Archives of Microbiology

, Volume 182, Issue 1, pp 18–29

Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO

  • Julie Schwedock
  • Tara L. Harmer
  • Kathleen M. Scott
  • Harm J. Hektor
  • Angelica P. Seitz
  • Matthew C. Fontana
  • Daniel L. Distel
  • Colleen M. Cavanaugh
Original Paper

Abstract

Chemoautotrophic endosymbionts residing in Solemya velum gills provide this shallow water clam with most of its nutritional requirements. The cbb gene cluster of the S. velum symbiont, including cbbL and cbbS, which encode the large and small subunits of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), was cloned and expressed in Escherichia coli. The recombinant RubisCO had a high specific activity, ∼3 μmol min−1 mg protein −1, and a KCO2 of 40.3 μM. Based on sequence identity and phylogenetic analyses, these genes encode a form IA RubisCO, both subunits of which are closely related to those of the symbiont of the deep-sea hydrothermal vent gastropod Alviniconcha hessleri and the photosynthetic bacterium Allochromatium vinosum. In the cbb gene cluster of the S. velum symbiont, the cbbLS genes were followed by cbbQ and cbbO, which are found in some but not all cbb gene clusters and whose products are implicated in enhancing RubisCO activity post-translationally. cbbQ shares sequence similarity with nirQ and norQ, found in denitrification clusters of Pseudomonas stutzeri and Paracoccus denitrificans. The 3′ region of cbbO from the S. velum symbiont, like that of the three other known cbbO genes, shares similarity to the 3′ region of norD in the denitrification cluster. This is the first study to explore the cbb gene structure for a chemoautotrophic endosymbiont, which is critical both as an initial step in evaluating cbb operon structure in chemoautotrophic endosymbionts and in understanding the patterns and forces governing RubisCO evolution and physiology.

Keywords

RubisCO Symbiosis Chemosynthesis Solemya velum Ribulose 1,5-bisphosphate carboxylase/oxygenase KCO2 

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A (2003) A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 302:286–290CrossRefPubMedGoogle Scholar
  3. Ausubel F, Brent R, Kingston R, Moore D, Seidman J, Smith J, Struhl K (1994) Current protocols in molecular biology. Wiley, New YorkGoogle Scholar
  4. Bartnikas TB, Tosques IE, Laratta WP, Shi J, Shapleigh JP (1997) Characterization of the nitric oxide reductase-encoding region in Rhodobacter sphaeroides 2.4.3. J Bacteriol 179:3534–3540PubMedGoogle Scholar
  5. de Boer APN, van der Oost J, Reijnders WNM, Westerhoff HV, Stouthamer AH, van Spanning RJ (1996) Mutational analysis of the nor gene cluster which encodes nitric-oxide reductase from Paracoccus denitrificans. Eur J Biochem 242:592–600PubMedGoogle Scholar
  6. Cavanaugh CM (1983) Symbiotic chemoautotrophic bacteria in marine invertebrates from sulphide-rich habitats. Nature (London) 302:58–61Google Scholar
  7. Cavanaugh CM (1994) Microbial symbiosis: patterns of diversity in the marine environment. Amer Zool 34:79–89Google Scholar
  8. Cavanaugh CM, Robinson JJ (1996) CO2 fixation in chemoautotroph-invertebrate symbioses: expression of Form I and Form II RubisCO. In: Lindstrom ME, Tabita FR (eds) Microbial growth on C1 compounds. Kluwer, Dordrecht, pp 285–292Google Scholar
  9. Cavanaugh CM, Abbott MS, Veenhuis M (1988) Immunochemical localization of ribulose 1,5 bisphosphate carboxylase in the symbiont containing gills of Solemya velum (Bivalvia: Mollusca). Proc Natl Acad Sci USA 85:7786–7789Google Scholar
  10. Childress JJ, Fisher CR (1992) The biology of hydrothermal vent animals: physiology, biochemistry, and autotrophic symbioses. Oceanogr Mar Biol Annu Rev 30:337–441Google Scholar
  11. Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol Biol Evol 13:873–882PubMedGoogle Scholar
  12. Dubilier N, Giere O, Distel DL, Cavanaugh CM (1995) Characterization of chemoautotrophic bacterial symbionts in a gutless marine worm (Oligochaeta, Annelida) by phylogenetic 16S rRNA sequence analysis and in situ hybridization. Appl Environ Microbiol 61:2346–2350PubMedGoogle Scholar
  13. Eisenthal R, Cornish-Bowden A (1974) The direct linear plot. A new graphical procedure for estimating enzyme kinetic parameters. Biochem J 139:715–720PubMedGoogle Scholar
  14. Elsaied H, Naganuma T (2001) Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygense large-subunit genese from deep-sea microorganisms. Appl Environ Microbiol 67:1751–1765CrossRefPubMedGoogle Scholar
  15. Englert C, Kruger K, Offner S, Pfeifer F (1992) Three different but related gene clusters encoding gas vesicles in halophilic archaea. J Mol Biol 227:586–592PubMedGoogle Scholar
  16. Faith DP (1991) Cladistic permutation tests for monophyly and nonmonophyly. Syst Zool 40:366–375Google Scholar
  17. Finn MW, Tabita FR (2003) Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea. J Bacteriol 185:3049–3059CrossRefPubMedGoogle Scholar
  18. Goffredi S, Childress J, Desaulniers N, Lee R, Lallier F, Hammond D (1997) Inorganic carbon acquisition by the hydrothermal vent tubeworm Riftia pachyptila depends upon high external pCO2 and upon proton-equivalent ion transport by the worm. J Exp Biol 200:883–896PubMedGoogle Scholar
  19. Goloubinoff P, Gatenby AA, Lorimer GH (1989) GroE heat-shock proteins promote assembly of foreign prokaryotic ribulose bisphosphate carboxylase oligomers in Escherichia coli. Nature 337:44–47CrossRefPubMedGoogle Scholar
  20. Guy RD, Fogel ML, Berry JA (1993) Photosynthetic fractionation of the stable isotopes of oxygen and carbon. Plant Physiol 101:37–47PubMedGoogle Scholar
  21. Hanson TE, Tabita FR (2001) A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc Natl Acad Sci USA 98:4397–4402CrossRefPubMedGoogle Scholar
  22. Hayashi NR, Arai H, Kodama T, Igarashi Y (1997) The novel genes, cbbQ and cbbO, located downstream from the RubisCO genes of Pseudomonas hydrogenothermophila, affect the conformational states and activity of RubisCO. Biochem Biophys Res Commun 241:565–569CrossRefPubMedGoogle Scholar
  23. Hayashi NR, Arai H, Kodama T, Igarashi Y (1999) The cbbQ genes, located downstream of the form I and form II RubisCO genes, affect the activity of both RubisCOs. Biochem Biophys Res Commun 265:177–183CrossRefPubMedGoogle Scholar
  24. Hernandez JM, Baker SH, Lorbach SC, Shively JM, Tabita FR (1996) Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans. J Bacteriol 178:347–356PubMedGoogle Scholar
  25. Horken KM, Tabita FR (1999) Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities. Arch Biochem Biophys 361:183–194CrossRefPubMedGoogle Scholar
  26. Igarashi Y, Kodama T (1996) Genes related to carbon dioxide fixation in Hydrogenovibrio marinus and Pseudomonas hydrogenothermophilia. In: Lidstrom ME, Tabita FR (eds) Microbial growth on C1 compounds. Kluwer, Dordecht, pp 88–93Google Scholar
  27. Jannasch H (1989) The microbial basis of life at deep-sea hydrothermal vents. ASM News 55:413–416Google Scholar
  28. Knight S, Andersson I, Branden CI (1990) Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site. J Mol Biol 215:113–160PubMedGoogle Scholar
  29. Krueger DM, Cavanaugh CM (1997) Phylogenetic diversity of bacterial symbionts of Solemya hosts based on comparative sequence analysis of 16S rRNA genes. Appl Enivron Microbiol 63:91–98Google Scholar
  30. Kusian B, Bowien B (1997) Organization and regulation of cbb CO2 assimilation genes in autotrophic bacteria. FEMS Microbiol Rev 21:135–155CrossRefPubMedGoogle Scholar
  31. Li N, Cannon MC (1998) Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli. J Bacteriol 180:2450–2458PubMedGoogle Scholar
  32. Li LA, Tabita FR (1997) Maximum activity of recombinant ribulose 1,5-bisphosphate carboxylase/oxygenase of Anabaena sp. strain CA requires the product of the rbcX gene. J Bacteriol 179:3793–3796PubMedGoogle Scholar
  33. Martin WJ, Zeng LC, Ahmed K, Roy M (1994) Cytomegalovirus-related sequence in an atypical cytopathic virus repeatedly isolated from a patient with chronic fatigue syndrome. Am J Pathol 145:440–451PubMedGoogle Scholar
  34. Meade HM, Long SR, Ruvkun GB, Brown SE, Ausubel FM (1982) Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol 149:114–122PubMedGoogle Scholar
  35. Murphy BA, Grundy FJ, Henkin TM (2002) Prediction of gene function in methylthioadenosine recycling from regulatory signals. J Bacteriol 184:2314–2318CrossRefPubMedGoogle Scholar
  36. Nelson D, Fisher C (1995) Chemoautotrophic and methanotrophic endosymbiotic bacteria at deep-sea vents and seeps. In: Karl D (ed) Microbiology of deep-sea hydrothermal vents. CRC, Boca RatonGoogle Scholar
  37. Niyogi SK, Foote RS, Mural RJ, Larimer FW, Mitra S, Soper TS, Machanoff R, Hartman FC (1986) Nonessentiality of histidine 291 of Rhodospirillum rubrum ribulose-bisphosphate carboxylase/oxygenase as determined by site-directed mutagenesis. J Biol Chem 261:10087–10092PubMedGoogle Scholar
  38. Paoli GC, Soyer F, Shively J, Tabita FR (1998) Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer. Microbiology 144(Pt 1):219–227PubMedGoogle Scholar
  39. Parkinson JS, Kofoid EC (1992) Communication modules in bacterial signaling proteins. Annu Rev Genet 26:71–112CrossRefPubMedGoogle Scholar
  40. Pfennig N, Truper HG (1992) The family Chromatiaceae. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH (eds) The Prokaryotes: a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn. Springer, Berlin Heidelberg New York, pp 3200–3221Google Scholar
  41. Read BA, Tabita FR (1992) Amino acid substitutions in the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase that influence catalytic activity of the holoenzyme. Biochemistry 31:519–525PubMedGoogle Scholar
  42. Reznikoff WS, Siegele DA, Cowing DW, Gross CA (1985) The regulation of transcription initiation in bacteria. Annu Rev Genet 19:355–387CrossRefPubMedGoogle Scholar
  43. Robinson JJ (1997) Biochemistry and molecular biology of RubisCO expression and stable carbon isotope fractionation in chemoautotrophic symbioses. Harvard University, CambridgeGoogle Scholar
  44. Robinson JJ, Cavanaugh CM (1995) Expression of form I and form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubsico) in chemoautotrophic symbioses: implications for the interpretation of stable carbon isotope ratios. Limnol Oceanogr 40:1496–1502Google Scholar
  45. Robinson JJ, Stein JL, Cavanaugh CM (1998) Cloning and sequencing of a form II ribulose-1,5-biphosphate carboxylase/oxygenase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila. J Bacteriol 180:1596–1599PubMedGoogle Scholar
  46. Robinson JJ, Scott KM, Swanson ST, O’Leary MH, Horken K, Tabita FR, Cavanaugh CM (2003) Kinetic isotope effect and characterization of form II RubisCO from the chemoautotrophic endosymbionts of the hydrothermal vent tubeworm Riftia pachyptila. Limnol Oceanogr 48:48–54Google Scholar
  47. Roeske CA, O’Leary MH (1984) Carbon isotope effects on the enzyme-catalyzed craboxylation of ribulose bisphosphate. Biochemistry 23:6275–6284Google Scholar
  48. Roeske CA, O’Leary MH (1985) Carbon isotope effect on carboxylation of ribulose bisphosphate catalyzed by ribulosebisphosphate carboxylase from Rhodospirillum rubrum. Biochemistry 24:1603–1607PubMedGoogle Scholar
  49. Sakurai N, Sakurai T (1998) Genomic DNA cloning of the region encoding nitric oxide reductase in Paracoccus halodenitrificans and a structure model relevant to cytochrome oxidase. Biochem Biophys Res Commun 243:400–406CrossRefPubMedGoogle Scholar
  50. Saraste M, Sibbald PR, Wittinghofer A (1990) The P-loop—a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 15:430–434CrossRefPubMedGoogle Scholar
  51. Sarbu SM, Kane TC, Kinkle BK (1996) A chemoautotrophically based cave ecosystem. Science 272:1953–1955PubMedGoogle Scholar
  52. Schaferjohann J, Bednarski R, Bowien B (1996) Regulation of CO2 assimilation in Ralstonia eutropha: premature transcription termination within the cbb operon. J Bacteriol 178:6714–6719PubMedGoogle Scholar
  53. Schneider G, Knight S, Andersson I, Branden CI, Lindqvist Y, Lundqvist T (1990) Comparison of the crystal structures of L2 and L8S8 Rubisco suggests a functional role for the small subunit. Embo J 9:2045–2050PubMedGoogle Scholar
  54. Schneider G, Lindqvist Y, Branden CI (1992) RUBISCO: structure and mechanism. Annu Rev Biophys Biomol Struct 21:119–143CrossRefPubMedGoogle Scholar
  55. Scott KM, Schwedock J, Schrag DP, Cavanaugh CM (2004) Influence of form IA RubisCO and environmental disolved inorganic carbon on the del13C of the clam-bacterial chemoautotrophic symbions Solemya velum. Environ Microbiol (in press)Google Scholar
  56. Sekowska A, Danchin A (2002) The methionine salvage pathway in Bacillus subtilis. BMC Microbiol 2:8CrossRefPubMedGoogle Scholar
  57. Stein JL, Felbeck H (1993) Kinetic and physical properties of a recombinant RuBisCO from a chemoautotrophic endosymbiont. Mol Mar Biol Biotechnol 2:280–290PubMedGoogle Scholar
  58. Stein J, Cary S, Hessler R, Ohta S, Vetter R, Childress J, Felbeck H (1988) Chemoautotrophic symbiosis in a hydrothermal vent gastropod. Biol Bull 174:373–378Google Scholar
  59. Stein JL, Haygood M, Felbeck H (1990) Nucleotide sequence and expression of a deep-sea ribulose-1,5-bisphosphate carboxylase gene cloned from a chemoautotrophic bacterial endosymbiont. Proc Natl Acad Sci USA 87:8850–8854PubMedGoogle Scholar
  60. Swofford DL (1999) PAUP*. Phylogenetic analysis using parsimony (*and Other Methods), 4th edn. Sinauer Associates, SunderlandGoogle Scholar
  61. Tabita FR (1988) Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol Rev 52:155–189PubMedGoogle Scholar
  62. Tabita FR (1995) The biochemistry and metabolic regulation of carbon metabolism and CO2 fixation in purple bacteria. In: Blankenship RE, Madigan MT, Bauer CE (eds) Anoxygenic photosynthetic bacteria. Kluwer, DordrechtGoogle Scholar
  63. Tabita FR (1999) Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynthesis Res 60:1–28CrossRefGoogle Scholar
  64. Viale AM, Kobayashi H, Akazawa T (1989) Expressed genes for plant-type ribulose 1,5-bisphosphate carboxylase/oxygenase in the photosynthetic bacterium Chromatium vinosum, which possesses two complete sets of the genes. J Bacteriol 171:2391–2400PubMedGoogle Scholar
  65. Viale AM, Kobayashi H, Akazawa T (1990) Distinct properties of Escherichia coli products of plant-type ribulose-1,5-bisphosphate carboxylase/oxygenase directed by two sets of genes from the photosynthetic bacterium Chromatium vinosum. J Biol Chem 265:18386–18392PubMedGoogle Scholar
  66. Wilmot DB, Vetter RD (1992) Oxygen- and nitrogen-dependent sulfer metabolism in the thiotrophic clam Solemya reidi. Biol Bull 182:444–453Google Scholar
  67. Yaguchi T, Chung SY, Igarashi Y, Kodama T (1994) Cloning and sequence of the L2 form of RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. Biosci Biotechnol Biochem 58:1733–1737PubMedGoogle Scholar
  68. Yanofsky C, Platt T, Crawford IP, Nichols BP, Christie GE, Horowitz H, VanCleemput M, Wu AM (1981) The complete nucleotide sequence of the tryptophan operon of Escherichia coli. Nucleic Acids Res 9:6647–6668PubMedGoogle Scholar
  69. Yokota A, Kitaoka S (1985) Correct pK values for dissociation constant of carbonic acid lower the reported Km values of ribulose bisphosphate carboxylase to half. Presentation of a nomograph and an equation for determining the pK values. Biochem Biophys Res Commun 131:1075–1079PubMedGoogle Scholar
  70. Yokoyama K, Hayashi NR, Arai H, Chung SY, Igarashi Y, Kodama T (1995) Genes encoding RubisCO in Pseudomonas hydrogenothermophila are followed by a novel cbbQ gene similar to nirQ of the denitrification gene cluster from Pseudomonas species. Gene 153:75–79CrossRefPubMedGoogle Scholar
  71. Yu C, Lee AM, Bassler BL, Roseman S (1991) Chitin utilization by marine bacteria. A physiological function for bacterial adhesion to immobilized carbohydrates. J Biol Chem 266:24260–24267PubMedGoogle Scholar
  72. Zengel JM, Mueckl D, Lindahl L (1980) Protein L4 of the E. coli ribosome regulates an eleven gene r protein operon. Cell 21:523–535CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Julie Schwedock
    • 1
    • 2
  • Tara L. Harmer
    • 1
  • Kathleen M. Scott
    • 1
    • 3
  • Harm J. Hektor
    • 1
  • Angelica P. Seitz
    • 1
  • Matthew C. Fontana
    • 1
  • Daniel L. Distel
    • 1
    • 4
  • Colleen M. Cavanaugh
    • 1
  1. 1.Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUSA
  2. 2.Genomic Profiling SystemsBedfordUSA
  3. 3.Department of BiologyUniversity of South FloridaTampaUSA
  4. 4.Department of Biochemistry, Microbiology, and Molecular BiologyUniversity of MaineOronoUSA

Personalised recommendations