1887

Chapter 11 : Sensing, Signal Transduction, and Posttranslational Modification

Author: Peter J. Kennelly1
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: Department of Biochemistry, Mail Stop 0308, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
Content Type: Monograph
Publication Year: 2007

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

Sensing, Signal Transduction, and Posttranslational Modification, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815516/9781555813918_Chap11-1.gif /docserver/preview/fulltext/10.1128/9781555815516/9781555813918_Chap11-2.gif

Abstract:

This chapter focuses on other modalities of signal transduction, including intracellular second messengers, feedback regulation, and posttranslational modifications such as the phosphorylation-dephosphorylation of proteins. Empirical studies of archaeal-archaeal and archaeal-bacterial communication have been few in number and preliminary in nature. Inspection of archaeal genomes has revealed them to be devoid of homologs of the prototypic bacterial quorum-sensing proteins LuxS and LuxR. Two-component systems differ in several fundamental respects from protein-serine/threonine/tyrosine phosphorylation cascades. First, autophosohorylation is the predominant mechanism of phosphorylation in the two-component system, whereas protein-serine/threonine/tyrosine phosphorylation cascades rely primarily on phosphotransfer reactions catalyzed by protein kinases that are distinct from the phosphoacceptor protein. Second, the chemical nature of the phosphoryl moieties formed during two-component signaling differs significantly from that of protein-serine/threonine/tyrosine phosphorylation. Posttranslational modifications have discussed and demonstrated, at least in some instances, to modulate the function of one or more target proteins from the or other organisms. It is widely presumed that (poly)ADP-ribosylation regulates the functional properties of proteins, as is the case with other covalent modifications such as protein phosphorylation-dephosphorylation. Given that the members of the bacterial domain have been the subject of decades of intensive study, it appears highly likely that the will not only be found to contain new sensor-response mechanisms and molecules, but that they will provide new insights into this vital process in other organisms as well.

Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Sensing, Signal Transduction, and Posttranslational Modification
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815516.ch11-1,webId=/content/author/10.1128/9781555815516.ch11-1,properties={foaf_givenname=Peter J., foaf_name=Peter J. Kennelly, foaf_surname=Kennelly, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815516.ch11-aff1]]}]]
Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
/content/10.1128/9781555815516.ch11.ch11fig01
Figure 1.
Environmental variables and internal cues known or likely to be monitored by members of the
10.1128/9781555815516/f0225-01_thmb.gif
10.1128/9781555815516/f0225-01.gif
Image of Figure 1.
Figure 1.

Environmental variables and internal cues known or likely to be monitored by members of the

Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555815516.ch11.ch11fig02
Figure 2.
Basic elements of biological sensor-response pathways. (A) Hypothetical multistep signal transduction pathway in which an external signal (open diamond) interacts with a transmembrane receptor complex to activate a target protein. The sensor-response pathway comprises two steps. In the first, the transmission domain of the receptor complex produces a second messenger (filled circle) that, in turn, serves as an allosteric activator for a second transmission domain (hatched circle) that catalyzes the covalent modification (open triangle) of the target (open quadrilateral). In this example, binding of the allosteric ligand and covalent modification both activate their respective target proteins by altering their conformation. (B) Hypothetical multistep biosynthetic pathway that is subject to feedback inhibition by one of the products of the final enzyme in the pathway (filled diamond). In this case, the indicator metabolite binds to and allosterically activates a sensor-transmitter fusion protein that subsequently binds to and inhibits the activity of the first enzyme in the pathway (target). The second and third enzymes in the pathway are denoted by diagonal hatching and cross hatching, respectively. See Table 1 for definitions of terms used.
10.1128/9781555815516/f0228-01_thmb.gif
10.1128/9781555815516/f0228-01.gif
Image of Figure 2.
Figure 2.

Basic elements of biological sensor-response pathways. (A) Hypothetical multistep signal transduction pathway in which an external signal (open diamond) interacts with a transmembrane receptor complex to activate a target protein. The sensor-response pathway comprises two steps. In the first, the transmission domain of the receptor complex produces a second messenger (filled circle) that, in turn, serves as an allosteric activator for a second transmission domain (hatched circle) that catalyzes the covalent modification (open triangle) of the target (open quadrilateral). In this example, binding of the allosteric ligand and covalent modification both activate their respective target proteins by altering their conformation. (B) Hypothetical multistep biosynthetic pathway that is subject to feedback inhibition by one of the products of the final enzyme in the pathway (filled diamond). In this case, the indicator metabolite binds to and allosterically activates a sensor-transmitter fusion protein that subsequently binds to and inhibits the activity of the first enzyme in the pathway (target). The second and third enzymes in the pathway are denoted by diagonal hatching and cross hatching, respectively. See Table 1 for definitions of terms used.

Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555815516.ch11.ch11fig03
Figure 3.
Phosphorylation of phosphohexosemutase from . Ser-309 on the phosphohexosemutase inhibits catalysis by electrosterically interfering with the binding of substrate phosphohexoses.
10.1128/9781555815516/f0238-01_thmb.gif
10.1128/9781555815516/f0238-01.gif
Image of Figure 3.
Figure 3.

Phosphorylation of phosphohexosemutase from . Ser-309 on the phosphohexosemutase inhibits catalysis by electrosterically interfering with the binding of substrate phosphohexoses.

Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555815516.ch11.ch11fig04
Figure 4.
Examples of typical architectures of two-component signal transduction cascades. Shown are schematic representations of three hypothetical two-component signal transduction cascades. For each example, an external signal (open diamond) activates a histidine kinase (hatched oval) by binding to its transmembrane receptor domain (open pentagon). Response regulator domains are represented as diagonally striped rectangles. Output domains (filled circles and filled hexagons); Hpt domains (open triangles); phosphoryl transfer events (hatched arrows); conserved histidine (H) and conserved aspartate (D) residues within each two-component domain. A basic two-component signaling cascade (left); an extended two-component cascade employing a hybrid histidine kinase, i.e., one that is fused to a response regulator domain, and phosphoryl shuttle via an Hpt domain (middle); a branched two-component cascade whose right-hand branch includes an response regulator domain-Hpt domain fusion protein that serves as a phosphoryl group shuttle bridging the histidine kinase to a downstream target response regulator protein (right).
10.1128/9781555815516/f0242-01_thmb.gif
10.1128/9781555815516/f0242-01.gif
Image of Figure 4.
Figure 4.

Examples of typical architectures of two-component signal transduction cascades. Shown are schematic representations of three hypothetical two-component signal transduction cascades. For each example, an external signal (open diamond) activates a histidine kinase (hatched oval) by binding to its transmembrane receptor domain (open pentagon). Response regulator domains are represented as diagonally striped rectangles. Output domains (filled circles and filled hexagons); Hpt domains (open triangles); phosphoryl transfer events (hatched arrows); conserved histidine (H) and conserved aspartate (D) residues within each two-component domain. A basic two-component signaling cascade (left); an extended two-component cascade employing a hybrid histidine kinase, i.e., one that is fused to a response regulator domain, and phosphoryl shuttle via an Hpt domain (middle); a branched two-component cascade whose right-hand branch includes an response regulator domain-Hpt domain fusion protein that serves as a phosphoryl group shuttle bridging the histidine kinase to a downstream target response regulator protein (right).

Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555815516.ch11.ch11fig05
Figure 5.
Redox regulation of coenzyme F metabolism in Enzyme names are italicized. Events that stimulate (plus sign) or inhibit (minus sign) enzymatic activity; cysteine sulfhydryl groups (SH); cystine disulfides (S—S).
10.1128/9781555815516/f0246-01_thmb.gif
10.1128/9781555815516/f0246-01.gif
Image of Figure 5.
Figure 5.

Redox regulation of coenzyme F metabolism in Enzyme names are italicized. Events that stimulate (plus sign) or inhibit (minus sign) enzymatic activity; cysteine sulfhydryl groups (SH); cystine disulfides (S—S).

Citation: Kennelly P. 2007. Sensing, Signal Transduction, and Posttranslational Modification, p 224-259. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815516.ch11
1. Adams, M. W. W.,, J. F. Holden,, A. L. Menon,, G. J. Schut,, A. M. Grunden,, C. Hu,, A. M. Hutchins,, F. E. Jenney, Jr.,, C. Kim,, K. Ma,, G. Pan,, R. Roy,, R. Sapra,, S. V. Story, and, M. F. J. M. Verhagen. 2001. Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183: 716– 724.
2. Alam, M.,, M. Lebert,, D. Oesterhelt, and, G. L. Hazelbauer. 1989. Methyl-accepting chemotaxis proteins in Halobacterium halobium. EMBO J. 8: 631– 639.
3. Albers, S. V. and, A. J. M. Driessen. 2002. Signal peptides of secreted proteins of the archaeon Sulfolobus solfataricus: a genomic survey. Arch. Microbiol. 177: 209– 216.
4. Allen, M. D.,, A. M. Buckle,, S. C. Cordell,, J. Lowe, and, M. Bycroft. 2003. The crystal structure of AF1521, a protein from Archaeoglobus fulgidus with homology to the non-histone domain of MacroH2A, J. Mol. Biol. 330: 503– 511.
5. Alonso, A.,, S. Burkhalter,, J. Sasin,, L. Tautz,, J. Bogets,, H. Huynh,, M. C. D. Bremer,, L. J. Holsinger,, A. Godzik, and, T. Mustelin. 2004. The minimal essential core of a cysteine-based protein-tyrosine phosphatase revealed by a novel 16-kDa VH1-like phosphatase, VHZ. J. Biol. Chem. 279: 35768– 35774.
6. Amaro, A. M., and, C. A. Jerez. 1984. Methylation of ribosomal proteins in bacteria: Evidence of conserved modification of the eubacterial 50S subunit. J. Bacteriol. 158: 84– 93.
7. Anantharaman, V., and, L. Aravind. 2000. Cache—a signaling domain common to animal Ca 2+-channel subunits and a class of prokaryotic chemotaxis receptors. Trends Biochem. Sci. 25: 535– 537.
8. Anantharaman, V., and, L. Aravind. 2001. The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem. Sci. 26: 579– 591.
9. Anantharaman, V.,, E. V. Koonin, and, L. Aravind. 2001. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J. Mol. Biol. 307: 1271– 1292.
10. Angermayr, M.,, A. Roidl, and, W. Brandlow. 2002. Yeast Rio1p is the founding member of a novel subfamily of protein serine kinases involved in control of cell cycle progression. Mol. Microbiol. 44: 309– 324.
11. Appleby, J. L.,, J. S. Parkinson, and, R. B. Bourret. 1996. Signal transduction via the multi-step phosphorelay: not necessarily a road less traveled. Cell 86: 845– 848.
12. Arai, M.,, M. Ikeda, and, T. Shimizu. 2003. Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene 304: 77– 86.
13. Aravind, L. 2001. The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation. Trends Biochem. Sci. 26: 273– 275.
14. Aravind, L.,, V. Anantharaman, and, L. M. Iyer. 2003. Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective. Curr. Opin. Microbiol. 6: 490– 497.
15. Aravind, L. and, E. V. Koonin. 1999. DNA-binding proteins and evolution of transcription regulation in the Archaea. Nucleic Acids Res. 27: 4658– 4670.
16. Aravind, L., and, C. P. Ponting. 1997. The GAF domain: An evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci. 22: 458– 459.
17. Arent, S.,, P. Harris,, K. F. Jensen, and, S. Larsen. 2005. Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus. Biochemistry 44: 883– 892.
18. Ashby, M. K. 2004. Survey of the number of two-component response regulator genes in the complete and annotated genome sequences of prokaryotes. FEMS Microbiol. Lett. 231: 277– 281.
19. Ashby, M. K. 2006. Distribution, structure, and diversity of “bacterial” genes encoding two-component proteins in the Euryarchaeota. Archaea 2: 11– 30.
20. Baker, M. D.,, P. M. Wolanin, and, J. B. Stock. 2005. Signal transduction in bacterial chemotaxis. BioEssays 28: 9– 22.
21. Baker-Austin, C.,, M. Dopson,, M. Wexler,, R. G. Sawers, and, P. L. Bond. 2005. Molecular insight into extreme copper resistance in the extremophilic archaeon ’Ferroplasma acidar-manus’ Fer1. Microbiology 151: 2637– 2646.
22. Baliga, N. S.,, S. P. Kennedy,, W. V. Ng,, L. Hood, and, S. Das-Sarma. 2001. Genomic and genetic dissection of an archaeal regulon. Proc. Natl. Acad. Sci. USA 98: 2521– 2525.
23. Barford, D. 1996. Molecular mechanisms of the protein serine/threonine phosphatases. Trends Biochem. Sci. 21: 407– 412.
24. Bartig, D.,, K. Lemkemeier,, J. Frank,, F. Lottspeich, and, F. Klink. 1992. The archaebacterial hypusine-containng protein. Strucutral features suggest common ancestry with eu-karyotic translation initiation factor 5A. Eur. J. Biochem. 204: 751– 758.
25. Baumann, H.,, T. Lundback,, R. Ladenstein, and, T. Hard. 1994. Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus. Nat. Struct. Biol. 1: 808– 819.
26. Bell, S. D.,, C. H. Botting,, B. N. Wardelworth,, S. P. Jackson, and, M. F. White. 2002. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296: 148– 151.
27. Bhaduri, A., and, R. Sowdhamini. 2005. Genome-wide survey of prokaryotic O-phosphatases. J. Mol. Biol. 352: 736– 752.
28. Bidle, K. A. 2003. Differential expression of genes influenced by changing salinity using RNA arbitrarily primed PCR in the archaeal halophile Haloferax volcanii. Extremophiles 7: 1– 7.
29. Bienkowska, J. R.,, H. Hartman, and, T. F. Smith. 2004. A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells? Protein Eng. 16: 897– 904.
30. Bini, E. and, P. Blum. 2001. Archaeal catabolite repression: a gene regulatory paradigm. Adv. Appl. Microbiol. 50: 39– 367.
31. Bolhuis, A. 2002. Protein transport in the halophilic archaeon Halobacterium sp. NRC-1: A major role for the twin-arginine translocation pathway. Microbiology 148: 3335– 3346.
32. Bonete, M. J.,, F. Perez-Pomares,, J. Ferrer, and, M. L. Camacho. 1996. NAD-glutamate dehydrogenase from Halobacterium halobium: Inhibition and activation by TCA intermediates and amino acids. Biochim. Biophys. Acta 1289: 14– 24.
33. Bonete, M. J.,, M. L. Camacho, and, E. Cadenas. 1989. Kinetic mechanism of Halobacterium halobium NAD +-glutamate dehydrogenase. Biochim. Biophys. Ada 24: 150– 155.
34. Bonete, M. J.,, M. L. Camacho, and, E. Cadenas. 1990. Analysis of the kinetic mechanism of halophilic NADP-dependent glutamate dehydrogenase. Biochim. Biophys. Ada 5: 305– 310.
35. Boonyaratanakornkit, B. B.,, A. J. Simpson,, T. A. Whitehead,, C. M. Fraser,, N. M. A. El-Sayed, and, D. S. Clark. 2005. Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. Environ. Microbiol. 7: 789– 797.
36. Botsford, J. L, and, J. G. Harman. 1992. Cyclic AMP in prokaryotes. Microbiol. Rev. 56: 100– 122.
37. Bourret, R. B., and, A. M. Stock. 2002. Molecular information processing: Lessons from bacterial chemtaxis. J. Biol. Chem. 277: 9625– 9628
38. Brabbban A. D.,, E. N. Orcutt, and, S. H. Zinder. 1999. Interactions between nitrogen fixation and osmoregulation in the methanogenic archaeon Methanosarcina barkeri 227. Appl. Environ. Microbiol. 65: 1222– 1227.
39. Brasen, C, and, P. Schonheit. 2004. Regulation of acetate and acetyl-CoA converting enzymes during growth on acetate and/or glucose in the halophilic archaeon Haloarcula marismortui. FEMS Microbiol. Lett. 241: 21– 26.
40. Brinkman, A. B.,, S. D. Bell,, R. J. Lebbink,, W. M. deVos, and, J. van der Oost. 2002. The Sulfolobus sol-fataricus Lrp-like protein LysM regulates lysine biosynthesis in response to lysine availability. J. Biol. Chem. 277: 29537– 29549.
41. Brochier, C,, P. Lopez-Garcia, and, D. Moreira. 2004. Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria. Gene 330: 169– 176.
42. Brooun, A.,, J. Bell,, T. Freitas,, R. W. Larsen, and, M. Alam. 1998. An archaeal aeotaxis transducer combines subunit I core structures of eukaryotic cytochrome c oxidase and eu-bacterial methyl-accepting chemotaxis proteins. J. Bacteriol. 180: 1642– 1646.
43. Brooun, A.,, W. Zhang, and, M. Alam. 1997. Primary structure and functional analysis of the soluble transducer protein HtrXI in the archaeon Halobacterium salinarium. J. Bacteriol. 179: 2963– 2968.
44. Brunner, N. A.,, H. Brinkmann,, B. Siebers, and, R. Hensel. 1998. NAD +-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. J. Biol. Chem. 273: 6149– 6156.
45. Brunner, N. A.,, B. Siebers, and, R. Hensel. 2001. Role of two different glyceraldehydes-3-phosphate dehydrogenases in controlling the reversible Embden-Meyerhof-Parnas pathway in Thermoproteus tenax: Regulation on protein and transcript level. Extremophiles 5: 101– 109.
46. Buss, J. E., and, J. T. Stull. 1983. Measurement of chemical phosphate in proteins. Methods Enzymol. 99: 7– 14.
47. Byrnes, W. M., and, V. L. Vilker. 2004. Extrinsic factors potassium chloride and glycerol induce thermostability in recombinant anthranilate synthase from Archaeoglobus fulgidus. Extremophiles 8: 455– 462.
48. Cabello, P.,, M. D. Roldan, and, C. Moreno-Vivian. 2004. Nitrate reduction and the nitrogen cycle in archaea. Microbiology 150: 3527– 3546.
49. Cai, X., and, J. Lytton. 2004. The cation/Ca 2+ exchanger superfamily: phylogenetic analysis and structural implications. Mol. Biol. Evol. 21: 1692– 1703.
50. Cardona, S.,, F. Remonsellez,, N. Guiliani, and, C. A. Jerez. 2001. The glycogen-bound polyphosphate kinase from Sulfolobus acidocaldarius is actually a glycogen synthase. Appl. Environ. Microbiol. 67: 4773– 4780.
51. Cech, T. R. 1993. The efficiency and versatility of catalytic RNA: Implications for an RNA world. Gene 135: 33– 36.
52. Cho, H. S.,, J. G. Pelton,, D. Yan,, S. Kustu, and, D. E. Wemmer. 2001. Phosphoaspartates in bacterial signal transduction. Curr. Opin. Struct. Biol. 11: 679– 684.
53. Ciulla, R. A.,, S. Burggraf,, K. O. Stetter, and, M. F. Roberts. 1994. Occurrence and role of di-myo-inositol-1,1 (prm1)-phosphate in Methanococcus igneus. Appl. Environ. Microbiol. 60: 3660– 3664.
54. Clemens, M. J. 2004. Targets and mechanisms for the regulation of translation in malignant transformation. Oncogene 23: 3180– 3188.
55. Cohen, P. T. W. 2002. Protein phosphatase 1—targeted in many directions. J. Cell Sci. 115: 241– 256.
56. Cohen-Kupiec, R.,, C. Blank, and, J. A. Leigh. 1997. Tran-scriptional regulation in Archaea: In vivo demonstration of a repressor binding site in a methanogen. Proc. Natl. Acad. Sci. USA 94: 1316– 1320.
57. Condo, L.,, D. Ruggero,, R. Reinhardt, and, P. Londel. 1998. A novel amino-peptidase associated with the 60 kDa chaper-onin in the thermophilic archaeon Sulfolobus sol-fataricus. Mol. Microbiol. 29: 775– 785.
58. Cosgrove, M. S., and, C. Wolberger. 2005. How does the his-tone code work? Biochem. Cell Biol. 83: 468– 476.
59. Daas, P. J. H.,, R. W. Wassenaar,, P. Willemsen,, R. J. Theunissen,, J. T. Keltjens,, C. van der Drift, and, G. D. Vogels. 1996. Purification and properties of an enzyme involved in the ATP-dependent activation of the methanol:2-mercaptoethanesul-fonic acid methyltransferase reaction in Methanosarcina barkeri. J. Biol. Chem. 271: 22339– 22345.
60. D’Amours, D.,, S. Desnoyers,, I. D’Silva, and, G. G. Poirier. 1999. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem. J. 342: 249– 268.
61. D’Argenio, D. A., and, S. I. Miller. 2004. Cyclic di-GMP as a bacterial second messenger. Microbiology 150: 2497– 2502.
62. DasSarma, S.,, S. P. Kennedy,, B. Berquist,, W. V. Ng,, N. S. Baliga,, J. L. Spudich,, M. P. Krebs,, J. A. Eisen,, C. H. Johnson, and, L. Hood. 2001. Genomic perspective on the photo-biology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth. Res. 70: 3– 17.
63. De Biase, A.,, A. J. L. Macario, and, E. C. De Macario. 2002. Effect of heat stress on promoter binding by transcription factors in the cytosol of the archaeon Methanosarcina mazeii. Gene 282: 189– 197.
64. De Felice, M.,, L. Esposito,, B. Pucci,, F. Carpentieri,, M. De Falco,, M. Rossi, and, F. M. Pisani. 2003. Biochemical characterization of a CDC6-like protein from the crenarchaeon Sulfolobus sol-fataricus. J. Biol. Chem. 278: 46424– 46431.
65. De Hertogh, B.,, A. C. Lantin,, P. V. Baret, and, A. Goffeau. 2004. The archaeal P-Type ATPases. J. Bioenerg. Biomemb. 36: 135– 142.
66. De Vendittis, E.,, M. R. Amatruda,, G. Raimo, and, V. Boc-chini. 1997. Heterologous expression in Escherichia coli of the gene encoding an archaeal thermoacidophilic elongation factor 2. Properties of the recombinant protein. Biochimie 79: 303– 308.
67. Diefenbach, J., and, A. Burkle. 2005. Introduction to poly (ADP-ribose) metabolism. Cell. Mol. Life Sci. 62: 721– 730.
68. DiRuggiero, J.,, D. Dunn,, D. L. Maeder,, R. Holley-Shanks,, J. Chatard,, R. Horlacher,, R. T. Robb,, W. Boos, and, R. B. Weiss. 2000. Evidence of recent lateral gene transfer among hyperthermophilic Archaea. Mol. Microbiol. 38: 684– 693.
69. Dodsworth, J. A.,, N. C. Cady, and, J. A. Leigh. 2005. 2-Oxo-glutarate and the PII homologues Nifl 1 and Nifl 2 regulate nitrogenase activity in cell extracts of Methanaococcus mari-paludis, Mol. Microbiol. 56: 1527– 1538.
70. Dominguez, D. C. 2004. Calcium signaling in bacteria. Mol. Microbiol. 54: 291– 297.
71. Durbecq, V.,, T. L. Thia-Toong,, D. Charlier,, V. Villeret,, M. Roovers,, R. Wattiez,, C. Legrain, and, N. Glansdorff. 1999. Aspartate carbamoyltransferase from the thermoaci-dophilic archaeon Sulfolobus acidocaldarius. Eur. J. Biochem. 264: 233– 241.
72. Ehlers, C,, K. Weidenbach,, K. Veit,, K. Forchhammer, and, R. A. Schmitz. 2005. Unique mechanistic features of post-translational regulation of glutamine synthetase activity in Methanosarcina mazei strain Gö1 in response to nitrogen availability. Mol. Microbiol. 55: 1841– 1854.
73. Ehrmann, M., and, T. Clausen. 2004. Proteolysis as a regulatory mechanism. Annu. Rev. Genet. 38: 709– 724.
74. Eichler, J., and, M. W. W. Adams. 2005. Posttranslational protein modification in Archaea. Microbiol. Mol. Biol. Rev. 69: 393– 425.
75. Eliasson, R.,, E. Pontis,, A. Jordan, and, P. Reichard. 1999. Allosteric control of three B 12-dependent (class II) ribonu-cleotide reductases. J. Biol. Chem. 274: 7182– 7189.
76. Ermler, U.,, W. Grabarse,, S. Shima,, M. Goubeaud, and, R. K. Thaure. 1997. Crystal structure of methyl-coenzyme M reductase: The key enzyme of biological methane formation. Science 278: 1457– 1462.
77. Ettema, T. J. G.,, A. B. Brinkman,, T. H. Tani,, J. B. Rafferty, and, J. van der Oost. 2002. A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes. J. Biol. Chem. 277: 37464– 37468.
78. Ettema, T. J. G,, M. A. Hyunen,, W. M. de Vos, and, J. van der Oost. 2003. TRASH: A novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking, and resistance. Trends Biochem. Sci. 28: 170– 173.
79. Ettema, T. J. G.,, K. S. Makarova,, G. L. Jellema,, H. J. Gier-man,, E. V. Koonin,, M. A. Huynen,, W. M. de Vos, and, J. van der Oost. 2004. Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. J. Bacteriol. 186: 7754– 7762.
80. Fabret, C.,, V. A. Feher, and, J. A. Hoch. 1999. Two-component signal transduction in Bacillus subtilis: How one organism sees its world. J. Bacteriol. 181: 1975– 1983.
81. Facchin, S.,, S. Sarno,, O. Marin,, R. Lopreiato,, G. Sartori, and, L. A. Pinna. 2002. Acidophilic nature of yeast PID261/BUD32, a putative ancestor of eukaryotic protein kinases. Biochem. Biophys. Res. Commun. 296: 1366– 1371.
82. Faraone-Mennella, M. R., and, B. Farina. 1995. In the thermophilic archaeon Sulfolobus sol-fataricus a DNA-binding protein is in vitro (ADPribosyl)ated. Biochem. Biophys. Res. Commun. 208: 55– 62.
83. Faraone-Mennella, M. R.,, A. Gambacorta,, B. Nicolaus, and, B. Farina. 1998. Purification and biochemical characterization of a poly(ADP-ribose) polymerase-like enzyme from the thermophilic archaeon Sulfolobus sol-fataricus. Biochem. J. 335: 441– 447.
84. Faraone-Mennella, M. R.,, G. Piccialli,, P. De Luca,, S. Castel-lano,, A. Giordano,, D. Rigano,, L. De Napoli, and, B. Farina. 2002. Interaction of the ADP-ribosylating enzyme from the hyperthermophilic archaeon S. sol-fataricus with DNA and ss-oligo deoxy ribonucleotides. J. Cell. Biochem. 85: 146– 157.
85. Febbraio, F.,, A. Andolfo,, F. Tanfani,, R. Briante,, F. Gentile,, S. Formisano,, C. Vaccaro,, A. Scire,, E. Bertoli,, P. Pucci, and, R. Nucci. 2004. Thermal stability and aggregation of Sulfolobus sol-fataricus β-glycosidase are dependent upon the N-∈-methylation of specific lysyl residues. J. Biol. Chem. 279: 10185– 10194.
86. Fiorentino, G.,, R. Cannio,, M. Rossi, and, S. Bartolucci. 2003. Transcriptional regulation of the gene encoding and alcohol dehydrogenase in the archaeon Sulfolobus sol-fataricus involves multiple factors and control elements. J. Bacteriol. 185: 3926– 3934.
87. Fischer, R. S.,, C. A. Bonner,, D. R. Boone, and, R. A. Jensen. 1993. Clues from a halophilic methanogen about aromatic amino-acid biosynthesis in Archaebacteria. Arch. Microbiol. 160: 440– 446.
88. Forbes, A. J.,, S. M. Patrie,, G. K. Taylor,, Y. B. Kim,, L. Jiang, and, N. L. Kelleher. 2004. Targeted analysis and discovery of posttranslational modifications in proteins from methano-genic Archaea by top-down MS. Proc. Natl. Acad. Sci. USA 2: 2678– 2683.
89. Freitas, T. A. K.,, S. Hou,, E. M. Dioum,, J. A. Saito,, J. New-house,, G. Gonzalez,, M. A. Gilles-Gonzalez, and, M. Alam. 2004. Ancestral hemoglobins in Archaea. Proc. Natl. Acad. Sci. USA 101: 6675– 6690.
90. Fujiwara, S.,, A. Yamanaka,, K. Hirooka,, A. Kobayashi,, T. Imanaka, and, E. Fukusaki. 2004. Temperature-dependent modulation of farnesyl diphosphate/geranylgeranyl diphosphate synthase from hyperthermophilic Archaea. Biochem. Biophys. Res. Commun. 325: 1066– 1074.
91. Fujitaki, J. M., and, R. A. Smith. 1984. Techniques in the detection and characterization of phosphoramidate-containing proteins. Methods Enzymol. 107: 23– 36.
92. Fusi, P,, M. Grisa,, E. Mombelli,, R. Consonni,, P. Tortora, and, M. Vanoni. 1995. Expression of s synthetic gene encoding P2 ribonuclease from the extreme thermoacidophilic archaebacterium Sulfolobus solfactaricus in mesophylic host. Gene 154: 99– 103.
93. Fusi, P.,, M. Grisa,, G. Tedeschi,, A. Megri,, A. Guerritore, and, P. Tortora. 1995. An 8.5-kDa ribonuclease from the extreme thermophilic archaebacterium Sulfolobus sol-fataricus. FEBS Lett. 360: 187– 190.
94. Galperin, M. Y. 2004. Bacterial signal transduction network in a genomic prespective. Environ. Microbiol. 6: 552– 567.
95. Galperin, M. Y. 2005. A census of membrane-bound and in-tracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC Microbiol. 5: 35.
96. Galperin, M. Y.,, A. N. Nikolskaya, and, E. V. Koonin. 2001. Novel domains of the prokaryotic two-component signal transduction system. FEMS Microbiol. Lett. 203: 11– 21.
97. Gast, D. A.,, U. Jenal,, A. Wasserfallen, and, T. Leisinger. 1994. Regulation of tryptophan biosynthesis in Methanobacterium thermoautotrophicum Marburg. J. Bacteriol. 176: 4590– 4596.
98. Goldman, S.,, K. Hecht,, H. Eisenberg, and, M. Mevarech. 1990. Extracellular Ca 2+-dependent inducible alkaline phos-phatase from the extremely halophilic archaebacterium Haloarcula marismortui. J. Bacteriol. 172: 7065– 7070.
99. Goodchild, A.,, M. Raftery,, N. F. W. Saunders,, M. Guilhaus, and, R. Cavicchioli. 2005. Cold adaptation of the Antarctic archaeon, Methanococcus burtonii assessed by proteomics using ICAT J. Proteome Res. 4: 473– 480.
100. Goodchild, A.,, N. F. W. Saunders,, H. Ertan,, M. Raftery,, M. Guilhaus,, P. M. G. Curmi, and, R. Cavicchioli. 2004. A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcus burtonii. Mol. Microbiol. 53: 309– 321.
101. Grabarse, W.,, F. Mahlert,, S. Shima,, R. K. Thauer, and, U. Ermler. 2000. Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: Unusual amino acid modification, conservation and adaptation. J. Mol. Biol. 303: 329– 344.
102. Grabowski, B., and, Z. Kelman. 2001. Autophosphorylation of archaeal Cdc6 homologs is regulated by DNA. J. Bacteriol. 183: 5459– 5464.
103. Grebe, T. W., and, J. B. Stock. 1999. The histidine protein ki-nase superfamily. Adv. Microbial Physiol. 41: 139– 227.
104. Gregory, P. D.,, K. Wagner, and, W. Horz. 2001. Histone acetylation and chromatin remodeling. Exp. Cell Res. 265: 195– 202.
105. Griffith, S. C.,, M. R. Sawaya,, D. R. Boutz,, N. Thapar,, J. E. Katz,, C. Clarke, and, T. O. Yeates. 2001. Crystal structure of protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. J. Mol. Biol. 313: 1103– 1116.
106. Gropp, F., and, M. C. Betlach. 1994. The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor. Proc. Natl. Acad. Sci. USA 91: 5474– 5479.
107. Hack, E. S.,, T. Vorobyova,, J. B. Sakash,, J. M. West,, C. P. Ma-col,, G. Herve,, M. K. Williams, and, E. R. Kantrowitz. 2000. Characterization of the aspartate transcarbamoylase from Methanococcus jannaschii. J. Biol. Chem. 275: 15820– 15827.
108. Hao, B.,, W. Gong,, T. K. Ferguson,, C. M. James,, J. A. Krzycki, and, M. K. Chan. 2002. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296: 1462– 1466.
109. Haseltine, C.,, R. Montalvo-Rodriguex,, E. Bini,, A. Carl, and, P. Blum. 1999. Coordinate transcriptional control in the hyperthermophilic archaeon Sulfolobus sol-fataricus. J. Bacteriol. 181: 3920– 3927.
110. Heinemeyer, W.,, M. Fischer,, T. Krimmer,, U. Stachon, and, D. H. Wolf. 1997. The active sites of the eukaryotic 20 S pro-teasome and their involvement in subunit precursor processing. J. Biol. Chem. 272: 25200– 25209.
111. Hensel, R., and, H. Konig. 1988. Thermoadaption of methanogenic bacteria by intracellular ion concentration. FEMS Microbiol. Lett. 49: 75– 79.
112. Hildebrand, E., and, N. Dencher. 1975. Two photosystems controlling behavioural responses of Halobacterium halobium. Nature 257: 46– 48.
113. Ho, Y. S. J.,, L. M. Burden, and, J. H. Hurley. 2000. Structure of AGF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. EMBO J. 19: 5288– 5299.
114. Hoch, J. A. 2000. Two-component and phosphorelay signal transduction. Curr. Opin. Microbiol. 3: 165– 170.
115. Hoff, W. D.,, K. H. Jung, and, J. L. Spudich. 1997. Molecular mechanism of photosignaling by archaeal sensory rhodopsins. Annu. Rev. Biophys. Biomol. Struct. 26: 223– 258.
116. Holden, J. F., and, J. A. Baross. 1993. Enhanced thermotoler-ance and temperature-induced changes in protein composition in the hyperthermophilic archaeon ES4. J. Bacteriol. 175: 2839– 2843.
117. Hou, S.,, A. Brooun,, H. S. Yu,, T. Freitas, and, M. Alam. 1998. Sensory rhodopsin II transducer HrtII is also responsible for serine chemotaxis in the archaeon Halobacterium salinarium. J. Bacteriol. 180: 1600– 1602.
118. Hou, S.,, R. W. Larsen,, D. Boudko,, C. W. Riley,, E. Karatan,, M. Zimmer,, G. W. Ordal, and, M. Alam. 2000. Myoglobinlike aerotaxis transducers in Archaea and Bacteria. Nature 403: 540– 544.
119. Hsing, W., and, T. J. Silhavy. 1997. Function of conserved his-tidine-243 in phosphatase activity of EnvZ, the sensor for porin osmoregulation in Escherichia coli. J. Bacteriol. 179: 3729– 3735.
120. Huffman, J. L.,, H. Li,, R. H. White, and, J. A. Tainer. 2003. Structural basis for recognition and catalysis by the bifunc-tional dCTP deaminase and dUTPase from Methanococcus jannaschii. J. Mol. Biol. 331: 885– 896.
121. Irvine, R. F. 2003. 20 years of Ins(1,4,5)P 3, and 40 years before. Nat. Rev. Mol. Cell Biol. 4: 586– 590.
122. Irving, J. A.,, P. J. M. Steenbakkers,, A. M. Lesk,, H. J. M. Op den Camp,, R. N. Pike, and, J. C. Whisstock. 2002. Serpins in prokaryotes. Mol. Biol. Evol. 19: 1881– 1890.
123. Izzo, V.,, E. Notomista,, A. Picardi,, F. Pennacchio, and, A. Di Donato. 2005. The thermophilic archaeon Sulfolobus solfataricus is able to grow on phenol. Res. Microbiol. 156: 677– 689.
124. Jager, A.,, R. Samorski,, F. Pfeifer, and, G. Klug. 2002. Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase. Nucleic Acids Res. 30: 5436– 5443.
125. Jansson, B. P. M.,, L. Malandrin, and, H. E. Johansson. 2000. Cell cycle arrest in Archaea by the hypusination inhibitor N 1-guanyl-1,7-diaminoheptane. J. Bacteriol. 182: 1158– 1161.
126. Jensen, K. F.,, S. Arent,, S. Larsen, and, L. Schack. 2005. Al-losteric properties of the GTP activated and CTP inhibited uracil phosphoibosyltransferase from the thermoacidophilic archaeon Sulfolobus sol-fataricus. FEBS J. 272: 1440– 1453.
127. Jensen, R. A.,, T. A. d’Amato, and, L. I. Hochstein. 1988. An extreme-halophilic archaebacterium possesses the interlock type of prephenate dehydratase characteristic of Gram-positive eubacteria. Arch. Microbiol. 148: 365– 371.
128. Jeon, S.-J.,, S. Fujiwara,, M. Takagi,, M. Tanaka, and, T. Imanaka. 2002. T&-PTP, a protein-tyrosine phosphatase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1: enzymatic characteristics and identification of its substrate proteins. Biochem. Biophys. Res. Commun. 295: 508– 514.
129. Jiang, Y.,, A. Lee,, J. Chen,, M. Cadene,, B. T. Chait, and, R. MacKinnon. 2002. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 30: 516– 522.
130. Jing, H.,, J. Takagi,, J. Liu,, S. Lindgren,, R. Zhang,, A. Joachimiak,, J. Wang, and, T. A. Springer. 2002. Archaeal surface layer proteins contain β propeller, PKD, and β helix domains and are related to metazoan cell surface proteins. Structure 10: 1453– 1464.
131. Johnson, M. R.,, C. I. Montero,, S. B. Conners,, K. R. Shockley,, S. L. Bridger, and, R. M. Kelly. 2005. Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritime. Mol. Microbiol. 55: 664– 674.
132. Jones, J. B.,, G. L. Dilworth, and, T. C. Stadtman. 1979. Occurrence of selenocysteine in the selenium-dependent formate dehydrogenase of Methanococcus vannielii. Arch. Biochem. Biophys. 195: 255– 260.
133. Kaidoh, K.,, S. Miyauchi,, A. Abe,, S. Tanabu,, T. Nara, and, N. Kamo. 1996. Rhodamine 123 efflux transporter in Haloferax volcanii is induced when cultured under ’metabolic stress’ by amino acids: the efflux system resembles that in a doxorubicin-resistant mutant. Biochem. J. 314: 355– 359.
134. Kappler, U.,, I. Lindsay, and, A. G. McEwan. 2005. Respiratory gene clusters of Metallosphaera sedula—differential expression and transcriptional organization. Microbiology. 151: 35– 43.
135. Karras, G. I.,, G. Kustatscher,, H. R. Buhecha,, M. D. Allen,, C. Pugieux,, F. Sait,, M. Bycroft, and, A. G. Ladurner. 2005. The macro domain is an ADP-ribose binding module. EMBO J. 24: 1911– 1920.
136. Kennelly, P. J. 2001. Protein phosphatases: a phylogenetic perspective. Chem. Rev. 101: 2291– 2312.
137. Kennelly, P. J. 2002. Protein kinases and protein phosphatases in prokaryotes: A genomic perspective. FEMS Microbiol. Lett. 206: 1– 8.
138. Kennelly, P. J. 2003. Archaeal protein kinases and protein phosphatases—insights from genomics and biochemistry. Biochem. J. 370: 373– 389.
139. Kessel, M., and, F. Klink. 1980. Archaebacterial elongation factor is ADP-ribosylated by diphtheria toxin. Nature 287: 250– 251.
140. Kessler, P. S., and, J. A. Leigh. 1999. Genetics of nitrogen regulation in Methanococcus maripaludis. Genetics 152: 1343– 1351.
141. Khristich, C. J., and, G. W. Ordal. Bacillus subtilis CheD is a chemorecpetoor modification enzyme required for chemotaxiis. J. Biol. Chem. 277: 25356– 25362.
142. Kim, D.-J., and, S. Forst. 2001. Genomic analysis of the histi-dine kinase superfamily in bacteria and archaea. Microbiology 147: 1197– 1212.
143. Kim, A. D.,, D. E. Graham,, S. H. Seeholzer, and, G. D. Markham. 2000. S-Adenosylmethionine decarboxylase from the archaeon Methanococcus jannaschii: Identification of a novel family of pyruvoyl enzymes. J. Bacteriol. 182: 6667– 6672.
144. Kim, S., and, S. B. Lee. 2005. Identification and characterization of Sulfolobus sol-fataricus D-gluconate dehydratase: a key enzyme in the non-phosphorylated Entner-Doudoroff pathway. Biochem. J. 387: 271– 280.
145. Kim, J. W.,, H. A. Terc,, L. O. Flowers,, M. Whiteley, and, T. L. Peeples. 2001. Novel, thermostable family-13-like glycoside hydrolase from Methanococcus jannaschii. Folia Microbiol. 46: 475– 481.
146. Kirby, J. R.,, C. J. Khristich,, M. M. Saulmon,, M. A. Zimmer,, L. F. Garriity,, I. B. Zhulin, and, G. W. Ordal. 2001. CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. Mol. Microbiol. 42: 573– 585.
147. Kloda, A., and, B. Martinac. 2001. Structural and functional differences between two homologous mechanosensitive channels of Methanococcus jannaschii. EMBO J. 20: 1888– 1896.
148. Kloda, A., and, B. Martinac. 2001. Mechanosensitive channel of Thermoplasma, the cell wall-less Archaea: Cloning and molecular characterization. Cell Biochem. Biophys. 34: 321– 347.
149. Kloda, A., and, B. Martinac. 2002. Common evolutionary origins of mechanosensitive ion channels in Archaea, Bacteria and cell-walled Eukaraya. Archaea 1: 35– 44.
150. Klussmann, S.,, P. Franke,, U. Bergmann,, S. Kostka, and, B. Wittmann-Liebold. 1993. N-Terminal modification and amino-acid sequence of the ribosomal protein HmaS7 from Haloarcula marismortui and homology studies to other ribosomal proteins. Biol. Chem. Hoppe-Seyler 374: 305– 312.
151. Knapp, S.,, A. Karshikoff,, K. D. Berndt,, P. Christova,, B. Atanasov, and, R. Ladenstein. 1996. Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus sol-fataricus. J. Mol. Biol. 264: 1132– 1144.
152. Koch, M. K., and, D. Oesterhelt. 2005. MpcT is the transducer for membrane potential changes in Halobacterium sali-narium. Mol. Microbiol. 55: 1681– 1694.
153. Kokoeva, M. V., and, D. Oesterhelt. 2000. BasT, a membrane-bound transducer protein for amino acid detection in Halobacterium salinarium. Mol. Microbiol. 35: 647– 656.
154. Kokoeva, M. V.,, K. F. Storch,, C. Klein, and, D. Oesterhelt. 2002. A novel mode of sensory transduction in Archaea: binding protein-mediated chemotaxis towards osmoprotectants and amino acids. EMBO J. 21: 2312– 2322.
155. Koonin, E. V.,, K. S. Makarova,, I. B. Rogozin,, L. Davidovic,, M. C. Letellier, and, L. Pellegrini. 2003. The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Genome Biol. 4: R19.1- R19.12.
156. Koretke, K. K.,, A. N. Lupas,, P. V. Warren,, M. Rosenberg, and, J. R. Brown. 2000. Evolution of the two-component regulatory system. Mol. Biol. Evol. 17: 1956– 1970.
157. Krzycki, J. A. 2005. The direct genetic encoding of pyrrolysine. Curr. Opin. Microbiol. 8: 706– 712.
158. Kuo, M. M.-C,, W. J. Haynes,, S. H. Loukin,, C. Kung, and, Y. Saimi. 2005. Prokaryotic K + channels: from crystal structures to diversity. FEMS Microbiol. Rev. 29: 961– 985.
159. Kuo, Y. P.,, D. K. Thompson,, A. St. Jean,, R. L. Charlebois, and, C. J. Daniels. 1977. Characterization of two heat shock genes from Haloferax volcanii: A model system for transcription regulation in the Archaea. J. Bacteriol. 179: 6318– 6324.
160. Labedan, B.,, A. Boyen,, M. Baetens,, D. Charlier,, P. Chen,, R. Cunin,, V. Durbeco,, N. Glansdorff,, G. Herv,, C. Legrain,, Z. Liang,, C. Purcarea,, M. Roovers,, R. Sanchez,, T. L. Toong,, M. Van de Casteel,, F. van Vliet,, Y. Xu, and, Y. F. Zhang. 1999. The evolutionary history of carbamoyltransferases: a complex set of paralogous genes was already present in the last universal common ancestor. J Mol Evol. 49: 461– 473.
161. Labedan, B.,, Y. Xu,, D. G. Naumoff, and, N. Glansdorff. 2003. Using quaternary structures to assess the evolutionary history of proteins: the case of the aspartate carbamoyltransferase. Mol. Biol. Evol. 21: 364– 373.
162. Lai, M. C.,, D. R. Yang, and, M. J. Chuang. 1999. Regulatory factors associated with synthesis of the osmolyte glycine betaine in the halophilic methanoarchaeon Methanohalophilus portucalensis. Appl. Environ. Microbiol. 65: 828– 833.
163. Lai, X.,, H. Shao,, F. Hao, and, L. Haung. 2002. Biochemical characterization of an ATP-dependent DNA ligase from the hyperthermophilic crenarchaeon Sulfolobus shibatae. Extremophiles 6: 469– 477.
164. Lam, W. L.,, S. M. Logan, and, W. F. Doolittle. 1992. Genes for tryptophan Biosynthesis in the halophilic archaebacterium Haloferax volcanii: The trpDFEG cluster. J. Bacteriol. 174: 1694– 1697.
165. Lange, M.,, T. Tolker-Nielsen,, S. Molin, and, B. K. Ahring. 2000. In situ reverse transcription-PCR for monitoring gene expression in individual Methanosarcina mazei S-6 cells. Appl. Environ. Microbiol. 66: 1796– 1800.
166. LaPaglia, C., and, P. L. Hartzell. 1997. Stress-induced production of biofilm in the hyperthermophile Archaeoglobus fulgidus. Appl. Environ. Microbiol. 63: 3158– 3163.
167. LaRonde-LaBlanc, N., and, A. Wlodawer. 2004. Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases. Structure 12: 1585– 1594.
168. LaRonde-LeBlanc, N.,, T. Guszczynski,, T. Copeland, and, A. Wlodawer. 2005. Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes. FEBS J. 272: 2800– 2810.
169. LaRonde-LeBlanc, N.,, T. Guszczynski,, T. Copeland, and, A. Wlodawer. 2005. Structure and activity of the atypical serine kinase Rio1. FEBS J. 272: 3698– 3713.
170. LaRonde-LeBlanc, N., and, A. Wlodawer. 2005. A family portrait of the RIO kinases. J. Biol. Chem. 280: 37297– 37300.
171. LaRonde-LeBlanc, N., and, A. Wlodawer. 2005. The RIO kinases: An atypical protein kinase family required for ribo-some biogenesis and cell cylce progression. Biochim. Biophys. Acta 1754: 14– 24.
172. Le Dain, A. C.,, N. Saint,, A. Kloda,, A. Ghazi, and, B. Martinac. 1998. Mechanosensitive ion channels of the archaeon Haloferax volcanii. J. Biol. Chem. 273: 12116– 12119.
173. Lee, C. H.,, J. W. Jung,, A. Yee,, C. H. Arrowsmith, and, W. Lee. 2004. Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum. Protein Sci. 13: 1148– 1154.
174. Lee, M. S.,, W. A. Joo, and, C. W. Kim. 2004. Identification of a novel protein D3UPCA from Halobacterium salinarum and prediction of its function, Proteomics 4: 3622– 3631.
175. Leichtling, B. H.,, H. V. Rickenberg,, R. J. Seely,, D. E. Fahrney, and, N. R. Pace. 1986. The occurrence of cyclic AMP in Archaebacteria. Biochem. Biophys. Res. Commun. 136: 1078– 1082.
176. Leigh, J. A. 2000. Nitrogen fixation in methanogens: The archaeal perspective. Curr. Issues Mol. Biol. 2: 125– 131.
177. Lemker, T.,, G. Gruber,, R. Schmid, and, V. Muller. 2003. Defined subcomplexes of the A 1 ATPase from the archaeon Methanosarcina mazei Gö1: biochemical properties and re-dox regulation. FEBS Lett. 544: 206– 209.
178. Leng, J.,, A. J. Cameron,, S. Buckel, and, P. J. Kennelly. 1995. Isolation and cloning of a protein-serine/threonine phos-phatase from an archaeon. J. Bacteriol. 177: 6510– 6517.
179. Leonard, C. J.,, L. Aravind, and, E. V. Koonin. 1998. Novel families of putative protein kinases in Bacteria and Archaea: evolution of the ’eukaryotic’ protein kinase superfamily. Genome Res. 8: 1038– 1047.
180. Li, H.,, H. Xu,, D. E. Graham, and, R. H. White. 2003. The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase. J. Biol. Chem. 278: 11100– 11106.
181. Li, R.,, M. B. Potters,, L. Shi, and, P. J. Kennelly. 2005. The protein phosphatases of Synechocystis sp. strain PCC6803: Open reading frames sll1033 and sll1387 encode enzymes that exhibit both protein-serine and protein-tyrosine phosphatase activity in vitro. J. Bacteriol. 187: 5877– 5884.
182. Lie, T. J., and, J. A. Leigh. 2002. Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source. J. Bacteriol. 184: 5301– 5306.
183. Lindbeck, J. C.,, E. A. Goulbourne, Jr.,, M. S. Johnson, and, B. L. Taylor. 1995. Aerotaxis in Halobacterium salinarium is methylation-dependent. Microbiology 141: 2945– 2953.
184. Lipscomb, W. N. 1994. Aspartate transcarbamylase from Escherichia coli: activity and regulation. Adv. Enzymol. Relat. Areas Mol. Biol. 68: 67– 151.
185. Lobo, A. L., and, S. H. Zinder. 1990. Nitrogenase in the ar-chaebacterium Methanosarcina barkeri 227. J. Bacteriol. 172: 6789– 6796.
186. Lopalco, P.,, S. Lobasso,, F. Babudri, and, A. Corcelli. 2004. Osmotic shock stimulates de novo synthesis of two cardiolipins in an extreme halophilic archaeon. J. Lipid Res. 45: 194– 201.
187. Lorentzen, E.,, R. Hensel,, T. Knura,, H. Ahmed, and, E. Pohl. 2004. Structural basis of allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde 3-phos-phate dehydrogenase from Thermoproteus tenax. J. Mol. Biol. 341: 815– 828.
188. Lower, B. H.,, K. M. Bischoff, and, P. J. Kennelly. 2000. The archaeon Sulfolobus sol-fataricus contains a membrane-associated protein kinase that preferentially phosphorylates thre-onine residues. J. Bacteriol. 182: 3452– 3459.
189. Lower, B. H., and, P. J. Kennelly. 2002. The membrane-associated protein-serine/threonine kinase from Sulfolobus sol-fataricus is a glycoprotein. J. Bacteriol. 184: 2614– 2619.
190. Lower, B. H., and, P. J. Kennelly. 2003. Open reading frame sso2387 from the archaeon Sulfolobus sol-fataricus encodes a polypeptide with protein-serine kinase activity. J. Bacteriol. 185: 3436– 3445.
191. Lower, B. H.,, M. B. Potters, and, P. J. Kennelly. 2004. A phos-phoprotein from the archaeon Sulfolobus sol-fataricus with protein-serine kinase activity. J. Bacteriol. 186: 463– 472.
192. Lundback, T.,, H. Hansson,, S. Knapp,, R. Ladenstein, and, T. Hard. 1998. Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus sol-fataricus. J. Mol. Biol. 276: 775– 786.
193. Luo, H. W.,, H. Zhang,, T. Suzuki,, S. Hattori, and, Y. Kama-gata. 2002. Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs. Appl. Environ. Microbiol. 68: 1173– 1179.
194. Ma, K.,, H. Loessner,, J. Heider,, M. K. Johnson, and, M. W. W. Adams. 1995. Effects of elemental sulfur on the metabolism of the deep-sea hyperthermophilic archaeon Thermococcus strain ES-1: Characterization of a sulfur-regulated, non-heme iron alcohol dehydrogenase. J. Bacteriol. 177: 4748– 4756.
195. Mai, B.,, G. Frey,, R. V. Swanson,, E. J. Mathur, and, K. O. Stetter. 1998. Molecular cloning and functional expression of a protein-serine/threonine phosphatase from the hyperthermophilic archaeon Pyrodictium abyssi TAG11. J. Bacteriol. 180: 4030– 4035.
196. Manning, G.,, G. D. Plowman,, T. Hunter, and, S. Sudarsanam. 2002. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27: 514– 520.
197. Manning, G.,, D. B. Whyte,, R. Martinez,, T. Hunter, and, S. Sudarsanam. 2002. The protein kinase complement of the human kinase. Science 298: 1912– 1934.
198. Manzur, K. L., and, M. M. Zhou. 2005. An archaeal SET domain protein exhibits distinct lysine methyltransferase activity towards DNA-associated protein MC1-a. FEBS Lett. 579: 3859– 3865.
199. Maras, B.,, V. Consalvi,, R. Chiaraluce,, L. Politi,, M. De Rosa,, F. Bossa,, R. Scandurra, and, D. Barra. 1992. The protein sequence of glutamate dehydrogenase from Sulfolobus sol-fataricus, a thermoacidophilic archaebacterium. Eur. J. Biochem. 203: 81– 87.
200. Marsh, V. L.,, S. Y. Peak-Chew, and, S. D. Bell. 2005. Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba. J. Biol. Chem. 280: 21122– 21128.
201. Marteinsson, V. T.,, A. L. Reysenbach,, J. L. Birrien, and, D. Prieur. 1999. A stress protein is induced in the deep-sea barophilic hyperthermophile Thermoccocus barophilus when grown under atmospheric pressure. Extremophiles 3: 277– 282.
202. Martin, D. D.,, R. A. Ciulla,, P. M. Robinson, and, M. R. Roberts. 2000. Switching osmolyte strategies: response of Methanococcus thermolithotrophicus to changes in external NaC1. Biochim. Biophys. Acta 1524: 1– 10.
203. Martins, L. O., and, H. Santos. 1995. Accumulation of man-nosylglycerate and di-myo-inositol-phosphate by Pyrococcus furiosus in response to salinity and temperature. Appl. Environ. Microbiol. 61: 3299– 3303.
204. Martins, L. O.,, R. Huber,, H. Huber,, K. O. Stetter,, M. S. Da Costa, and, H. Santos. 1997. Organic solutes in hyperthermophilic Archaea. Appl. Environ. Microbiol. 63: 896– 902.
205. Marwan, W.,, S. I. Bibikov,, M. Montrone, and, D. Oesterhelt. 1995. Mechanism of photosensory adaptation in Halobacterium salinarium. J. Mol. Biol. 246: 493– 499.
206. Marwan, W.,, W. Schafer, and, D. Oesterhelt. 1990. Signal transduction in Halobacterium depends on fumarate. EMBO J. 9: 355– 362.
207. Matsubara, M., and, T. Mizuno. 2000. The SixA phospho-his-tidine phosphatase modulates the ArcB phosphorelay signal transduction in Escherichia coli. FEBS Lett. 470: 118– 124.
208. Mattar, S.,, B. Scharf,, S. B. H. Kent,, K. Rodewald,, D. Oesterhelt, and, M. Engelhard. 1994. The primary structure of halo-cyanin, and archaeal blue copper protein, predicts a lipid anchor for membrane fixation. J. Biol. Chem. 269: 14939– 14945.
209. Michiels, J.,, C. Xi,, J. Verhaert, and, J. Vanderleyden. 2002. The Functions of Ca 2+ in bacteria: a role for EF-hand proteins? Trends Microbiol. 10: 87– 93.
210. Mojica, F. J. M.,, E. Cisneros,, C. Ferrer,, F. Rodriguez-Valera, and, G. Juez. 1997. Osmotically induced response in representatives of halophilic prokaryotes: The bacterium Halo-monas elongata and the archaeon Haloferax volcanii. J. Bacteriol. 179: 5471– 5481.
211. Montrone, M.,, W. Marwan,, H. Grunberg,, S. Mubeleck,, C. Starostzik, and, D. Oesterhelt. 1993. Sensory rhodopsin-con-trolled release of the switch factor fumarate in Halobacterium salinarium. Mol. Microbiol. 10: 1077– 1085.
212. Montrone, M.,, D. Oesterhelt, and, W. Marwan. 1996. Phos-phorylation-independent bacterial chemoresponses correlate with changes in the cytoplasmic level of fumarate. J. Bacteriol. 178: 6882– 6887.
213. Morona, J. K.,, R. Morona,, D. C. Miller, and, J. C. Paton. 2002. Streptococcus pneumoniae capsule biosynthesis protein CpsB is a novel manganese-dependent phosphotyrosine-protein phosphatase. J. Bacteriol. 184: 577– 583.
214. Mougel, C, and, I. B. Zhulin. 2001. CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem. Sci. 26: 582– 584.
215. Nauhaus, K.,, T. Treude,, A. Boetius, and, M. Kruger. 2005. Environmental regulation of the anaerobic oxidation of methane: A comparison of ANME-I and ANME-II communities. Environ. Microbiol. 7: 98– 106.
216. Neelon, K.,, Y. Wang,, B. Stec, and, M. F. Roberts. 2005. Probing the mechanism of the Archaeoglobus fulgidus inositol-1-phospate synthase, J. Biol. Chem. 280: 11475– 11482.
217. Nercessian, D.,, R. E. De Castro, and, R. D. Conde. 2002. Ubiquitin-like proteins in halobacteria. J. Basic Microbiol. 42: 277– 283.
218. Ninfa, A. J., and, P. Jiang. 2005. PII signal transduction proteins: sensors of a-ketoglutarate that regulate nitrogen metabolism. Curr. Opin. Microbiol. 8: 168– 173.
219. Norberg, P.,, J. G. Kaplan, and, D. J. Kushner. 1973. Kinetics and regulation of the salt-dependent aspartate transcarbamy-lase of Halobacterium cutirubrum, J. Bacteriol. 113: 680– 686.
220. Oppermann, U. C. T,, S. Knapp,, V. Bonetto,, R. Ladenstein, and, H. Jornvall. 1998. Isolation and structure of repressor-like proteins from the archaeon Sulfolobus sol-fataricus. FEBS Lett. 432: 141– 144.
221. Overmann, J., and, K. Schubert. 2002. Phototrophic consortia: Model systems for symbiotic interrelations between prokaryotes. Arch. Microbiol. 177: 201– 208.
222. Paggi, R. A.,, C. B. Martone,, C. Fuqua, and, R. E. De Castro. 2003. Detection of quorum sensing signals in the haloalkaliphilic archaeon Natronococcus occultus. FEMS Microbiol. Lett. 221: 49– 52.
223. Pappenheimer, A. M. Jr.,, P. C. Dunlop,, K. W. Adolph, and, J. W. Bodley. 1983. Occurrence of diphthamide in archaebacteria. J. Bacteriol. 153: 1342– 1347.
224. Pardee, A. B., and, G. P.-V. Reddy. 2003. Beginning of feedback inhibition, allostery, and multi-protein complexes. Gene 321: 17– 23.
225. Parkinson, J. S. 2003. Bacterial chemotaxis: a new player in response regulator dephosphorylation. J. Bacteriol. 185: 1492– 1494.
226. Peeples, T. L., and, R. M. Kelly. 1995. Bioenergetic response of the extreme thermoacidophile Metallosphaera sedula to thermal and nutritional stresses. Appl. Environ. Microbiol. 61: 2314– 2321.
227. Pei, J., and, N. V. Grishin. 2001. GGDEF domain is homologous to adenylyl cyclase. Proteins: Struct. Funct. Genet. 42: 210– 216.
228. Perazzona, B., and, J. L. Spudich. 1999. Identification of methylation sites and effects of phototaxis stimuli on transducer methylation in Halobacterium salinarium. J. Bacteriol. 181: 5676– 5683.
229. Perraud, A.-L.,, V. Weiss, and, R. Gross. 1999. Signballing pathways in two-component phosphorelay systems. Trends Microbiol. 7: 115– 120.
230. Pfeifer, F.,, D. Gregor,, A. Hofacker,, P. Plosser, and, P. Zimmermann. 2002. Regulation of gas vesicle formation in halophilic Archaea. J. Mol. Microbiol. Biotechnol. 4: 175– 181.
231. Pfluger, K.,, S. Baumann,, G. Gottschalk,, W. Lin,, H. Santos, and, V. Muller. 2003. Lysine-2,3-aminomutase and β-lysine acetyltransferase genes of methanogenic Archaea are salt induced and are essential for the biosynthesis of N ε-acetyl-β-lysine and growth at high salinity. Appl. Environ. Microbiol. 69: 6047– 6055.
232. Phipps, B. M.,, A. Hoffmann,, K. O. Stetter, and, W. Baumeister. 1991. A novel ATPase complex selectively accumulated upon heat shock is a major cellular component of thermophilic archaebacteria. EMBO J. 10: 1711– 1722.
233. Ponting, C. P.,, L. Aravind,, J. Schultz,, P. Bork, and, E. V. Koonin. 1999. Eukaryotic signaling domain homologues in Archaea and Bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289: 729– 745.
234. Porat, I.,, B. W. Waters,, Q. Teng, and, W. B. Whitman. 2004. Two biosynthetic pathways for aromatic amino acids in the archaeon Methanococcus maripaludis. J. Bacteriol. 186: 4940– 4950.
235. Purcarea, C,, G. Herve,, M. M. Ladjimi, and, R. Cunin. 1997. Aspartate transcarbamylase from the deep-sea hyperthermophilic archaeon Pyrococcus abyssi: genetic organization, structure, and expression in Escherichia coli. J. Bacteriol. 179: 4143– 4157.
236. Rashid, N.,, J. Cornista,, S. Ezaki,, T. Fukui,, H. Atomi, and, T. Imanaka. 2002. Characterization of an archaeal cyclodex-trin glucanotransferase with a novel C-terminal domain. J. Bacteriol. 184: 777– 784.
237. Ray, W. K.,, S. M. Keith,, A. M. DeSantis,, J. P. Hunt,, T. J. Larson,, R. F. Helm, and, P. J. Kennelly. 2005. A phosphohexo-mutase from the archaeon Sulfolobus sol-fataricus is covalently modified by phosphorylation on serine. J. Bacteriol. 187: 4270– 4275.
238. Reizer, J.,, A. Reizer,, M. Perego, and, M. H. Saier, Jr. 1997. Characterization of a family of bacterial response regulator aspartyl-phosphate (RAP) phosphatases. Microb. Comp. Genomics 2: 103– 111.
239. Reuter, C. J.,, S. J. Kaczowka, and, J. A. Maupin-Furlow. 2004. Differential regulation of the PanA and PanB protea-some-activating nucleotidase and 20S proteasomal proteins of the haloarchaeon Haloferax volcanii. J. Bacteriol. 186: 7763– 7772.
240. Riera, J.,, F. T. Robb,, R. Weiss, and, M. Fontecave. 1997. Ri-bonucleotide reductase in the archaeon Pyrococcus furiosus: A critical enzyme in the evolution of DNA genomes? Proc. Natl. Acad. Sci. USA 94: 475– 478.
241. Rigden, K. J. and, M. Y. Galperin. 2004. The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution. J. Mol. Biol. 343: 971– 984.
242. Roberts, T. H.,, J. Hejgaard,, N. F. W. Saunders,, R. Cavicchi-oli, and, P. J. G. Curmi. 2004. Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J. Mol. Evol. 59: 437– 447.
243. Robertson, D. E.,, M. Lai,, R. P. Gunsalus, and, M. F. Roberts. 1992. Composition, variation, and dynamics of major osmotic solutes in Methanohalophilus strain FDF1. Appl. Environ. Microbiol. 58: 2438– 2443.
244. Rohlin, L.,, J. D. Trent,, K. Salmon,, U. Kim,, R. P. Gunsalus, and, J. C. Liao. 2005. Heat shock response of Archaeoglobus fulgidus. J. Bacteriol. 187: 6046– 6057.
245. Roosild, T. P.,, S. Miller,, I. R. Booth, and, S. Choe. 2002. A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch. Cell 109: 781– 791.
246. Rotharmel, T, and, G. Wagner. 1995. Isolation and characterization of a calmodulin-like protein from Halobacterium salinarium. J. Bacteriol. 177: 864– 866.
247. Rother, M.,, P. Boccazzi,, A. Bose,, M. A. Pritchett, and, W. W. Metcalf. 2005. Methanol-dependent gene expression demonstrates that methyl-coenzyme M reductase is essential for Methanosarcina acetivorans C2A and allows isolation of mutants with defects in regulation of the methanol utilization pathway. J. Bacteriol. 187: 5552– 5559.
248. Rudiger, A.,, P. L. Jorgensen, and, G. Antranikian. 1995. Isolation and characterization of a heat-stable pullulanase from the hyperthermophilic archaeon Pyrococcus woesei after cloning and expression of its gene in Escherichia coli. Appl. Environ. Microbiol. 61: 567– 575.
249. Rudolph, J., and, D. Oesterhelt. 1995. Chemotaxis and phototaxis require a CheA histidine kinase in the archaeon Halobacterium salinarium. EMBO J. 14: 667– 673.
250. Rudolph, J., and, D. Oesterhelt. 1996. Deletion analysis of the che operon in the archaeon Halobacterium salinarium. J. Mol. Biol. 258: 548– 554.
251. Rudolph, J.,, N. Tolliday,, C. Schmitt,, S. C. Schuster, and, D. Oesterhelt. 1995. Phosphorylation in halobacterial signal transduction. EMBO J. 14: 4249– 4257.
252. Ruppert, U.,, A. Irmler,, N. Kloft, and, K. Forchhammer. 2002. The novel protein phosphatase PphA from Synechocystis PCC 6803 controls dephosphorylation of the signaling protein PII. Mol. Microbiol. 44: 855– 864.
253. Ruta, V., and, R. MacKinnon. 2004. Localization of the voltage-sensor toxin receptor on KvAP. Biochemistry 43: 10071– 10079.
254. Ruta, V.,, Y. Jiang,, A. Lee,, J. Chen, and, R. MacKinnon. 2003. Functional analysis of an archaebacterial voltage-dependent K + channel. Nature 422: 180– 185.
255. Sako, Y.,, K. Takai,, A. Uchida, and, Y. Ishida. 1996. Purification and characterization of phosphoenolpyruvate carboxy-lase from the hyperthermophilic archaeon Methanothermus sociabilis. FEBS Lett. 392: 148– 152.
256. Sako, Y.,, K. Takai,, T. Nishizaka, and, Y. Ishida. 1997. Biochemical relationship of phosphoenolpyruvate carboxylases (PEPCs) from the thermophilic Archaea. FEMS Microbiol. Lett. 153: 159– 165.
257. Salerno, V.,, A. Napoli,, M. F. White,, M. Rossi, and, M. Ciaramella. 2003. Transcriptional response to DNA damage in the archaeon Sulfolobus sol-fataricus. Nucleic Acids Res. 31: 6127– 6138.
258. Savchenko, A.,, C. Vieille,, S. Kang, and, J. G. Zeikus. 2002. Pyrococcus furiosus a-amylase is stabilized by calcium and zinc. Biochemistry 41: 6193– 6201.
259. Scharf, B., and, E. K. Wolff. 1994. Phototactic behavior of the archaebacterial Natronobacterium pharaonis. FEBS Lett. 340: 114– 116.
260. Schmiz, A. 1981. Methylation of membrane proteins is involved in chemosensory and photosensory behavior in Halobacterium halobium. FEBS Lett. 125: 205– 207.
261. Schmiz, A., and, E. Hildebrand. 1979. Chemosensory responses of Halobacterium halobium. J. Bacteriol. 140: 749– 753.
262. Schofield, L. R.,, M. L. Patchett, and, E. B. Parker. 2003. Expression, purification, and characterization of 3-deoxy-D- ara-bm o-heptulosonate 7-phosphate synthase from Pyrococcus furiosus. Protein Expr. Purif 34: 17– 27.
263. Schut, G. J.,, S. D. Brehm,, S. Datta, and, M. W. W. Adams. 2003. Whole-genome DNA microarray analysis of a hyper-thermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J. Bacteriol. 185: 3935– 3947.
264. Selmer, T,, J. Kahnt,, M. Goubeaud,, S. Shima,, W. Grabarse,, U. Ermler, and, R. K. Thauer. 2000. The biosynthesis of methylated amino acids in the active site region of methyl-coenzyme M reductase. J. Biol. Chem. 275: 3755– 3760.
265. Sesti, F.,, S. Rajan,, R. Gonzalez-Colsao,, N. Nikolaeva, and, S. A. N. Goldstein. Hyperpolarization moves S$ sensors inward to open MVP, a methanococcal voltage-gated potassium channel. Nat. Neurosci. 6: 353– 361.
266. Sham, S.,, L. Calzolai,, P. L. Wang,, K. Bren,, H. Haarklau,, P. S. Brereton,, M. W. W. Adams, and, G. N. La Mar. 2002. A solution NMR molecular model for the aspartate-ligated, cubane cluster containing ferredoxin from the hyperthermophilic archeaon Pyrococcus furiosus. Biochemistry 41: 12498– 12508.
267. Shenoy, A. R., and, S. S. Visweswariah. 2004. Class III nucleotide cyclases in bacteria and archaebacteria: Lineage-specific expansion of adenylyl cyclases and a dearth of guanylyl cyclases. FEBS Lett. 561: 11– 21.
268. Shi, L.,, M. Potts, and, P. J. Kennelly. 1998. The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait. FEMS Microbiol. Rev. 22: 229– 253.
269. Shockley, K. R.,, D. E. Ward,, S. R. Chhabra,, S. B. Conners,, C. I. Montero, and, R. M. Kelly. 2003. Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl. Environ. Microbiol. 69: 2365– 2371.
270. Skarphol, K.,, J. Waukau, and, S. A. Forst. 1997. Role of His243 in thhe phosphatase activity of EnvZ in Escherichia coli. J. Bacteriol. 179: 1413– 1416.
271. Sment, K. A., and, J. Konisky. 1989. Chemotaxis in the archaebacterium Methanococcus voltae. J. Bacteriol. 171: 2870– 2872.
272. Smith, R. J. 1995. Calcium and bacteria. Adv. Microb. Physiol. 37: 83– 133.
273. Soares, J. A.,, L. Zhang,, R. L. Pitsch,, N. M. Kleinholz,, R. B. Jones,, J. J. Wolff,, J. Amster,, K. B. Green-Church, and, J. A. Krzycki. 2005. The residue mass of L-pyrrolysine in three distinct methylamine methyltransferases. J. Biol. Chem. 280: 36962– 36969.
274. Solow, B.,, J. C. Young, and, P. J. Kennelly. 1997. Gene cloning and expression and characterization of a toxin-sensitive protein phosphatase from the methanogenic archaeon Methanosarcina thermophila TM-1. J. Bacteriol. 179: 5072– 5075.
275. Sowers, K. R., and, R. P. Gunsalus. 1995. Halotolerance in Methanosarcina spp.: role of N ε-acetyl-β-lysine, α-glutamate, glycine betaine, and K + as compatible solutes for osmotic adaptation. Appl. Environ. Microbiol. 61: 4382– 4388.
276. Spreter, T,, M. Pech, and, B. Beatrix. 2005. The crystal structure of archaeal nascent polypeptide-associated complex (NAC) reveals a unique fold and the presence of a ubiquitin-associated domain. J. Biol. Chem. 280: 15849– 15854.
277. Spudich, E. N., and, J. L. Spudich. 1981. Photosensitive phosphoproteins in halobacteria: Regulatory coupling of transmembrane proton flux and protein dephosphorylation. J. Cell Biol. 91: 895– 900.
278. Spudich, J. L., and, W. Stoeckenius. 1979. Photosensory and chemosensory behavior of Halobacterium halobium. Photo-biochem. Photobiophys. 1: 43– 53.
279. Spudich, J. L., and, W. Stoeckenius. 1980. Light-mediated retinal-dependent reversible phosphorylation of Halobacterium proteins. J. Biol. Chem. 255: 5501– 5503.
280. Spudich, E. N.,, T. Takahashi, and, J. L. Spudich. 1989. Sensory rhodopsins I and II modulate the methylation/demethy-lation system in Halobacterium halobium phototaxis. Proc. Natl. Acad. Sci. USA 86: 7746– 7750.
281. Stan-Lotter, H.,, E. Doppler,, M. Jarosch,, C. Radax,, C. Gruber, and, K. Inatomi. 1999. Isolation of a chymotrypsinogen B-like enzyme from the archaeon Natronomonas pharaonis and other halobacteria. Extremophiles 3: 153– 161.
282. Stieglitz, K. A.,, B. A. Seaton,, J. F. Head,, B. Stec, and, M. F. Roberts. 2003. Unexpected similarity in regulation between an archaeal inositol monophosphatase/fructose bisphos-phatase and chloroplast fructose bisphosphatase. Protein Sci. 12: 760– 767.
283. Stock, J., and, S. De Re. 2000. Signal transduction: Response regulators on and off. Curr. Biol. 10: R420- R424.
284. Stock, A. M.,, V. L. Robinson, and, P. N. Goudreau. 2000. Two-component signal transduction. Annu. Rev. Biochem. 69: 182– 215.