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: 617-973-5321

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

Campus Address:
Office: Donohue Building, Room 513
Lab: Archer Building, Room 631

Courses I teach (and links to materials)

FALL - CHEM 331 (Biochemistry I)
FALL - CHEM 428 (Research Seminar I)

SPRING - CHEM L333 (Advanced Biochemical Techniques and Research)
SPRING - CHEM 429 (Research Seminar II)

FALL 2005 (at MIT), course 7.341 (advanced seminar on bacterial molecular and cellular biology)

Education

(2002-2007) Jane Coffin Childs Postdoctoral 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

Research

I am interested in two broad questions in biology:

1. How do proteins come together to form a complex molecular machine, capable of such tasks like 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?

B. subtilis cells with YddE-GFP.
GREEN (YddE fused to GFP), 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.

Current Members of the Berkmen Lab

Maria at the bench

Erin

Stephanie!

Maria Levicheva - Biochemistry Major, Honors Program, May 2009
For CHEM L333, Maria began construction of a his-tagged YddE. For CHEM L428/L429, we hope to purify YddE and test whether it can bind and hydrolyze ATP in vitro.

Erin Cross - Biochemistry Major, May 2009
Erin is extending her CHEM L333 project for CHEM L428/L429. She will be using fluorescence microscopy to analyze what parts of YddE are required for localization to the cell poles.

Stephanie Laurer - Biochemistry Major, May 2012
As a new research assistant, Stephanie will help determine which other proteins in ICEBs1 are required for YddE to localize properly.

Former Members of the Berkmen Lab and/or CHEM L333 Lab

Morgan in CHEM L333 Spring 2008

Emma-Kate Loveday - Biochemistry Major, May 2008
For her CHEM L428/L429 project, Emma-Kate constructed two variants of YddE and tested their effects on mating. She found that the Walker B (ATP hydrolysis domain) of YddE is essential for mating. She also found that the N-terminus of YddE does not contribute significantly to mating.


Morgan Turano - Biochemistry Forensics Science Major, December 2008
For her CHEM L333 project, Morgan cloned a his-tagged YddE Walker A mutant protein.

Publications

Vrentas CE, Gaal T, Berkmen MB, Rutherford ST, Haugen SP, Ross W, Gourse RL. (2008) Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J Mol Biol, 277(2): 551-64.

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 postdoctoral fellow in Jon Beckwith's lab at Harvard Medical School.

Now he is at the biotechnology 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, practice my Turkish, and travel.

Kaan at 1 year