Benutzer:Asw-hamburg/Methanogene

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MAP

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ProteobakterienRickettsialesCyanobakterienFirmicutesEuryarchaeotaCrenarchaeotaLokiarchaeotaDiaphoretickesGlaucophytaPlantaeExcavataAmorphaeaFungiAnimaliaArchaeaBakterienEukaryoten
Abb. 2. Zeitskala in Milliarden Jahren vor heute

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Origin of eukaryotes

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The three-domains tree and the Eocyte hypothesis.[1]
Phylogenetic tree showing the relationship between the eukaryotes and other forms of life.[2] Eukaryotes are colored red, archaea green and bacteria blue.

Fossils

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The origin of the eukaryotic cell is considered a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The timing of this series of events is hard to determine; Knoll (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some acritarchs are known from at least 1.65 billion years ago, and the possible alga Grypania has been found as far back as 2.1 billion years ago.[3]

Organized living structures have been found in the black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryotic life could have evolved at that time.[4] Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a red alga, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago.[5]

Biomarkers suggest that at least stem eukaryotes arose even earlier. The presence of steranes in Australian shales indicates that eukaryotes were present in these rocks dated at 2.7 billion years old.[6][7]

Relationship to Archaea

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Eukaryotes are more closely related to Archaea than Bacteria, at least in terms of nuclear DNA and genetic machinery, and one controversial idea is to place them with Archaea in the clade Neomura. However, in other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:

  • Eukaryotes resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a eubacterium, and the nucleus from an archaeon,[8] from a virus,[9][10] or from a pre-cell.[11][12]
  • Eukaryotes developed from Archaea, and acquired their eubacterial characteristics from the proto-mitochondrion.
  • Eukaryotes and Archaea developed separately from a modified eubacterium.

The chronocyte hypothesis for the origin of the eukaryotic cell[13] postulates that a primitive eukaryotic cell was formed by the endosymbiosis of both archaea and bacteria by a third type of cell, termed a chronocyte.

Endomembrane system and mitochondria

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ProteobakterienRickettsialesCyanobakterienFirmicutesEuryarchaeotaCrenarchaeotaLokiarchaeotaDiaphoretickesGlaucophytaPlantaeExcavataAmorphaeaFungiAnimaliaArchaeaBakterienEukaryoten
Zelle 3

The origins of the endomembrane system and mitochondria are also unclear.[14] The phagotrophic hypothesis proposes that eukaryotic-type membranes lacking a cell wall originated first, with the development of endocytosis, whereas mitochondria were acquired by ingestion as endosymbionts.[15] The syntrophic hypothesis proposes that the proto-eukaryote relied on the proto-mitochondrion for food, and so ultimately grew to surround it. Here the membranes originated after the engulfment of the mitochondrion, in part thanks to mitochondrial genes (the hydrogen hypothesis is one particular version).[16]

In a study using genomes to construct supertrees, Pisani et al. (2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy between an archaea closely related to Thermoplasmatales and an α-proteobacterium, likely a symbiosis driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the α-proteobacterial endosymbiont.[17]

Hypotheses for the origin of eukaryotes

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Different hypotheses have been proposed as to how eukaryotic cells came into existence. These hypotheses can be classified into two distinct classes – autogenous models and chimeric models.

Autogenous models

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Vorlage:Plain image with caption

Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria.[18] According to this model, a large prokaryote developed invaginations in its plasma membrane in order to obtain enough surface area to service its cytoplasmic volume. As the invaginations differentiated in function, some became separate compartments—giving rise to the endomembrane system, including the endoplasmic reticulum, golgi apparatus, nuclear membrane, and single membrane structures such as lysosomes.[19] Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium, and it's assumed that all the eukaryotic lineages that did not acquire mitochondria went extinct.[20] Chloroplasts came about from another endosymbiotic event involving cyanobacteria. Since all eukaryotes have mitochondria, but not all have chloroplasts, mitochondria are thought to have come first. This is the serial endosymbiosis theory.

Some models propose that the origins of double layered organelles, such as mitochondria and chloroplasts, in the proto-eukaryotic cell is due to the compartmentalization of DNA vesicles that were formed from the secondary invaginations or more detailed infoldings of cellular membrane.Vorlage:Citation needed

Chimeric models

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Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell. Within these chimeric models, some studies further claim that mitochondria originated from a bacterial ancestor while others emphasize the role of endosymbiotic processes behind the origin of mitochondria.

Based on the process of mutualistic symbiosis, the hypotheses can be categorized as – the serial endosymbiotic theory (SET),[21][22][23] the hydrogen hypothesis (mostly a process of symbiosis where hydrogen transfer takes place among different species),[24] and the syntrophy hypothesis.[25][26]

According to serial endosymbiotic theory (championed by Dr. Lynn Margulis), a union between a motile anaerobic bacterium (like Spirochaeta) and a thermoacidophilic crenarchaeon (like Thermoplasma which is sulfidogenic in nature) gave rise to the present day eukaryotes. This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. The bacterium on the other hand, contributed the necessary fermentation products and electron acceptors along with its motility feature to the archaeon thereby gaining a swimming motility for the organism. From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alpha-proteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. For example, Thiodendron has been known to have originated via an ectosymbiotic process based on a similar syntrophy of sulfur existing between the two types of bacteria – Desulphobacter and Spirochaeta. However, such an association based on motile symbiosis have never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments.[27]

In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alpha-proteobacterium (the symbiont) gave rise to the eukaryotes. The host utilized hydrogen (H2) and carbon dioxide (Vorlage:CO2) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and Vorlage:CO2 as byproducts of anaerobic fermentation process. The host's methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation. Endosymbiotic gene transfer (EGT) acted as a catalyst for the host to acquire the symbionts' carbohydrate metabolism and turn heterotrophic in nature. Subsequently, the host's methane forming capability was lost. Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.

The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this theory, eukaryogenesis (i.e. origin of eukaryotic cells) occurred based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a delta-proteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alpha-proteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a delta-proteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus while the delta-proteobacterium contributed towards the cytoplasmic features. This theory incorporates two selective forces that were needed to be considered during the time of nucleus evolution – (a) presence of metabolic partitioning in order to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, and (b) prevention of abnormal biosynthesis of proteins that occur due to a vast spread of introns in the archaeal genes after acquiring the mitochondrion and the loss of methanogenesis.

Thus, the origin of eukaryotes by endosymbiotic processes has been broadly recognized and accepted so far. Mitochondria and plastids have been known to originate from a bacterial ancestor during parallel adaptation to anaerobiosis. However, there still remains a greater need in assessing the question of how much eukaryotic complexity is being originated via an implementation of these symbiogenetic theories.

Forterre 2015[28]

Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. (??)

The editors of research topic on “archaeal cell envelopes and surface structures” gave me the challenging task of drawing an updated version of the universal tree of life.

These observations suggest that thermal adaptation from LUCA to the ancestors of Archaea and Bacteria took place from cold to hot and not the other way around.

The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya.

a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. 


    Kasie Raymann, Céline Brochier-Armanet, and Simonetta Gribaldo

The two-domain tree of life is linked to a new root for the Archaea PNAS 2015 112 (21) 6670-6675; published ahead of print May 11, 2015, doi:10.1073/pnas.1420858112

Methanogene der Klasse I und III

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  • Stoffwechsel methanogener Archaea der Klasse I (links) und der Klasse III (rechts)
  • Obligat Wasserstoff oxidierender Methanbildner. 1 Methanofuran, 1a N-Carboxymethanofuran, [29], 1b Formyl-Methanofuran. 2 Tetrahydromethanopterin (H4MPT), 2a Formyl-H4MPT, 2b Methenyl-H4MPT, 2c Methylen-H4MPT, 2d Methyl-H4MPT. 3 Coenzym M (H-S-CoM), 3a Methyl-S-CoM. 4' Bifurkierende Heterodisulfid-Reduktase, 4a Heterodisulfid, 4b Coenzym B. RCoA Reduktiver Acetyl-CoA-Weg
    Obligat Wasserstoff oxidierender Methanbildner.
    1 Methanofuran, 1a N-Carboxymethanofuran, [29], 1b Formyl-Methanofuran. 2 Tetrahydromethanopterin (H4MPT), 2a Formyl-H4MPT, 2b Methenyl-H4MPT, 2c Methylen-H4MPT, 2d Methyl-H4MPT. 3 Coenzym M (H-S-CoM), 3a Methyl-S-CoM. 4' Bifurkierende Heterodisulfid-Reduktase, 4a Heterodisulfid, 4b Coenzym B. RCoA Reduktiver Acetyl-CoA-Weg
  • Methanosarcina mazei bei Wachstum auf Wasserstoff (grüne Pfeile) und Acetat (blaue Pfeile).
    Methanosarcina mazei bei Wachstum auf Wasserstoff (grüne Pfeile) und Acetat (blaue Pfeile).

Taxonomie

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2016 [30]

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Sand

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e--
Donor 		e--
Acceptor 		End-
produkt 		Typ Beispiel
CO O2 CO2 CO verwertende Bakterien Carboxydothermus hydrogenoformans
Fe2+ O2 Fe3+ Eisenoxidierende Mikroorganismen [31] Sulfolobus acidocaldarius, Acidithiobacillus ferrooxidans
H2 O2 H2O Knallgasbakterien[32][33] Cupriavidus metallidurans, Aquifex aeolicus
H2 CO2 CH4 Methanbildner Archaea
H2 SO42− H2S H2 nutzende Desulfurikanten[32] Desulfobacteraceae
HPO32− SO42− HPO42− + H2S δ-Proteobacteria Desulfotignum phosphitoxidans[34]
NH3 O2 NO2- Ammoniakoxidierer[35] Nitrosomonas
NH3 NO2- N2 Anammox-Bakterien[36] Planctomycetes
NO2- O2 NO3- Nitritoxidierer[37] Nitrobacter
S0 O2 SO42− Schwefeloxidierende Bakterien Chemotrophe Rhodobacteraceae
Thiotrichales und Acidithiobacillus thiooxidans
S0 NO3- SO42− Schwefeloxidierende Bakterien[38] Thiobacillus denitrificans
S2− O2 S0 chemotrophe Schwefelpurpurbakterien Halothiobacillaceae
  1. ↑ Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R., Embley, T. M.: The archaebacterial origin of eukaryotes. In: Proc Natl Acad Sci USA. 105. Jahrgang, Nr. 51, 2008, S. 20356–61, doi:10.1073/pnas.0810647105, PMID 19073919, PMC 2629343 (freier Volltext), bibcode:2008PNAS..10520356C.
  2. ↑ Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P: Toward automatic reconstruction of a highly resolved tree of life. In: Science. 311. Jahrgang, Nr. 5765, 2006, S. 1283–7, doi:10.1126/science.1123061, PMID 16513982, bibcode:2006Sci...311.1283C.
  3. ↑ Andrew H. Knoll, Javaux, E.J, Hewitt, D., Cohen, P.: Eukaryotic organisms in Proterozoic oceans. In: Philosophical Transactions of the Royal Society B. 361. Jahrgang, Nr. 1470, 2006, S. 1023–38, doi:10.1098/rstb.2006.1843, PMID 16754612, PMC 1578724 (freier Volltext).
  4. ↑ A. E. Albani, S. Bengtson, D. E. Canfield, A. Bekker, R. MacChiarelli, A. Mazurier, E. U. Hammarlund, P. Boulvais, J. J. Dupuy, C. Fontaine, F. T. Fürsich, F. O. Gauthier-Lafaye, P. Janvier, E. Javaux, F. O. Ossa, A. C. Pierson-Wickmann, A. Riboulleau, P. Sardini, D. Vachard, M. Whitehouse, A. Meunier: Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago. In: Nature. 466. Jahrgang, Nr. 7302, 2010, S. 100–104, doi:10.1038/nature09166, PMID 20596019, bibcode:2010Natur.466..100A.
  5. ↑ S Bengtson, V Belivanova, B Rasmussen, M Whitehouse: The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older. In: Proceedings of the National Academy of Sciences of the United States of America. 106. Jahrgang, Nr. 19, 2009, S. 7729–34, doi:10.1073/pnas.0812460106, PMID 19416859, PMC 2683128 (freier Volltext), bibcode:2009PNAS..106.7729B.
  6. ↑ Brocks JJ, Logan GA, Buick R, Summons RE: Archean molecular fossils and the early rise of eukaryotes. In: Science. 285. Jahrgang, Nr. 5430, August 1999, S. 1033–6, doi:10.1126/science.285.5430.1033, PMID 10446042 (sciencemag.org).
  7. ↑ Ward P: Mass extinctions: the microbes strike back. In: New Scientist. 9. Februar 2008, S. 40–3 (newscientist.com).
  8. ↑ Martin W: Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. In: Curr. Opin. Microbiol. 8. Jahrgang, Nr. 6, Dezember 2005, S. 630–7, doi:10.1016/j.mib.2005.10.004, PMID 16242992.
  9. ↑ Takemura M: Poxviruses and the origin of the eukaryotic nucleus. In: J. Mol. Evol. 52. Jahrgang, Nr. 5, Mai 2001, S. 419–25, doi:10.1007/s002390010171, PMID 11443345.
  10. ↑ Bell PJ: Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? In: J. Mol. Evol. 53. Jahrgang, Nr. 3, September 2001, S. 251–6, doi:10.1007/s002390010215, PMID 11523012.
  11. ↑ Wächtershäuser G: From pre-cells to Eukarya—a tale of two lipids. In: Mol. Microbiol. 47. Jahrgang, Nr. 1, Januar 2003, S. 13–22, doi:10.1046/j.1365-2958.2003.03267.x, PMID 12492850.
  12. ↑ Wächtershäuser G: From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. In: Philosophical Transactions of the Royal Society B. 361. Jahrgang, Nr. 1474, Oktober 2006, S. 1787–1808, doi:10.1098/rstb.2006.1904, PMID 17008219, PMC 1664677 (freier Volltext).
  13. ↑ Hartman H. & Fedorov A.: The origin of the eukaryotic cell: A genomic investigation. In: PNAS. 99. Jahrgang, Nr. 3, 2002, S. 1420–1425, doi:10.1073/pnas.032658599, PMID 11805300, PMC 122206 (freier Volltext), bibcode:2002PNAS...99.1420H.
  14. ↑ Jékely G: Origin of eukaryotic endomembranes: a critical evaluation of different model scenarios. In: Adv. Exp. Med. Biol. (= Advances in Experimental Medicine and Biology). 607. Jahrgang, 2007, S. 38–51, doi:10.1007/978-0-387-74021-8_3, PMID 17977457.
  15. ↑ Cavalier-Smith T: The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. In: Int. J. Syst. Evol. Microbiol. 52. Jahrgang, Pt 2, 1. März 2002, S. 297–354, doi:10.1099/00207713-52-2-297, PMID 11931142 (sgmjournals.org).
  16. ↑ Martin W, Müller M: The hydrogen hypothesis for the first eukaryote. In: Nature. 392. Jahrgang, Nr. 6671, März 1998, S. 37–41, doi:10.1038/32096, PMID 9510246, bibcode:1998Natur.392...37M.
  17. ↑ Pisani D, Cotton JA, McInerney JO: Supertrees disentangle the chimerical origin of eukaryotic genomes. In: Mol Biol Evol. 24. Jahrgang, Nr. 8, 2007, S. 1752–60, doi:10.1093/molbev/msm095, PMID 17504772.
  18. ↑ A. Latorre, Durban, A., Moya, A., Pereto, J.: The role of symbiosis in eukaryotic evolution. Origins and evolution of life – An astrobiological perspective. 2011, Kap. 21, S. 326–339.
  19. ↑ J Ayala S: Transport and internal organization of membranes: vesicles, membrane networks and GTP-binding proteins. In: Journal of Cell Science. 107. Jahrgang, Nr. 107, 1. April 1994, S. 753–763, PMID 8056835 (biologists.org [abgerufen am 27. März 2013]).
  20. ↑ William F Martin: The Origin of Mitochondria. In: Scitable. Nature education, abgerufen am 27. März 2013.
  21. ↑ L. Margulis: Origin of Eukaryotic Cells. Yale University Press, New Haven, London 1970.
  22. ↑ L. Margulis: Symbiosis in Cell Evolution. W. H. Freeman, New York 1993.
  23. ↑ L. Margulis, Dolan, M.F., Guerrero, R.: The chimeric eukaryote:origin of the nucleus from the Karyomastigont in Amitochondriate protists. In: Proceedings of the National Academy of Sciences of the United States of America. 97. Jahrgang, Nr. 13, 2000, S. 6954–6959, doi:10.1073/pnas.97.13.6954, PMID 10860956, PMC 34369 (freier Volltext), bibcode:2000PNAS...97.6954M.
  24. ↑ W. Martin, M. Müller: The hydrogen hypothesis for the first eukaryote. In: Nature. 392. Jahrgang, Nr. 6671, 1998, S. 37–41, doi:10.1038/32096, PMID 9510246, bibcode:1998Natur.392...37M.
  25. ↑ D. Moreira, Lopez-Garcia, P.: Symbiosis between methanogenic Archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. In: Journal of Molecular Evolution. 47. Jahrgang, Nr. 5, 1998, S. 517–530, doi:10.1007/PL00006408, PMID 9797402.
  26. ↑ P. Lopez-Garcia, Moreira, D.: Selective forces for the origin of the eukaryotic nucleus. In: BioEssays. 28. Jahrgang, Nr. 5, 2006, S. 525–533, doi:10.1002/bies.20413, PMID 16615090.
  27. ↑ A. Latorre, Durban, A., Moya, A., Pereto, J.: The role of symbiosis in eukaryotic evolution. Origins and evolution of life – An astrobiological perspective. 2011, S. 326–339.
  28. ↑ Patrick Forterre: The universal tree of life: an update. In: Frontiers in Microbiology. Nr. 6, 2015, doi:10.3389/fmicb.2015.00717 (frontiersin.org).
  29. ↑ Bartoschek, S., Vorholt, J. A., Thauer, R. K., Geierstanger, B. H. and Griesinger, C. (2000), N-Carboxymethanofuran (carbamate) formation from methanofuran and CO2 in methanogenic archaea. European Journal of Biochemistry, 267: 3130–3138. doi:10.1046/j.1432-1327.2000.01331.x
  30. ↑ Mark Alexander Lever: A New Era of Methanogenesis Research. In: Trends in Microbiology. 2016, doi:10.1016/j.tim.2015.12.005 (sciencedirect.com).
  31. ↑ Meruane G, Vargas T: Bacterial oxidation of ferrous iron by Acidithiobacillus ferrooxidans in the pH range 2.5–7.0. In: Hydrometallurgy. 71. Jahrgang, Nr. 1, 2003, S. 149-58, doi:10.1016/S0304-386X(03)00151-8 (uchile.cl [PDF]).
  32. ↑ a b Libert M, Esnault L, Jullien M, Bildstein O: Molecular hydrogen: an energy source for bacterial activity in nuclear waste disposal. In: Physics and Chemistry of the Earth. 2010 (nantes2010.com [PDF]).
  33. ↑ M. Guiral, C. Aubert, M.-T. Giudici-Orticoni: Hydrogen metabolism in the hyperthermophilic bacterium Aquifex aeolicus. In: Biochemical Society Transactions. 33. Jahrgang, Nr. 1, 2005, S. 22–24 (biochemsoctrans.org).
  34. ↑ Schink, Bernhard, et al. Desulfotignum phosphitoxidans sp. nov., a new marine sulfate reducer that oxidizes phosphite to phosphate. Archives of microbiology 177.5 (2002): 381-391.
  35. ↑ Zwolinski, Michele D. "Lithotroph." Weber State University. p. 7.
  36. ↑ Kartal B, Kuypers MM, Lavik G, Schalk J, Op den Camp HJ, Jetten MS, Strous M: Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium. In: Environmental Microbiology. 9. Jahrgang, Nr. 3, 2007, S. 635-42, doi:10.1111/j.1462-2920.2006.01183.x, PMID 17298364.
  37. ↑ "Nitrifying bacteria." PowerShow. p. 12.
  38. ↑ Zwolinski, Michele D. "Lithotroph." Weber State University. p. 3.
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