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 several interacting protein components of the conjugation machinery of the model bacterium Bacillus subtilis (ConB, ConC, ConD, ConE, ConG, ConQ, and CwlT). Our research uses a combination of bioinformatics, molecular, cellular and biochemical approaches to provide insight into how these 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.

Besides bacterial mating, I have two other research interests. In my Advanced Biochemical Techniques and Research course (CHEM L332), my students explore the biochemical underpinnings of metabolic disease and cancer caused by mutations in fumarase, the Krebs cycle enzyme and tumor suppressor. In addition, I am collaborating with Celeste Peterson (Professor, Department of Biology, Suffolk University) to explore the use virtual reality for teaching visualization of biomolecular structure (proteins, DNA) in our courses.

All of my research is conducted by Suffolk University undergraduate students. 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

Recent Publications

• Garcia I, Cornely K, Peterson CN, and Berkmen MB. (2024) Roles of the oncometabolite enantiomers of 2-hydroxyglutarate and their metabolism by diverse dehydrogenases. Essays in Biochemistry, in press.
• Murthy* AC, Aleksanyan* N, Morton* GM, Toyoda* HC, Kalashyan* M, Chen* S, Ragucci* AE, Broulidakis* MP, Swerdlow* KJ, Bui* MNN, Muccioli* M, Berkmen MB. (2023) Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis. Journal of Bacteriology, 206(6): e0003323.
• 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.

Recent Oral Presentations

• 2024
  22nd International Conference on Gram-positive Microorganisms, Bloomington, IN
• 2024
  Discover BMB – annual meeting of the American Society for Biochemistry and Molecular Biology (ASBMB), San Antonio, TX
• 2022
  Advances in Molecular and Cellular Biology & their Clinical & Biotechnology Applications, Madison, WI
• 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

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

• 2023-2025
  National Science Foundation IUSE Grant – Conference (Co-PI): Training STEM educators on the use of virtual reality for teaching biomolecular visualization
• 2024
  ASBMB annual meeting travel award
• 2016-2024
  New England Biolabs Course Support Award (with Department of Biology)
  
• 2016-2022
  National Science Foundation RUI Grant (PI): Molecular analysis of two interacting components of the conjugation machinery of Bacillus subtilis
• 2021 and 2022
  Suffolk University Experiential Learning Grant
• 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 (PI): Characterization of a conserved ATPase required for conjugation of Bacillus subtilis