The van Operons

Introduction

During bacterial cell wall (peptidoglycan) synthesis, two molecules of D-alanine are joined by a D-Ala:D-Ala ligase protein (Ddl). The resulting D-Ala:D-Ala dipeptide is added to uracil diphosphate-N-acetylmuramic acid-tripeptide, forming a pentapeptide. This species is attached to a lipid carrier, after which it is further modified to complete the peptidoglycan building block. The lipid carrier is then flipped to the outside of the cytoplasmic membrane, and the building block is added to the growing peptidoglycan chain through transglycosylation. Subsequently, the resulting peptidoglycan wall is strengthened by cross-links, which are catalyzed by transpeptidases that connect D-Ala:D-Ala groups on adjacent peptidoglycan chains. Click to learn more about the cell wall biosynthesis pathway.

In the growing peptidoglycan matrix (outside the bacterial cell), vancomycin binds to the D-alanyl-D-alanine C-terminus of the pentapeptide group. This introduces steric hindrance and prevents the necessary transpeptidase enzymes (penicillin-binding proteins or PBPs), from accessing the terminal D-Ala:D-Ala units and completing cell wall synthesis (Reynolds, 1989). This significantly weakens the cell, leaving it susceptible to osmotic lysis (Roper et al., 2000). Learn more about the mechanism of vancomycin action.

One common way bacteria become resistant to vancomycin is to alter the antibiotic’s target - i.e., replacing the terminal D-alanine residue of the pentapeptide group with either a D-lactate or D-serine residue (Figure 1). While vancomycin binds to the D-Ala:D-Ala terminus with high affinity (Figure 2), it has low affinity for termini with either D-lactate or D-serine (Munita and Arias, 2016).

Learn about other mechanisms of vancomycin resistance.

Gene clusters, called van operons, code for enzymes that alter the vancomycin target, leading to vancomycin resistance. These van operons are discussed here in detail.

Figure 1. Cartoon depicting the reduced affinity of vancomycin for the modified D-Ala:D-Ser or D-Ala:D-Lac terminal units of lipid II, which allows for the PBP enzymes to resume their function in completing cell wall biosynthesis.

The van Operons

The van operons are found in many types of bacteria and are thought to have originated within the bacterial species that produce glycopeptide antibiotics. Clinically, the most important bacterial pathogens containing van operons are the Enterococci, in which many variants of these operons have been found. Currently, nine types of operons have been identified in Enterococci, and are named types A, B, C, D, E, G, L, M, and N. There are both similarities and differences between the different van operons. Three key features of these operons are discussed here.

Altered Target

Each contains a minimal set of genes that encode the necessary remodeling enzymes; these enzymes degrade the D-Ala:D-Ala peptide and synthesize either D-Ala:D-lactate or D-Ala:D-Ser to replace it. Vancomycin and its peptide target form five hydrogen bonds with Di-acetyl-Lysine-D-Ala-D-Ala (PDB ID: 1FVM, Figure 2). Substitution of the terminal D-Ala with D-lactate results in the loss of one hydrogen bond (Roper et al., 2000), which decreases vancomycin’s affinity for the peptide 1,000-fold (Munita and Arias, 2016). On the other hand, the affinity of vancomycin for peptides ending in D-Ala:D-Ser is only about seven-fold lower than its affinity for D-Ala:D-Ala, so operons producing this structure are associated with a lower level of resistance (Courvalin, 2006).

Figure 2. Vancomycin forms five hydrogen bonds with di-acetyl-lysine-D-Ala:D-Ala (PDB ID: 1FVM, Nitanai et al., 2009). The substitution of D-lactate for the terminal D-Ala results in the loss of one hydrogen bond (shown by arrow); this loss significantly reduces vancomycin’s affinity for the peptide.

Operon regulation

Each operon also encodes two proteins, VanS and VanR, that form a two-component system that regulates the expression of the remodeling genes. These proteins are further discussed in the context of the vanA operon later.

Remodeling Enzymes

Different operons encode different remodeling enzymes, depending on whether the remodeling process replaces D-Ala:D-Ala with D-Ala:D-Lac or D-Ala:D-Ser. For example, the vanA, vanB, vanD, and vanM operons, which produce cell-wall peptides ending with D-Lac, include vanH, a gene encoding a dehydrogenase that converts pyruvate into D-lactate (Guffey and Loll, 2021; see Figure 3B). In contrast, the vanC, vanE, vanG, vanL, and vanN operons, which produce cell-wall peptides ending with D-Ser, contain the vanT gene, which encodes a serine racemase that converts L-serine to D-serine (see Figure 3C).

Figure 3. Comparison of different Van gene clusters. A. Steps in the biosynthesis of uridine diphosphate N-acetylmuramic acid pentapeptide with D-Ala:D-Ala termination. Vancomycin binds to this target with high affinity. B. Steps in the resistant pathway leading to the production of uridine diphosphate N-acetylmuramic acid pentapeptide with D-Ala:D-Lac termination. Vancomycin has reduced affinity for this product. C. Steps in the resistant pathway leading to the production of uridine diphosphate N-acetylmuramic acid pentapeptide with D-Ala:D-Ser termination. Vancomycin has reduced affinity for this product.

The vanA operon

The vanA operon, named after the VanA ligase protein, confers high-level vancomycin resistance by substituting the terminal D-alanine residue with D-lactate. The vanA operon confers resistance not only to vancomycin but also to the related glycopeptide antibiotic teicoplanin. The minimum inhibitory concentration (MIC) of vancomycin in vanA strains is 64-100 mg/L, while that for teicoplanin is 16-512 mg/L, which is also considered high-level resistance (Courvalin, 2006).

Type-A vancomycin resistance is carried by transposon 1546, a mobile genetic element first detected in a plasmid in Enterococcus faecium (Courvalin, 2006). The vanA operon in Tn1546 encodes seven proteins (Courvalin, 2006).

Two of the proteins coded by the van operons are VanR and VanS (Figure 4) which make up a gene expression regulatory system for the remainder of the operon (Roper et al., 2000). These two proteins control gene expression at the transcriptional level (Arthur et al., 1992). The operon contains two promoters, PR and PH; PR is upstream of the vanS and vanR genes, while PH is upstream of the genes encoding the remodeling enzymes. VanS is a membrane-bound histidine kinase that serves as a sensory protein. It modulates the phosphorylation state of VanR, a transcriptional activator needed for initiation at both promoters (Arthur and Quintiliani, 2001). Phosphorylation of VanR activates it as a transcription factor.

Figure 4. Schematic of vanA operon organization. The vanRS regulatory system is shown, in which the vanS sensor protein (colored red) initiates the signal transduction pathway. In inducing conditions, the VanR protein (colored blue) accepts the phosphate group from vanS and activates the transcription of resistance genes.

The VanS sensor enzyme has an N-terminal glycopeptide sensor domain and a C-terminal cytoplasmic kinase domain (Figure 5). The sensor domain detects the presence of the antibiotic and transduces a signal to the cytoplasmic domain (Arthur and Quintiliani, 2001). The mechanism by which VanS senses glycopeptide antibiotics is currently unknown. In any case, in vanA strains, both vancomycin and teicoplanin activate VanS. It was also found that moenomycin A, which is not a glycopeptide antibiotic, is also an activator of VanS. This suggests that VanS may be activated by a cell-wall intermediate (i.e., lipid II) which accumulates on the outside face of the cytoplasmic membrane when either moenomycin A or the glycopeptide antibiotics are used (Hong et al., 2008).

The cytoplasmic domain of VanS catalyzes ATP-dependent autophosphorylation of a histidine residue and then transfers the phosphate group to an aspartate residue in VanR (Courvalin, 2006). The cytoplasmic domain contains a dimerization and histidine-phosphorylation domain (DHp) and a catalytic and ATP-binding domain (CA). The structure of the VanS CA domain is known (Figure 5, Grasty et al., 2023).

Figure 5: Linear representation of the VanS protein and the structure of the CA domain of VanSA histidine kinase (PDB ID 8dvq, Grasty et al., 2023)

The VanR protein has two main domains - an N-terminal response-regulatory domain (colored blue in Figure 6), and a C-terminal DNA-binding domain (colored orange in Figure 6, Maciunas et al., 2021). An Asp residue (Asp51) at the center of the response regulatory domain is phosphorylated by VanS kinase. Part of the N-terminal domain is disordered in the inactive form of this protein (PDB ID 7lz9), but becomes ordered in the active form (PDB ID 7lza), allowing the protein to form dimers (not shown here). The conformational change resulting from phosphorylation allows the DNA binding domain to bind to the promoter regions of the operon. A side-by-side comparison of the inactive and active forms of VanR is shown in Figure 6.

Figure 6. Structure of the VanR protein: A. Inactive form of the protein (PDB ID 7lz9), and B. Active form of the protein (PDB ID 7lza, Maciunas et al., 2021)

The phosphorylation of VanR increases its affinity for both promoters, which activates the transcription of the resistance genes (Arthur and Quintiliani, 2001). Additionally, an amplification loop is created in which the binding of phosphorylated VanR to PR increases the transcription of vanR itself. This cycle results in the eventual accumulation of phosphorylated VanR (Arthur and Quintiliani, 2001). VanS can also act as a phosphatase that dephosphorylates VanR in non-inducing conditions (i.e., in the absence of the antibiotic; Courvalin, 2006). Consequently, VanS is needed for negative control of transcription to prevent the accumulation of phosphorylated VanR when the resistance proteins are no longer needed (Arthur and Quintiliani, 2001).

The next protein encoded by the operon is VanH, a dehydrogenase that reduces pyruvate to D-lactate (Courvalin, 2006), which is not otherwise produced by Enterococci. Thus, VanH is necessary for vancomycin resistance to build the required precursors for the modified cell wall (Cetinkaya, Falk, and Mayhall, 2000).

The next gene in the operon codes for the VanA protein. VanA utilizes the product of vanH and forms an ester bond between D-Ala and D-Lac to create a depsipeptide for the peptidoglycan cell wall (Figure 7, Walsh et al., 1996). Endogenous D-Ala:D-Ala ligase catalyzes the formation of a peptide bond between two D-alanine molecules; this product is then added to the stem peptide of UDP-muramic acid, a component of lipid II. VanA catalyzes a similar reaction, first binding and phosphorylating the D-alanine residue, then forming an ester bond with the second substrate, D-Lac, via a nucleophilic reaction. D-Ala:D-Ala ligase proteins share a 40% sequence identity with the VanA ligase and have similar functions. However, VanA differs from the D-Ala:D-Ala ligase enzymes in its selectivity for D-lactate (Roper et al., 2000). VanA can catalyze both peptide bond and ester bond formation but shows a preference for the latter. The imidazole ring of VanA residue His244 favors lactate binding over D-alanine, repelling the alanine zwitterion and attracting the negatively charged lactate to the second subsite (Roper et al., 2000).

Figure 7. The vanA ligase enzyme is shown. The conformation of the Histidine-244 residue is shown. The conformation of the residue is significant in allowing passage of D-lactate into the subsite and it brings the necessary chemistry for the switch between peptide and ester bond formation (PDB 1E4E, Roper et al., 2000).

In addition to the creation of these low-affinity precursors, the elimination of high-affinity precursors is also needed for resistance (Courvalin, 2006). Susceptible D-Ala:D-Ala can still be created from host D-Ala:D-Ala ligase enzymes, as well as from VanA's bifunctionality; this necessitates the proteins VanX and VanY to ensure resistance. VanX is a D,D-dipeptidase that hydrolyzes any D-Ala:D-Ala dipeptides synthesized (Courvalin, 2006). The structure of VanX from Enterococcus faecium shows that it is a globular, α+β class enzyme (Figure 8, Bussiere et al., 1998). The active site contains a zinc ion coordinated by His116, Asp123, His184, and a structural water. The Glu181 functions as a catalytic base while Arg71, within the hydrogen-bonding distance of the catalytic water, functions as a transition state stabilizer.

Figure 8. Structure of VanX from Enterococcus faecium (PDB ID 1r44, Bussiere et al., 1998). The inset shows a closeup of the active site with catalytic residues (in pink) and bound zinc.

The next protein coded by this operon is VanY, a D,D-carboxypeptidase. This enzyme removes the C-terminal D-Ala residue of D-Ala:D-Ala precursors that have escaped vanX hydrolysis (Abadía-Patiño et al., 2004). Since the VanY ortholog present in the vanB operon is the most important in vancomycin resistance (Kim et al., 2018), it is discussed in the VanB type operon section. The function of the final protein in the vanA operon, VanZ, is currently unknown (Roper et al., 2000).

The vanB operon

The vanB operon (Figure 9) is named after the VanB ligase protein and confers a variable level of resistance with MIC of vancomycin ranging from 4-1000 mg/L (Courvalin, 2006). Just like vanA, vanB operons also confer resistance by adding a D-lactate terminal in the lipid II peptidoglycan precursors. The vanB resistance gene clusters are primarily carried on Tn916-like conjugative elements, however, two related elements Tn5382 and Tn1549 have been identified in strains in the US and Europe (Courvalin, 2006). VanA strains have high levels of resistance to both vancomycin and teicoplanin. However, vanB strains only confer resistance to vancomycin since this operon is only induced by vancomycin (Courvalin, 2006).

Figure 9. Schematic of VanB operon organization.

The next enzyme coded by the vanB operon is VanY, a D,D-carboxypeptidase. This recognizes the peptidyl-D-Ala:D-Ala terminus of lipid II and hydrolyses the terminal D-Ala. This step creates the substrate for the D-Ala:D-Lac ligase. The VanY_B protein has a transmembrane segment (not shown in Figure 10), and short N- and C-terminal domains around the main carboxypeptidase domain (Figure 10, PDB ID 5zhw). The D-Ala:D-Ala substrate binds to the active site, near Glu or E238 (the proton donor/acceptor participating in the catalysis).

Figure 10. Linear representation of the VanYB protein and the structure of D-Ala:D-Ala carboxypeptidase domain (PDB ID 5zhw, Kim et al., 2018)

The vanY gene in the operon is followed by vanW. This gene is exclusive to vanB strains and currently has an unknown function (Courvalin, 2006). The next 3 proteins are VanH, VanB, and VanX which are very similar to the VanH, VanA, and VanX proteins in the vanA type resistance (Evers and Courvalin, 1996). Here too, VanH functions as a dehydrogenase which creates the D-lactate. VanB uses the D-lactate as a substrate to create D-Ala:D-Lac dipeptides, while VanX is a D,D-dipeptidase that eliminates any susceptible D-Ala:D-Ala precursors.

The vanC operon

The vanC operon encodes low-level resistance to vancomycin, with MICs ranging from 2-32 mg/L (Courvalin, 2006). VanC is intrinsic to E. gallinarum, E. casseliflavus, and E. flavescens, and this operon is located chromosomally. Moreover, like vanB strains, vanC strains are still susceptible to teicoplanin (Courvalin, 2006).

The proteins coded by the vanC operon (in order) are VanC, VanXY_C, vanT, and then the vanRS regulatory system (Figure 11).

Figure 11. Schematic of VanC operon organization.

The VanT protein is a membrane-bound serine racemase, which converts L-serine to D-serine. An example of a VanT enzyme is shown in the vanG operon section. D-serine substitutes the terminal D-alanine, similar to how D-lactate does in vanA and vanB (Courvalin, 2006). D-serine will be used by the vanC ligase enzyme to create the D-Ala:D-Ser dipeptide.

The structure of D-Ala:D-Ser bound to vancomycin (PDB ID 8G82, Figure 12) shows that it forms similar hydrogen bonds as the D-Ala:D-Ala substrate. However, the extra hydroxyl group changes the size of the antibiotic leading to its weaker binding to the antibiotic (Park et al., 2024).

Figure 12. Structure of vancomycin bound to D-Ala:D-Ser (PDB ID 8G82, Park et al., 2024)

VanA and vanB strains contain separate vanX and VanY proteins, which have D,D-dipeptidase and D,D-carboxypeptidase functions, respectively. In the vanC operon, the vanXY_C protein has both functions allowing for the elimination of peptides ending in D-Ala:D-Ala to ensure resistance (Courvalin, 2006).

The vanD operon

The vanD operon encodes moderate-level resistance to vancomycin (MIC of 64-128 mg/L) and teicoplanin (MIC of 4-62 mg/L). The vanD operon is located only chromosomally and is not transferable by conjugation, and resistance is due to the production of D-Ala:D-Lac ending precursors (Courvalin, 2006). The operon begins with a vanRS gene expression regulatory system, followed by vanY (D,D-carboxypeptidase), vanH (dehydrogenase), vanD (D-alanine:D-lactate ligase), and vanX (D,D-dipeptidase) (Figure 13). Despite having a vanX protein, there is negligible D,D-dipeptidase activity; while this could lead to the retention of susceptibility, the endogenous D-Ala:D-Ala ligase is inactive so vancomycin resistance is preserved (Courvalin, 2006).

Figure 13. Schematic of vanD operon organization.

Notably, vanD is expressed constitutively rather than inducibly due to mutations in the vanRS genes. It was found that there was no difference between the precursors produced by induced and uninduced cells, demonstrating that there is no requirement for glycopeptides to be present for D-Ala:D-Lac to be produced (Depardieu et al., 2003b).

The vanE operon

The vanE operon encodes low-level resistance to vancomycin (MIC of 8-32 mg/L) and remains susceptible to teicoplanin. This type of resistance is located only chromosomally (Courvalin, 2006). vanE (Figure 14) has a similar organization and biochemistry as the vanC operon. The first gene codes for the VanE ligase, which catalyzes the synthesis of D-Ala:D-Ser dipeptide. The next protein is VanXYE, a bifunctional D,D-dipeptidase and D,D-carboxypeptidase; followed by vanTE, which is a membrane-bound serine racemase that converts L-serine to D-serine. Downstream of this is the VanRS gene expression regulation system (Abadía-Patiño et al., 2004).

Figure 14. Schematic of VanE operon organization.

The vanG operon

The vanG operon encodes low-level resistance to vancomycin (MIC of 16 mg/L) and remains susceptible to teicoplanin. This operon is found chromosomally and confers resistance by producing precursors that end in D-Ala:D-Ser. The operon begins with vanU, vanR, and vanS genes, whose products regulate gene expression (Figure 15).

Figure 15. Schematic of vanG operon organization.

While the VanRS proteins are functional, VanU provides an additional level of regulation by binding to the PUG regulatory promoter. By competing with VanR, VanU negatively autoregulates the transcription of vanURS genes from that promoter (Depardieu et al., 2015). This repression was demonstrated in mutants without vanU, which showed higher transcriptional levels for vanR and vanS. This additional level of regulation benefits the bacteria by reducing the fitness cost of resistance.

In the presence of vancomycin, vanG mutants without vanU showed less relative growth indicating resistance is more costly in the absence of the VanU protein (Depardieu et al., 2015). Downstream of vanURS is vanY. However, the VanY protein contains a frameshift mutation disabling its D,D-carboxypeptidase function (Depardieu et al., 2003a). The next protein is VanW with an unknown function, followed by the VanG, a D-Ala:D-Ser ligase; VanXY_G, a bifunctional enzyme with D,D-dipeptidase and D,D-carboxypeptidase activities.

Finally, VanT_G, a serine racemase, is required to produce D-Ala:D-Ser-terminating pentapeptides. The main function of this enzyme is to convert L-Ser to D-Ser. The VanT protein has two domains - an N-terminal membrane-bound domain (shown in the linear representation of the protein at the top of Figure 16) that potentially takes up L-Ser and a C-terminal cytoplasmic domain that catalyzes the enzyme’s function (Figure 16). Bacteria have PLP-dependent alanine racemases that catalyze the conversion of L-Ala to D-Ala. These enzymes are required for cell wall synthesis. The catalytic domain of VanT_G and alanine racemases are similar in structure, suggesting that the former may have evolved from alanine racemases. However, the VanT enzyme has a larger active site to accommodate D-Ser, and the membrane-bound N-terminal domain may have a role to play in its specificity for L-Ser (Meziane-Cherif et al., 2015).

Figure 16. Linear representation of the VanTG protein and the structure of serine racemase (PDB ID 4ecl, Meziane-Cherif et al., 2015)

Other van Operons

A few other van operons have also been identified, e.g., vanL, vanM, and vanN (Figure 17). While the organization of the operons vanL and vanN are similar to vanE, that of vanM is similar to vanD.

Figure 17. Schematic of genes organized in vanL, M, and N operons.

A summary of the various van operons leading to resistances is included in Table 1.

Table 1. Types of van operons seen in vancomycin-resistant Enterococci (VRE) and some of their key properties (Ahmed and Baptiste, 2018)

Clinical Implications of Resistance Through van Operons

Until the 1980s, vancomycin was regarded as the last-resort antibiotic for managing severe infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and other multidrug-resistant gram-positive pathogens. However, since that time vancomycin-resistant strains of Enterococci (VRE) have been spreading rapidly. While all these strains confer resistance to vancomycin, they have proved to contain a variety of operons containing different van genes.

Most common van operons, e.g., the vanA gene cluster, are carried on transposons or plasmids. They are transferred between different enterococci by conjugation and/or through transposition; notably this method of transmission could conceivably transfer resistance to non-enterococcal species. The emergence of vancomycin resistance in Enterococcus and Staphylococcus aureus has become a serious public health concern for human and animal health (Ahmed and Baptiste, 2018.) Recently, a vanA operon was found integrated into the bacteria, via homologous recombination. Thus instead of possibly losing the gene (e.g., absence of inducers), chromosomal integration ensures vertical transmission of these gene clusters through generations (Vo et al., 2024).

The emergence of vancomycin and multi-drug resistance in different bacteria warrants careful attention, continuous monitoring, and antimicrobial stewardship.

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April 2025, Sameer Ahmad, Shuchismita Dutta; Reviewed by Dr. Patrick Loll
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/amr-mech/van-operon