Melanie Barker Berkmen, PhD
Associate Professor
Department of Chemistry and Biochemistry

Phone: 617-973-5321
Fax: 617-573-8668
Email: mberkmen@suffolk.edu
Office: Somerset Building, Rm. 831
Website

Education

  • PhD, University of Wisconsin, Madison
  • BS, University of Dayton, summa cum laude

Research Interests

Bacteria have the remarkable ability to acquire new genes in a process known as mating, or conjugation. Mating has played a profound role in bacterial evolution by spreading genes that allow bacteria to adapt to new environments or gain resistance to various antibiotics. During conjugation, DNA is transferred from one cell to another through a specialized translocation channel in the membrane. Many of the molecular mechanisms behind the conjugation process remain a mystery. My research group focuses on characterizing ConB and ConE, two critical interacting protein components of the conjugation machinery of the model bacterium Bacillus subtilis. Our research uses a combination of bioinformatics, molecular, cellular and biochemical approaches to provide insight into how these two proteins function, interact, and localize within the cell. As these proteins are conserved, our findings will apply to the conjugation machinery of numerous Gram-positive bacteria, including many important human pathogens, and provide a deeper understanding of a major mechanism mediating horizontal gene transfer.

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

2016-2019 - National Science Foundation RUI Grant: Molecular analysis of two interacting components of the conjugation machinery of Bacillus subtilis
2016 - New England Biolabs Course Support Award (with Dr. Edith Enyedy)
2012-2016 - National Science Foundation RUI Grant: Characterization of a Conserved ATPase Required for Conjugation of Bacillus subtilis
2015-2016 – Suffolk University Summer Stipend Award
2010-2011 - Suffolk University Summer Stipend Award
2008-2009 - Suffolk University Summer Stipend Award
2007-2008 - Suffolk University Summer Stipend Award

Recent Publications

*Indicates a Suffolk University undergraduate student co-author

Auchtung JM, Aleksanyan* N, Bulku* A, Berkmen MB. (in press) Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis. Plasmid.

Leonetti* CT, Hamada* MA, Laurer* SJ, Broulidakis* MP, Swerdlow* KJ, Lee CA, Grossman AD, Berkmen MB. (2015) Critical components of the conjugation machinery of the integrative and conjugative element ICEBs1 of Bacillus subtilis. Journal of Bacteriology, 197(15): 2558-67.

Berkmen MB, Murthy AC, Broulidakis MP. (2014) An Inquiry-Based Laboratory Module to Promote Understanding of the Scientific Method and Bacterial Conjugation. J Micriobiol & Biol Educ., 15(2): 321-2.

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

2016 University of Wisconsin-Madison, Madison, WI
2015 Brandeis University, Waltham, MA
2014 Emmanuel College, Boston, MA
2013 Pennsylvania State University, University Park, PA
2013 7th International Conference on Gram-positive microorganisms, Montecatini Terme, Italy
2013 Massachusetts Institute of Technology, Cambridge, MA
2011 University of Massachusetts-Boston, Boston, MA
2010 University of Massachusetts-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 106 - Biotechnology and its Applications in Medicine, Agriculture and the Law
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