C. ulcerans can infect humans and a variety of wild and domestic animals that act as a reservoir. Manifestations can be asymptomatic, or cause damage to the respiratory tract, mastitis and gangrenous dermatitis (Hacker et al. 2016; Tiwari et al. 2008). Non-toxigenic strains can be classified as tox-negative or non-toxigenic but tox gene-bearing (NTTB) (Dangel et al. 2019; Fuursted et al. 2015). C. silvaticum is a recently described NTTB species close to C. ulcerans that causes caseous lymphadenitis in wild animals such as wild boar and roe deer, which are reservoirs, and domestic pigs (Dangel et al. 2020). Its potential host range is unknown, and It could potentially cause zoonotic infections (Viana et al. 2020).
Subtractive genomics, as the name suggests, is an approach based on several steps of filtering proteomic sequences, in order to select and identify final proteins that are indispensable to microorganisms and that are not homologous to the host. This methodology is widely used in reverse vaccinology, a method which includes subtractive genomics, modeling, docking and other in silico techniques in order to predict vaccine and drug targets, without financial expense and in a short time (Hassan et al. 2018; Masignani et al. 2019). The Bexsero vaccine for Neisseria meningitidis (Christodoulides and Heckels 2017) and Engerix-B vaccine for Hepatitis B (Keating and Noble 2003) were developed using these approaches.
We predicted nine vaccine targets, four drug targets and four probable dug molecules for C. ulcerans and C. silvaticum using reverse vaccinology and in silico drug targeting (Tables 1 and 2). Among nine predicted vaccine targets, four were annotated as subunits of ABC transporters. Two are substrate-binding protein for manganese (Mn) and zinc (Zn), one for phosphate, and one is a permease for glutamate. Both metals are vital for several organisms, required by transcriptional transporters and regulators and oxidative stress response (Mn), and several ribosomal proteins and tRNA synthetases (Zn). The acquisition of both metals is disputed with the host and those ABC transporters are required for colonization (Juttukonda and Skaar 2015; Nies and Grass 2009). One of the transporter’s subunits (mntA) is in PAI 3 (Fig. 2). Glutamate is an essential metabolite that plays an important role in the metabolism of nitrogen and carbon. The ABC glutamate transporter has already been characterized in other bacterial genera and is a known vaccine target, considering its indispensable role in the survival of the bacterium (Bhatia et al. 2014). Phosphate is essential for energy metabolism and is a component of nucleic acids, phospholipids, and other cell molecules. The Phosphate ABC transporter, substrate-binding protein PstS is part of the complex PstSACB involved in phosphate import (Santos-Beneit 2015). Inactivation of the pstS gene increased the susceptibility to penicillin in Streptococcus pneumoniae (Soualhine et al. 2005). The transport of these essential nutrients makes those proteins promising vaccine candidates.
Among the non-transporter vaccine target candidates is a bifunctional protein from the Phospholipase/Thioesterase family, with the gene located in pathogenicity island PAI 6 (Fig. 2). This enzyme is involved in the non-ribosomal synthesis of peptides, including antimicrobial peptides (Santucci et al. 2018; Schneider and Marahiel 1998). The Integral membrane protein belong to the “Putative Actinobacterial Holin-X, holin superfamily III”. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to lysogenize their hosts (InterPro entry IPR009937). The other three candidates are hypothetical proteins classified by InterProScan as “Papain-like cysteine peptidase superfamily” (InterPro entry IPR038765) (PATRIC ID 996634.5.peg.652), “Calcium-dependent phosphotriesterase” (SSF63829) (996634.5.peg.1276) and a transmembrane protein (996634.5.peg.823).
Within the drug targets, DtxR was the only predicted virulence factor. It is an iron-dependent repressor in prokaryotes that regulates the expression of genes involved in iron homeostasis and virulence factors, such as diphtheria toxin (tox) (WHITE et al., 1998). DtxR regulates genes according to the concentration of Fe2+ ions in the environment, allowing to adjust iron uptake. It is considered a virulence factor due to its importance for host colonization (Merchant and Spatafora 2014). Furthermore, DxtR has been considered an attractive drug target due to its role in regulating genes involved in iron homeostasis in bacteria, and such genes are generally virulence factors (Cheng et al. 2018; Parise et al. 2021). Residue SER 70 is hydrogen bonded to the nitrogen of the aromatic ring, THR 159 is hydrogen bonded to the third oxygen of the compound and residues ARG 69 and LEU 135 have hydrophobic interactions with the three aromatic rings.
Uridine Monophosphate Kinase is an important enzyme that acts on the metabolism of pyrimidines in bacteria, specifically on uridine monophosphate (UMP). It converts UMP to UDP that is later used in the nucleoside biosynthesis. UMPK plays an essential role in the production of nucleotides that are constituents of nucleic acids. This enzyme is of interest, as It has been recognized as a potential drug target for tuberculosis (ARVIND et al. 2013) as It also plays a role in regulating the balance of pyrimidine and purine nucleosides. In addition, It is structurally different from the eukaryotic UMP kinases (Rostirolla et al. 2011), which makes It a more attractive candidate. ASP 79 makes two hydrogen bonds with NH (NH-O), GLY 21 makes two hydrogen bonds with the first oxygen of the molecule. The 2D image shows hydrogen bonding of MET 140 to the last nitrogen. MET 83 shows hydrophobic interaction with the last aromatic ring.
The Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic protein that participates in the glucose metabolic pathway and in the production of organic acid when oxygen is scarce (Altenhoff and Dessimoz 2009; Teramoto et al. 2010). In some genera, It has been shown that reducing FBA leads to cell death. This enzyme is present in the membrane and exposed on the bacterium's cell surface, and its association to virulence is already know as It binds to human plasminogen and mammalian cells (Shams et al. 2014). FBA and other proteins are expressed under conditions of alkaline stress, which indicates that this enzyme is also involved in the physiological breakdown of the bacterium during environmental changes. For these reasons, this protein has previously been recognized as a potential candidate for drug and vaccine targets in various pathogens such as bacteria, fungi and parasites of animals and humans (Pirovich et al. 2021)(Shams et al. 2014). SER 53 is hydrogen bonded to two oxygens (one from the pentose), HIS 212 is hydrogen bonded to an oxygen at the ligand end, and THR 29 is hydrogen bonded to one oxygen (O = S = O). THR 29, THR 33 and GLN 280 have a hydrophobic interaction with naphthalene.
The AcrR family of transcriptional regulators belongs to the one-component system and is associated with several essential cellular mechanisms of bacteria and archaea, such as cell signaling, carbon, nitrogen and lipid metabolism, amino acid metabolism and cofactor metabolism, production of antibiotics, among other physiological factors. They normally act as repressors, having different regulatory mechanisms in different species of bacteria, which can be positive or negative. In addition, these regulators play a key role in antibiotic resistance (Cuthbertson and Nodwell 2013). For these reasons, proteins from this family have been identified as a broad-spectrum drug target (Deng et al. 2013) and for novel treatments (Gonzáles et al. 2018). ARG 21 has two hydrogen bonds with the oxygen that is attached to the aromatic ring, ARG 92 has a hydrogen bond with an oxygen of the ligand. The two aromatic rings show hydrophobic interactions with VAL 73 and ARG 69.