Found at: doi:10.1371/journal.pone.0010433.s012 (0.02 MB XLS)

**Table S5** Transcription factors - meta analysis. Transcription factors across 965 organisms, including 673 bacteria (source: http://www.transcriptionfactor.org/). Note that this table consist of multiple sheets: Sheet 1, DBDOverview - general information and data from DBD; Sheet 2, DBD organism - breakdown of transcriptional regulators for each of the organisms listed in Table 2 and *E. coli* K-12; Sheet 3, MageReplicon - distribution of transcriptional regulators across the four replicons of CH34, using MaGe data.

Found at: doi:10.1371/journal.pone.0010433.s013 (0.62 MB XLS)

**Table S6** Functional distribution and chromosomal location of *C. metallidurans* CH34 genes implicated in iron uptake and -metabolism.

Found at: doi:10.1371/journal.pone.0010433.s014 (0.12 MB DOC)

**Table S7** Signal transduction systems. Domain profiles of *C. metallidurans* CH34 and related organisms listed in Table 2 and *E. coli* K-12 (source: http://mistdb.com/). Only domains that occur 10 times or more in CH34 are considered. Extreme underrepresentations of domains (according to actual numbers versus genome size) are shaded in orange. Rows 25–27 hold the distributions of predicted one-component and two-component signal transduction systems (denoted as 1CST and 2CST, respectively) as well as the total number of predicted systems. The latter was used to calculate the proportional number (in percentages) of proteins putatively involved in signal transduction.

Found at: doi:10.1371/journal.pone.0010433.s015 (0.02 MB XLS)

**Table S8** Prevalence of Bug domains according to the MiST2 database. Distribution of 2,377 proteins with Bug domains across 1,216 complete and draft, bacterial and archaeal genomes (source: http://mistdb.com). Organisms without Bug domain-containing proteins are omitted from the table.

## References

1. Fergusson JE (1990) The Heavy Elements: Chemistry, Environmental Impact, and Health Effects. Oxford, UK: Pergamon Press.

2. Adriano DC (2001) Trace Elements in Terrestrial Environments: Biogeochemistry, Bioavailability, and Risks of Metals. New-YorkUS: Springer-Verlag.

3. Mergeay M, Houba C, Gerits J (1978) Extrachromosomal inheritance controlling resistance to cadmium, cobalt, copper and zinc ions: evidence from curing in a *Pseudomonas* [proceedings]. Arch Int Physiol Biochim 86: 440-442.

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

5. 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: 15-25.

6. Mergeay M (2000) Bacteria adapted to industrial biotopes: the metal resistant *Ralstonia*. In: Hengge-Aronis R, Storz G, eds. Bacterial Stress Responses. Washington, DC: ASM Press. pp 403-414.

7. 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. Berlin: Springer Berlin/Heidelberg. pp 209-238.

8. Mergeay M, Monchy S, Vallaees T, Auquier V, Benotmane A, et al. (2003) *Ralstonia metallidurans*, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev 27: 385-410.

9. Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, et al. (1985) *Alcaligenes eutrophus* CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162: 328-334.

10. Monchy S, Benotmane MA, Janssen P, Vallaees T, Taghavi S, et al. (2007) Plasmids pMOL28 and pMOL30 of *Cupriavidus metallidurans* are specialized in the maximal viable response to heavy metals. J Bacteriol 189: 7417-7425.

Found at: doi:10.1371/journal.pone.0010433.s016 (0.07 MB XLS)

**Table S9** Functional distribution and chromosomal location of *C. metallidurans* CH34 genes involved in polyester (PHA/PHB) biosynthesis and degradation.

Found at: doi:10.1371/journal.pone.0010433.s017 (0.06 MB DOC)

**Table S10** *C. metallidurans* CH34 genes for DNA repair and stress-related regulators.

Found at: doi:10.1371/journal.pone.0010433.s018 (0.08 MB DOC)

**Table S11** *C. metallidurans* CH34 genes encoding universal stress proteins (UspA superfamily) that are induced by a variety of starvation- and stress-conditions.

Found at: doi:10.1371/journal.pone.0010433.s019 (0.04 MB DOC)

## Acknowledgments

We thank A. D. Woodhead for excellent scientific editing of the manuscript and D. Vallenet and Z. Rouy of Génoscope (Centre National de Séquençage, Evry, France) for implementing additional features in MaGe and their essential advice in genome annotation. We are also grateful to I. T. Paulsen and Q. Ren for advice and data analyses using TransAAP, and to L. Ulrich for providing SQL-derived data from the Microbial Signal Transduction database (MistDB and MiST2).

## Author Contributions

Wrote the paper: PJJ RVH HM PM NM NL AL SM ST DvdL MM. Coordinated the genome annotation: PJJ. Contributed to genome annotation: RVH HM PM NM SM MM. Performed genome data analysis: PJJ. Analysed genome information: PJJ RVH HM PM NM SM CM ST DvdL MM. Organised, reviewed, and edited the manuscript: PJJ. Performed bioinformatics: PJJ PM CM. Performed associated miscellaneous bioinformatics: SMcC. Performed genetic experiments and the sequencing and finishing of the genome: AM MAB TV AL SM ST JD. Maintained and updated the Cupriavidu2Scope project with her team: CM. Developed and applied methods to identify and correct misassemblies in the original shotgun assembly: SMcC.

11. Nies A, Nies DH, Silver S (1989) Cloning and expression of plasmid genes encoding resistances to chromate and cobalt in *Alcaligenes eutrophus*. J Bacteriol 171: 5065-5070.

12. 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: 5648-5653.

13. Nies DH, Silver S (1989) Plasmid-determined inducible efflux is responsible for resistance to cadmium, zinc, and cobalt in *Alcaligenes eutrophus*. J Bacteriol 171: 896-900.

14. Reith F, Rogers SL, McPhail DC, Webb D (2006) Biomineralization of gold: biofilms on bacterioform gold. Science 313: 233-236.

15. Novick RP, Roth C (1968) Plasmid-linked resistance to inorganic salts in *Staphylococcus aureus*. J Bacteriol 95: 1335-1342.

16. Nies DH (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51: 730-750.

17. Silver S, Misra TK (1988) Plasmid-mediated heavy metal resistances. Annu Rev Microbiol 42: 717-743.

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

19. Lejeune P, Mergeay M, Van Gijsegem F, Faelen M, Gerits J, et al. (1983) Chromosome transfer and R-prime plasmid formation mediated by plasmid pULB113 (RP4::mini-Mu) in *Alcaligenes eutrophus* CH34 and *Pseudomonas fluorescens* 6.2. J Bacteriol 155: 1015-1026.

20. Van Gijsegem F, Toussaint A (1982) Chromosome transfer and R-prime formation by an RP4::mini-Mu derivative in *Escherichia coli*, *Salmonella typhimurium*, *Klebsiella pneumoniae*, and *Proteus mirabilis*. Plasmid 7: 30-44.

21. Mergeay M, Lejeune P, Sadouk A, Gerits J, Fabry L (1987) Shuttle transfer (or retrotransfer) of chromosomal markers mediated by plasmid pULB113. Mol Gen Genet 209: 61-70.

<figure><img src="image_36.png" /></figure>
Found at: doi:10.1371/journal.pone.0010433.s012 (0.02 MB XLS)

**Table S5** Transcription factors - meta analysis. Transcription factors across 965 organisms, including 673 bacteria (source: http://www.transcriptionfactor.org/). Note that this table consist of multiple sheets: Sheet 1, DBDOverview - general information and data from DBD; Sheet 2, DBD organism - breakdown of transcriptional regulators for each of the organisms listed in Table 2 and *E. coli* K-12; Sheet 3, MageReplicon - distribution of transcriptional regulators across the four replicons of CH34, using MaGe data.

Found at: doi:10.1371/journal.pone.0010433.s013 (0.62 MB XLS)

**Table S6** Functional distribution and chromosomal location of *C. metallidurans* CH34 genes implicated in iron uptake and -metabolism.

Found at: doi:10.1371/journal.pone.0010433.s014 (0.12 MB DOC)

**Table S7** Signal transduction systems. Domain profiles of *C. metallidurans* CH34 and related organisms listed in Table 2 and *E. coli* K-12 (source: http://mistdb.com/). Only domains that occur 10 times or more in CH34 are considered. Extreme underrepresentations of domains (according to actual numbers versus genome size) are shaded in orange. Rows 25–27 hold the distributions of predicted one-component and two-component signal transduction systems (denoted as 1CST and 2CST, respectively) as well as the total number of predicted systems. The latter was used to calculate the proportional number (in percentages) of proteins putatively involved in signal transduction.

Found at: doi:10.1371/journal.pone.0010433.s015 (0.02 MB XLS)

**Table S8** Prevalence of Bug domains according to the MiST2 database. Distribution of 2,377 proteins with Bug domains across 1,216 complete and draft, bacterial and archaeal genomes (source: http://mistdb.com). Organisms without Bug domain-containing proteins are omitted from the table.

## References

1. Fergusson JE (1990) The Heavy Elements: Chemistry, Environmental Impact, and Health Effects. Oxford, UK: Pergamon Press.

2. Adriano DC (2001) Trace Elements in Terrestrial Environments: Biogeochemistry, Bioavailability, and Risks of Metals. New-YorkUS: Springer-Verlag.

3. Mergeay M, Houba C, Gerits J (1978) Extrachromosomal inheritance controlling resistance to cadmium, cobalt, copper and zinc ions: evidence from curing in a *Pseudomonas* [proceedings]. Arch Int Physiol Biochim 86: 440-442.

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

5. 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: 15-25.

6. Mergeay M (2000) Bacteria adapted to industrial biotopes: the metal resistant *Ralstonia*. In: Hengge-Aronis R, Storz G, eds. Bacterial Stress Responses. Washington, DC: ASM Press. pp 403-414.

7. 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. Berlin: Springer Berlin/Heidelberg. pp 209-238.

8. Mergeay M, Monchy S, Vallaees T, Auquier V, Benotmane A, et al. (2003) *Ralstonia metallidurans*, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev 27: 385-410.

9. Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, et al. (1985) *Alcaligenes eutrophus* CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162: 328-334.

10. Monchy S, Benotmane MA, Janssen P, Vallaees T, Taghavi S, et al. (2007) Plasmids pMOL28 and pMOL30 of *Cupriavidus metallidurans* are specialized in the maximal viable response to heavy metals. J Bacteriol 189: 7417-7425.

Found at: doi:10.1371/journal.pone.0010433.s016 (0.07 MB XLS)

**Table S9** Functional distribution and chromosomal location of *C. metallidurans* CH34 genes involved in polyester (PHA/PHB) biosynthesis and degradation.

Found at: doi:10.1371/journal.pone.0010433.s017 (0.06 MB DOC)

**Table S10** *C. metallidurans* CH34 genes for DNA repair and stress-related regulators.

Found at: doi:10.1371/journal.pone.0010433.s018 (0.08 MB DOC)

**Table S11** *C. metallidurans* CH34 genes encoding universal stress proteins (UspA superfamily) that are induced by a variety of starvation- and stress-conditions.

Found at: doi:10.1371/journal.pone.0010433.s019 (0.04 MB DOC)

## Acknowledgments

We thank A. D. Woodhead for excellent scientific editing of the manuscript and D. Vallenet and Z. Rouy of Génoscope (Centre National de Séquençage, Evry, France) for implementing additional features in MaGe and their essential advice in genome annotation. We are also grateful to I. T. Paulsen and Q. Ren for advice and data analyses using TransAAP, and to L. Ulrich for providing SQL-derived data from the Microbial Signal Transduction database (MistDB and MiST2).

## Author Contributions

Wrote the paper: PJJ RVH HM PM NM NL AL SM ST DvdL MM. Coordinated the genome annotation: PJJ. Contributed to genome annotation: RVH HM PM NM SM MM. Performed genome data analysis: PJJ. Analysed genome information: PJJ RVH HM PM NM SM CM ST DvdL MM. Organised, reviewed, and edited the manuscript: PJJ. Performed bioinformatics: PJJ PM CM. Performed associated miscellaneous bioinformatics: SMcC. Performed genetic experiments and the sequencing and finishing of the genome: AM MAB TV AL SM ST JD. Maintained and updated the Cupriavidu2Scope project with her team: CM. Developed and applied methods to identify and correct misassemblies in the original shotgun assembly: SMcC.

11. Nies A, Nies DH, Silver S (1989) Cloning and expression of plasmid genes encoding resistances to chromate and cobalt in *Alcaligenes eutrophus*. J Bacteriol 171: 5065-5070.

12. 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: 5648-5653.

13. Nies DH, Silver S (1989) Plasmid-determined inducible efflux is responsible for resistance to cadmium, zinc, and cobalt in *Alcaligenes eutrophus*. J Bacteriol 171: 896-900.

14. Reith F, Rogers SL, McPhail DC, Webb D (2006) Biomineralization of gold: biofilms on bacteriiform gold. Science 313: 233-236.

15. Novick RP, Roth C (1968) Plasmid-linked resistance to inorganic salts in *Staphylococcus aureus*. J Bacteriol 95: 1335-1342.

16. Nies DH (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51: 730-750.

17. Silver S, Misra TK (1988) Plasmid-mediated heavy metal resistances. Annu Rev Microbiol 42: 717-743.

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

19. Lejeune P, Mergeay M, Van Gijsegem F, Faelen M, Gerits J, et al. (1983) Chromosome transfer and R-prime plasmid formation mediated by plasmid pULB113 (RP4::mini-Mu) in *Alcaligenes eutrophus* CH34 and *Pseudomonas fluorescens* 6.2. J Bacteriol 155: 1015-1026.

20. Van Gijsegem F, Toussaint A (1982) Chromosome transfer and R-prime formation by an RP4::mini-Mu derivative in *Escherichia coli*, *Salmonella typhimurium*, *Klebsiella pneumoniae*, and *Proteus mirabilis*. Plasmid 7: 30-44.

21. Mergeay M, Lejeune P, Sadouk A, Gerits J, Fabry L (1987) Shuttle transfer (or retrotransfer) of chromosomal markers mediated by plasmid pULB113. Mol Gen Genet 209: 61-70.

<figure><img src="image_36.png" /></figure>
22. Sadouk A, Mergeay M (1993) Chromosome mapping in *Alcaligenes eutrophus* CH34. Mol Gen Genet 240: 181-187.

23. Diels L, Dong Q, van der Lelie D, Baeyens W, Mergeay M (1995) The *cze* operon of *Alcaligenes eutrophus* CH34: from resistance mechanism to the removal of heavy metals. J Ind Microbiol 14: 142-153.

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<figure><img src="image_37.png" /></figure>
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136. Braud A, Jezequel K, Bazot S, Lebeau T (2009) Enhanced phytoextraction of an agricultural Cr- and Pb-contaminated soil by bioaugmentation with siderophore-producing bacteria. Chemosphere 74: 280-286.

137. Brickman TJ, Armstrong SK (1996) The ornithine decarboxylase gene odc is required for alcaligin siderophore biosynthesis in *Bordetella* spp.: Putrescine is a precursor of alcaligin. J Bacteriol 178: 54-60.

138. Gilis A, Corbisier P, Baeyens W, Taghavi S, Mergeay M, et al. (1998) Effect of the siderophore alcaligin E on the bioavailability of Cd to *Alcaligenes eutrophus* CH34. J Ind Microbiol Biotechnol 20: 61-68.

139. Garg RP, Yindeeyoungyeon W, Gilis A, Denny TP, Van Der Lelie D, et al. (2000) Evidence that *Ralstonia eutropha* (*Alcaligenes eutrophus*) contains a functional homologue of the *Ralstonia solanacearum* Phc cell density sensing system. Mol Microbiol 38: 359-367.

140. Galperin MY, Gomelsky M (2005) Bacterial signal transduction modules: from genomics to biology. ASM News 71: 326-333.

141. Ulrich LE, Zhulin IB (2007) MiST: a microbial signal transduction database. Nucleic Acids Res 35: D386-390.

142. Antoine R, Raze D, Locht C (2000) Genomics of *Bordetella pertussis* toxins. Int J Med Microbiol 290: 301-305.

143. Herrou J, Bompard C, Antoine R, Leroy A, Rucktooa P, et al. (2007) Structure-based mechanism of ligand binding for periplasmic solute-binding protein of the Bug family. J Mol Biol 373: 954-964.

144. Huvent I, Belrhali H, Antoine R, Bompard C, Locht C, et al. (2006) Crystal structure of *Bordetella pertussis* BugD solute receptor unveils the basis of ligand binding in a new family of periplasmic binding proteins. J Mol Biol 356: 1014-1026.

145. Antoine R, Huvent I, Chemlal K, Deray I, Raze D, et al. (2005) The periplasmic binding protein of a tripartite tricarboxylate transporter is involved in signal transduction. J Mol Biol 351: 799-809.

146. von Wintzingerode F, Schattke A, Siddiqui RA, Rosick U, Gobel UB, et al. (2001) *Bordetella petrii* sp. nov., isolated from an anaerobic bioreactor, and emended description of the genus *Bordetella*. Int J Syst Evol Microbiol 51: 1257-1265.

147. Wang F, Grundmann S, Schmid M, Dorfler U, Roherer S, et al. (2007) Isolation and characterization of 1,2,4-trichlorobenzene mineralizing *Bordetella* sp. and its bioremediation potential in soil. Chemosphere 67: 896-902.

148. Gross R, Guzman CA, Sebhiahi M, dos Santos VA, Pieper DH, et al. (2008) The missing link: *Bordetella petrii* is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic *Bordetella*. BMC Genomics 9: 449.

149. Fry NK, Duncan J, Malnick H, Warner M, Smith AJ, et al. (2005) *Bordetella petrii* clinical isolate. Emerg Infect Dis 11: 1131-1133.

150. Stark D, Riley LA, Harkness J, Marriott D (2007) *Bordetella petrii* from a clinical sample in Australia: isolation and molecular identification. J Med Microbiol 56: 435-437.

151. Cummings CA, Bootsma HJ, Relman DA, Miller JF (2006) Species- and strain-specific control of a complex, flexible regulon by *Bordetella* BvgAS. J Bacteriol 188: 1775-1785.

152. Masuda N, Church GM (2002) *Escherichia coli* gene expression responsive to levels of the response regulator EvgA. J Bacteriol 184: 6225-6234.

153. Kulasekara HD, Ventre I, Kulasekara BR, Lazdunski A, Filloux A, et al. (2005) A novel two-component system controls the expression of *Pseudomonas aeruginosa* fimbrial cup genes. Mol Microbiol 55: 368-380.

154. Clarke BR, Pearce R, Roberts IS (1999) Genetic organization of the *Escherichia coli* K10 capsule gene cluster: identification and characterization of two conserved regions in group III capsule gene clusters encoding polysaccharide transport functions. J Bacteriol 181: 2279-2285.

155. Russo TA, Wenderoth S, Carlino UB, Merrick JM, Lesse AJ (1998) Identification, genomic organization, and analysis of the group III capsular polysaccharide genes *kpsD*, *kpsM*, *kpsT*, and *kpsE* from an extraintestinal isolate of *Escherichia coli* (CP9, O4/K54/H5). J Bacteriol 180: 338-349.

156. Arrecubieta C, Hammarton TC, Barrett B, Chareonsudjai S, Hodson N, et al. (2001) The transport of group 2 capsular polysaccharides across the periplasmic space in *Escherichia coli*. Roles for the KpsE and KpsD proteins. J Biol Chem 276: 4245-4250.

157. Vimr ER, Steenbergen SM (2009) Early molecular-recognition events in the synthesis and export of group 2 capsular polysaccharides. Microbiology 155: 9-15.

158. Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, et al. (2001) Analysis of the chromosome sequence of the legume symbiont *Sinorhizobium meliloti* strain 1021. Proc Natl Acad Sci U S A 98: 9877-9882.

159. Kiss E, Kereszt A, Barta F, Stephens S, Reuhs BL, et al. (2001) The *rkp-3* gene region of *Sinorhizobium meliloti* Rm41 contains strain-specific genes that determine K antigen structure. Mol Plant Microbe Interact 14: 1395-1403.

160. Friedman L, Kolter R (2004a) Genes involved in matrix formation in *Pseudomonas aeruginosa* PA14 biofilms. Mol Microbiol 51: 675-690.

161. Vasseur P, Vallet-Gely I, Soscia C, Genin S, Filloux A (2005) The *pel* genes of the *Pseudomonas aeruginosa* PAK strain are involved at early and late stages of biofilm formation. Microbiology 151: 985-997.

162. Friedman L, Kolter R (2004b) Two genetic loci produce distinct carbohydrate-rich structural components of the *Pseudomonas aeruginosa* biofilm matrix. J Bacteriol 186: 4457-4465.

163. Guiné V, Spadini L, Sarret G, Muris M, Delolme C, et al. (2006) Zinc sorption to three gram-negative bacteria: combined titration, modeling, and EXAFS study. Environ Sci Technol 40: 1806-1813.

164. Clough SJ, Flavier AB, Schell MA, Denny TP (1997) Differential Expression of Virulence Genes and Motility in *Ralstonia (Pseudomonas) solanacearum* during Exponential Growth. Appl Environ Microbiol 63: 844-850.

165. Lutke-Eversloh T, Steinbuchel A (1999) Biochemical and molecular characterization of a succinate semialdehyde dehydrogenase involved in the catabolism of 4-hydroxybutyric acid in *Ralstonia eutropha*. FEMS Microbiol Lett 181: 63-71.

166. Harwood CS, Burchhardt G, Herrmann H, Fuchs G (1998) Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiology Reviews 22: 439-458.

167. Harrison FH, Harwood CS (2005) The *pimFABCD* operon from *Rhodopseudomonas palustris* mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation. Microbiology 151: 727-736.

168. Siedow A, Cramm R, Siddiqui RA, Friedrich B (1999) A megaplasmid-borne anaerobic ribonucleotide reductase in *Alcaligenes eutrophus* H16. J Bacteriol 181: 4919-4928.

169. Cramm R (2009) Genomic view of energy metabolism in *Ralstonia eutropha* H16. J Mol Microbiol Biotechnol 16: 38-52.

170. Roth JR, Lawrence JG, Bobik TA (1996) Cobalamin (coenzyme B12): synthesis and biological significance. Annu Rev Microbiol 50: 137-181.

171. Warren MJ, Raux E, Schubert HL, Escalante-Semerenca JC (2002) The biosynthesis of adenosylcobalamin (vitamin B12). Nat Prod Rep 19: 390-412.

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195. Notomista E, Lahm A, Di Donato A, Tramontano A (2003) Evolution of bacterial and archaean multicomponent monooxygenases. J Mol Evol 56: 435-445.

196. Cafaro V, Izzo V, Scognamiglio R, Notomista E, Capasso P, et al. (2004) Phenol hydroxylase and toluene/o-xylene monooxygenase from *Pseudomonas stutzeri* OX1: interplay between two enzymes. Appl Environ Microbiol 70: 2211-2219.

197. Kageyama C, Ohta T, Hiraoka K, Suzuki M, Okamoto T, et al. (2005) Chlorinated aliphatic hydrocarbon-induced degradation of trichloroethylene in *Wautersia numadzuensis* sp. nov. Arch Microbiol 183: 56-65.

198. Pérez-Pantoja D, De la Iglesia R, Pieper DH, Gonzalez B (2008) Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium *Cupriavidus necator* JMP134. FEMS Microbiol Rev 32: 736-794.

199. Lenz RW, Marchessault RH (2005) Bacterial polyesters: biosynthesis, biodegradable plastics and biotechnology. Biomacromolecules 6: 1-8.

200. Khanna S, Srivastava AK (2005) Recent Advances in microbial polyhydrox-yalkanoates. Process Biochemistry 40: 607-619.

201. York GM, Lupberger J, Tian J, Lawrence AG, Stubbe J, et al. (2003) *Ralstonia eutropha* H16 encodes two and possibly three intracellular poly[D(-)-3-hydroxybutyrate] depolymerase genes. J Bacteriol 185: 3788-3794.

202. Kobayashi T, Shiraki M, Abe T, Sugiyama A, Saito T (2003) Purification and properties of an intracellular 3-hydroxybutyrate-oligomer hydrolase (PhaZ2) in *Ralstonia eutropha* H16 and its identification as a novel intracellular poly(3-hydroxybutyrate) depolymerase. J Bacteriol 185: 3485-3490.

203. Kobayashi T, Uchino K, Abe T, Yamazaki Y, Saito T (2003) Novel intracellular 3-hydroxybutyrate-oligomer hydrolase in *Wautersia eutropha* H16. J Bacteriol 187: 5129-5135.

204. Saegusa H, Shiraki M, Saito T (2002) Cloning of an intracellular D(-)-3-hydroxybutyrate-oligomer hydrolase gene from *Ralstonia eutropha* H16 and identification of the active site serine residue by site-directed mutagenesis. J Biosci Bioeng 94: 106-112.

205. Sugiyama A, Kobayashi T, Shiraki M, Saito T (2004) Roles of poly(3-hydroxybutyrate) depolymerase and 3HB-oligomer hydrolase in bacterial PHB metabolism. Curr Microbiol 48: 424-427.

206. Taghavi S, van der Lelie D, Mergeay M (1994) Electroporation of *Alcaligenes eutrophus* with (mega) plasmids and genomic DNA fragments. Appl Environ Microbiol 60: 3585-3591.

207. Rocha EP, Cornet E, Michel B (2005) Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet 1: e15.

208. Low DA, Weyand NJ, Mahan MJ (2001) Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun 69: 7197-7204.

209. Palma M, Zurita J, Ferreras JA, Worgall S, Larone DH, et al. (2005) *Pseudomonas aeruginosa* SoxR does not conform to the archetypal paradigm for

SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infect Immun 73: 2958-2966.

210. Defrance M, Janky R, Sand O, van Helden J (2008) Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoc 3: 1589-1603.

211. Siegele DA (2005) Universal stress proteins in *Escherichia coli*. J Bacteriol 187: 6253-6254.

212. Sousa MC, McKay DB (2001) Structure of the universal stress protein of *Haemophilus influenzae*. Structure 9: 1135-1141.

213. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.

214. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.

215. Ghai R, Hain T, Chakraborty T (2004) GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5: 198.

216. Gao F, Zhang CT (2008) Ori-Finder: a web-based system for finding *oriCs* in unannotated bacterial genomes. BMC Bioinformatics 9: 79.

217. Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21: 108-110.

218. Sakakibara Y, Osana Y, Popendorf K (2007) Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes. Nihon Hansenbyo Gakkai Zasshi 76: 251-256.

219. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.

220. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.

221. Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, et al. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics 16: 915-922.

222. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.

223. Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, et al. (2002) Genome sequence of the plant pathogen *Ralstonia solanacearum*. Nature 415: 497-502.

224. Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, et al. (2006) *Burkholderia xenovorans* LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 103: 15280-15287.

225. Audic S, Robert C, Campagna B, Parinello H, Claverie JM, et al. (2007) Genome analysis of *Minibacterium massiliensis* highlights the convergent evolution of water-living bacteria. PLoS Genet 3: e138.

226. Muller D, Médigue C, Koechler S, Barbe V, Barakat M, et al. (2007) A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 3: e53.

<figure><img src="image_40.png" /></figure>
194. Jendrossek D, Kruger N, Steinbuchel A (1990) Characterization of alcohol dehydrogenase genes of derepressible wild-type *Alcaligenes eutrophus* H16 and constitutive mutants. J Bacteriol 172: 4844-4851.

195. Notomista E, Lahm A, Di Donato A, Tramontano A (2003) Evolution of bacterial and archaean multicomponent monooxygenases. J Mol Evol 56: 435-445.

196. Cafaro V, Izzo V, Scognamiglio R, Notomista E, Capasso P, et al. (2004) Phenol hydroxylase and toluene/o-xylene monooxygenase from *Pseudomonas stutzeri* OX1: interplay between two enzymes. Appl Environ Microbiol 70: 2211-2219.

197. Kageyama C, Ohta T, Hiraoka K, Suzuki M, Okamoto T, et al. (2005) Chlorinated aliphatic hydrocarbon-induced degradation of trichloroethylene in *Wautersia numadzuensis* sp. nov. Arch Microbiol 183: 56-65.

198. Pérez-Pantoja D, De la Iglesia R, Pieper DH, Gonzalez B (2008) Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium *Cupriavidus necator* JMP134. FEMS Microbiol Rev 32: 736-794.

199. Lenz RW, Marchessault RH (2005) Bacterial polyesters: biosynthesis, biodegradable plastics and biotechnology. Biomacromolecules 6: 1-8.

200. Khanna S, Srivastava AK (2005) Recent Advances in microbial polyhydrox-yalkanoates. Process Biochemistry 40: 607-619.

201. York GM, Lupberger J, Tian J, Lawrence AG, Stubbe J, et al. (2003) *Ralstonia eutropha* H16 encodes two and possibly three intracellular poly[D(-)-3-hydroxybutyrate] depolymerase genes. J Bacteriol 185: 3788-3794.

202. Kobayashi T, Shiraki M, Abe T, Sugiyama A, Saito T (2003) Purification and properties of an intracellular 3-hydroxybutyrate-oligomer hydrolase (PhaZ2) in *Ralstonia eutropha* H16 and its identification as a novel intracellular poly(3-hydroxybutyrate) depolymerase. J Bacteriol 185: 3485-3490.

203. Kobayashi T, Uchino K, Abe T, Yamazaki Y, Saito T (2003) Novel intracellular 3-hydroxybutyrate-oligomer hydrolase in *Wautersia eutropha* H16. J Bacteriol 187: 5129-5135.

204. Saegusa H, Shiraki M, Saito T (2002) Cloning of an intracellular D(-)-3-hydroxybutyrate-oligomer hydrolase gene from *Ralstonia eutropha* H16 and identification of the active site serine residue by site-directed mutagenesis. J Biosci Bioeng 94: 106-112.

205. Sugiyama A, Kobayashi T, Shiraki M, Saito T (2004) Roles of poly(3-hydroxybutyrate) depolymerase and 3HB-oligomer hydrolase in bacterial PHB metabolism. Curr Microbiol 48: 424-427.

206. Taghavi S, van der Lelie D, Mergeay M (1994) Electroporation of *Alcaligenes eutrophus* with (mega) plasmids and genomic DNA fragments. Appl Environ Microbiol 60: 3585-3591.

207. Rocha EP, Cornet E, Michel B (2005) Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet 1: e15.

208. Low DA, Weyand NJ, Mahan MJ (2001) Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun 69: 7197-7204.

209. Palma M, Zurita J, Ferreras JA, Worgall S, Larone DH, et al. (2005) *Pseudomonas aeruginosa* SoxR does not conform to the archetypal paradigm for

SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infect Immun 73: 2958-2966.

210. Defrance M, Janky R, Sand O, van Helden J (2008) Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoc 3: 1589-1603.

211. Siegele DA (2005) Universal stress proteins in *Escherichia coli*. J Bacteriol 187: 6253-6254.

212. Sousa MC, McKay DB (2001) Structure of the universal stress protein of *Haemophilus influenzae*. Structure 9: 1135-1141.

213. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.

214. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.

215. Ghai R, Hain T, Chakraborty T (2004) GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5: 198.

216. Gao F, Zhang CT (2008) Ori-Finder: a web-based system for finding *oriCs* in unannotated bacterial genomes. BMC Bioinformatics 9: 79.

217. Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21: 108-110.

218. Sakakibara Y, Osana Y, Popendorf K (2007) Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes. Nihon Hansenbyo Gakkai Zasshi 76: 251-256.

219. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.

220. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.

221. Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, et al. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics 16: 915-922.

222. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.

223. Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, et al. (2002) Genome sequence of the plant pathogen *Ralstonia solanacearum*. Nature 415: 497-502.

224. Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, et al. (2006) *Burkholderia xenovorans* LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 103: 15280-15287.

225. Audic S, Robert C, Campagna B, Parinello H, Claverie JM, et al. (2007) Genome analysis of *Minibacterium massiliensis* highlights the convergent evolution of water-living bacteria. PLoS Genet 3: e138.

226. Muller D, Médigue C, Koechler S, Barbe V, Barakat M, et al. (2007) A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 3: e53.

<figure><img src="image_40.png" /></figure>