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Volumn 113, Issue 4, 2014, Pages 306-315

Insights into the history of a bacterial group II intron remnant from the genomes of the nitrogen-fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); SINORHIZOBIUM MEDICAE; SINORHIZOBIUM MELILOTI;

EID: 84927176265     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2014.32     Document Type: Article
Times cited : (13)

References (60)
  • 1
    • 34447549172 scopus 로고    scopus 로고
    • Horizontal gene transfer and homologous recombination drive the evolution of the nitrogen-fixing symbionts of Medicago species
    • Bailly X, Olivieri I, Brunel B, Cleyet-Marel J-C, Bena G (2007). Horizontal gene transfer and homologous recombination drive the evolution of the nitrogen-fixing symbionts of Medicago species. J Bacteriol 189: 5223-5236.
    • (2007) J Bacteriol , vol.189 , pp. 5223-5236
    • Bailly, X.1    Olivieri, I.2    Brunel, B.3    Cleyet-Marel, J.-C.4    Bena, G.5
  • 2
    • 0033933642 scopus 로고    scopus 로고
    • High-resolution physical map of the pSymb megaplasmid and comparison of the three replicons of Sinorhizobium meliloti strain 1021
    • Barloy-Hubler F, Capela D, Batut J, Galibert F (2000). High-resolution physical map of the pSymb megaplasmid and comparison of the three replicons of Sinorhizobium meliloti strain 1021. Curr Microbiol 41: 109-113.
    • (2000) Curr Microbiol , vol.41 , pp. 109-113
    • Barloy-Hubler, F.1    Capela, D.2    Batut, J.3    Galibert, F.4
  • 3
  • 4
    • 84871339426 scopus 로고    scopus 로고
    • Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizo-bium meliloti
    • Biondi E, Toro N, Bazzicalupo M, Martínez-Abarca F (2011). Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizo-bium meliloti. Mob Genet Elements 1: 1-7.
    • (2011) Mob Genet Elements , vol.1 , pp. 1-7
    • Biondi, E.1    Toro, N.2    Bazzicalupo, M.3    Martínez-Abarca, F.4
  • 6
    • 0035859877 scopus 로고    scopus 로고
    • Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021
    • Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J et al. (2001). Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc Natl Acad Sci USA 98: 9877-9882.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 9877-9882
    • Capela, D.1    Barloy-Hubler, F.2    Gouzy, J.3    Bothe, G.4    Ampe, F.5    Batut, J.6
  • 7
    • 79551475230 scopus 로고    scopus 로고
    • Splicing of the Sinorhizobium meliloti RmInt1group II intron provides evidence of retroelement behavior
    • Chillón I, Martínez-Abarca F, Toro N (2010). Splicing of the Sinorhizobium meliloti RmInt1group II intron provides evidence of retroelement behavior. Nucleic Acids Res 39: 1095-1104.
    • (2010) Nucleic Acids Res , vol.39 , pp. 1095-1104
    • Chillón, I.1    Martínez-Abarca, F.2    Toro, N.3
  • 10
    • 0036795276 scopus 로고    scopus 로고
    • The dispersal of five group II introns among natural populations of Escherichia coli
    • Dai LX, Zimmerly S (2002). The dispersal of five group II introns among natural populations of Escherichia coli. RNA 8: 1294-1307.
    • (2002) RNA , vol.8 , pp. 1294-1307
    • Dai, L.X.1    Zimmerly, S.2
  • 11
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignmentof conserved genomic sequence with rearrangements
    • Darling AC, Mau B, Blattner FR, Perna NT (2004). Mauve: multiple alignmentof conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
    • (2004) Genome Res , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 12
    • 0002687402 scopus 로고
    • Origins and evolutionary relationships of retroelements
    • Morse SS (ed.) Raven Press: New York
    • Eickbush TH (1994). Origins and evolutionary relationships of retroelements. In: Morse SS (ed.) The Evolutionary Biology of Viruses. Raven Press: New York, pp 121-157.
    • (1994) The Evolutionary Biology of Viruses , pp. 121-157
    • Eickbush, T.H.1
  • 13
    • 19544370548 scopus 로고    scopus 로고
    • Dispersal and evolution of the Sinorhizobium meliloti group II RmInt1 intron in bacteria that interact with plants
    • Fernandez-Lopez M, Munoz-Adelantado E, Gillis M, Willems A, Toro N (2005). Dispersal and evolution of the Sinorhizobium meliloti group II RmInt1 intron in bacteria that interact with plants. Mol Biol Evol 22: 1518-1528.
    • (2005) Mol Biol Evol , vol.22 , pp. 1518-1528
    • Fernandez-Lopez, M.1    Munoz-Adelantado, E.2    Gillis, M.3    Willems, A.4    Toro, N.5
  • 14
    • 0035859832 scopus 로고    scopus 로고
    • The complete sequence of the 1, 683-kb pSymB megaplasmid from the N-2-fixing endosymbiont Sinorhizobium meliloti
    • Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorhölter FJ et al. (2001). The complete sequence of the 1, 683-kb pSymB megaplasmid from the N-2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci USA 98: 9889-9894.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 9889-9894
    • Finan, T.M.1    Weidner, S.2    Wong, K.3    Buhrmester, J.4    Chain, P.5    Vorhölter, F.J.6
  • 15
    • 27144444025 scopus 로고    scopus 로고
    • Diversification of DNA sequences in the symbiotic genome of Rhizobium etli
    • Flores M, Morales L, Avila A, González V, Bustos P, García D et al. (2005). Diversification of DNA sequences in the symbiotic genome of Rhizobium etli. J Bacteriol 187: 7185-7192.
    • (2005) J Bacteriol , vol.187 , pp. 7185-7192
    • Flores, M.1    Morales, L.2    Avila, A.3    González, V.4    Bustos, P.5    García, D.6
  • 17
    • 2942526836 scopus 로고    scopus 로고
    • Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumesMicrobiol
    • Gage DJ (2004). Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumesMicrobiol. Mol Biol Rev 68: 280-300.
    • (2004) Mol Biol Rev , vol.68 , pp. 280-300
    • Gage, D.J.1
  • 18
    • 79955837064 scopus 로고    scopus 로고
    • Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti
    • Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S et al. (2011). Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomic 12: 235.
    • (2011) BMC Genomic , vol.12 , pp. 235
    • Galardini, M.1    Mengoni, A.2    Brilli, M.3    Pini, F.4    Fioravanti, A.5    Lucas, S.6
  • 19
    • 84876520217 scopus 로고    scopus 로고
    • Replicon-dependent bacterial genome evolution: The case of Sinorhizobium meliloti
    • Galardini M, Pini F, Bazzicalupo M, Biondi EG, Mengoni A (2013). Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. Genome Biol Evol 5: 542-558.
    • (2013) Genome Biol Evol , vol.5 , pp. 542-558
    • Galardini, M.1    Pini, F.2    Bazzicalupo, M.3    Biondi, E.G.4    Mengoni, A.5
  • 20
    • 0035958746 scopus 로고    scopus 로고
    • The composite genome of the legume symbiont Sinorhizobium meliloti
    • Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F et al. (2001). The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668-672.
    • (2001) Science , vol.293 , pp. 668-672
    • Galibert, F.1    Finan, T.M.2    Long, S.R.3    Puhler, A.4    Abola, P.5    Ampe, F.6
  • 21
    • 0025760427 scopus 로고
    • Structuralcom-plexity of the symbiotic plasmid of Rhizobium leguminosarum bv. Phaseoli
    • Girard ML, Flores M, Brom S, Romero D, Palacios R, Dávila G (1991). Structuralcom-plexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli. J Bacteriol 173: 2411-2419.
    • (1991) J Bacteriol , vol.173 , pp. 2411-2419
    • Girard, M.L.1    Flores, M.2    Brom, S.3    Romero, D.4    Palacios, R.5    Dávila, G.6
  • 24
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 25
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
    • (2010) Syst Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 26
    • 77950802816 scopus 로고    scopus 로고
    • Introducing the bacterial 'chromid': Not a chromosome, not a plasmid
    • Harrison PW, Lower RPJ, Kim NKD, Young JPW (2010). Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol 18: 141-148.
    • (2010) Trends Microbiol , vol.18 , pp. 141-148
    • Harrison, P.W.1    Rpj, L.2    Nkd, K.3    Jpw, Y.4
  • 27
    • 63049137897 scopus 로고    scopus 로고
    • Principles of c-di-GMP signalling in bacteria
    • Hengge R (2009). Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7: 263-273.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 263-273
    • Hengge, R.1
  • 28
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 29
    • 33845403359 scopus 로고    scopus 로고
    • Mechanisms of cyclic-di-GMP signaling in bacteria
    • Jenal U, Malone J (2006). Mechanisms of cyclic-di-GMP signaling in bacteria. Ann Rev Genet 40: 385-407.
    • (2006) Ann Rev Genet , vol.40 , pp. 385-407
    • Jenal, U.1    Malone, J.2
  • 30
    • 0037436328 scopus 로고    scopus 로고
    • DNA target site requirements for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain
    • Jiménez-Zurdo JI, García-Rodŕiguez FM, Barrientos-Durán A, Toro N (2003). DNA target site requirements for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain. J Mol Biol 326: 413-423.
    • (2003) J Mol Biol , vol.326 , pp. 413-423
    • Jiménez-Zurdo, J.I.1    García-Rodŕiguez, F.M.2    Barrientos-Durán, A.3    Toro, N.4
  • 31
    • 84871274823 scopus 로고    scopus 로고
    • Selection-driven extinction dynamics for group II introns in Enterobacteriales
    • Leclercq S, Cordaux R (2012). Selection-driven extinction dynamics for group II introns in Enterobacteriales. PLoS One 7: e52268.
    • (2012) PLoS One , vol.7 , pp. e52268
    • Leclercq, S.1    Cordaux, R.2
  • 33
    • 34250632806 scopus 로고    scopus 로고
    • Genomes of the symbiotic nitrogen-fixing bacteria of legumes
    • MacLean AM, Finan TM, Sadowsky MJ (2007). Genomes of the symbiotic nitrogen-fixing bacteria of legumes. Plant Physiol 144: 615-622.
    • (2007) Plant Physiol , vol.144 , pp. 615-622
    • Maclean, A.M.1    Finan, T.M.2    Sadowsky, M.J.3
  • 34
    • 0031744472 scopus 로고    scopus 로고
    • Characterization and splicing in vivo of a Sinorhizobium meliloti group II intron associated with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily
    • Martínez-Abarca F, Zekri S, Toro N (1998). Characterization and splicing in vivo of a Sinorhizobium meliloti group II intron associated with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily. Mol Microbiol 28: 1295-1306.
    • (1998) Mol Microbiol , vol.28 , pp. 1295-1306
    • Martínez-Abarca, F.1    Zekri, S.2    Toro, N.3
  • 35
    • 3042725448 scopus 로고    scopus 로고
    • The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming
    • Martínez-Abarca F, Barrientos-Durán A, Fernández-López M, Toro N (2004). The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming. Nucleic Acids Res 32: 2880-2888.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2880-2888
    • Martínez-Abarca, F.1    Barrientos-Durán, A.2    Fernández-López, M.3    Toro, N.4
  • 38
    • 0029066770 scopus 로고
    • Structure and activities of group II introns
    • Michel F, Ferat JL (1995). Structure and activities of group II introns. Annu Rev Biochem 64: 435-461.
    • (1995) Annu Rev Biochem , vol.64 , pp. 435-461
    • Michel, F.1    Ferat, J.L.2
  • 39
    • 63549105637 scopus 로고    scopus 로고
    • The ribozyme core of group II introns: A structure in want of partners
    • Michel F, Costa M, Westhof E (2009). The ribozyme core of group II introns: a structure in want of partners. Trends Biochem Sci 34: 189-199.
    • (2009) Trends Biochem Sci , vol.34 , pp. 189-199
    • Michel, F.1    Costa, M.2    Westhof, E.3
  • 40
    • 0027434086 scopus 로고
    • Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function
    • Mohr G, Perlman PS, Lambowitz AM (1993). Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res 21: 4991-4997.
    • (1993) Nucleic Acids Res , vol.21 , pp. 4991-4997
    • Mohr, G.1    Perlman, P.S.2    Lambowitz, A.M.3
  • 41
    • 77954729219 scopus 로고    scopus 로고
    • Mechanisms used for genomic proliferation by thermophilic group II Introns
    • Mohr G, Ghanem E, Lambowitz AM (2010). Mechanisms used for genomic proliferation by thermophilic group II Introns. PLoS Biol 8: e1000391.
    • (2010) PLoS Biol , vol.8 , pp. e1000391
    • Mohr, G.1    Ghanem, E.2    Lambowitz, A.M.3
  • 42
    • 0034892720 scopus 로고    scopus 로고
    • Ectopic transposition of a group II intron in natural bacterial populations
    • Muñoz E, Villadas PJ, Toro N (2001). Ectopic transposition of a group II intron in natural bacterial populations. Mol Microbiol 41: 645-652.
    • (2001) Mol Microbiol , vol.41 , pp. 645-652
    • Muñoz, E.1    Villadas, P.J.2    Toro, N.3
  • 44
    • 77954288890 scopus 로고    scopus 로고
    • An alignment confidence score capturing robustness to guide tree uncertainty
    • Penn O, Privman E, Landan G, Graur D, Pupko T (2010). An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol 27: 1759-1767.
    • (2010) Mol Biol Evol , vol.27 , pp. 1759-1767
    • Penn, O.1    Privman, E.2    Landan, G.3    Graur, D.4    Pupko, T.5
  • 45
    • 80053440204 scopus 로고    scopus 로고
    • Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419
    • Reeve W, Chain P, O'Hara G, Ardley J, Nandesena K, Bräu L et al. (2010). Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci 2: 77-86.
    • (2010) Stand Genomic Sci , vol.2 , pp. 77-86
    • Reeve, W.1    Chain, P.2    O'Hara, G.3    Ardley, J.4    Nandesena, K.5    Bräu, L.6
  • 47
    • 84874914744 scopus 로고    scopus 로고
    • Cyclic di-GMP: The first 25 years of a universal bacterial second messenger
    • Römling U, Galperin MY, Gomelsky M (2013). Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77: 1-52.
    • (2013) Microbiol Mol Biol Rev , vol.77 , pp. 1-52
    • Römling, U.1    Galperin, M.Y.2    Gomelsky, M.3
  • 48
    • 0037073484 scopus 로고    scopus 로고
    • Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein
    • San Filippo J, Lambowitz AM (2002). Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein. J Mol Biol 324: 933-951.
    • (2002) J Mol Biol , vol.324 , pp. 933-951
    • San Filippo, J.1    Lambowitz, A.M.2
  • 50
    • 70349274104 scopus 로고    scopus 로고
    • Structural and mechanistic determinants of c-di-GMP signalling
    • Schirmer T, Jenal U (2009). Structural and mechanistic determinants of c-di-GMP signalling. Nature Rev Microbiol 7: 724-735.
    • (2009) Nature Rev Microbiol , vol.7 , pp. 724-735
    • Schirmer, T.1    Jenal, U.2
  • 51
    • 79961211358 scopus 로고    scopus 로고
    • The complete genome sequence of the dominant Sinorhizobiummeliloti field isolate SM11 extends the S. Meliloti pan-genome
    • Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H et al. (2011). The complete genome sequence of the dominant Sinorhizobiummeliloti field isolate SM11 extends the S. meliloti pan-genome. J Biotech 155: 20-33.
    • (2011) J Biotech , vol.155 , pp. 20-33
    • Schneiker-Bekel, S.1    Wibberg, D.2    Bekel, T.3    Blom, J.4    Linke, B.5    Neuweger, H.6
  • 52
    • 50649097946 scopus 로고    scopus 로고
    • Group II introns in eubacteria and archaea: ORF-less introns and new varieties
    • Simon DM, Clarke NA, McNeil BA, Johnson I, Pantuso D, Dai L et al. (2008). Group II introns in eubacteria and archaea: ORF-less introns and new varieties. RNA 14: 1704-1713.
    • (2008) RNA , vol.14 , pp. 1704-1713
    • Simon, D.M.1    Clarke, N.A.2    McNeil, B.A.3    Johnson, I.4    Pantuso, D.5    Dai, L.6
  • 53
    • 34250635510 scopus 로고    scopus 로고
    • Legume evolution: Where do nodules and mycorrhizas fit in?
    • Sprent JI, James EK (2007). Legume evolution: Where do nodules and mycorrhizas fit in? Plant Physiol 144: 575-581.
    • (2007) Plant Physiol , vol.144 , pp. 575-581
    • Sprent, J.I.1    James, E.K.2
  • 54
    • 84873965566 scopus 로고    scopus 로고
    • Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies
    • Sugawara M, Epstein B, Badgley BD, Unno T, Xu L, Reese J et al. (2013). Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies. Genome Biol 14: R17.
    • (2013) Genome Biol , vol.14 , pp. R17
    • Sugawara, M.1    Epstein, B.2    Badgley, B.D.3    Unno, T.4    Xu, L.5    Reese, J.6
  • 55
    • 84861893794 scopus 로고    scopus 로고
    • Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
    • Tian CF, Zhou YJ, Zhang YM, Li QQ, Zhang YZ, Li DF et al. (2012). Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Natl Acad Sci USA 109: 8629-8634.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 8629-8634
    • Tian, C.F.1    Zhou, Y.J.2    Zhang, Y.M.3    Li, Q.Q.4    Zhang, Y.Z.5    Li, D.F.6
  • 56
    • 84872793413 scopus 로고    scopus 로고
    • Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties
    • Toro N, Martínez-Abarca F (2013). Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties. PLoS One 8: e55102.
    • (2013) PLoS One , vol.8 , pp. e55102
    • Toro, N.1    Martínez-Abarca, F.2
  • 57
    • 0033979041 scopus 로고    scopus 로고
    • The glutamine synthetases of rhizobia: Phylogenetics and evolutionary implications
    • Turner SL, Young JPW (2000). The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Mol Biol Evol 17: 309-319.
    • (2000) Mol Biol Evol , vol.17 , pp. 309-319
    • Turner, S.L.1    Jpw, Y.2
  • 60
    • 79960634800 scopus 로고    scopus 로고
    • Selfish genetic elements, genetic conflict, and evolutionary innovation
    • Werren JH (2011). Selfish genetic elements, genetic conflict, and evolutionary innovation. Proc Natl Acad Sci USA 108: 10863-10870.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 10863-10870
    • Werren, J.H.1


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