Comparative genomics for mycobacterial peptidoglycan remodelling enzymes reveals extensive genetic multiplicity

Abstract

BackgroundMycobacteria comprise diverse species including non-pathogenic, environmental organisms, animal disease agents and human pathogens, notably Mycobacterium tuberculosis. Considering that the mycobacterial cell wall constitutes a significant barrier to drug penetration, the aim of this study was to conduct a comparative genomics analysis of the repertoire of enzymes involved in peptidoglycan (PG) remodelling to determine the potential of exploiting this area of bacterial metabolism for the discovery of new drug targets.ResultsWe conducted an in silico analysis of 19 mycobacterial species/clinical strains for the presence of genes encoding resuscitation promoting factors (Rpfs), penicillin binding proteins, endopeptidases, L,D-transpeptidases and N-acetylmuramoyl-L-alanine amidases. Our analysis reveals extensive genetic multiplicity, allowing for classification of mycobacterial species into three main categories, primarily based on their rpf gene complement. These include the M. tuberculosis Complex (MTBC), other pathogenic mycobacteria and environmental species. The complement of these genes within the MTBC and other mycobacterial pathogens is highly conserved. In contrast, environmental strains display significant genetic expansion in most of these gene families. Mycobacterium leprae retains more than one functional gene from each enzyme family, underscoring the importance of genetic multiplicity for PG remodelling. Notably, the highest degree of conservation is observed for N-acetylmuramoyl-L-alanine amidases suggesting that these enzymes are essential for growth and survival.ConclusionPG remodelling enzymes in a range of mycobacterial species are associated with extensive genetic multiplicity, suggesting functional diversification within these families of enzymes to allow organisms to adapt.

Phytochemical-mediated Protein Expression Profiling and the Potential Applications in Therapeutic Drug Target Identifications

“…Recently, proteomic study has reported on the C.formosana-mediated down-regulated bacterial enzymes (triacylglycerol lipase, Nacetylmuramoyl-L-alanine amidase), upon exposure to C. formosana methanol extract(Yong et al., in press). The later amidase is especially noteworthy, as it was previously reported by others as a bacterial enzyme with functional role in the biosynthesis of peptidoglycans, an important building component in bacterial cell walls(Machowski et al, 2014). Nevertheless, further work is still needed to pinpoint which phytochemicals in the C. formosana extract are exactly responsible for this phenomenon.…”

“…Specifically, its rhodomyrtone (a xanthene derivative) was pinpointed as the potent phytochemical with anti-bacterial activity, parallel with inhibition potentials of commercial antibiotics. For instance, rhodomyrtone was reported with an MIC value of 0.39-0.78 µg/ml against MRSA strain, comparable to that of the commercial vancomycin (MIC: 1 25. …”

“…The situation is grimmer if taking into account the decreasing antibiotic candidate in the pharmaceutical development pipeline. In view of this situation, increasing researches are aiming toward the identification of potentially useful antibacterial compounds or materials, especially those which specifically target critical enzymes in bacterial pathways (Machowski et al, 2014;Smith et al, 2013).…”

The hydrolase LpqI primes mycobacterial peptidoglycan recycling

“…The genome of M tuberculosis encodes many lytic enzymes, including at least five Resuscitation Promoting Factors (Rpfs) and greater than 10 peptidases and amidases in addition to penicillin binding proteins with potential lytic activities 24 . The Rpfs are most likely lytic transglycosylases with the product of RpfB having been recently confirmed as a GlcNAc-1,6-anhydroMurNAc disaccharide 25 .…”

Resuscitation-promoting factors are important determinants of the pathophysiology inMycobacterium tuberculosisinfection

“…In Mtb, Rpf represent inviting targets for intervention. They are important virulence factors, they lack human homologs ensuring a high degree of drug specificity and their extracellular nature means small molecule inhibitors do not need to enter the cell for biological activity (Kana et al, 2008;Machowski et al, 2014). Inhibitors of Rpf, such as 2-nitrophenylthiocyanates, could be given to patients with LTBI who need treatment with anti-TNFa inhibitors to prevent the reactivation of tuberculosis (Demina et al, 2009;Kaprelyants et al, 2012).…”