"
The beast and its Achilles heel:
A novel target to fight multi-resistant pathogenic bacteria
DAC Team
In order to find new antibacterial compounds, we focused on the signaling molecule bis-(3’,5’)-cyclic dimeric adenosine monophosphate (c-di-AMP) as it has proven to be an essential second messenger in many pathogenic Gram-positive bacteria (Witte et al., 2008). It was reported to have a crucial functions in cell wall synthesis and spore formation in Bacillus subtilis (Oppenheimer-Shaanan et al., 2011; Mehne et al., 2013). Interestingly, both absence and excess of c-di-AMP have detrimental effects on cell growth and morphology (Luo and Helmann, 2012; Mehne et al, 2013).
Knowing this information it makes sense that we take a closer look at the enzyme, the diadenylate cyclase, which produces c-di-AMP. The cyclase domain is conserved among several Gram-positive bacteria like B. subtilis, Streptococcus pneumoniae, Staphylococcus aureus and Listeria monocytogenes (Corrigan and Gründling, 2013). So far, the diadenylate cyclase DisA from B. subtilis has been purified (Witte et al., 2008). However, the purification and crystallization of DisA comes along with some difficulties so we decided to concentrate on the diadenylate cyclase in L. monocytogenes, DacA. As the cloning of the full-length (273 aa) membrane-bound DacA (Lmo2120) into Escherichia coli failed, we excluded the trans-membrane domains meaning we chopped off the first 100 amino acids. Nevertheless, the resulting truncated part still included the essential cyclase domain, and therefore represents one of our favorite BioBricks: [http://parts.igem.org/Part:BBa_K1045003 BBa_K1045003]!
Conducting several experiments we proved that the truncated DacA protein ([http://parts.igem.org/Part:BBa_K1045003 BBa_K1045003]) was not only active in vivo, but also in vitro. Moreover, we were able to purify the diadenylate cyclase in large scale for determining its protein structure! One can now further search for chemical compounds that interfere with the activity of the cyclase by computational modeling.
Following, the experiments will be explained in more detail. However, if you wish to get even more details, please visit the Parts Registry or our LabBook.
The truncated DacA protein ([http://parts.igem.org/Part:BBa_K1045003 BBa_K1045003]) was extended with an N-terminal Step-tag allowing easy purification steps. Moreover, this construct was brought under the control of a T7-promoter enabling us to induce the expression by addition of Isopropyl--D-thiogalactopyranosid (IPTG). This was then cloned into the E. coli strain BL21. (The Gram-negative bacterium E. coli does not produce c-di-AMP and is not severely affected by the signaling molecule in contrast to Gram-positive bacteria.)
In order to analyze the cyclase activity in vivo, the E. coli clones were induced to express the protein by the addition of IPTG. The cells were then lysed to extract c-di-AMP from the cells.
By performing SDS gel electrophoresis it was nicely shown that the desired protein was highly expressed (Fig. 1). Furthermore, the presence of c-di-AMP in the supernatant of the lysed bacteria was confirmed using LC-MS/MS. Thus, one can conclude that our truncated DacA protein codes for an active adenylate cyclase domain in vivo.
Fig. 1. Confirmation of the high expression of DacA. The SDS gel electrophoresis confirmed the high expression of DacA Lmo2120 in three biological replicates showing a thick band at about 20 kDa; Lane 1: Thermo Scientific PageRuler Plus Prestained Protein Ladder.
Diadenylate cyclases catalyze the condensation reaction of two molecules ATP to a single molecule c-di-AMP while releasing two pyrophosphate molecules consisting of the β-γ-phosphates of each ATP (Fig. 2). In order to analyze the cyclase activity of DacA in vitro, we performed an assay in which these pyrophosphate molecules were used as evidence for the reaction. Among other things, the assay included a pyrophosphatase that cleaves the pyrophosphate molecule in free phosphate molecules, malachite-green and molybdate. Malachite-green forms a complex with free phosphate molecules and molybdate that can be measured due to its absorption spectrum. With this in vitro assay the concentration of free phosphate molecules and thus the conversion rate of ATP to c-di-AMP was analyzed.
