Genetics of Archaea

Kevin R. Sowers; Paul H. Blum; Shiladitya Dassarma

doi:10.1128/9781555817497.ch33

Chapter 33 : Genetics of Archaea

Authors: Kevin R. Sowers, Paul H. Blum, Shiladitya Dassarma

Content Type: Reference

Publication Year: 2007

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817497

Chapter DOI: 10.1128/9781555817497.ch33

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Abstract:

In recent years several laboratories have developed effective plating techniques, identifying genetic markers that do not target cell wall synthesis, fusing archaeal promoters with recombinant genes, and isolating native vectors and promiscuous nonnative vectors. This chapter focuses on tractable systems that are currently available for the Archaea. Due to fundamental differences between gene transfer systems for each archaeal branch, the chapter is divided into three inclusive sections covering the halophilic and methanogenic Euryarchaeota and the hyperthermophilic Crenarchaeota. Despite varying degrees of difficulty growing Archaea, all three systems are routinely used by laboratories conducting research on archaeal genetics and can be mastered by anyone with a fundamental knowledge of microbial genetic techniques. Under low oxygen tension, Halobacterium sp. NRC-1 induces purple membrane patches in the cell membrane and buoyant gas vesicles intracellularly, which increases the availability of light and oxygen and allows a period of light-driven proton pumping and phototrophic growth. Targeted manipulation of the chromosome by directed recombination was recently added to the growing list of approaches for the genetic analysis of Sulfolobus solfataricus. Plasmids that do not replicate in S. solfataricus can be used to introduce DNA into the genome.

Citation: Sowers K, Blum P, Dassarma S. 2007. Genetics of Archaea, p 800-824. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch33

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Genetics of Archaea

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FIGURE 1

Haloarchaeal shuttle vector pNG168. This plasmid contains the E. coli pTZ19r replicon and the Halobacterium NRC-1 pNRC100 minimal replication region. The bla gene provides selection with ampicillin in E. coli, and the hmg gene provides selection with mevinolin in haloarchaea. The multiple cloning site is located in the lacZα fragment gene and permits blue-white screening in E. coli. The plasmid is available from ATCC (catalog no. MBA-77) and the sequence is available in GenBank (accession no. AY291460).

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FIGURE 1

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FIGURE 2

Gene knockout and replacement in the halophilic Euryarchaeota. The example shown is for selection and counterselection with ura3. A cloned haloarchaeal target gene (geneX) in a plasmid vector, which does not replicate in haloarchaea, is used for PCR amplification (primers designated by arrowheads) and recircularization to provide for a precisely deleted gene. The plasmid is introduced into a ∆ura3 haloarchaeon by transformation. Integrants are selected by uracil prototrophy using uracil dropout plates. Excisants are selected for by plating on plates containing 5- FOA. Depending on the site of the recombination (1 or 2), different outcomes are possible. Alternatively, mevinolin selection can also be used for integration and the pyrE2 gene can be used for selection and counterselection.

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FIGURE 2

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FIGURE 3

Recombinant plasmid showing construction typical for an E. coli-Methanosarcina shuttle vector. The construct includes the pir-dependent R6K ori for replication of the plasmid in pir + E. coli and the bla gene for selection of E. coli transformants with ampicillin; pC2A ori and repA for replication in Methanosarcina spp.; and pac under transcriptional control of the archaeal methyl-coenzyme M reductase mcrB gene for selection of methansarcinal recombinants on puromycin. Filled and open elements represent genes from the Bacteria and Archaea, respectively.

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FIGURE 3

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FIGURE 4

Random gene mutagenesis in Methanosarcina with an E. coli-Methanosarcina shuttle vector containing a transposable element. pJK60 is a modified E. coli-Methanosarcina shuttle vector that contains the puromycin resistance pac gene, the R6K E. coli plasmid origin of replication, and the kanamycin resistance aph gene flanked by the transposable elements of the insect marinerfamily Himar1 transposon. The transposase is expressed in the methanogen from the methyl-coenzyme M reductase gene (mcrB) from Methanosarcina barkeri. The vector is transformed into Methanosarcina spp. and transposed into random sites in the genome, and then puromycin-resistant colonies with the desired phenotype are selected. The transposed DNA is purified and digested with EcoRI, and the fragments are closed by treatment with T4 ligase. The circular DNA is transformed into E. coli, the DNA is repurified from kanamycin-resistant clones, and then DNA flanking the transposable element is sequenced to identify the disrupted gene.

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FIGURE 4

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FIGURE 5

Reporter vector pWLG30+lacZ for detecting archaeal promoter strength based on β-galactosidase activity. This Escherichia-Methanococcus shuttle vector includes a bacterial ori for replication of the plasmid in E. coli and the bla gene for selection of E. coli transformants with ampicillin; methanococcal pURB500 for replication in Methanococcus maripaludis; and pac under transcriptional control of the archaeal methyl-coenzyme M reductase mcrB gene for selection of methanococcal recombinants on puromycin. The methanococcal hmvA hydrogenase promoter is fused upstream of lacZ for measuring expression of hydrogenase by β-galactosidase activity. Filled and open elements represent genes from the Bacteria and Archaea, respectively.

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FIGURE 5

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FIGURE 6

Specialized apparatus for plating methanogenic Euryarchaeota. (A) Anaerobic glove box used for plating methanogenic Archaea. The gas phase is composed of a mixture of N2, CO2, and H2 in a volume ratio of 75:20:5. The CO2 maintains the equilibrium of the carbonate buffer at a neutral pH, the H2 combined with palladium catalyst pellets located in the glove box reduces any oxygen that may diffuse into the chamber, and the N2 is inert. Lower figures show anaerobic jars for incubation of colony clones on solidified medium. Examples include a modified glass canning jar (B), a commercial jar manufactured by TORBAL (C), and a modified paint pressure tank (D). Photo in panel D is courtesy of W. B. Whitman.

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FIGURE 6

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FIGURE 7

Transformation enrichment culture time courses. S. solfataricus PBL2025 (circles) and PBL2030 (triangles and squares) were transformed with plasmids pLacS (filled circles) or pMalA (filled triangles and squares) to growth on lactose (circles), glycogen (triangles), or starch (squares). Untransformed control cultures were PBL2025 (open circles) and PBL2030 (open triangles and open squares).

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FIGURE 7

References

/content/book/10.1128/9781555817497.chap33

1. Allen, M. B. 1959. Studies with Cyanidium caldarium, an anomalously pigmented chlorophyte. Arch. Mikrobiol. 32: 270– 277.

2. Allers, T.,, and M. Mevarech. 2005. Archaeal genetics— the third way. Nat. Rev. Genet. 6: 58– 73.

3. Apolinario, E. E.,, K. M. Jackson,, and K. R. Sowers. 2005. Development of a plasmid-mediated reporter system for in vivo monitoring of gene expression in the archaeon Methanosarcina acetivorans. Appl. Environ Microbiol. 71: 4914– 4918.

4. Apolinario, E. E.,, and K. R. Sowers. 1996. Plate colonization of Methanococcus maripaludis and Methanosarcina thermophila in a modified canning jar. FEMS Microbiol. Lett. 145: 131– 137.

5. Aravalli, R. N.,, and R. A. Garrett. 1997. Shuttle vectors for hyperthermophilic archaea. Extremophiles 1: 183– 191.

6. Argyle, J. L.,, D. L. Tumbula,, and J. A. Leigh. 1996. Neomycin resistance as a selectable marker in Methanococcus maripaludis. Appl. Environ. Microbiol. 62: 4233– 4237.

7. Balch, W. E.,, G. E. Fox,, L. J. Magrum,, C. R. Woese,, and R. S. Wolfe. 1979. Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 43: 260– 296.

8. Balch, W. E.,, and R. S. Wolfe. 1976. New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl. Environ. Microbiol. 32: 781– 791.

9. Baliga, N. S.,, S. J. Bjork,, R. Bonneau,, M. Pan,, C. Iloanusi,, M. C. Kottemann,, L. Hood,, and J. DiRuggiero. 2004. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14: 1025– 1035.

10. Baliga, N. S.,, B. R. Bonneau,, M. T. Facciotti,, M. Pan,, G. Glusman,, E. W. Deutsch,, P. Shannon,, Y. Chiu,, R. S. Weng,, R. R. Gan,, P. Hung,, S. V. Date,, E. Marcotte,, L. Hood,, and W. V. Ng. 2004. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14: 2221– 2234.

11. Baliga, N.,, and S. DasSarma. 1999. Saturation mutagenesis of the TATA-box and upstream activator sequence in the haloarchaeal bop gene promoter. J. Bacteriol. 181: 2513– 2518.

12. Baliga, N. S.,, and S. DasSarma. 2000. Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity. Mol. Microbiol. 36: 1175– 1183.

13. Baliga, N. S.,, S. P. Kennedy,, W. V. Ng,, L. Hood,, and S. DasSarma. 2001. Genomic and genetic dissection of an archaeal regulon. Proc. Natl. Acad. Sci. USA 98: 2521– 2525.

14. Bartus, C. L.,, V. P. Jaakola,, R. Reusch,, H. H. Valentine,, P. Heikinheimo,, A. Levay,, L. T. Potter,, H. Heimo,, A. Goldman,, and G. J. Turner. 2003. Downstream coding region determinants of bacterio-opsin, muscarinic acetylcholine receptor and adrenergic receptor expression in Halobacterium salinarum. Biochim. Biophys. Acta 1610: 109– 123.

15. Beneke, S.,, H. Bestgen,, and A. Klein. 1995. Use of the Escherichia coli uidA gene as a reporter in Methanococcus voltae for the analysis of the regulatory function of the intergenic region between the operons encoding seleniumfree hydrogenases. Mol. Gen. Genet. 248: 225– 228.

16. Bitan-Banin, R. O. G, and M. Mevarech. 2003. Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene. J. Bacteriol. 185: 772– 778.

17. Blank, C. E.,, P. S. Kessler,, and J. A. Leigh. 1995. Genetics in methanogens: transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene. J. Bacteriol. 177: 5773– 5777.

18. Blaseio, U.,, and F. Pfeifer. 1990. Transformation of Halobacterium halobium: development of vectors and investigation of gas vesicle synthesis. Proc. Natl. Acad. Sci. USA 87: 6772– 6776.

19. Boccazzi, P.,, K. J. Zhang,, and W. W. Metcalf. 2000. Generation of dominant selectable markers for resistance to pseudomonic acid by cloning and mutagenesis of the ileS gene from the archaeon Methanosarcina barkeri Fusaro. J. Bacteriol. 182: 2611– 2618.

20. Bock, A.,, and O. Kandler,. 1985. Antibiotic sensitivity of archaebacteria. In C. R. Woese, and R. S. Wolfe (ed.), The Bacteria. A Treatise on Structure and Function, vol. VIII. Academic Press, Inc., New York.

21. Bowen, T. L.,, and W. B. Whitman. 1987. Incorporation of exogenous purines and pyrimidines by Methanococcus voltae and isolation of analog-resistant mutants. Appl. Environ. Microbiol. 53: 1822– 1826.

22. Brock, T. D.,, K. M. Brock,, R. T. Belly,, and R. L. Weiss. 1972. Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch. Mikrobiol. 84: 54– 68.

23. Cannio, R.,, P. Contursi,, M. Rossi,, and S. Bartolucci. 1998. An autonomously replicating transforming vector for Sulfolobus solfataricus. J. Bacteriol. 180: 3237– 3240.

24. Charlebois, R. L.,, L. C. Schalkwyk,, J. D. Hofman,, and W. F. Doolittle. 1991. Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2. J. Mol. Biol. 222: 509– 524.

25. Cohen-Kupiec, R.,, C. Blank,, and J. A. Leigh. 1997. Transcriptional regulation in Archaea: In vivo demonstration of a repressor binding site in a methanogen. Proc. Natl. Acad. Sci. USA 94: 1316– 1320.

26. Danner, S.,, and J. Soppa. 1996. Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection. Mol. Microbiol. 19: 1265– 1276.

27. DasSarma, S. 1989. Mechanisms of genetic variability in Halobacterium halobium: the purple membrane and gas vesicle mutations. Can. J. Microbiol. 35: 65– 72.

28. DasSarma, S., 2003. Genome sequence of an extremely halophilic archaeon. In T. R. C. M. Fraser, and K. E. Nelson (ed.), Microbial Genomes. Humana Press, Inc, Totowa, NJ.

29. DasSarma, S.,, and P. Arora. 2002. Halophiles, p. 458– 466. In Encyclopedia of Life Sciences. Macmillan Press, London, England.

30. DasSarma, S.,, P. Arora,, F. Lin,, E. Molinari,, and L. R. Yin. 1994. Wild-type gas vesicle formation requires at least ten genes in the gvp gene cluster of Halobacterium halobium plasmid pNRC100. J. Bacteriol. 176: 7646– 7652.

31. DasSarma, S.,, and E. M. Fleischmann (ed.). 1995. Halophiles, vol. 1. Archaea: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, NY.

32. Deppenmeier, U.,, A. Johann,, T. Hartsch,, R. Merkl,, R. A. Schmitz,, R. Martinez-Arias,, A. Henne,, A. Wiezer,, S. Bäumer,, C. Jacobi,, H. Brüggemann,, T. Lienard,, A. Christmann,, M. Bömeke,, S. Steckel,, A. Bhattacharyya,, A. Lykidis,, R. Overbeek,, H.-P. Klenk,, R. P. Gunsalus,, H. J. Fritz,, and G. Gottschalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between Bacteria and Archaea. J. Mol. Microbiol. Biotechnol. 4: 453– 461.

33. Dyall-Smith, M. L.,, and W. F. Doolittle. 1994. Construction of composite transposons for halophilic Archaea. Can. J. Microbiol. 40: 922– 929.

34. Ehlers, C.,, K. Weidenbach,, K. Veit,, U. Deppenmeier,, W. W. Metcalf,, and R. A. Schmitz. 2005. Development of genetic methods and construction of a chromosomal glnK1 mutant in Methanosarcina mazei strain Go1. Mol. Genet. Genomics 273: 290– 298.

35. Elferink, M. G.,, C. Schleper,, and W. Zillig. 1996. Transformation of the extremely thermoacidophilic archaeon Sulfolobus solfataricus via a self-spreading vector. FEMS Microbiol. Lett. 137: 31– 35.

36. Falb, M.,, F. Pfeiffer,, P. Palm,, K. Rodewald,, V. Hickmann,, J. Tittor,, and D. Oesterhelt. 2005. Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res. 15: 1336– 1343.

37. Firtel, M.,, G. B. Patel,, and T. J. Beveridge. 1995. S layer regeneration in Methanococcus voltae protoplasts. Microbiology 141: 817– 824.

38. Fuller, A.,, G. Banks,, G. Mellows,, K. Barrow,, M. Woolford,, and E. Chain. 1971. Pseudomonic acid: an antibiotic produced by Pseudomonas fluorescens. Nature 234: 416– 417.

39. Galagan, J. E.,, C. Nusbaum,, A. Roy,, M. G. Endrizzi,, P. Macdonald,, W. FitzHugh,, S. Calvo,, R. Engels,, S. Smirnov,, D. Atnoor,, A. Brown,, N. Allen,, J. Naylor,, N. Stange-Thomann,, K. DeArellano,, R. Johnson,, L. Linton,, P. McEwan,, K. McKernan,, J. Talamas,, A. Tirrell,, W. J. Ye,, A. Zimmer,, R. D. Barber,, I. Cann,, D. E. Graham,, D. A. Grahame,, A. M. Guss,, R. Hedderich,, C. Ingram- Smith,, H. C. Kuettner,, J. A. Krzycki,, J. A. Leigh,, W. X. Li,, J. F. Liu,, B. Mukhopadhyay,, J. N. Reeve,, K. Smith,, T. A. Springer,, L. A. Umayam,, O. White,, R. H. White,, E. C. de Macario,, J. G. Ferry,, K. F. Jarrell,, H. Jing,, A. J. L. Macario,, I. Paulsen,, M. Pritchett,, K. R. Sowers,, R. V. Swanson,, S. H. Zinder,, E. Lander,, W. W. Metcalf,, and B. Birren. 2002. The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12: 532– 542.

40. Gardner, W. L.,, and W. B. Whitman. 1999. Expression vectors for Methanococcus maripaludis: overexpression of acetohydroxyacid synthase and beta-galactosidase. Genetics 152: 1439– 1447.

41. Gernhardt, P.,, O. Possot,, M. Foglino,, L. Sibold,, and A. Klein. 1990. Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene. Mol. Gen. Genet. 22: 273– 279.

42. Grant, W. D.,, and H. Larsen,. 1984. Extremely halophilic archaeobacteria, p. 2216– 2233. In S. Staley (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.

43. Gregor, D.,, and F. Pfeifer. 2001. Use of a halobacterial bgaH reporter gene to analyse the regulation of gene expression in halophilic archaea. Microbiology 147: 1745– 1754.

44. Grogan, D. W.,, G. T. Carver,, and J. W. Drake. 2001. Genetic fidelity under harsh conditions: analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Proc. Natl. Acad. Sci. USA 98: 7928– 7933.

45. Grogan, D. W.,, and J. E. Hansen. 2003. Molecular characteristics of spontaneous deletions in the hyperthermophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 185: 1266– 1272.

46. Guy, C. P.,, S. Haldenby,, A. Brindley,, D. A. Walsh,, G. S. Briggs,, M. J. Warren,, T. Allers,, and E. L. Bolt. 2006. Interactions of RadB, a DNA repair protein in Archaea, with DNA and ATP. J. Mol. Biol. 358: 46– 56.

47. Harris, J. E.,, and P. A. Pinn. 1985. Bacitracin-resistant mutants of a mesophilic Methanobacterium species. Arch. Microbiol. 143: 151– 153.

48. Haseltine, C.,, R. Montalvo-Rodriguez,, A. Carl,, E. Bini,, and P. Blum. 1999. Extragenic pleiotropic mutations that repress glycosyl hydrolase expression in the hyperthermophilic archaeon Sulfolobus solfataricus. Genetics 152: 1353– 1361.

49. Haseltine, C.,, R. Montalvo-Rodriguez,, E. Bini,, A. Carl,, and P. Blum. 1999. Coordinate transcriptional control in the hyperthermophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 181: 3920– 3927.

50. Hendrickson, E. L.,, R. Kaul,, Y. Zhou,, D. Bovee,, P. Chapman,, J. Chung,, E. C. de Macario,, J. A. Dodsworth,, W. Gillett,, D. E. Graham,, M. Hackett,, A. K. Haydock,, A. Kang,, M. L. Land,, R. Levy,, T. J. Lie,, T. A. Major,, B. C. Moore,, I. Porat,, A. Palmeiri,, G. Rouse,, C. Saenphimmachak,, D. Soll,, S. Van Dien,, T. Wang,, W. B. Whitman,, Q. Xia,, Y. Zhang,, F. W. Larimer,, M. V. Olson,, and J. A. Leigh. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J. Bacteriol. 186: 6956– 6969.

51. Heymann, J. A.,, W. A. Havelka,, and D. Oesterhelt. 1993. Homologous overexpression of a light-driven anion pump in an archaebacterium. Mol. Microbiol. 7: 623– 630.

52. Hoang, V.,, E. Bini,, V. Dixit,, M. Drozda,, and P. Blum. 2004. The role of cis-acting sequences governing catabolite repression control of lacS expression in the archaeon Sulfolobus solfataricus. Genetics 167: 1563– 1572.

53. Holmes, M. L.,, and M. L. Dyall-Smith. 1990. A plasmid vector with a selectable marker for halophilic archaebacteria. J. Bacteriol. 172: 756– 761.

54. Holmes, M. L.,, and M. L. Dyall-Smith. 1991. Mutations in DNA gyrase result in novobiocin resistance in halophilic archaebacteria. J. Bacteriol. 173: 642– 648.

55. Jones, W. J.,, W. B. Whitman,, F. D. Fields,, and R. S. Wolfe. 1983. Growth and plating efficiency of methanococci on agar media. Appl. Environ. Microbiol. 46: 220– 226.

56. Jung, K. H.,, and J. L. Spudich. 1998. Suppressor mutation analysis of the sensory rhodopsin I-transducer complex: insights into the color-sensing mechanism. J. Bacteriol. 180: 2033– 2042.

57. Jussofie, A.,, F. Mayer,, and G. Gottschalk. 1986. Methane formation from methanol hydrogen by protoplasts of new methanogenic isolates and inhibition on by dicyclohexylcarbodiimide. Arch. Microbiol. 146: 245– 249.

58. Kandler, O.,, and H. Hippe. 1977. Lack of peptidoglycan in the cell walls of Methanosarcina barkeri. Arch. Microbiol. 113: 57– 60.

59. Kennedy, S. P.,, W. V. Ng,, S. L. Salzberg,, L. Hood,, and S. DasSarma. 2001. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res. 11: 1641– 1650.

60. Krebs, M. P.,, R. Mollaaghababa,, and H. G. Khorana. 1993. Gene replacement in Halobacterium halobium and expression of bacteriorhodopsin mutants. Proc. Natl. Acad. Sci. USA 90: 1987– 1991.

61. Krebs, M. P.,, E. N. Spudich,, H. G. Khorana,, and J. L. Spudich. 1993. Synthesis of a gene for sensory rhodopsin I and its functional expression in Halobacterium halobium. Proc. Natl. Acad. Sci. USA 90: 3486– 3490.

62. Lam, W. L.,, and W. F. Doolittle. 1992. Mevinolin-resistant mutations identify a promoter and the gene for a eukaryote-like 3-hydroxy-3-methylglutaryl-coenzyme A reductase in the archaebacterium Haloferax volcanii. J. Biol. Chem. 267: 5829– 5834.

63. Lam, W. L.,, and W. F. Doolittle. 1989. Shuttle vectors for the archaebacterium Halobacterium volcanii. Proc. Natl. Acad. Sci. USA 86: 5478– 5482.

64. Lange, M.,, and B. K. Ahring. 2001. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea. FEMS Microbiol. Rev. 25: 553– 571.

64.a. Maeder, D. L.,, I. Anderson,, T. Brettin,, D. Bruce,, P. Gilna,, C. S. Han,, A. Lapidus,, W. W. Metcalf,, E. Saunders,, R. Tapia,, and K. R. Sowers. 2006. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J. Bacteriol. 188: 7922– 7931.

65. Mankin, A. S.,, I. M. Zyrianova,, V. K. Kagramanova,, and R. A. Garrett. 1992. Introducing mutations into the single- copy chromosomal 23S rRNA gene of the archaeon Halobacterium halobium by using an rRNA operon-based transformation system. Proc. Natl. Acad. Sci. USA 89: 6535– 6539.

66. Martusewitsch, E.,, C. W. Sensen,, and C. Schleper. 2000. High spontaneous mutation rate in the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by transposable elements. J. Bacteriol. 182: 2574– 2581.

67. McCready, S.,, and L. Marcello. 2003. Repair of UV damage in Halobacterium salinarum. Biochem. Soc. Trans. 31: 694– 698.

68. McCready, S.,, J. A. Muller,, I. Boubriak,, B. R. Berquist,, W. L. Ng,, and S. Dassarma. 2005. UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1. Saline Syst. 1: 3.

69. Metcalf, W. W., 1999. Genetic analysis in the domain Archaea, p. 277– 326. In M. C. Smith, and R. E. Sockett (ed.), Genetic Methods for Diverse Prokaryotes, vol. 29. Academic Press, New York.

70. Metcalf, W. W.,, W. Jiang,, and B. L. Wanner. 1994. Use of rep technique for allele replacement to construct new Escherichia coli hosts for maintenance of R6K g origin plasmids at different copy numbers. Gene 138: 1– 7.

71. Metcalf, W. W.,, J. K. Zhang,, E. Apolinario,, K. R. Sowers,, and R. S. Wolfe. 1997. A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors. Proc. Natl. Acad. Sci. USA 94: 2626– 2631.

72. Metcalf, W. W.,, J. K. Zhang,, and R. S. Wolfe. 1998. An anaerobic, intrachamber incubator for growth of Methanosarcina spp. on methanol-containing solid media. Appl. Environ. Microbiol. 64: 768– 770.

73. Meuer, J.,, H. C. Kuettner,, J. K. Zhang,, R. Hedderich,, and W. W. Metcalf. 2002. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferridoxin in methanogenesis and carbon fixation. Proc. Natl. Acad. Sci. USA 99: 5632– 5637.

74. Miller, J. H. 1992. A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory Press, Plainview, NY.

75. Moore, B. C.,, and J. A. Leigh. 2005. Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. J. Bacteriol. 187: 972– 979.

76. Muller, J. A.,, and S. DasSarma. 2005. Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors. J. Bacteriol. 187: 1659– 1667.

77. Ng, W.-L.,, P. Arora,, and S. DasSarma. 1994. Large deletions in class III gas-vesicles deficient mutants of Halobacterium halobium. Syst. Appl. Microbiol. 16: 560– 568.

78. Ng, W.-L.,, S. A. Ciufo,, T. M. Smith,, R. E. Bumgarner,, D. Baskin,, J. Faust,, B. Hall,, C. Loretz,, J. Seto,, J. Slagel,, L. Hood,, and S. DasSarma. 1998. Snapshot of a large dynamic replicon from a halophilic archaeon: Megaplasmid or minichromosome? Genome Res. 8: 1131– 1141.

79. Ng, W. L.,, and S. DasSarma. 1993. Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100. J. Bacteriol. 175: 4584– 4596.

80. Ng, W. V.,, S. P. Kennedy,, G. G. Mahairas,, B. Berquist,, M. Pan,, H. D. Shukla,, S. R. Lasky,, N. S. Baliga,, V. Thorsson,, J. Sbrogna,, S. Swartzell,, D. Weir,, J. Hall,, T. A. Dahl,, R. Welti,, Y. A. Goo,, B. Leithauser,, K. Keller,, R. Cruz,, M. J. Danson,, D. W. Hough,, D. G. Maddocks,, P. E. Jablonski,, M. P. Krebs,, C. M. Angevine,, H. Dale,, T. A. Isenbarger,, R. F. Peck,, M. Pohlschroder,, J. L. Spudich,, K. W. Jung,, M. Alam,, T. Freitas,, S. Hou,, C. J. Daniels,, P. P. Dennis,, A. D. Omer,, H. Ebhardt,, T. M. Lowe,, P. Liang,, M. Riley,, L. Hood,, and S. DasSarma. 2000. Genome sequence of Halobacterium species NRC-1. Proc. Natl. Acad. Sci. USA 97: 12176– 12181.

81. Ni, B. F.,, M. Chang,, A. Duschl,, J. Lanyi,, and R. Needleman. 1990. An efficient system for the synthesis of bacteriorhodopsin in Halobacterium halobium. Gene 90: 169– 172.

82. Nieuwlandt, D. T.,, and C. J. Daniels. 1990. An expression vector for the archaebacterium Haloferax volcanii. J. Bacteriol. 172: 7104– 7110.

83. Nomura, S.,, and Y. Harada. 1998. Functional expression of green fluorescent protein derivatives in Halobacterium salinarum. FEMS Microbiol. Lett. 167: 287– 293.

84. Patenge, N.,, A. Haase,, H. Bolhuis,, and D. Oesterhelt. 1995. The gene for a halophilic beta-galactosidase ( bgaH) of Haloferax alicantei as a reporter gene for promoter analyses in Halobacterium salinarum. EMBO J. 14: 667– 673.

85. Patenge, N.,, and J. Soppa. 1999. Extensive proteolysis inhibits high-level production of eukaryal G protein-coupled receptors in the archaeon Haloferax volcanii. FEMS Microbiol. Lett. 171: 27– 35.

86. Peck, R. F.,, S. DasSarma,, and M. P. Krebs. 2000. Homologous gene knockout in the archaeon Halobacterium with ura3 as a counterselectable marker. Mol. Microbiol. 35: 667– 676.

87. Peck, R. F.,, C. Echavarri-Erasun,, E. A. Johnson,, W. V. Ng,, S. P. Kennedy,, L. Hood,, S. DasSarma,, and M. P. Krebs. 2001. brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium. J. Biol. Chem. 276: 5739– 5744.

88. Peck, R. F.,, E. A. Johnson,, and M. P. Krebs. 2002. Identification of a lycopene beta-cyclase required for bacteriorhodopsin biogenesis in the archaeon Halobacterium salinarum. J. Bacteriol. 184: 2889– 2897.

89. Piatibratov, M.,, S. Hou,, A. Brooun,, J. Yang,, H. Chen,, and M. Alam. 2000. Expression and fast-flow purification of a polyhistidine-tagged myoglobin-like aerotaxis transducer. Biochim. Biophys. Acta 1524: 149– 154.

90. Possot, O.,, P. Gernhardt,, A. Klein,, and L. Sibold. 1988. Analysis of drug resistance in the archaebacterium Methanococcus voltae with respect to potential use in genetic engineering. Appl. Environ. Microbiol. 54: 734– 740.

91. Prisco, A.,, M. Moracci,, M. Rossi,, and M. Ciaramella. 1995. A gene encoding a putative membrane protein homologous to the major facilitator superfamily of transporters maps upstream of the beta-glycosidase gene in the archaeon Sulfolobus solfataricus. J. Bacteriol. 177: 1614– 1619.

92. Pritchett, M. A.,, J. K. Zhang,, and W. W. Metcalf. 2004. Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea. Appl. Environ. Microbiol. 70: 1425– 1433.

93. Reilly, M. S.,, and D. W. Grogan. 2001. Characterization of intragenic recombination in a hyperthermophilic archaeon via conjugational DNA exchange. J. Bacteriol. 183: 2943– 2946.

94. Reuter, C. J.,, and J. A. Maupin-Furlow. 2004. Analysis of proteasome-dependent proteolysis in Haloferax volcanii cells, using short-lived green fluorescent proteins. Appl. Environ. Microbiol. 70: 7530– 7538.

95. Robb, F. T.,, and A. R. Place (ed.). 1995. Thermophiles, vol. 3. Archaea: A Laboroatory Manual. Cold Spring Harbor Laboratory Press, Plainview, NY.

96. Rolfsmeier, M.,, and P. Blum. 1995. Purification and characterization of a maltase from the extremely thermophilic crenarchaeote Solfataricus solfataricus. J. Bacteriol. 177: 482– 485.

97. Rolfsmeier, M.,, C. Haseltine,, A. C. E. Bini,, and P. Blum. 1998. Molecular characterization of the a-glucosidase gene ( malA) from the hyperthermophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 180: 1287– 1295.

98. Rother, M.,, and W. W. Metcalf. 2005. Genetic technologies for Archaea. Curr. Opin. Microbiol. 8: 745– 751.

99. Rother, M.,, A. Resch,, W. L. Gardner,, W. B. Whitman,, and A. Böck. 2001. Heterologous expression of archaeal selenoprotein genes directed by the SECIS element located in the 3' non-translated region. Mol. Microbiol. 40: 900– 908.

100. Sandbeck, K. A.,, and J. A. Leigh. 1991. Recovery of an integration shuttle vector from tandem repeats in Methanococcus maripaludis. Appl. Environ. Microbiol. 57: 2762– 2763.

101. Schelert, J.,, V. Dixit,, V. Hoang,, J. Simbahan,, M. Drozda,, and P. Blum. 2004. Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus using gene disruption. J. Bacteriol. 186: 427– 437.

102. Schleper, C.,, R. Roder,, T. Singer,, and W. Zillig. 1994. An insertion element of the extremely thermophilic archaeon Sulfolobus solfataricus transposes into the endogenous β-galactosidase gene. Mol. Gen. Genet. 243: 91– 96.

103. She, Q.,, R. K. Singh,, F. Confalonieri,, Y. Zivanovic,, G. Allard,, M. J. Awayez,, C. C. Chan-Weiher,, I. G. Clausen,, B. A. Curtis,, A. D. Moors,, G. Erauso,, C. Fletcher,, P. M. Gordon,, I. H.-d. Jong,, A. C. Jeffries,, C. J. Kozera,, N. Medina,, X. Peng,, H. P. Thi-Ngoc,, P. Redder,, M. E. Schenk,, C. Theriault,, N. Tolstrup,, R. L. Charlebois,, W. F. Doolittle,, M. Duguet,, T. Gaasterland,, R. A. Garrett,, M. A. Ragan,, C. W. Sensen,, and J. V. d. Oost. 2001. The complete genome of the Crenarchaeote Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98: 7835– 7840.

104. Smith, P. H.,, and R. E. Hungate. 1958. Isolation and characterization of Methanobacterium ruminatium n. sp. J. Bacteriol. 75: 713– 718.

105. Sowers, K. R.,, S. F. Baron,, and J. G. Ferry. 1984. Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl. Environ. Microbiol. 47: 971– 978.

106. Sowers, K. R.,, J. E. Boone,, and R. P. Gunsalus. 1993. Disaggregation of Methanosarcina spp. and growth as single cells at elevated osmolarity. Appl. Environ. Microbiol. 59: 3832– 3839.

107. Sowers, K. R.,, and R. P. Gunsalus. 1988. Adaptation for growth at various saline concentrations by the archaebacterium Methanosarcina thermophila. J. Bacteriol. 170: 998– 1002.

108. Sowers, K. R.,, and H. J. Schreier (ed.). 1995. Methanogens, vol. 2. Archaea: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

109. Sowers, K. R.,, and H. J. Schreier,. 1995. Techniques for anaerobic growth, p. 15– 55. In F. T. Robb,, K. R. Sowers,, S. DasSharma,, A. R. Place,, H. J. Schreier,, and E. M. Fleischmann (ed.), Archaea: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, NY.

110. Sowers, K. R.,, and H. J. Schreier. 1999. Gene transfer systems for the archaea. Trends Microbiol. 7: 212– 219.

111. Stathopoulos, C.,, W. Kim,, T. Li,, I. Anderson,, B. Deutsch,, S. Palioura,, W. Whitman,, and D. Soll. 2001. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. USA 98: 14292– 14297.

112. Stedman, K. M.,, C. Schleper,, E. Rumpf,, and W. Zillig. 1999. Genetic requirements for the function of the archaeal virus SSV1 in Sulfolobus solfataricus: construction and testing of viral shuttle vectors. Genetics 152: 1397– 1405.

113. Stoeckenius, W.,, R. H. Lozier,, and R. A. Bogomolni. 1979. Bacteriorhodopsin and the purple membrane of halobacteria. Biochim. Biophys. Acta 505: 215– 278.

114. Stuart, E. S.,, F. Morshed,, M. Sremac,, and S. DasSarma. 2001. Antigen presentation using novel particulate organelles from halophilic archaea. J. Biotechnol. 88: 119– 128.

115. Tu, D.,, G. Blaha,, P. B. Moore,, and T. A. Steitz. 2005. Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted. Extremophiles 9: 427– 435.

116. Tumbula, D. L.,, T. L. Bowen,, and W. B. Whitman,. 1995. Growth of methanogens on solidified medium, p. 49– 55. In F. T. Robb,, A. R. Place,, K. R. Sowers,, H. J. Schreier,, S. DasSarma,, and E. M. Fleischmann (ed.), Archaea: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, NY.

117. Tumbula, D. L.,, T. L. Bowen,, and W. B. Whitman. 1997. Characterization of pURB500 from the archaeon Methanococcus maripaludis and construction of a shuttle vector. J. Bacteriol. 179: 2976– 2986.

118. Tumbula, D. L.,, and W. B. Whitman. 1999. Genetics of Methanococcus: possibilities for functional genomics in Archaea. Mol. Microbiol. 33: 1– 7.

119. Wang, G.,, S. P. Kennedy,, S. Fasiludeen,, C. Rensing,, and S. DasSarma. 2004. Arsenic resistance in Halobacterium sp. strain NRC-1 examined by using an improved gene knockout system. J. Bacteriol. 186: 3187– 3194.

120. Wolin, E. A.,, M. J. Wolin,, and R. S. Wolfe. 1963. Formation of methane by bacterial extracts. J. Biol. Chem. 238: 2882– 2886.

121. Wood, G. E.,, A. K. Haydock,, and J. A. Leigh. 2003. Function and regulation of the formate dehydrogenase genes of the methanogenic Archaeon Methanococcus maripaludis. J. Bacteriol. 185: 2548– 2554.

122. Woods, W. G.,, K. Ngui,, and M. L. Dyall-Smith. 1999. An improved transposon for the halophilic archaeon Haloarcula hispanica. J. Bacteriol. 181: 7140– 7142.

123. Woodson, D.,, R. Peck,, M. Krebs,, and J. Escalante- Semerena. 2003. The cobY gene of the Archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis. J. Bacteriol. 185: 311– 316.

124. Worthington, P.,, P. Blum,, F. Perez-Pomares,, and T. Elthon. 2003. Large scale cultivation of acidophilic hyperthermophiles for recovery of secreted proteins. Appl. Environ. Microbiol. 69: 252– 257.

125. Worthington, P.,, V. Hoang,, P. Perez-Pomares,, and P. Blum. 2003. Targeted disruption of the a-amylase gene in the hyperthermophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 185: 482– 488.

126. Zhang, J. K.,, M. A. Pritchett,, D. J. Lampe,, H. M. Robertson,, and W. W. Metcalf. 2000. In vivo transposon mutagenesis of the methanogenic archaeon Methanosarcina acetivorans C2A using a modified version of the insect mariner-family transposable element Himar1. Proc. Natl. Acad. Sci. USA 97: 9665– 9670.

127. Zhang, J. K.,, A. K. White,, H. C. Kuettner,, P. Boccazzi,, and W. W. Metcalf. 2002. Directed mutagenesis and plasmid-based complementation in the methanogenic archaeon Methanosarcina acetivorans C2A demonstrated by genetic analysis of proline biosynthesis. J. Bacteriol. 184: 1449– 1454.

128. Zibat, A. 2001. Efficient transformation of Halobacterium salinarum by a “freeze and thaw” technique. Biotechniques. 31: 1010– 1012.

129. Zillig, W.,, H. P. Arnold,, I. Holz,, D. Prangishvili,, A. Schweier,, K. Stedman,, Q. She,, H. Phan,, R. Garrett,, and J. K. Kristjansson. 1998. Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles 2: 131– 140.

130. Zillig, W.,, K. O. Stetter,, S. Wunderl,, W. Schulz,, H. Priess,, and J. Scholz. 1980. The Sulfolobus-“Caldariella” group: taxonomy on the basis of the structure of DNAdependent RNA polymerases. Arch. Microbiol. 125: 259– 269.

Tables

Genetics of Archaea

/content/10.1128/9781555817497.chap33.tab33-1

TABLE 1

Archaeal genomic sequences

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TABLE 1

Archaeal genomic sequences

/content/10.1128/9781555817497.chap33.tab33-2

TABLE 2

Archaeal strain characteristics and sources a

a ATCC, American Type Culture Collection (http://www.atcc.org/); DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (http://www.dsmz.de/); JCM, Japan Collection of Microorganisms (http://www.jcm.riken.go.jp/); OCM, Oregon Collection of Methanogens (http://methanogens.pdx.edu/).

10.1128/9781555817497/tab33-2_thmb.gif

10.1128/9781555817497/tab33-2.gif

TABLE 2

Archaeal strain characteristics and sources a

/content/10.1128/9781555817497.chap33.tab33-3

TABLE 3

Archaeal genetic vectors

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TABLE 3

Archaeal genetic vectors

/content/10.1128/9781555817497.chap33.tab33-4

TABLE 4

Selectable genetic markers for Archaea

a SCES, sole carbon and energy source.

10.1128/9781555817497/tab33-4_thmb.gif

10.1128/9781555817497/tab33-4.gif

TABLE 4

Selectable genetic markers for Archaea

a SCES, sole carbon and energy source.