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John Thompson, Ph.D.

John Thompson, Ph.D.Senior Investigator
Chief, Microbial Biochemistry and Genetics Section

National Institute of Dental Research
BETHESDA MD 20892-4352

Phone: 301-496-4083
Fax: 301-402-0396

Biographical Sketch

In 1960, I was admitted to the Honors School of Leeds University where I obtained both B.Sc. and Ph.D. degrees in biochemistry under the guidance of Professor Frank C. Happold (who pioneered the establishment of biochemistry in the core curriculum of English Universities). The subject of my Ph.D. thesis pertained to the biochemical, physiological and enzymological aspects of solute transport in marine bacteria. Upon completion of my thesis in 1967, Professor Robert A. MacLeod at MacDonald College of McGill University suggested that I pursue my research endeavors (initially as a post –doctoral fellow, later research associate) in his lab in Montreal. In 1973, I accepted the tenured position of research biochemist in the New Zealand Dairy Research Institute in Palmerston North, where I was introduced to the attractions, and unique aspects of the physiology and biochemistry, of the lactic acid bacteria. In a turning point of my career, I initiated a program of research into the regulatory mechanisms involved in the transport and metabolism of sugars by Lactococcus lactis and related dairy organisms. These studies led, in 1980, to an invitation from Professor Milton H. Saier Jr., to spend a sabbatical year as a Warner-Lambert research fellow in his lab in the Biology Department, University of California in San Diego. A chance encounter that year (at the ASM meeting in Miami) with members of the Microbiology Section of the National Institute of Dental and Craniofacial Research (NIDCR) culminated with an invitation (and an NIH Director’s Award) to spend 1981 as a special expert at the NIDCR in Bethesda. Thirty years later, I continue my research at the NIH, where I am presently senior investigator and chief of the Microbial Biochemistry and Genetics Section, Laboratory of Cell and Developmental Biology, NIDCR.

Research Interests/Scientific Focus

Molecular structure of sucrose-6P and its five phosphorylated isomers

This program examines the molecular basis for regulation of transport and dissimilation of carbohydrates and amino acids by oral microorganisms. Other research activities include the cloning and site - directed mutagenesis of genes, and the expression, purification and functional analysis of metabolic enzymes. In 2007, a collaboration was initiated between the Microbial Biochemistry and Genetics Section and the Microbiology Institute of the Chinese Academy of Sciences in Beijing. The investigation pertained to the mechanism(s) of infection and pathogenicity of Streptococcus suis in humans. This fruitful endeavor resulted in the first purification, crystallization and enzymatic characterization of two important enzymes: gluconate 5-dehydrogenase (Ga5DH) and D-mannonate dehydrogenase (ManD), respectively. These metabolic enzymes are potential targets for therapeutic intervention and inhibition of growth of this pathogenic organism.

Areas of specialization in the section include the chemical and enzymatic syntheses of unique sugar phosphates. Significantly, our laboratory has effected the first preparation of the five phosphorylated isomers of sucrose, trivially designated: trehalulose-6’P, turanose-6’P, maltulose-6’P, leucrose-6’P and palatinose-6’P. These disaccharide phosphates are formed during membrane translocation via the bacterial phosphoenolpyruvate -dependent: sugar phospho-transferase system (PEP-PTS) in a variety of non-oral bacteria, including:- Bacillus subtilis, Fusobacterium mortiferum, Klebsiella pneumoniae and Clostridium acetobutylicum. Prior to their fermentation by the glycolytic pathway, the phosphorylated isomers are hydrolyzed intracellularly by a catalytically unique NAD+ and Mn2+-dependent phospho-glycosyl hydrolase assigned to the Family GH4 of the glycosyl hydrolase (GH) superfamily.

In a multi-national collaboration with researchers in the USA, Canada, England and France, we have determined the crystal structure, active-site residues, and catalytic mechanism of the NAD+ and Mn2+-dependent phospho -a-glucosidase (GlvA) from Bacillus subtilis. GlvA and its homologs cleave the O- glycosyl linkage of disaccharide 6’-phosphates (including, the phosphorylated isomers of sucrose, see Fig.) via a sequence of oxidation-elimination-addition and reduction reactions. From the results of kinetic analyses, kinetic isotope effects (KIE) and Brønsted analyses, we have established that oxidation and deprotonation are the rate-limiting steps in a catalytic mechanism that had been unanticipated in the past six decades of study of glycoside hydrolysis. Sucrose isomers are not fermented by cariogenic mutans streptococci and consequently, these disaccharides are increasingly used as substitutes for dietary sucrose.

Unexpectedly, and contrary to general belief, our recent studies show that certain residents of the oral cavity (for example, Leptotrichia species) readily utilize these ostensibly “non-metabolizable” compounds. As genetic information accumulates in the Human Oral Microbiome Database (HOMD;, it is probable that genomic ‘mining’ will reveal similar cariogenic potential in other oral microorganisms. The inter-species transfer of genetic material is well documented, and one could hypothesize that the industrial scale use of sucrose isomers might encourage the dissemination of these metabolic genes to presently non-pathogenic species in the oral microbiome. It remains to be seen therefore, whether extensive use of sucrose isomers will impact upon the species composition, or ecological distribution of the oral microflora in health and disease. In this context our research program is of particular relevance to oral health and the mission of NIDCR.

Selected Publications

1. Thompson, J. 1989. N5- (L-1-Carboxyethyl)-L-ornithine: NADP+ oxido-reductase from Streptococcus lactis: Purification and partial characterization. J. Biol. Chem. 264:9592-9601. PMID: 2498334

2. Thompson, J., Nguyen, N. Y., Sackett, D. L., and Donkersloot, J. A. 1991. Transposon-encoded sucrose metabolism in Lactococcus lactis subsp. lactis: purification of sucrose 6-phosphate hydrolase and genetic linkage to N5- (L-1-carboxyethyl)-L-ornithine synthase in strain K1. J. Biol. Chem. 266:14573-14579. PMID: 1650362

3. Thompson, J., Pikis, A., Ruvinov, S. B., Henrissat, B., Yamamoto, H., and Sekiguchi, J. 1998. The gene glvA of Bacillus subtilis 168 encodes a metal-requiring, NAD(H)-dependent 6-phospho-α-glucosidase: Assignment to family 4 of the glycosylhydrolase superfamily. J. Biol. Chem. 273:27347-27356. PMID: 9765262

4. Cisar, J. O., Xu, D-Q., Thompson, J., Swaim, W., Hu, L., and Kopecko, D. J. 2000. An alternative interpretation of nanobacteria – induced biomineralization. Proc. Natl. Acad. Sci. USA 97:11511-11515. PMID: 11027350

5. Thompson, J., Robrish, S. A., Immel. S., Lichtenthaler, F. W., Hall, B. G., and Pikis, A. 2001. Metabolism of sucrose and its five linkage-isomeric α-D-glucosyl-D-fructoses by Klebsiella pneumoniae: participation and properties of sucrose-6-phosphate hydrolase and phospho-α-glucosidase. J. Biol. Chem. 276:37415-37425. PMID: 11473129

6. Thompson, J., Lichtenthaler, F. W., Peters, S., and Pikis, A. 2002. β-Glucoside kinase (BglK) from Klebsiella pneumoniae: Purification, properties and preparative synthesis of 6-phospho-β-D-glucosides. J. Biol. Chem. 277:34310-34321. PMID: 12110692

7. Yip, V. L. Y., Varrot, A., Davies, G. J., Rajan, S. S., Yang, X., Thompson, J., Anderson, W. F., and Withers, S. G. 2004. An unusual mechanism of glycoside hydrolysis involving redox and elimination steps by a family 4 β-glycosidase from Thermotoga maritima. J. Am. Chem. Soc. 126:8354-8355. PMID: 15237973

8. Thompson, J., Hess., and Pikis, A. 2004. Genes malh and pagl of Clostridium acetobutylicum ATCC 824 encode NAD+- and Mn2+ -dependent phospho-α-glucosidase(s). J. Biol. Chem. 279: 1553-1561. PMID: 14570887

9. Rajan, S. S., Yang, X., Collart, F., Yip., V. L. Y., Withers, S. G., Varrot, A., Thompson, J., Davies., G. J., and Anderson, W.F. 2004. Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ - dependent phospho-α-glucosidase from Bacillus subtilis. Structure: 12: 1619-1629. PMID: 15341727

10. Pikis, A., Hess, S., Arnold, I., Erni, B., and Thompson, J. 2006. Genetic requirements for growth of Escherichia coli K-12 on methyl-α-D-glucopyranoside and the five α-D-glucosyl-D-fructose isomers of sucrose. J. Biol. Chem. 281:17900-17908. PMID: 16636060

11. Yip, V. L. Y., Thompson, J., and Withers, S. G. 2007. Mechanism of GlvA from Bacillus subtilis: A detailed kinetic analysis of a 6-phospho-α-glucosidase from glycoside hydrolase Family 4. Biochemistry 46: 9840 -9852. PMID: 17676871

12. Zhang, Q., Peng, H., Gao, F., Lui, Y., Cheng, H., Thompson, J., and Gao, G. F. 2009. Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: crystal structures of the substrate-free and quaternary complex enzyme. Protein Sci. 18: 294-303. PMID: 19177572

13. Thompson, J., and Pikis, A. 2012. Metabolism of sugars by genetically diverse species of oral Leptotrichia. Mol. Oral. Microbiol. 27: 34-44. PMID: 22230464
14. Thompson, J., Pikis, A., Rich, J., Hall, B. G., and Withers, S. G. 2013. α-Galacturonidase(s): a new class of Family 4 glycoside hydrolases with strict specificity and a unique CHEV active site motif. FEBS Lett. 587: 799-803. PMID: 23416295

15. Yu, W-L., Jiang, Y-L., Pikis, A., Cheng, W., Bai, X-H., Ren, Y-M., Thompson, J., Zhou, C-Z., and Chen, Y. 2013. Structural insights into the substrate specificity of a 6-phospho-β-glucosidase BglA-2 from Streptococcus pneumoniae TIGR4. J. Biol. Chem. 288: 14949-14958. PMID: 23580646

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This page last updated: February 26, 2014