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Professor |
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?
See website for: Bioinformatics, Proteomics and Genomics Program
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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? These studies are funded by an NIH grant to Dr. Blumenthal, with subcontracts to laboratories at Minnesota (http://www.cbs.umn.edu/BMBB/faculty/Khodursky.A.B.shtml and http://www.micab.umn.edu/faculty/Kapur.html) and Stanford (http://schoolniklab.stanford.edu/).
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.
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?
Current grant funding:
NIH (NIAID) - Conservation and Adaptation of a Regulon Across Genera
NSF (MCB) - Genetic Switch Controlled by an Unusual Family of Transcription Activators
Representative publications:
Mruk, Iwona and Blumenthal, R.M. (2009) Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. Nucleic Acids Research, 37(3):983-98.
Lintner, R.E., Mishra, P.K., Srivastava, P., Martinez-Vaz, B.M., Khodursky, A.B., and Blumenthal, R.B. (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. S-adenosylmethionine-dependent methyltransferases: Structures and functions. River Edge (NJ): World Scientific; 1999.
(http://books.google.com/books?id=oUCKHnsZuukC ).
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.
