Robert Blumenthal, Ph.D.
笔谤辞蹿别蝉蝉辞谤听
Office: HEB 229A
Phone: (419) 383-5422
Fax: (419) 383-3002
E-mail Address: robert.blumenthal@utoledo.edu
Five Nucleic Acids Research (NAR) cover articles by Drs. Bob Blumenthal and Xiaodong Cheng
Distinguished University Professor,听2012
Outstanding听Researcher Award,听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: 听Bioinformatics, Proteomics and Genomics Program听听
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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?
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 ().
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 鈥淎doMet鈥� or 鈥淪AM鈥�). 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) -
NIH (NIAID) -
Representative publications:
Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases.Curr Opin Struct Biol. 2022 Jul 29;75:102433. doi: 10.1016/j.sbi.2022.102433. Online ahead of print.PMID:听35914495听Review.
Enzymatic Characterization of In Vitro Activity of RNA Methyltransferase PCIF1 on DNA. Biochemistry. 2022 May 23;61(11):1005-13. doi: 10.1021/acs.biochem.2c00134. Online ahead of print.PMID:听35605980听Free PMC article.
Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140. DNA Repair (Amst). 2022 Feb 26;113:103306. doi: 10.1016/j.dnarep.2022.103306. Online ahead of print.PMID:听35255310听Free article.
Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs.听J Biol Chem. 2022 Apr;298(4):101751. doi: 10.1016/j.jbc.2022.101751. Epub 2022 Feb 19.PMID:听35189146听Free PMC article.
. Repurposing epigenetic inhibitors to target the听Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA.听Epigenetics. 2021 Sep 15:1-12. doi: 10.1080/15592294.2021.1976910. Online ahead of print.PMID:听34523387
Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat Commun. 2021 Jun 8;12(1):3436. doi: 10.1038/s41467-021-23693-w.PMID:听34103525听Free PMC article.
Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions. Nucleic Acids Res. 2021 Nov 18;49(20):11629-11642. doi: 10.1093/nar/gkab460.PMID:听34086966听Free PMC article.
Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res. 2021 May 21;49(9):5084-5094. doi: 10.1093/nar/gkab276.PMID:听33877329听Free PMC article.
Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima.听J Biol Chem. 2021 Jan-Jun;296:100270. doi: 10.1016/j.jbc.2021.100270. Epub 2021 Jan 9.PMID:听33428944听Free PMC article.
听Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla.听Microbiology (Reading).听2020 Oct 21;.听doi: 10.1099/mic.0.000980.听[Epub ahead of print]听PubMed PMID: 33085588.听
.听A Role for N6-Methyladenine in DNA Damage Repair.听Trends Biochem Sci.听2020 Oct 16;.听doi: 10.1016/j.tibs.2020.09.007.听[Epub ahead of print]听Review.听PubMed PMID: 33077363.听
听Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.听Nucleic Acids Res.听2020 Oct 9;48(18):10329-10341.听doi: 10.1093/nar/gkaa604.听PubMed PMID: 32663306; PubMed Central PMCID: PMC7544203.听
Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences.听Nucleic Acids Res.听2020 Oct 9;48(18):10034-10044.听doi: 10.1093/nar/gkaa446.听PubMed PMID: 32453412; PubMed Central PMCID: PMC7544214.听
.听Detection of DNA Modifications by Sequence-Specific Transcription Factors.听J Mol Biol.听2019 Oct 15;.听doi: 10.1016/j.jmb.2019.09.013.听[Epub ahead of print]听Review.听PubMed PMID: 31626807; PubMed Central PMCID: PMC7156337.听
听Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.听Nucleic Acids Res.听2019 Sep 19;47(16):8375-8387.听doi: 10.1093/nar/gkz381.听PubMed PMID: 31081034; PubMed Central PMCID: PMC6895265.听
.听Structural basis for effects of CpA modifications on C/EBP尾 binding of DNA.听Nucleic Acids Res.听2019 Feb 28;47(4):1774-1785.听doi: 10.1093/nar/gky1264.听PubMed PMID: 30566668; PubMed Central PMCID: PMC6393304.听
听Detecting and interpreting DNA methylation marks.听Curr Opin Struct Biol.听2018 Dec;53:88-99.听doi: 10.1016/j.sbi.2018.06.004.听Epub 2018 Jul 19.听Review.听PubMed PMID: 30031306; PubMed Central PMCID: PMC6322410.听
听Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites.听Nucleic Acids Res.听2018 May 4;46(8):3864-3877.听doi: 10.1093/nar/gkx1274.听PubMed PMID: 29294058; PubMed Central PMCID: PMC5934627.听
Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence.听J Biol Chem.听2017 Sep 29;292(39):15994-16002.听doi: 10.1074/jbc.M117.805754.听Epub 2017 Aug 11.听PubMed PMID: 28801461; PubMed Central PMCID: PMC5625032.
. Complementation of a metK-deficient E. coli strain with heterologous AdoMet synthetase genes. Microbiology. 2017 Nov 7. doi: 10.1099/mic.0.000565.
听 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.
. Evolution of a global regulator: Lrp in four orders of 纬-Proteobacteria. BMC听 evolutionary biology. 2016; 16(1):111. PubMed [journal] PMID: 27206730, PMCID: PMC4875751.
. 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.
. 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.
. Structural basis for Klf4 recognition of methylated DNA. Nucleic acids research. 2014; 42(8):4859-67. PubMed [journal] PMID: 24520114, PMCID: PMC4005678.
. Producing proficient methyl donors from alternative substrates of S-adenosylmethionine synthetase. Biochemistry. 2014; 53(9):1521-6. PubMed [journal] PMID: 24528526, PMCID: PMC3985469.
. 2013. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res. 41: 6045-6057. PMC3695507. []
. 2013. Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. BMC Evol. Biol. 13: 218 (11pp).听
. 2013. A common mode of recognition for methylated CpG. Trends Biochem Sci 38: 177-183.
. 2013. Emergence, origin, and function of neutrophil-dendritic cell hybrids in experimentally induced inflammatory lesions in mice. Blood 121: 1690-1700.
., and Mukundan, D. 2011. Higher incidence of perineal community acquired MRSA infections
among toddlers. BMC Pediatrics,听11:96 听http://www.biomedcentral.com/1471-2431/11/96.
.听2011. Recognition of DNA by the Helix-Turn-Helix global regulatory protein Lrp is modulated by the amino terminus. J. Bacteriol.;193:3794-3803.
听 2010. Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.听 BMC Molecular Biology, 11:87.
听 2010.听Coordinated chromatin control:听structural and functional linkage of DNA and
histone methylation. Biochem. 49:2999-3008.
听 2009听 Tuning the relative affinities for activating and repressing operators of
a temporally regulated restriction-modification system.听 Nucleic Acids Research,听37(3):983-98.听听听
听 2008听 Limited functional conservation of a global regulator among related bacterial
genera: Lrp in Escherichia, Proteus and Vibrio.听 BMC Microbiology 2008, 8:60.听听听 听听听
听 2008听 Mammalian DNA methyltransferases: A structural perspective.听 Structure 16(3), 331-496.
(2008)听 Real-time kinetics of restriction-modification gene expression after entry
into a new host cell.听 Nucleic Acids Res. 36:2581-2593.听听
2007听Regulatory circuit based on autogenous activation-repression: roles of C-boxes
and spacer sequences in control of the PvuII restriction-modification system.听 Nucleic Acids Res.听听35:6935-6952.
听 2007 Integration of regulatory signals through involvement of multiple global regulators:
control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR.听 BMC Microbiol. 7:1471-2180.听
2005 Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved
among restriction-modification systems. J. Bacteriol. 87:488-497.
2003 Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 28:329-335.
听2003 A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31:1805-1812.
2002 Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:13471-13476.
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.
2002 Mobility of a restriction-modification system revealed by its genetic contexts in three hosts. J. Bacteriol., 184:2411-2419.
2002 Cytosines do it, thymines do it, even pseudouridines do it 脨 base flipping by an enzyme that acts on RNA. Structure, 10:127-129.
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.
2001 Activation from a distance: roles of Lrp and integration host factor in transcriptional
activation of gltBDF. J. Bacteriol. 183:3910-3918.
2001 A Taq attack displaces bases. Nature Struct. Biol. 8:101-103.
2000 Recognition of native DNA methylation by the PvuII restriction endonuclease. Nucleic Acids Res. 28:3143-3150.
听 2000 Role and Mechanism of Action of C.PvuII, a Regulatory Protein Conserved among
Restriction-Modification Systems. J. Bact. 182:477-487.
1999 Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG
sites. Nucleic Acids Res. 27:1032-1038.
听听听听听听听听
1999)Mapping regulatory networks in microbial cells. Trends Microbiol. 7:320-328.
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.
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.
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.
1997 Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25:2702-2715.
1997 A genetic and functional analysis of the unusually large variable region in
the M鈥�.AAluI DNA-(cytosine C5)-methyltransferase. Mol. Gen. Genet. 257:14-22.
1997 Expression, purification, mass spectrometry, crystallization and multiwavelength
anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
European J. Biochem. 247:1009-1018.
(1996) Experimental analysis of global gene regulation in Escherichia coli [review].
Progress in Nucl. Acid Res. & Molec. Bio. 55:1-86.
(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.
(1996) Finding a basis for flipping bases. Structure 4:639-645.
Host-mediated modification of PvuII restriction in mycobacterium tuberculosis. J. Bacteriology 178:78-84.
(1995) Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association. Gene 157:193-199.
1995 Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that
carries the genes of the PvuII restriction-modification system. Gene 157:78-79.
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.
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.
听 1993 Assignment of enzymatic function to specific protein regions of cobalamin-dependent
methionine synthase from Escherichia coli. Biochemistry 32:9290-9295.
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.
1993 The M. AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region. Nucl. Acids Res. 21:905-911.
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.,听Blumenthal, R.M.,听ed.听Modification of Nuclear DNA and its Regulatory Proteins. Volume 101, Pages 1-488
(2011). ISBN: 978-0-12-387685-0.听听听听听听听听 听
Cheng, X., Blumenthal, R.M., ed. S-adenosylmethionine-dependent methyltransferases: Structures and functions. River Edge (NJ): World Scientific; 1999.听听听 (听).
Book Chapters
Schubert, H.L., Blumenthal, R.M., and Cheng, X. 2005听 Protein methyltransferases: their distribution among the five
structural classes of AdoMet-dependent methyltransferases.听 In: The Enzymes, vol.
24, Protein Methylation (Clarke, S.G., and F. Tamanoi, eds.).听 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.听 In: Restriction Endonucleases (A.
Pingoud, ed.).听 Berlin: Springer-Verlag, 14:361-392.
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听
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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