Melanie Barker Berkmen
Assistant Professor of Chemistry and Biochemistry at Suffolk University
How to contact me:
Email: mberkmen at suffolk.edu
Office Phone: 617-973-5321
Department of Chemistry and Biochemistry
41 Temple St.
Boston, MA 02114
Office: Donahue Building, Room 513
Biochemistry Lab: Archer Building, Room 631
Courses I teach
FALL - CHEM 331 (Biochemistry I)
FALL - CHEM L331 (Biochemistry Lab)
FALL - CHEM L111 (General Chemistry Lab I)
SPRING - CHEM L333 (Advanced Biochemistry Research Lab)
SPRING - CHEM 429 (Research & Seminar II)
Previously Taught Courses
FALL - CHEM 428 (Research & Seminar I)
SPRING - CHEM L111 (General Chemistry Lab I)
FALL 2005 (at MIT), course 7.341 (advanced seminar on bacterial molecular and cellular biology)
(2002-2007) Jane Coffin Childs Postdoctoral Fellow
Massachusetts Insitute of Technology, Cambridge, MA
Laboratory of Alan D. Grossman
(2001) Ph.D., Cellular and Molecular Biology
University of Wisconsin-Madison, Madision, WI
Laboratory of Richard L. Gourse
(1995) B.S., Biochemistry
University of Dayton, Dayton, OH, summa cum laude
I am interested in two broad questions in biology:
1. How do proteins come together to form a complex molecular machine, capable of such tasks like DNA transport through a membrane (e.g. in bacterial mating)?
2. How are the proteins that make up a complex molecular machine targeted to the correct location in the bacterial cell?
Bacterial mating or conjugation is the transfer of DNA from one bacterium to another via direct cell-to-cell contact through a mating pore. My current research uses the genetically-tractable bacterium Bacillus subtilis as a model system to explore the function and subcellular localization of a putative component of the bacterial mating pore apparatus. I have been characterizing the protein ConE (formerly YddE) which is encoded on the B. subtilis conjugal element ICEBs1. ConE is related to proteins encoded on conjugal elements in numerous bacteria, including the Gram-positive pathogens S. aureus, C. difficile, and L. monocytogenes. ConE belongs to a large superfamily of ATP-dependent pumps involved in the extrusion of proteins and DNA through membrane pores. I have shown that ConE and its ATPase domain are essential for mating of ICEBs1. In addition, ConE-GFP localizes at the cell poles, in close association with the membrane (see Figure). Given ConE’s localization, ATPase domain, and essentiality in conjugation, I propose that ConE and its homologs are the essential membrane-associated ATPase component of the Gram-positive mating pore apparatus. I plan on analyzing the role of ConE in conjugation, exploring its functional domains, and investigating its subcellular localization through a combination of bioinformatics, molecular, cellular, and biochemical techniques. Our research is funded through an NSF-RUI grant from 2012-2015.
Current Members of the Berkmen Lab
Matt Broulidakis - Biochemistry Major
Matt joined out lab under the NSF grant in the summer of 2012 as a research assistant. He has been responsible for running mating assays and will soon be monitoring the localization of ConE-GFP under various conditions.
Georgeanna Morton - Biochemistry Major
Geogeanna became a research assistant under the NSF grant in the summer of 2012. She is now responsible for purifying His6-ConE mutants and testing the oligomerization of each using Blue Native-PAGE.
Azul Pinochet Barros - Philosophy/Biology Major
Azul joined the lab in the spring of 2012. With an interest in cyanobacteria, Azul was very determined to be involved in bacterial growth, so she was assigned the task of optimizing the protocol for growing competent cells.
Kyle Swerdlow - Biochemistry Major
Kyle started working as a research assistant in fall of 2011 working very closely with Gianna Mancuso on the optimization of His6-ConE. After making many attempts to optimize the protocol, Kyle compiled the results and presented his research at the 2012 ACS national conference as well as the 2012 STEM conference at Suffolk University. Kyle is now using bacterial two-hybrid analysis to piece together key players in the ICEBs1 conjugation machinery.
Gianna Mancuso - Biochemistry Major
Gianna has been working as a research assistant since the spring of 2011. After helping Stephanie work on mating assays, her main objective was to optimize the purification of His6-ConE. She, along with Kyle Swerdlow, worked on this task and the research was presented at the 2012 ACS national conference and 2012 STEM conference at Suffolk University.
Former Members of the Berkmen Lab
Stephanie Laurer - B.S. Biochemistry, May 2012
As a research assistant, Stephanie used mating assays to determine that addition of a His6-tag on the N-terminus of ConE does not interfere with ConE's ability to support mating. She presented this research with Bridget at the 2010 ACS National Meeting in San Francisco and at the Suffolk Science Banquet where they won a poster award. She also helped clone several ICEBs1 genes. On the side, Stephanie had an interest in genetically modified food. During her first year at Suffolk, she used a PCR-based assay to detect the Bt gene in corn. She found that at least half of the samples she tested (6 of 11) were genetically modified. She presented this work at the 2009 Suffolk science banquet where her poster won first place. She now acts as Clinical Coordinating Assistant in the Oncology department at Mass General Hospital.
Bridget Giarusso - B.S. Biochemistry, May 2011
As a research assistant, Bridget used mating assays to determine that addition of a His6-tag on the N-terminus of ConE does not interfere with ConE's ability to support mating. She presented this research with Stephanie at the 2010 ACS National Meeting in San Francisco and at the Suffolk Science Banquet where they won a poster award. She helped clone several ICEBs1 genes.
Matt Hamada - B.S. Biochemistry, December 2010
For CHEM L333, Matt cloned the yddC gene encoded on the ICEBs1 conjugative element. For CHEM L428/L429, Matt used fluorescence microscopy to determine whether yddC and other ICEBs1 genes are required for ConE to localize at the cell poles. He presented his research with Cori at the 2009 Boston Bacterial Meeting. Currently, Matt is working as a laboratory research technician.
Cori Leonetti - B.S. Biochemistry, May 2010
For CHEM L333, Cori helped clone the yddB gene encoded on the ICEBs1 conjugative element. Cori extended her CHEM L333 project for CHEM L428/L429. She tested whether yddB and other ICEBs1 genes are required for mating. Cori presented her research with Matt at the 2009 Boston Bacterial Meeting. Cori is now a graduate student at Arizona State University studying microbiology.
Erin Cross - B.S. Biochemistry, May 2009
In CHEM L333, Erin and her class mates attempted to clone various C-terminal truncations of YddE fused to GFP. For CHEM L428/L429, she used fluorescence microscopy to analyze what parts of YddE are required for localization to the cell poles. She found that the C-terminal half of YddE is critical for localization. In addition, she found the YddE-GFP localizes at the cell poles, even when the upstream gene yddD is not expressed in cis. She presented this work at the national ACS meeting in March 2009 and at the 2009 Suffolk Science Banquet where her poster won 3rd place. Erin is now working as a laboratory research technicial.
Maria Muccioli (formerly Levicheva) - B.S. Biochemistry, Honors Program, May 2009
For CHEM L333, Maria began construction of a his-tagged YddE. For CHEM L428/L429, she purified and characterized His6-YddE to enable future students to perform ATPase assays to determine whether YddE can hydrolyze ATP in vitro. She presented this work at the national ACS meeting in March 2009. Maria is now a graduate student in the molecular and cellular biology Ph.D. program at Ohio University.
Tamara Wong - B.S. Biochemistry Forensic Science, May 2009
Tamara cloned the His6-YddE construct so that we can test whether this protein can support mating. In addition, Tamara purified His6-YddE to enable future ATPase assays.
Emma-Kate Loveday - B.S. Biochemistry, May 2008
For her CHEM L428/L429 project, Emma-Kate constructed two variants of YddE and tested their effects on mating. She found that the Walker B (ATP hydrolysis domain) of YddE is essential for mating. She also found that the N-terminus of YddE does not contribute significantly to mating. She presented her work at the Boston Bacterial Meeting in June 2008 and the Cold Spring Harbor Molecular Genetics of Bacteria and Phages Meeting in August 2008. Emma is now a graduate student in the microbiology and immunology Ph.D. program at the University of British Columbia supported by an NSF Fellowship.
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. J Bacteriol, 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 site 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 Bacteriol, 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 Bacteriol, 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.
Singer SS, Henkels K, Deucher A, Barker MM, Singer J, Trulzsch T. (1996) Growth hormone and aging change rat liver fatty acid binding protein levels. J Amer Coll Nutr 15: 169-174.
In my free time I like to travel, snowboard, practice my Turkish, and eat delicious food.