The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

BMC Genomics

Colleen M Cavanaugh²  Jonathan A Eisen⁶  Jenna Morgan Lang⁶  Dongying Wu⁶  Tanja Woyke¹  Irene LG Newton³  Frank J Stewart⁴  Raghav Sharma⁴  Guus Roeselers⁵  Li Liao⁷  Kristina M Fontanez⁸  Wesley T Loo²  Shelbi L Russell²  Oleg Dmytrenko² 

[1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA;Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, 4081 Biological Laboratories, Cambridge, MA 02138, USA;Department of Biology, Indiana University, 1001 East 3rd Street, Jordan Hall, Bloomington, IN 47405, USA;School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA;Microbiology & Systems Biology Group, TNO, Utrechtseweg 48, Zeist, Utrecht 3704HE, The Netherlands;UC Davis Genome Center, 451 East Health Sciences Drive, Davis, CA 95616-8816, USA;SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China;Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street, Cambridge, MA 02139, USA

关键词: Mobile genetic elements;    Motility;    Heterotrophy;    Pyrophosphate-dependent phosphofructokinase;    Calvin cycle;    H⁺/Na⁺ -membrane cycles;    Respiratory flexibility;    Sulfur oxidation;    Chemosynthesis;    Symbiosis;   

Others  :  1128433
DOI  :  10.1186/1471-2164-15-924

 received in 2014-04-03, accepted in 2014-09-23,  发布年份 2014

【 摘 要 】

Background

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced.

Results

Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host.

Conclusions

The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.

【 授权许可】

   
2014 Dmytrenko et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Sagan L: On the origin of mitosing cells. J Theor Biol 1967, 14:225-274.
• [2]Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, Knight R: Our microbial selves: what ecology can teach us. EMBO Rep 2011, 12:775-784.
• [3]Dilworth MJ, James EK, Sprent JI: Nitrogen-Fixing Leguminous Symbioses. Kluwer Academic Pub; 2008.
• [4]Clark EL, Karley AJ, Hubbard SF: Insect endosymbionts: manipulators of insect herbivore trophic interactions? Protoplasma 2010, 244:25-51.
• [5]Cavanaugh CM, McKiness Z, Newton I, Stewart FJ: Marine chemosynthetic symbioses. In The Prokaryotes - Prokaryotic Biology and Symbiotic Associations 3rd edition. Edited by Rosenberg E. 2013, 579-607.
• [6]Toft C, Andersson SGE: Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet 2010, 11:465-475.
• [7]Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng J-F: One bacterial cell, one complete genome. PLoS One 2010, 5:1-8.
• [8]Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, Woyke T, Hentschel U: Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J 2013, 7:2287-2300.
• [9]Dubilier N, Bergin C, Lott C: Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Micro 2008, 6:725-740.
• [10]Cavanaugh CM: Symbiotic chemoautotrophic bacteria in marine invertebrates from sulphide-rich habitats. Nature 1983, 302:58-61.
• [11]Eisen JA, Smith SW, Cavanaugh CM: Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. J Bacteriol 1992, 174:3416-3421.
• [12]Cavanaugh CM, Abbott M, Veenhuis M: Immunochemical localization of ribulose-1, 5-bisphosphate carboxylase in the symbiont-containing gills of Solemya velum (Bivalvia: Mollusca). P Natl Acad Sci USA 1988, 85:7786-7789.
• [13]Scott KM, Cavanaugh CM: CO2 uptake and fixation by endosymbiotic chemoautotrophs from the bivalve Solemya velum. Appl Environ Microb 2007, 73:1174-1179.
• [14]Conway N, Capuzzo J, Fry B: The role of endosymbiotic bacteria in the nutrition of Solemya velum: evidence from a stable isotope analysis of endosymbionts and host. Limnol Oceanogr 1989, 34:249-255.
• [15]Krueger DM, Gallager S, Cavanaugh CM: Suspension feeding on phytoplankton by Solemya velum, a symbiont-containing clam. Mar Ecol-Prog Ser 1992, 86:145-151.
• [16]Cary SC: Vertical transmission of a chemoautotrophic symbiont in the protobranch bivalve, Solemya reidi. Mol Mar Biol Biotechnol 1994, 3:121-130.
• [17]Krueger DM, Gustafson RG, Cavanaugh CM: Vertical transmission of chemoautotrophic symbionts in the bivalve Solemya velum (Bivalvia: Protobranchia). Biol Bull 1996, 190:195-202.
• [18]Peek A, Vrijenhoek R, Gaut B: Accelerated evolutionary rate in sulfur-oxidizing endosymbiotic bacteria associated with the mode of symbiont transmission. Mol Biol Evol 1998, 15:1514.
• [19]Hurtado LA, Mateos M, Lutz RA, Vrijenhoek RC: Coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam Calyptogena magnifica. Appl Environ Microb 2003, 69:2058-2064.
• [20]Kuwahara H, Yoshida T, Takaki Y, Shimamura S, Nishi S, Harada M, Matsuyama K, Takishita K, Kawato M, Uematsu K: Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Curr Biol 2007, 17:881-886.
• [21]Kuwahara H, Takaki Y, Yoshida T, Shimamura S, Takishita K, Reimer JD, Kato C, Maruyama T: Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. Extremophiles 2008, 12:365-374.
• [22]Newton I, Woyke T, Auchtung T, Dilly G, Dutton R, Fisher M, Fontanez K, Lau E, Stewart FJ, Richardson P: The Calyptogena magnifica chemoautotrophic symbiont genome. Science 2007, 315:998-1000.
• [23]Newton I, Girguis PR, Cavanaugh CM: Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts. BMC Genomics 2008, 9:585. BioMed Central Full Text
• [24]Peek A, Feldman R, Lutz R, Vrijenhoek R: Cospeciation of chemoautotrophic bacteria and deep sea clams. Proc Natl Acad Sci U S A 1998, 95:9962.
• [25]Stewart FJ, Young CR, Cavanaugh CM: Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Mol Biol Evol 2008, 25:673-687.
• [26]Stewart FJ, Young C, Cavanaugh CM: Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Mol Biol Evol 2009, 26:1391-1404.
• [27]Stewart FJ, Baik AHY, Cavanaugh CM: Genetic subdivision of chemosynthetic endosymbionts of Solemya velum along the Southern New England coast. Appl Environ Microb 2009, 75:6005-6007.
• [28]Krueger DM, Cavanaugh CM: Phylogenetic diversity of bacterial symbionts of Solemya hosts based on comparative sequence analysis of 16S rRNA genes. Appl Environ Microb 1997, 63:91.
• [29]Moran NA: Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A 1996, 93:2873-2878.
• [30]Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O’Neill SL, Eisen JA: Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2004, 2:E69.
• [31]Robidart J, Bench S, Feldman R, Novoradovsky A, Podell S, Gaasterland T, Allen E, Felbeck H: Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol 2008, 10:727-737.
• [32]Gardebrecht A, Markert S, Sievert SM, Felbeck H, Thürmer A, Albrecht D, Wollherr A, Kabisch J, Le Bris N, Lehmann R, Daniel R, Liesegang H, Hecker M, Schweder T: Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. ISME J 2012, 6:766-776.
• [33]Nakagawa S, Shimamura S, Takaki Y, Suzuki Y, Murakami S-I, Watanabe T, Fujiyoshi S, Mino S, Sawabe T, Maeda T, Makita H, Nemoto S, Nishimura S-I, Watanabe H, Watsuji T-O, Takai K: Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont. ISME J 2014, 8:40-51.
• [34]Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N: Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 2006, 443:950-955.
• [35]Wu M, Eisen JA: A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008, 9:1-11.
• [36]Murphy FV, Ramakrishnan V: Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat Struct Mol Biol 2004, 11:11251-11252.
• [37]Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278:631-637.
• [38]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
• [39]Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC: Integrative analysis of environmental sequences using MEGAN4. Genome Res 2011, 21:1552-1560.
• [40]Stewart FJ, Dmytrenko O, DeLong E: Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Frontiers Microbiol 2011, 2:1-10.
• [41]Frigaard N-U, Dahl C: Sulfur metabolism in phototrophic sulfur bacteria. Adv Microb Physiol 2009, 54:103-200.
• [42]Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD, Hallam SJ: Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 2009, 326:578-582.
• [43]Dahl C, Prange A: Bacterial sulfur globules: occurrence, structure and metabolism. Inclusions in Prokaryotes Microbiology Monographs, Volume 1 2006, 21-51.
• [44]Friedrich C, Bardischewsky F, Rother D, Quentmeier A, Fischer J: Prokaryotic sulfur oxidation. Curr Opin Microbiol 2005, 8:253-259.
• [45]Fisher C, Childress J, ARP A, BROOKS J, DISTEL D, Favuzzi J, Macko S, Newton A, Powell M, Somero G, SOTO T: Physiology, morphology, and biochemical composition of Riftia pachyptila at Rose Garden in 1985. Deep-Sea Res 1988, 35:1745-1758.
• [46]Vetter RD: Elemental sulfur in the gills of three species of clams containing chemoautotrophic symbiotic bacteria: a possible inorganic energy storage compound. Mar Biol 1985, 88:33-42.
• [47]Childress JJ, Girguis PR: The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities. J Exp Biol 2011, 214:312-325.
• [48]Cort JR, Selan U, Schulte A, Grimm F, Kennedy MA, Dahl C: Allochromatium vinosum DsrC: Solution-state NMR structure, redox properties, and interaction with DsrEFH, a protein essential for purple sulfur bacterial sulfur oxidation. J Mol Biol 2008, 382:692-707.
• [49]Oliveira TF, Vonrhein C, Matias PM, Venceslau SS, Pereira IAC, Archer M: Purification, crystallization and preliminary crystallographic analysis of a dissimilatory DsrAB sulfite reductase in complex with DsrC. J Struct Biol 2008, 164:236-239.
• [50]Ghosh W, Dam B: Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. Fems Microbiol Rev 2009, 33:999-1043.
• [51]Chen C, Rabourdin B, Hammen C: The effect of hydrogen sulfide on the metabolism of Solemya velum and enzymes of sulfide oxidation in gill tissue. Comp Biochem Physiol B Biochem Mol Biol 1987, 88:949-952.
• [52]Biegel E, Schmidt S, González JM, Müller V: Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell Mol Life Sci 2011, 68:613-634.
• [53]Bruschi M, Guerlesquin F: Structure, function and evolution of bacterial ferredoxins. Fems Microbiol Rev 1988, 4:155-175.
• [54]Kovács KL, Kovács AT, Maróti G, Mészáros LS, Balogh J, Latinovics D, Fülöp A, Dávid R, Dorogházi E, Rákhely G: The hydrogenases of Thiocapsa roseopersicina. Biochem Soc Trans 2005, 33:61-63.
• [55]Burgdorf T, Lenz O, Buhrke T, van der Linden E, Jones A, Albracht S, Friedrich B: [NiFe]-hydrogenases of Ralstonia eutropha H16: Modular enzymes for oxygen-tolerant biological hydrogen oxidation. J Mol Microb Biotech 2005, 10:181-196.
• [56]Vignais PM, Billoud B: Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 2007, 107:4206-4272.
• [57]Maroti J, Farkas A, Nagy IK, Maroti G, Kondorosi E, Rakhely G, Kovacs KL: A second soluble hox-type nife enzyme completes the hydrogenase set in Thiocapsa roseopersicina BBS. Appl Environ Microbiol 2010, 76:5113-5123.
• [58]Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, Dubilier N: Hydrogen is an energy source for hydrothermal vent symbioses. Nature 2011, 476:176-180.
• [59]Bogachev AV, Verkhovsky MI: Na+-translocating NADH: quinone oxidoreductase: progress achieved and prospects of investigations. Biochem (Moscow) 2005, 70:143-149.
• [60]Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H: Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 2000, 407:81-86.
• [61]Pickering BS, Oresnik IJ: Formate-dependent autotrophic growth in Sinorhizobium meliloti. J Bacteriol 2008, 190:6409.
• [62]Benoit S, Abaibou H, Mandrand-Berthelot M-A: Topological analysis of the aerobic membrane-bound formate dehydrogenase of Escherichia coli. J Bacteriol 1998, 180:6625.
• [63]Preisig O, Zufferey R, Thony-Meyer L, Appleby C, Hennecke H: A high-affinity cbb3-type cytochrome oxidase terminates the symbiosis- specific respiratory chain of Bradyrhizobium japonicum. J Bacteriol 1996, 178:1532.
• [64]Pitcher RS, Watmough NJ: The bacterial cytochrome cbb3 oxidases. Biochim Biophys Acta Bioenerg 2004, 1655:388-399.
• [65]Nunoura T, Sako Y, Wakagi T, Uchida A: Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense. Microbiol (Reading, Engl) 2003, 149:673-688.
• [66]Otten MF, Stork DM, Reijnders WN, Westerhoff HV, Van Spanning RJ: Regulation of expression of terminal oxidases in Paracoccus denitrificans. Eur J Biochem 2001, 268:2486-2497.
• [67]Krueger DM, Roeselers G, Sigman D, Cavanaugh CM: Nitrogen nutrition in the symbiosis Solemya velum. in preparation
• [68]Potter LC, Millington P, Griffiths L, Thomas GH, Cole JA: Competition between Escherichia coli strains expressing either a periplasmic or a membrane-bound nitrate reductase: does Nap confer a selective advantage during nitrate-limited growth? Biochem J 1999, 344(Pt 1):77-84.
• [69]Zemmelink H, Houghton L, Sievert S, Frew N, Dacey J: Gradients in dimethylsuffide, dimethylsulfoniopropionate, dimethylsulfoxide, and bacteria near the sea surface. Mar Ecol-Prog Ser 2005, 295:33-42.
• [70]Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jorgensen BB, Huntemann M, Gloeckner FO, Amann R, Koopman WJH, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD: Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 2007, 5:1923-1937.
• [71]McCrindle SL, Kappler U, McEwan AG: Microbial dimethylsulfoxide and trimethylamine-N-oxide respiration. Adv Microb Physiol 2005, 50:147-198.
• [72]Häse CC, Fedorova ND, Galperin MY, Dibrov PA: Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons. Microbiol Mol Biol Rev 2001, 65:353-370. table of contents
• [73]Mulkidjanian AY, Dibrov P, Galperin MY: The past and present of sodium energetics: may the sodium-motive force be with you. Biochim Biophys Acta 2008, 1777:985-992.
• [74]Robinson J, Cavanaugh CM: Expression of form I and form II Rubisco in chemoautotrophic symbioses: implications for the interpretation of stable carbon isotope values. Limnol Oceanogr 1995, 40:1496-1502.
• [75]Reshetnikov AS, Rozova ON, Khmelenina VN, Mustakhimov II, Beschastny AP, Murrell JC, Trotsenko YA: Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Methylococcus capsulatus Bath. FEMS Microbiol Lett 2008, 288:202-210.
• [76]Markert S, Gardebrecht A, Felbeck H, Sievert SM, Klose J, Becher D, Albrecht D, Thürmer A, Daniel R, Kleiner M, Hecker M, Schweder T: Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics 2011, 11:3106-3117.
• [77]Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J, Chang Y-J, Shah M, VerBerkmoes NC, Zarzycki J, Fuchs G, Markert S, Hempel K, Voigt B, Becher D, Liebeke M, Lalk M, Albrecht D, Hecker M, Schweder T, Dubilier N: Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci 2012, 109:E1173-E1182.
• [78]Bassham J, Benson A, Calvin M: The path of carbon in photosynthesis. J Biol Chem 1950, 185:781-787.
• [79]Fenton A, Paricharttanakul N, Reinhart G: Identification of substrate contact residues important for the allosteric regulation of phosphofructokinase from Eschericia coli. Biochemistry 2003, 42:6453-6459.
• [80]Purves J, Cockayne A, Moody PCE, Morrissey JA: Comparison of the regulation, metabolic functions, and roles in virulence of the glyceraldehyde-3-phosphate dehydrogenase homologues gapA and gapB in Staphylococcus aureus. Infect Immun 2010, 78:5223-5232.
• [81]Wood AP, Aurikko JP, Kelly DP: A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy? Fems Microbiol Rev 2004, 28:335-352.
• [82]Han SO, Inui M, Yukawa H: Effect of carbon source availability and growth phase on expression of Corynebacterium glutamicum genes involved in the tricarboxylic acid cycle and glyoxylate bypass. Microbiology 2008, 154:3073-3083.
• [83]Lee R, Thuesen E, Childress J: Ammonium and free amino acids as nitrogen sources for the chemoautotrophic symbiosis Solemya reidi Bernard (Bivalvia: Protobranchia). J Exp Mar Biol Ecol 1992, 158:75-91.
• [84]Liao L, Wankel SD, Wu M, Cavanaugh CM, Girguis PR: Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae. Mol Ecol 2013.
• [85]Lee RW, Childress JJ: Assimilation of inorganic nitrogen by marine invertebrates and their chemoautotrophic and methanotrophic symbionts. Appl Environ Microb 1994, 60:1852-1858.
• [86]Bourbonnais A, Lehmann MF, Butterfield DA, Juniper SK: Subseafloor nitrogen transformations in diffuse hydrothermal vent fluids of the Juan de Fuca Ridge evidenced by the isotopic composition of nitrate and ammonium. Geochem Geophys Geosyst 2012, 13:1-23.
• [87]Hentschel U, Felbeck H: Nitrate respiration in the hydrothermal vent tubeworm Riftia pachyptila. Nature 1993, 366:338-340.
• [88]Lee R, Robinson J, Cavanaugh CM: Pathways of inorganic nitrogen assimilation in chemoautotrophic bacteria-marine invertebrate symbioses: expression of host and symbiont glutamine synthetase. J Exp Biol 1999, 202(Pt 3):289-300.
• [89]Girguis PR, Lee RW, Desaulniers N, Childress JJ, Pospesel M, Felbeck H, Zal F: Fate of nitrate acquired by the tubeworm Riftia pachyptila. Appl Environ Microbiol 2000, 66:2783-2790.
• [90]Beckers G, Bendt AK, Kramer R, Burkovski A: Molecular identification of the urea uptake system and transcriptional analysis of urea transporter and urease-encoding genes in Corynebacterium glutamicum. J Bacteriol 2004, 186:7645.
• [91]De Cian M, Regnault M, Lallier FH: Nitrogen metabolites and related enzymatic activities in the body fluids and tissues of the hydrothermal vent tubeworm Riftia pachyptila. J Exp Biol 2000, 203:2907-2920.
• [92]Joyner JL, Peyer SM, Lee RW: Possible roles of sulfur-containing amino acids in a chemoautotrophic bacterium-mollusc symbiosis. Biol Bull 2003, 205:331-338.
• [93]Conway N, Howes B, McDowell Capuzzo J, Turner R, Cavanaugh CM: Characterization and site description of Solemya borealis (Bivalvia; Solemyidae), another bivalve-bacteria symbiosis. Mar Biol 1992, 112:601-613.
• [94]Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T: Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J Biol Chem 1997, 272:23031-23036.
• [95]Conway N, McDowell Capuzzo J: Incorporation and utilization of bacterial lipids in the Solemya velum symbiosis. Mar Biol 1991, 108:277-291.
• [96]Karow M, Georgopoulos C: Isolation and characterization of the Escherichia coli msbB gene, a multicopy suppressor of null mutations in the high-temperature requirement gene htrB. J Bacteriol 1992, 174:702-710.
• [97]Moran N, McCutcheon J, Nakabachi A: Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 2008, 42:165-190.
• [98]Nussbaumer AD, Fisher CR, Bright M: Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 2006, 441:345-348.
• [99]Cavanaugh CM: Symbiosis of chemoautotrophic bacteria and marine invertebrates. In PhD Thesis. Cambridge, MA, USA: Harvard University, Department of Organismic and Evolutionary Biology; 1985.
• [100]Fisher C, Childress J: Organic carbon transfer from methanotrophic symbionts to the host hydrocarbon-seep mussel. Symbiosis 1992, 12:221-235.
• [101]Saurin W, Hofnung M, Dassa E: Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters. J Mol Evol 1999, 48:22-41.
• [102]van de Velde W, Zehirov G, Szatmari A, Debreczeny M, Ishihara H, Kevei Z, Farkas A, Mikulass K, Nagy A, Tiricz H: Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 2010, 327:1122-1125.
• [103]Paau AS, Bloch CB, Brill WJ: Developmental fate of Rhizobium meliloti bacteroids in alfalfa nodules. J Bacteriol 1980, 143:1480-1490.
• [104]Stewart FJ, Cavanaugh CM: Bacterial endosymbioses in Solemya (Mollusca: Bivalvia)—model systems for studies of symbiont–host adaptation. Antonie Van Leeuwenhoek 2006, 90:343-360.
• [105]Whitchurch CB, Leech AJ, Young MD, Kennedy D, Sargent JL, Bertrand JJ, Semmler ABT, Mellick AS, Martin PR, Alm RA, Hobbs M, Beatson SA, Huang B, Nguyen L, Commolli JC, Engel JN, Darzins A, Mattick JS: Characterization of a complex chemosensory signal transduction system which controls twitching motility in Pseudomonas aeruginosa. Mol Microbiol 2004, 52:873-893.
• [106]Newton ILG, Bordenstein SR: Correlations between bacterial ecology and mobile DNA. Curr Microbiol 2011, 62:198-208.
• [107]Plague GR, Dunbar HE, Tran PL, Moran NA: Extensive proliferation of transposable elements in heritable bacterial symbionts. J Bacteriol 2008, 190:777-779.
• [108]Gil R, Latorre A, Moya A: Evolution of prokaryote-animal symbiosis from a genomics perspective. In Microbiology Monographs, Volume 19. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010:207-233.
• [109]Cordaux R, Pichon S, Ling A, Pérez P, Delaunay C, Vavre F, Bouchon D, Grève P: Intense transpositional activity of insertion sequences in an ancient obligate endosymbiont. Mol Biol Evol 2008, 25:1889-1896.
• [110]Chafee ME, Funk DJ, Harrison RG, Bordenstein SR: Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations. Mol Biol Evol 2010, 27:501-505.
• [111]Roeselers G, Newton ILG: On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves. Appl Microbiol Biotechnol 2012, 94:1-10.
• [112]Gil R, Sabater-Muñoz B, Latorre A, Silva FJ, Moya A: Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci U S A 2002, 99:4454-4458.
• [113]Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA: Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol 2006, 4:1079-1092.
• [114]Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, et al.: Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
• [115]Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM: Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012.
• [116]Pacific Biosciences. [http://www.pacb.com webcite]
• [117]English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA: Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLoS ONE 2012, 7:e47768.
• [118]Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679.
• [119]Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:1-11. BioMed Central Full Text
• [120]Besemer J, Lomsadze A, Borodovsky M: GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001, 29:2607.
• [121]Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 2007, 23:1282-1288.
• [122]Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I: RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res 2014, 42:D553-D559.
• [123]Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F: The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics 2012, 13:1-5. BioMed Central Full Text
• [124]Standard operating procedure for the annotations of genomes and metagenomes submitted to the integrated microbial genomes expert review (IMG-ER) system [http://img.jgi.doe.gov/w/doc/img_er_ann.pdf webcite]
• [125]Gao F, Zhang C-T, Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 2009, 9:1-6.
• [126]Bprom. [http://www.softberry.com webcite]
• [127]Emanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007, 2:953-971.
• [128]Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
• [129]Robinson DG, Lee M-C, Marx CJ: OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences. Nucleic Acids Res 2012, 40:e174.
• [130]Bi D, Xu Z, Harrison EM, Tai C, Wei Y, He X, Jia S, Deng Z, Rajakumar K, Ou H-Y: ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res 2012, 40(Database issue):D621-D626.
• [131]Leplae R, Lima-Mendez G, Toussaint A: ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 2010, 38(Database issue):D57-D61.