A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099 T

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Siddaramappa, Shivakumara ^a   Challacombe, Jean F ^a   DeCastro, Rosana E ^b   Pfeiffer, Friedhelm ^c   Sastre, Diego E ^b   Giménez, María I ^b   Paggi, Roberto A ^b   Detter, John C ^a   Davenport, Karen W ^a   Goodwin, Lynne A ^a   Kyrpides, Nikos ^d   Tapia, Roxanne ^a   Pitluck, Samuel ^d   Lucas, Susan ^d   Woyke, Tanja ^d   Maupin Furlow, Julie A ^e  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSIDAD NACIONAL DE MAR DEL PLATA   (Argentina)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^d DOE JOINT GENOME INSTITUTE   (United States)

^e UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; COBALAMIN; COENZYME F420; CYTOCHROME; ENZYME; HEME; PEPTIDASE; PEPTIDE; POLYSACCHARIDE; PROTEINASE; PROTON; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RIBOFLAVIN; THIAMINE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN;

AEROBIC METABOLISM; ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL SURVIVAL; BIOSYNTHESIS; CARBOHYDRATE SYNTHESIS; CHEMOTAXIS; CONTROLLED STUDY; ELECTRON TRANSPORT; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOMICS; GLYCOSYLATION; METABOLIC STRESS; NATRIALBA MAGADII; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOTAXIS; PROTEIN SECRETION; REPLICON; SALINITY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; ARCHAEAL GENOME; CHROMOSOME; CHROMOSOME MAP; COENZYME; COMPARATIVE STUDY; GENETICS; HALOBACTERIALES; METABOLISM;

ARCHAEAL PROTEINS; CHROMOSOME MAPPING; CHROMOSOMES, ARCHAEAL; COENZYMES; GENOME, ARCHAEAL; GENOMICS; HALOBACTERIACEAE;

EID: 84860504598     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-165     Document Type: Article

References (131)

1. Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008, 36:6688-6719. 10.1093/nar/gkn668, 2588523, 18948295.
2. Gross ST. Introduction to Archaea. Practical Handbook of Microbiology 2009, 663-674. CRC Press, Taylor & Francis Group, LLC, Boca Raton, FL, Goldman E, Green LH, 2.
3. Ventosa A. Unusual micro-organisms from unusual habitats: hypersaline environments. Prokaryotic Diversity: Mechanisms and Significance 2006, 223-254. Cambridge University Press, New York, Logan NA, Lappin-Scott HM, Oyston PCF.
4. Cuadros-Orellana S, Pohlschröder M, Durrant LR. Isolation and characterization of halophilic archaea able to grow in aromatic compounds. Int Biodeterior Biodegradation 2006, 57:151-154.
5. Soppa J. From genomes to function: haloarchaea as model organisms. Microbiology 2006, 152:585-590. 10.1099/mic.0.28504-0, 16514139.
6. Grant WD, Ross HNM. The ecology and taxonomy of halobacteria. FEMS Microbiol Lett 1986, 39:9-15.
7. Grant WD. Cultivation of aerobic alkaliphiles. Method Microbiol 2006, 35:439-449.
8. DeRosa M, Gambacorta A, Grant WD, Lanzotti V, Nicolaus B. Polar lipids and glycine betaine from haloalkaliphilic archaebacteria. J Gen Microbiol 1988, 134:205-211.
9. Kamekura M, Dyall-Smith ML, Upasani V, Ventosa A, Kates M. Diversity of alkaliphilic halobacteria: proposals for transfer ofNatronobacterium vacuolatum,Natronobacterium magadii, andNatronobacterium pharaonistoHalorubrum,Natrialba, andNatronomonasgen. nov., respectively, asHalorubrum vacuolatumcomb. nov.,Natrialba magadiicomb. nov., andNatronomonas pharaoniscomb. nov., respectively. Int J Syst Bacteriol 1997, 47:853-857. 10.1099/00207713-47-3-853, 9226918.
10. Kamekura MD-S, Dyallsmith ML. Taxonomy of the familyHalobacteriaceaeand the description of two new generaHalorubrobacteriumandNatrialba. J Gen Microbiol 1995, 41:333-350.
11. Tindall BJ, Ross HNM, Grant WD. Natronobacteriumgen. nov. andNatronococcusgen. nov., two new genera of haloalkaliphilic archaebacteria. Syst Appl Microbiol 1984, 5:41-57.
12. Oren A. The OrderHalobacteriales. The Prokaryotes 2006, 113-164. Springer, New York, Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E.
13. Kamekura M. Diversity of members of the familyHalobacteriaceae. Microbiology and Biogeochemistry of Hypersaline Environments 1999, 13-26. CRC Press, Boca Raton, FL, Oren A.
14. Desmarais D, Jablonski PE, Fedarko NS, Roberts MF. 2-Sulfotrehalose, a novel osmolyte in haloalkaliphilic archaea. J Bacteriol 1997, 179:3146-3153. 179091, 9150208.
15. Polosina Y, Jarrell KF, Fedorov OV, Kostyukova AS. Nucleoside diphosphate kinase from haloalkaliphilic archaeonNatronobacterium magadii: purification and characterization. Extremophiles 1998, 2:333-338. 10.1007/s007920050076, 9783181.
16. Giménez MI, Studdert CA, Sánchez JJ, De Castro RE. Extracellular protease ofNatrialba magadii: purification and biochemical characterization. Extremophiles 2000, 4:181-188. 10.1007/s007920070033, 10879563.
17. Serganova I, Ksenzenko V, Serganov A, Meshcheryakova I, Pyatibratov M, Vakhrusheva O, Metlina A, Fedorov O. Sequencing of flagellin genes fromNatrialba magadiiprovides new insight into evolutionary aspects of archaeal flagellins. J Bacteriol 2002, 184:318-322. 10.1128/JB.184.1.318-322.2002, 134749, 11741874.
18. Katoh R, Ngata S, Ozawa A, Ohshima T, Kamekura M, Misono H. Purification and characterization of leucine dehydrogenase from an alkaliphilic halophile,Natronobacterium magadiiMS-3. J Mol Catal B: Enzym 2003, 23:231-238.
19. Kamekura M. Diversity of extremely halophilic bacteria. Extremophiles 1998, 2:289-295. 10.1007/s007920050071, 9783176.
20. Horikoshi K. Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 1999, 63:735-750. 98975, 10585964.
21. Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L. Low-pass sequencing for microbial comparative genomics. BMC Genomics 2004, 5:3. 10.1186/1471-2164-5-3, 331400, 14718067.
22. Saunders E, Tindall BJ, Fahnrich R, Lapidus A, Copeland A, Del Rio TG, Lucas S, Chen F, Tice H, Cheng JF, et al. Complete genome sequence ofHaloterrigena turkmenicatype strain (4 k). Stand Genomic Sci 2010, 2:107-116. 10.4056/sigs.681272, 3035258, 21304683.
23. Falb M, Pfeiffer F, Palm P, Rodewald K, Hickmann V, Tittor J, Oesterhelt D. Living with two extremes: conclusions from the genome sequence ofNatronomonas pharaonis. Genome Res 2005, 15:1336-1343. 10.1101/gr.3952905, 1240075, 16169924.
24. Falb M, Muller K, Konigsmaier L, Oberwinkler T, Horn P, von Gronau S, Gonzalez O, Pfeiffer F, Bornberg-Bauer E, Oesterhelt D. Metabolism of halophilic archaea. Extremophiles 2008, 12:177-196. 10.1007/s00792-008-0138-x, 2262144, 18278431.
25. Ng W-L, Yang C-F, Halladay JT, Arora P, DasSarma S. Isolation of genomic and plasmid DNAs fromHalobacterium halobium. Archaea, a Laboratory Manual: Halophiles 1995, 179-184. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, DasSarma S, Fleischmann EM.
26. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. 10.1186/1471-2164-9-75, 2265698, 18261238.
27. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403. 10.1101/gr.2289704, 442156, 15231754.
28. Darling AE, Treangen TJ, Messeguer X, Perna NT. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol Biol 2007, 396:135-152. 10.1007/978-1-59745-515-2_10, 18025691.
29. Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30:2478-2483. 10.1093/nar/30.11.2478, 117189, 12034836.
30. Witte A, Baranyi U, Klein R, Sulzner M, Luo C, Wanner G, Kruger DH, Lubitz W. Characterization ofNatronobacterium magadiiphage φCh1, a unique archaeal phage containing DNA and RNA. Mol Microbiol 1997, 23:603-616. 10.1046/j.1365-2958.1997.d01-1879.x, 9044293.
31. Klein R, Greineder B, Baranyi U, Witte A. The structural protein E of the archaeal virus φCh1: evidence for processing inNatrialba magadiiduring virus maturation. Virology 2000, 276:376-387. 10.1006/viro.2000.0565, 11040128.
32. Klein R, Baranyi U, Rossler N, Greineder B, Scholz H, Witte A. Natrialba magadiivirus φCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol Microbiol 2002, 45:851-863. 10.1046/j.1365-2958.2002.03064.x, 12139629.
33. Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T. Genetic and physical mapping of DNA replication origins inHaloferax volcanii. PLoS Genet 2007, 3:e77. 10.1371/journal.pgen.0030077, 1868953, 17511521.
34. Filee J, Siguier P, Chandler M. Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 2007, 71:121-157. 10.1128/MMBR.00031-06, 1847376, 17347521.
35. Brussow H. Prophage genomics. The bacteriophages 2006, 17-25. Oxford University Press, New York, Calendar R.
36. Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D. Haloquadratum walsbyi: limited diversity in a global pond. PLoS One 2011, 6:e20968. 10.1371/journal.pone.0020968, 3119063, 21701686.
37. Klug G, Evguenieva-Hackenberg E, Omer AD, Dennis PP, Marchfelder A. RNA processing. Archaea: Molecular and Cellular Biology 2007, 158-174. ASM Press, Washington, DC, Cavicchioli R.
38. Boucher Y, Douady CJ, Sharma AK, Kamekura M, Doolittle WF. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 2004, 186:3980-3990. 10.1128/JB.186.12.3980-3990.2004, 419955, 15175312.
39. Krulwich TA. Alkaliphilic prokaryotes. The Prokaryotes 2006, 283-308. Springer, New York, Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, 3.
40. Konstantinidis K, Tebbe A, Klein C, Scheffer B, Aivaliotis M, Bisle B, Falb M, Pfeiffer F, Siedler F, Oesterhelt D. Genome-wide proteomics ofNatronomonas pharaonis. J Proteome Res 2007, 6:185-193. 10.1021/pr060352q, 17203963.
41. Paul S, Bag SK, Das S, Harvill ET, Dutta C. Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol 2008, 9:R70. 10.1186/gb-2008-9-4-r70, 2643941, 18397532.
42. Oren A. Intracellular salt concentrations and ion metabolism in halophilic microorganisms. Halophilic Microorganisms and their Environments 2002, 207-232. Kluwer Academic, Dordrecht, The Netherlands, Oren A.
43. Roberts MF. Organic compatible solutes of halotolerant and halophilic microorganisms. Saline Syst 2005, 1:5. 10.1186/1746-1448-1-5, 1224877, 16176595.
44. Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst 2008, 4:2. 10.1186/1746-1448-4-2, 2329653, 18412960.
45. Martin DD, Ciulla RA, Roberts MF. Osmoadaptation in archaea. Appl Environ Microbiol 1999, 65:1815-1825. 91261, 10223964.
46. Wei Y, Liu J, Ma Y, Krulwich TA. Three putative cation/proton antiporters from the soda lake alkaliphileAlkalimonas amylolyticaN10 complement an alkali-sensitiveEscherichia colimutant. Microbiology 2007, 153:2168-2179. 10.1099/mic.0.2007/007450-0, 2538799, 17600061.
47. Kurz M. Compatible solute influence on nucleic acids: many questions but few answers. Saline Syst 2008, 4:6. 10.1186/1746-1448-4-6, 2430576, 18522725.
48. Sherwood JE, Stagnitti F, Kokkinn MJ, Williams WD. Dissolved oxygen concentrations in hypersaline waters. Limnol Oceanogr 1991, 36:235-250.
49. Oren A. The ecology of the extremely halophilic archaea. FEMS Microbiol Rev 1994, 13:415-439.
50. Ochsenreiter T, Pfeifer F, Schleper C. Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles 2002, 6:267-274. 10.1007/s00792-001-0253-4, 12215811.
51. Siezen RJ, Leunissen JA. Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci 1997, 6:501-523. 2143677, 9070434.
52. De Castro RE, Ruiz DM, Giménez MI, Silveyra MX, Paggi RA, Maupin-Furlow JA. Gene cloning and heterologous synthesis of a haloalkaliphilic extracellular protease ofNatrialba magadii(Nep). Extremophiles 2008, 12:677-687. 10.1007/s00792-008-0174-6, 2614922, 18553052.
53. Bourne DG, Riddles P, Jones GJ, Smith W, Blakeley RL. Characterisation of a gene cluster involved in bacterial degradation of the cyanobacterial toxin microcystin LR. Environ Toxicol 2001, 16:523-534. 10.1002/tox.10013, 11769251.
54. Maupin-Furlow JA, Humbard MA, Kirkland PA, Li W, Reuter CJ, Wright AJ, Zhou G. Proteasomes from structure to function: perspectives from Archaea. Curr Top Dev Biol 2006, 75:125-169.
55. Humbard MA, Miranda HV, Lim JM, Krause DJ, Pritz JR, Zhou G, Chen S, Wells L, Maupin-Furlow JA. Ubiquitin-like small archaeal modifier proteins (SAMPs) inHaloferax volcanii. Nature 2010, 463:54-60. 10.1038/nature08659, 2872088, 20054389.
56. Miranda HV, Nembhard N, Su D, Hepowit N, Krause DJ, Pritz JR, Phillips C, Soll D, Maupin-Furlow JA. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc Natl Acad Sci U S A 2011, 108:4417-4422. 10.1073/pnas.1018151108, 3060232, 21368171.
57. Sastre DE, Paggi RA, De Castro RE. The Lon protease from the haloalkaliphilic archaeonNatrialba magadiiis transcriptionally linked to a cluster of putative membrane proteases and displays DNA-binding activity. Microbiol Res 2011, 166:304-313. 10.1016/j.micres.2010.07.002, 20869220.
58. Franzetti B, Schoehn G, Hernandez JF, Jaquinod M, Ruigrok RW, Zaccai G. Tetrahedral aminopeptidase: a novel large protease complex from archaea. EMBO J 2002, 21:2132-2138. 10.1093/emboj/21.9.2132, 125989, 11980710.
59. Konaklieva MI, Plotkin BJ. The relationship between inhibitors of eukaryotic and prokaryotic serine proteases. Mini Rev Med Chem 2004, 4:721-739.
60. Giménez MI, Sánchez JJ, De Castro RE. Detection of an intracellular protease inhibitor in archaea. Curr Microbiol 2003, 46:334-339. 10.1007/s00284-002-3861-z, 12732960.
61. Bolhuis A. The archaeal Sec-dependent protein translocation pathway. Philos Trans R Soc Lond B Biol Sci 2004, 359:919-927. 10.1098/rstb.2003.1461, 1693384, 15306407.
62. Pohlschröder M, Dilks KC. Protein translocation into and across archaeal cytoplasmic membranes. Archaea: Molecular and Cellular Biology 2007, 369-384. ASM Press, Washington, DC, Cavicchioli R.
63. Ellen AF, Zolghadr B, Driessen AM, Albers SV. Shaping the archaeal cell envelope. Archaea 2010, 2010:608243. 2910488, 20671907.
64. Storf S, Pfeiffer F, Dilks K, Chen ZQ, Imam S, Pohlschröder M. Mutational and bioinformatic analysis of haloarchaeal lipobox-containing proteins. Archaea 2010, 2010:410975. 2945643, 20886060.
65. Haft DH, Payne SH, Selengut JD. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol 2012, 194:36-48. 10.1128/JB.06026-11, 3256604, 22037399.
66. Burda P, Aebi M. The dolichol pathway of N-linked glycosylation. Biochim Biophys Acta 1999, 1426:239-257. 10.1016/S0304-4165(98)00127-5, 9878760.
67. Magidovich H, Eichler J. Glycosyltransferases and oligosaccharyltransferases in Archaea: putative components of the N-glycosylation pathway in the third domain of life. FEMS Microbiol Lett 2009, 300:122-130. 10.1111/j.1574-6968.2009.01775.x, 19765088.
68. Oren A. Biotechnological applications and potentials of halophilic microorganisms. Halophilic Microorganisms and their Environments 2002, 357-390. Kluwer Academic Publishers, Dordrecht, The Netherlands, Oren A.
69. Bali S, Lawrence AD, Lobo SA, Saraiva LM, Golding BT, Palmer DJ, Howard MJ, Ferguson SJ, Warren MJ. Molecular hijacking of siroheme for the synthesis of heme andd1 heme. Proc Natl Acad Sci U S A 2011, 108:18260-18265. 10.1073/pnas.1108228108, 3215036, 21969545.
70. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem 2002, 277:48949-48959. 10.1074/jbc.M208965200, 12376536.
71. Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J. Thiamin biosynthesis in prokaryotes. Arch Microbiol 1999, 171:293-300. 10.1007/s002030050713, 10382260.
72. Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 2007, 315:1003-1006. 10.1126/science.1135999, 17303759.
73. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res 2002, 30:3141-3151. 10.1093/nar/gkf433, 135753, 12136096.
74. Fischer M, Bacher A. Biosynthesis of vitamin B2: structure and mechanism of riboflavin synthase. Arch Biochem Biophys 2008, 474:252-265. 10.1016/j.abb.2008.02.008, 18298940.
75. Fischer M, Bacher A. Biosynthesis of vitamin B2: a unique way to assemble a xylene ring. Chembiochem 2011, 12:670-680. 10.1002/cbic.201000681, 21404408.
76. Graham DE, White RH. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat Prod Rep 2002, 19:133-147. 10.1039/b103714p, 12013276.
77. White RH. Biosynthesis of the methanogenic cofactors. Vitam Horm 2001, 61:299-337.
78. Graham DE. A new role for coenzyme F420in aflatoxin reduction by soil mycobacteria. Mol Microbiol 2010, 78:533-536. 10.1111/j.1365-2958.2010.07358.x, 21038477.
79. Taylor MC, Jackson CJ, Tattersall DB, French N, Peat TS, Newman J, Briggs LJ, Lapalikar GV, Campbell PM, Scott C, et al. Identification and characterization of two families of F420H2-dependent reductases fromMycobacteriathat catalyse aflatoxin degradation. Mol Microbiol 2010, 78:561-575. 10.1111/j.1365-2958.2010.07356.x, 3034190, 20807200.
80. Lin XL, White RH. Occurrence of coenzyme F420and its γ-monoglutamyl derivative in nonmethanogenic archaebacteria. J Bacteriol 1986, 168:444-448. 213475, 3093465.
81. Selengut JD, Haft DH. Unexpected abundance of coenzyme F420-dependent enzymes inMycobacterium tuberculosisand other actinobacteria. J Bacteriol 2010, 192:5788-5798. 10.1128/JB.00425-10, 2953692, 20675471.
82. Selengut JD, Rusch DB, Haft DH. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. BMC Bioinformatics 2010, 11:52. 10.1186/1471-2105-11-52, 3098086, 20102603.
83. Green JM, Nichols BP, Matthews RG. Folate biosynthesis, reduction, and polyglutamylation. Escherichia coli and Salmonella: cellular and molecular biology 1996, 665-673. ASM Press, Washington, D.C, Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley MA, Schaechter M, Umbarger HE, 2.
84. Lucock M. Folic acid: nutritional biochemistry, molecular biology, and role in disease processes. Mol Genet Metab 2000, 71:121-138. 10.1006/mgme.2000.3027, 11001804.
85. de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 2007, 8:245. 10.1186/1471-2164-8-245, 1971073, 17645794.
86. Lascelles J. Synthesis of tetrapyrroles by microorganisms. Physiol Rev 1961, 41:417-441.
87. Warren MJ, Smith AG, Deery E, Rose R-S. Biosynthesis of siroheme and coenzyme F430. Tetrapyrroles: Birth, Life and Death 2009, 344-351. Springer, New York, Warren MJ, Smith AG.
88. Zappa S, Li K, Bauer CE. The tetrapyrrole biosynthetic pathway and its regulation inRhodobacter capsulatus. Adv Exp Med Biol 2010, 675:229-250. 10.1007/978-1-4419-1528-3_13, 2883787, 20532744.
89. Maggio-Hall LA, Escalante-Semerena JC. In vitrosynthesis of the nucleotide loop of cobalamin bySalmonella typhimuriumenzymes. Proc Natl Acad Sci U S A 1999, 96:11798-11803. 10.1073/pnas.96.21.11798, 18366, 10518530.
90. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the vitamin B12metabolism and regulation in prokaryotes. J Biol Chem 2003, 278:41148-41159. 10.1074/jbc.M305837200, 12869542.
91. Woodson JD, Peck RF, Krebs MP, Escalante-Semerena JC. ThecobYgene of the archaeonHalobacteriumsp. strain NRC-1 is required for de novo cobamide synthesis. J Bacteriol 2003, 185:311-316. 10.1128/JB.185.1.311-316.2003, 141819, 12486068.
92. Woodson JD, Escalante-Semerena JC. CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12precursor cobinamide in archaea. Proc Natl Acad Sci U S A 2004, 101:3591-3596. 10.1073/pnas.0305939101, 373507, 14990804.
93. Kajiwara Y, Santander PJ, Roessner CA, Perez LM, Scott AI. Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes. J Am Chem Soc 2006, 128:9971-9978. 10.1021/ja062940a, 16866557.
94. Raux E, Leech HK, Beck R, Schubert HL, Santander PJ, Roessner CA, Scott AI, Martens JH, Jahn D, Thermes C, et al. Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin inBacillus megaterium. Biochem J 2003, 370:505-516. 10.1042/BJ20021443, 1223173, 12408752.
95. Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN. Crystal structure of the vitamin B12biosynthetic cobaltochelatase, CbiXS, fromArchaeoglobus fulgidus. J Struct Funct Genomics 2006, 7:37-50. 10.1007/s10969-006-9008-x, 16835730.
96. Moss J, Lane MD. The biotin-dependent enzymes. Adv Enzymol Relat Areas Mol Biol 1971, 35:321-442.
97. Schneider G, Lindqvist Y. Structural enzymology of biotin biosynthesis. FEBS Lett 2001, 495:7-11. 10.1016/S0014-5793(01)02325-0, 11322938.
98. Rodionov DA, Mironov AA, Gelfand MS. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res 2002, 12:1507-1516. 10.1101/gr.314502, 187538, 12368242.
99. Burns D, Dyall-Smith ML. Cultivation of haloarchaea. Methods Microbiol 2006, 35:535-552.
100. Kisker C, Schindelin H, Rees DC. Molybdenum-cofactor-containing enzymes: structure and mechanism. Annu Rev Biochem 1997, 66:233-267. 10.1146/annurev.biochem.66.1.233, 9242907.
101. Schwarz G, Mendel RR. Molybdenum cofactor biosynthesis and molybdenum enzymes. Annu Rev Plant Biol 2006, 57:623-647. 10.1146/annurev.arplant.57.032905.105437, 16669776.
102. Magalon A, Frixon C, Pommier J, Giordano G, Blasco F. In vivointeractions between gene products involved in the final stages of molybdenum cofactor biosynthesis inEscherichia coli. J Biol Chem 2002, 277:48199-48204. 10.1074/jbc.M205806200, 12372836.
103. Khomyakova M, Bukmez O, Thomas LK, Erb TJ, Berg IA. A methylaspartate cycle in haloarchaea. Science 2011, 331:334-337. 10.1126/science.1196544, 21252347.
104. Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D. The genome of the square archaeonHaloquadratum walsbyi: life at the limits of water activity. BMC Genomics 2006, 7:169. 10.1186/1471-2164-7-169, 1544339, 16820047.
105. Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV. Evolutionary primacy of sodium bioenergetics. Biol Direct 2008, 3:13. 10.1186/1745-6150-3-13, 2359735, 18380897.
106. Steinert K, Wagner V, Kroth-Pancic PG, Bickel-Sandkotter S. Characterization and subunit structure of the ATP synthase of the halophilic archaeonHaloferax volcaniiand organization of the ATP synthase genes. J Biol Chem 1997, 272:6261-6269. 10.1074/jbc.272.10.6261, 9045643.
107. Mukohata Y, Yoshida M. The H+-translocating ATP synthase inHalobacterium halobiumdiffers from F0F1-ATPase/synthase. J Biochem 1987, 102:797-802.
108. Scharf B, Wittenberg R, Engelhard M. Electron transfer proteins from the haloalkaliphilic archaeonNatronobacterium pharaonis: possible components of the respiratory chain include cytochromebcand a terminal oxidase cytochromeba3. Biochemistry 1997, 36:4471-4479. 10.1021/bi962312d, 9109654.
109. Gomes CM, Bandeiras TM, Teixeira M. A new type-II NADH dehydrogenase from the archaeonAcidianus ambivalens: characterization and in vitro reconstitution of the respiratory chain. J Bioenerg Biomembr 2001, 33:1-8.
110. Sreeramulu K, Schmidt CL, Schafer G, Anemuller S. Studies of the electron transport chain of the euryarcheonHalobacterium salinarum: indications for a type II NADH dehydrogenase and a complex III analog. J Bioenerg Biomembr 1998, 30:443-453. 10.1023/A:1020538129400, 9932647.
111. DiSpirito AA, Kunz RC, Choi D-W, Zahn JA. Respiration in methanotrophs. Respiration in Archaea and Bacteria: Diversity of Prokaryotic Respiratory Systems 2004, 149-168. Springer, Dordrecht, The Netherlands, Zannoni D.
112. Mattar S, Engelhard M. Cytochromeba3fromNatronobacterium pharaonis-an archaeal four-subunit cytochrome-c-type oxidase. Eur J Biochem 1997, 250:332-341. 10.1111/j.1432-1033.1997.0332a.x, 9428682.
113. Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, Rodewald K, Ruepp A, Soppa J, Tittor J, Oesterhelt D. Evolution in the laboratory: the genome ofHalobacterium salinarumstrain R1 compared to that of strain NRC-1. Genomics 2008, 91:335-346. 10.1016/j.ygeno.2008.01.001, 18313895.
114. Xu XM, Moller SG. Iron-sulfur clusters: biogenesis, molecular mechanisms, and their functional significance. Antioxid Redox Signal 2011, 15:271-307. 10.1089/ars.2010.3259, 20812788.
115. Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction. Annu Rev Biochem 2000, 69:183-215. 10.1146/annurev.biochem.69.1.183, 10966457.
116. Engelhard M, Schmies G, Wegener AA. Archeabacterial phototaxis. Photoreceptors and Light Signalling 2003, 1-39. The Royal Society of Chemistry, Cambridge, U.K, Batschauer A.
117. Peck RF, Echavarri-Erasun C, Johnson EA, Ng WV, Kennedy SP, Hood L, DasSarma S, Krebs MP. brpandblhare required for synthesis of the retinal cofactor of bacteriorhodopsin inHalobacterium salinarum. J Biol Chem 2001, 276:5739-5744. 10.1074/jbc.M009492200, 11092896.
118. Szurmant H, Ordal GW. Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiol Mol Biol Rev 2004, 68:301-319. 10.1128/MMBR.68.2.301-319.2004, 419924, 15187186.
119. Koch MK, Staudinger WF, Siedler F, Oesterhelt D. Physiological sites of deamidation and methyl esterification in sensory transducers ofHalobacterium salinarum. J Mol Biol 2008, 380:285-302. 10.1016/j.jmb.2008.04.063, 18514223.
120. Schlesner M, Miller A, Streif S, Staudinger WF, Muller J, Scheffer B, Siedler F, Oesterhelt D. Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus. BMC Microbiol 2009, 9:56. 10.1186/1471-2180-9-56, 2666748, 19291314.
121. Thomas NA, Bardy SL, Jarrell KF. The archaeal flagellum: a different kind of prokaryotic motility structure. FEMS Microbiol Rev 2001, 25:147-174. 10.1111/j.1574-6976.2001.tb00575.x, 11250034.
122. Streif S, Staudinger WF, Marwan W, Oesterhelt D. Flagellar rotation in the archaeonHalobacterium salinarumdepends on ATP. J Mol Biol 2008, 384:1-8. 10.1016/j.jmb.2008.08.057, 18786541.
123. Fedorov OV, Pyatibratov MG, Kostyukova AS, Osina NK, Tarasov VY. Protofilament as a structural element of flagella of haloalkalophilic archaebacteria. Can J Microbiol 1994, 40:45-53.
124. Patenge N, Berendes A, Engelhardt H, Schuster SC, Oesterhelt D. Theflagene cluster is involved in the biogenesis of flagella inHalobacterium salinarum. Mol Microbiol 2001, 41:653-663. 10.1046/j.1365-2958.2001.02542.x, 11532133.
125. Chaban B, Ng SY, Kanbe M, Saltzman I, Nimmo G, Aizawa S, Jarrell KF. Systematic deletion analyses of theflagenes in the flagella operon identify several genes essential for proper assembly and function of flagella in the archaeon,Methanococcus maripaludis. Mol Microbiol 2007, 66:596-609. 10.1111/j.1365-2958.2007.05913.x, 17887963.
126. Ghosh A, Hartung S, van der Does C, Tainer JA, Albers SV. Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding. Biochem J 2011, 437:43-52. 10.1042/BJ20110410, 3213642, 21506936.
127. Pyatibratov MG, Leonard K, Tarasov VY, Fedorov OV. Two immunologically distinct types of protofilaments can be identified inNatrialba magadiiflagella. FEMS Microbiol Lett 2002, 212:23-27. 10.1111/j.1574-6968.2002.tb11239.x, 12076782.
128. Selb RM. Construction of mutants ofNatrialba magadiiand φCh1. PhD thesis 2010, Universität Wien, Molecular Biology Department, .
129. Reiter M. Gene regulation of φCh1: characterization of ORF49 and further characterization of the origin of replication of the halophage φCh1. PhD thesis 2010, Universität Wien, Molecular Biology Department, .
130. Berquist BR, Soneja J, DasSarma S. Comparative genomic survey of information transfer systems in two diverse extremely halophilic Archaea,Halobacteriumsp. strain NRC-1 andHaloarcula marismortui. Adaptation to Life at High Salt Concentrations in Archaea, Bacteria, and Eukarya 2005, 148-182. Springer, Dordrecht, The Netherlands, Gunde-Cimerman N, Oren A, Plemenitaš A.
131. Thomm M. Transcription: mechanism and regulation. Archaea: Molecular and Cellular Biology 2007, 139-157. ASM Press, Washington, DC, Cavicchioli R.