristane 1 2,6,10,15,19-pentamethylicosane (PMI) 1 2,6,10,14,18-pentamethylicosane 1 squalane farnesane 6 Less Common Acyclic Isoprenoids C30 HBI C25 HBI C20 HBI Diatom sources botryococcane Botryococcus braunii 17 18 19 lycopene 2' 2 4 6 8 tomato carotenoid 3 7 9 16 1 5 Probable algal hydrocarbon lycopane ? from lycapodiene 7 Polar Lipid Precursors of Acyclic Isoprenoids O O phytane OH archaeol HO O caldarchaeol O O O OH biphytane O O O OH chrenarchaeol O HO 8 Stereochemistry of archaeal and bacterial lipids 9 33 34 35 36 10 Polar Lipid Precursors of Acyclic Isoprenoids CCommommon heaon head gdroups g of bacteria and archaea OOOOO OOOOO OOOOO HHHHHOOOOO OOOOOHHHHH OOOOO HOHOHOHOHO OOOOO OOOOO OOOOOHHHHH OOOOO OOOOOHHHHH NNNNNHHHHH22222 PPPPP PPPPP PPPPP PPPPP PPPPP PPPPP OOOOOHHHHH OOOOO OOOOO OOOOO OOOOO HHHHHOOOOO OOOOO OOOOO HHHHHOOOOO OOOOO OOOOO OOOOO OOOOOHHHHH OOOOO OOOOO OOOOO OOOOO OOOOO HHHHHOOOOO OHOHOHOHOH HHHHH22222NNNNN OOOOOHHHHH OOOOOHHHHH OOOOOHHHHH NNNNN OOOOO OOOOO OOOOOHHHHH NNNNNHHHHH22222 HHHHHOOOOO OOOOOHHHHH HHHHHOOOOO OOOOOHHHHH ethanethanoooollllaminamine (e (PEPE)))) glglglglycycereroooollll ( PG)PG) seserrrrinininine (e (PSPS)))) cccchohollllinininine (ePCPC ()))) aminaminooooppppententaaaannnnetetretetroooollll ( AAAAPT)PT) ininininoooositositollll ( PI)PI) hexohexohexohexosesesese ( ararararcccchaea)haea)haea)haea) CCCommonommommon core lililipidspidpids of bactesbacteribacteriarrii aaofa bacte CCommommon core onlilipidpid cores of archaeaa OOO RRR RRR OOOO OOO RRR OOO OOO OOOO OOOO OOOO RRR OOO OOO OOO OOO RRR OOOO OOO OOO RRR OOOO OOOO OOOO OOO OOO OOOO ddii--esteresterddii--etethherer mixedmixed ArArchachaeoleol CalCalCaldardardarccchaehaehaeooolll 11 Favored Mass Spectrometric Fragmentations 57 253 x50 267 71 323 352 85 127 183 ?? 12 Crocetane – Phytane Distinction crocetane phytane crocetane phytane GC-FID (a) 282-169; 0.6%, 1.9 Full Scan (RIC) (b) 196-127; 100%, 2.1 169 Da (RIC from FS) (c) 196-126; 63%, 2.3 169 Da (SIR) (d) 168-182; 13%, 11.7 183 Da (SIR) (e) 182-127; 40%, 0.1 GC-MS-MS GC and GC-MS (SIR) 13 Crocetane – Phytane Distinction 14 Regular C25 vs PMI Distinction Ace Lake Modern Wilkinson 1 W. Terrace Sed. 1 PMI C25 reg C25 reg 100% 100% 100% (a) 266-197 Da (a) (a) 2.4% 68% 76% (b) 252-197 Da (b (b) ) 26% 4% 26% (c) 352-267 Da (c) (c) 35.48 36.18 35.48 36.18 36.18 35.48 Ret. Time (mins) One thin peak+ one compound All fat peaks = more than one compound 15 Regular C25 vs PMI & HBI Distinction O R O O 2,6,10,14,14-pentamethylicosane Carbon chains of Halobacterium core lipid 2,6,10,15,19-pentamethylicosane (PMI) Found as a free hydrocarbon in some methanogens A „highly branched isoprenoid‟ (HBI) from a diatom 16 I25 Reg PMI Unknowns 1 2 Distinguishing C25 (a) Monterey Isoprenoids (b) Byilkaoora-3 note peak shapes (c) Monterey + Byilkaoora-3 (d) W. Terrace-1 Partial 183Figure Da (SIR) 6 chromatograms of (a) Monterey Formation showing elution position of PMI; (b) Byilkaoora-3 showing elution position of I25 reg; (c) Monterey + Byilkaoora-3 mixture showing relative elution order of PMI and I25 reg isomers (NB. only partially resolved); (d) West Terrace-1 which has a peak at the same position as the I25 reg isomer and no peak at the earlier retention time of PMI. Unknown peaks 1 (Monterey) and 2 (West Terrace-1) elute after I25 reg. Chromatogram 17time range = 36 sec. phytane reduction/dehydration/reduction OH E-3, 7R, 11R, 15-tetramethylhexadec-2-enol = phytol oxidation/decarboxylation/reduction = 6(R), 10(S) - pristane 6(S), 10(R) - pristane 6(R), 10(R) - pristane 6(S), 10(S) - pristane 18 Pristane to Phytane Ratio Pr/Ph • An empirical parameter that was originally used to classify Australian oils; high in oils from land plant OM (Powell & McKirdy, 1973) • Empirical correlation with depositional environment (Didyk et al., 1978) – <1 strongly reducing or evaporitic environments (correlates with Gammacerane) – 1-4 reducing marine and lacustrine environments – >4 terrestrial aquatic environments d13C of Pr and Ph generally similar • Pr/Ph probably reflects redox control on diagenesis of phytol 19 40.0 35.0 Kangaroo Is. Strand OB 30.0 OA Sawpit 25.0 Bass GA1 GA2 20.0 GB Migr %C27 Sterane 15.0 10.0 5.0 0.0 0.0 2.0 4.0 6.0 8.0 10.0 12.0 Pristane/Phytane 20 1.0 0.9 Bonaparte/Petrel 0.8 Bonaparte/Timor Bonaparte/Vulcan 0.7 Canning Carnarvon/Barrow Carnarvon/Dampier 0.6 Carnarvon/Beagle Carnarvon/Exmouth 0.5 Browse Perth Indo/Bintuni nC27/nC17 0.4 Indo/Seram Indo/Timor 0.3 0.2 0.1 0.0 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 Pr/Ph 21 Botryococcus braunii isoprenoids 22 C30 Botryococcene C31-C33 Botryoccanes C30 C31 C32 C33 C33 23 some cultured B braunii strains 434 350 lake sediments (Maoming) and 350 434 Oils (Duri of Sumatra) 266 434 350 182 lake sediments (Maniguin) and Oils (Minas and Duri of Sumatra) 210 294 24 Text has been removed due to copyright restrictions. Please see: Abstract, John K. Volkman, et al. "C25 and C30 Highly Branched Isoprenoid Alkenes in Laboratory Cultures of Two Marine diatoms." Organic Geochemistry 21, no. 3-4 (March-April 1994): 407-414. 25 Courtesy Elsevier, Inc., http://www.sciencedirect.com. Used with permission. 26 Courtesy Elsevier, Inc., http://www.sciencedirect.com. Used with permission. 27 Science 23 April 2004: Vol. 304. no. 5670, pp. 584 – 587 The Rise of the Rhizosolenid Diatoms Jaap S. Sinninghe Damsté,1* Gerard Muyzer,1,2 Ben Abbas,1 Sebastiaan W. Rampen,1 Guillaume Massé,3 W. Guy Allard,3 Simon T. Belt,3 Jean-Michel Robert,4 Steven J. Rowland,3 J. Michael Moldowan,5 Silvana M. Barbanti,5,6 Frederick J. Fago,5 Peter Denisevich,5 Jeremy Dahl,5 Luiz A. F. Trindade,6 Stefan Schouten1 The 18S ribosomal DNA molecular phylogeny and lipid composition of over 120 marine diatoms showed that the capability to biosynthesize highly branched isoprenoid (HBI) alkenes is restricted to two specific phylogenetic clusters, which independently evolved in centric and pennate diatoms. 28 Fig. 1. Neighbor-joining phylogenetic tree based on nearly complete 18S rRNA sequences of diatoms. Some of the sequences were published before (5); 86 others (see table S1 for details) were determined in this study. The sequences of Coccoid haptophyte and Emiliania huxleyi were used as outgroups but were pruned from the tree. Bolidomonas mediterranea is a sister group of the diatoms. The This image has been removed due to copyright tree was created with the use of the Jukes Cantor restrictions. Please see Figure 1 on http://www.sciencemag.org/cgi/content/full/304/5670/584. model. HBI-biosynthesizing strains are indicated in red. Diatoms in green were tested but did not contain HBI alkenes; diatoms in black were not tested for the presence of HBI alkenes. The scale bar indicates 10% sequence variation. The inset shows the structure of C25 HBI alkane (27) and parent skeleton of C25 HBI unsaturated alkenes (7–11) produced by diatoms. Note that the odd non HBI-biosynthesizing Rhizosolenia strain, R. robusta, falls completely out of the Rhizosolenia phylogenetic cluster, indicating that its morphological classification as a Rhizosolenia diatom is probably wrong. 29 Methane seeps: Anaerobic oxidation of methane (AOM) 30 Image courtesy of Victoria Orphan. Used with permission. Sediment Core from a methane-rich Monterey cold seep This is a chemistry “profile” from the core 1 Methane (µM) 1 2 4 6 8 00 20 00 00 00 00 0 0 0 0 (cm) 4 CH 4 SO4 Bacteria feed on methane and sulfate 8 sediment o theintDepth o theintDepth 12 16 0 5 10 15 20 25 30 Sulfate (mM) Image courtesy of Victoria Orphan. Used with permission. 31 Anaerobic oxidation of methane The “consortium hypothesis” 2- SO4 Reversed Intermediate Sulfate- CH 4 Methanogen Product Reducing CO2 Bacterium HS- Hoehler et al., Global Biogeochemical Cycles 8, 451-463 (1994) Geochim. Cosmochim. Acta 62, 1745-1756 (1998) 32 NATURE |VOL 29 APRIL 1999 803 Text has been removed due to copyright restrictions. Please see http://www.nature.com/nature/journal/v398/n6730/abs/398802a0.html.
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