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.