1. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Chapter 18 The Archaea

2. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2 Archaea many features in common with Eukarya –genes encoding protein: replication, transcription, translation features in common with Bacteria –genes for metabolism other elements are unique to Archaea –unique rRNA gene structure –capable of methanogenesis

3. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3 Archaea highly diverse with respect to morphology, physiology, reproduction, and ecology best known for growth in anaerobic, hypersaline, pH extremes, and high- temperature habitats also found in marine arctic temperature and tropical waters

4. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 4 Archaeal Taxonomy five major physiological and morphological groups

5. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 5 Table 18.1

6. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 6 Archaeal Taxonomy two phyla based on Bergey’s Manual –Euryarchaeota –Crenarchaeota 16S rRNA and SSU rRNA analysis also shows –Group I are Thaumarchaeota –Group II are Korachaeota

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9. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9 Archaeal Cell Surfaces cell envelopes –varied S layers attached to plasma membrane –pseudomurein (peptidoglycan-like polymer) –complex polysaccharides, proteins, or glycoproteins found in some other species –only Ignicoccus has outer membrane flagella closely resemble bacterial type IV pili

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11. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 11 Archaeal Membrane Lipids differ from Bacteria and Eukarya in having branched chain hydrocarbons attached to glycerol by ether linkages polar phospholipids, sulfolipids, glycolipids, and unique lipids are also found in archaeal membranes

12. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 12 Archaeal Lipids and Membranes Bacteria/Eukaryotes fatty acids attached to glycerol by ester linkages Archaea branched chain hydrocarbons attached to glycerol by ether linkages some have diglycerol tetraethers

13. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 13 Figure 18.4

14. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 14 Archaeal Genetics and Molecular Biology like Bacteria –have circular chromosome –may have plasmids like Eukarya –have histone-like proteins –self-splicing introns in few

15. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 15 Archaeal DNA Replication and Cell Division like Eukarya –replication origin flanking genes –DNA polymerases –replication eukaryotic like proteins helicase MCM, SSBs, PCNA sliding clamp –endosomal sorting proteins in cell division like Bacteria – bidirectional

16. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 16 Archaeal Transcription transcription machinery is like Eukarya –RNA polymerases II and III –transcription factors, TBP and TFB –promoters regulation of transcription is like Bacteria –may have polycistronic mRNA –transcription regulators some transcription regulators are unique to Archaea

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18. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 18 Archaeal Transcription like Bacteria –70S ribosomes –leaders similar to Shine-Dalgarno like Eukarya –antibiotics do not bind ribosomes –sensitive to eukaryotic inhibitor –mRNA transcripts have no leader methionine initiator tRNA archaeal unique –tRNA and 2 unusual amino acids

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20. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 20 Archaeal Protein Secretion many similarities in all 3 domains like Bacteria –signal recognition particle binds pre- protein –secrete folded proteins through TAT like Eukarya –Sec-dependent pathway proteins

21. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 21 Archaeal Metabolism great variation among the different archaeal groups organotrophy, autotrophy, and phototrophy have been observed differ from other groups in glucose catabolism, pathways for CO 2 fixation, and the ability of some to synthesize methane

22. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 22 Carbohydrate Metabolism similarities in eukaryotes and bacteria 3 pathways unique to Archaea –modified Embden-Meyerhof –2 modified Entner-Duodoroff

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25. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 25 Thermostability of Proteins proteins remain folded at extremely high temperatures –hydrophobic core –increasing ionic interactions, atomic packing density –additional hydrogen bonds –shorter loop structures –chaperones refold denatured proteins

26. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 26 Thermostability of DNA DNA does not denature –reverse DNA gyrase induces positive supercoils enhancing DNA thermostability –increase cytoplasmic solute concentration preventing purines and pyrimidines –Archaeal histones contribute to stability

27. Red colors will be in your exam Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 27

28. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 28 Phylum Crenarchaeota most are extremely thermophilic –hyperthermophiles (hydrothermal vents) most are strict anaerobes some are acidophiles many are sulfur-dependent –for some, used as electron acceptor in anaerobic respiration –for some, used as electron source

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31. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 31 Crenarchaeota… include organotrophs and lithotrophs (sulfur-oxidizing and hydrogen-oxidizing) contains 25 genera –two best studied are Sulfolobus and Thermoproteus

32. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 32 Genus Thermoproteus long thin rod, bent or branched –cell walls composed of glycoprotein thermoacidophiles –70–97 °C –pH 2.5–6.5 anaerobic metabolism –lithotrophic on sulfur and hydrogen –organotrophic on sugars, amino acids, alcohols, and organic acids using elemental sulfur as electron acceptor autotrophic using CO or CO 2 as carbon source

33. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 33 Genus Sulfolobus irregularly lobed, spherical shaped –cell walls contain lipoproteins and carbohydrates thermoacidophiles –70–80°C –pH 2–3 metabolism –lithotrophic on sulfur using oxygen (usually) or ferric iron as electron acceptor –organotrophic on sugars and amino acids

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35. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 35 Phylum Crenarchaeota - 2 group I archaea –archaeal unique membrane lipid, crenarchaeol is widespread in nature marine waters rice paddies, soil, freshwater recent growth of mesophilic archaea –capable of nitrification (ammonia to nitrate)

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37. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 37 Phylum Euryarchaeota consists of many classes, orders, and families often divided informally into five major groups –methanogens –halobacteria –thermoplasms –extremely thermophilic S 0 -metabolizers –sulfate-reducers

38. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 38 Methanogens all methanogenic microbes are Archaea –called methanogens: produce methane methanogenesis –last step in the degradation of organic compounds –occurs in anaerobic environments e.g., animal rumens e.g., anaerobic sludge digesters e.g., within anaerobic protozoa

39. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 39 Methanogens 26 genera, largest group of cultured archaea –differ in morphology –16S rRNA –cell walls –membrane lipids

40. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 40 Figure 18.13

41. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 41 Table 18.2

42. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 42 Methanogens unique anaerobic production of methane –hydrogen, CO 2 oxidation –coenzymes, cofactors –ATP production linked with methanogenesis

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45. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 45 Ecological and Practical Importance of Methanogens important in wastewater treatment can produce significant amounts of methane –can be used as clean burning fuel and energy source –is greenhouse gas and may contribute to global warming can oxidize iron –contributes significantly to corrosion of iron pipes

46. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 46 Halobacteria order Halobacteriales; 17 genera in one family, Halobacteriaceae extreme halophiles (halobacteria) –require at least 1.5 M NaCl cell wall disintegrates if [NaCl] < 1.5 M –growth optima near 3–4 M NaCl aerobic, respiratory, chemoheterotrophs with complex nutritional requirements

47. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 47 Strategies to Cope with Osmotic Stress increase cytoplasmic osmolarity –use compatible solutes (small organics) “salt-in” approach –use antiporters and symporters to increase concentration of KCl and NaCl to level of external environment acidic amino acids in proteins

48. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 48 Figure 18.16

49. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 49 e.g., Halobacterium salinarium (H. halobium) has unique type of photosynthesis –not chlorophyll based –uses modified cell membrane (purple membrane) contains bacteriorhodopsin –absorption of light by bacteriorhodopsin drives proton transport, creating PMF for ATP synthesis

50. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 50 Features of Halobacterium Rhodopsins bacteriorhodopsin –chromophore similar to retinal –seven membrane spanning domains –purple aggregates in membrane halorhodopsin –light energy to transport chloride ions 2 sensory rhodopsins –flagellar attached photoreceptors

51. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 51 Proteorhodopsin now known to be widely distributed among bacteria and archaea –found in marine bacterioplankton using DNA sequence analysis of uncultivated organisms –also found in cyanobacteria

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54. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 54 Thermoplasms class Thermoplasmata three different genera –Thermoplasmataceae –Picrophilaceae –Ferroplasmataceae thermoacidophiles lack cell walls

55. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 55 Genus Thermoplasma thermoacidophiles; grow in refuse piles of coal mines at 55–59°C, pH 1–2, FeS cell structure –shape depends on temperature –may be flagellated and motile –cell membrane strengthened by diglycerol tetraethers, lipopolysaccharides, and glycoproteins –nucleosome-like structures formed by association of DNA with histonelike proteins

56. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 56 Genus Picrophilus irregularly shaped cocci, 1 to 5  M diameter –large cytoplasmic cavities that are not membrane bound –no cell wall –has S-layer outside plasma membrane thermoacidophiles –47–65°C (optimum 60°C) –pH <3.5 (optimum 0.7) aerobic

57. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 57 Extremely Thermophilic S 0 -Reducers class Thermococci; one order, Thermococcales one family containing three genera, Thermococcus, Paleococcus, Pyrococcus motile by flagella optimum growth temperatures 88–100°C strictly anaerobic reduce sulfur to sulfide

58. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 58 Sulfate-Reducing Archaea class Archaeoglobi; order Archaeoglobales; one family with one genus, Archaeoglobus irregular coccoid cells –cell walls consist of glycoprotein subunits extremely thermophilic –optimum 83°C –isolated from marine hydrothermal vents

59. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 59 Sulfate-Reducing Archaea - 2 metabolism –can be lithotrophic (H 2 ) or organotrophic (lactate or glucose) –use sulfate, sulfite, or thiosulfite as electron acceptor –possess some methanogen coenzymes

60. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 60 Aciduliprofundum newly characterized thermophilic euryarchaeote –acidophile, requires pH 3.3 to 5.8 –thermophile, 60–75 o C for growth –inhabit hydrothermal vents –sulfur- and iron-reducing heterotroph first thermoacidophile in sulfide rich areas may be important in iron and sulfur cycling