메뉴 건너뛰기




Volumn 8, Issue 7, 2016, Pages 2241-2258

Osmoadaptative strategy and its molecular signature in obligately halophilic heterotrophic protists

Author keywords

Ectoine; Extremophile; Hypersaline; Osmoregulation; Salt in; Salt out

Indexed keywords

CARRIER PROTEIN; PROTOZOAL PROTEIN; TRANSCRIPTOME;

EID: 85015647587     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evw152     Document Type: Article
Times cited : (53)

References (106)
  • 1
    • 0030727942 scopus 로고    scopus 로고
    • Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques
    • Aljanabi SM, Martinez I. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25:4692-4693.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4692-4693
    • Aljanabi, S.M.1    Martinez, I.2
  • 3
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • 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.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 4
    • 0027478050 scopus 로고
    • Ectoine accumulation and osmotic regulation in Brevibacterium linens
    • Bernard T, et al. 1993. Ectoine accumulation and osmotic regulation in Brevibacterium linens. J Gen Microbiol. 139:129-136.
    • (1993) J Gen Microbiol , vol.139 , pp. 129-136
    • Bernard, T.1
  • 5
    • 84904815625 scopus 로고    scopus 로고
    • SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information
    • Biasini M, et al. 2014. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42:W252-W258.
    • (2014) Nucleic Acids Res , vol.42 , pp. W252-W258
    • Biasini, M.1
  • 6
    • 0035958656 scopus 로고    scopus 로고
    • The osmophobic effect: Natural selection of a thermodynamic force in protein folding
    • Bolen DW, Baskakov IV. 2001. The osmophobic effect: natural selection of a thermodynamic force in protein folding. J Mol Biol. 310:955-963.
    • (2001) J Mol Biol , vol.310 , pp. 955-963
    • Bolen, D.W.1    Baskakov, I.V.2
  • 7
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 8
    • 84862676601 scopus 로고    scopus 로고
    • Aggregative multi-cellularity evolved independently in the eukaryotic supergroup Rhizaria
    • Brown MW, Kolisko M, Silberman JD, Roger AJ. 2012. Aggregative multi-cellularity evolved independently in the eukaryotic supergroup Rhizaria. Curr Biol. 22:1123-1127.
    • (2012) Curr Biol , vol.22 , pp. 1123-1127
    • Brown, M.W.1    Kolisko, M.2    Silberman, J.D.3    Roger, A.J.4
  • 9
    • 84859945474 scopus 로고    scopus 로고
    • The evolutionary history of haptophytes and cryptophytes: Phylogenomic evidence for separate origins
    • Burki F, Okamoto N, Pombert JF, Keeling PJ. 2012. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc R Soc Lond [Biol]. 279:2246-2254.
    • (2012) Proc R Soc Lond [Biol] , vol.279 , pp. 2246-2254
    • Burki, F.1    Okamoto, N.2    Pombert, J.F.3    Keeling, P.J.4
  • 10
    • 57149120517 scopus 로고    scopus 로고
    • Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses
    • Bursy J, et al. 2008. Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses. Appl Environ Microbiol. 74:7286-7296.
    • (2008) Appl Environ Microbiol , vol.74 , pp. 7286-7296
    • Bursy, J.1
  • 11
    • 35748980013 scopus 로고    scopus 로고
    • Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase
    • Bursy J, Pierik AJ, Pica N, Bremer E. 2007. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase. J Biol Chem. 282:31147-31155.
    • (2007) J Biol Chem , vol.282 , pp. 31147-31155
    • Bursy, J.1    Pierik, A.J.2    Pica, N.3    Bremer, E.4
  • 12
    • 4844224263 scopus 로고    scopus 로고
    • Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043
    • Calderón MI, et al. 2004. Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043. Microbiol-SGM. 150: 3051-3063.
    • (2004) Microbiol-SGM , vol.150 , pp. 3051-3063
    • Calderón, M.I.1
  • 13
    • 0032586949 scopus 로고    scopus 로고
    • Role of N gamma-acetyldiaminobutyrate as an enzyme stabilizer and an intermediate in the biosynthesis of hydroxyectoine
    • Cánovas D, et al. 1999. Role of N gamma-acetyldiaminobutyrate as an enzyme stabilizer and an intermediate in the biosynthesis of hydroxyectoine. Appl Environ Microbiol. 65:3774-3779.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3774-3779
    • Cánovas, D.1
  • 14
    • 62149097585 scopus 로고    scopus 로고
    • Osmotic responses of Dunaliella to the changes of salinity
    • Chen H, Jiang J-G. 2009. Osmotic responses of Dunaliella to the changes of salinity. J Cell Physiol. 219:251-258.
    • (2009) J Cell Physiol , vol.219 , pp. 251-258
    • Chen, H.1    Jiang, J.-G.2
  • 15
    • 20144377620 scopus 로고    scopus 로고
    • Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    • Chen HL, Zhou HX. 2005. Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res. 33:3193-3199.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3193-3199
    • Chen, H.L.1    Zhou, H.X.2
  • 16
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    • Chevreux B, et al. 2004. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14:1147-1159.
    • (2004) Genome Res , vol.14 , pp. 1147-1159
    • Chevreux, B.1
  • 17
    • 54249105870 scopus 로고    scopus 로고
    • Morphology and molecular phylogeny of Trimyema koreanum n. Sp., a ciliate from the hypersaline water of a solar saltern
    • Cho BC, Park JS, Xu KD, Choi JK. 2008. Morphology and molecular phylogeny of Trimyema koreanum n. sp., a ciliate from the hypersaline water of a solar saltern. J Eukaryot Microbiol. 55:417-426.
    • (2008) J Eukaryot Microbiol , vol.55 , pp. 417-426
    • Cho, B.C.1    Park, J.S.2    Xu, K.D.3    Choi, J.K.4
  • 18
    • 0032516807 scopus 로고    scopus 로고
    • Multiple sorting pathways between the late Golgi and the vacuole in yeast
    • Conibear E, Stevens TH. 1998. Multiple sorting pathways between the late Golgi and the vacuole in yeast. Biochim Biophys Acta. 140:211-230.
    • (1998) Biochim Biophys Acta , vol.140 , pp. 211-230
    • Conibear, E.1    Stevens, T.H.2
  • 19
    • 0034128816 scopus 로고    scopus 로고
    • The alpha-amylase gene amyH of the moderate halophile Halomonas meridiana: Cloning and molecular characterization
    • Coronado MJ, et al. 2000. The alpha-amylase gene amyH of the moderate halophile Halomonas meridiana: cloning and molecular characterization. Microbiology 146:861-868.
    • (2000) Microbiology , vol.146 , pp. 861-868
    • Coronado, M.J.1
  • 20
    • 77954403053 scopus 로고    scopus 로고
    • BMGE (block mapping and gathering with entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments
    • Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 10:210.
    • (2010) BMC Evol Biol , vol.10 , pp. 210
    • Criscuolo, A.1    Gribaldo, S.2
  • 21
    • 84872054814 scopus 로고    scopus 로고
    • An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content
    • 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.
    • (2013) J Biol Chem , vol.288 , pp. 581-588
    • Deole, R.1    Challacombe, J.2    Raiford, D.W.3    Hoff, W.D.4
  • 22
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 23
    • 0032563113 scopus 로고    scopus 로고
    • Electrostatic contributions to the stability of halophilic proteins
    • Elcock AH, McCammon JA. 1998. Electrostatic contributions to the stability of halophilic proteins. J Mol Biol. 280:731-748.
    • (1998) J Mol Biol , vol.280 , pp. 731-748
    • Elcock, A.H.1    McCammon, J.A.2
  • 24
    • 84860833690 scopus 로고    scopus 로고
    • The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales
    • Elevi Bardavid R, Oren A. 2012. The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales. Extremophiles 16:567-572.
    • (2012) Extremophiles , vol.16 , pp. 567-572
    • Elevi Bardavid, R.1    Oren, A.2
  • 25
    • 0034697980 scopus 로고    scopus 로고
    • Predicting sub-cellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson O, Nielsen H, Brunak S, von Heijne G. 2000. Predicting sub-cellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 300:1005-1016.
    • (2000) J Mol Biol , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    Von Heijne, G.4
  • 26
    • 84898056889 scopus 로고    scopus 로고
    • Morphology, ontogenesis and molecular phylogeny of Platynematum salinarum nov. Spec., a new scuticociliate (Ciliophora, Scuticociliatia) from a solar saltern
    • Foissner W, Jung J-H, Filker S, Rudolph J, Stoeck T. 2014. Morphology, ontogenesis and molecular phylogeny of Platynematum salinarum nov. spec., a new scuticociliate (Ciliophora, Scuticociliatia) from a solar saltern. Eur J Protistol. 50:174-184.
    • (2014) Eur J Protistol , vol.50 , pp. 174-184
    • Foissner, W.1    Jung, J.-H.2    Filker, S.3    Rudolph, J.4    Stoeck, T.5
  • 27
    • 0030010138 scopus 로고    scopus 로고
    • Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin
    • Frolow F, Harel M, Sussman JL, Mevarech M, Shoham M. 1996. Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin. Nat Struct Biol. 3:452-458.
    • (1996) Nat Struct Biol , vol.3 , pp. 452-458
    • Frolow, F.1    Harel, M.2    Sussman, J.L.3    Mevarech, M.4    Shoham, M.5
  • 28
    • 0028783450 scopus 로고
    • Osmoadaptation in bacteria
    • Galinski EA. 1995. Osmoadaptation in bacteria. Adv Microb Physiol. 37:272-328.
    • (1995) Adv Microb Physiol , vol.37 , pp. 272-328
    • Galinski, E.A.1
  • 29
    • 33744769732 scopus 로고    scopus 로고
    • The ectD gene, which is involved in the synthesis of the compatible solute hydroxyectoine, is essential for thermo-protection of the halophilic bacterium Chromohalobacter salexigens
    • García-Estepa R, et al. 2006. The ectD gene, which is involved in the synthesis of the compatible solute hydroxyectoine, is essential for thermo-protection of the halophilic bacterium Chromohalobacter salexigens. J Bacteriol. 188:3774-3784.
    • (2006) J Bacteriol , vol.188 , pp. 3774-3784
    • García-Estepa, R.1
  • 30
    • 0026074320 scopus 로고
    • Role of organic osmolytes in adaptation of renal cells to high osmolarity
    • Garcia-Perez A, Burg MB. 1991. Role of organic osmolytes in adaptation of renal cells to high osmolarity. J Membr Biol. 119:1-13.
    • (1991) J Membr Biol , vol.119 , pp. 1-13
    • Garcia-Perez, A.1    Burg, M.B.2
  • 31
    • 0028029829 scopus 로고
    • Signal-mediated retrieval of a membrane protein from the Golgi to the ER in yeast
    • Gaynor EC, Heesen ST, Graham TR, Aebi M, Emr SD. 1994. Signal-mediated retrieval of a membrane protein from the Golgi to the ER in yeast. J Cell Biol. 127:653-665.
    • (1994) J Cell Biol , vol.127 , pp. 653-665
    • Gaynor, E.C.1    Heesen, S.T.2    Graham, T.R.3    Aebi, M.4    Emr, S.D.5
  • 32
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr MG, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29:644-652.
    • (2011) Nat Biotechnol , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 34
    • 42949116727 scopus 로고    scopus 로고
    • Heterotrophic protozoa from hypersaline environments
    • Gunde-Cimerman N, Oren A, Plemenitaš A, editors. Dordrecht: Springer.
    • Hauer G, Rogerson A. 2005. Heterotrophic protozoa from hypersaline environments. In: Gunde-Cimerman N, Oren A, Plemenitaš A, editors. Adaptation to life at high salt concentrations in archaea, bacteria, and eukarya. Dordrecht: Springer. p. 519-539.
    • (2005) Adaptation to Life at High Salt Concentrations in Archaea, Bacteria, and Eukarya , pp. 519-539
    • Hauer, G.1    Rogerson, A.2
  • 35
    • 84960089630 scopus 로고    scopus 로고
    • BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS
    • Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. 2016. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32:767-769.
    • (2016) Bioinformatics , vol.32 , pp. 767-769
    • Hoff, K.J.1    Lange, S.2    Lomsadze, A.3    Borodovsky, M.4    Stanke, M.5
  • 36
    • 0036282743 scopus 로고    scopus 로고
    • Osmotic stress signaling and osmoadaptation in yeasts
    • Hohmann S. 2002. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev. 66:300-372.
    • (2002) Microbiol Mol Biol Rev , vol.66 , pp. 300-372
    • Hohmann, S.1
  • 37
    • 84908432708 scopus 로고    scopus 로고
    • Crystal structure of the ectoine hydroxylase, a snapshot of the active site
    • Höppner A, Widderich N, Lenders M, Bremer E, Smits SHJ. 2014. Crystal structure of the ectoine hydroxylase, a snapshot of the active site. J Biol Chem. 289:29570-29583.
    • (2014) J Biol Chem , vol.289 , pp. 29570-29583
    • Höppner, A.1    Widderich, N.2    Lenders, M.3    Bremer, E.4    Smits, S.H.J.5
  • 38
    • 34547560275 scopus 로고    scopus 로고
    • Wolf PSORT: Protein localization predictor
    • Horton P, et al. 2007. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35:W585-W587.
    • (2007) Nucleic Acids Res , vol.35 , pp. W585-W587
    • Horton, P.1
  • 40
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • Käll L, Krogh A, Sonnhammer ELL. 2004. A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 338:1027-1036.
    • (2004) J Mol Biol , vol.338 , pp. 1027-1036
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 41
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • 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.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 42
    • 84903286893 scopus 로고    scopus 로고
    • The marine microbial eukaryote transcriptome sequencing project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
    • Keeling PJ, et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12:e1001889.
    • (2014) PLoS Biol , vol.12 , pp. e1001889
    • Keeling, P.J.1
  • 43
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, et al. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1
  • 44
    • 0032705896 scopus 로고    scopus 로고
    • Accumulation of myo-inositol in Actinidia seedlings subjected to salt stress
    • Klages K, Boldingh H, Smith GS. 1999. Accumulation of myo-inositol in Actinidia seedlings subjected to salt stress. Ann Bot. 84:521-527.
    • (1999) Ann Bot , vol.84 , pp. 521-527
    • Klages, K.1    Boldingh, H.2    Smith, G.S.3
  • 45
    • 33746174612 scopus 로고    scopus 로고
    • Hypersaline conditions induce changes in cell-wall melanization and colony structure in a halophilic and a xerophilic black yeast species of the genus Trimmatostroma
    • Kogej T, Gorbushina AA, Gunde-Cimerman N. 2006. Hypersaline conditions induce changes in cell-wall melanization and colony structure in a halophilic and a xerophilic black yeast species of the genus Trimmatostroma. Mycol Res. 110:713-724.
    • (2006) Mycol Res , vol.110 , pp. 713-724
    • Kogej, T.1    Gorbushina, A.A.2    Gunde-Cimerman, N.3
  • 46
    • 32044455999 scopus 로고    scopus 로고
    • Halophilic fungus Hortaea werneckii and the halotolerant fungus Aureobasidium pullulans maintain low intracellular cation concentrations in hypersaline environments
    • Kogej T, Ramos J, Plemenitaš A, Gunde-Cimerman N. 2005. Halophilic fungus Hortaea werneckii and the halotolerant fungus Aureobasidium pullulans maintain low intracellular cation concentrations in hypersaline environments. Appl Environ Microbiol. 71:6600-6605.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 6600-6605
    • Kogej, T.1    Ramos, J.2    Plemenitaš, A.3    Gunde-Cimerman, N.4
  • 47
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 305:567-580.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.L.4
  • 48
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. 1982. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 49
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25R25.
    • (2009) Genome Biol , vol.10 , pp. R25R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 50
    • 0016139829 scopus 로고
    • Salt-dependent properties of proteins from extremely halophilic bacteria
    • Lanyi JK. 1974. Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol Rev. 38:272-290.
    • (1974) Bacteriol Rev , vol.38 , pp. 272-290
    • Lanyi, J.K.1
  • 51
    • 84911429068 scopus 로고    scopus 로고
    • AliView: A fast and lightweight alignment viewer and editor for large datasets
    • Larsson A. 2014. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30:3276-3278.
    • (2014) Bioinformatics , vol.30 , pp. 3276-3278
    • Larsson, A.1
  • 52
    • 84896735766 scopus 로고    scopus 로고
    • Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law CW, Chen Y, Shi W, Smyth GK. 2014. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15:R29.
    • (2014) Genome Biol , vol.15 , pp. R29
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 53
    • 84876263777 scopus 로고    scopus 로고
    • EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments
    • Leng N, et al. 2013. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29:1035-1043.
    • (2013) Bioinformatics , vol.29 , pp. 1035-1043
    • Leng, N.1
  • 54
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 55
    • 0026598013 scopus 로고
    • Enzyme stabilization by ectoine-type compatible solutes: Protection against heating, freezing and drying
    • Lippert K, Galinski EA. 1992. Enzyme stabilization by ectoine-type compatible solutes: protection against heating, freezing and drying. Appl Microbiol Biotechnol. 37:61-65.
    • (1992) Appl Microbiol Biotechnol , vol.37 , pp. 61-65
    • Lippert, K.1    Galinski, E.A.2
  • 56
    • 71449098882 scopus 로고    scopus 로고
    • Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways
    • Lo C-C, Bonner CA, Xie G, D'Souza M, Jensen RA. 2009. Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol Mol Biol Rev. 73:594-651.
    • (2009) Microbiol Mol Biol Rev , vol.73 , pp. 594-651
    • Lo, C.-C.1    Bonner, C.A.2    Xie, G.3    D'Souza, M.4    Jensen, R.A.5
  • 57
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:550.
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 58
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • Lunter G, Goodson M. 2011. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21:936-939.
    • (2011) Genome Res , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 59
    • 3142617489 scopus 로고    scopus 로고
    • A novel salt-tolerant L-myo-inositol-1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice - Molecular cloning, bacterial overexpression, characterization, and functional introgression into tobacco-conferring salt tolerance phenotype
    • Majee M, et al. 2004. A novel salt-tolerant L-myo-inositol-1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice - Molecular cloning, bacterial overexpression, characterization, and functional introgression into tobacco-conferring salt tolerance phenotype. J Biol Chem. 279:28539-28552.
    • (2004) J Biol Chem , vol.279 , pp. 28539-28552
    • Majee, M.1
  • 60
    • 58449113058 scopus 로고    scopus 로고
    • Genome analysis of the anaerobic thermoha-lophilic bacterium Halothermothrix orenii
    • Mavromatis K, et al. 2009. Genome analysis of the anaerobic thermoha-lophilic bacterium Halothermothrix orenii. PLoS One 4:e4192.
    • (2009) PLoS One , vol.4
    • Mavromatis, K.1
  • 61
    • 84875578097 scopus 로고    scopus 로고
    • Using tablet for visual exploration of second-generation sequencing data
    • Milne I, et al. 2013. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 14:193-202.
    • (2013) Brief Bioinform , vol.14 , pp. 193-202
    • Milne, I.1
  • 62
    • 77952808412 scopus 로고    scopus 로고
    • Evaluation of computational methods for secreted protein prediction in different eukaryotes
    • Min XJ. 2010. Evaluation of computational methods for secreted protein prediction in different eukaryotes. J Proteomics Bioinform. 3:143-147.
    • (2010) J Proteomics Bioinform , vol.3 , pp. 143-147
    • Min, X.J.1
  • 64
    • 0030472453 scopus 로고    scopus 로고
    • NMR analyses of compatible solutes in a halotolerant Brevibacterium sp
    • Nagata S, Adachi K, Sano H. 1996. NMR analyses of compatible solutes in a halotolerant Brevibacterium sp. Microbiology 142:3355-3362.
    • (1996) Microbiology , vol.142 , pp. 3355-3362
    • Nagata, S.1    Adachi, K.2    Sano, H.3
  • 65
    • 39549086808 scopus 로고    scopus 로고
    • Efficient cyclic system to yield ectoine using Brevibacterium sp JCM 6894 subjected to osmotic downshock
    • Nagata S, et al. 2008. Efficient cyclic system to yield ectoine using Brevibacterium sp JCM 6894 subjected to osmotic downshock. Biotechnol Bioeng. 99:941-948.
    • (2008) Biotechnol Bioeng , vol.99 , pp. 941-948
    • Nagata, S.1
  • 67
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H, Engelbrecht J, Brunak S, von Heijne G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
    • (1997) Protein Eng , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 68
    • 0033022073 scopus 로고    scopus 로고
    • Bioenergetic aspects of halophilism
    • Oren A. 1999. Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev. 63:334-348.
    • (1999) Microbiol Mol Biol Rev , vol.63 , pp. 334-348
    • Oren, A.1
  • 70
    • 0012498466 scopus 로고    scopus 로고
    • Intracellular salt concentration and ion metabolism in halophilic microorganisms
    • Seckbach J, editor. Dordrecht: Kluwyer Academic Publishers.
    • Oren A. 2002b. Intracellular salt concentration and ion metabolism in halophilic microorganisms. In: Seckbach J, editor. Halophilic microorganisms and their environments. Dordrecht: Kluwyer Academic Publishers. p. 207-231.
    • (2002) Halophilic Microorganisms and Their Environments , pp. 207-231
    • Oren, A.1
  • 71
    • 42949104034 scopus 로고    scopus 로고
    • Microbial life at high salt concentrations: Phylogenetic and metabolic diversity
    • Oren A. 2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 4:2.
    • (2008) Saline Syst , vol.4 , pp. 2
    • Oren, A.1
  • 72
    • 84890305097 scopus 로고    scopus 로고
    • Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes
    • Oren A. 2013. Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes. Front Microbiol. 4:315.
    • (2013) Front Microbiol , vol.4 , pp. 315
    • Oren, A.1
  • 73
    • 23944462637 scopus 로고    scopus 로고
    • How to be moderately halophilic with broad salt tolerance: Clues from the genome of Chromohalobacter salexigens
    • Oren A, Larimer F, Richardson P, Lapidus A, Csonka LN. 2005. How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens. Extremophiles 9:275-279.
    • (2005) Extremophiles , vol.9 , pp. 275-279
    • Oren, A.1    Larimer, F.2    Richardson, P.3    Lapidus, A.4    Csonka, L.N.5
  • 74
    • 84155188826 scopus 로고    scopus 로고
    • Effects of different ion compositions on growth of obligately halophilic protozoan Halocafeteria seosinensis
    • Park JS. 2012. Effects of different ion compositions on growth of obligately halophilic protozoan Halocafeteria seosinensis. Extremophiles 16:161-164.
    • (2012) Extremophiles , vol.16 , pp. 161-164
    • Park, J.S.1
  • 75
    • 33751117187 scopus 로고    scopus 로고
    • Halocafeteria seosinensis gen. Et sp. Nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern
    • Park JS, Cho BC, Simpson AGB. 2006. Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern. Extremophiles 10:493-504.
    • (2006) Extremophiles , vol.10 , pp. 493-504
    • Park, J.S.1    Cho, B.C.2    Simpson, A.G.B.3
  • 76
    • 0242491573 scopus 로고    scopus 로고
    • Active flagellates grazing on prokaryotes in high salinity waters of a solar saltern
    • Park JS, Kim HJ, Choi DH, Cho BC. 2003. Active flagellates grazing on prokaryotes in high salinity waters of a solar saltern. Aquat Microb Ecol. 33:173-179.
    • (2003) Aquat Microb Ecol , vol.33 , pp. 173-179
    • Park, J.S.1    Kim, H.J.2    Choi, D.H.3    Cho, B.C.4
  • 77
    • 80053093217 scopus 로고    scopus 로고
    • Characterization of Pharyngomonas kirbyi (=“Macropharyngomonas halophila” nomen nudum), a very deep-branching, obligately halophilic Heterolobosean
    • Park JS, Simpson AGB. 2011. Characterization of Pharyngomonas kirbyi (=“Macropharyngomonas halophila” nomen nudum), a very deep-branching, obligately halophilic Heterolobosean. Protist 162:691-709.
    • (2011) Protist , vol.162 , pp. 691-709
    • Park, J.S.1    Simpson, A.G.B.2
  • 78
    • 84937135179 scopus 로고    scopus 로고
    • Diversity of heterotrophic protists from extremely hypersaline habitats
    • Park JS, Simpson AGB. 2015. Diversity of heterotrophic protists from extremely hypersaline habitats. Protist 166:422-437.
    • (2015) Protist , vol.166 , pp. 422-437
    • Park, J.S.1    Simpson, A.G.B.2
  • 79
    • 34347336591 scopus 로고    scopus 로고
    • Ultrastructure and phylogenetic placement within Heterolobosea of the previously unclassified, extremely halophilic heterotrophic flagellate Pleurostomum flabella-tum (Ruinen 1938)
    • Park JS, Simpson AGB, Lee WJ, Cho BC. 2007. Ultrastructure and phylogenetic placement within Heterolobosea of the previously unclassified, extremely halophilic heterotrophic flagellate Pleurostomum flabella-tum (Ruinen 1938). Protist 158:397-413.
    • (2007) Protist , vol.158 , pp. 397-413
    • Park, J.S.1    Simpson, A.G.B.2    Lee, W.J.3    Cho, B.C.4
  • 80
    • 47149088683 scopus 로고    scopus 로고
    • Molecular signature of hypersaline adaptation: Insights from genome and proteome composition of halophilic prokaryotes
    • Paul S, Bag SK, Das S, Harvill ET, Dutta C. 2008. Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol. 9:R70.
    • (2008) Genome Biol , vol.9 , pp. R70
    • Paul, S.1    Bag, S.K.2    Das, S.3    Harvill, E.T.4    Dutta, C.5
  • 81
    • 0037314097 scopus 로고    scopus 로고
    • Matrix2png: A utility for visualizing matrix data
    • Pavlidis P, Noble WS. 2003. Matrix2png: a utility for visualizing matrix data. Bioinformatics 19:295-296.
    • (2003) Bioinformatics , vol.19 , pp. 295-296
    • Pavlidis, P.1    Noble, W.S.2
  • 82
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 8:785-786.
    • (2011) Nat Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 83
    • 84891757311 scopus 로고    scopus 로고
    • EggNOG v4.0: Nested orthology inference across 3686 organisms
    • Powell S, et al. 2014. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42:D231-D239.
    • (2014) Nucleic Acids Res , vol.42 , pp. D231-D239
    • Powell, S.1
  • 84
  • 85
    • 0024044384 scopus 로고
    • Effect of extreme salt concentrations on the physiology and biochemistry of Halobacteroides acet-oethylicus
    • Rengpipat S, Lowe SE, Zeikus JG. 1988. Effect of extreme salt concentrations on the physiology and biochemistry of Halobacteroides acet-oethylicus. J Bacteriol. 170:3065-3071.
    • (1988) J Bacteriol , vol.170 , pp. 3065-3071
    • Rengpipat, S.1    Lowe, S.E.2    Zeikus, J.G.3
  • 86
    • 24644509270 scopus 로고    scopus 로고
    • Cloning, purification, and characterization of diaminobutyrate acetyltransferase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z
    • Reshetnikov AS, Mustakhimov II, Khmelenina VN, Trotsenko YA. 2005. Cloning, purification, and characterization of diaminobutyrate acetyltransferase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Biochem (Mosc). 70:878-883.
    • (2005) Biochem (Mosc) , vol.70 , pp. 878-883
    • Reshetnikov, A.S.1    Mustakhimov, I.I.2    Khmelenina, V.N.3    Trotsenko, Y.A.4
  • 87
    • 84867364321 scopus 로고    scopus 로고
    • Phytools: An R package for phylogenetic comparative biology (and other things)
    • Revell LJ. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 3:217-223.
    • (2012) Methods Ecol Evol , vol.3 , pp. 217-223
    • Revell, L.J.1
  • 88
    • 41349119604 scopus 로고    scopus 로고
    • PCCA: A program for phylogenetic canonical correlation analysis
    • Revell LJ, Harrison AS. 2008. PCCA: a program for phylogenetic canonical correlation analysis. Bioinformatics 24:1018-1020.
    • (2008) Bioinformatics , vol.24 , pp. 1018-1020
    • Revell, L.J.1    Harrison, A.S.2
  • 89
    • 0034620588 scopus 로고    scopus 로고
    • Halophilic adaptation: Novel solvent protein interactions observed in the 2.9 and 2.6 Å resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui
    • Richard SB, Madern D, Garcin E, Zaccai G. 2000. Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 Å resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui. Biochemistry 39:992-1000.
    • (2000) Biochemistry , vol.39 , pp. 992-1000
    • Richard, S.B.1    Madern, D.2    Garcin, E.3    Zaccai, G.4
  • 90
    • 84926507971 scopus 로고    scopus 로고
    • Limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie ME, et al. 2015. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43:e47.
    • (2015) Nucleic Acids Res , vol.43 , pp. e47
    • Ritchie, M.E.1
  • 92
    • 33747154433 scopus 로고    scopus 로고
    • High-yield cultivation of Marinococcus M52 for production and recovery of hydroxyectoine
    • Schiraldi C, Maresca C, Catapano A, Galinski EA, De Rosa M. 2006. High-yield cultivation of Marinococcus M52 for production and recovery of hydroxyectoine. Res Microbiol. 157:693-699.
    • (2006) Res Microbiol , vol.157 , pp. 693-699
    • Schiraldi, C.1    Maresca, C.2    Catapano, A.3    Galinski, E.A.4    De Rosa, M.5
  • 93
    • 0032760945 scopus 로고    scopus 로고
    • Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes
    • Schofield CJ, Zhang ZH. 1999. Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes. Curr Opin Struct Biol. 9:722-731.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 722-731
    • Schofield, C.J.1    Zhang, Z.H.2
  • 94
    • 79953168805 scopus 로고    scopus 로고
    • Natural and engineered hydroxyectoine production based on the Pseudomonas stutzeri ectABCD-ask gene cluster
    • Seip B, Galinski EA, Kurz M. 2011. Natural and engineered hydroxyectoine production based on the Pseudomonas stutzeri ectABCD-ask gene cluster. Appl Environ Microbiol. 77:1368-1374.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 1368-1374
    • Seip, B.1    Galinski, E.A.2    Kurz, M.3
  • 95
    • 0026699271 scopus 로고
    • The predominant role of recently discovered tetrahydropyrimidine for the osmoadaptation of halophilic eubacteria
    • Severin J, Wohlfarth A, Galinski EA. 1992. The predominant role of recently discovered tetrahydropyrimidine for the osmoadaptation of halophilic eubacteria. J Gen Microbiol. 138:1629-1638.
    • (1992) J Gen Microbiol , vol.138 , pp. 1629-1638
    • Severin, J.1    Wohlfarth, A.2    Galinski, E.A.3
  • 96
    • 0005201001 scopus 로고
    • Lipid composition of the plasma membrane of the halotolerant alga, Dunaliella salina
    • Sheffer M, Fried A, Gottlieb HE, Tietz A, Avron M. 1986. Lipid composition of the plasma membrane of the halotolerant alga, Dunaliella salina. Biochim Biophys Acta. 857:165-172.
    • (1986) Biochim Biophys Acta , vol.857 , pp. 165-172
    • Sheffer, M.1    Fried, A.2    Gottlieb, H.E.3    Tietz, A.4    Avron, M.5
  • 97
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
    • Stamatakis A, Ludwig T, Meier H. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463.
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 98
    • 84924283510 scopus 로고    scopus 로고
    • Living at the limits: Evidence for microbial eukaryotes thriving under pressure in deep anoxic, hypersaline habitats
    • Stoeck T, et al. 2014. Living at the limits: evidence for microbial eukaryotes thriving under pressure in deep anoxic, hypersaline habitats. Adv Ecol. 2014:532687.
    • (2014) Adv Ecol , vol.2014 , pp. 532687
    • Stoeck, T.1
  • 99
    • 80052309177 scopus 로고    scopus 로고
    • A specialized aspartokinase enhances the biosynthesis of the osmoprotectants ectoine and hydroxyectoine in Pseudomonas stutzeri A1501
    • Stöveken N, et al. 2011. A specialized aspartokinase enhances the biosynthesis of the osmoprotectants ectoine and hydroxyectoine in Pseudomonas stutzeri A1501. J Bacteriol. 193:4456-4468.
    • (2011) J Bacteriol , vol.193 , pp. 4456-4468
    • Stöveken, N.1
  • 100
    • 0242487523 scopus 로고    scopus 로고
    • Estimation of rates-across-sites distributions in phylogenetic substitution models
    • Susko E, Field C, Blouin C, Roger AJ. 2003. Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst Biol. 52:594-603.
    • (2003) Syst Biol , vol.52 , pp. 594-603
    • Susko, E.1    Field, C.2    Blouin, C.3    Roger, A.J.4
  • 101
    • 0037264650 scopus 로고    scopus 로고
    • Plasma membrane mono-amine transporters: Structure, regulation and function
    • Torres GE, Gainetdinov RR, Caron MG. 2003. Plasma membrane mono-amine transporters: structure, regulation and function. Nature Rev Neurosci. 4:13-25.
    • (2003) Nature Rev Neurosci , vol.4 , pp. 13-25
    • Torres, G.E.1    Gainetdinov, R.R.2    Caron, M.G.3
  • 102
    • 0024571667 scopus 로고
    • Species-specific variation in signal peptide design - Implications for protein secretion in foreign hosts
    • Vonheijne G, Abrahmsen L. 1989. Species-specific variation in signal peptide design - implications for protein secretion in foreign hosts. FEBS Lett. 244:439-446.
    • (1989) FEBS Lett , vol.244 , pp. 439-446
    • Vonheijne, G.1    Abrahmsen, L.2
  • 103
    • 84899541925 scopus 로고    scopus 로고
    • Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms
    • Widderich N, et al. 2014. Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. Plos One 9: e93809e93809.
    • (2014) Plos One , vol.9
    • Widderich, N.1
  • 105
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 106
    • 84894319739 scopus 로고    scopus 로고
    • Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales
    • Youssef NH, 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.
    • (2014) Isme J , vol.8 , pp. 636-649
    • Youssef, N.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.