Berkmen

Melanie Berkmen

Me at the scope

Bio

Hi. My name is Melanie Barker Berkmen.
I am an assistant professor of biochemistry at Suffolk University. Welcome to my webpage!

How to contact me:
email: mberkmen at suffolk.edu
phone: to be determined

address:
Suffolk University
Department of Chemistry and Biochemistry
41 Temple St.
Boston, MA 02114

Education

(2002-2007) 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

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.

(2004-2005)Co-chair of the organizing committee for the 2005 Boston Bacterial Meeting
http://mcb.harvard.edu/losick/BBM2005/

(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

Research

I am interested in two broad questions in biology:

1. How do proteins come together to form a functional molecular machine, capable of the complex task of DNA transport through a membrane (e.g. in bacterial mating)?

2. How are the proteins that make up a complex molecular machine targeted to the correct location in the bacterial cell in order for them to function properly.

B. subtilis cells with YddE-GFP.
Color code:
GREEN (YddE fused to Green Fluorescent Protein)
RED (membrane)
BLUE (DNA)

Bacterial mating or conjugation is the transfer of DNA from one bacterium to another via direct cell-to-cell contact through a mating pore. My current research uses the genetically-tractable bacterium Bacillus subtilis as a model system to explore the function and subcellular localization of a putative component of the bacterial mating pore apparatus. I have been characterizing the protein YddE which is encoded on the B. subtilis conjugal element ICEBs1. YddE is related to proteins encoded on conjugal elements in numerous bacteria, including the Gram-positive pathogens S. aureus, C. difficile, and L. monocytogenes. YddE belongs to a large superfamily of ATP-dependent pumps involved in the extrusion of proteins and DNA through membrane pores. I have shown that YddE and its ATPase domain are essential for mating of ICEBs1. In addition, YddE localizes at the cell poles, in close association with the membrane (see Figure). 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, and investigating its subcellular localization through a combination of bioinformatics, molecular, cellular, and biochemical techniques.

Publications

Wang JD, Berkmen MB, Grossman AD. (2007) Genome-wide co-orientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis, PNAS, 104(13): 5608-5613.

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.

Personal

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.

In my free time, I like to cook, play with my son Kaan, learn Turkish, and travel.

Kaan at 2 months