Abstract
Three genes from Arabidopsis thaliana with high sequence similarity to gamma carbonic anhydrase (γCA), a Zn containing enzyme from Methanosarcina thermophila(CAM), were identified and characterized. Evolutionary and structural analyses predict that these genes code for active forms of γCA. Phylogenetic analyses reveal that these Arabidopsis gene products cluster together with CAM and related sequences from α and γ proteobacteria, organisms proposed as the mitochondrial endosymbiont ancestor. Indeed, in vitro and in vivo experiments indicate that these gene products are transported into the mitochondria as occurs with several mitochondrial protein genes transferred, during evolution, from the endosymbiotic bacteria to the host genome. Moreover, putative CAM orthologous genes are detected in other plants and green algae and were predicted to be imported to mitochondria. Structural modeling and sequence analysis performed in more than a hundred homologous sequences show a high conservation of functionally important active site residues. Thus, the three histidine residues involved in Zn coordination (His 81, 117 and 122), Arg 59, Asp 61, Gin 75, and Asp 76 of CAM are conserved and properly arranged in the active site cavity of the models. Two other functionally important residues (Glu 62 and Glu 84 of CAM) are lacking, but alternative amino acids that might serve to their roles are postulated. Accordingly, we propose that photosynthetic eukaryotic organisms (green algae and plants) contain γCAs and that these enzymes codified by nuclear genes are imported into mitochondria to accomplish their biological function.
Similar content being viewed by others
References
Adler, L., Brundell, J., Falkbring, S.O. and Nyman, P.O. 1972. Carbonic anhydrase from Neisseria sicca, strain 6021. I. Bacterial growth and purification of the enzyme. Biochim. Biophys. Acta 284: 298–310.
Alber, B.E. and Ferry, J.G. 1994. A carbonic anhydrase from the archaeon Methanosarcina thermophila. Proc. Natl. Acad. Sci. USA 91: 6909–6913.
Alber, B.E. and Ferry, J.G. 1996. Characterization of heterologously produced carbonic anhydrase from Methanosarcina thermophila. J. Bacteriol. 178: 3270–3274.
Badger, M.R. and Price, G.D. 1994. The role of carbonic anhydrase in photosynthesis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 45: 369–392.
Badger, M.R. and Price, G.D. 2003. CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution. J. Exp. Bot. 54: 609–622.
Becker, D., Kemper, E., Schell, J. and Masterson, R. (1992) New plant binary vectors with selectable markers located proximal to the left T-DNA border. Plant Mol. Biol. 20, 1195–1197.
Boriacksjodin, P.A., Heck, R.W., Laipis, P.J., Silverman, D., and Christianson, D. 1995. Structure determination of murine mitochondrial carbonic-anhydrase-V at 2.45-Angstrom resolution-implications for catalytic proton-transfer and inhibitor design. Proc. Natl. Acad. Sci. USA 92: 10949–10953.
Braus-Stromeyer, S.A., Schnappauf, G., Braus, G., Gossner, A. and Drake, H. 1997. Carbonic anhydrase in Acetobacterium woodii and other acetogenic bacteria. J. Bacteriol. 179: 7197–200.
Brooks, B.R., Bruccoleri, R., Olafson, B., Swaminathan, S. and Karplis, M. 1983. A program for macromolecular energy, minimization and dynamics calculations. J. Comp. Chem. 4: 105–113.
Brown, J. 2001 Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst. Biol. 50: 497–512.
Brown, J., Douady, C., Italia, M., Marshall, W. and Stanhope, M. 2001. Universal trees based on large combined protein sequence data sets. Nature Genet. 28: 281–285.
Chirica, L.C., Elleby, B., Jonsson, B. and Lindskog, S. 1997. The complete sequence, expression in Escherichia coli, purification and some properties of carbonic anhydrase from Neisseria gonorrhoeas. Eur. J. Biochem. 244: 755–760.
Clough, S.J. and Bent, A.F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16: 735–737.
Cox, E., McLendon, G., Morel, F.M., Lane, T.W., Prince, R.C., Pickering, I.J. and George, G.N. 2000. The active site structure of Thalassiosira weissflogii carbonic anhydrase 1. Biochemistry 2000 39: 12128–12130.
Douce, R., Bourguignon, J., Brouquisse, R. and Neuburger, M. 1987. Isolation of plant mitochondria: general principles and criteria of integrity. Methods Enzymol. 148: 403–415.
Echeverria, M., Martin, M.T., Ricard, B. and Litvak, S. 1986. A DNA topoisomerase type I from wheat mitochondria. Plant Mol. Biol. 6, 417–427.
Eriksson, M., Karlsson, K., Ramazanov, Z., Gardestrom, G. and Samuelsson, G. 1996. Discovery of an algal mitochondrial carbonic anhydrase: molecular cloning and characterization of a low-CO2-induced polypeptide in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 93: 12031–12034.
Eubel, H., Jansch, L. and Braun, H.-P. 2003. New insights into the respiratory chain of plant mitochondria. Supercomplexes and a unique composition of complex II. Plant Physiol. 133: 274–286.
Farré, J.C. and Araya, A. 2001. Gene expression in isolated plant mitochondria: high fidelity of transcription, splicing and editing of a transgene product in electroporated organelles. Nucl. Acids Res. 29: 2484–2491.
Felsenstein, J. (1993). PHYLIP (Phytogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seatle.
Figueroa, P., Gómez, I., Holuigue, L., Araya, A. and Jordana, X. 1999. Transfer of rps14 from the mitochondrion to the nucleus in maize implied integration within a gene encoding the iron-sulfur subunit of succinate dehydrogenase and expression by alternative splicing. Plant J. 18: 601–609.
Fukuzawa, H., Fujiwara, S., Yamamoto, Y., Dionisio-Sese, M. and Miyachi, S. 1990. cDNA cloning, sequence, and expression of carbonic anhydrase in Chlamydomonas reinhardtii: regulation by environmental CO2 concentration. Proc. Natl. Acad. Sci. USA 87: 4383–4387.
González-Meler, M.A., Rubas-Carbo, M., Siedow, J. and Drake, B.G. 1996. Direct inhibition of plant mitochondrial respiration by elevated CO2. Plant Physiol. 112: 1349–1355.
Gray, M.W., Burger, G. and Lang, B.F. 1999. Mitochondrial evolution. Science 283: 1476–1481.
Guilloton, M.B., Korte, J., Lamblin, A., Fuchs, J. and Anderson, P. 1992. Carbonic anhydrase in Escherichia coli. A product of the cyn operon. J. Biol. Chem. 267: 3731–3734.
Heazlewood, J.L., Howell, K. and Millar, A.M. 2003. Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plantspecific subunits. Biochim. Biophys. Acta. 1604: 159–169.
Henrick, K. and Thornton, J.M. 1998. PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23: 358–361.
Henry, R.P. 1996. Multiple roles of carbonic anhydrase in cellular transport and metabolism. Annu. Rev. Physiol. 58: 523–538.
Hewett-Emmett, D. and Tashian, R.E. 1996. Functional diversity, conservation, and convergence in the evolution of the alpha-, beta-, and gamma-carbonic anhydrase gene families. Mol. Phylogenet. Evol. 5: 50–77.
Hewett-Emmett, D. 2000. Evolution and distribution of the carbonic anhydrase gene families. In: W.R. Chegwidden, N.D. Carter and Y.H. Edwards (Eds.) The Carbonic Anhdyrases. New Horizons, Birkha¨ user Verlag, Basel, pp. 29–76.
Iverson, T.M., Alber, B.E., Kisker, C., Ferry, J.G. and Rees, D.C. 2000. A closer look at the active site of gammaclass carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39: 9222–9231.
Kaplan, A. and Reinhold, L. 1999. CO2 concentrating mechanisms in photosynthetic microorganisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 539–570.
Kisker, C., Schindelin, H., Alber, B.E., Ferry, J.G. and Rees, D.C. 1996. A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. EMBO J. 15: 2323–2330.
Laemmli, Y.K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophacie T4. Nature 227: 680–685.
Lane, T.W. and Morel, F.M. 2000. A biological function for cadmium in marine diatoms. Proc. Natl. Acad. Sci. USA 97: 4627–4631.
Lesburg, C.A., Huang, C.C., Christianson, D. and Fierke, C.A. 1997. Histidine carboxamide ligand substitutions in the zinc binding site of carbonic anhydrase II alter metal coordination geometry but retain catalytic activity. Biochemistry 36: 15780–15791.
Li, W., Jaroszewski, L. and Godzik, A. 2002. Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 15: 643–649.
Maeda, S., Badger, M.R. and Price, G.D. 2002. Novel gene products associated with NdhD3/D4-containing NDH-1 complexes are involved in photosynthetic CO2 hydration in the cyanobacterium, Synechococcus sp. PCC7942. Mol. Microbiol 43: 425–435.
Mathur, J. and Koncz, C. 1998. Protoplast isolation, culture, and regeneration. Methods Mol. Biol. 82: 35–42.
Meldrum, N.U. and Roughton, F.J. 1933. Carbonic anhydrase: its preparation and properties. J. Physiol. 80: 113–141.
Meller, J. and Elber, R. 2001. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins 45: 241–261.
Merlin, C., Masters, M., McAteer, S. and Coulson, A. 2003. Why is carbonic anhydrase essential to Escherichia coli? J. Bacteriol. 185: 6415–6424.
Millar, A.H., Sweetlove, L.J., Giegé, P. and Leaver, C.L. 2001. Analysis of the Arabidopsis mitochondrial proteome. Plant Physiol. 127: 1711–1727.
Mori, K., Ogawa, Y., Ebihara, K., Tamura, N., Tashiro, K., Kuwahara, T., Mukoyama, M., Sugawara, A., Ozaki, S., Tanaka, I. and Nakao, K. 1999. Isolation and characterization of CA XIV, a novel membrane-bound carbonic anhydrase from mouse kidney. J. Biol. Chem. 274: 15701–15705.
Moroney, J.V., Bartlett, S.G., and Samuelsson, G. (2001). Carbonic anhydrases in plants and algae. Plant Cell Environ. 24: 141–153.
Parisi, G. and Echave, J. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol. Biol. Evol. 18: 750–756.
Parisi, G., Fornasari, M. and Echave, J. 2000. Evolutionary analysis of gamma-carbonic anhydrase structurally related proteins. Mol. Phylogenet. Evol. 14: 323–334.
Price, G.D., Hewit, S.M., Harrison, K. and Badger, M.R. 1993. Analysis of genomic DNA region from the cyanobacteria Synechococcus sp. strain PCC7942 involved in carboxysome assembly and function. J. Bacteriol. 175: 2871–2879.
Qian, M., Earnhardt, J., Wadhwa, N., Tu, C., Laipis, P. and Silverman, D. 1999. Proton transfer to residues of basic pK(a) during catalysis by carbonic anhydrase. Biochim. Biophys. Acta. 1434: 1–5.
Raetz, C.R. and Roderick, S.L. 1995. A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science 270: 997–1000.
Raven, J.A. 2001. A role for mitochondrial carbonic anhydrase in limiting CO2 leakage from low CO2-grown cells of Chlamydomonas reinhardtii. Plant Cell Environ. 24: 261–264.
Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779–815.
Sambrook, J. and Russell, D. 2001. Molecular Cloning, a Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York.
Sanchez, R. and Sali, A. 1998. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. USA 95: 13597–13602.
Shi, J., Blundell, T.L. and Mizuguchi, K. 2001. FUGUE: sequence-structure homology recognition using environmentspecific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310: 243–257.
Sippl, M.J. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355–362.
Smith, K., Jakubzick, S.C., Whittam, T.S. and Ferry, J.G. 1999. Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Proc. Natl. Acad. Sci. USA. 96: 15184–15189.
Thompson, J.D., Gibson, T.D., Plewniak, F., Jeanmougin, F. and Higgins, D.G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids. Res. 25: 4876–4882.
Tripp, B.C. and Ferry, J.G. 2000. A structure-function study of a proton transport pathway in the gamma-class carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39: 9232–9240.
Tripp, B., Bell, C., Cruz, F., Krebs, C. and Ferry, J.G. 2004. A role for iron in an ancient carbonic anhydrase. J. Biol. Chem. 279: 6683–6687.
Tu, C.K., Rowlett, R., Tripp, B.C., Ferry, J.G. and Silverman, D.N. 2002. Chemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta-and gamma-class. Biochemistry 41: 15429–15435.
Vaara, M. 1992. Eight bacterial proteins, including UDP-Nacetylglucosamine acyltransferase (LpxA) and three other transferases of Escherichia coli, consist of a six-residue periodicity theme. FEMS Microbiol Lett. 76: 249–254.
Veitch, F.P. and Blankenship, L.C. 1963. Carbonic anhydrase in bacteria. Nature 197: 76–77.
Yagawa, Y., Shiraiwa, Y. and Miyachi, S. 1984. Plant Cell Physiol 25: 775–783.
Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555–556.
Zabaleta, E., Heiser V., Grohmann, L. and Brennicke, A. 1998. Promoters of nuclear-encoded respiratory chain complex I genes from Arabidopsis thaliana contain a region essential for anther/pollen specific expression. Plant J. 15: 49–59.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Parisi, G., Perales, M., Fornasari, M. et al. Gamma carbonic anhydrases in plant mitochondria. Plant Mol Biol 55, 193–207 (2004). https://doi.org/10.1007/s11103-004-0149-7
Issue Date:
DOI: https://doi.org/10.1007/s11103-004-0149-7