Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

PLoS Genetics

Volumn 10, Issue 11, 2014, Pages

  Becker, Erin A ^a   Seitzer, Phillip M ^a,b,c   Tritt, Andrew ^d   Larsen, David ^a   Krusor, Megan ^a   Yao, Andrew I ^a,b   Wu, Dongying ^d   Madern, Dominique ^e,f,g   Eisen, Jonathan A ^a   Darling, Aaron E ^h   Facciotti, Marc T ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Davis   (United States)

^c PROTEOME SOFTWARE INC   (United States)

^d DOE JOINT GENOME INSTITUTE   (United States)

^e UNIV GRENOBLE ALPES   (France)

^f CNRS   (France)

^g INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^h UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORIDE; MAGNESIUM; POTASSIUM; SODIUM; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ADAPTATION; ARTICLE; BACTERIUM; CLADISTICS; GENE SEQUENCE; GENOME; HALOBACTERIALES; HALOPHILIC ARCHAEON; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; NONHUMAN; OSMOADAPTATION; OSMOLARITY; OSMOSIS; PHYLOGENY; POTASSIUM TRANSPORT; SHOCK; SODIUM TRANSPORT; ARCHAEAL GENOME; ARCHAEON; GENETICS; HUMAN; METAGENOMICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SALINITY;

ADAPTATION, PHYSIOLOGICAL; ARCHAEA; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENOME, ARCHAEAL; HUMANS; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; OSMOLAR CONCENTRATION; PHYLOGENY; SALINITY; TATA-BOX BINDING PROTEIN;

EID: 84912059789     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004784     Document Type: Article

References (115)

1. Vogel BF, Hansen LT, Mordhorst H, Gram L, (2010) The survival of Listeria monocytogenes during long term desiccation is facilitated by sodium chloride and organic material. Int J Food Microbiol 140: 192–200 doi:10.1016/j.ijfoodmicro.2010.03.035
2. Finn S, Händler K, Condell O, Colgan A, Cooney S, et al. (2013) ProP is required for the survival of desiccated Salmonella enterica serovar typhimurium cells on a stainless steel surface. Appl Environ Microbiol 79: 4376–4384 doi:10.1128/AEM.00515-13
3. Jogaiah S, Govind SR, Tran L-SP, (2013) Systems biology-based approaches toward understanding drought tolerance in food crops. Crit Rev Biotechnol 33: 23–39 doi:10.3109/07388551.2012.659174
4. Chen Q, Duan E, (2011) Aquaporins in sperm osmoadaptation: an emerging role for volume regulation. Acta Pharmacol Sin 32: 721–724 doi:10.1038/aps.2011.35
5. Bettari L, Fiuzat M, Felker GM, O'Connor CM, (2012) Significance of hyponatremia in heart failure. Heart Fail Rev 17: 17–26 doi:10.1007/s10741-010-9193-3
6. Levillain O, Schmolke M, Guder W, (2001) Influence of dehydratation on glycerophosphorylcholine and choline distribution along the rat nephron. Pflugers Arch - Eur J Physiol 442: 218–222 doi:10.1007/s004240100534
7. Maallem S, Wierinckx A, Lachuer J, Kwon MH, Tappaz ML, (2008) Gene expression profiling in brain following acute systemic hypertonicity: novel genes possibly involved in osmoadaptation. J Neurochem 105: 1198–1211 doi:10.1111/j.1471-4159.2008.05222.x
8. Verbalis JG, (2003) Disorders of body water homeostasis. Best Pract Res Clin Endocrinol Metab 17: 471–503 doi:10.1016/S1521-690X(03)00049-6
9. Falb M, Müller K, Königsmaier L, Oberwinkler T, Horn P, et al. (2008) Metabolism of halophilic archaea. Extremophiles 12: 177–196 doi:10.1007/s00792-008-0138-x
10. Bowers KJ, Wiegel J, (2011) Temperature and pH optima of extremely halophilic archaea: a mini-review. Extremophiles 15: 119–128 doi:10.1007/s00792-010-0347-y
11. Soppa J, (2006) From genomes to function: haloarchaea as model organisms. Microbiology 152: 585–590 doi:10.1099/mic.0.28504-0
12. Soppa J, (2011) Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of Haloferax volcanii. Archaea 2011: 602408 doi:10.1155/2011/602408
13. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75 doi:10.1186/1471-2164-9-75
14. NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (n.d.). Available: http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html. Accessed 17 April 2013.
15. Altschul S, (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402 doi:10.1093/nar/25.17.3389
16. Enright AJ, Van Dongen S, Ouzounis CA, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575–1584.
17. Seitzer P, Huynh TA, Facciotti MT, (2013) JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. BMC Bioinformatics 14: 18 doi:10.1186/1471-2105-14-18
18. Tritt A, Eisen JA, Facciotti MT, Darling AE, (2012) An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7: e42304 doi:10.1371/journal.pone.0042304
19. Walsh DA, Bapteste E, Kamekura M, Doolittle WF, (2004) Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 21: 2340–2351 doi:10.1093/molbev/msh248
20. Wu D, Jospin G, Eisen JA, (2013) Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 8: e77033 doi:10.1371/journal.pone.0077033
21. Tindall BJ, (2003) Taxonomic problems arising in the genera Haloterrigena and Natrinema. Int J Syst Evol Microbiol 53: 1697–1698 doi:10.1099/ijs.0.02529-0
22. Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R, et al. (2010) Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. Int J Syst Evol Microbiol 60: 2398–2408 doi:10.1099/ijs.0.017160-0
23. Kuzniar A, van Ham RCHJ, Pongor S, Leunissen JAM, (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 24: 539–551 doi:10.1016/j.tig.2008.08.009
24. Tatusov RL, Galperin MY, Natale DA, Koonin E V, (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 33–36.
25. Nelson-Sathi S, Dagan T, Landan G, Janssen A., Steel M, et al. (2012) Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci 109. doi: 10.1073/pnas.1209119109.
26. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P, (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245–252 doi:10.1038/nrmicro1852
27. Kelly S, Wickstead B, Gull K, (2011) Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc Biol Sci 278: 1009–1018 doi:10.1098/rspb.2010.1427
28. Makarova KS, Yutin N, Bell SD, Koonin EV, (2010) Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol 8: 731–741 doi:10.1038/nrmicro2406
29. Gogarten JP, Townsend JP, (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3: 679–687 doi:10.1038/nrmicro1204
30. Barthelmebs L, Lecomte B, Divies C (2000) Inducible Metabolism of Phenolic Acids inPediococcus pentosaceus Is Encoded by an Autoregulated Operon Which Involves a New Class of Negative Transcriptional Regulator Inducible Metabolism of Phenolic Acids in Pediococcus pentosaceus Is Encoded by an Auto. doi: 10.1128/JB.182.23.6724–6731.2000.Updated.
31. Huillet E, Velge P, Vallaeys T, Pardon P, (2006) LadR, a new PadR-related transcriptional regulator from Listeria monocytogenes, negatively regulates the expression of the multidrug efflux pump MdrL. FEMS Microbiol Lett 254: 87–94 doi:10.1111/j.1574-6968.2005.00014.x
32. Daniels CJ, McKee a H, Doolittle WF, (1984) Archaebacterial heat-shock proteins. EMBO J 3: 745–749.
33. Coker JA, DasSarma S, (2007) Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA. BMC Genet 8: 61 doi:10.1186/1471-2156-8-61
34. Dutta C, Paul S, (2012) Microbial lifestyle and genome signatures. Curr Genomics 13: 153–162 doi:10.2174/138920212799860698
35. Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, et al. (2010) The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 5: e9605 doi:10.1371/journal.pone.0009605
36. De Rosa M, Gambacorta A, (1988) The lipids of archaebacteria. Prog Lipid Res 27: 153–175.
37. Yamauchi K, Doi K, Yoshida Y, Kinoshita M, (1993) Archaebacterial lipids: highly proton-impermeable membranes from 1,2-diphytanyl-sn-glycero-3-phosphocholine. Biochim Biophys Acta 1146: 178–182.
38. Bidle KA, Hanson TE, Howell K, Nannen J, (2007) HMG-CoA reductase is regulated by salinity at the level of transcription in Haloferax volcanii. Extremophiles 11: 49–55 doi:10.1007/s00792-006-0008-3
39. Kokoeva MV, Storch K, Klein C, Oesterhelt D (2002) A novel mode of sensory transduction in archaea: binding protein-mediated chemotaxis towards osmoprotectants and amino acids. 21.
40. Goh F, Jeon YJ, Barrow K, Neilan BA, Burns BP, (2011) Osmoadaptive strategies of the archaeon Halococcus hamelinensis isolated from a hypersaline stromatolite environment. Astrobiology 11: 529–536 doi:10.1089/ast.2010.0591
41. Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, et al. (2014) Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. ISME J 8: 636–649 doi:10.1038/ismej.2013.165
42. Kempf B, Bremer E, (1998) Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch Microbiol 170: 319–330.
43. Spanheimer R, Müller V, (2008) The molecular basis of salt adaptation in Methanosarcina mazei Gö1. Arch Microbiol 190: 271–279 doi:10.1007/s00203-008-0363-9
44. Corratgé-Faillie C, Jabnoune M, Zimmermann S, Véry A-A, Fizames C, et al. (2010) Potassium and sodium transport in non-animal cells: the Trk/Ktr/HKT transporter family. Cell Mol Life Sci 67: 2511–2532 doi:10.1007/s00018-010-0317-7
45. Levina N, Tötemeyer S, Stokes NR, Louis P, Jones MA, et al. (1999) Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity. EMBO J 18: 1730–1737 doi:10.1093/emboj/18.7.1730
46. Oren A, (1999) Bioenergetic Aspects of Halophilism. Microbiol Mol Biol Rev 63: 334.
47. Müller V, Oren A, (2003) Metabolism of chloride in halophilic prokaryotes. Extremophiles 7: 261–266 doi:10.1007/s00792-003-0332-9
48. Duschl A, Wagner G, (1986) Primary and secondary chloride transport in Halobacterium halobium. J Bacteriol 168: 548–552.
49. Warmuth S, Zimmermann I, Dutzler R, (2009) X-ray structure of the C-terminal domain of a prokaryotic cation-chloride cotransporter. Structure 17: 538–546 doi:10.1016/j.str.2009.02.009
50. Accardi A, Miller C, (2004) Secondary active transport mediated by a prokaryotic homologue of ClC Cl- channels. Nature 427: 803–807 doi:10.1038/nature02314
51. Iyer R, Iverson TM, Accardi A, Miller C, (2002) A biological role for prokaryotic ClC chloride channels. 419: 7–9 doi:10.1038/nature01003.1
52. Hezayen FF, Rehm BH, Tindall BJ, Steinbüchel A, (2001) Transfer of Natrialba asiatica B1T to Natrialba taiwanensis sp. nov. and description of Natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the Archaea from Egypt that produces extracellular poly (glutamic). Int J Syst Evol Microbiol 51: 1133–1142.
53. Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, et al. (2012) A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 13: 165 doi:10.1186/1471-2164-13-165
54. Orellana MV, Pang WL, Durand PM, Whitehead K, Baliga NS, (2013) A role for programmed cell death in the microbial loop. PLoS One 8: e62595 doi:10.1371/journal.pone.0062595
55. Holtmann G, Bremer E (2004) Thermoprotection of Bacillus subtilis by Exogenously Provided Glycine Betaine and Structurally Related Compatible Solutes: Involvement of Opu Transporters Thermoprotection of Bacillus subtilis by Exogenously Provided Glycine Betaine and Structurally Rela. doi: 10.1128/JB.186.6.1683.
56. Tschapek B, Pittelkow M, Sohn-Bösser L, Holtmann G, Smits SHJ, et al. (2011) Arg149 is involved in switching the low affinity, open state of the binding protein AfProX into its high affinity, closed state. J Mol Biol 411: 36–52 doi:10.1016/j.jmb.2011.05.039
57. Wood JM, Bremer E, Csonka LN, Kraemer R, Poolman B, et al. (2001) Osmosensing and osmoregulatory compatible solute accumulation by bacteria. Comp Biochem Physiol A Mol Integr Physiol 130: 437–460.
58. Santos H, Costa MS, (2002) Minireview Compatible solutes of organisms that live in hot saline environments. 4: 501–509.
59. Lamark T, Kaasen I, Eshoo MW, Falkenberg P, McDougall J, et al. (1991) DNA sequence and analysis of the bet genes encoding the osmoregulatory choline-glycine betaine pathway of Escherichia coli. Mol Microbiol 5: 1049–1064.
60. Boch J, Kempf B, Schmid R, Bremer E, Boch J, et al. (1996) Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: characterization of the gbsAB genes. 178.
61. Madern D, Ebel C, Zaccai G, (2000) Halophilic adaptation of enzymes. Extremophiles 4: 91–98.
62. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, et al. (2000) Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97: 12176–12181 doi:10.1073/pnas.190337797
63. Soppa J, Baumann A, Brenneis M, Dambeck M, Hering O, et al. (2008) Genomics and functional genomics with haloarchaea. Arch Microbiol 190: 197–215 doi:10.1007/s00203-008-0376-4
64. Zaccai G, (2013) Hydration shells with a pinch of salt. Biopolymers 99: 233–238 doi:10.1002/bip.22154
65. Talon R, Coquelle N, Madern D, Girard E, (2014) An experimental point of view on hydration/solvation in halophilic proteins. Front Microbiol 5: 66 doi:10.3389/fmicb.2014.00066
66. Deole R, Challacombe J, Raiford DW, Hoff WD, (2013) An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content. J Biol Chem 288: 581–588 doi:10.1074/jbc.M112.420505
67. Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, et al. (2014) Data Dryad Package. Data Dryad. doi: 10.5061/dryad.1546n.
68. Schwartz R, Ting CS, King J, (2001) Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. Genome Res 11: 703–709 doi:10.1101/gr.158701
69. Bolhuis H, Palm P, Wende A, Falb M, Rampp M, et al. (2006) The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7: 169 doi:10.1186/1471-2164-7-169
70. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, et al. (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6: 81–93 doi:10.1038/ismej.2011.78
71. Daubin V, Lerat E, Perrière G, (2003) The source of laterally transferred genes in bacterial genomes. Genome Biol 4: R57 doi:10.1186/gb-2003-4-9-r57
72. Oren A, Arahal DR, Ventosa A, (2009) Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 59: 637–642 doi:10.1099/ijs.0.008904-0
73. Goodrich JA, Tjian R, (2010) Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet 11: 549–558 doi:10.1038/nrg2847
74. Reichlen MJ, Murakami KS, Ferry JG, (2010) Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans. J Bacteriol 192: 1511–1517 doi:10.1128/JB.01165-09
75. Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, et al. (2011) Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol 7: 554 doi:10.1038/msb.2011.87
76. Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, et al. (2007) General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A 104: 4630–4635 doi:10.1073/pnas.0611663104
77. Teufel K, Bleiholder A, Griesbach T, Pfeifer F, (2008) Variations in the multiple tbp genes in different Halobacterium salinarum strains and their expression during growth. Arch Microbiol 190: 309–318 doi:10.1007/s00203-008-0383-5
78. Soppa J, (1999) Transcription initiation in Archaea: facts, factors and future aspects. Mol Microbiol 31: 1295–1305.
79. Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, et al. (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2: e243 doi:10.7717/peerj.243
80. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, et al. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7: 455–457 doi:10.1038/nmeth.1457
81. Adey A, Morrison HG, Asan, Xun X, Kitzman JO, et al. (2010) Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 11: R119 doi:10.1186/gb-2010-11-12-r119
82. Edgar RC, (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113 doi:10.1186/1471-2105-5-113
83. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307–321 doi:10.1093/sysbio/syq010
84. Paradis E, Claude J, Strimmer K, (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20: 289–290 doi:10.1093/bioinformatics/btg412
85. Rambaut A (2012) FigTree v12.05: http://tree.bio.ed.ac.uk/software/figtree/.
86. Moreno-Hagelsieb G, Latimer K, (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24: 319–324 doi:10.1093/bioinformatics/btm585
87. Heinrich (2012) org.knowceans.util.Samplers. Available: http://www.arbylon.net/projects/knowceans-tools/doc/org/knowceans/util/Samplers.html. Accessed 2 September 2012.
88. Katoh K, Misawa K, Kuma K, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059–3066.
89. Darriba D, Taboada GL, Doallo R, Posada D, (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27: 1164–1165 doi:10.1093/bioinformatics/btr088
90. Fredslund J, (2006) PHY.FI: fast and easy online creation and manipulation of phylogeny color figures. BMC Bioinformatics 7: 315 doi:10.1186/1471-2105-7-315
91. Letunic I, Bork P, (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475–8 doi:10.1093/nar/gkr201
92. Letunic I, Bork P, (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127–128 doi:10.1093/bioinformatics/btl529
93. MATLAB and Statistics Toolbox Release 2012b, The MathWorks, Inc., Natick, Massachusetts, United States. (n.d.).
94. Woodward O (2009) export_fig.
95. Holland RCG, Down TA, Pocock M, Prlić A, Huen D, et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics 24: 2096–2097 doi:10.1093/bioinformatics/btn397
96. Schmeing TM, Moore PB, Steitz TA (2003) Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit: 1345–1352. doi: 10.1261/rna.5120503.The.
97. Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, et al. (2000) Small Ribosomal Subunit ° Resolution at 3. 3 A. 102: 615–623.
98. The PyMOL Molecular Graphics System, Version 1.5.04, Schrödinger, LLC. (n.d.).
99. Arnold K, Bordoli L, Kopp J, Schwede T, (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195–201 doi:10.1093/bioinformatics/bti770
100. Littlefield O, Korkhin Y, Sigler PB, (1999) The structural basis for the oriented assembly of a TBP/TFB/promoter complex. Proc Natl Acad Sci U S A 96: 13668–13673.
101. Kobayashi K, Saito K, Ishitani R, Ito K, Nureki O, (2012) Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex. Nucleic Acids Res 40: 9319–9328 doi:10.1093/nar/gks660
102. Killick R, Eckley I (2012) Changepoint: an R package for changepoint analysis. R package version 0.6.1.
103. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.69. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
104. Price MN, Dehal PS, Arkin AP, (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641–1650 doi:10.1093/molbev/msp077
105. Price M (n.d.) Fast Tree-Comparison Tools. Distributed by the author. Department of Computational and Theoretical Biology, Lawrence Berkeley National Laboratory.
106. Eddy S, (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23: 205–211.
107. MATLAB and Bioinformatics Toolbox Release 2012b, The MathWorks, Inc., Natick, Massachusetts, United States. (n.d.).
108. Eisen M, Spellman P, Brown P, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863–14868.
109. Lynch EA, Langille MGI, Darling A, Wilbanks EG, Haltiner C, et al. (2012) Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One 7: e41389 doi:10.1371/journal.pone.0041389
110. Roh SW, Nam Y-D, Nam S-H, Choi S-H, Park H-S, et al. (2010) Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon. J Bacteriol 192: 4528–4529 doi:10.1128/JB.00663-10
111. Jiang X, Wang S, Cheng H, Huo Y, Zhang X, et al. (2011) Genome sequence of Halobiforma lacisalsi AJ5, an extremely halophilic archaeon which harbors a bop gene. J Bacteriol 193: 7023–7024 doi:10.1128/JB.06282-11
112. Burns BP, Gudhka RK, Neilan B a, (2012) Genome sequence of the halophilic archaeon Halococcus hamelinensis. J Bacteriol 194: 2100–2101 doi:10.1128/JB.06599-11
113. Han J, Zhang F, Hou J, Liu X, Li M, et al. (2012) Complete genome sequence of the metabolically versatile halophilic archaeon Haloferax mediterranei, a poly(3-hydroxybutyrate-co-3-hydroxyvalerate) producer. J Bacteriol 194: 4463–4464 doi:10.1128/JB.00880-12
114. Malfatti S, Tindall BJ, Schneider S, Fähnrich R, Lapidus A (2009) Complete genome sequence of Halogeometricum borinquense type strain (PR3 T): 150–158. doi: 10.4056/23264.
115. Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, et al. (2012) A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 13: 165 doi:10.1186/1471-2164-13-165