Crossroads of Antibiotic Resistance and Biosynthesis

Abstract

The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.

Keywords: adjuvant; antibiotic resistance; combination therapy; hybrid antibiotics; natural product biosynthesis.

Figure 1.

The ancient antibiotics sisomicin and tetracycline are enzymatically inactivated by aminoglycoside acetyltransferase AAC(2’)-Ia and tetracycline monooxygenase TetX, respectively. The plazomicin and eravacycline scaffolds are derived from the parent sisomicin and tetracycline scaffolds, respectively, and were FDA approved for human use in 2018. Plazomicin and eravacycline have been structurally optimized to overcome some of the established clinical resistance mechanisms for aminoglycoside and tetracycline antibiotics, respectively, and could potentially select for new clinical resistance mechanisms of ancient origin, such as enzymatic inactivation.

Figure 2.

Macrolide resistance in producers and competing microbes.

Figure 3.

Reversible modification of tabtoxinine-beta-lactam (TBL) by amino acid ligase TblF to form the pro-drug TBL-Thr dipeptide in P. syringae. Irreversible modification of TBL by GNAT acetyltransferase Ttr confers resistance in competing microbes.

Figure 4.

Resistance evolves with chemistry. (a) Hydrolysis of strained beta-lactam ring in penicillin by a beta-lactamase. (b) Oxidation of electron rich C11a-enol in tetracycline by a tetracycline destructase C4a-flavin peroxy intermediate.

Figure 5.

Evolution of antibiotic inactivating enzymes. (a) Evolution of beta-lactamases from target d,d-transpeptidases. (b) Evolution of protein kinase into a macrolide inactivating enzyme. (c) Evolution of a tetracycline inactivating enzyme (“antibiotic destructase”) from a biosynthetic flavin monooxygenase (“antibiotic constructase”). (d) Evolution of an endiyne self-sacrificing protein from a substrate binding protein.

Figure 6.

Comparison of macrolide inactivating enzymes used for resistance (macrolide esterase), self-protection (macrolide glycosyltransferase), and general metabolic housekeeping (demethylase) in microbes. Chemical modifications of the macrolide erythromycin are highlighted in blue with the site of functional group modification highlighted by a yellow circle.

Figure 7.

Dissemination of ARGs from soil to the human gut. Ancient antibiotic resistance to the natural cephalosporin can be a source of resistance to the man-made cephalosporin used in hospitals when ARGs from a BGC are mobilized on plasmids. This natural phenomenon can be leveraged for resistance-guided antibiotic discovery (left) to prospect for new antibiotics and functional metagenomic screens (right) to prospect for emerging resistance. The image of soil was obtained from pixabay.com and is free for use in the public domain.

Figure 8.

Co-production of antibiotic (black) and adjuvant (blue) to overcome resistance during microbial competition. (a) Transcription of the beta-lactam “super” BGC in S. clavuligerus results in co-production of cephamycin C and clavulanic acid, a beta-lactam antibiotic/beta-lactamase inhibitor combination that rescues beta-lactam antibacterial activity against competing microbes expressing beta-lactamase resistance enzymes. (b) Similarly, co-production of anhydrotetracycline (aTC), a tetracycline destructase inhibitor, and tetracycline (TC), a ribosome inhibitor, might provide a competitive advantage against microbes expressing tetracycline destructase resistance enzymes.

Figure 9.

Co-production of synergistic antibiotic combinations to improve potency and limit resistance development. (a) Sulfazecin and bulgecin BGCs in Paraburkholderia acidophila ATCC 31363 are arranged as a “super cluster”. (b) Mupirocin and jessenpeptin BGCs in amoeba-associated Pseudomonas sp. QS1027 are co-regulated by LuxR/LuxI-type quorum sensing (QS) systems. Genes are color coded blue or black to match biosynthetic products (green genes are regulatory).

Figure 10.

Biosynthesis and activation of hybrid antibiotics to improve potency, engage multiple biological targets, and limit resistance development. (a) Albomycin BGC from Streptomyces sp. ATCC 700974 encodes an amide synthetase AbmC that presumably ligates the siderophore and Ser-tRNA synthetase inhibitor components to form the hybrid sideromycin antibiotic. (b) Thiomarinol BGC from Pseudoalteromonas spp. SANK73390 encodes for a CoA-ligase TmlU and acyl transferase HolE that ligates the mupirocin and holomycin components to form the hybrid thiomarinol antibiotic. Genes are color coded to match biosynthetic products.

Figure 11.

Biosynthetic promiscuity as a source of antibiotic cocktails. (a) Pikromycin biosynthesis in Streptomyces venezuelae produces a pool of 12- and 14-membered macrolides with varying degrees of side chain oxidation. Genes are color coded as defined in the legend where the color of biosynthetic genes match the structural fragment derived from catalysis by enzyme gene products. (b) Prochlorosin biosynthesis in Prochlorococcus MIT9313 generates a library of structurally diverse lantipeptides with unique ring topologies from genetically encoded precursor peptides and a single lanthionine synthetase ProcM with low substrate selectivity. The procM gene is shown in red while all genes encoding product precursor peptides are shown in blue.