Melanie Berkmen, PhD

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.

All of my research is conducted by Suffolk University undergraduate students, partially funded through a grant from the National Science Foundation. Please see me if you are interested in joining my lab!

Employment History

• 2021-present
  Suffolk University, Boston, MA, Professor of Biochemistry
• 2013-2021
  Suffolk University, Boston, MA, Associate Professor of Biochemistry
• 2007-2013
  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

Recent Publications

• Peterson CN, Tavana* SZ, Akinleye* OP, Johnson WH, Berkmen MB. (2020) An idea to explore: Use of augmented reality for teaching three-dimensional biomolecular structures. Biochemistry and Molecular Biology Education, 48:276-282.
• Grocott* O, Phanor* SK, Fung F, Thibert RL, Berkmen MB. (2019) Clinical report and biochemical analysis of a patient with fumarate hydratase deficiency. American Journal of Medical Genetics Part A, 182A:504-507.
• Bulku* A, Weaver TM, Berkmen MB. (2018) Biochemical characterization of two clinically-relevant human fumarase variants defective for oligomerization. The Open Biochemistry Journal, 12:1-15.
• Auchtung JM, Aleksanyan* N, Bulku* A, Berkmen MB. (2016) Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis. Plasmid, 86: 14-25.
• 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 Microbiol & 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

• 2019
  Northeastern University, Boston, MA
• 2016
  Type IV Secretion Systems in Gram-negative and Gram-positive Bacteria, Beilngries, Germany
• 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

Grants & Awards

• 2016-2022
  National Science Foundation RUI Grant: Molecular analysis of two interacting components of the conjugation machinery of Bacillus subtilis
• 2021
  Suffolk University Experiential Learning Grant
• 2016-2019
  New England Biolabs Course Support Award (with Department of Biology)
• 2019
  Marion and Jasper White Foundation Travel Fellowship
• 2017
  College of Arts and Science Dean’s Award for Excellence in Teaching
• 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