Melanie Barker Berkmen, PhD
Associate 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, summa cum laude

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 specialized DNA translocation channel. 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

2008-2011 (summers), Massachusetts Institute of Technology, Cambridge, MA, Visiting Scientist in the laboratory of Alan Grossman

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

Grants and Awards

2012-2015 National Science Foundation RUI Grant: Characterization of a Conserved ATPase
Required for Conjugation of Bacillus subtilis
2010-2011 Suffolk University Summer Stipend Award
2008-2009 Suffolk University Summer Stipend Award
2007-2008 Suffolk University Summer Stipend Award

Recent Publications

Berkmen MB, Laurer SJ*, Giarusso BK*, Romero R*. (2013) The integrative and conjugative element ICEBs1 of Bacillus subtilis. In Bacterial Integrative Mobile Genetic Elements. (Roberts AP, Mullany P ed.). Landes Biosciences, Austin, TX.

Martinez II KA, Kitko RD, Mershon JP, Adcox HE, Malek KA, Berkmen MB, Slonczewski JL. (2012) Cytoplasmic pH response to acid stress in individual cells of Escherichia coli and Bacillus subtilis observed by fluorescence ratio imaging microscopy. Applied and Envir. Microbiol., 78(10):3706-14.

Babic, A, Berkmen MB, Lee CA, Grossman AD. (2011) Efficient gene transfer in bacterial cell chains. mBio, 2(2):e00027-11.

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.

Oral Presentations

2013 7th  International Conference on Gram-positive microorganisms, Montecatini Terme, Italy
2013 Massachusetts Institute of Technology, Cambridge, MA
2011 University of Massasachusetts-Boston, Boston, MA
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 Genomics of Gram-positive Microorganisms, Tirrenia, Italy

Professional Activities

2010-present, Member of the American Society for Biochemistry and Molecular Biology
2004-present, Member of the American Society for Microbiology

Courses Taught

CHEM L111 - General Chemistry I Laboratory
CHEM L112 - General Chemistry II Laboratory
CHEM 331 - Biochemistry I
CHEM L331 - Biochemistry I Laboratory
CHEM L333 - Advanced Biochemical Techniques and Research
CHEM 428 - Research and Seminar I
CHEM 429 - Research and Seminar II
CHEM L432 - Advanced Biochemistry Research Laboratory