Mehmet Berkmen
Staff Scientist, Gene Expression Division
Education:
1992
1993
2000
2000-2006
B.S. in Biotechnology, Imperial College of Science and Technology, London
M.S. in Biotechnology, University of Reading, England
Ph.D. in Microbiology, University of Vienna, Austria and University of Houston,
TX
Postdoctoral fellowship in Microbiology and Molecular Genetics, Harvard Medical
School, Boston, MA
Research Interests:
We are interested in understanding the molecular mechanisms that govern oxidative
folding of proteins. Many important proteins require disulfide bonds for their folding and stability,
including antibodies, interferons, proteases and signaling proteins. The formation of the correct
disulfide bonds in a protein requires the coordinated activity of enzymes belonging to the
thioredoxin family. In eukaryotes, disulfide bond formation is compartmentalized to the
endoplasmic reticulum where 30% of all proteins fold; of those, half are predicted to form
disulfide bonds. In prokaryotes, disulfide bond formation occurs in the periplasm. A deep
understanding of the processes involved in disulfide bond formation is critical to the production
of complex disulfide-bonded proteins.
Our research focuses on how disulfide bond formation is catalyzed. In addition, we are
interested in how mis-oxidized proteins are isomerized back to their native correctly folded state.
We investigate these principles in vivo using the model organism E. coli. Specifically, our
research is focused on understanding the mechanisms of forming disulfide bonds within the two
distinct compartments of E. coli, the reducing cytoplasm and the oxidizing periplasm. We hope
to, (i) improve our understanding of the mechanism of oxidative-folding, (ii) identify novel
enzymes which can assist in the oxidative-folding of proteins and (iii) engineer mutant E. coli
strains which can express at high yields multi-disulfide bonded proteins.
Publications:
1.
Ke N., Landgraf D., Paulsson J. and Berkmen M. (2014) Bringing the periplasm to light:
Use of Halo tag in visualizing periplasmic proteins (in progress)
2.
Chatelle C., Kraemer S., Ren G., Chmura C., Marechal N., Boyd D., Roggemans C., Ke
N., Riggs P., Bardwell J. and Berkmen M. (2014) Converting a sulfenic acid reductase
(DsbG) into a disulfide bond isomerase (DsbC), using mutant alkaline phosphatase in
the periplasm of Escherichia coli. (in submission)
3.
M. P Robinson, Ke N., Lobstein J., Szkodny A., Mansell T. J., Tuckey C., Riggs P.,
Colussi P., Noren C., Taron C., DeLisa M. P. and Berkmen M. (2014) Bypassing
membranes: exceptional expression of functional IgGs in the cytoplasm of engineered
Escherichia coli (Under review)
4.
Ke N. and Berkmen M. (2014) Production of disulfide-bonded proteins in Escherichia
coli. Current protocols in molecular biology / edited by Frederick M Ausubel [et al] 2014,
108:16 11B 11-16 11B 21.
5.
Lobstein J., Emrich C., Jeans C., Faulkner M., Riggs P. and Berkmen M. (2012) SHuffle,
a novel Escherichia coli protein expression strain capable of correctly folding disulfide
bonded proteins in its cytoplasm. Microbial Cell Factories. 11(56):
6.
Berkmen M., (2012) Oxidative folding of proteins in Escherichia coli. BioProcess
International. 25(5): 48-54
7.
Samuelson C. J., Causey B. T. and Berkmen M. (2012) Disulfide-bonded protein
production in E. coli. Genetic Engineering & Biotechnology News. Vol. 32, No. 3, page
35.
8.
Berkmen M., (2012) Production of disulfide-bonded proteins in Escherichia coli. Protein
Expr Purif. Vol 82, No 1: 240–251
9.
Hemmis, C., Berkmen, M., Eser, M., and Schildbach, J. (2011) TrbB from conjugative
plasmid F is a unique disulfide isomerase that requires DsbD for redox state
maintenance, Submitted.
10.
Shouldice, S., Cho, S.H., Boyd, D., Heras, B., Eser, M., Beckwith, J., Riggs, P., Martin,
J., Berkmen, M. (2010) In vivo oxidative protein folding can be facilitated by oxidation–
reduction cycling. Mol. Micro. 75: 13–28.
11.
Dutton, R., Boyd, D., Berkmen, M. and Beckwith, J. (2008) Diversity in disulfide bond
formation capacity and mechanism across bacterial species. PNAS 105(33): 11933–
11938.
12.
Berkmen, M. and Beckwith, J. (2006) Disulfide bond formation in the E. coli periplasm.
(A chapter in the book “The Periplasm”, Michael Ehrmann (ed.), ASM Press.)
13.
Berkmen, M., Boyd, D. and Beckwith, J. (2004) The non-consecutive disulfide bond of
Escherichia coli phytase (appA) renders it dependent on the protein disulfide isomerase,
DsbC. J. Biol. Chem. 2005 280(12):11387-11394.
14.
Schierle, C., Berkmen, M., Huber, D., Kumamoto, C. and Beckwith, J. (2003) The DsbA
signal sequence directs efficient, cotranslational export of passenger proteins to the
Escherichia coli periplasm via the signal recognition particle pathway. J. Bacteriol. 185:
5706-5713.
15.
Berkmen, M. and Benedik, M.J. (2002) Multi-copy repression of Serratia marcescens
nuclease expression by dinI. Curr. Microbiol. 44: 44-8
16.
Barlow, T., Berkmen, M., Georgellis, D., Bayr, L., Arvidson, S. and von Gabain, A.
(1998) RNase E, the major player in mRNA degradation is down-regulated in
Escherichia coli during a transient growth retardation (diauxic lag). Biol. Chem. 379: 3338.
17.
Berkmen, M., Benedik, M.J., and Bläsi, U. (1997) The Serratia marcescens NucE
Protein Functions as a Holin in Escherichia coli. J. Bacteriol. 179: 6522-6524.