Overview
Aminoglycoside Modifying Enzymes
Beta lactamase

Overview

Introduction

Ever since Alexander Fleming’s famous discovery of penicillin in 1928, antibiotics have continued to revolutionize medicine, allowing treatment of infections and making it possible for patient to have surgical procedures with full and speedy recovery. However, as the threat of antimicrobial resistance (AMR) continues to grow, the benefits of using antibiotics is diminishing. Why is this significant? When a bacterium is resistant to the effects of a certain antibiotic, the bacterium will not die even in the presence of that antibiotic. So if a physician prescribes the antibiotic to treat a bacterial infection, but the bacteria are resistant to the drug, the drug will not work and patient management is significantly complicated. Antimicrobial resistant infections claim at least 50,000 lives annually in the US and Europe alone (Review on Antimicrobial Resistance, 2014). Staphylococcus aureus is one of the most prevalent causes of bacterial infection in humans, and approximately 60% of these infections are resistant to a drug called methicillin, causing an estimated 11,000 deaths per year (Ali, Rafiq, & Ratcliffe, 2018). These numbers will only continue to rise with the continued misuse of antibiotics, and medicine will regress significantly as these drugs lose their utility over time (Ali, Rafiq, & Ratcliffe, 2018). The goal now is to control the dangers of AMR and preserve the function of clinical antibiotic use. Understanding the mechanisms of antibiotic resistance is critical for developing ways to combat AMR and to develop new antibiotics to uphold the modern practice of medicine.

The Source of Resistance: Genes

While antibiotic resistance is seemingly a modern issue, this crisis predates the market use of antibiotics beginning in the 1940s (Munita & Arias, 2016). Resistance genes to β-lactam, tetracycline and glycopeptide antibiotics were identified in 30,000 year old Beringian permafrost sediments found in Yukon, Canada (D’Costa et al., 2011). Why were such genes present in a time before humans began using antibiotics? This is because organisms, such as fungi, have been coexisting with bacteria for millennia, and in order to survive they evolved mechanisms, such as producing antibiotic molecules, in order to kill the bacteria that they competed with. In response bacteria, with their high degree of genetic plasticity, also evolved ways to survive in these circumstances. In an environment now filled with antibiotic molecules from organisms like fungi, bacteria developed various resistance mechanisms in order to ensure their own survival (Figure 1). These mechanisms are encoded as genes found in bacterial DNA, the same way hair and eye color are encoded in human DNA. These genes can be spread from commensal and environmental species to pathogenic bacteria, giving them an "acquired" resistance (von Wintersdorff et al., 2016).

Figure 1. Depiction of natural selection, causing resistant bacteria to emerge and susceptible bacteria to be eliminated. This is due to antibiotic molecules synthesized by organisms, such as fungi, which share the same niche as the bacteria.
Figure 1. Depiction of natural selection, causing resistant bacteria to emerge and susceptible bacteria to be eliminated. This is due to antibiotic molecules synthesized by organisms, such as fungi, which share the same niche as the bacteria.

Acquired resistance genes can come about through mutations or spread through horizontal gene transfer (HGT, Figure 2). Among the mechanisms of HGT, conjugation has the greatest influence in the dissemination of resistance genes. Conjugation is the transfer of mobile genetic elements, such as plasmids and transposons, through a pili structure which assembles between 2 adjacently located bacteria. Transduction is the HGT mechanism in which bacterial DNA is transferred via bacteriophages which infect one bacterium, take up bacterial DNA, and transfer the DNA to another bacteriophage susceptible bacteria. Finally, transformation is the acquisition of foreign DNA into a competent bacterial cell (von Wintersdorff et al., 2016).

Figure 2. Depiction of the fundamental methods of horizontal gene transfer. Cartoons created using Servier Medical Art.
Figure 2. Depiction of the fundamental methods of horizontal gene transfer. Cartoons created using Servier Medical Art.

Along with these horizontal gene transfer mechanisms, mutations provide a way for new bacterial genotypes to form (Thomas & Nielsen, 2005). With a means for resistance genes to spread, the increased selection pressure from anthropological antibiotic use creates the perfect environment for resistant bacteria to dominate. From 2000 to 2010, global human antibiotic use increased by 36%, reaching nearly 74 billion standard units (von Wintersdorff et al., 2016). Antibiotic use is even greater in animals, as it is used to increase growth and lengthen life in farming conditions. This incessant use of antibiotics allows for strains with resistance genotypes to proliferate and dominate, increasing the pool of resistant bacteria, while susceptible bacteria selectively die off. This increases the prevalence of resistance, further strengthens infections from antibiotics, and can even lead to the development of superbugs. Learn more about development of antimicrobial resistance and why we should care about it.

Resistance Mechanisms

It is established that genes are the source of not only bacterial resistance, but the dissemination of resistance as well. But how do genes actually stop bacterial cells from dying? Resistance genes encode proteins which carry out the functions needed for the resistance mechanisms. Resistance to one antibiotic class can be accomplished through multiple pathways, and one bacterium can harbor multiple mechanisms by having multiple resistance genes. The major mechanisms of antibiotic resistance are classified into the following categories (Munita & Arias, 2016) and summarized in Figure 3:

Major Category CARD Ontology
1. Modification of antimicrobial molecule Antibiotic Inactivation
2. Decreased permeability to the antibiotic target
A. Modified Porins Reduced Permeability to Antibiotic
B. Efflux Pumps Antibiotic Efflux
3. Modification of target site
Antibiotic Target Alteration
Antibiotic Target Replacement
Antibiotic Target Protection
4. Global Cellular Adaptations modification to cell morphology
Figure 3: Depiction of the different resistance mechanism types. Green layer between inner and outer membrane is the peptidoglycan layer. The outer membrane shown in the figure is only present in gram negative bacteria; gram positive bacteria have the green peptidoglycan layer as their outermost layer. Cartoons created using Servier Medical Art.
Figure 3: Depiction of the different resistance mechanism types. Green layer between inner and outer membrane is the peptidoglycan layer. The outer membrane shown in the figure is only present in gram negative bacteria; gram positive bacteria have the green peptidoglycan layer as their outermost layer. Cartoons created using Servier Medical Art.

Modification of Antimicrobial Molecule

The antibiotic modification mechanism is a pathway which entails chemically altering antibiotic molecules to render them ineffective. Bacteria may possess enzymes which may do one of two things:

  1. Add certain chemical groups to the antibiotic molecule
  2. Break bonds within the antibiotic molecule

An example of resistance caused by adding chemical groups to the drug molecule is through the aminoglycoside modifying enzymes (AMEs). AMEs catalyze acetylation, phosphorylation, and adenylation of aminoglycoside antibiotics. These reactions involve transferring chemical groups to the antibiotic drug molecule which causes steric hindrance (Figure 4 and 5), which simply means the altered antibiotic is now too big to bind to its target, rendering it ineffective in killing bacteria (Munita & Arias, 2016).

Figure 4. Schematic of aminoglycoside modifying enzyme classes. [AMP = adenosine monophosphate; NH2 = amino group; OH = hydroxyl group] (Ramirez & Tolmasky, 2010).
Figure 4. Schematic of aminoglycoside modifying enzyme classes. [AMP = adenosine monophosphate; NH2 = amino group; OH = hydroxyl group] (Ramirez & Tolmasky, 2010).
Figure 5. Example chemical transformations catalyzed by the aminoglycoside enzymes. Figure created using ChemDraw.
Figure 5. Example chemical transformations catalyzed by the aminoglycoside enzymes. Figure created using ChemDraw.

Antibiotic modification also encompasses breaking bonds within the drug molecule. The famous example of this form of resistance is through the β-lactamase enzymes which destroy drugs in the class of antibiotics known as β-lactams. β-lactam antibiotics are named after their 4 membered amide ring which is critical to their function in killing bacteria (Fernandes, Amador, and Prudêncio, 2013). β-Lactamase enzymes inactivate β-Lactam antibiotics by breaking the amide bond (shown in red in Figure 6). Breaking this bond opens the β-Lactam ring which takes away its potential to kill the bacteria.

Figure 6. Structural formula of Penicillin G, a β-lactam, and the resulting destroyed molecule after enzymatic destruction of the amide bond. The amine ring is colored red and blue. The amide bond which breaks is colored in red. Figure created using ChemDraw.
Figure 6. Structural formula of Penicillin G, a β-lactam, and the resulting destroyed molecule after enzymatic destruction of the amide bond. The amine ring is colored red and blue. The amide bond which breaks is colored in red. Figure created using ChemDraw.

The discovery of β-Lactamase mediated resistance initiated the development of new β-Lactam drugs that preserved bactericidal functions despite these enzymes. However, the creation of new drugs was always accompanied by the evolution of new β-Lactamases which could destroy them. This arms race between synthetic chemists and bacteria has resulted in many β-Lactamase enzymes and β-Lactam drugs.

Learn more about β-Lactam antibiotics, their targets in the bacterial cell, and the β-Lactamase enzyme mediated drug resistance.

Reduced Permeability to the Antibiotic

Antibiotic drugs with targets inside of the cell require mechanisms that allow them to penetrate the cell membrane and access their intracellular target sites. Decreasing this permeability, or the ability of an antibiotic to access the intracellular domain, is another mode of action for resistance. The cell membrane of bacteria is made from a phospholipid bilayer consisting of non-polar, hydrophobic fatty acids forming the interior of the bilayer, and polar, hydrophilic phosphate molecules forming the exterior. This bilayer is relatively impervious to polar, hydrophilic molecules. Thus, hydrophilic antibiotic molecules, such as β-Lactams and tetracyclines, may use aqueous diffusion channels, also known as porin proteins, to cross the cell membrane to access their target (Munita & Arias, 2016). Porins are integral proteins, which means they span the entire length of the cellular membrane, which allow polar hydrophilic molecules into the cell which normally cannot diffuse through the lipid bilayer of the cell.

By changing the types of porins that are expressed, or the level of porin expression, certain antibiotics can no longer enter the cell to access their targets, thus creating resistance. For example, in the bacteria Klebsiella Pneumoniae, decreased susceptibility to β-Lactam drugs results from a switch in porin expression to OmpK36 which has a smaller channel size, allowing less of the drug to pass into the cell (Dutzler et al., 1999, Figure 7).

Figure 7: A monomer of the osmoporin OmpK36 is shown in relative position in the outer cell membrane of a Klebsiella Pneumoniae (gram-negative) bacterium. It’s smaller channel size leads to decreased β-Lactams permeability [PDB ID: 1OSM] (Dutzler et al., 1999). Cartoons created using Servier Medical Art.
Figure 7: A monomer of the osmoporin OmpK36 is shown in relative position in the outer cell membrane of a Klebsiella Pneumoniae (gram-negative) bacterium. It’s smaller channel size leads to decreased β-Lactams permeability [PDB ID: 1OSM] (Dutzler et al., 1999). Cartoons created using Servier Medical Art.

Another mechanism of antimicrobial resistance is decreasing antibiotic permeability into the cellular domain is by actively pumping them back out. Efflux pumps are enzymatic “machines” that are capable of extruding antibiotic molecules from the cell. There are 5 major classes of efflux pumps which differ in their structure, energy source, substrate specificity, and distribution among bacteria:
1. Major facilitator superfamily (MFS)
2. Small multidrug resistance family (SMR)
3. Resistance-nodulation-cell-division family (RND)
4. ATP-binding cassette family (ABC)
5. Multidrug and toxic compound extrusion family (MATE)

Shown below is the AcrAB-TolC system, found in E. coli. This efflux pump extrudes antibiotics by the orchestrated functions of 3 separate proteins: AcrB, AcrA, and TolC (Figure 8).

Figure 8. AcrAB-TolC system shown in relative location in an E. coli cell (gram negative), PDB ID 5O66, (Wang et al., 2017). Cartoons created using Servier Medical Art.
Figure 8. AcrAB-TolC system shown in relative location in an E. coli cell (gram negative), PDB ID 5O66, (Wang et al., 2017). Cartoons created using Servier Medical Art.

The AcrB protein is a protein located in the inner membrane which binds the antibiotic molecules found in the cell. The AcrA protein serves as a linking protein to the TolC protein. TolC is a protein channel located in the outer membrane. Through conformational changes in these proteins, antibiotics are pumped out of TolC and into the extracellular environment (Munita & Arias, 2016).

Modifications of Target Site

Bacteria can confer resistance by modifying the target site of the drug itself. There are numerous components to the cell wall biosynthesis pathway, so there are many different ways to alter a drug target and confer drug resistance. Click to learn more about the cell wall biosynthesis pathway.

These modifications result in decreased affinity between the target site and the drug. Bacteria can alter their target sites in 4 ways: a. Protection of target site; b. Gene alterations (pre-translational modifications); c. Enzymatic alterations (post-translational modifications); and d. Substitution of original target

Protection of Target Site

Target site protection entails preventing the antibiotic from reaching its target through mechanisms other than decreased permeability. An example of this is the TetM enzyme. TetM dislodges tetracycline antibiotic molecules from their binding site in the ribosome of the bacterial cell. Additionally, TetM prevents rebinding of the drug by altering the ribosomal conformation (Munita & Arias, 2016).

Genetic Alterations of the Target Site

Bacteria can modify the genes which encode the target site. This is known as pre-translational alterations. By altering the RNA (the "blueprint" of a protein), once the RNA is translated into a protein, the protein will contain the modified target site that the drug has less affinity for. These modifications can arise from point mutations in genes. An example of this is through a point mutation in the rpoB gene which encodes the bacterial RNA polymerase. This genetic alteration changes the target site of the antibiotic rifamycin; rifamycin now has decreased affinity for this new target site, resulting in resistance (Munita & Arias, 2016).

Enzymatic Alterations

Post-translational enzymatic alteration of a target site occurs once the protein has already been translated from the RNA; these alterations can be fulfilled through many pathways. One classical example is through the Erm enzymes which confer macrolide resistance. These enzymes can transfer methyl groups to an adenine residue in the bacterial ribosome. Macrolides target the ribosome but with the steric hindrance from the methyl groups on the binding site for the drug, the drug has reduced affinity for its target, resulting in resistance (Munita & Arias, 2016).

Substitution of the Original Target

Replacement of the target site for a less susceptible target (with reduced affinity) while preserving biochemical function is another resistance mechanism that bacteria have evolved. In vancomycin resistant Enterococci, the susceptible target site is replaced with one that has reduced affinity from vancomycin. Vancomycin binds to terminal D-Alanyl-D-Alanine units of the pentapeptide group of the peptidoglycan cell wall. Resistant bacteria have completely substituted the final D-Alanine unit for other units such as D-Lactate or D-Serine. Vancomycin has reduced affinity for these units, resulting in reduced antibiotic action, and in other words, vancomycin resistance (Munita & Arias, 2016).

Global Cell Adaptations

The final category of resistance mechanism is global cell adaptations, which entails complex cellular changes to resist antibiotic molecules. These mechanisms can be manifested in diverse ways. Daptomycin resistance is the noteworthy resistance mechanism from this category. Daptomycin is a lipopeptide antibiotic that complexes with calcium ions, giving the molecule an overall positive charge. The molecule passes into the membrane, forms oligomers, and creates a pore-like structure in the cell membrane which results in bacterial death (Figure 9, Munita & Arias, 2016).

Figure 9. Process by which Daptomycin causes cell death is shown, sequenced chronologically from top to bottom. Cartoons created using Servier Medical Art.
Figure 9. Process by which Daptomycin causes cell death is shown, sequenced chronologically from top to bottom. Cartoons created using Servier Medical Art.

To confer resistance to daptomycin, resistant strains of Enterococci use a mutated regulatory system which modifies the cell membrane to have a positive charge which repels the cationic daptomycin-calcium complexes, resulting in daptomycin resistance (Arias et al., 2011).

Conclusion

These resistance mechanisms form the basis of the immeasurable threat of AMR. While these classifications may be simple, they encompass a diverse array of mechanisms, many of which require more investigation. Moreover, many mechanisms active in nature have yet to be described in scientific literature. For these reasons, AMR is a difficult crisis for scientists to combat, yet its threat on patients grows everyday. For every drug used in treatment, a resistance mechanism exists. With the genetic plasticity of bacteria, there is the potential for these mechanisms to spread, rendering the antibiotics mankind depends on ineffective. The World Health Organization has ranked AMR as one of the top 10 health threats of the as of 2019 (WHO, 2019), and for good reason. The impending post-antibiotic era will result in the collapse of current medical protocols and treatment, and we will be left with no way to manage ailments that were once treatable.

References

Ali, J., Rafiq, Q., and Ratcliffe, E. (2018) Antimicrobial resistance mechanisms and potential synthetic treatments. Future Science OA 4, FSO290.

Arias, C., Panesso, D., McGrath, D., Qin, X., Mojica, M., Miller, C., Diaz, L., Tran, T., Rincon, S., Barbu, E., Reyes, J., Roh, J., Lobos, E., Sodergren, E., Pasqualini, R., Arap, W., Quinn, J.,

Shamoo, Y., Murray, B., and Weinstock, G. (2011) Genetic Basis for In Vivo Daptomycin Resistance in Enterococci. New England Journal of Medicine 365, 892-900.

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Dutzler, R., Rummel, G., Albertí, S., Hernández-Allés, S., Phale, P., Rosenbusch, J., Benedí, V., and Schirmer, T. (1999) Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae. Structure 7, 425-434.

Fernandes, R., Amador, P., and Prudêncio, C. (2013) β-Lactams. Reviews in Medical Microbiology 24, 7-17.

Munita, J., and Arias, C. (2016) Mechanisms of Antibiotic Resistance. Virulence Mechanisms of Bacterial Pathogens, Fifth Edition 481-511.

Ramirez, M., and Tolmasky, M. (2010) Aminoglycoside modifying enzymes. Drug Resistance Updates 13, 151-171.

Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations. 2014.

Thomas, C., and Nielsen, K. (2005) Mechanisms of and Barriers to, Horizontal Gene Transfer between Bacteria. Nature Reviews Microbiology 3, 711-721.

von Wintersdorff, C., Penders, J., van Niekerk, J., Mills, N., Majumder, S., van Alphen, L., Savelkoul, P., and Wolffs, P. (2016) Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Frontiers in Microbiology 7.

Wang, Z., Fan, G., Hryc, C., Blaza, J., Serysheva, I., Schmid, M., Chiu, W., Luisi, B., and Du, D. (2017) An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. eLife 6.

World Health Organization (2019) Ten health issues WHO will tackle this year. Who.int.

Authors: Sameer Ahmed, Helen Gao


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