Overview of the Protease Network Model
Gram-positive organisms account for 80% of all the community-acquired and > 60% of hospital-acquired bacterial infections in infants, children and adolescents (19766890). The emergence of Gram-positive drug resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pneumoniae and Enterococcus is a global public health problem. The antibiotics currently used in clinical practice either disrupt bacterial membrane or inhibit protein synthesis. Resistance to these antibiotics might be resolved using a new class of antibiotics with a different mechanism of action (12111749, 10873842, 10708847). Bacterial proteases are implicated in bacterial virulence, playing critical role in the host-pathogen interactions (12111749, 8981341, 10941781). They are ubiquitous in occurrence and important to the survival and growth of the bacteria (12111749, 10708847). This makes them ideal candidates as drug targets. Bacterial protease inhibitors, thus, represent a novel antibiotic class that is relatively unexplored and potentially an important field.
To identify novel bacterial protease targets, it is important to elucidate the bacterial protease degradome and its function and effect on the pathway networks. Databases like Degradome (18776217), ProLysED (16128617 ), CutDB (17142225 ) and MEROPS (17991683 ) provide important information on proteases from prokaryotic and eukaryotic organisms based on experimental data and manually curated or automated annotations. However, it is critical to understand the role of proteases by modeling them in the context of multiple components such as protein signaling networks and complex biochemical pathways that can influence or be influenced by their activity.
Therefore, using Pathway Logic (PL), we are developing a comprehensive computational model of interactions of proteases from multiple Gram-positive bacteria. Using this model of Protease-network, we can analyze systems at multiple levels of details and highlight subtle but potentially important regulatory differences between species. We can also identify key proteases and proteins by comparing different pathways or networks within and across the species and predict how these molecules, if inhibited or avoided could affect a pathway or the network. A guided tour of this model can be found here . You can browse and analyse the Pathway Logic protease network model using the Pathway Logic Assistant client . Just click on the link and follow instructions. The guide includes suggestions for subnets to explore and instructions for creating them using the Pathway Logic Assistant viewer.
As an initial step, we have developed a model network with 30 proteases from 9 different Gram-positive bacteria, namely, Staphylococcus aureus, Bacillus subtilis, Bacillus anthracis, Corynebacterium diphtheriae, Clostridium perfringens, Clostridium difficile, Listeria monocytogenes, Lactobacillus plantarum and Streptococcus pyogenes. The 30 proteases belonging to serine, metalloprotease, or cysteine family of peptidases and Type I and Type II Signal peptidases (SPases) used to develop the protease network model are listed in the following Table.
| Proteases | Function or similarity |
|---|---|
| AprE (subtilisin E) | Extracellular serine protease |
| Bpr (bacillopeptidase F) | Extracellular serine protease |
| ClpCP | Cytoplasmic ATP dependent serine protease |
| ClpEP | Cytoplasmic ATP dependent serine protease |
| ClpXP | Cytoplasmic ATP dependent serine protease |
| CodWX | Cytoplasmic ATP dependent serine protease |
| CtpB | Cytoplasmic serine protease |
| Epr | Extracellular serine protease |
| FtsH | Membrane ATP dependent metalloprotease |
| HtrA (DegP) | Membrane serine protease |
| LonA | Cytoplasmic ATP dependent serine protease |
| LonB | Cytoplasmic ATP dependent serine protease |
| Lsp | Membrane Type II SPase |
| LytE | Cell wall peptidase |
| Mpr | Extracellular metalloprotease |
| NprB | Extracellular metalloprotease |
| NprE | Extracellular metalloprotease |
| PrsW (YpdC) | Membrane protease |
| RasP (YluC) | Membrane metalloprotease |
| SipS | Membrane Type I SPase |
| SipT | Membrane Type I SPase |
| SipV | Membrane Type I SPase |
| SpeB | Extracellular cysteine protease |
| SpoIVB | Cytoplasmic serine protease |
| SpoIVFB | Membrane metalloprotease |
| SrtA | Membrane cysteine protease-transpeptidase |
| SrtB | Membrane cysteine protease-transpeptidase |
| SrtF | Membrane protease-transpeptidase |
| Vpr | Extracellular serine protease |
| WprA | Cell wall serine protease |
Note that the ClpCP, ClpEP, ClpXP and CodWX proteases are complexes represented as ClpC:ClpP, ClpE:ClpP, ClpP:ClpX and CodW:CodX in our model to make this information explicit.