메뉴 건너뛰기




Volumn 9, Issue 2, 2009, Pages 153-166

Bacterial intein-like domains of predatory bacteria: A new domain type characterized in Bdellovibrio bacteriovorus

Author keywords

Bioinformatics; Comparative genomics; Modifications; Protein dynamics

Indexed keywords

BACTERIAL PROTEIN; PROTEIN BD2400; UNCLASSIFIED DRUG;

EID: 63649162825     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-008-0106-7     Document Type: Article
Times cited : (11)

References (49)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2
  • 2
    • 0037222296 scopus 로고    scopus 로고
    • Distribution and function of new bacterial intein-like protein domains
    • Amitai G, Belenkiy O et al (2003) Distribution and function of new bacterial intein-like protein domains. Mol Microbiol 47(1):61-73
    • (2003) Mol Microbiol , vol.47 , Issue.1 , pp. 61-73
    • Amitai, G.1    Belenkiy, O.2
  • 3
    • 0034885813 scopus 로고    scopus 로고
    • Analysis of phenotypic diversity among host-independent mutants of Bdellovibrio bacteriovorus 109J
    • Barel G, Jurkevitch E (2001) Analysis of phenotypic diversity among host-independent mutants of Bdellovibrio bacteriovorus 109J. Arch Microbiol 176(3):211-216
    • (2001) Arch Microbiol , vol.176 , Issue.3 , pp. 211-216
    • Barel, G.1    Jurkevitch, E.2
  • 4
    • 11144323264 scopus 로고    scopus 로고
    • Fate of predator and prey proteins during growth of Bdellovibrio bacteriovorus on Escherichia coli and Pseudomonas syringae prey
    • Barel G, Sirota A et al (2005) Fate of predator and prey proteins during growth of Bdellovibrio bacteriovorus on Escherichia coli and Pseudomonas syringae prey. J Bacteriol 187(1):329-335
    • (2005) J Bacteriol , vol.187 , Issue.1 , pp. 329-335
    • Barel, G.1    Sirota, A.2
  • 5
    • 1842580753 scopus 로고    scopus 로고
    • Improving large-scale proteomics by clustering of mass spectrometry data
    • Beer I, Barnea E et al (2004) Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics 4(4):950-960
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 950-960
    • Beer, I.1    Barnea, E.2
  • 6
    • 0014748695 scopus 로고
    • Ultrastructure and cell division of a facultatively parasitic strain of Bdellovibrio bacteriovorus
    • Burnham JC, Hashimoto T et al (1970) Ultrastructure and cell division of a facultatively parasitic strain of Bdellovibrio bacteriovorus. J Bacteriol 101(3):997-1004
    • (1970) J Bacteriol , vol.101 , Issue.3 , pp. 997-1004
    • Burnham, J.C.1    Hashimoto, T.2
  • 7
    • 0033555277 scopus 로고    scopus 로고
    • The structure of a PKD domain from polycystin-1: Implications for polycystic kidney disease
    • Bycroft M, Bateman A et al (1999) The structure of a PKD domain from polycystin-1: Implications for polycystic kidney disease. EMBO J 18(2):297-305
    • (1999) EMBO J , vol.18 , Issue.2 , pp. 297-305
    • Bycroft, M.1    Bateman, A.2
  • 8
    • 32044468517 scopus 로고    scopus 로고
    • Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans
    • Choi J, Nam K et al (2005) Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans. J Mol Biol 356(5):1093-1106
    • (2005) J Mol Biol , vol.356 , Issue.5 , pp. 1093-1106
    • Choi, J.1    Nam, K.2
  • 9
    • 33750492267 scopus 로고    scopus 로고
    • Elimination of in vivo cleavage between target protein and intein in the intein-mediated protein purification systems
    • Cui C, Zhao W et al (2006) Elimination of in vivo cleavage between target protein and intein in the intein-mediated protein purification systems. Protein Expr Purif 50(1):74-81
    • (2006) Protein Expr Purif , vol.50 , Issue.1 , pp. 74-81
    • Cui, C.1    Zhao, W.2
  • 10
    • 33846072572 scopus 로고    scopus 로고
    • Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations
    • Dassa B, Amitai G et al (2007) Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations. Biochemistry 46(1):322-330
    • (2007) Biochemistry , vol.46 , Issue.1 , pp. 322-330
    • Dassa, B.1    Amitai, G.2
  • 12
    • 3543025094 scopus 로고    scopus 로고
    • Protein splicing and auto-cleavage of bacterial intein-like domains lacking a C′-flanking nucleophilic residue
    • Dassa B, Haviv H et al (2004a) Protein splicing and auto-cleavage of bacterial intein-like domains lacking a C′-flanking nucleophilic residue. J Biol Chem 279(31):32001-32007
    • (2004) J Biol Chem , vol.279 , Issue.31 , pp. 32001-32007
    • Dassa, B.1    Haviv, H.2
  • 13
    • 4744359173 scopus 로고    scopus 로고
    • New type of polyubiquitin-like genes with intein-like autoprocessing domains
    • Dassa B, Yanai I et al (2004b) New type of polyubiquitin-like genes with intein-like autoprocessing domains. Trends Genet 20(11):538-542
    • (2004) Trends Genet , vol.20 , Issue.11 , pp. 538-542
    • Dassa, B.1    Yanai, I.2
  • 14
    • 33750901290 scopus 로고    scopus 로고
    • A new alpha-proteobacterial clade of Bdellovibrio-like predators: Implications for the mitochondrial endosymbiotic theory
    • Davidov Y, Huchon D et al (2006) A new alpha-proteobacterial clade of Bdellovibrio-like predators: Implications for the mitochondrial endosymbiotic theory. Environ Microbiol 8(12):2179-2188
    • (2006) Environ Microbiol , vol.8 , Issue.12 , pp. 2179-2188
    • Davidov, Y.1    Huchon, D.2
  • 15
    • 57149090496 scopus 로고    scopus 로고
    • Proteome-based comparative analyses of growth stages reveal new cell-cycle dependent functions in the predatory bacterium Bdellovibrio bacteriovorus
    • Dori-Bachash M, Dassa B et al (2008) Proteome-based comparative analyses of growth stages reveal new cell-cycle dependent functions in the predatory bacterium Bdellovibrio bacteriovorus. Appl Environ Microbiol 74(23):7152-7162
    • (2008) Appl Environ Microbiol , vol.74 , Issue.23 , pp. 7152-7162
    • Dori-Bachash, M.1    Dassa, B.2
  • 16
    • 21444456479 scopus 로고    scopus 로고
    • Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure
    • Frenkel-Morgenstern M, Voet H et al (2005) Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure. Bioinformatics 21(13):2950-2956
    • (2005) Bioinformatics , vol.21 , Issue.13 , pp. 2950-2956
    • Frenkel-Morgenstern, M.1    Voet, H.2
  • 17
    • 0035710229 scopus 로고    scopus 로고
    • An overview of real-time quantitative PCR: Applications to quantify cytokine gene expression
    • Giulietti A, Overbergh L et al (2001) An overview of real-time quantitative PCR: Applications to quantify cytokine gene expression. Methods 25(4):386-401
    • (2001) Methods , vol.25 , Issue.4 , pp. 386-401
    • Giulietti, A.1    Overbergh, L.2
  • 18
    • 0029002967 scopus 로고
    • Polycystic kidney disease: The complete structure of the PKD1 gene and its protein
    • The International Polycystic Kidney Disease Consortium
    • Gluecksmann-Kuis MA, Tayber O, Woolf EA, Bougueleret L, Deng N, Alperin GD, Iris F, Hawkins F et al (1995) Polycystic kidney disease: The complete structure of the PKD1 gene and its protein. The International Polycystic Kidney Disease Consortium. Cell 81(2):289-298
    • (1995) Cell , vol.81 , Issue.2 , pp. 289-298
    • Gluecksmann-Kuis, M.A.1    Tayber, O.2    Woolf, E.A.3    Bougueleret, L.4    Deng, N.5    Alperin, G.D.6    Iris, F.7    Hawkins, F.8
  • 19
    • 0024313938 scopus 로고
    • Unbalanced growth as a normal feature of development of Bdellovibrio bacteriovorus
    • Gray KM, Ruby EG (1989) Unbalanced growth as a normal feature of development of Bdellovibrio bacteriovorus. Arch Microbiol 152(5):420-424
    • (1989) Arch Microbiol , vol.152 , Issue.5 , pp. 420-424
    • Gray, K.M.1    Ruby, E.G.2
  • 20
    • 0342813091 scopus 로고    scopus 로고
    • Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins
    • Hall TM, Porter JA et al (1997) Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins. Cell 91:85-97
    • (1997) Cell , vol.91 , pp. 85-97
    • Hall, T.M.1    Porter, J.A.2
  • 21
    • 33751172146 scopus 로고    scopus 로고
    • Comprehensive analysis of gene expression patterns of Hedgehog-related genes
    • Hao L, Johnsen R et al (2006) Comprehensive analysis of gene expression patterns of Hedgehog-related genes. BMC Genomics 7:280
    • (2006) BMC Genomics , vol.7 , pp. 280
    • Hao, L.1    Johnsen, R.2
  • 22
    • 0016708649 scopus 로고
    • Ribonucleic acid destruction and synthesis during intraperiplasmic growth of Bdellovibrio bacteriovorus
    • Hespell RB, Miozzari GF et al (1975) Ribonucleic acid destruction and synthesis during intraperiplasmic growth of Bdellovibrio bacteriovorus. J Bacteriol 123(2):481-491
    • (1975) J Bacteriol , vol.123 , Issue.2 , pp. 481-491
    • Hespell, R.B.1    Miozzari, G.F.2
  • 23
    • 0028825276 scopus 로고
    • Automated construction and graphical presentation of protein blocks from unaligned sequences
    • Henikoff S, Henikoff JG et al (1995) Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163:17-26
    • (1995) Gene , vol.163 , pp. 17-26
    • Henikoff, S.1    Henikoff, J.G.2
  • 24
    • 34250166196 scopus 로고    scopus 로고
    • Phylogenetic diversity and evolution of predatory prokaryotes
    • In: Jurkevitch E (ed) Springer-Verlag, Heidelberg
    • Jurkevitch E, Davidov Y (2007) Phylogenetic diversity and evolution of predatory prokaryotes. In: Jurkevitch E (ed) Predatory prokaryotes - biology, ecology, and evolution. Springer-Verlag, Heidelberg
    • (2007) Predatory Prokaryotes - Biology, Ecology, and Evolution
    • Jurkevitch, E.1    Davidov, Y.2
  • 25
    • 33751201804 scopus 로고    scopus 로고
    • Bdellovibrio: Growth and development during the predatory cycle
    • Lambert C, Morehouse KA et al (2006) Bdellovibrio: Growth and development during the predatory cycle. Curr Opin Microbiol 9(6):639-644
    • (2006) Curr Opin Microbiol , vol.9 , Issue.6 , pp. 639-644
    • Lambert, C.1    Morehouse, K.A.2
  • 26
    • 0034511180 scopus 로고    scopus 로고
    • Protein-splicing intein: Genetic mobility, origin, and evolution
    • Liu XQ (2000) Protein-splicing intein: Genetic mobility, origin, and evolution. Annu Rev Genet 34:61-76
    • (2000) Annu Rev Genet , vol.34 , pp. 61-76
    • Liu, X.Q.1
  • 27
    • 2942742564 scopus 로고    scopus 로고
    • Novel lipid modifications of secreted protein signals
    • Mann RK, Beachy PA (2004) Novel lipid modifications of secreted protein signals. Annu Rev Biochem 73:891-923
    • (2004) Annu Rev Biochem , vol.73 , pp. 891-923
    • Mann, R.K.1    Beachy, P.A.2
  • 28
    • 0018784261 scopus 로고
    • Keilin's respiratory chain concept and its chemiosmotic consequences
    • Mitchell P (1979) Keilin's respiratory chain concept and its chemiosmotic consequences. Nature 206:1148-1159
    • (1979) Nature , vol.206 , pp. 1148-1159
    • Mitchell, P.1
  • 29
    • 0036208814 scopus 로고    scopus 로고
    • Molecular analysis of the gene encoding a novel chitin-binding protease from Alteromonas sp. strain O-7 and its role in the chitinolytic system
    • Miyamoto K, Nukui E et al (2002) Molecular analysis of the gene encoding a novel chitin-binding protease from Alteromonas sp. strain O-7 and its role in the chitinolytic system. J Bacteriol 184(7):1865-1872
    • (2002) J Bacteriol , vol.184 , Issue.7 , pp. 1865-1872
    • Miyamoto, K.1    Nukui, E.2
  • 30
    • 33744503690 scopus 로고    scopus 로고
    • Overexpression, purification and crystallization of the two C-terminal domains of the bifunctional cellulase ctCel9D-Cel44A from Clostridium thermocellum
    • Najmudin S, Guerreiro CI et al (2005) Overexpression, purification and crystallization of the two C-terminal domains of the bifunctional cellulase ctCel9D-Cel44A from Clostridium thermocellum. Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 12):1043-1045
    • (2005) Acta Crystallograph Sect F Struct Biol Cryst Commun , vol.61 , Issue.PART 12 , pp. 1043-1045
    • Najmudin, S.1    Guerreiro, C.I.2
  • 31
    • 0037881919 scopus 로고    scopus 로고
    • Zinc ion effects on individual Ssp DnaE intein splicing steps: Regulating pathway progression
    • Nichols NM, Benner JS, Martin DD, Evans TC Jr (2003) Zinc ion effects on individual Ssp DnaE intein splicing steps: Regulating pathway progression. Biochemistry 42(18):5301-5311
    • (2003) Biochemistry , vol.42 , Issue.18 , pp. 5301-5311
    • Nichols, N.M.1    Benner, J.S.2    Martin, D.D.3    Evans Jr., T.C.4
  • 32
    • 3543142392 scopus 로고    scopus 로고
    • Mutational analysis of protein splicing, cleavage, and self-association reactions mediated by the naturally split Ssp DnaE intein
    • Nichols NM, Evans TC Jr (2004) Mutational analysis of protein splicing, cleavage, and self-association reactions mediated by the naturally split Ssp DnaE intein. Biochemistry 43(31):10265-10276
    • (2004) Biochemistry , vol.43 , Issue.31 , pp. 10265-10276
    • Nichols, N.M.1    Evans Jr., T.C.2
  • 33
    • 24044553899 scopus 로고    scopus 로고
    • Role of the N-terminal polycystic kidney disease domain in chitin degradation by chitinase A from a marine bacterium, Alteromonas sp. strain O-7
    • Orikoshi H, Nakayama S et al (2005) Role of the N-terminal polycystic kidney disease domain in chitin degradation by chitinase A from a marine bacterium, Alteromonas sp. strain O-7. J Appl Microbiol 99(3):551-557
    • (2005) J Appl Microbiol , vol.99 , Issue.3 , pp. 551-557
    • Orikoshi, H.1    Nakayama, S.2
  • 34
    • 0033782899 scopus 로고    scopus 로고
    • Protein splicing and related forms of protein autoprocessing
    • Paulus H (2000) Protein splicing and related forms of protein autoprocessing. Annu Rev Biochem 69:447-496
    • (2000) Annu Rev Biochem , vol.69 , pp. 447-496
    • Paulus, H.1
  • 35
    • 0028214350 scopus 로고
    • Protein splicing elements: Inteins and exteins - A definition of terms and recommended nomenclature
    • Perler FB, Davis EO et al (1994) Protein splicing elements: Inteins and exteins - a definition of terms and recommended nomenclature. Nucleic Acids Res 22:1125-1127
    • (1994) Nucleic Acids Res , vol.22 , pp. 1125-1127
    • Perler, F.B.1    Davis, E.O.2
  • 36
    • 0031938897 scopus 로고    scopus 로고
    • Modular organization of inteins and C-terminal autocatalytic domains
    • Pietrokovski S (1998) Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci 7:64-71
    • (1998) Protein Sci , vol.7 , pp. 64-71
    • Pietrokovski, S.1
  • 37
    • 0035425040 scopus 로고    scopus 로고
    • Intein spread and extinction in evolution
    • Pietrokovski S (2001) Intein spread and extinction in evolution. Trends Genet 17:465-472
    • (2001) Trends Genet , vol.17 , pp. 465-472
    • Pietrokovski, S.1
  • 38
    • 0034595699 scopus 로고    scopus 로고
    • Structural insights into the protein splicing mechanism of PI-SceI
    • Poland BW, Xu MQ et al (2000) Structural insights into the protein splicing mechanism of PI-SceI. J Biol Chem 275:16408-16413
    • (2000) J Biol Chem , vol.275 , pp. 16408-16413
    • Poland, B.W.1    Xu, M.Q.2
  • 39
    • 9144236808 scopus 로고    scopus 로고
    • A predator unmasked: Life cycle of Bdellovibrio bacteriovorus from a genomic perspective
    • Rendulic S, Jagtap P et al (2004) A predator unmasked: Life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science 303(5658):689-692
    • (2004) Science , vol.303 , Issue.5658 , pp. 689-692
    • Rendulic, S.1    Jagtap, P.2
  • 40
    • 0011238463 scopus 로고
    • Intraperiplasmic growth-life in a cozy environment
    • In: Schlessinger D (ed) American Society for Microbiology, Washington, D.C
    • Rittenberg SC, Thomashow MF (1979) Intraperiplasmic growth-life in a cozy environment. In: Schlessinger D (ed) Microbiology - 1979. American Society for Microbiology, Washington, D.C
    • (1979) Microbiology - 1979
    • Rittenberg, S.C.1    Thomashow, M.F.2
  • 41
    • 0346176148 scopus 로고
    • Cell-envelope modifications accompanying intracellular growth of Bdellovibrio bacteriovorus
    • In: Moulder JW (ed) CRC, Boca Raton, Fla
    • Ruby E (1989) Cell-envelope modifications accompanying intracellular growth of Bdellovibrio bacteriovorus. In: Moulder JW (ed) Intracellular parasitism. CRC, Boca Raton, Fla, pp 17-34
    • (1989) Intracellular Parasitism , pp. 17-34
    • Ruby, E.1
  • 42
    • 0026100921 scopus 로고
    • A workbench for multiple alignment construction and analysis
    • Schuler GD, Altschul SF et al (1991) A workbench for multiple alignment construction and analysis. Proteins 9(3):180-190
    • (1991) Proteins , vol.9 , Issue.3 , pp. 180-190
    • Schuler, G.D.1    Altschul, S.F.2
  • 43
    • 2342503863 scopus 로고    scopus 로고
    • Rescue of protein splicing activity from a Magnetospirillum magnetotacticum intein-like element
    • Southworth MW, Yin J, Perler FB (2004) Rescue of protein splicing activity from a Magnetospirillum magnetotacticum intein-like element. Biochem Soc Trans 32(Pt 2):250-254
    • (2004) Biochem Soc Trans , vol.32 , Issue.PART 2 , pp. 250-254
    • Southworth, M.W.1    Yin, J.2    Perler, F.B.3
  • 44
    • 0032189925 scopus 로고    scopus 로고
    • Disulfide bond formation in the Escherichia coli cytoplasm: An in vivo role reversal for the thioredoxins
    • Stewart EJ, Aslund F, Beckwith J (1998) Disulfide bond formation in the Escherichia coli cytoplasm: An in vivo role reversal for the thioredoxins. EMBO J 17:5543-5550
    • (1998) EMBO J , vol.17 , pp. 5543-5550
    • Stewart, E.J.1    Aslund, F.2    Beckwith, J.3
  • 45
    • 34547787590 scopus 로고    scopus 로고
    • Development of a novel genetic system to create markerless deletion mutants of Bdellovibrio bacteriovorus
    • Steyert SR, Pineiro SA (2007) Development of a novel genetic system to create markerless deletion mutants of Bdellovibrio bacteriovorus. Appl Environ Microbiol 73(15):4717-4724
    • (2007) Appl Environ Microbiol , vol.73 , Issue.15 , pp. 4717-4724
    • Steyert, S.R.1    Pineiro, S.A.2
  • 47
    • 0001353754 scopus 로고
    • Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism
    • Stolp H, Starr MP (1963) Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. Antonie Van Leeuwenhoek 29:217-248
    • (1963) Antonie Van Leeuwenhoek , vol.29 , pp. 217-248
    • Stolp, H.1    Starr, M.P.2
  • 48
    • 33846817517 scopus 로고    scopus 로고
    • Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum
    • Williams TI, Combs JC et al (2006) Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum. Appl Microbiol Biotechnol 74:422-432
    • (2006) Appl Microbiol Biotechnol , vol.74 , pp. 422-432
    • Williams, T.I.1    Combs, J.C.2
  • 49
    • 2942733563 scopus 로고    scopus 로고
    • New knowledge from old: In silico discovery of novel protein domains in Streptomyces coelicolor
    • Yeats C, Bentley S et al (2003) New knowledge from old: In silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol 3:3
    • (2003) BMC Microbiol , vol.3 , pp. 3
    • Yeats, C.1    Bentley, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.