Co-reporter:Abraham J. Waldman, Tai L. Ng, Peng Wang, and Emily P. Balskus
Chemical Reviews April 26, 2017 Volume 117(Issue 8) pp:5784-5784
Publication Date(Web):April 4, 2017
DOI:10.1021/acs.chemrev.6b00621
Natural products that contain functional groups with heteroatom-heteroatom linkages (X–X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X–X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X–X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X–X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
Co-reporter:B. J. Levin;Y. Y. Huang;S. C. Peck;Y. Wei;E. P. Balskus;A. Martínez-del Campo;C. Huttenhower;E. A. Franzosa;J. A. Marks
Science 2017 Volume 355(Issue 6325) pp:
Publication Date(Web):10 Feb 2017
DOI:10.1126/science.aai8386
Chemically guided functional profiling
The big challenge posed by the microbiota living in or on humans is working out what they do for us. Microorganisms generate large quantities of peptides and proteins that may have profound systemic effects on the host. Levin et al. took microbial metagenome data and used a combination of bioinformatic tools to generate a network that clusters sequences of enzymes sharing similar biological functions (see the Perspective by Glasner). Experiments verified these homology and structural-chemical inferences. The analysis identified enzymes involved in anaerobic short-chain fatty acid production and L-proline biosynthesis, both of which are key mediators of healthy microbiota-host symbioses.
Science, this issue p. eaai8386; see also p. 577
Co-reporter:Vayu Maini Rekdal;Nitzan Koppel
Science 2017 Volume 356(Issue 6344) pp:
Publication Date(Web):
DOI:10.1126/science.aag2770
One person's meat is another's poison
The human gut is packed with actively metabolizing microorganisms. These have a transformative effect on what we ingest—whether food, drugs, or pollutants. Koppel et al. review the distinguishing features of microbial xenobiotic metabolism, its interaction with somatic metabolism, and interindividual variation. Depending on the functional composition of microorganisms in the gut, the subsequent products may have nutritionally beneficial effects, modify pharmaceuticals, or be toxic. All of these consequences of our companion microbes can have important impacts on human health and well-being.
Science, this issue p. eaag2770
Co-reporter:Kymberleigh A. Romano, Ana Martinez-del Campo, Kazuyuki Kasahara, Carina L. Chittim, ... Federico E. Rey
Cell Host & Microbe 2017 Volume 22, Issue 3(Volume 22, Issue 3) pp:
Publication Date(Web):13 September 2017
DOI:10.1016/j.chom.2017.07.021
•Gut bacteria compete with the host for choline, decreasing bioavailability•Microbial choline degradation depletes methyl-donor metabolites•Microbial choline utilization alters in utero epigenetic programming of the brain•Mice with choline-consuming gut microbiota display altered behaviorCholine is an essential nutrient and methyl donor required for epigenetic regulation. Here, we assessed the impact of gut microbial choline metabolism on bacterial fitness and host biology by engineering a microbial community that lacks a single choline-utilizing enzyme. Our results indicate that choline-utilizing bacteria compete with the host for this nutrient, significantly impacting plasma and hepatic levels of methyl-donor metabolites and recapitulating biochemical signatures of choline deficiency. Mice harboring high levels of choline-consuming bacteria showed increased susceptibility to metabolic disease in the context of a high-fat diet. Furthermore, bacterially induced reduction of methyl-donor availability influenced global DNA methylation patterns in both adult mice and their offspring and engendered behavioral alterations. Our results reveal an underappreciated effect of bacterial choline metabolism on host metabolism, epigenetics, and behavior. This work suggests that interpersonal differences in microbial metabolism should be considered when determining optimal nutrient intake requirements.Download high-res image (215KB)Download full-size image
Co-reporter:Li Zha, Matthew R. Wilson, Carolyn A. Brotherton, and Emily P. Balskus
ACS Chemical Biology 2016 Volume 11(Issue 5) pp:1287
Publication Date(Web):February 18, 2016
DOI:10.1021/acschembio.6b00014
Colibactin is a human gut bacterial genotoxin of unknown structure that has been linked to colon cancer. The biosynthesis of this elusive metabolite is directed by the pks gene cluster, which encodes a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly line that is hypothesized to use the unusual polyketide building block aminomalonate. This biosynthetic pathway is thought to initially produce an inactive intermediate (precolibactin) that is processed to the active toxin. Here, we report the first in vitro biochemical characterization of the PKS components of the pks enzymatic assembly line. We evaluate PKS extender unit utilization and show that ClbG, a freestanding acyltransferase (AT) from the pks gene cluster, recognizes aminomalonyl-acyl carrier protein (AM-ACP) and transfers this building block to multiple PKS modules, including a cis-AT PKS ClbI. We also use genetics to explore the in vivo role of ClbG in colibactin and precolibactin biosynthesis. Unexpectedly, production of previously identified pks-associated metabolites is dramatically increased in a ΔclbP/ΔclbG mutant strain, enabling the first structure elucidation of a bithiazole-containing candidate precolibactin. This work provides new insights into the unusual biosynthetic capabilities of the pks gene cluster, offers further support for the hypothesis that colibactin directly damages DNA, and suggests that additional, uncharacterized pks-derived metabolites containing aminomalonate play critical roles in genotoxicity.
Co-reporter:Emily P. Balskus
ACS Infectious Diseases 2016 Volume 2(Issue 7) pp:453
Publication Date(Web):June 17, 2016
DOI:10.1021/acsinfecdis.6b00100
Microbial communities occupy essentially every habitat on earth and have profound effects on our environment and human health. The National Microbiome Initiative will provide a framework for interdisciplinary microbiome research. The challenges inherent in discovering and understanding microbiome functions, especially those associated with infectious disease, present countless opportunities for chemists.
Co-reporter:Dr. Stephen Wallace ; Emily P. Balskus
Angewandte Chemie 2016 Volume 128( Issue 20) pp:6127-6131
Publication Date(Web):
DOI:10.1002/ange.201600966
Abstract
Synthetic biology has enabled the production of many value-added chemicals via microbial fermentation. However, the problem of low product titers from recombinant pathways has limited the utility of this approach. Methods to increase metabolic flux are therefore critical to the success of metabolic engineering. Here we demonstrate that vitamin E-derived designer micelles, originally developed for use in synthetic chemistry, are biocompatible and accelerate flux through a styrene production pathway in Escherichia coli. We show that these micelles associate non-covalently with the bacterial outer-membrane and that this interaction increases membrane permeability. In addition, these micelles also accommodate both heterogeneous and organic-soluble transition metal catalysts and accelerate biocompatible cyclopropanation in vivo. Overall, this work demonstrates that these surfactants hold great promise for further application in the field of synthetic biotechnology, and for expanding the types of molecules that can be readily accessed from renewable resources via the combination of microbial fermentation and biocompatible chemistry.
Co-reporter:Dr. Stephen Wallace ; Emily P. Balskus
Angewandte Chemie International Edition 2016 Volume 55( Issue 20) pp:6023-6027
Publication Date(Web):
DOI:10.1002/anie.201600966
Abstract
Synthetic biology has enabled the production of many value-added chemicals via microbial fermentation. However, the problem of low product titers from recombinant pathways has limited the utility of this approach. Methods to increase metabolic flux are therefore critical to the success of metabolic engineering. Here we demonstrate that vitamin E-derived designer micelles, originally developed for use in synthetic chemistry, are biocompatible and accelerate flux through a styrene production pathway in Escherichia coli. We show that these micelles associate non-covalently with the bacterial outer-membrane and that this interaction increases membrane permeability. In addition, these micelles also accommodate both heterogeneous and organic-soluble transition metal catalysts and accelerate biocompatible cyclopropanation in vivo. Overall, this work demonstrates that these surfactants hold great promise for further application in the field of synthetic biotechnology, and for expanding the types of molecules that can be readily accessed from renewable resources via the combination of microbial fermentation and biocompatible chemistry.
Co-reporter:H. Nakamura, J. X. Wang and E. P. Balskus
Chemical Science 2015 vol. 6(Issue 7) pp:3816-3822
Publication Date(Web):14 Apr 2015
DOI:10.1039/C4SC03132F
The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.
Co-reporter:Carolyn A. Brotherton, Matthew Wilson, Gary Byrd, and Emily P. Balskus
Organic Letters 2015 Volume 17(Issue 6) pp:1545-1548
Publication Date(Web):March 10, 2015
DOI:10.1021/acs.orglett.5b00432
Colibactin is a structurally uncharacterized, genotoxic natural product produced by commensal and pathogenic strains of E. coli that harbor the pks island. A new metabolite has been isolated from a pks+ E. coli mutant missing an essential biosynthetic enzyme. The unusual azaspiro[2.4] bicyclic ring system of this molecule provides new insights into colibactin biosynthesis and suggests a mechanism through which colibactin and other pks-derived metabolites may exert genotoxicity.
Co-reporter:Abraham J. Waldman;Yakov Pechersky;Dr. Peng Wang;Jennifer X. Wang; Emily P. Balskus
ChemBioChem 2015 Volume 16( Issue 15) pp:
Publication Date(Web):
DOI:10.1002/cbic.201500461
Co-reporter:Dr. Stephen Wallace ; Emily P. Balskus
Angewandte Chemie 2015 Volume 127( Issue 24) pp:7212-7215
Publication Date(Web):
DOI:10.1002/ange.201502185
Abstract
The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small-molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non-native reactivity into metabolic pathways for small-molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non-natural phenyl cyclopropanes directly from D-glucose in single-vessel fermentations. This process is the first example of the combination of nonbiological carbene-transfer reactivity with cellular metabolism for small-molecule production.
Co-reporter:Dr. Stephen Wallace ; Emily P. Balskus
Angewandte Chemie International Edition 2015 Volume 54( Issue 24) pp:7106-7109
Publication Date(Web):
DOI:10.1002/anie.201502185
Abstract
The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small-molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non-native reactivity into metabolic pathways for small-molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non-natural phenyl cyclopropanes directly from D-glucose in single-vessel fermentations. This process is the first example of the combination of nonbiological carbene-transfer reactivity with cellular metabolism for small-molecule production.
Co-reporter:Abraham J. Waldman;Yakov Pechersky;Dr. Peng Wang;Jennifer X. Wang; Emily P. Balskus
ChemBioChem 2015 Volume 16( Issue 15) pp:2172-2175
Publication Date(Web):
DOI:10.1002/cbic.201500407
Abstract
Diazo groups are found in a range of natural products that possess potent biological activities. Despite longstanding interest in these metabolites, diazo group biosynthesis is not well understood, in part because of difficulties in identifying specific genes linked to diazo formation. Here we describe the discovery of the gene cluster that produces the o-diazoquinone natural product cremeomycin and its heterologous expression in Streptomyces lividans. We used stable isotope feeding experiments and in vitro characterization of biosynthetic enzymes to decipher the order of events in this pathway and establish that diazo construction involves late-stage N−N bond formation. This work represents the first successful production of a diazo-containing metabolite in a heterologous host, experimentally linking a set of genes with diazo formation.
Co-reporter:Abraham J. Waldman and Emily P. Balskus
Organic Letters 2014 Volume 16(Issue 2) pp:640-643
Publication Date(Web):January 2, 2014
DOI:10.1021/ol403714g
Lomaiviticin biosynthesis is thought to utilize a propionyl starter unit for a type II polyketide synthase (PKS). Discovery of the lomaiviticin (lom) biosynthetic gene cluster suggested an unusual method for starter unit generation involving a bifunctional acyltransferase/decarboxylase (AT/DC) thus far observed only in type I PKS pathways. In vitro biochemical characterization of AT/DC Lom62 confirmed its ability to generate a propionyl-acyl carrier protein (ACP), revealing a new role for this enzymatic activity within natural product biosynthesis.
Co-reporter:Smaranda Craciun, Jonathan A. Marks, and Emily P. Balskus
ACS Chemical Biology 2014 Volume 9(Issue 7) pp:1408
Publication Date(Web):May 22, 2014
DOI:10.1021/cb500113p
The recently identified glycyl radical enzyme (GRE) homologue choline trimethylamine-lyase (CutC) participates in the anaerobic conversion of choline to trimethylamine (TMA), a widely distributed microbial metabolic transformation that occurs in the human gut and is linked to disease. The proposed biochemical function of CutC, C–N bond cleavage, represents new reactivity for the GRE family. Here we describe the in vitro characterization of CutC and its activating protein CutD. We have observed CutD-mediated formation of a glycyl radical on CutC using EPR spectroscopy and have demonstrated that activated CutC processes choline to trimethylamine and acetaldehyde. Surveys of potential alternate CutC substrates uncovered a strict specificity for choline. Homology modeling and mutagenesis experiments revealed essential CutC active site residues. Overall, this work establishes that CutC is a GRE of unique function and a molecular marker for anaerobic choline metabolism.
Co-reporter:Dr. Gopal Sirasani;Liuchuan Tong ; Emily P. Balskus
Angewandte Chemie International Edition 2014 Volume 53( Issue 30) pp:7785-7788
Publication Date(Web):
DOI:10.1002/anie.201403148
Abstract
Organic chemists and metabolic engineers use orthogonal technologies to construct essential small molecules such as pharmaceuticals and commodity chemicals. While chemists have leveraged the unique capabilities of biological catalysts for small-molecule production, metabolic engineers have not likewise integrated reactions from organic synthesis with the metabolism of living organisms. Reported herein is a method for alkene hydrogenation which utilizes a palladium catalyst and hydrogen gas generated directly by a living microorganism. This biocompatible transformation, which requires both catalyst and microbe, and can be used on a preparative scale, represents a new strategy for chemical synthesis that combines organic chemistry and metabolic engineering.
Co-reporter:Dr. Gopal Sirasani;Liuchuan Tong ; Emily P. Balskus
Angewandte Chemie 2014 Volume 126( Issue 30) pp:7919-7922
Publication Date(Web):
DOI:10.1002/ange.201403148
Abstract
Organic chemists and metabolic engineers use orthogonal technologies to construct essential small molecules such as pharmaceuticals and commodity chemicals. While chemists have leveraged the unique capabilities of biological catalysts for small-molecule production, metabolic engineers have not likewise integrated reactions from organic synthesis with the metabolism of living organisms. Reported herein is a method for alkene hydrogenation which utilizes a palladium catalyst and hydrogen gas generated directly by a living microorganism. This biocompatible transformation, which requires both catalyst and microbe, and can be used on a preparative scale, represents a new strategy for chemical synthesis that combines organic chemistry and metabolic engineering.
Co-reporter:Jeffrey E. Janso, Brad A. Haltli, Alessandra S. Eustáquio, Kerry Kulowski, Abraham J. Waldman, Li Zha, Hitomi Nakamura, Valerie S. Bernan, Haiyin He, Guy T. Carter, Frank E. Koehn, Emily P. Balskus
Tetrahedron 2014 70(27–28) pp: 4156-4164
Publication Date(Web):
DOI:10.1016/j.tet.2014.03.009
Co-reporter:Carolyn A. Brotherton
Journal of the American Chemical Society 2013 Volume 135(Issue 9) pp:3359-3362
Publication Date(Web):February 13, 2013
DOI:10.1021/ja312154m
Commensal Escherichia coli residing in the human gut produce colibactin, a small-molecule genotoxin of unknown structure that has been implicated in the development of colon cancer. Colibactin biosynthesis is hypothesized to involve a prodrug resistance strategy that entails initiation of biosynthesis via construction of an N-terminal prodrug scaffold and late-stage cleavage of this structural motif during product export. Here we describe the biochemical characterization of the prodrug synthesis, elongation, and cleavage enzymes from the colibactin biosynthetic pathway. We show that nonribosomal peptide synthetases ClbN and ClbB assemble and process an N-acyl-d-asparagine prodrug scaffold that serves as a substrate for the periplasmic d-amino peptidase ClbP. In addition to affording information about structural features of colibactin, this work reveals the biosynthetic logic underlying the prodrug resistance strategy and suggests that cytotoxicity requires amide bond cleavage.
Co-reporter:Dr. Yunmi Lee;Afoma Umeano; Emily P. Balskus
Angewandte Chemie International Edition 2013 Volume 52( Issue 45) pp:11800-11803
Publication Date(Web):
DOI:10.1002/anie.201307033
Co-reporter:Dr. Yunmi Lee;Afoma Umeano; Emily P. Balskus
Angewandte Chemie 2013 Volume 125( Issue 45) pp:12016-12019
Publication Date(Web):
DOI:10.1002/ange.201307033
Co-reporter:Hitomi Nakamura ; Hilary A. Hamer ; Gopal Sirasani
Journal of the American Chemical Society 2012 Volume 134(Issue 45) pp:18518-18521
Publication Date(Web):October 29, 2012
DOI:10.1021/ja308318p
The cylindrocyclophanes are a family of natural products that share a remarkable paracyclophane carbon scaffold. Using genome sequencing and bioinformatic analyses, we have discovered a biosynthetic gene cluster involved in the assembly of cylindrocyclophane F. Through a combination of in vitro enzyme characterization and feeding studies, we confirm the connection between this gene cluster and cylindrocyclophane production, elucidate the chemical events involved in initiating and terminating an unusual type I polyketide synthase assembly line, and discover that macrocycle assembly involves functionalization of an unactivated carbon center.
Co-reporter:Smaranda Craciun
PNAS 2012 Volume 109 (Issue 52 ) pp:21184-21185
Publication Date(Web):2012-12-26
DOI:10.1073/pnas.1215689109
Choline and trimethylamine (TMA) are small molecules that play central roles in biological processes throughout all kingdoms
of life. These ubiquitous metabolites are linked through a single biochemical transformation, the conversion of choline to
TMA by anaerobic microorganisms. This metabolic activity, which contributes to methanogenesis and human disease, has been
known for over a century but has eluded genetic and biochemical characterization. We have identified a gene cluster responsible
for anaerobic choline degradation within the genome of a sulfate-reducing bacterium and verified its function using both a
genetic knockout strategy and heterologous expression in Escherichia coli. Bioinformatics and electron paramagnetic resonance (EPR) spectroscopy revealed the involvement of a C–N bond cleaving glycyl
radical enzyme in TMA production, which is unprecedented chemistry for this enzyme family. Our discovery provides the predictive
capabilities needed to identify choline utilization clusters in numerous bacterial genomes, underscoring the importance and
prevalence of this metabolic activity within the human microbiota and the environment.
Co-reporter:Stephen Wallace, Emily P Balskus
Current Opinion in Biotechnology (December 2014) Volume 30() pp:1-8
Publication Date(Web):1 December 2014
DOI:10.1016/j.copbio.2014.03.006
•Efforts to combine organic and biological synthesis are increasing.•Sequestering non-enzymatic and enzyme catalysts can overcome incompatibility.•Organic chemistry inspires engineering of non-biological reactivity into enzymes.•Non-enzymatic reactions can be integrated with cellular metabolism.Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecule production. We highlight recent advances in combining enzymatic and non-enzymatic catalysis in vitro, discuss the application of design principles from organic chemistry for engineering non-biological reactivity into enzymes, and describe the development of biocompatible chemistry that can be interfaced with microbial metabolism.Download high-res image (167KB)Download full-size image
Co-reporter:H. Nakamura, J. X. Wang and E. P. Balskus
Chemical Science (2010-Present) 2015 - vol. 6(Issue 7) pp:NaN3822-3822
Publication Date(Web):2015/04/14
DOI:10.1039/C4SC03132F
The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.