Abstract
Mycobacterium sp. strain KMS was isolated from soils where remediation of polycyclic aromatic hydrocarbons was active. This isolate is a competent plant root colonizer through utilization of an array of carbon substrates available in the root exudates. Bioinformatic analyses based on the KMS genome propose pathways for C4- and C3-intermediate conversions during growth of the isolate on substrates requiring gluconeogenesis. Expression of candidate genes for these pathways was compared using semi-quantitative RT-PCR from cells grown on acetate, succinate, benzoate, or pyrene as sole carbon sources requiring gluconeogenesis during growth. Expression was examined for cells grown on fructose and mannitol, where gluconeogenesis would not be essential. Transcript accumulation in cells grown on all the carbon sources confirmed expression from genes involved in the glyoxylate shunt and a gene encoding a novel enzyme to complete the tricarboxylic acid cycle, a membrane-associated malate:quinone oxidoreductase (MQO). Transcript accumulations for genes encoding phosphoenolpyruvate carboxykinase, malic enzyme, and phosphoenolpyruvate synthase were weak for mannitol growth but were detected for the other carbon sources. Activities for PEP synthase and the membrane-associated MQO were confirmed in cell extracts at different levels indicating feasibility of their function in production of PEP for gluconeogenesis in this soil Mycobacterium.
Similar content being viewed by others
References
Bertin C, Yang X, Weston LA (2003) The role of exudates and allelochemicals in the rhizosphere. Plant Soil 256:67–83
Beste DJ, Bonde B, Hawkins N et al (2011) ¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathog 7:e1002091
Brennan PJ, Nikaido H (1995) The envelope of mycobacteria. Annu Rev Biochem 64:29–63
Brennan PJ (2003) Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis. Tuberculosis 83:91–97
Bruland N, Voss I, Brämer C et al (2010) Unravelling the C3/C4 carbon metabolism in Ralstonia eutropha H16. J Appl Microbiol 109:79–90
Child R, Miller CD, Liang Y et al (2007) Polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates: their association with plant roots. Appl Microbiol Biotechnol 75:655–663
Child R, Miller CD, Liang Y et al (2007) Pyrene mineralization by Mycobacterium sp. strain KMS in a barley rhizosphere. J Environ Qual 36:1260–1265
Cooper RA, Kornberg HL (1965) Net formation of phosphoenolpyruvate from pyruvate by Escherichia coli. Biochim Biophys Acta 104:618–620
de Carvalho LPS, Fischer SM, Marrero J et al (2010) Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates. Chem Biol 17:1122–1131
Gourdon P, Baucher MF, Lindley ND et al (2000) Cloning of the malic enzyme gene from Corynebacterium glutamicum and role of the enzyme in lactate metabolism. Appl Environ Microbiol 66:2981–2987
Höner Zu, Bentrup K, Miczak A, Swenson DL et al (1999) Characterization of activity and expression of isocitrate lyase in Mycobacterium avium and Mycobacterium tuberculosis. J Bacteriol 181:7161–7167
Hutchins AM, Holden JF, Adams MW (2001) Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 183:709–715
Kather B, Stingl K, van der Rest ME et al (2000) Another unusual type of citric acid cycle enzyme in Helicobacter pylori: the malate:quinone oxidoreductase. J Bacteriol 182:3204–3209
Kim YH, Engesser KH, Cerniglia CE (2003) Two polycyclic aromatic hydrocarbon o-quinone reductases from a pyrene-degrading Mycobacterium. Arch Biochem Biophys 416:209–217
Kim SJ, Kweon O, Jones RC et al (2007) Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J Bacteriol 189:464–472
Kim SJ, Kweon O, Jones RC et al (2008) Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19:859–881
Kitagawa W, Miyauchi K, Masai E et al (2001) Cloning and characterization of benzoate catabolic genes in the gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. J Bacteriol 183:6598–6606
Kornberg HL (1966) The role and control of the glyoxylate cycle in Escherichia coli. Biochem J 99:1–11
Kretzschmar U, Rückert A, Jeoung JH et al (2002) Malate:quinone oxidoreductase is essential for growth on ethanol or acetate in Pseudomonas aeruginosa. Microbiology 148:3839–3847
Imanaka H, Yamatsu A, Fukui T et al (2006) Phosphoenolpyruvate synthase plays an essential role for glycolysis in the modified Embden-Meyerhof pathway in Thermococcus kodakarensis. Mol Microbiol 61:898–909
Lewis DH, Smith DC (1967) Sugar alcohols (polyols) in fungi and green plants: distribution, physiology and metabolism. New Phytol 66:143–184
Liang Y, Gardner DR, Miller CD et al (2006) Study of biochemical pathways and enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS. Appl Environ Microb 72:7821–7828
Liu K, Yu J, Russell DG (2003) pckA-deficient Mycobacterium bovis BCG shows attenuated virulence in mice and in macrophages. Microbiology 149:1829–1835
Marrero J, Rhee KY, Schnappinger D et al (2010) Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection. Proc Natl Acad Sci USA 107:9819–9824
Miller CD, Hall K, Liang YN et al (2004) Isolation and characterization of polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates from soil. Microb Ecol 48:230–238
Molenaar D, van der Rest ME, Petrović S (1998) Biochemical and genetic characterization of the membrane-associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum. Eur J Biochem 254:395–403
Molenaar D, van der Rest ME, Drysch A et al (2000) Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum. J Bacteriol 182:6884–6891
Niersbach M, Kreuzaler F, Geerse RH et al (1992) Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase. Mol Gen Genet 231:332–336
Pliego C, Kamiova F, Lugtenberg B (2011) Plant growth-promoting bacteria: fundamentals and exploitation. In: Bacteria in agrobiology: crop ecosystems. Springer, Berlin. doi:10.1007/978-3-642-18357-7_11
Riedel C, Rittmann D, Dangel P et al (2001) Characterization of the phosphoenolpyruvate carboxykinase gene from Corynebacterium glutamicum and significance of the enzyme for growth and amino acid production. J Mol Microbiol Biotechnol 3:573–583
Titgemeyer F, Amon J, Parche S et al (2007) A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis. J Bacteriol 189:5903–5915
Tjaden B, Plagens A, Dörr C et al (2006) Phosphoenolpyruvate synthetase and pyruvate, phosphate dikinase of Thermoproteus tenax: key pieces in the puzzle of archaeal carbohydrate metabolism. Mol Microbiol 60:287–298
van der Rest ME, Frank C, Molenaar D (2000) Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli. J Bacteriol 182:6892–6899
Wisselink HW, Weusthuis RA, Eggink G et al (2002) Mannitol production by lactic acid bacteria: a review. Int Dairy J 12:151–161
Zhang C, Anderson AJ (2012) Multiplicity of genes for aromatic ring-hydroxylating dioxygenases in Mycobacterium isolate KMS and their regulation. Biodegradation. doi:10.1007/s10532-012-9535-z
Zhang C, Anderson AJ (2012) Utilization of pyrene and benzoate in Mycobacterium isolate KMS is regulated differentially by catabolic repression. J App Microbiol. doi:10.1002/jobm.201100480
Acknowledgments
The authors thank Dr. C. Dimkpa and Dr. D. Welker for comments on the manuscript and the JGI for the funding for sequencing and annotation of the genome. The study was supported in part by the Utah Agricultural Experiment Station, paper number 3045.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Zhang, C., Anderson, A.J. The Gluconeogenic Pathway in a Soil Mycobacterium Isolate with Bioremediation Ability. Curr Microbiol 66, 122–131 (2013). https://doi.org/10.1007/s00284-012-0248-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00284-012-0248-7