메뉴 건너뛰기




Volumn 8, Issue 1, 2012, Pages

Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: Influences on polyester production

Author keywords

Biopolyesters; Genome evolution; Halomonadaceae; Halomonas; Halomonas boliviensis; Halophilic bacterium; Polyhydroxyalkanoates; Population genetics

Indexed keywords

ADAPTATION; BACTERIUM; CARBOHYDRATE; CHROMOSOME; GENE TRANSFER; GENOME; GLUCOSE; METABOLISM; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; POLYMER; POLYMORPHISM; POPULATION GENETICS; PROTEIN; RECOMBINATION;

EID: 84862981182     PISSN: 20469063     EISSN: None     Source Type: Journal    
DOI: 10.1186/2046-9063-8-9     Document Type: Article
Times cited : (15)

References (47)
  • 1
    • 0027020232 scopus 로고
    • The nearly neutral theory of molecular evolution
    • Ohta T. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 1992, 23:263-286.
    • (1992) Annu Rev Ecol Syst , vol.23 , pp. 263-286
    • Ohta, T.1
  • 2
    • 79952201675 scopus 로고    scopus 로고
    • The tree and net components of prokaryote evolution
    • 10.1093/gbe/evq062, 2997564, 20889655
    • Puigbò P, Wolf YI, Koonin EV. The tree and net components of prokaryote evolution. Genome Biol Evol 2010, 2:745-756. 10.1093/gbe/evq062, 2997564, 20889655.
    • (2010) Genome Biol Evol , vol.2 , pp. 745-756
    • Puigbò, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 3
    • 13144257707 scopus 로고    scopus 로고
    • The genetic theory of adaptation: a brief history
    • Orr H. The genetic theory of adaptation: a brief history. Nature Reviews 2005, 6:119-127.
    • (2005) Nature Reviews , vol.6 , pp. 119-127
    • Orr, H.1
  • 4
    • 68149093715 scopus 로고    scopus 로고
    • Search for a 'Tree of Life' in the thicket of the phylogenetic forest
    • Puigbò P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biology 2009, 8:1-17.
    • (2009) J Biology , vol.8 , pp. 1-17
    • Puigbò, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 5
    • 79952835117 scopus 로고    scopus 로고
    • Harvesting evolutionary signals in a forest of prokaryotic gene trees
    • Schliep K, Lopez P, Lapointe FJ, Bapteste E. Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol 2010, 28:1393-1405.
    • (2010) Mol Biol Evol , vol.28 , pp. 1393-1405
    • Schliep, K.1    Lopez, P.2    Lapointe, F.J.3    Bapteste, E.4
  • 6
    • 80055030247 scopus 로고    scopus 로고
    • Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships
    • 10.1186/1475-2859-10-88, 3227634, 22040376
    • Cai L, Tan D, Aibaidula G, Dong X, Chen J, Tian W, Chen G. Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships. Microb Cell Fact 2011, 10:88. 10.1186/1475-2859-10-88, 3227634, 22040376.
    • (2011) Microb Cell Fact , vol.10 , pp. 88
    • Cai, L.1    Tan, D.2    Aibaidula, G.3    Dong, X.4    Chen, J.5    Tian, W.6    Chen, G.7
  • 7
    • 42949104034 scopus 로고    scopus 로고
    • Microbial life at high salt concentrations: phylogenetic and metabolic diversity
    • 10.1186/1746-1448-4-2, 2329653, 18412960
    • Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 2008, 4:2. 10.1186/1746-1448-4-2, 2329653, 18412960.
    • (2008) Saline Systems , vol.4 , pp. 2
    • Oren, A.1
  • 8
    • 23944462637 scopus 로고    scopus 로고
    • How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens
    • 10.1007/s00792-005-0442-7, 15902510
    • Oren A, Larimer F, Richardson P, Lapidus A, Csonka LN. How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens. Extremophiles 2005, 9:275-279. 10.1007/s00792-005-0442-7, 15902510.
    • (2005) Extremophiles , vol.9 , pp. 275-279
    • Oren, A.1    Larimer, F.2    Richardson, P.3    Lapidus, A.4    Csonka, L.N.5
  • 9
    • 79952810798 scopus 로고    scopus 로고
    • A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T
    • 3187862, 20849449
    • Schvibbert K, et al. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Environ Microbiol 2010, 13:1973-1994. 3187862, 20849449.
    • (2010) Environ Microbiol , vol.13 , pp. 1973-1994
    • Schvibbert, K.1
  • 10
    • 84862907458 scopus 로고    scopus 로고
    • Draft genome sequence of Halomonas sp. strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil
    • Lin Y, et al. Draft genome sequence of Halomonas sp. strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil. J Bacteriol 2011, 194:199-200.
    • (2011) J Bacteriol , vol.194 , pp. 199-200
    • Lin, Y.1
  • 11
    • 33646498780 scopus 로고    scopus 로고
    • Organic compatible solutes of halotolerant and halophilic microorganism
    • 10.1186/1746-1448-1-5, 1224877, 16176595
    • Roberts MF. Organic compatible solutes of halotolerant and halophilic microorganism. Saline Systems 2005, 1:5. 10.1186/1746-1448-1-5, 1224877, 16176595.
    • (2005) Saline Systems , vol.1 , pp. 5
    • Roberts, M.F.1
  • 12
    • 78651313713 scopus 로고    scopus 로고
    • Molecular population genetics and selection in the glycolytic pathway
    • 10.1242/jeb.046458, 3183487, 21177937
    • Eanes WF. Molecular population genetics and selection in the glycolytic pathway. J Exp Biol 2011, 214:165-171. 10.1242/jeb.046458, 3183487, 21177937.
    • (2011) J Exp Biol , vol.214 , pp. 165-171
    • Eanes, W.F.1
  • 13
    • 0033369552 scopus 로고    scopus 로고
    • Analysis of selection on enzyme polymorphism
    • Eanes WF. Analysis of selection on enzyme polymorphism. Annu Rev Ecol Syst 1999, 30:301-326.
    • (1999) Annu Rev Ecol Syst , vol.30 , pp. 301-326
    • Eanes, W.F.1
  • 14
    • 0022410121 scopus 로고
    • Limits of adaptation: the evolution of selective neutrality
    • 1202663, 3932127
    • Hartl D, Dykhuizen D, Dean A. Limits of adaptation: the evolution of selective neutrality. Genetics 1985, 111:655-674. 1202663, 3932127.
    • (1985) Genetics , vol.111 , pp. 655-674
    • Hartl, D.1    Dykhuizen, D.2    Dean, A.3
  • 15
    • 2942665971 scopus 로고    scopus 로고
    • Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile bacterium isolated from soil around a Bolivian hypersaline lake
    • 10.1099/ijs.0.02800-0, 15143014
    • Quillaguamán J, Hatti-Kaul R, Mattiasson B, Alvarez MT, Delgado O. Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile bacterium isolated from soil around a Bolivian hypersaline lake. Int J Syst Evol Microbiol 2004, 54:721-725. 10.1099/ijs.0.02800-0, 15143014.
    • (2004) Int J Syst Evol Microbiol , vol.54 , pp. 721-725
    • Quillaguamán, J.1    Hatti-Kaul, R.2    Mattiasson, B.3    Alvarez, M.T.4    Delgado, O.5
  • 17
    • 77951976828 scopus 로고    scopus 로고
    • High productivity of ectoines by Halomonas boliviensis using a combined two-step fed-batch culture and milking process
    • 10.1016/j.jbiotec.2010.03.003, 20223266
    • Van-Thuoc D, Guzmán H, Quillaguamán J, Hatti-Kaul R. High productivity of ectoines by Halomonas boliviensis using a combined two-step fed-batch culture and milking process. J Biotechnol 2010, 147:46-51. 10.1016/j.jbiotec.2010.03.003, 20223266.
    • (2010) J Biotechnol , vol.147 , pp. 46-51
    • Van-Thuoc, D.1    Guzmán, H.2    Quillaguamán, J.3    Hatti-Kaul, R.4
  • 18
    • 27844436145 scopus 로고    scopus 로고
    • Poly(β-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1
    • Quillaguamán J, Delgado O, Mattiasson B, Hatti-Kaul R. Poly(β-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1. Enzyme Microb Technol 2006, 38:148-154.
    • (2006) Enzyme Microb Technol , vol.38 , pp. 148-154
    • Quillaguamán, J.1    Delgado, O.2    Mattiasson, B.3    Hatti-Kaul, R.4
  • 19
    • 0042344160 scopus 로고    scopus 로고
    • Bacterial and other biological systems for polyester production
    • 10.1016/S0167-7799(98)01194-9, 9807839
    • Steinbüchel A, Füchtenbush B. Bacterial and other biological systems for polyester production. Trends Biotechnol 1998, 16:419-427. 10.1016/S0167-7799(98)01194-9, 9807839.
    • (1998) Trends Biotechnol , vol.16 , pp. 419-427
    • Steinbüchel, A.1    Füchtenbush, B.2
  • 20
    • 33947594416 scopus 로고    scopus 로고
    • Polyhydroxyalkanoates: biodegradable polymers with a range of applications
    • Philip S, Keshavarz T, Roy I. Polyhydroxyalkanoates: biodegradable polymers with a range of applications. J Chem Technol Biotechnol 2007, 82:233-247.
    • (2007) J Chem Technol Biotechnol , vol.82 , pp. 233-247
    • Philip, S.1    Keshavarz, T.2    Roy, I.3
  • 21
    • 0030298096 scopus 로고    scopus 로고
    • Plastic bacteria? Progress and prospects for polyhydroxyalkanoate production in bacteria
    • Lee SY. Plastic bacteria? Progress and prospects for polyhydroxyalkanoate production in bacteria. Trends Biotechnol 1996, 14:431-438.
    • (1996) Trends Biotechnol , vol.14 , pp. 431-438
    • Lee, S.Y.1
  • 22
    • 0032900321 scopus 로고    scopus 로고
    • Factors affecting the economics of polyhydroxyalkanoate production by bacterial fermentation
    • Choi J, Lee S. Factors affecting the economics of polyhydroxyalkanoate production by bacterial fermentation. Appl Microbiol Biotechnol 1998, 51:13-21.
    • (1998) Appl Microbiol Biotechnol , vol.51 , pp. 13-21
    • Choi, J.1    Lee, S.2
  • 23
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • 10.1093/bioinformatics/btm009, 2387122, 17237039
    • Delcher A, Bratke K, Powers E, Salzberg S. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
    • (2007) Bioinformatics , vol.23 , pp. 673-679
    • Delcher, A.1    Bratke, K.2    Powers, E.3    Salzberg, S.4
  • 24
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: an updated version includes eukaryotes
    • Tatusov R, et al. The COG database: an updated version includes eukaryotes. BMC Bioinforma 2003, 4:41.
    • (2003) BMC Bioinforma , vol.4 , pp. 41
    • Tatusov, R.1
  • 26
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • 10.1093/nar/gkh340, 390337, 15034147
    • Edgar R. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.1
  • 27
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 10:2731-2739.
    • (2011) Mol Biol Evol , vol.10 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 28
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson D, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006, 23:254-267.
    • (2006) Mol Biol Evol , vol.23 , pp. 254-267
    • Huson, D.1    Bryant, D.2
  • 30
    • 0141808594 scopus 로고    scopus 로고
    • Production of medium-chain-length polyhydroxyalkanoates by high-cell-density cultivation of Pseudomonas putida under phosphorus limitation
    • 10.1002/(SICI)1097-0290(20000520)68:4<466::AID-BIT12>3.0.CO;2-T, 10745215
    • Lee SY, Wong HH, Choi J, Lee SH, Lee SC, Han CS. Production of medium-chain-length polyhydroxyalkanoates by high-cell-density cultivation of Pseudomonas putida under phosphorus limitation. Biotechnol Bioeng 2000, 68:466-470. 10.1002/(SICI)1097-0290(20000520)68:4<466::AID-BIT12>3.0.CO;2-T, 10745215.
    • (2000) Biotechnol Bioeng , vol.68 , pp. 466-470
    • Lee, S.Y.1    Wong, H.H.2    Choi, J.3    Lee, S.H.4    Lee, S.C.5    Han, C.S.6
  • 31
    • 23244444597 scopus 로고    scopus 로고
    • Optimization of ectoine synthesis through fed-batch fermentation of Brevibacterium epidermis
    • Onraedt A, Wlcarius B, Soetaert W, Vandamme E. Optimization of ectoine synthesis through fed-batch fermentation of Brevibacterium epidermis. Biotechnol Prog 2005, 21:1206-1212.
    • (2005) Biotechnol Prog , vol.21 , pp. 1206-1212
    • Onraedt, A.1    Wlcarius, B.2    Soetaert, W.3    Vandamme, E.4
  • 32
    • 0034916345 scopus 로고    scopus 로고
    • Chromohalobacter salexigens sp. nov., a moderately halophilic species that includes Halomonas elongata DSM 3043 and ATCC 33174
    • Arahal DR, García MT, Vargas C, Cánovas D, Nieto JJ, Ventosa A. Chromohalobacter salexigens sp. nov., a moderately halophilic species that includes Halomonas elongata DSM 3043 and ATCC 33174. Int J Syst Evol Microbiol 2001, 51:1457-1462.
    • (2001) Int J Syst Evol Microbiol , vol.51 , pp. 1457-1462
    • Arahal, D.R.1    García, M.T.2    Vargas, C.3    Cánovas, D.4    Nieto, J.J.5    Ventosa, A.6
  • 34
    • 0028929048 scopus 로고
    • Convergent evolution of amino acid usage in archaebacterial and eubacterial linages adapted to high salt
    • 10.1016/0923-2508(96)80889-8, 7652205
    • Gandbhir M, Rashed I, Marlière P, Mutzel R. Convergent evolution of amino acid usage in archaebacterial and eubacterial linages adapted to high salt. Res Microbiol 1995, 146:113-120. 10.1016/0923-2508(96)80889-8, 7652205.
    • (1995) Res Microbiol , vol.146 , pp. 113-120
    • Gandbhir, M.1    Rashed, I.2    Marlière, P.3    Mutzel, R.4
  • 35
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • 10.1038/217624a0, 5637732
    • Kimura M. Evolutionary rate at the molecular level. Nature 1968, 217:624-626. 10.1038/217624a0, 5637732.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 36
    • 0030219466 scopus 로고    scopus 로고
    • The neutral theory is dead. Long live the neutral theory
    • 10.1002/bies.950180812, 8760341
    • Kreitman M. The neutral theory is dead. Long live the neutral theory. Bioessays 1996, 18:678-683. 10.1002/bies.950180812, 8760341.
    • (1996) Bioessays , vol.18 , pp. 678-683
    • Kreitman, M.1
  • 37
    • 33644874819 scopus 로고    scopus 로고
    • From genomics to chemical genomics: new developments in KEGG
    • 10.1093/nar/gkj102, 1347464, 16381885
    • Kanehisa M, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357. 10.1093/nar/gkj102, 1347464, 16381885.
    • (2006) Nucleic Acids Res , vol.34
    • Kanehisa, M.1
  • 38
    • 21244444248 scopus 로고    scopus 로고
    • Poly(β-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1 using starch hydrolysate as substrate
    • 10.1111/j.1365-2672.2005.02589.x, 15960675
    • Quillaguamán J, Hashim S, Bento F, Mattiasson B, Hatti-Kaul R. Poly(β-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1 using starch hydrolysate as substrate. J Appl Microbiol 2005, 99:151-157. 10.1111/j.1365-2672.2005.02589.x, 15960675.
    • (2005) J Appl Microbiol , vol.99 , pp. 151-157
    • Quillaguamán, J.1    Hashim, S.2    Bento, F.3    Mattiasson, B.4    Hatti-Kaul, R.5
  • 39
    • 0032537589 scopus 로고    scopus 로고
    • The pyruvate dehydrogenase multi-enzyme comples from Gram-negative bacteria
    • 10.1016/S0167-4838(98)00079-X, 9655933
    • de Kok A, Hengeveld AF, Martin A, Westphal AH. The pyruvate dehydrogenase multi-enzyme comples from Gram-negative bacteria. Biochim Biophys Acta 1998, 1385:353-366. 10.1016/S0167-4838(98)00079-X, 9655933.
    • (1998) Biochim Biophys Acta , vol.1385 , pp. 353-366
    • de Kok, A.1    Hengeveld, A.F.2    Martin, A.3    Westphal, A.H.4
  • 40
    • 8844250928 scopus 로고
    • Central metabolism of the Archaea
    • Danson MJ. Central metabolism of the Archaea. New Compr Biochem 1993, 26:1-24.
    • (1993) New Compr Biochem , vol.26 , pp. 1-24
    • Danson, M.J.1
  • 41
    • 0034025564 scopus 로고    scopus 로고
    • 2-oxoacid dehydrogenase mutienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions
    • Jolley KA, et al. 2-oxoacid dehydrogenase mutienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions. Microbiology 2000, 146:1061-1069.
    • (2000) Microbiology , vol.146 , pp. 1061-1069
    • Jolley, K.A.1
  • 42
    • 0023413802 scopus 로고
    • Confidence interval for the number of selectively neutral amino acid polymorphism
    • 10.1073/pnas.84.17.6225, 299043, 3306673
    • Sawyer S, Dykhuizen D, Hartl D. Confidence interval for the number of selectively neutral amino acid polymorphism. Proc Natl Acad Sci USA 1987, 84:6225-6228. 10.1073/pnas.84.17.6225, 299043, 3306673.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6225-6228
    • Sawyer, S.1    Dykhuizen, D.2    Hartl, D.3
  • 43
    • 76849099236 scopus 로고    scopus 로고
    • Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects
    • 10.1007/s00253-009-2397-6, 20024541
    • Quillaguamán J, Guzmán H, Van-Thuoc D, Hatti-Kaul R. Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects. Appl Microbiol Biotechnol 2010, 85:1687-1696. 10.1007/s00253-009-2397-6, 20024541.
    • (2010) Appl Microbiol Biotechnol , vol.85 , pp. 1687-1696
    • Quillaguamán, J.1    Guzmán, H.2    Van-Thuoc, D.3    Hatti-Kaul, R.4
  • 45
    • 0001156391 scopus 로고
    • Production of copolyesters of 3-hydroxybutyrate and 3-hydroxyvalerate by Alcaligenes eutrophus from butyric and pentanoic acids
    • Doi Y, Tamaki A, Kunioka M, Soga K. Production of copolyesters of 3-hydroxybutyrate and 3-hydroxyvalerate by Alcaligenes eutrophus from butyric and pentanoic acids. Appl Microbiol Biotechnol 1988, 28:330-334.
    • (1988) Appl Microbiol Biotechnol , vol.28 , pp. 330-334
    • Doi, Y.1    Tamaki, A.2    Kunioka, M.3    Soga, K.4
  • 46
    • 0028171091 scopus 로고
    • Comparison of recombinant Escherichia coli strains for synthesis and accumulation of poly-(3-hydroxybutyric acid) and morphological changes
    • 10.1002/bit.260441110, 18618646
    • Lee SY, Lee KM, Chang HN, Steinbüchel A. Comparison of recombinant Escherichia coli strains for synthesis and accumulation of poly-(3-hydroxybutyric acid) and morphological changes. Biotechnol Bioeng 1994, 44:1337-1347. 10.1002/bit.260441110, 18618646.
    • (1994) Biotechnol Bioeng , vol.44 , pp. 1337-1347
    • Lee, S.Y.1    Lee, K.M.2    Chang, H.N.3    Steinbüchel, A.4
  • 47
    • 0026464544 scopus 로고
    • Production of poly-β-hydroxybutyrate by Azotobacter vinelandii UWD in media containing sugars and complex nitrogen
    • Page WJ. Production of poly-β-hydroxybutyrate by Azotobacter vinelandii UWD in media containing sugars and complex nitrogen. Appl Microbiol Biotechnol 1992, 38:117-121.
    • (1992) Appl Microbiol Biotechnol , vol.38 , pp. 117-121
    • Page, W.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.