메뉴 건너뛰기




Volumn 104, Issue 4, 2013, Pages 509-520

Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: Unexpected findings

Author keywords

Planctomycetes; Prokaryotic E2 ubiquitin; Prokaryotic STKs

Indexed keywords

GUANOSINE TRIPHOSPHATASE; PROTEIN SERINE THREONINE KINASE; UBIQUITIN CONJUGATING ENZYME E2;

EID: 84890554291     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-013-9993-2     Document Type: Article
Times cited : (13)

References (38)
  • 1
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • 10.1093/bioinformatics/bti263 15647292 10.1093/bioinformatics/bti263 1:CAS:528:DC%2BD2MXjsl2ns7Y%3D
    • Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21(9):2104-2105. doi: 10.1093/bioinformatics/bti263
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 3
    • 82555169810 scopus 로고    scopus 로고
    • GTPases in bacterial cell polarity and signaling
    • doi: 10.1016/j.mib.2011.09.001
    • Bulyha I, Hot E, Huntley S, Sogaard-Andersen L (2011) GTPases in bacterial cell polarity and signalling. Curr Opin Microbiol 14(6):726-733. doi: 10.1016/j.mib.2011.09.001
    • (2011) Curr Opin Microbiol , vol.14 , Issue.6 , pp. 726-733
    • Bulyha, I.1    Hot, E.2    Huntley, S.3    Sogaard-Andersen, L.4
  • 4
    • 84861817863 scopus 로고    scopus 로고
    • Regulation of prokaryotic gene expression by eukaryotic-like enzymes
    • 10.1016/j.mib.2011.12.006 22221896 10.1016/j.mib.2011.12.006 1:CAS:528:DC%2BC38XkvF2isb8%3D
    • Burnside K, Rajagopal L (2012) Regulation of prokaryotic gene expression by eukaryotic-like enzymes. Curr Opin Microbiol 15(2):125-131. doi: 10.1016/j.mib.2011.12.006
    • (2012) Curr Opin Microbiol , vol.15 , Issue.2 , pp. 125-131
    • Burnside, K.1    Rajagopal, L.2
  • 5
    • 42649124278 scopus 로고    scopus 로고
    • Anatomy of the E2 ligase fold: Implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation
    • 10.1016/j.jsb.2007.12.006 18276160 10.1016/j.jsb.2007.12.006 1:CAS:528:DC%2BD1cXlslGqtr8%3D
    • Burroughs AM, Jaffee M, Iyer LM, Aravind L (2008) Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J Struct Biol 162(2):205-218. doi: 10.1016/j.jsb.2007.12. 006
    • (2008) J Struct Biol , vol.162 , Issue.2 , pp. 205-218
    • Burroughs, A.M.1    Jaffee, M.2    Iyer, L.M.3    Aravind, L.4
  • 6
    • 0037665941 scopus 로고    scopus 로고
    • Transcription regulation and environmental adaptation in bacteria
    • 12823939 10.1016/S0966-842X(03)00103-3 1:CAS:528:DC%2BD3sXkvVCmsLw%3D
    • Cases I, de Lorenzo V, Ouzounis CA (2003) Transcription regulation and environmental adaptation in bacteria. Trends Microbiol 11(6):248-253
    • (2003) Trends Microbiol , vol.11 , Issue.6 , pp. 248-253
    • Cases, I.1    De Lorenzo, V.2    Ouzounis, C.A.3
  • 7
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • 11485799 10.1016/S0168-9525(01)02348-4 1:CAS:528:DC%2BD3MXlsFyltbs%3D
    • Devos D, Valencia A (2001) Intrinsic errors in genome annotation. Trends Genet 17(8):429-431
    • (2001) Trends Genet , vol.17 , Issue.8 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 8
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • 20180275 10.1142/9781848165632-0019
    • Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23(1):205-211
    • (2009) Genome Inform , vol.23 , Issue.1 , pp. 205-211
    • Eddy, S.R.1
  • 12
    • 27144551296 scopus 로고    scopus 로고
    • Intracelullar compartmentation in Planctomycetes
    • 10.1146/annurev.micro.59.030804.121258 10.1146/annurev.micro.59.030804. 121258 1:CAS:528:DC%2BD2MXht1Shs7fL
    • Fuerst JA (2005) Intracelullar compartmentation in Planctomycetes. Ann Rev Microbiol 59:299-328. doi: 10.1146/annurev.micro.59.030804.121258
    • (2005) Ann Rev Microbiol , vol.59 , pp. 299-328
    • Fuerst, J.A.1
  • 13
    • 79958071293 scopus 로고    scopus 로고
    • Metagenomics and the protein universe
    • 10.1016/j.sbi.2011.03.010 21497084 10.1016/j.sbi.2011.03.010 1:CAS:528:DC%2BC3MXnsVyitL0%3D
    • Godzik A (2011) Metagenomics and the protein universe. Curr Opin Struct Biol 21(3):398-403. doi: 10.1016/j.sbi.2011.03.010
    • (2011) Curr Opin Struct Biol , vol.21 , Issue.3 , pp. 398-403
    • Godzik, A.1
  • 14
    • 68049139485 scopus 로고    scopus 로고
    • Estimating maximum likelihood phylogenies with PhyML
    • 10.1007/978-1-59745-251-9-6 19378142 10.1007/978-1-59745-251-9-6 1:CAS:528:DC%2BD1MXmvVSqtbw%3D
    • Guindon S, Delsuc F, Dufayard JF, Gascuel O (2009) Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537:113-137. doi: 10.1007/978-1-59745-251-9-6
    • (2009) Methods Mol Biol , vol.537 , pp. 113-137
    • Guindon, S.1    Delsuc, F.2    Dufayard, J.F.3    Gascuel, O.4
  • 15
    • 33747219426 scopus 로고    scopus 로고
    • The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains
    • 10.1186/gb-2006-7-7-r60 16859499 10.1186/gb-2006-7-7-r60
    • Iyer LM, Burroughs AM, Aravind L (2006) The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Genome Biol 7(7):R60. doi: 10.1186/gb-2006-7-7-r60
    • (2006) Genome Biol , vol.7 , Issue.7 , pp. 60
    • Iyer, L.M.1    Burroughs, A.M.2    Aravind, L.3
  • 17
    • 33947226782 scopus 로고    scopus 로고
    • Structural and functional diversity of the microbial kinome
    • 10.1371/journal.pbio.0050017 17355172 10.1371/journal.pbio.0050017
    • Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2007) Structural and functional diversity of the microbial kinome. PLoS Biol 5(3):e17. doi: 10.1371/journal.pbio.0050017
    • (2007) PLoS Biol , vol.5 , Issue.3 , pp. 17
    • Kannan, N.1    Taylor, S.S.2    Zhai, Y.3    Venter, J.C.4    Manning, G.5
  • 18
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • 10.1093/nar/gki198 15661851 10.1093/nar/gki198 1:CAS:528: DC%2BD2MXhtV2qsbc%3D
    • Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33(2):511-518. doi: 10.1093/nar/gki198
    • (2005) Nucleic Acids Res , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 19
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • 10.1038/nrg2386 18591983 10.1038/nrg2386 1:CAS:528:DC%2BD1cXpsVOku7k%3D
    • Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9(8):605-618. doi: 10.1038/nrg2386
    • (2008) Nat Rev Genet , vol.9 , Issue.8 , pp. 605-618
    • Keeling, P.J.1    Palmer, J.D.2
  • 20
    • 33845873289 scopus 로고    scopus 로고
    • Interactive tree of life (iTOL): An online tool for phylogenetic tree display and annotation
    • 10.1093/bioinformatics/btl529 17050570 10.1093/bioinformatics/btl529 1:CAS:528:DC%2BD28XhtlGktLzN
    • Letunic I, Bork P (2007) Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23(1):127-128. doi: 10.1093/bioinformatics/btl529
    • (2007) Bioinformatics , vol.23 , Issue.1 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 21
    • 77950421915 scopus 로고    scopus 로고
    • Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution
    • 10.1111/j.1574-6976.2010.00209.x 20132312 10.1111/j.1574-6976.2009.00209. x 1:CAS:528:DC%2BC3cXlt1Kisrs%3D
    • Moliner C, Fournier PE, Raoult D (2010) Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 34(3):281-294. doi: 10.1111/j.1574-6976.2010.00209.x
    • (2010) FEMS Microbiol Rev , vol.34 , Issue.3 , pp. 281-294
    • Moliner, C.1    Fournier, P.E.2    Raoult, D.3
  • 22
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • 10.1006/jmbi.2000.4042 10964570 10.1006/jmbi.2000.4042 1:CAS:528:DC%2BD3cXmtVGntr8%3D
    • Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302(1):205-217. doi: 10.1006/jmbi.2000.4042
    • (2000) J Mol Biol , vol.302 , Issue.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 23
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata
    • 10.1093/nar/gkr1100 22135293 10.1093/nar/gkr1100 1:CAS:528: DC%2BC3MXhs12hur%2FJ
    • Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40(Database issue):D571-579. doi: 10.1093/nar/gkr1100
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE , pp. 571-579
    • Pagani, I.1    Liolios, K.2    Jansson, J.3    Chen, I.M.4    Smirnova, T.5    Nosrat, B.6    Markowitz, V.M.7    Kyrpides, N.C.8
  • 24
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of Phylogenetics and Evolution in R language
    • 14734327 10.1093/bioinformatics/btg412 1:CAS:528:DC%2BD2cXms1eitg%3D%3D
    • Paradis E, Claude J, Strimmer K (2004) APE: analyses of Phylogenetics and Evolution in R language. Bioinformatics 20(2):289-290
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 25
    • 79952426399 scopus 로고    scopus 로고
    • Eukaryote-like serine/threonine kinases and phosphatases in bacteria
    • 10.1128/MMBR.00042-10 21372323 10.1128/MMBR.00042-10 1:CAS:528: DC%2BC3MXlsVequ7o%3D
    • Pereira SF, Goss L, Dworkin J (2011) Eukaryote-like serine/threonine kinases and phosphatases in bacteria. Microbiol Mol Biol Rev 75(1):192-212. doi: 10.1128/MMBR.00042-10
    • (2011) Microbiol Mol Biol Rev , vol.75 , Issue.1 , pp. 192-212
    • Pereira, S.F.1    Goss, L.2    Dworkin, J.3
  • 26
    • 57349107073 scopus 로고    scopus 로고
    • Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome
    • 10.1073/pnas.0806851105 18836084 10.1073/pnas.0806851105 1:CAS:528:DC%2BD1cXht1yitrfM
    • Perez J, Castaneda-Garcia A, Jenke-Kodama H, Muller R, Munoz-Dorado J (2008) Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome. Proc Natl Acad Sci USA 105(41):15950-15955. doi: 10.1073/pnas.0806851105
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.41 , pp. 15950-15955
    • Perez, J.1    Castaneda-Garcia, A.2    Jenke-Kodama, H.3    Muller, R.4    Munoz-Dorado, J.5
  • 27
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • 10.1006/jmbi.2000.5197 11743721 10.1006/jmbi.2000.5197 1:CAS:528:DC%2BD3MXptVOlsro%3D
    • Remm M, Storm CE, Sonnhammer EL (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314(5):1041-1052. doi: 10.1006/jmbi.2000.5197
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 28
    • 56349151939 scopus 로고    scopus 로고
    • The regulation of salt transport and blood pressure by the WNK-SPAK/OSR1 signalling pathway
    • 10.1242/jcs.029223 18843116 10.1242/jcs.029223 1:CAS:528: DC%2BD1cXhsVaitLrE
    • Richardson C, Alessi DR (2008) The regulation of salt transport and blood pressure by the WNK-SPAK/OSR1 signalling pathway. J Cell Sci 121(Pt 20):3293-3304. doi: 10.1242/jcs.029223
    • (2008) J Cell Sci , vol.121 , Issue.PART 20 , pp. 3293-3304
    • Richardson, C.1    Alessi, D.R.2
  • 29
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • 12912839 10.1093/bioinformatics/btg180 1:CAS:528:DC%2BD3sXntlKms7k%3D
    • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572-1574
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 30
    • 84878297375 scopus 로고    scopus 로고
    • Three-dimensional reconstruction of bacteria with a complex endomembrane system
    • 10.1371/journal.pbio.1001565 23700385 10.1371/journal.pbio.1001565 1:CAS:528:DC%2BC3sXptlygsrg%3D
    • Santarella-Mellwig R, Pruggnaller S, Roos N, Mattaj IW, Devos DP (2013) Three-dimensional reconstruction of bacteria with a complex endomembrane system. PLoS Biol 11(5):e1001565. doi: 10.1371/journal.pbio.1001565
    • (2013) PLoS Biol , vol.11 , Issue.5 , pp. 1001565
    • Santarella-Mellwig, R.1    Pruggnaller, S.2    Roos, N.3    Mattaj, I.W.4    Devos, D.P.5
  • 31
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
    • 10.1371/journal.pcbi.1000605 20011109 10.1371/journal.pcbi.1000605
    • Schnoes AM, Brown SD, Dodevski I, Babbitt PC (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5(12):e1000605. doi: 10.1371/journal.pcbi.1000605
    • (2009) PLoS Comput Biol , vol.5 , Issue.12 , pp. 1000605
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 32
    • 33744927902 scopus 로고    scopus 로고
    • The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
    • 10.1016/j.copbio.2006.05.005 16704931 10.1016/j.copbio.2006.05.005 1:CAS:528:DC%2BD28Xls1aktrc%3D
    • Wagner M, Horn M (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17(3):241-249. doi: 10.1016/j.copbio.2006.05.005
    • (2006) Curr Opin Biotechnol , vol.17 , Issue.3 , pp. 241-249
    • Wagner, M.1    Horn, M.2
  • 34
    • 77649200259 scopus 로고    scopus 로고
    • A primer on metagenomics
    • 10.1371/journal.pcbi.1000667 20195499 10.1371/journal.pcbi.1000667
    • Wooley JC, Godzik A, Friedberg I (2010) A primer on metagenomics. PLoS Comput Biol 6(2):e1000667. doi: 10.1371/journal.pcbi.1000667
    • (2010) PLoS Comput Biol , vol.6 , Issue.2 , pp. 1000667
    • Wooley, J.C.1    Godzik, A.2    Friedberg, I.3
  • 35
    • 77949513721 scopus 로고    scopus 로고
    • The evolutionary history of protein domains viewed by species phylogeny
    • 10.1371/journal.pone.0008378 20041107 10.1371/journal.pone.0008378
    • Yang S, Bourne PE (2009) The evolutionary history of protein domains viewed by species phylogeny. PLoS One 4(12):e8378. doi: 10.1371/journal.pone. 0008378
    • (2009) PLoS One , vol.4 , Issue.12 , pp. 8378
    • Yang, S.1    Bourne, P.E.2
  • 36
    • 12244257804 scopus 로고    scopus 로고
    • Phylogeny determined by protein domain content
    • 10.1073/pnas.0408810102 15630082 10.1073/pnas.0408810102 1:CAS:528:DC%2BD2MXptFSksA%3D%3D
    • Yang S, Doolittle RF, Bourne PE (2005) Phylogeny determined by protein domain content. Proc Natl Acad Sci USA 102(2):373-378. doi: 10.1073/pnas. 0408810102
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.2 , pp. 373-378
    • Yang, S.1    Doolittle, R.F.2    Bourne, P.E.3
  • 38
    • 78649642175 scopus 로고    scopus 로고
    • Pseudokinases-remnants of evolution or key allosteric regulators?
    • 10.1016/j.sbi.2010.10.001 21074407 10.1016/j.sbi.2010.10.001 1:CAS:528:DC%2BC3cXhsV2js77L
    • Zeqiraj E, van Aalten DM (2010) Pseudokinases-remnants of evolution or key allosteric regulators? Curr Opin Struct Biol 20(6):772-781. doi: 10.1016/j.sbi.2010.10.001
    • (2010) Curr Opin Struct Biol , vol.20 , Issue.6 , pp. 772-781
    • Zeqiraj, E.1    Van Aalten, D.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.