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Genomic Context of Metal Response Genes in Cupriavidus metallidurans with a Focus on Strain CH34

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Abstract

Cupriavidus metallidurans CH34 has been studied for over 30 years, mostly because of its resistance to numerous heavy metals. Many of these metal resistance determinants were rapidly associated with native megaplasmids. However, its genome sequencing and whole genome expression profiling not only revealed the complex structure of its multiple replicons and complex responses to metals, but also revealed the presence of unnoticed/unstudied metal resistance determinants on the different replicons. In this chapter, the genomic context of the metal response genes in C. metallidurans CH34 will be described with a focus on its mobilome including insertion sequence elements, transposons, integrative and conjugative elements and genomic islands.

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References

  • Alvarez AF, Rodriguez C, Georgellis D (2013) Ubiquinone and menaquinone electron carriers represent the yin and yang in the redox regulation of the ArcB sensor kinase. J Bacteriol 195(13):3054–3061

    CAS  Google Scholar 

  • Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrere S, Cruveiller S, Dossat C, Lajus A, Marchetti M, Poinsot V, Rouy Z, Servin B, Saad M, Schenowitz C, Barbe V, Batut J, Medigue C, Masson-Boivin C (2008) Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res 18(9):1472–1483

    CAS  Google Scholar 

  • Bentley SD, Corton C, Brown SE, Barron A, Clark L, Doggett J, Harris B, Ormond D, Quail MA, May G, Francis D, Knudson D, Parkhill J, Ishimaru CA (2008) Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation. J Bacteriol 190(6):2150–2160

    CAS  Google Scholar 

  • Bernard R, El Ghachi M, Mengin-Lecreulx D, Chippaux M, Denizot F (2005) BcrC from Bacillus subtilis acts as an undecaprenyl pyrophosphate phosphatase in bacitracin resistance. J Biol Chem 280(32):28852–28857

    CAS  Google Scholar 

  • Bersch B, Derfoufi KM, De Angelis F, Auquier V, Ekende EN, Mergeay M, Ruysschaert JM, Vandenbussche G (2011) Structural and metal binding characterization of the C-terminal metallochaperone domain of membrane fusion protein SilB from Cupriavidus metallidurans CH34. Biochemistry 50(12):2194–2204

    CAS  Google Scholar 

  • Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009) Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genom 10:468

    Google Scholar 

  • Bondarczuk K, Piotrowska-Seget Z (2013) Molecular basis of active copper resistance mechanisms in gram-negative bacteria. Cell Biol Toxicol 29(6):397–405

    CAS  Google Scholar 

  • Borremans B, Hobman JL, Provoost A, Brown NL, van der Lelie D (2001) Cloning and functional analysis of the pbr lead resistance determinant of Ralstonia metallidurans CH34. J Bacteriol 183(19):5651–5658

    CAS  Google Scholar 

  • Brim H, Heyndrickx M, de Vos P, Wilmotte A, Springael D, Schlegel HG, Mergeay M (1999) Amplified rDNA restriction analysis and further genotypic characterisation of metal-resistant soil bacteria and related facultative hydrogenotrophs. Syst Appl Microbiol 22(2):258–268

    CAS  Google Scholar 

  • Brown NL, Evans LR (1991) Transposition in prokaryotes: transposon Tn501. Res Microbiol 142(6):689–700

    CAS  Google Scholar 

  • Busby JN, Panjikar S, Landsberg MJ, Hurst MR, Lott JS (2013) The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device. Nature 501(7468):547–550

    CAS  Google Scholar 

  • Chen WJ, Hsieh FC, Hsu FC, Tasy YF, Liu JR, Shih MC (2014) Characterization of an insecticidal toxin and pathogenicity of Pseudomonas taiwanensis against insects. PLoS Pathog 10(8):e1004288

    Google Scholar 

  • Collard JM, Provoost A, Taghavi S, Mergeay M (1993) A new type of Alcaligenes eutrophus CH34 zinc resistance generated by mutations affecting regulation of the cnr cobalt-nickel resistance system. J Bacteriol 175(3):779–784

    CAS  Google Scholar 

  • Collard JM, Corbisier P, Diels L, Dong Q, Jeanthon C, Mergeay M, Taghavi S, van der Lelie D, Wilmotte A, Wuertz S (1994) Plasmids for heavy metal resistance in Alcaligenes eutrophus CH34: mechanisms and applications. FEMS Microbiol Rev 14(4):405–414

    CAS  Google Scholar 

  • Diaz-Perez C, Cervantes C, Campos-Garcia J, Julian-Sanchez A, Riveros-Rosas H (2007) Phylogenetic analysis of the chromate ion transporter (CHR) superfamily. FEBS J 274(23):6215–6227

    CAS  Google Scholar 

  • Diels L, Mergeay M (1990) DNA probe-mediated detection of resistant bacteria from soils highly polluted by heavy metals. Appl Environ Microbiol 56(5):1485–1491

    CAS  Google Scholar 

  • Diels L, Faelen M, Mergeay M, Nies D (1985) Mercury transposons from plasmids governing multiple resistance to heavy metals in Alcaligenes eutrophus CH34. Arch Physiol Biochem 93:27–28

    Google Scholar 

  • Diels L, Sadouk A, Mergeay M (1989) Large plasmids governing multiple resistances to heavy metals—a genetic approach. Toxicol Environ Chem 23(1–4):79–89

    CAS  Google Scholar 

  • Diels L, Dong QH, van der Lelie D, Baeyens W, Mergeay M (1995) The czc operon of Alcaligenes eutrophus CH34: from resistance mechanism to the removal of heavy metals. J Ind Microbiol 14(2):142–153

    CAS  Google Scholar 

  • Don RH, Pemberton JM (1981) Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J Bacteriol 145(2):681–686

    CAS  Google Scholar 

  • Don RH, Pemberton JM (1985) Genetic and physical map of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pJP4. J Bacteriol 161(1):466–468

    CAS  Google Scholar 

  • Dong Q, Sadouk A, van der Lelie D, Taghavi S, Ferhat A, Nuyten JM, Borremans B, Mergeay M, Toussaint A (1992) Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351. J Bacteriol 174(24):8133–8138

    CAS  Google Scholar 

  • Dubarry N, Pasta F, Lane D (2006) ParABS systems of the four replicons of Burkholderia cenocepacia: new chromosome centromeres confer partition specificity. J Bacteriol 188(4):1489–1496

    CAS  Google Scholar 

  • Fricke WF, Kusian B, Bowien B (2009) The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae. J Microbiol Biotechnol 16(1–2):124–135

    CAS  Google Scholar 

  • Friedrich B, Hogrefe C, Schlegel HG (1981) Naturally occurring genetic transfer of hydrogen-oxidizing ability between strains of Alcaligenes eutrophus. J Bacteriol 147(1):198–205

    CAS  Google Scholar 

  • Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3(9):722–732

    CAS  Google Scholar 

  • Grass G, Grosse C, Nies DH (2000) Regulation of the cnr cobalt and nickel resistance determinant from Ralstonia sp. strain CH34. J Bacteriol 182(5):1390–1398

    CAS  Google Scholar 

  • Gstalder ME, Faelen M, Mine N, Top EM, Mergeay M, Couturier M (2003) Replication functions of new broad host range plasmids isolated from polluted soils. Res Microbiol 154(7):499–509

    CAS  Google Scholar 

  • Haines AS, Akhtar P, Stephens ER, Jones K, Thomas CM, Perkins CD, Williams JR, Day MJ, Fry JC (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology 152(Pt 9):2689–2701

    CAS  Google Scholar 

  • Haines AS, Jones K, Batt SM, Kosheleva IA, Thomas CM (2007) Sequence of plasmid pBS228 and reconstruction of the IncP-1alpha phylogeny. Plasmid 58(1):76–83

    CAS  Google Scholar 

  • Harrison PW, Lower RP, Kim NK, Young JP (2010) Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid. Trends Microbiol 18(4):141–148

    CAS  Google Scholar 

  • Henard CA, Tapscott T, Crawford MA, Husain M, Doulias PT, Porwollik S, Liu L, McClelland M, Ischiropoulos H, Vazquez-Torres A (2014) The 4-cysteine zinc-finger motif of the RNA polymerase regulator DksA serves as a thiol switch for sensing oxidative and nitrosative stress. Mol Microbiol 91(4):790–804

    CAS  Google Scholar 

  • Hong KW, Thinagaran D, Gan HM, Yin WF, Chan KG (2012) Whole-genome sequence of Cupriavidus sp. strain BIS7, a heavy-metal-resistant bacterium. J Bacteriol 194(22):6324

    CAS  Google Scholar 

  • Hubner A, Hendrickson W (1997) A fusion promoter created by a new insertion sequence, IS1490, activates transcription of 2,4,5-trichlorophenoxyacetic acid catabolic genes in Burkholderia cepacia AC1100. J Bacteriol 179(8):2717–2723

    CAS  Google Scholar 

  • Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40(Database issue): D306–D312

    Google Scholar 

  • Hynninen A, Touze T, Pitkanen L, Mengin-Lecreulx D, Virta M (2009) An efflux transporter PbrA and a phosphatase PbrB cooperate in a lead-resistance mechanism in bacteria. Mol Microbiol 74(2):384–394

    CAS  Google Scholar 

  • Inaoka T, Ochi K (2012) Undecaprenyl pyrophosphate involvement in susceptibility of Bacillus subtilis to rare earth elements. J Bacteriol 194(20):5632–5637

    CAS  Google Scholar 

  • Jackson AP, Thomas GH, Parkhill J, Thomson NR (2009) Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genom 10:584

    Google Scholar 

  • Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M (2010) The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS ONE 5(5):e10433

    Google Scholar 

  • Juhnke S, Peitzsch N, Hubener N, Grosse C, Nies DH (2002) New genes involved in chromate resistance in Ralstonia metallidurans strain CH34. Arch Microbiol 179(1):15–25

    CAS  Google Scholar 

  • Kanjee U, Ogata K, Houry WA (2012) Direct binding targets of the stringent response alarmone (p)ppGpp. Mol Microbiol 85(6):1029–1043

    CAS  Google Scholar 

  • Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV, Nikiforov VG (1995) Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol Microbiol 17(6):1189–1200

    CAS  Google Scholar 

  • Klockgether J, Wurdemann D, Reva O, Wiehlmann L, Tummler B (2007) Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 189(6):2443–2459

    CAS  Google Scholar 

  • Klockgether J, Wurdemann D, Wiehlmann L, Tummler B (2008) Transcript profiling of the Pseudomonas aeruginosa genomic islands PAGI-2 and pKLC102. Microbiology 154(Pt 6):1599–1604

    CAS  Google Scholar 

  • Koskiniemi S, Lamoureux JG, Nikolakakis KC, de Roodenbeke CTK, Kaplan MD, Low DA, Hayes CS (2013) Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci U S A 110(17):7032–7037

    CAS  Google Scholar 

  • Koskiniemi S, Garza-Sanchez F, Sandegren L, Webb JS, Braaten BA, Poole SJ, Andersson DI, Hayes CS, Low DA (2014) Selection of orphan Rhs toxin expression in evolved Salmonella enterica serovar Typhimurium. PLoS Genet 10(3):e1004255

    Google Scholar 

  • Kung VL, Khare S, Stehlik C, Bacon EM, Hughes AJ, Hauser AR (2012) An rhs gene of Pseudomonas aeruginosa encodes a virulence protein that activates the inflammasome. Proc Natl Acad Sci U S A 109(4):1275–1280

    CAS  Google Scholar 

  • Larbig KD, Christmann A, Johann A, Klockgether J, Hartsch T, Merkl R, Wiehlmann L, Fritz HJ, Tummler B (2002) Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol 184(23):6665–6680

    CAS  Google Scholar 

  • Leao SC, Matsumoto CK, Carneiro A, Ramos RT, Nogueira CL, Lima JD, Jr., Lima KV, Lopes ML, Schneider H, Azevedo VA, da Costa da Silva A (2013) The detection and sequencing of a broad-host-range conjugative IncP-1beta plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii. PLoS One 8(4): e60746

    Google Scholar 

  • Legatzki A, Grass G, Anton A, Rensing C, Nies DH (2003) Interplay of the Czc system and two P-type ATPases in conferring metal resistance to Ralstonia metallidurans. J Bacteriol 185(15):4354–4361

    CAS  Google Scholar 

  • Li LG, Cai L, Zhang T (2013) Genome of Cupriavidus sp. HMR-1, a heavy metal-resistant bacterium. Genome Announc 1(1):e00202–e00212

    Google Scholar 

  • Liesegang H, Lemke K, Siddiqui RA, Schlegel HG (1993) Characterization of the inducible nickel and cobalt resistance determinant cnr from pMOL28 of Alcaligenes eutrophus CH34. J Bacteriol 175(3):767–778

    CAS  Google Scholar 

  • Lin H, Li TY, Xie MH, Zhang Y (2007) Characterization of the variants, flanking genes, and promoter activity of the Leifsonia xyli subsp. cynodontis insertion sequence IS1237. J Bacteriol 189(8):3217–3227

    CAS  Google Scholar 

  • Lykidis A, Perez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, Gonzalez B, Kyrpides NC (2010) The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS ONE 5(3):e9729

    Google Scholar 

  • Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62(3):725–774

    CAS  Google Scholar 

  • Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183(19):5684–5697

    CAS  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Google Scholar 

  • Mela F, Fritsche K, Boersma H, van Elsas JD, Bartels D, Meyer F, de Boer W, van Veen JA, Leveau JH (2008) Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol 66(1):45–62

    CAS  Google Scholar 

  • Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Van Gijsegem F (1985) Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162(1):328–334

    CAS  Google Scholar 

  • Mergeay M, Monchy S, Janssen P, Van Houdt R, Leys N (2009) Megaplasmids in Cupriavidus genus and metal resistance. In: Schwartz E (ed) Microbial megaplasmids, vol 11., Microbiology MonographsSpringer, Berlin, pp 209–238

    Google Scholar 

  • Merlin C, Springael D, Toussaint A (1999) Tn4371: a modular structure encoding a phage-like integrase, a Pseudomonas-like catabolic pathway, and RP4/Ti-like transfer functions. Plasmid 41(1):40–54

    CAS  Google Scholar 

  • Mijnendonckx K, Provoost A, Monsieurs P, Leys N, Mergeay M, Mahillon J, Van Houdt R (2011) Insertion sequence elements in Cupriavidus metallidurans CH34: distribution and role in adaptation. Plasmid 65(3):193–203

    CAS  Google Scholar 

  • Mijnendonckx K, Provoost A, Ott CM, Venkateswaran K, Mahillon J, Leys N, Van Houdt R (2013) Characterization of the survival ability of Cupriavidus metallidurans and Ralstonia pickettii from space-related environments. Microb Ecol 65(2):347–360

    CAS  Google Scholar 

  • Minakhina S, Kholodii G, Mindlin S, Yurieva O, Nikiforov V (1999) Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases. Mol Microbiol 33(5):1059–1068

    CAS  Google Scholar 

  • Mindlin S, Petrova M (2013) Mercury resistance transposons. In: Roberts AP, Mullany P (eds) Bacterial integrative mobile genetic elements. Landes Biosciences, Austin, pp 33–52

    Google Scholar 

  • Mira A, Klasson L, Andersson SG (2002) Microbial genome evolution: sources of variability. Curr Opin Microbiol 5(5):506–512

    CAS  Google Scholar 

  • Miyazaki R, Minoia M, Pradervand N, Sentchilo V, Sulser S, Reinhard F, van der Meer JR (2013) The clc element and related genomic islands in Proteobacteria. In: Roberts AP, Mullany P (eds) Bacterial integrative mobile genetic elements. Landes Bioscience, Austin, pp 261–272

    Google Scholar 

  • Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B, Mergeay M, Taghavi S, van der Lelie D, Vallaeys T (2006a) Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34. Microbiology 152(Pt 6):1765–1776

    CAS  Google Scholar 

  • Monchy S, Vallaeys T, Bossus A, Mergeay M (2006b) Metal transport ATPase genes from Cupriavidus metallidurans CH34: a transcriptomic approach. Int J Environ Anal Chem 86(9):677–692

    CAS  Google Scholar 

  • Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S, van der Lelie D, Mergeay M (2007) Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 189(20):7417–7425

    CAS  Google Scholar 

  • Monsieurs P, Moors H, Van Houdt R, Janssen PJ, Janssen A, Coninx I, Mergeay M, Leys N (2011) Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals 24(6):1133–1151

    CAS  Google Scholar 

  • Monsieurs P, Provoost A, Mijnendonckx K, Leys N, Gaudreau C, Van Houdt R (2013) Genome sequence of Cupriavidus metallidurans Strain H1130, isolated from an invasive human infection. Genome Announc 1(6):e01051–e01013

    Google Scholar 

  • Monsieurs P, Mijnendonckx K, Provoost A, Venkateswaran K, Ott CM, Leys N, Van Houdt R (2014) Genome sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, isolated from space equipment. Genome Announc 2(4):e00719–e00714

    Google Scholar 

  • Nies DH (1995) The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J Bacteriol 177(10):2707–2712

    CAS  Google Scholar 

  • Nies A, Nies DH, Silver S (1990) Nucleotide sequence and expression of a plasmid-encoded chromate resistance determinant from Alcaligenes eutrophus. J Biol Chem 265(10):5648–5653

    CAS  Google Scholar 

  • Nies DH, Koch S, Wachi S, Peitzsch N, Saier MH Jr (1998) CHR, a novel family of prokaryotic proton motive force-driven transporters probably containing chromate/sulfate antiporters. J Bacteriol 180(21):5799–5802

    CAS  Google Scholar 

  • Overmars L, Kerkhoven R, Siezen RJ, Francke C (2013) MGcV: the microbial genomic context viewer for comparative genome analysis. BMC Genom 14:209

    CAS  Google Scholar 

  • Paul BJ, Berkmen MB, Gourse RL (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. Proc Natl Acad Sci USA 102(22):7823–7828

    CAS  Google Scholar 

  • Poehlein A, Kusian B, Friedrich B, Daniel R, Bowien B (2012) Complete genome sequence of the type strain Cupriavidus necator N-1. J Bacteriol 193(18):5017

    Google Scholar 

  • Poole SJ, Diner EJ, Aoki SK, Braaten BA, de Roodenbeke CTK, Low DA, Hayes CS (2011) Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLoS Genet 7(8):e1002217

    CAS  Google Scholar 

  • Remenant B, de Cambiaire JC, Cellier G, Jacobs JM, Mangenot S, Barbe V, Lajus A, Vallenet D, Médigue C, Fegan M, Allen C, Prior P (2011) Ralstonia syzygii, the blood disease bacterium and some Asian Ralstonia solanacearum strains form a single genomic species despite divergent lifestyles. PLoS One 6(9): e24356

    Google Scholar 

  • Ricker N, Qian H, Fulthorpe RR (2013) Phylogeny and organization of recombinase in trio (RIT) elements. Plasmid 70(2):226–239

    CAS  Google Scholar 

  • Ryan MP, Pembroke JT, Adley CC (2009) Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements. BMC Microbiol 9:242

    Google Scholar 

  • Sadouk A, Mergeay M (1993) Chromosome mapping in Alcaligenes eutrophus CH34. Mol Gen Genet 240(2):181–187

    CAS  Google Scholar 

  • Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thébault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415(6871):497–502

    CAS  Google Scholar 

  • Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD, Concepcion RN, Ohta H (2006) Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. Int J Syst Evol Microbiol 56(Pt 5): 973–978

    Google Scholar 

  • Sawana A, Adeolu M, Gupta RS (2014) Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 5:429

    Google Scholar 

  • Schmidt T, Schlegel HG (1989) Nickel and cobalt resistance of various bacteria isolated from soil and highly polluted domestic and industrial wastes. FEMS Microbiol Lett 62(5):315–328

    CAS  Google Scholar 

  • Schmidt T, Stoppel RD, Schlegel HG (1991) High-level nickel resistance in Alcaligenes xylosoxydans 31A and Alcaligenes eutrophus KTO2. Appl Environ Microbiol 57(11):3301–3309

    CAS  Google Scholar 

  • Schneider D, Lenski RE (2004) Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol 155(5):319–327

    CAS  Google Scholar 

  • Schneider D, Faure D, Noirclerc-Savoye M, Barrière AC, Coursange E, Blot M (2000) A broad-host-range plasmid for isolating mobile genetic elements in gram-negative bacteria. Plasmid 44(2):201–207

    CAS  Google Scholar 

  • Schwartz E (2009) Microbial megaplasmids. Microbiology Monographs. Springer, Berlin

    Google Scholar 

  • Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G (2003) Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis. J Mol Biol 332(2):369–383

    CAS  Google Scholar 

  • Sen D, Van der Auwera GA, Rogers LM, Thomas CM, Brown CJ, Top EM (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol 77(22):7975–7983

    CAS  Google Scholar 

  • Sharma P, Stagge S, Bekker M, Bettenbrock K, Hellingwerf KJ (2013) Kinase activity of ArcB from Escherichia coli Is subject to regulation by both ubiquinone and demethylmenaquinone. PLoS ONE 8(10):e75412

    CAS  Google Scholar 

  • Siguier P, Gourbeyre E, Chandler M (2014) Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 38(5): 865–891

    Google Scholar 

  • Silver S, Phung LT (1996) Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50:753–789

    CAS  Google Scholar 

  • Sisto A, Cipriani MG, Morea M, Lonigro SL, Valerio F, Lavermicocca P (2010) An Rhs-like genetic element is involved in bacteriocin production by Pseudomonas savastanoi pv. savastanoi. Anton Leeuw Int J G 98(4):505–517

    CAS  Google Scholar 

  • Stokes HW, Elbourne LD, Hall RM (2007) Tn1403, a multiple-antibiotic resistance transposon made up of three distinct transposons. Antimicrob Agents Chemother 51(5):1827–1829

    CAS  Google Scholar 

  • Taghavi S, Lesaulnier C, Monchy S, Wattiez R, Mergeay M, van der Lelie D (2009) Lead(II) resistance in Cupriavidus metallidurans CH34: interplay between plasmid and chromosomally-located functions. Anton Leeuw Int J G 96(2):171–182

    CAS  Google Scholar 

  • Talat ME (2000) Genetic mechanism of heavy metal resistance of Pseudomonas aeruginosa CMG103. PhD thesis, University of Karachi, Karachi

    Google Scholar 

  • Tauch A, Schneiker S, Selbitschka W, Puhler A, van Overbeek LS, Smalla K, Thomas CM, Bailey MJ, Forney LJ, Weightman A, Ceglowski P, Pembroke T, Tietze E, Schroder G, Lanka E, van Elsas JD (2002) The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. Microbiology 148(Pt 6):1637–1653

    CAS  Google Scholar 

  • Tibazarwa C, Wuertz S, Mergeay M, Wyns L, van der Lelie D (2000) Regulation of the cnr cobalt and nickel resistance determinant of Ralstonia eutropha (Alcaligenes eutrophus) CH34. J Bacteriol 182(5):1399–1409

    CAS  Google Scholar 

  • Timotius K, Schlegel HG (1987) Aus Abwässern isolierte nickel-resistente Bakterien. Nachrichten der Akademie der Wissenschaften Göttingen II Math-Physik Klasse 3:15–23

    Google Scholar 

  • Top E, Desmet I, Verstraete W, Dijkmans R, Mergeay M (1994) Exogenous isolation of mobilizing plasmids from polluted soils and sludges. Appl Environ Microbiol 60(3):831–839

    CAS  Google Scholar 

  • Touchon M, Rocha EP (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 24(4):969–981

    CAS  Google Scholar 

  • Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D (2003) The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol 69(8):4837–4845

    CAS  Google Scholar 

  • Tseng SP, Hsueh PR, Tsai JC, Teng LJ (2007) Tn6001, a transposon-like element containing the bla VIM-3-harboring integron In450. Antimicrob Agents Chemother 51(11):4187–4190

    CAS  Google Scholar 

  • Van der Auwera GA, Krol JE, Suzuki H, Foster B, Van Houdt R, Brown CJ, Mergeay M, Top EM (2009) Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Anton Leeuw Int J G 96(2): 193–204

    Google Scholar 

  • van Elsas JD, Gardener BB, Wolters AC, Smit E (1998) Isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere. Appl Environ Microbiol 64(3):880–889

    Google Scholar 

  • Van Houdt R, Mergeay M (2012) Plasmids as secondary chromosomes. In: Bell E, Bond J, Klinman J, Masters B, Wells R (eds) Molecular life sciences: an encyclopedic reference: springerreference (www.springerreference.com)

  • Van Houdt R, Monchy S, Leys N, Mergeay M (2009) New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria. Anton Leeuw Int J G 96:205–226

    Google Scholar 

  • Van Houdt R, Leplae R, Lima-Mendez G, Mergeay M, Toussaint A (2012a) Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. Mob DNA 3(1):6

    Google Scholar 

  • Van Houdt R, Monsieurs P, Mijnendonckx K, Provoost A, Janssen A, Mergeay M, Leys N (2012b) Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans. BMC Genom 13:111

    Google Scholar 

  • Van Houdt R, Toussaint A, Ryan MP, Pembroke JT, Mergeay M, Adley CC (2013) The Tn4371 ICE family of bacterial mobile genetic elements. In: Roberts AP, Mullany P (eds) Bacterial integrative mobile genetic elements. Landes Bioscience, Austin, pp 179–200

    Google Scholar 

  • Wagner A, Lewis C, Bichsel M (2007) A survey of bacterial insertion sequences using IScan. Nucleic Acids Res 35(16):5284–5293

    CAS  Google Scholar 

  • Yang F, Pecina DA, Kelly SD, Kim SH, Kemner KM, Long DT, Marsh TL (2010) Biosequestration via cooperative binding of copper by Ralstonia pickettii. Environ Technol 31(8–9):1045–1060

    CAS  Google Scholar 

  • Youderian P, Hartzell PL (2007) Triple mutants uncover three new genes required for social motility in Myxococcus xanthus. Genetics 177(1):557–566

    CAS  Google Scholar 

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Van Houdt, R., Mergeay, M. (2015). Genomic Context of Metal Response Genes in Cupriavidus metallidurans with a Focus on Strain CH34. In: Mergeay, M., Van Houdt, R. (eds) Metal Response in Cupriavidus metallidurans. SpringerBriefs in Molecular Science(). Springer, Cham. https://doi.org/10.1007/978-3-319-20594-6_2

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