Global evolution of glycosylated polyene macrolide antibiotic biosynthesis
Introduction
Antibiotics are the most important secondary metabolites of environmental microbes. They can not only eliminate or inhibit the competitors in living environments, but also play signaling and regulatory roles in microbial communities (Aminov, 2009). Meanwhile, many types of antibiotics are essential for ecological balance and harmonious coexistence of the producers and their hosts. Polyene macrolides (PEMs) are a series of widespread polyketide antibiotics (Jørgensen et al., 2009) as the main anti-pathogenic fungal agents of many actinomycetes in diverse environments, as well as the primary weapons (from symbiotic actinomycetes) used by leaf-cutting ants to protect their fungus culture gardens (Haeder et al., 2009). Moreover, some of PEMs have been successfully developed as antifungal drugs and food preservatives (Caffrey et al., 2016).
PEMs possess large macrolactone rings with a series of conjugated double bonds and can be classified according to the modification patterns: the glycosylated PEMs (gPEMs) such as nystatin (Fig. 1b) and the non-glycosylated PEMs (nPEMs) such as filipin. Currently, most of PEMs isolated from nature and widely used in clinics and industries are gPEMs, which have been well studied in biosynthetic pathways. To date, a total of ten gPEM biosynthetic gene clusters have been completely sequenced, designated as nys (for nystatin) (Fjaervik & Zotchev, 2005), amph (for amphotericin) (Caffrey et al., 2001), cpp (for NPP) (Kim et al., 2009), fsc (for FR-008/candicidin) (Chen et al., 2003), pim (Aparicio et al., 2000)/sgn (Wang et al., 2016)/scn (Du et al., 2011) (for pimaricin), tetr (Cao et al., 2012)/ttm (Ren et al., 2014) (for tetramycin) and ace (for 67-121C) (Sheehan et al., 2017). Also, per (for perimycin) (Hutchinson et al., 2010), rim (for rimocidin/CE-108) (Seco et al., 2004), can (for candicidin) (Gil & Campelo-Diez, 2003) and nyp (for nystatin P1) (Barke et al., 2010) were partially identified (Fig. 1a). We have noticed that almost all of the natural gPEMs used as antibiotics or preservatives are 26/28-membered rings with tetraene structures or 38-membered rings with heptaene/heptaene-like structures. Interestingly, although there are large differences among the macrolactone rings, the basic skeleton and tailoring parts are quite conserved, containing an exocyclic carboxyl group and an unusual sugar moiety named mycosamine (Fig. 1b). As expected, all identified gPEM biosynthetic pathways are similar substantially.
gPEM biosynthesis begins with a repetitive decarboxylative condensation of an activated starter unit with methylmalonyl- or malonyl-CoA-derived extender units to form a growing polyketide chain, catalyzed by type I polyketide synthases (PKSs). Following the cyclization of polyketide chain, a type of cytochrome P450 (P450I) participates in the formation of the carboxyl group. GDP-mannose 4, 6 dehydratase (GMD) and GDP-ketosugar aminotransferase (GKA) take part in sugar biosynthesis and the sugar moiety is attached to the macrolactone ring by glycosyltransferase (GT) after the formation of the carboxyl group. Then oxidation in the polyol region (if necessary) is completed by another type of P450 (P450II). The similar biosynthetic processes and widespread distribution provide more possibilities to explore how gPEMs got so variform structures and spread to every corner of the world.
To investigate the development of gPEM biosynthetic pathways in nature, we searched for the possible gPEM clusters in current actinomycetes genome database, collecting considerable candidate and transitional clusters, providing abundant phenotypic transitions for gPEM evolution. Based on the comparative analysis of gPEM clusters, we discovered the most conserved parts of gPEM biosynthesis and constructed phylogeny using best-preserved GT and GKA. Accordingly, ancestral gPEM clusters at different evolutionary stages were proposed. Then possible evolutionary histories of gPEMs were also discussed in detail. The results revealed that gPEMs evolved from small rings to large rings and continuously increased structural diversity for better bioactivities or host preference. Meanwhile, co-evolution of functionally related proteins and environmental effects balanced the conservation and variation during evolutionary process. Moreover, frequent horizontal gene transfers (HGTs) might play fundamental roles in distribution of gPEMs. Our studies not only interpreted the origination and development of gPEMs but also provided an efficient alternative method for investigating the evolutionary processes of specific metabolites through mining current massive data.
Section snippets
Genomic sequences and resources
All identified gPEM clusters were retrieved from GenBank (Table S1) and sorted out according to relevant literatures. Sequences of gPEM biosynthetic proteins were obtained from the National Center for Biotechnology Information (NCBI: http://www.ncbi.nlm.nih.gov/) (Table S2).
Identification of candidate and transitional gPEM clusters
Putative gPEM cluster searches were done by using MultiGeneBlast (Medema et al., 2013). Chromosome segments containing more than three types of homologous gPEM proteins (identities > 40%) were considered as potential
Identification of gPEM biosynthetic clusters
Similarity retrieval of gPEM biosynthetic clusters showed us a rich resource of gPEM biosynthetic pathways, including 130 candidate clusters, 38 transitional clusters and 14 fragmental clusters (Table S1). Identified gPEM clusters are all from Streptomyces, Pseudonocardia (only cpp) or Couchioplanes (only ace). Interestingly, all strains containing candidate clusters are either Streptomyces or Pseudonocardia, and the latter harbors c-type clusters exclusively. Thus, gPEM clusters should develop
Conclusions
Actinomycetes generally live in quite complex survivable environments and always undergo fierce competitions for existence. They had to produce various antibiotics aiming at the main competitors or beneficial to the hosts, and continuously increase the antibiotic diversities under natural selection. Here we took gPEMs as the breakthrough to reveal the origination and development of antibiotics taking full advantage of current massive data. We have not only proposed ancestral and transitional
Declarations of interest
None.
Acknowledgements
This work was supported by the National Key R&D Program of China (2017YFD0201400), the National Natural Science Foundation of China (31370091), and the Funds for Creative Research Groups of China (21621004). Dr. Jianjun Qiao was supported by the New Century Outstanding Talent Support Program, Education Ministry of China.
References (41)
- et al.
A complex multienzyme system encoded by five polyketide synthase genes is involved in the biosynthesis of the 26-membered polyene macrolide pimaricin in Streptomyces natalensis
Chem. Biol.
(2000) - et al.
Mechanisms of multidrug transporters
FEMS Microbiol. Rev.
(1997) - et al.
Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes
Chem. Biol.
(2001) - et al.
Organizational and mutational analysis of a complete FR-008/candicidin gene cluster encoding a structurally related polyene complex
Chem. Biol.
(2003) - et al.
Redesign of polyene macrolide glycosylation: engineered biosynthesis of 19-(O)-perosaminyl-amphoteronolide B
Chem. Biol.
(2010) - et al.
Cholesterol oxidases act as signaling proteins for the biosynthesis of the polyene macrolide pimaricin
Chem. Biol.
(2007) - et al.
Enhancement of nystatin production by redirecting precursor fluxes after disruption of the tetramycin gene from Streptomyces ahygroscopicus
Microbiol. Res.
(2014) - et al.
Molecular control of polyene macrolide biosynthesis: direct binding of the regulator PimM to eight promoters of pimaricin genes and identification of binding boxes
J. Biol. Chem.
(2011) - et al.
Starter unit choice determines the production of two tetraene macrolides, rimocidin and CE-108, in Streptomyces diastaticus var. 108
Chem. Biol.
(2004) - et al.
Structure-based phylogeny of polyene macrolide antibiotic glycosyltransferases
Gene
(2012)
Iteratively improving natamycin production in Streptomyces gilvosporeus by a large operon-reporter based strategy
Metab. Eng.
The role of antibiotics and antibiotic resistance in nature
Environ. Microbiol.
Identification of PimR as a positive regulator of pimaricin biosynthesis in Streptomyces natalensis
J. Bacteriol.
Polyene antibiotic biosynthesis gene clusters
Appl. Microbiol. Biotechnol.
A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus
BMC Biol.
Biosynthetic engineering of polyene macrolides towards generation of improved antifungal and antiparasitic agents
Curr. Top Med. Chem.
Polyene macrolide biosynthesis in streptomyces and related bacteria: recent advances from genome sequencing and experimental studies
Appl. Microbiol. Biotechnol.
Genome mining of the biosynthetic gene cluster of the polyene macrolide antibiotic tetramycin and characterization of a P450 monooxygenase involved in the hydroxylation of the tetramycin B polyol segment
Chembiochem.
Functional manipulations of the tetramycin positive regulatory gene ttmRIV to enhance the production of tetramycin A and nystatin A1 in Streptomyces ahygroscopicus
J. Ind. Microbiol. Biotechnol.
Catalytic promiscuity of ancestral easterases and hydroxynitrile lyases
J. Am. Chem. Soc.
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These authors contributed equally to this work.