Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. Two sets of structural genes (cbbLS-1 and -2) for form I RubisCO have been previously identified in the Mycobacterium sp. strain JC1, which is able to grow on carbon monoxide (CO) or methanol as sole sources of carbon and energy. Northern blot and reverse transcriptase PCR showed that the cbbLS-1 and -2 genes are expressed in cells grown on either carbon monoxide (CO) or methanol, but not in cells grown in nutrient broth. A promoter assay revealed that the cbbLS-2 promoter has a higher activity than the cbbLS-1 promoter in both CO- and methanol-grown cells, and that the activities of both promoters were higher in CO-grown cells than in methanol-grown cells. A gel mobility shift assay and footprinting assays showed that CbbR expressed in Escherichia coli from a cbbR gene, which is located downstream of cbbLS-1 and transcribed in the same orientation as that of the cbbLS genes, specifically bound to the promoter regions of the cbbLS-1 and -2 genes containing inverted repeat sequence. A DNase I footprinting assay revealed that CbbR protected positions −59 to −3 and −119 to −78 of the cbbLS-1 and -2 promoters, respectively. Overexpression of CbbR induced the transcription of RubisCO genes in Mycobacterium sp. strain JC1 grown in nutrient broth. Our results suggest that the CbbR product from a single cbbR gene may positively regulate two cbbLS operons in the Mycobacterium sp. strain JC1 as is the case for Rhodobacter sphaeroides and Cupriavidus necator.
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References
Ashida, H., Y. Saito, C. Kojima, K. Kobayashi, N. Ogasawara, and A. Yokota. 2003. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 302, 286–290.
Cho, J.W., H.S. Yim, and Y.M. Kim. 1985. Acinetobacter isolate growing with carbon monoxide. Kor. J. Microbiol. 23, 1–8.
Dangel, A.W., J.L. Gibson, A.P. Janssen, and F.R. Tabita. 2005. Residues that influence in vivo and in vitro CbbR function in Rhodobacter sphaeroides and identification of a specific region critical for co-inducer recognition. Mol. Microbiol. 57, 1397–1414.
Delwiche, C.F. and J.D. Palmer. 1996. Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13, 873–882.
Dhandayuthapani, S., M. Mudd, and V. Deretic. 1997. Interactions of OxyR with the promoter region of the oxyR and ahpC genes from Mycobacterium leprae and Mycobacterium tuberculosis. J. Bacteriol. 179, 2401–2409.
Dubbs, J.M., T.H. Bird, C.E. Bauer, and F.R. Tabita. 2000. Interaction of CbbR and RegA* transcription regulators with the Rhodobacter sphaeroides cbb I promoter-operator region. J. Biol. Chem. 275, 19224–19230.
Dubbs, P., J.M. Dubbs, and F.R. Tabita. 2004. Effector-mediated interaction of CbbRI and CbbRII regulators with target sequences in Rhodobacter capsulatus. J. Bacteriol. 186, 8026–8035.
Dubbs, J.M. and F.R. Tabita. 2003. Interactions of the cbb II promoter-operator region with CbbR and RegA (PrrA) regulators indicate distinct mechanisms to control expression of the two cbb operons of Rhodobacter sphaeroides. J. Biol. Chem. 278, 16443–16450.
Ellis, R.J. 1979. The most abundant protein in the world. Trends Biochem. Sci. 4, 241–244.
English, R.S., C.A. Williams, S.C. Lorbach, and J.M. Shively. 1992. Two forms of ribulose-1,5-bisphosphate carboxylase/oxygenase from Thiobacillus denitrificans. FEMS Microbiol. Lett. 94, 111–120.
Finn, M.W. and F.R. Tabita. 2003. Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea. J. Bacteriol. 185, 3049–3059.
Frias, J.E., E. Flores, and A. Herrero. 2000. Activation of the Anabaena nir operon promoter requires both NtcA (CAP family) and NtcB (LysR family) transcription factors. Mol. Microbiol. 38, 613–625.
Gibson, J.L., D.L. Falcone, and F.R. Tabita. 1991. Nucleotide sequence, transcriptional analysis, and expression of genes encoded within the form I CO2 fixation operon of Rhodobacter sphaeroides. J. Biol. Chem. 266, 14646–14653.
Gibson, J.L. and F.R. Tabita. 1977a. Different molecular forms of D-ribulose-1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides. J. Biol. Chem. 252, 943–949.
Gibson, J.L. and F.R. Tabita. 1977b. Isolation and preliminary characterization of two forms of ribulose 1,5-biphosphate carboxylase from Rhodopseudomonas capsulata. J. Bacteriol. 132, 818–823.
Gibson, J.L. and F.R. Tabita. 1993. Nucleotide sequence and functional analysis of cbbR, a positive regulator of the Calvin cycle operons of Rhodobacter sphaeroides. J. Bacteriol. 175, 5778–5784.
Gomez, M. and I. Smith. 2000. Determinants of mycobacterial gene expression, p. 111–129. In G.F. Hatfull and J.W.R. Jacobs (eds.), Molecular Genetics of Mycobacteria, American Society for Microbiology, Washington, D.C., USA.
Heinhorst, S., S.H. Baker, D.R. Johnson, P.S. Davies, G.C. Cannon, and J.M. Shively. 2002. Two copies of form I RuBisCO genes in Acidithiobacillus ferrooxidans ATCC 23270. Curr. Microbiol. 45, 115–117.
Howard, N.S., J.E. Gomez, C. Ko, and W.R. Bishai. 1995. Color selection with a hygromycin-resistance-based Escherichia coli-mycobacterial shuttle vector. Gene 166, 181–182.
Jouanneau, Y. and F.R. Tabita. 1986. Independent regulation of synthesis of form I and form II ribulose bisphosphate carboxylase-oxygenase in Rhodopseudomonas sphaeroides. J. Bacteriol. 165, 620–624.
Kang, C.M., D.W. Abbott, S.T. Park, C.C. Dascher, L.C. Cantley, and R.N. Husson. 2005. The Mycobacterium tuberculosis serine/threonine kinases PknA and PknB: substrate identification and regulation of cell shape. Genes Dev. 19, 1692–1704.
Kim, Y.M. and G.D. Hegeman. 1981. Purification and some properties of carbon monoxide dehydrogenase from Pseudomonas carboxydohydrogena. J. Bacteriol. 148, 904–911.
Kim, E.Y., Y.T. Ro, and Y.M. Kim. 1997. Purification and some properties of ribulose 1,5-bisphosphate carboxylases/oxygenases from Acinetobacter sp. strain JC1 and Hydrogenophaga pseudoflava. Mol. Cells 7, 380–388.
Kusano, T., T. Takeshima, C. Inoue, and K. Sugawara. 1991. Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans. J. Bacteriol. 173, 7313–7323.
Kusian, B., R. Bednarski, M. Husemann, and B. Bowien. 1995. Characterization of the duplicate ribulose-1,5-bisphosphate carboxylase genes and cbb promoters of Alcaligenes eutrophus. J. Bacteriol. 177, 4442–4450.
Kusian, B. and B. Bowien. 1995. Operator binding of the CbbR protein, which activates the duplicate cbb CO2 assimilation operons of Alcaligenes eutrophus. J. Bacteriol. 177, 6568–6574.
Kusian, B. and B. Bowien. 1997. Organization and regulation of cbb CO2 assimilation genes in autotrophic bacteria. FEMS Microbiol. Rev. 21, 135–155.
Laemmli, U.K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.
Leblanc, B. and T. Moss. 1994. DNase I footprinting. Methods Mol. Biol. 30, 1–10.
Li, H., M.R. Sawaya, F.R. Tabita, and D. Eisenberg. 2005. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure 13, 779–789.
Maxam, A.M. and W. Gilbert. 1980. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65, 499–560.
McFall, S.M., M.R. Parsek, and A.M. Chakrabarty. 1997. 2-Chloro-muconate and ClcR-mediated activation of the clcABD operon: In vitro transcriptional and DNase I footprint analyses. J. Bacteriol. 179, 3655–3663.
Paoli, G.C., N. Strom Morgan, F.R. Tabita, and J.M. Shively. 1995. Expression of the cbbLcbbS and cbbM genes and distinct organization of the cbb Calvin cycle structural genes of Rhodobacter capsulatus. Arch. Microbiol. 164, 396–405.
Park, S.W., E.H. Hwang, H.S. Jang, J.H. Lee, B.S. Kang, J.I. Oh, and Y.M. Kim. 2009. Presence of the duplicate genes encoding a phylogenetically new subgroup of form I ribulose 1,5-bisphosphate carboxylase/oxygenase in Mycobacterium sp. strain JC1 DSM 3803. Res. Microbiol. 160, 159–165.
Park, S.W., E.H. Hwang, H. Park, J.A. Kim, J. Heo, K.H. Lee, T. Song, E. Kim, Y.T. Ro, S.W. Kim, and Y.M. Kim. 2003. Growth of mycobacteria on carbon monoxide and methanol. J. Bacteriol. 185, 142–147.
Parsek, M.R., S.M. McFall, D.L. Shinabarger, and A.M. Chakrabarty. 1994. Interaction of two LysR-type regulatory proteins CatR and ClcR with heterologous promoters: functional and evolutionary implications. Proc. Natl. Acad. Set USA 91, 12393–12397.
Ro, Y.T., J.G. Seo, J. Lee, D. Kim, I.K. Chung, T.U. Kim, and Y.M. Kim. 1997. Growth on methanol of a carboxydobacterium, Acinetobacter sp. strain JC1 DSM 3803. J. Microbiol. 35, 30–39.
Sambrook, J., E.F. Fristh, and T. Manniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd. ed. Cold Spring Harbor Laboratory, New York, N.Y., USA.
Schell, M.A. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47, 597–626.
Seo, J.G., S.W. Park, H. Park, S.Y. Kim, Y.T. Ro, E. Kim, J.W. Cho, and Y.M. Kim. 2007. Cloning, characterization and expression of a gene encoding dihydroxyacetone synthase in Mycobacterium sp. strain JC1 DSM 3803. Microbiology 153, 4174–4182.
Sherman, D.R., M. Voskuil, D. Schnappinger, R. Liao, M.I. Harrell, and G.K. Schoolnik. 2001. Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding α-crystallin. Proc. Natl. Acad. Sci. USA 98, 7534–7539.
Shively, J.M., W. Devore, and L. Stratford. 1986. Molecular evolution of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). FEMS Microbiol. Lett. 37, 251–257.
Smith, S.A. and F.R. Tabita. 2002. Up-regulated expression of the cbb I and cbb II operons during photoheterotrophic growth of a ribulose 1,5-bisphosphate carboxylase-oxygenase deletion mutant of Rhodobacter sphaeroides. J. Bacteriol. 184, 6721–6724.
Song, T., H. Lee, Y.H. Park, E. Kim, Y.T. Ro, S.W. Kim, and Y.M. Kim. 2002. Reclassification of a carboxydobacterium, Acinetobacter sp. strain JC1 DSM 3803, as Mycobacterium sp. strain JC1 DSM 3803. J. Microbiol. 40, 237–240.
Stoner, M.T. and J.M. Shively. 1993. Cloning and expression of the D-ribulose-1,5-bis-phosphate carboxylase/oxygenase form II gene from Thiobacillus intermedius in Escherichia coli. FEMS Microbiol. Lett. 107, 287–292.
Tabita, F.R., T.E. Hanson, H.Y. Li, S. Satagopan, J. Singh, and S. Chan. 2007. Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol. Mol. Biol. Rev. 71, 576–599.
Tourova, T.P., E.M. Spiridonova, I.A. Berg, B.B. Kuznetsov, and D.Y. Sorokin. 2006. Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium. Microbiology 152, 2159–2169.
Toyoda, K., Y. Yoshizawa, H. Arai, M. Ishii, and Y. Igarashi. 2005. The role of two CbbRs in the transcriptional regulation of three ribulose-1,5-bisphosphate carboxylase/oxygenase genes in Hydrogenovibrio marinus strain MH-110. Microbiology 151, 3615–3625.
Uchino, Y. and A. Yokota. 2003. “Green-like” and “red-like” RubisCO cbbL genes in Rhodobacter azotoformans. Mol. Biol. Evol. 20, 821–830.
Van Keulen, G., L. Girbal, E.R.E. Van Den Bergh, L. Dijkhuizen, and W.G. Meijer. 1998. The LysR-type transcriptional regulator CbbR controlling autotrophic CO2 fixation by Xanthobacter flavus is an NADPH sensor. J. Bacteriol. 180, 1411–1417.
Van Keulen, G., A. Ridder, L. Dijkhuizen, and W.G. Meijer. 2003. Analysis of DNA binding and transcriptional activation by the LysR-type transcriptional regulator CbbR of Xanthobacter flavus. J. Bacteriol. 185, 1245–1252.
Viale, A.M., H. Kobayashi, and T. Akazawa. 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, 2391–2400.
Vichivanives, P., T.H. Bird, C.E. Bauer, and F.R. Tabita. 2000. Multiple regulators and their interactions in vivo and in vitro with the cbb regulons of Rhodobacter capsulatus. J. Mol. Biol. 300, 1079–1099.
Wang, L., J.D. Helmann, and S.C. Winans. 1992. The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite. Cell 69, 659–667.
Watson, G.M.F. and F.R. Tabita. 1997. Microbial ribulose 1,5-bis-phosphate carboxylase/oxygenase: A molecule for phylogenetic and enzymological investigation. FEMS Microbiol. Lett. 146, 13–22.
Weber, K. and M. Osborn. 1969. The reliability of molecular weight determination by dodecyl sulfate-polyacrylamide gel electrophoresis. J. Biol. Chem. 244, 4406–4412.
Yaguchi, T., S.Y. Chung, Y. Igarashi, and T. Kodama. 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, 1733–1737.
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Lee, J.H., Park, D.O., Park, S.W. et al. Expression and regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in Mycobacterium sp. strain JC1 DSM 3803. J Microbiol. 47, 297–307 (2009). https://doi.org/10.1007/s12275-008-0210-3
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DOI: https://doi.org/10.1007/s12275-008-0210-3