Hi. My name is Melanie Barker Berkmen.
I am a post-doc in Alan Grossman's lab at MIT. I am starting my own lab in the fall.
How to contact me:
MIT Department of Biology
31 Ames St, Building 68, Room 540D
Cambridge, MA 02139
(2002-present) Jane Coffin Childs Post-Doctoral Fellow
Massachusetts Insitute of Technology, Cambridge, MA
Laboratory of Alan D. Grossman
(2001) Ph.D., Cellular and Molecular Biology
University of Wisconsin-Madison, Madision, WI
Laboratory of Richard L. Gourse
(1995) B.S., Biochemistry
University of Dayton, Dayton, OH, summa cum laude
My husband, Mehmet Berkmen, is also a microbiologist. He was a post-doc in Jon Beckwith's lab at Harvard Medical School.
Now he is at the biotech company New England Biolabs, where he is developing Escherichia coli strains and plasmids for recombinant protein production.
Here are some of the things that I am doing when I am not in the scope room, cooking, learning Turkish, or playing with my son Kaan (born December 21, 2006).
Teaching and supervisory experience
(Fall 2005) Co-instructor for an undergraduate seminar class at MIT
I co-taught a literature-based class on DNA dynamics in the tiny bacterial cell with Lyle Simmons. Each week we discussed two papers exploring bacterial DNA replication, chromosome and plasmid partitioning, conjugation, or cell shape. http://web.mit.edu/biology/www/undergrad/adv-ugsem.html
(2004-2005)Co-chair of the organizing committee for the 2005 Boston Bacterial Meeting
(2003-present) Active Participant in the Howard Hughes Medical Institutes Extended Education Group
http://www.cfkeep.org/html/snapshot.php?id=29045795 led by Graham Walker at MIT
(2005-present) Question consultant for the 2005 National Biology Olympiad
for high school students in collaboration with the Center for Excellence in Education in McLean, VA http://www.cee.org/usabo/index.shtml
(Each Spring 2004-present) Volunteer assistant/instructor for the "Science Field Trip to MIT"
that involved ~90 students from four Boston area high schools and their teachers. In 2004, I helped run a lab exercise based on microscopic observation of zebrafish embryos. In 2005 and 2006, Jenny Auchtung and I designed and ran a lab exercise based on bacterial responses to starvation and stress. We had the high school students act as CSI agents and discover whether the "mysterious white powder" found in an envelope was Bacillus spores or harmless. http://www.cfkeep.org/html/snapshot.php?id=84010578
I am interested in two broad questions in biology:
1. How do proteins come together to form a functional molecular machine, capable of complex tasks such as RNA synthesis or DNA transport?
2. How are the proteins that make up a complex molecular machine targeted to the correct location in the cell in order for them to function properly.
My interest in understanding how molecular machines function began with my graduate work on Escherichia coli RNA polymerase (RNAP). Employing biochemical, biophysical, and molecular genetic methods, I investigated the mechanistic details by which the small molecule guanosine tetraphosphate (ppGpp) acts as both a positive and negative regulator of transcription initiation in E. coli. I found that ppGpp shortens the half-lives of RNAP-promoter complexes formed on all promoters, even those promoters unaffected by ppGpp in vivo. The kinetic properties of a particular promoter determined whether or not the effect of ppGpp on half-life results in inhibition. Furthermore, I found that ppGpp stimulated amino acid promoter activity in vivo, but not in purified transcription assays. These and other data led me to propose that direct inhibition of the highly transcribed rRNA genes by ppGpp results in a dramatic increase in the free RNAP concentration, which leads to an increase in initiation from amino acid biosynthesis promoters that are rate-limited for binding RNAP. My results demonstrated that dissecting the details of the interactions between molecules (in this case, RNAP, promoter DNA, and ppGpp) could provide keys to understanding complex physiological phenomena.
For my postdoctoral work, I turned to the broad question of how molecular machines are localized to their correct subcellular addresses in bacteria. My work initially focused on how the replication machinery and the origin of replication are positioned in B. subtilis and whether the location of one influences the position of the other. I found that the replication machinery co-localizes with the origin immediately after initiation, indicating that replication initiates near midcell. Several lines of evidence indicated that the location of the origin at the time of initiation establishes the position of the replication machinery. I also discovered that origin positioning is independent of origin sequences and the site of replication initiation. My results provide new insights into how the replication machinery is dynamically positioned in the cell and refine our current understanding of the spatial and temporal events of the B. subtilis replication cycle.
My current research focus also uses B. subtilis as a model system but has shifted to exploring the function and subcellular localization of a different complex molecular machine, the Gram-positive mating pore. I have been characterizing YddE, a protein that is essential for mating of the B. subtilis conjugal element ICEBs1. yddE is encoded on ICEBs1 and is related to genes on conjugal elements in numerous bacteria, including the Gram-positive pathogens Staphylococcus aureus, Clostridium difficile, and L. monocytogenes. Containing Walker A and B box ATPase motifs, YddE belongs to a large superfamily of ATP-dependent pumps involved in the extrusion of proteins and DNA through membrane pores. Given the precedent of Gram-negative conjugation systems and given YddE’s localization, ATPase domain, and essentiality in conjugation, I propose that YddE and its homologs are the essential membrane-associated ATPase component of the Gram-positive mating pore apparatus. I plan on analyzing the role of YddE in conjugation, exploring its functional domains, investigating its subcellular localization, and identifying any YddE-interacting proteins.
Wang JD, Berkmen MB, Grossman AD. Genome-wide co-orientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis, PNAS, in press.
Berkmen MB and Grossman AD. (2007) Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA. Mol Microbiol, 63(1): 150-165.
Berkmen MB, Grossman AD. (2006) Spatial and temporal organization of the Bacillus subtilis replication cycle. Mol. Microbiol, 62(1): 57-71.
Haugen SP, Berkmen MB, Ross W, Gaal T, Ward C, Gourse RL. (2006) rRNA promoter regulation by nonoptimal binding of σ region 1.2: An additional recognition element for RNA polymerase. Cell, 125(6): 1069-1082.
Paul BJ, Berkmen MB, Gourse RL (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. PNAS, 102(22):7823-8.
Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL (2004) DksA: A critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell, 118(3): 311-322.
Wang JD, Rokop ME, Barker MM, Hanson NR, Grossman AD (2004) Multi-copy plasmids affect replisome positioning in Bacillus subtilis. J Bact, 186(21):7084-90.
Barker MM, Gourse RL (2002) Control of stable RNA synthesis. In Translation Mechanisms. (Lapointe J, Brakier-Gingras L. ed.). Landes Biosciences, Austin, TX.
Barker MM, Gourse RL (2001) Regulation of rRNA transcription correlates with nucleoside triphosphate sensing. J Bact, 183, 6315-6323.
Barker MM, Gaal T, Josaitis CA, Gourse RL. (2001) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 305(4): 673-688.
Barker MM, Gaal T, Gourse RL (2001) Mechanism of regulation of transcription initiation by ppGpp II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol 305(4): 689-702.
Gourse RL, Gaal T, Aiyar SE, Barker MM, Estrem ST, Hirvonen CA, Ross W. (1998) Strength and regulation without transcription factors: Lessons from bacterial rRNA promoters. Cold Spring Harb Sym 63: 131-139.
Singer SS, Henkels K, Deucher A, Barker MM, Singer J, Trulzsch T. (1996) Growth hormone and aging change rat liver fatty acid binding protein levels. J Amer Coll Nutr 15: 169-174.
Back to the Grossman Lab Webpage
Guest Biochemistry Lecture on Purine Biosynthesis at Suffolk University
Lecture on April 12, 2007
Here are notes in PDF format that you can download from my lecture.
If you would like a copy of the handout that I passed out in class OR if you have any questions about my lecture or grad school or how to get into grad school, feel free to email me at:
You should also check out wikipedia's websites on purines and caffeine:
And you should feel VERY lucky that you did not have to do a music video on purine metabolism, like these poor guys had to do for their biochemistry class. Check out this YouTube video on the chemistry of chocolate and caffeine...set to the tune of Fergalicious: