Melanie Berkmen, Assistant Professor

Melanie Barker Berkmen, PhD

Assistant Professor
Department of Chemistry and Biochemistry

Phone: 617.973.5321
Fax: 617.573.8668 
Email: mberkmen@suffolk.edu
Office: Donahue Building, Rm. 513
Website

Education

• PhD, University of Wisconsin, Madison
• BS, University of Dayton

Research Interests

I am interested in two broad questions in biology:

1. How do proteins come together to form a molecular machine, capable of complex tasks such as DNA transport through a membrane (e.g. in bacterial mating)?
2. How are the proteins that make up a machine targeted to the correct location in the cell?

Bacterial mating or conjugation is the transfer of DNA from one bacterium to another through a mating pore. Conjugation is thought to have played a profound role in evolution by spreading genes that allow bacteria to adapt to and colonize new niches. Our long-term goal is to understand the mating machinery of the conjugative element ICEBs1 in the genetically-tractable bacterium Bacillus subtilis. We have found that the ConE protein is a critical component of the ICEBs1 mating machinery. ConE is essential for mating, localizes to the membrane predominantly at the cell poles, and belongs to the HerA/FtsK superfamily of ATP-dependent pumps. We are currently analyzing the role of ConE in conjugation, exploring its interacting partners, and investigating its subcellular localization through a combination of bioinformatics, molecular, cellular, and biochemical techniques. As ConE is related to proteins found in the pathogens Staphylococcus aureus, Clostridium difficile, and Listeria monocytogenes, we hope our studies will reveal new insights into the workings of the mating machinery of numerous bacteria.

Employment

2007-present, Suffolk University, Boston, MA, Assistant Professor of Biochemistry

2008-present (summers), Massachusetts Institute of Technology, Cambridge, MA, Visiting Scientist in the laboratory of Alan Grossman

2002-2007, Massachusetts Institute of Technology, Cambridge, MA, Postdoctoral Fellow in the laboratory of Alan Grossman

Fellowships and Awards

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. Journal of Bacteriology, 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 sire 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.

Presentations

2010 University of Massaschusetts-Amherst, Amherst, MA
2009 Bogazici University, Istanbul, Turkey
2009 Wellesley College, Wellesley, MA
2008 Sabanci University, Istanbul, Turkey
2008 Suffolk University, Boston, MA
2007 Functional Gemonics of Gram-positive Microorganisms, Tirrenia, Italy
2007 Clark University, Worcester, MA
2006 Boston Bacterial Meeting, Boston, MA
2005 ASM Conference on Prokaryotic Development, Vancouver, Canada
2004 Molecular Genetics of Bacteria and Phages, Cold Spring Harbor, NY

Professional Activities

2010-present, Member of the American Society for Biochemistry and Molecular Biology
2004-present, Member of the American Society For Microbiology
2004-2005, Co-chair of the organizing committee of the Boston Bacterial Meeting

Courses Taught

CHEM 331 - Biochemistry I (Fall semesters)
CHEM L333 - Advanced Biochemical Techniques and Research (Spring semesters)
CHEM 428 - Research and Seminar I (Fall semesters)
CHEM 429 - Research and Seminar II (Spring semesters)
Advanced Seminar in Microbial Cellular and Molecular Biology (Fall, 2005, MIT)