Medical Microbiology and Immunology




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Medical Microbiology and Immunology
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Robert Blumenthal, Ph.D.

Director, Program in Bioinformatics & Proteomics/Genomics

Office: HEB 243
Phone: (419) 383-5422
Fax: (419) 383-3002
E-mail Address:

Article by Xiaodong Cheng and R.M. Blumenthal is in the top 10 most accessed articles of 2010 for the journal Biochemistry:  
 Read the UT NEWS review April 22, 2011
"Coordinated Chromatin Control: Structural and Functional Linkage of DNA and Histone Methylation”  

Distinguished University Professor, 2012
Recipient of NIH Grant (Co-PI), 2011

Outstanding Researcher Award, 2010

How bacteria control the expression and distribution of their genes

  • How do regulatory networks evolve to serve the needs of their diverse hosts?
  • To what extent do conserved regulators play the same roles in different species?
  • How do activators stimulate RNA polymerase at promoters?
  • How are restriction systems controlled to prevent cell suicide?
  • How do restriction systems affect the gene flow between bacteria?
  • What are the best strategies for selectively interfering with bacterial quorum sensing?

See website for:  Bioinformatics, Proteomics and Genomics Program  

Dr. Blumenthal grew up in microbiology labs - his father, Dr. Harold J. Blumenthal (1926-2003), studied the metabolism of Gram-positive bacteria and was chair of the microbiology department at Loyola University (Chicago) for many years. The younger Dr. Blumenthal majored in microbiology at Indiana University (A.B. 1972), and earned his M.S. (1975) and Ph.D. (1977) in microbiology at the University of Michigan in the lab of Dr. Fred Neidhardt. His thesis focused on a proteomic analysis of transcription termination factor effects in the bacterium Escherichia coli. This was followed by postdoctoral work with Dr. Pat Dennis at the University of British Columbia (regulation of RNA polymerase synthesis), Dr. Lorne Babiuk at the University of Saskatchewan (gene regulation in rotavirus), and Nobel laureate Dr. Rich Roberts at the Cold Spring Harbor Laboratory (adenoviral RNA splicing, regulation of restriction-modification systems, bioinformatics). He has also spent two sabbatical leaves at the University of Michigan with Dr. Rowena Matthews (catalysis of methyltransfer, DNA-protein interactions).

Dr. Blumenthal's lab focuses on two areas critical to understanding the development of bacterial pathogenicity and antibiotic resistance - the mechanics and logic of gene regulation in bacteria, and the flow of genes between bacteria. These problems are related to one another: conserved regulatory mechanisms can improve a gene's mobility if the gene is properly regulated in new host cells, while the extent of gene flow between bacteria depends on the relative levels of expression of restriction endonucleases, modification methyltransferases, and recombination enzymes in the recipient cells. Many of these questions are designed to refine bioinformatic analyses of microbial genome sequences by testing some of the underlying assumptions.

Architecture of the Lrp regulon in various bacteria. The Leucine-responsive Regulatory Protein (Lrp) directly controls over 70 genes and operons in Escherichia coli (and indirectly controls several hundred more), and among the directly-controlled genes are many associated with virulence. Lrp is highly conserved among bacteria ranging from E. coli and Salmonella typhi through Vibrio cholerae and even, to a lesser extent, Haemophilus influenzae. Do the regulatory networks (regulons) controlled by Lrp have the same basic structure in all of these different bacteria? If not, how has the regulon structure changed? What are the implications of any changes found on bioinformatic predictions of gene regulation from genome sequences?

Control of restriction-modification systems by an unusual transcriptional activator. In our studies of the PvuII restriction-modification system, isolated from the Gram-negative urinary tract pathogen Proteus vulgaris, we discovered that the restriction endonuclease gene is controlled by an activator. This activator is found in a variety of other restriction-modification systems, including some from Gram-positive organisms such as Bacillus; surprisingly, the activators from Proteus and Bacillus work in both genera. Even more surprising is the fact that these activators have only about 9.5 kDa subunit masses. How does this new type of activator work? These studies are funded by an NSF grant to Dr. Blumenthal, and include collaboration with a mathematical modelling laboratory (Dr. Michael Savageau, UC-Davis).

Effects of Restriction-modification systems on gene flow
. Restriction-modification systems reduce the average size of chromosomally-integrated fragments following DNA transfer between two bacteria. It has been suggested that this size reduction increases the spread of beneficial mutations by physically separating them from linked deleterious sequences. This contrasts with the general assumption that restriction-modification systems reduce gene flow by cutting up incoming DNA. Which of these models is correct?

Preventing bacterial disease without killing the bacteria. This research area combines interest in the spread of antibiotic resistance with interest in methyltransferases (which use the methyl donor S-adenosyl-L-methionine, also known as “AdoMet” or “SAM”). Dr. Blumenthal is co-PI on an NIH grant project led by Dr. Ronald Viola (UT, Chemistry) to develop chemical agents that interfere with bacterial quorum sensing. By not directly killing the bacteria, these agents should generate weaker selective pressure for development of resistance, yet they should help protect patients by reducing bacterial production of certain virulence factors.

Prior grant funding:

NSF (MCB) - Regulation of Type II Restriction-Modification Systems
NIH (NIAID) - Selective Agents to Block Virulence in Gram Negative Pathogens

Representative publications:

NCBI My Bibliography

Samuel Hong, Dongxue Wang, John R. Horton, Xing Zhang, Samuel H. Speck, Robert M. Blumenthal, Xiaodong Cheng. Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucl Acids Research. 2017. gkx057. doi: 10.1093/nar/gkx057.

Unoarumhi Y, Blumenthal RM, Matson JS. Evolution of a global regulator: Lrp in four orders of γ-Proteobacteria. BMC  evolutionary biology. 2016; 16(1):111. PubMed [journal] PMID: 27206730, PMCID: PMC4875751.

Horton JR, Zhang X, Blumenthal RM, Cheng X. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic acids research. 2015; 43(8):4296-308. PubMed [journal] PMID: 25845600, PMCID: PMC4417163.

Zhao M, Wijayasinghe YS, Bhansali P, Viola RE, Blumenthal RM. A surprising range of modified-methionyl S-adenosylmethionine analogues support bacterial growth. Microbiology (Reading, England). 2015; 161(Pt 3):674-82. PubMed [journal] PMID: 25717169, PMCID: PMC4339656.

Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X. Structural basis for Klf4 recognition of methylated DNA. Nucleic acids research. 2014; 42(8):4859-67. PubMed [journal] PMID: 24520114, PMCID: PMC4005678.

Wijayasinghe YS, Blumenthal RM, Viola RE. Producing proficient methyl donors from alternative substrates of S-adenosylmethionine synthetase. Biochemistry. 2014; 53(9):1521-6. PubMed [journal] PMID: 24528526, PMCID: PMC3985469.

Williams K, Savageau MA, Blumenthal RM. 2013. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res. 41: 6045-6057. PMC3695507. [Featured article]

Liang J, Blumenthal RM. 2013. Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. BMC Evol. Biol. 13: 218 (11pp). 

Liu, Y., Zhang, X., Blumenthal, R.M., and Cheng, X. 2013. A common mode of recognition for methylated CpG. Trends Biochem Sci 38: 177-183.

Geng, S., Matsushima, H., Okamoto, T., Yao, Y. Lu, R., Page, K., Blumenthal, R.M., Ward, N.L., Miyazaki, T., and Takashima, A. 2013. Emergence, origin, and function of neutrophil-dendritic cell hybrids in experimentally induced inflammatory lesions in mice. Blood 121: 1690-1700.

McCullough, A.C., Seifried, M., Zhao, X., Haase, J., Kabat, W.J., Yogev, R., Blumenthal, R.M., and Mukundan, D. 2011. Higher incidence of perineal community acquired MRSA infections among toddlers. BMC Pediatrics11:96

Hart, B.R., Mishra, P.K., Lintner, R.E., Hinerman, J.M., Herr, A.B., and Blumenthal, R.M. 2011. Recognition of DNA by the Helix-Turn-Helix global regulatory protein Lrp is modulated by the amino terminus. J. Bacteriol.;193:3794-3803.

Kaw, M.K. and Blumenthal, R.M.  2010. Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.  BMC Molecular Biology, 11:87.

Cheng, X. and Blumenthal, R.M.  2010. Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochem. 49:2999-3008.

Mruk, I. and Blumenthal, R.M.  2009  Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.  Nucleic Acids Research37(3):983-98.   

Lintner, R.E., Mishra, P.K., Srivastava, P., Martinez-Vaz, B.M., Khodursky, A.B., and Blumenthal, R.M.  2008  Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio.  BMC Microbiology 2008, 8:60.       

Cheng, Xiaodong and Blumenthal, R.M.  2008  Mammalian DNA methyltransferases: A structural perspective.  Structure 16(3), 331-496.

Mruk, Iwona, Blumenthal, R.M. (2008)  Real-time kinetics of restriction-modification gene expression after entry into a new host cell.  Nucleic Acids Res. 36:2581-2593.  

Mruk, Iwona, Preeti, Rajesh, Blumenthal, R.M. 2007 Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system.  Nucleic Acids Res.  35:6935-6952.

Paul, L., Mishra, P.K., Blumenthal, R.M., and Matthews, R.G.  2007 Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR.  BMC Microbiol. 7:1471-2180. 

Knowle, D., Lintner, R.E., Touma, Y.M., Blumenthal, R.M. 2005 Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems. J. Bacteriol. 87:488-497.

Schubert, H.L., Blumenthal, R.M., and Cheng, X. 2003 Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 28:329-335.

Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., et al. (47 authors total). 2003 A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31:1805-1812.

Tani, T.H., Khodursky, A., Blumenthal, R.M., Brown, P.O., and Matthews, R.G. 2002 Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:13471-13476.

Bujnicki, J.M., Feder, M., Radlinska, M., Blumenthal, R.M. 2002 Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m6A methyltransferase. J. Molec. Evol. 55:431-444.

Naderer, M., Brust, J.R., Knowle, D., Blumenthal, R.M. 2002 Mobility of a restriction-modification system revealed by its genetic contexts in three hosts. J. Bacteriol., 184:2411-2419.

Cheng, X., Blumenthal, R.M. 2002 Cytosines do it, thymines do it, even pseudouridines do it Ð base flipping by an enzyme that acts on RNA. Structure, 10:127-129.

Bujnicki, J.M., Blumenthal, R.M. and Rychlewski, L. 2002 Sequence analysis and structure prediction of 23S rRNA: m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. J. Mol. Microbiol. Biotechnol. 4:93-99.

Paul, L., Blumenthal, R.M. and Matthews, R.G. 2001 Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF. J. Bacteriol. 183:3910-3918.

Blumenthal, R.M. and Cheng, X. 2001 A Taq attack displaces bases. Nature Struct. Biol. 8:101-103.

Rice, M.R., and Blumenthal, R.M. 2000 Recognition of native DNA methylation by the PvuII restriction endonuclease. Nucleic Acids Res. 28:3143-3150.

Vijesurier, R.M., Carlock, L., Blumenthal, R.M. and Dunbar, J.C.  2000 Role and Mechanism of Action of C.PvuII, a Regulatory Protein Conserved among Restriction-Modification Systems. J. Bact. 182:477-487.

Rice, M.R., Koons, M.D. and Blumenthal, R.M. 1999 Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG sites. Nucleic Acids Res. 27:1032-1038.
VanBogelen, R.A., Greis, K.D., Blumenthal, R.M., Tani, T.M. and Matthews, R.G. 1999)Mapping regulatory networks in microbial cells. Trends Microbiol. 7:320-328.

Bhagwat, S.P., Rice, M.R., Matthews, R.G., and Blumenthal, R.M. 1997 Use of an inducible regulatory protein to identify members of a regulon: application to the regulon controlled by the leucine-responsive regulatory protein (Lrp) in Escherichia coli. J. of Bacteriology 179:6254-6263.

Wiese II, D.E., Ernsting, B.R., Blumenthal, R.M. and Matthews, R.G. 1997 A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli. J. Molec. Biol. 270:152-168.

Adams, G.M. and Blumenthal, R.M. 1997 The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine. Biochemistry 36:8284-8292.

Gong, W., O'Gara, M., Blumenthal, R.M. and Cheng, X. 1997 Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25:2702-2715.

Master, S.S. and Blumenthal, R.M. 1997 A genetic and functional analysis of the unusually large variable region in the M•.AAluI DNA-(cytosine C5)-methyltransferase. Mol. Gen. Genet. 257:14-22.

O'Gara, M., Adams, G.M., Gong, W., Kobayashi, R., Blumenthal, R.M., Cheng, X. 1997 Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). European J. Biochem. 247:1009-1018.

Blumenthal, R.M., Borst, D.W., Matthews, R.G. (1996) Experimental analysis of global gene regulation in Escherichia coli [review]. Progress in Nucl. Acid Res. & Molec. Bio. 55:1-86.

Borst, D.W., Blumenthal, R.M., Matthews, R.G. (1996) Use of an in vivo titration method to study a global regulator: effect of varying Lrp levels on expression of gltBDF in Escherichia coli. J. Bacteriology 178:6904-6912.

Cheng, X. and Blumenthal, R.M. (1996) Finding a basis for flipping bases. Structure 4:639-645.

van Soolingen, D., de Haas, P.E., Blumenthal, R.M., Kremer, K., Sluijter, M., Pijnenburg, J.E., Schouls, L.M., Thole, J.E., Dessens-Kroon, M.W., van Embden, J.D., and Hermans, P.W. (1996) Host-mediated modification of PvuII restriction in mycobacterium tuberculosis. J. Bacteriology 178:78-84.

Adams, G.M. and Blumenthal, R.M.
(1995) Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association. Gene 157:193-199.

Koons, C.,and Blumenthal, R.M. 1995 Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system. Gene 157:78-79.

Ferrario, M., Ernsting, B.R., Borst, D.W., Wiese, D.E. II, Blumenthal, R.M., Matthews, R.G. 1995 The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF. J. Bacteriology 177:103-113.

Malone, T., Blumenthal, R.M. and Cheng, X. 1995 Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Molec. Biol. 253:618-632.

Drummond, J.T., Huang, S., Blumenthal, R.M., and Matthews, R.G.  1993 Assignment of enzymatic function to specific protein regions of cobalamin-dependent methionine synthase from Escherichia coli. Biochemistry 32:9290-9295.

Ernsting, B.R., Denninger, J.W., Blumenthal, R.M., and Matthews, R.G. 1993 Regulation of the gitBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein? J. Bacteriology 175:7160-7169.

Zhang, B., Tao, T., Wilson, G.G., Blumenthal, R.M. 1993 The M. AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region. Nucl. Acids Res. 21:905-911.

Guan, L., Blumenthal, R.M., and Burnham, J.C. 1992 Analysis of macromolecular biosynthesis to define the quinolone-induced postantibiotic effect in Escherichia coli. Antimicrobial Agents & Chemotherapy 36:2118-2124.

Edited Books

Cheng, X., Blumenthal, R.M., ed. Modification of Nuclear DNA and its Regulatory Proteins. Volume 101, Pages 1-488 (2011). ISBN: 978-0-12-387685-0.

Cheng, X., Blumenthal, R.M., ed. S-adenosylmethionine-dependent methyltransferases: Structures and functions. River Edge (NJ): World Scientific; 1999.    ( ).

Book Chapters

Schubert, H.L., Blumenthal, R.M., and Cheng, X. 2005  Protein methyltransferases: their distribution among the five structural classes of AdoMet-dependent methyltransferases.  In: The Enzymes, vol. 24, Protein Methylation (Clarke, S.G., and F. Tamanoi, eds.).  Amsterdam: Elsevier, 24:3-28. 570 pp.

Horton, J.R. Blumenthal, R.M., and Cheng, X. 2004 Restriction endonucleases: structure of the conserved catalytic core and the role of metal ions in DNA cleavage.  In: Restriction Endonucleases (A. Pingoud, ed.).  Berlin: Springer-Verlag, 14:361-392.

Blumenthal, R.M.and Cheng, X. 2002 Restriction-modification systems. In: Modern Microbial Genetics, 2nd edition (Yasbin R.E. and Streips U.N., eds.). New York: Wiley. ISBN 0-471-38665-0  657pp

Fauman, E.B., Blumenthal, R.M., and Cheng, X. Structure and evolution of AdoMet-dependent methyltransferases. In: Cheng, X., Blumenthal, R.M., ed. S-adenosylmethionine-dependent methyltransferases: Structures and functions. River Edge (NJ): World Scientific, 1999. p. 1-38.


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Last Updated: 2/7/17