51
|
Lin Z, Torres JP, Tianero MD, Kwan JC, Schmidt EW. Origin of Chemical Diversity in Prochloron-Tunicate Symbiosis. Appl Environ Microbiol 2016; 82:3450-60. [PMID: 27037119 PMCID: PMC4959158 DOI: 10.1128/aem.00860-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Diversity-generating metabolism leads to the evolution of many different chemicals in living organisms. Here, by examining a marine symbiosis, we provide a precise evolutionary model of how nature generates a family of novel chemicals, the cyanobactins. We show that tunicates and their symbiotic Prochloron cyanobacteria share congruent phylogenies, indicating that Prochloron phylogeny is related to host phylogeny and not to external habitat or geography. We observe that Prochloron exchanges discrete functional genetic modules for cyanobactin secondary metabolite biosynthesis in an otherwise conserved genetic background. The module exchange leads to gain or loss of discrete chemical functional groups. Because the underlying enzymes exhibit broad substrate tolerance, discrete exchange of substrates and enzymes between Prochloron strains leads to the rapid generation of chemical novelty. These results have implications in choosing biochemical pathways and enzymes for engineered or combinatorial biosynthesis. IMPORTANCE While most biosynthetic pathways lead to one or a few products, a subset of pathways are diversity generating and are capable of producing thousands to millions of derivatives. This property is highly useful in biotechnology since it enables biochemical or synthetic biological methods to create desired chemicals. A fundamental question has been how nature itself creates this chemical diversity. Here, by examining the symbiosis between coral reef animals and bacteria, we describe the genetic basis of chemical variation with unprecedented precision. New compounds from the cyanobactin family are created by either varying the substrate or importing needed enzymatic functions from other organisms or via both mechanisms. This natural process matches successful laboratory strategies to engineer the biosynthesis of new chemicals and teaches a new strategy to direct biosynthesis.
Collapse
|
52
|
Sardar D, Tianero MD, Schmidt EW. Directing Biosynthesis: Practical Supply of Natural and Unnatural Cyanobactins. Methods Enzymol 2016; 575:1-20. [PMID: 27417922 DOI: 10.1016/bs.mie.2016.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The increasingly rapid accumulation of genomic information is revolutionizing natural products discovery. However, the translation of sequence data to chemical products remains a challenge. Here, we detail methods used to circumvent the supply problem of cyanobactin natural products, both by engineered synthesis in Escherichia coli and by using purified enzymes in vitro. Such methodologies exploit nature's strategies of combinatorial chemistry in the cyanobactin class of RiPP natural products. As a result, it is possible to synthesize a wide variety of natural and unnatural compounds.
Collapse
|
53
|
Sardar D, Schmidt EW. Combinatorial biosynthesis of RiPPs: docking with marine life. Curr Opin Chem Biol 2015; 31:15-21. [PMID: 26709871 DOI: 10.1016/j.cbpa.2015.11.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/17/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022]
Abstract
Ribosomally synthesized natural products are found in all forms of life. Their biosynthesis uses simple ribosomally synthesized peptides as starting materials that are transformed into complex structures via posttranslational modifications, enriched with elaborate chemical scaffolds that make them desirable as pharmacological tools. In addition, these natural products often exhibit combinatorial biosynthesis, making them attractive targets for engineering. An increasing knowledge of their biosynthetic machinery has provided key insights into their fascinating chemistry. Marine organisms have been a rich source of this class of natural products and here we review the lessons learned from marine life that enables exploitation of their potential for combinatorial engineering, opening up new routes for peptide-based drug discovery.
Collapse
|
54
|
Neves JLB, Lin Z, Imperial JS, Antunes A, Vasconcelos V, Olivera BM, Schmidt EW. Small Molecules in the Cone Snail Arsenal. Org Lett 2015; 17:4933-5. [PMID: 26421741 DOI: 10.1021/acs.orglett.5b02389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cone snails are renowned for producing peptide-based venom, containing conopeptides and conotoxins, to capture their prey. A novel small-molecule guanine derivative with unprecedented features, genuanine, was isolated from the venom of two cone snail species. Genuanine causes paralysis in mice, indicating that small molecules and not just polypeptides may contribute to the activity of cone snail venom.
Collapse
|
55
|
Teichert RW, Schmidt EW, Olivera BM. Constellation pharmacology: a new paradigm for drug discovery. Annu Rev Pharmacol Toxicol 2015; 55:573-89. [PMID: 25562646 DOI: 10.1146/annurev-pharmtox-010814-124551] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Constellation pharmacology is a cell-based high-content phenotypic-screening platform that utilizes subtype-selective pharmacological agents to elucidate the cell-specific combinations (constellations) of key signaling proteins that define specific cell types. Heterogeneous populations of native cells, in which the different individual cell types have been identified and characterized, are the foundation for this screening platform. Constellation pharmacology is useful for screening small molecules or for deconvoluting complex mixtures of biologically active natural products. This platform has been used to purify natural products and discover their molecular mechanisms. In the ongoing development of constellation pharmacology, there is a positive feedback loop between the pharmacological characterization of cell types and screening for new drug candidates. As constellation pharmacology is used to discover compounds with novel targeting-selectivity profiles, those new compounds then further help to elucidate the constellations of specific cell types, thereby increasing the content of this high-content platform.
Collapse
|
56
|
Sardar D, Lin Z, Schmidt EW. Modularity of RiPP Enzymes Enables Designed Synthesis of Decorated Peptides. ACTA ACUST UNITED AC 2015; 22:907-16. [PMID: 26165156 DOI: 10.1016/j.chembiol.2015.06.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/11/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Macrocyclases and other posttranslational enzymes afford derived peptides with improved properties for pharmaceutical and biotechnological applications. Here, we asked whether multiple posttranslational modifications could be simultaneously controlled and matched to rationally generate new peptide derivatives. We reconstituted the cyanobactin peptide natural products in vitro with up to five different posttranslational enzymes in a single tube. By manipulating the order of addition and identity of enzymes and exploiting their broad-substrate tolerance, we engineered the production of highly unnatural derivatives, including an N-C peptide macrocycle of 22 amino acids in length. In addition to engineering, this work better defines the macrocyclization mechanism, provides the first biochemical demonstration of Ser/Thr posttranslational prenylation, and is the first example of reconstitution of a native, multistep RiPP pathway with multiple enzymes in one pot. Overall, this work demonstrates how the modularity of posttranslational modification enzymes can be used to design and synthesize desirable peptide motifs.
Collapse
|
57
|
Kakule TB, Jadulco RC, Koch M, Janso JE, Barrows LR, Schmidt EW. Native promoter strategy for high-yielding synthesis and engineering of fungal secondary metabolites. ACS Synth Biol 2015; 4:625-33. [PMID: 25226362 PMCID: PMC4487227 DOI: 10.1021/sb500296p] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Strategies
are needed for the robust production of cryptic, silenced,
or engineered secondary metabolites in fungi. The filamentous fungus Fusarium heterosporum natively synthesizes the polyketide
equisetin at >2 g L–1 in a controllable manner.
We hypothesized that this production level was achieved by regulatory
elements in the equisetin pathway, leading to the prediction that
the same regulatory elements would be useful in producing other secondary
metabolites. This was tested by using the native eqxS promoter and eqxR regulator in F. heterosporum, synthesizing heterologous natural products in yields of ∼1
g L–1. As proof of concept for the practical application,
we resurrected an extinct pathway from an endophytic fungus with an
initial yield of >800 mg L–1, leading to the
practical
synthesis of a selective antituberculosis agent. Finally, the method
enabled new insights into the function of polyketide synthases in
filamentous fungi. These results demonstrate a strategy for optimally
employing native regulators for the robust synthesis of secondary
metabolites.
Collapse
|
58
|
Ruffner DE, Schmidt EW, Heemstra JR. Assessing the combinatorial potential of the RiPP cyanobactin tru pathway. ACS Synth Biol 2015; 4:482-92. [PMID: 25140729 PMCID: PMC4410914 DOI: 10.1021/sb500267d] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ribosomally produced natural products, the RiPPs, exhibit features that are potentially useful in the creation of large chemical libraries using simple mutagenesis. RiPPs are encoded on ribosomal precursor peptides, but they are extensively posttranslationally modified, endowing them with properties that are useful in drug discovery and biotechnology. In order to determine which mutations are acceptable, strategies are required to determine sequence selectivity independently of the context of flanking amino acids. Here, we examined the absolute sequence selectivity of the trunkamide cyanobactin pathway, tru. A series of random double and quadruple simultaneous mutants were synthesized and produced in Escherichia coli. Out of a total of 763 mutated amino acids examined in 325 unique sequences, 323 amino acids were successfully incorporated in 159 sequences, leading to >300 new compounds. Rules for tru sequence selectivity were determined, which will be useful for the design and synthesis of combinatorial biosynthetic libraries. The results are also interpreted in comparison to the known natural products of tru and pat cyanobactin pathways.
Collapse
|
59
|
Kakule TB, Zhang S, Zhan J, Schmidt EW. Biosynthesis of the Tetramic Acids Sch210971 and Sch210972. Org Lett 2015; 17:2295-7. [DOI: 10.1021/acs.orglett.5b00715] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
60
|
Schmidt EW. The secret to a successful relationship: lasting chemistry between ascidians and their symbiotic bacteria. INVERTEBRATE BIOLOGY : A QUARTERLY JOURNAL OF THE AMERICAN MICROSCOPICAL SOCIETY AND THE DIVISION OF INVERTEBRATE ZOOLOGY/ASZ 2015; 134:88-102. [PMID: 25937788 PMCID: PMC4414342 DOI: 10.1111/ivb.12071] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bioactive secondary metabolites are common components of marine animals. In many cases, symbiotic bacteria, and not the animals themselves, synthesize the compounds. Among marine animals, ascidians are good models for understanding these symbioses. Ascidians often contain potently bioactive secondary metabolites as their major extractable components. Strong evidence shows that ~8% of the known secondary metabolites from ascidians are made by symbiotic bacteria, and indirect evidence implicates bacteria in the synthesis of many more. Far from being "secondary" to the animals, secondary metabolites are essential components of the interaction between host animals and their symbiotic bacteria. These interactions have complex underlying biology, but the chemistry is clearly ascidian-species specific. The chemical interactions are ancient in at least some cases, and they are widespread among ascidians. Ascidians maintain secondary metabolic symbioses with bacteria that are phylogenetically diverse, indicating a convergent solution to obtaining secondary metabolites and reinforcing the importance of secondary metabolism in animal survival.
Collapse
|
61
|
Sardar D, Pierce E, McIntosh JA, Schmidt EW. Recognition sequences and substrate evolution in cyanobactin biosynthesis. ACS Synth Biol 2015; 4:167-76. [PMID: 24625112 PMCID: PMC4384831 DOI: 10.1021/sb500019b] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Ribosomally
synthesized and posttranslationally modified peptide
(RiPP) natural products are of broad interest because of their intrinsic
bioactivities and potential for synthetic biology. The RiPP cyanobactin
pathways pat and tru have been experimentally
shown to be extremely tolerant of mutations. In nature, the pathways
exhibit “substrate evolution”, where enzymes remain
constant while the substrates of those enzymes are hypervariable and
readily evolvable. Here, we sought to determine the mechanism behind
this promiscuity. Analysis of a series of different enzyme–substrate
combinations from five different cyanobactin gene clusters, in addition
to engineered substrates, led us to define short discrete recognition
elements within substrates that are responsible for directing enzymes.
We show that these recognition sequences (RSs) are portable and can
be interchanged to control which functional groups are added to the
final natural product. In addition to the previously assigned N- and
C-terminal proteolysis RSs, here we assign the RS for heterocyclization
modification. We show that substrate elements can be swapped in vivo leading to successful production of natural products
in E. coli. The exchangeability of these elements
holds promise in synthetic biology approaches to tailor peptide products in vivo and in vitro.
Collapse
|
62
|
Kakule TB, Lin Z, Schmidt EW. Combinatorialization of Fungal Polyketide Synthase–Peptide Synthetase Hybrid Proteins. J Am Chem Soc 2014; 136:17882-90. [DOI: 10.1021/ja511087p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
63
|
Jadulco R, Koch M, Kakule T, Schmidt EW, Orendt A, He H, Janso JE, Carter GT, Larson EC, Pond C, Matainaho T, Barrows LR. Isolation of pyrrolocins A-C: cis- and trans-decalin tetramic acid antibiotics from an endophytic fungal-derived pathway. JOURNAL OF NATURAL PRODUCTS 2014; 77:2537-2544. [PMID: 25351193 PMCID: PMC4251065 DOI: 10.1021/np500617u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 06/04/2023]
Abstract
Three new decalin-type tetramic acid analogues, pyrrolocins A (1), B (2), and C (3), were defined as products of a metabolic pathway from a fern endophyte, NRRL 50135, from Papua New Guinea. NRRL 50135 initially produced 1 but ceased its production before chemical or biological evaluation could be completed. Upon transfer of the biosynthetic pathway to a model host, 1-3 were produced. All three compounds are structurally related to equisetin-type compounds, with 1 and 3 having a trans-decalin ring system, while 2 has a cis-fused decalin. All were active against Mycobacterium tuberculosis, with the trans-decalin analogues 1 and 3 exhibiting lower MICs than the cis-decalin analogue 2. Here we report the isolation, structure elucidation, and antimycobacterial activities of 1-3 from the recombinant expression as well as the isolation of 1 from the wild-type fungus NRRL 50135.
Collapse
|
64
|
Lin Z, Koch M, Abdel Aziz MH, Galindo-Murillo R, Tianero MD, Cheatham TE, Barrows LR, Reilly CA, Schmidt EW. Oxazinin A, a pseudodimeric natural product of mixed biosynthetic origin from a filamentous fungus. Org Lett 2014; 16:4774-7. [PMID: 25188821 PMCID: PMC4168773 DOI: 10.1021/ol502227x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Indexed: 02/03/2023]
Abstract
A racemic, prenylated polyketide dimer, oxazinin A (1), was isolated from a novel filamentous fungus in the class Eurotiomycetes, and its structure was elucidated spectroscopically. The pentacyclic structure of oxazinin A (1) is a unique combination of benzoxazine, isoquinoline, and a pyran ring. Oxazinin A (1) exhibited antimycobacterial activity and modestly antagonized transient receptor potential (TRP) channels.
Collapse
|
65
|
Tianero MDB, Kwan JC, Wyche TP, Presson AP, Koch M, Barrows LR, Bugni TS, Schmidt EW. Species specificity of symbiosis and secondary metabolism in ascidians. ISME JOURNAL 2014; 9:615-28. [PMID: 25171330 DOI: 10.1038/ismej.2014.152] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/30/2014] [Accepted: 06/02/2014] [Indexed: 12/19/2022]
Abstract
Ascidians contain abundant, diverse secondary metabolites, which are thought to serve a defensive role and which have been applied to drug discovery. It is known that bacteria in symbiosis with ascidians produce several of these metabolites, but very little is known about factors governing these 'chemical symbioses'. To examine this phenomenon across a wide geographical and species scale, we performed bacterial and chemical analyses of 32 different ascidians, mostly from the didemnid family from Florida, Southern California and a broad expanse of the tropical Pacific Ocean. Bacterial diversity analysis showed that ascidian microbiomes are highly diverse, and this diversity does not correlate with geographical location or latitude. Within a subset of species, ascidian microbiomes are also stable over time (R=-0.037, P-value=0.499). Ascidian microbiomes and metabolomes contain species-specific and location-specific components. Location-specific bacteria are found in low abundance in the ascidians and mostly represent strains that are widespread. Location-specific metabolites consist largely of lipids, which may reflect differences in water temperature. By contrast, species-specific bacteria are mostly abundant sequenced components of the microbiomes and include secondary metabolite producers as major components. Species-specific chemicals are dominated by secondary metabolites. Together with previous analyses that focused on single ascidian species or symbiont type, these results reveal fundamental properties of secondary metabolic symbiosis. Different ascidian species have established associations with many different bacterial symbionts, including those known to produce toxic chemicals. This implies a strong selection for this property and the independent origin of secondary metabolite-based associations in different ascidian species. The analysis here streamlines the connection of secondary metabolite to producing bacterium, enabling further biological and biotechnological studies.
Collapse
|
66
|
Lin Z, Zachariah M, Marett L, Hughen RW, Teichert RW, Concepcion GP, Haygood MG, Olivera BM, Light AR, Schmidt EW. Griseorhodins D-F, neuroactive intermediates and end products of post-PKS tailoring modification in Griseorhodin biosynthesis. JOURNAL OF NATURAL PRODUCTS 2014; 77:1224-1230. [PMID: 24786728 PMCID: PMC4039362 DOI: 10.1021/np500155d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 06/03/2023]
Abstract
The griseorhodins belong to a family of extensively modified aromatic polyketides that exhibit activities such as inhibition of HIV reverse transcriptase and human telomerase. The vast structural diversity of this group of polyketides is largely introduced by enzymatic oxidations, which can significantly influence the bioactivity profile. Four new compounds, griseorhodins D-F, were isolated from a griseorhodin producer, Streptomyces sp. CN48+, based upon their enhancement of calcium uptake in a mouse dorsal root ganglion primary cell culture assay. Two of these compounds, griseorhodins D1 and D2, were shown to be identical to the major, previously uncharacterized products of a grhM mutant in an earlier griseorhodin biosynthesis study. Their structures enabled the establishment of a more complete hypothesis for the biosynthesis of griseorhodins and related compounds. The other two compounds, griseorhodins E and F, represent new products of post-polyketide synthase tailoring in griseorhodin biosynthesis and showed significant binding activity in a human dopamine active transporter assay.
Collapse
|
67
|
Kwan JC, Tianero MDB, Donia MS, Wyche TP, Bugni TS, Schmidt EW. Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella. PLoS One 2014; 9:e95850. [PMID: 24788869 PMCID: PMC4008419 DOI: 10.1371/journal.pone.0095850] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/31/2014] [Indexed: 12/19/2022] Open
Abstract
Natural products (secondary metabolites) found in marine invertebrates are often thought to be produced by resident symbiotic bacteria, and these products appear to play a major role in the symbiotic interaction of bacteria and their hosts. In these animals, there is extensive variation, both in chemistry and in the symbiotic bacteria that produce them. Here, we sought to answer the question of what factors underlie chemical variation in the ocean. As a model, we investigated the colonial tunicate Lissoclinum patella because of its rich and varied chemistry and its broad geographic range. We sequenced mitochondrial cytochrome c oxidase 1 (COXI) genes, and found that animals classified as L. patella fall into three phylogenetic groups that may encompass several cryptic species. The presence of individual natural products followed the phylogenetic relationship of the host animals, even though the compounds are produced by symbiotic bacteria that do not follow host phylogeny. In sum, we show that cryptic populations of animals underlie the observed chemical diversity, suggesting that the host controls selection for particular secondary metabolite pathways. These results imply novel approaches to obtain chemical diversity from the oceans, and also demonstrate that the diversity of marine natural products may be greatly impacted by cryptic local extinctions.
Collapse
|
68
|
Jacinto MPV, Flores MS, Lin Z, Concepcion GP, Schmidt EW, Faulkner S, Villaraza AJL. Synthesis and bioactivity of nobilamide B. RSC Adv 2014; 4:37609-37612. [PMID: 26167276 DOI: 10.1039/c4ra06873d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An alternative and facile solution/solid-phase approach is reported for the total synthesis of neuroactive peptide, nobilamide B. Z-Dhb was formed in solution via EDC/CuCl induced elimination. The solid-phase synthesis employed HBTU/Oxyma Pure™ coupling using Barlos resin. Synthetic nobilamide B was also found to be neuroactive in primary cultures of dorsal root ganglion (DRG) neurons.
Collapse
|
69
|
Lin Z, Marett L, Hughen RW, Flores M, Forteza I, Ammon MA, Concepcion GP, Espino S, Olivera BM, Rosenberg G, Haygood MG, Light AR, Schmidt EW. Neuroactive diol and acyloin metabolites from cone snail-associated bacteria. Bioorg Med Chem Lett 2013; 23:4867-9. [PMID: 23880542 PMCID: PMC3779075 DOI: 10.1016/j.bmcl.2013.06.088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/14/2013] [Accepted: 06/27/2013] [Indexed: 01/07/2023]
Abstract
The bacterium Gordonia sp. 647W.R.1a.05 was cultivated from the venom duct of the cone snail, Conus circumcisus. The Gordonia sp. organic extract modulated the action potential of mouse dorsal root ganglion neurons. Assay-guided fractionation led to the identification of the new compound circumcin A (1) and 11 known analogs (2-12). Two of these compounds, kurasoin B (7) and soraphinol A (8), were active in a human norepinephrine transporter assay with Ki values of 2575 and 867 nM, respectively. No neuroactivity had previously been reported for compounds in this structural class. Gordonia species have been reproducibly isolated from four different cone snail species, indicating a consistent association between these organisms.
Collapse
|
70
|
Kakule TB, Sardar D, Lin Z, Schmidt EW. Two related pyrrolidinedione synthetase loci in Fusarium heterosporum ATCC 74349 produce divergent metabolites. ACS Chem Biol 2013; 8:1549-57. [PMID: 23614392 DOI: 10.1021/cb400159f] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Equisetin synthetase (EqiS), from the filamentous fungus Fusarium heterosporum ATCC 74349, was initially assigned on the basis of genetic knockout and expression analysis. Increasing inconsistencies in experimental results led us to question this assignment. Here, we sequenced the F. heterosporum genome, revealing two hybrid polyketide-peptide proteins that were candidates for the equisetin synthetase. The surrounding genes in both clusters had the needed auxiliary genes that might be responsible for producing equisetin. Genetic mutation, biochemical analysis, and recombinant expression in the fungus enabled us to show that the initially assigned EqiS does not produce equisetin but instead produces a related 2,4-pyrrolidinedione, fusaridione A, that was previously unknown. Fusaridione A is methylated in the 3-position of the pyrrolidinedione, which has not otherwise been found in natural products, leading to spontaneous reverse-Dieckmann reactions. A newly described gene cluster, eqx, is responsible for producing equisetin.
Collapse
|
71
|
Lin Z, Torres JP, Ammon MA, Marett L, Teichert RW, Reilly CA, Kwan JC, Hughen RW, Flores M, Tianero MD, Peraud O, Cox JE, Light AR, Villaraza AJL, Haygood MG, Concepcion GP, Olivera BM, Schmidt EW. A bacterial source for mollusk pyrone polyketides. ACTA ACUST UNITED AC 2013; 20:73-81. [PMID: 23352141 DOI: 10.1016/j.chembiol.2012.10.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/11/2012] [Accepted: 10/24/2012] [Indexed: 12/29/2022]
Abstract
In the oceans, secondary metabolites often protect otherwise poorly defended invertebrates, such as shell-less mollusks, from predation. The origins of these metabolites are largely unknown, but many of them are thought to be made by symbiotic bacteria. In contrast, mollusks with thick shells and toxic venoms are thought to lack these secondary metabolites because of reduced defensive needs. Here, we show that heavily defended cone snails also occasionally contain abundant secondary metabolites, γ-pyrones known as nocapyrones, which are synthesized by symbiotic bacteria. The bacteria, Nocardiopsis alba CR167, are related to widespread actinomycetes that we propose to be casual symbionts of invertebrates on land and in the sea. The natural roles of nocapyrones are unknown, but they are active in neurological assays, revealing that mollusks with external shells are an overlooked source of secondary metabolite diversity.
Collapse
|
72
|
Abstract
Ribosomal peptide natural products (RiPPs) offer a new frontier for discovering and engineering bioactive small molecules. In this issue of Chemistry & Biology, Young and colleagues overcome hurdles that have slowed the development of RiPPs, leading to in vivo synthesis of new thiopeptide antibiotics.
Collapse
|
73
|
McIntosh JA, Lin Z, Tianero MDB, Schmidt EW. Aestuaramides, a natural library of cyanobactin cyclic peptides resulting from isoprene-derived Claisen rearrangements. ACS Chem Biol 2013; 8:877-83. [PMID: 23411099 DOI: 10.1021/cb300614c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report 12 cyanobactin cyclic peptides, the aestuaramides, from the cultivated cyanobacterium Lyngbya aestuarii. We show that aestuaramides are synthesized enzymatically as reverse O-prenylated tyrosine ethers that subsequently undergo a Claisen rearrangement to produce forward C-prenylated tyrosine. These results reveal that a nonenzymatic Claisen rearrangement dictates isoprene regiochemistry in a natural system. They also reveal one of the mechanisms that organisms use to generate structurally diverse compound libraries starting from simple ribosomal peptide pathways (RiPPs).
Collapse
|
74
|
Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1433] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
Collapse
|
75
|
Lin Z, Falkinham JO, Tawfik KA, Jeffs P, Bray B, Dubay G, Cox JE, Schmidt EW. Burkholdines from Burkholderia ambifaria: antifungal agents and possible virulence factors. JOURNAL OF NATURAL PRODUCTS 2012; 75:1518-1523. [PMID: 22988812 DOI: 10.1021/np300108u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Burkholdines are cyclic lipopeptides with unusual antifungal potency, making them promising leads as a new class of antifungal agents. However, a recent report using knockout mutagenesis indicates that these and related compounds, such as occidiofungins, xylocandins, and cepacidines, may also be synonymous with the long-known hemolytic virulence factors found in diverse Burkholderia isolates. Because of their possible roles in causing Burkholderia infections or curing fungal infections, it is important to fully define their structures and biological activities using pure compounds. Here, we report the structures of three further burkholdines, Bk-1119, Bk-1213, and Bk-1215, which were elucidated using spectroscopic methods. The absolute configuration of this compound class was determined for the first time using a combination of spectroscopy and chemical degradation techniques. Antifungal and hemolytic activities were assessed for five pure burkholdines, representative of the structural diversity of this lipopeptide class. All of the burkholdines were potent antifungal and hemolytic agents, validating their probable role in virulence. However, one of the burkholdines (Bk-1119) exhibited a >30-fold selectivity for fungi versus sheep erythrocytes and was more than 25-fold more potent than amphotericin against some fungal strains. Therefore, burkholdines have potential to selectively target fungal infections.
Collapse
|