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 ConE-GFP (green), membrane (red), and DNA (blue) shown.

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 ConE (formerly YddE) which is encoded on the B. subtilis conjugal element ICEBs1. ConE is related to proteins encoded on conjugal elements in numerous bacteria, including the Gram-positive pathogens S. aureus, C. difficile, and L. monocytogenes. ConE belongs to a large superfamily of ATP-dependent pumps involved in the extrusion of proteins and DNA through membrane pores. I have shown that ConE and its ATPase domain are essential for mating of ICEBs1. In addition, ConE-GFP localizes at the cell poles, in close association with the membrane (see Figure). Given ConE’s localization, ATPase domain, and essentiality in conjugation, I propose that ConE and its homologs are the essential membrane-associated ATPase component of the Gram-positive mating pore apparatus. I plan on analyzing the role of ConE 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

Stephanie and Bridget at their poster at the Suffolk University Science Banquet, Spring 2010

Bridget Giarusso - Biochemistry Major
As a research assistant, Bridget and Stephanie used mating assays to determine that addition of a His6-tag on the N-terminus of ConE does not interfere with ConE's ability to support mating. Since His6-ConE is functional for mating, we can purify His6-ConE and begin in vitro assays to determine whether it can bind ATP. She presented this research with Stephanie at the 2010 ACS National Meeting in San Francisco and at the Suffolk Science Banquet where they won a poster award. She is also helping to clone several ICEBs1 genes.

Stephanie Laurer - Biochemistry Major
As a research assistant, Stephanie and Bridget used mating assays to determine that addition of a His6-tag on the N-terminus of ConE does not interfere with ConE's ability to support mating. Since His6-ConE is functional for mating, we can purify His6-ConE and begin in vitro assays to determine whether it can bind ATP. She presented this research with Bridget at the 2010 ACS National Meeting in San Francisco and at the Suffolk Science Banquet where they won a poster award. She is also helping to clone several ICEBs1 genes. On the side, Stephanie has had an interest in genetically modified food. During her first year at Suffolk, she used a PCR-based assay to detect the Bt gene in corn. She found that at least half of the samples she tested (6 of 11) were genetically modified. She presented this work at the 2009 Suffolk science banquet where her poster won first place.

Former Members of the Berkmen Lab

Matt Hamada - B.S. Biochemistry, December 2010
For CHEM L333, Matt cloned the yddC gene encoded on the ICEBs1 conjugative element. For CHEM L428/L429, Matt used fluorescence microscopy to determine whether yddC and other ICEBs1 genes are required for ConE to localize at the cell poles. He presented his research with Cori at the 2009 Boston Bacterial Meeting.

Cori Leonetti - B.S. Biochemistry, May 2010
For CHEM L333, Cori helped clone the yddB gene encoded on the ICEBs1 conjugative element. Cori extended her CHEM L333 project for CHEM L428/L429. She tested whether yddB and other ICEBs1 genes are required for mating. Cori presented her research with Matt at the 2009 Boston Bacterial Meeting.

Erin Cross - B.S. Biochemistry, May 2009
In CHEM L333, Erin and her class mates attempted to clone various C-terminal truncations of YddE fused to GFP. For CHEM L428/L429, she used fluorescence microscopy to analyze what parts of YddE are required for localization to the cell poles. She found that the C-terminal half of YddE is critical for localization. In addition, she found the YddE-GFP localizes at the cell poles, even when the upstream gene yddD is not expressed in cis. She presented this work at the national ACS meeting in March 2009 and at the 2009 Suffolk Science Banquet where her poster won 3rd place.

Maria Muccioli (formerly Levicheva) - B.S. Biochemistry, Honors Program, May 2009
For CHEM L333, Maria began construction of a his-tagged YddE. For CHEM L428/L429, she purified and characterized His6-YddE to enable future students to perform ATPase assays to determine whether YddE can hydrolyze ATP in vitro. She presented this work at the national ACS meeting in March 2009. Maria is now a graduate student in the molecular and cellular biology Ph.D. program at Ohio University.

Tamara Wong - B.S. Biochemistry Forensic Science, May 2009
Tamara cloned the His6-YddE construct so that we can test whether this protein can support mating. In addition, Tamara purified His6-YddE to enable future ATPase assays.

Emma-Kate Loveday - B.S. Biochemistry, 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. She presented her work at the Boston Bacterial Meeting in June 2008 and the Cold Spring Harbor Molecular Genetics of Bacteria and Phages Meeting in August 2008. Emma is now a graduate student in the microbiology and immunology Ph.D. program at the University of British Columbia supported by an NSF Fellowship.

Publications

Berkmen MB, Lee CA, Loveday EK, Grossman AD. (2010) Polar positioning of a conjugation protein from the integrative and conjugative element ICEBs1 of Bacillus subtilis. J Bacteriol, 192(1):38-45.

Kitko RD, Cleeton RL, Armentrout EI, Lee GE, Noguchi K, Berkmen MB, Jones BD, Slonczewski JL. (2009) Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis. PLoS One, 4(12):e8255.

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 Bacteriol, 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 Bacteriol, 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 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 travel, snowboard, practice my Turkish, and eat delicious food.