Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A. 1977, 74: 5088-5090. 10.1073/pnas.74.11.5088.
Article
PubMed Central
PubMed
Google Scholar
Woese CR, Fox GE: The concept of cellular evolution. J Mol Evol. 1977, 10: 1-6. 10.1007/BF01796132.
Article
PubMed
Google Scholar
Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM: The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A. 2008, 105: 20356-20361. 10.1073/pnas.0810647105.
Article
PubMed Central
PubMed
Google Scholar
Williams TA, Foster PG, Cox CJ, Embley TM: An archaeal origin of eukaryotes supports only two primary domains of life. Nature. 2013, 504: 231-236. 10.1038/nature12779.
Article
PubMed
Google Scholar
Brochier-Armanet C, Forterre P, Gribaldo S: Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol. 2011, 14: 274-281. 10.1016/j.mib.2011.04.015.
Article
PubMed
Google Scholar
Koga Y: Thermal adaptation of the archaeal and bacterial lipid membranes. Archaea. 2012, 2012: 789652-10.1155/2012/789652.
Article
PubMed Central
PubMed
Google Scholar
Matsumi R, Atomi H, Driessen AJ, van der Oost J: Isoprenoid biosynthesis in Archaea–biochemical and evolutionary implications. Res Microbiol. 2011, 162: 39-52. 10.1016/j.resmic.2010.10.003.
Article
PubMed
Google Scholar
Sumper M, Berg E, Mengele R, Strobel I: Primary structure and glycosylation of the S-layer protein of Haloferax volcanii . J Bacteriol. 1990, 172: 7111-7118.
PubMed Central
PubMed
Google Scholar
Ellen AF, Zolghadr B, Driessen AM, Albers SV: Shaping the archaeal cell envelope. Archaea. 2010, 2010: 608243-10.1155/2010/608243.
Article
PubMed Central
PubMed
Google Scholar
Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA: The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One. 2010, 5: e9605-10.1371/journal.pone.0009605.
Article
PubMed Central
PubMed
Google Scholar
Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J: DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival. PLoS One. 2014, 4: e94819-10.1371/journal.pone.0094819.
Article
Google Scholar
Allers T, Mevarech M: Archaeal genetics - the third way. Nat Rev Genet. 2005, 6: 58-73. 10.1038/nrg1504.
Article
PubMed
Google Scholar
Leigh JA, Albers SV, Atomi H, Allers T: Model organisms for genetics in the domain Archaea: methanogens, halophiles. Thermococcales and Sulfolobales . FEMS Microbiol Rev. 2011, 35: 577-608. 10.1111/j.1574-6976.2011.00265.x.
Article
PubMed
Google Scholar
Giménez MI, Dilks K, Pohlschröder M: Haloferax volcanii twin-arginine translocation substrates include secreted soluble, C-terminally anchored and lipoproteins. Mol Microbiol. 2007, 66: 1597-1606. 10.1111/j.1365-2958.2007.06034.x.
Article
PubMed
Google Scholar
Storf S, Pfeiffer F, Dilks K, Chen ZQ, Imam S, Pohlschroder M: Mutational and bioinformatic analysis of haloarchaeal lipobox-containing proteins. Archaea. 2010, 2010: 410975-10.1155/2010/410975.
Article
PubMed Central
PubMed
Google Scholar
Zhou G, Kowalczyk D, Humbard MA, Rohatgi S, Maupin-Furlow JA: Proteasomal components required for cell growth and stress responses in the haloarchaeon Haloferax volcanii . J Bacteriol. 2008, 190: 8096-8105. 10.1128/JB.01180-08.
Article
PubMed Central
PubMed
Google Scholar
Cohen A, Lam WL, Charlebois RL, Doolittle WF, Schalkwyk LC: Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea. Proc Natl Acad Sci U S A. 1992, 89: 1602-1606. 10.1073/pnas.89.5.1602.
Article
PubMed Central
PubMed
Google Scholar
Watrin L, Prieur D: UV and ethyl methanesulfonate effects in hyperthermophilic archaea and isolation of auxotrophic mutants of Pyrococcus strains. Curr Microbiol. 1996, 33: 377-382. 10.1007/s002849900131.
Article
PubMed
Google Scholar
Lange C, Zerulla K, Breuert S, Soppa J: Gene conversion results in the equalization of genome copies in the polyploid haloarchaeon Haloferax volcanii . Mol Microbiol. 2011, 80: 666-677. 10.1111/j.1365-2958.2011.07600.x.
Article
PubMed
Google Scholar
Zhang JK, Pritchett MA, Lampe DJ, Robertson HM, Metcalf WW: In vivo transposon mutagenesis of the methanogenic archaeon Methanosarcina acetivorans C2A using a modified version of the insect mariner-family transposable element Himar1 . Proc Natl Acad Sci U S A. 2000, 97: 9665-9670. 10.1073/pnas.160272597.
Article
PubMed Central
PubMed
Google Scholar
Sarmiento F, Mrazek J, Whitman WB: Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis . Proc Natl Acad Sci U S A. 2013, 110: 4726-4731. 10.1073/pnas.1220225110.
Article
PubMed Central
PubMed
Google Scholar
Dyall-Smith ML, Doolittle WF: Construction of composite transposons for halophilic Archaea. Can J Microbiol. 1994, 40: 922-929. 10.1139/m94-148.
Article
PubMed
Google Scholar
Woods WG, Ngui K, Dyall-Smith ML: An improved transposon for the halophilic Archaeon Haloarcula hispanica . J Bacteriol. 1999, 181: 7140-7142.
PubMed Central
PubMed
Google Scholar
Craig NL, Craigie R, Gellert M, Lambowitz AM: Mobile DNA II. 2002, ASM Press, Washington D.C
Book
Google Scholar
Skipper KA, Andersen PR, Sharma N, Mikkelsen JG: DNA transposon-based gene vehicles - scenes from an evolutionary drive. J Biomed Sci. 2013, 20: 92-10.1186/1423-0127-20-92.
Article
PubMed Central
PubMed
Google Scholar
Goryshin IY, Jendrisak J, Hoffman LM, Meis R, Reznikoff WS: Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes. Nat Biotechnol. 2000, 18: 97-100. 10.1038/72017.
Article
PubMed
Google Scholar
Lamberg A, Nieminen S, Qiao M, Savilahti H: Efficient insertion mutagenesis strategy for bacterial genomes involving electroporation of in vitro-assembled DNA transposition complexes of bacteriophage Mu. Appl Environ Microbiol. 2002, 68: 705-712. 10.1128/AEM.68.2.705-712.2002.
Article
PubMed Central
PubMed
Google Scholar
Hamer L, Adachi K, Montenegro-Chamorro MV, Tanzer MM, Mahanty SK, Lo C, Tarpey RW, Skalchunes AR, Heiniger RW, Frank SA, Darveaux BA, Lampe DJ, Slater TM, Ramamurthy L, DeZwaan TM, Nelson GH, Shuster JR, Woessner J, Hamer JE: Gene discovery and gene function assignment in filamentous fungi. Proc Natl Acad Sci U S A. 2001, 98: 5110-5115. 10.1073/pnas.091094198.
Article
PubMed Central
PubMed
Google Scholar
Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung K, Dobry CJ, Gerstein MB, Craig NL, Snyder M: Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res. 2004, 14: 1975-1986. 10.1101/gr.2875304.
Article
PubMed Central
PubMed
Google Scholar
Cline SW, Schalkwyk LC, Doolittle WF: Transformation of the archaebacterium Halobacterium volcanii with genomic DNA. J Bacteriol. 1989, 171: 4987-4991.
PubMed Central
PubMed
Google Scholar
Cline SW, Lam WL, Charlebois RL, Schalkwyk LC, Doolittle WF: Transformation methods for halophilic archaebacteria. Can J Microbiol. 1989, 35: 148-152. 10.1139/m89-022.
Article
PubMed
Google Scholar
Bitan-Banin G, Ortenberg R, Mevarech M: Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene. J Bacteriol. 2003, 185: 772-778. 10.1128/JB.185.3.772-778.2003.
Article
PubMed Central
PubMed
Google Scholar
Haapa S, Taira S, Heikkinen E, Savilahti H: An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications. Nucleic Acids Res. 1999, 27: 2777-2784. 10.1093/nar/27.13.2777.
Article
PubMed Central
PubMed
Google Scholar
Yanisch-Perron C, Vieira J, Messing J: Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985, 33: 103-119. 10.1016/0378-1119(85)90120-9.
Article
PubMed
Google Scholar
Allers T, Ngo HP, Mevarech M, Lloyd RG: Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Appl Environ Microbiol. 2004, 70: 943-953. 10.1128/AEM.70.2.943-953.2004.
Article
PubMed Central
PubMed
Google Scholar
Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T: Genetic and physical mapping of DNA replication origins in Haloferax volcanii . PLoS Genet. 2007, 3: e77-10.1371/journal.pgen.0030077.
Article
PubMed Central
PubMed
Google Scholar
Delmas S, Shunburne L, Ngo HP, Allers T: Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination. PLoS Genet. 2009, 5: e1000552-10.1371/journal.pgen.1000552.
Article
PubMed Central
PubMed
Google Scholar
Grant SG, Jessee J, Bloom FR, Hanahan D: Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A. 1990, 87: 4645-4649. 10.1073/pnas.87.12.4645.
Article
PubMed Central
PubMed
Google Scholar
Meissner PS, Sisk WP, Berman ML: Bacteriophage lambda cloning system for the construction of directional cDNA libraries. Proc Natl Acad Sci U S A. 1987, 84: 4171-4175. 10.1073/pnas.84.12.4171.
Article
PubMed Central
PubMed
Google Scholar
Ronnekleiv M, Liaaen-Jensen S: Bacterial carotenoids 53*, C-50-carotenoids 23; Carotenoids of Haloferax volcanii versus other halophilic bacteria. Biochem Syst Ecol. 1995, 23: 627-634. 10.1016/0305-1978(95)00047-X.
Article
Google Scholar
Dogbo O, Laferriere A, D’Harlingue A, Camara B: Carotenoid biosynthesis: isolation and characterization of a bifunctional enzyme catalyzing the synthesis of phytoene. Proc Natl Acad Sci U S A. 1988, 85: 7054-7058. 10.1073/pnas.85.19.7054.
Article
PubMed Central
PubMed
Google Scholar
Sieiro C, Poza M, de Miguel T, Villa TG: Genetic basis of microbial carotenogenesis. Int Microbiol. 2003, 6: 11-16.
PubMed
Google Scholar
The UCSC Archaeal Genome Browser. [http://genome.ucsc.edu/]
Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM: The UCSC Archaeal Genome Browser. Nucleic Acids Res. 2006, 34: D407-D410. 10.1093/nar/gkj134.
Article
PubMed Central
PubMed
Google Scholar
Chan PP, Holmes AD, Smith AM, Tran D, Lowe TM: The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res. 2012, 40: D646-D652. 10.1093/nar/gkr990.
Article
PubMed Central
PubMed
Google Scholar
Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One. 2012, 7: e41389-10.1371/journal.pone.0041389.
Article
PubMed Central
PubMed
Google Scholar
Hamer L, DeZwaan TM, Montenegro-Chamorro MV, Frank SA, Hamer JE: Recent advances in large-scale transposon mutagenesis. Curr Opin Chem Biol. 2001, 5: 67-73. 10.1016/S1367-5931(00)00162-9.
Article
PubMed
Google Scholar
Choi KH, Kim KJ: Applications of transposon-based gene delivery system in bacteria. J Microbiol Biotechnol. 2009, 19: 217-228.
PubMed
Google Scholar
Ivics Z, Li MA, Mates L, Boeke JD, Nagy A, Bradley A, Izsvak Z: Transposon-mediated genome manipulation in vertebrates. Nat Methods. 2009, 6: 415-422. 10.1038/nmeth.1332.
Article
PubMed Central
PubMed
Google Scholar
Ivics Z, Izsvak Z: The expanding universe of transposon technologies for gene and cell engineering. Mob DNA. 2010, 1: 25-10.1186/1759-8753-1-25.
Article
PubMed Central
PubMed
Google Scholar
Filee J, Siguier P, Chandler M: Insertion sequence diversity in archaea. Microbiol Mol Biol Rev. 2007, 71: 121-157. 10.1128/MMBR.00031-06.
Article
PubMed Central
PubMed
Google Scholar
Savilahti H, Rice PA, Mizuuchi K: The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 1995, 14: 4893-4903.
PubMed Central
PubMed
Google Scholar
Haapa-Paananen S, Rita H, Savilahti H: DNA transposition of bacteriophage Mu. A quantitative analysis of target site selection in vitro . J Biol Chem. 2002, 277: 2843-2851. 10.1074/jbc.M108044200.
Article
PubMed
Google Scholar
Pajunen M, Turakainen H, Poussu E, Peränen J, Vihinen M, Savilahti H: High-precision mapping of protein-protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform. Nucleic Acids Res. 2007, 35: e103-10.1093/nar/gkm563.
Article
PubMed Central
PubMed
Google Scholar
Orsini L, Pajunen M, Hanski I, Savilahti H: SNP discovery by mismatch-targeting of Mu transposition. Nucleic Acids Res. 2007, 35: e44-10.1093/nar/gkm070.
Article
PubMed Central
PubMed
Google Scholar
Turakainen H, Saarimaki-Vire J, Sinjushina N, Partanen J, Savilahti H: Transposition-based method for the rapid generation of gene-targeting vectors to produce Cre/Flp-modifiable conditional knock-out mice. PLoS One. 2009, 4: e4341-10.1371/journal.pone.0004341.
Article
PubMed Central
PubMed
Google Scholar
Poussu E, Vihinen M, Paulin L, Savilahti H: Probing the Δ-complementing domain of E. coli β-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition. Proteins. 2004, 54: 681-692. 10.1002/prot.10467.
Article
PubMed
Google Scholar
Poussu E, Jäntti J, Savilahti H: A gene truncation strategy generating N- and C-terminal deletion variants of proteins for functional studies: mapping of the Sec1p binding domain in yeast Mso1p by a Mu in vitro transposition-based approach. Nucleic Acids Res. 2005, 33: e104-10.1093/nar/gni102.
Article
PubMed Central
PubMed
Google Scholar
Rasila TS, Vihinen M, Paulin L, Haapa-Paananen S, Savilahti H: Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PLoS One. 2012, 7: e37922-10.1371/journal.pone.0037922.
Article
PubMed Central
PubMed
Google Scholar
Jones DD: Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 β-lactamase to an amino acid deletion. Nucleic Acids Res. 2005, 33: e80-10.1093/nar/gni077.
Article
PubMed Central
PubMed
Google Scholar
Simm AM, Baldwin AJ, Busse K, Jones DD: Investigating protein structural plasticity by surveying the consequence of an amino acid deletion from TEM-1 β-lactamase. FEBS Lett. 2007, 581: 3904-3908. 10.1016/j.febslet.2007.07.018.
Article
PubMed
Google Scholar
Edwards WR, Busse K, Allemann RK, Jones DD: Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Res. 2008, 36: e78-10.1093/nar/gkn363.
Article
PubMed Central
PubMed
Google Scholar
Baldwin AJ, Busse K, Simm AM, Jones DD: Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Res. 2008, 36: e77-10.1093/nar/gkn358.
Article
PubMed Central
PubMed
Google Scholar
Pajunen MI, Pulliainen AT, Finne J, Savilahti H: Generation of transposon insertion mutant libraries for Gram-positive bacteria by electroporation of phage Mu DNA transposition complexes. Microbiology. 2005, 151: 1209-1218. 10.1099/mic.0.27807-0.
Article
PubMed
Google Scholar
Kiljunen S, Vilen H, Pajunen M, Savilahti H, Skurnik M: Nonessential genes of phage phiYeO3-12 include genes involved in adaptation to growth on Yersinia enterocolitica serotype O:3. J Bacteriol. 2005, 187: 1405-1414. 10.1128/JB.187.4.1405-1414.2005.
Article
PubMed Central
PubMed
Google Scholar
Krupovic M, Vilen H, Bamford JK, Kivelä HM, Aalto J, Savilahti H, Bamford DH: Genome characterization of lipid-containing marine bacteriophage PM2 by transposon insertion mutagenesis. J Virol. 2006, 80: 9270-9278. 10.1128/JVI.00536-06.
Article
PubMed Central
PubMed
Google Scholar
Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomaki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H: Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res. 2008, 36: e148-10.1093/nar/gkn801.
Article
PubMed Central
PubMed
Google Scholar
Krysan PJ, Young JC, Sussman MR: T-DNA as an insertional mutagen in Arabidopsis. Plant Cell. 1999, 11: 2283-2290. 10.1105/tpc.11.12.2283.
Article
PubMed Central
PubMed
Google Scholar
Holmes ML, Nuttall SD, Dyall-Smith ML: Construction and use of halobacterial shuttle vectors and further studies on Haloferax DNA gyrase. J Bacteriol. 1991, 173: 3807-3813.
PubMed Central
PubMed
Google Scholar
Blaseio U, Pfeifer F: Transformation of Halobacterium halobium: development of vectors and investigation of gas vesicle synthesis. Proc Natl Acad Sci U S A. 1990, 87: 6772-6776. 10.1073/pnas.87.17.6772.
Article
PubMed Central
PubMed
Google Scholar
Boucher U, Kamekura M, Doolittle WF: Origins and evolution of isoprenoid lipid biosynthesis in archaea. Mol Microbiol. 2004, 52: 515-527. 10.1111/j.1365-2958.2004.03992.x.
Article
PubMed
Google Scholar
Britton G, Liaaen-Jensen S, Phander H: Carotenoids. Vol. 4: Natural Functions. 2008, Basel, Switzerland, Basel
Book
Google Scholar
EMBOSS Water. [http://www.ebi.ac.uk/Tools/psa/emboss_water/]
Liu X, Miao D, Zhang F, Wu Z, Liu J, Xiang H: Characterization of the minimal replicon of pHM300 and independent copy number control of major and minor chromosomes of Haloferax mediterranei . FEMS Microbiol Lett. 2013, 339: 66-74. 10.1111/1574-6968.12052.
Article
PubMed
Google Scholar
Sambrook J, Russell DW: Molecular Cloning: A Laboratory Manual. 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 3
Google Scholar
Dyall-Smith M: The Halohandbook. [http://www.haloarchaea.com/resources/halohandbook/]
NCBI blast. [http://blast.ncbi.nlm.nih.gov]
KEGG PATHWAY Database. [http://www.genome.jp/kegg/pathway.html]
Academy of Finland. [http://www.aka.fi/en-GB/A/]
The Alliance of Science Organizations in Germany. [http://www.dfg.de/en/]
The National Science Foundation. [http://www.nsf.gov]
National Aeronautics and Space Administration. [http://www.nasa.gov]