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Salama S, Mostafa HS, Husseiny S, Sebak M. Actinobacteria as Microbial Cell Factories and Biocatalysts in The Synthesis of Chiral Intermediates and Bioactive Molecules; Insights and Applications. Chem Biodivers 2024; 21:e202301205. [PMID: 38155095 DOI: 10.1002/cbdv.202301205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Actinobacteria are one of the most intriguing bacterial phyla in terms of chemical diversity and bioactivities of their reported biomolecules and natural products, including various types of chiral molecules. Actinobacterial genera such as Detzia, Mycobacterium, and Streptomyces are among the microbial sources targeted for selective reactions such as asymmetric biocatalysis catalyzed by whole cells or enzymes induced in their cell niche. Remarkably, stereoselective reactions catalyzed by actinobacterial whole cells or their enzymes include stereoselective oxidation, stereoselective reduction, kinetic resolution, asymmetric hydrolysis, and selective transamination, among others. Species of actinobacteria function with high chemo-, regio-, and enantio-selectivity under benign conditions, which could help current industrial processing. Numerous selective enzymes were either isolated from actinobacteria or expressed from actinobacteria in other microbes and hence exploited in the production of pure organic compounds difficult to obtain chemically. In addition, different species of actinobacteria, especially Streptomyces species, function as natural producers of chiral molecules of therapeutic importance. Herein, we discuss some of the most outstanding contributions of actinobacteria to asymmetric biocatalysis, which are important in the organic and/or pharmaceutical industries. In addition, we highlight the role of actinobacteria as microbial cell factories for chiral natural products with insights into their various biological potentialities.
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Affiliation(s)
- Sara Salama
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, 62514, Beni-Suef, Egypt
| | - Heba Sayed Mostafa
- Food Science Department, Faculty of Agriculture, Cairo University, 12613, Giza, Egypt
| | - Samah Husseiny
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, 62517, Beni-Suef, Egypt
| | - Mohamed Sebak
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, 62514, Beni-Suef, Egypt
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2
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Steele AD, Kiefer AF, Shen B. The many facets of sulfur incorporation in natural product biosynthesis. Curr Opin Chem Biol 2023; 76:102366. [PMID: 37451204 PMCID: PMC10527158 DOI: 10.1016/j.cbpa.2023.102366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Sulfur-containing natural products (S-containing NPs) exhibit diverse chemical structures and biosynthetic machineries. Unraveling the intricate chemistry of S-incorporation requires innovative and multidisciplinary approaches. In this review, we surveyed the landscape of S-containing NP biosynthetic machineries, classified the S-incorporation chemistry into four distinct classes, and highlighted each of the four classes with representative examples from recent studies. All highlighted chemistry has been correlated to the genes encoding the biosynthetic machineries of the S-containing NPs, which open new opportunities to discover S-containing NPs through genome mining. These examples should inspire the community to explore uncharted territories in NP research, promoting further advancements in both novel S-containing NP discovery and S-incorporation chemistry.
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Affiliation(s)
- Andrew D Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States
| | - Alexander F Kiefer
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States; Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States; Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States; Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458, United States.
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3
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Sinner EK, Li R, Marous DR, Townsend CA. ThnL, a B12-dependent radical S-adenosylmethionine enzyme, catalyzes thioether bond formation in carbapenem biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2206494119. [PMID: 35969793 PMCID: PMC9407657 DOI: 10.1073/pnas.2206494119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Complex carbapenems are important clinical antibiotics used to treat recalcitrant infections. Their biosynthetic gene clusters contain three essential B12-dependent radical S-adenosylmethionine (rSAM) enzymes. The majority of characterized enzymes in this subfamily catalyze methyl transfer, but only one is required to sequentially install all methionine-derived carbons in complex carbapenems. Therefore, it is probable that the other two rSAM enzymes have noncanonical functions. Through a series of fermentation and in vitro experiments, we show that ThnL uses radical SAM chemistry to catalyze thioether bond formation between C2 of a carbapenam precursor and pantetheine, uniting initial bicycle assembly common to all carbapenems with later tailoring events unique to complex carbapenems. ThnL also catalyzes reversible thiol/disulfide redox on pantetheine. Neither of these functions has been observed previously in a B12-dependent radical SAM enzyme. ThnL expands the known activity of this subclass of enzymes beyond carbon-carbon bond formation or rearrangement. It is also the only radical SAM enzyme currently known to catalyze carbon-sulfur bond formation with only an rSAM Fe-S cluster and no additional auxiliary clusters.
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Affiliation(s)
- Erica K. Sinner
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Daniel R. Marous
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in carbapenem β-lactam antibiotic biosynthesis. Methods Enzymol 2022; 669:29-44. [PMID: 35644176 DOI: 10.1016/bs.mie.2021.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
ThnK and TokK are cobalamin-dependent radical S-adenosylmethionine enzymes that catalyze sequential methylations of a common carbapenem biosynthetic intermediate. ThnK was an early characterized member of the subfamily of cobalamin-dependent radical S-adenosylmethionine enzymes. Since initial publication of the ThnK function, the field has progressed, and we have made methodological strides in the expression and purification of this enzyme and its ortholog TokK. An optimized protocol for obtaining the enzymes in pure and active form has enabled us to characterize their reactions and gain greater insight into the kinetic behavior of the sequential methylations they catalyze. We share here the methods and strategy that we have developed through our study of these enzymes.
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Alotaibi SH, Amer HH, Touil N, Abdel-Moneim AS, Soliman MM, Zaki YH. Synthesis, Characterization and Molecular Docking of New Nucleosides and Schiff Bases Derived from Ampyrone as Antiviral Agents to Contain the COVID-19 Virus. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2045329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Saad H. Alotaibi
- Department of Chemistry, Turabah University College, Taif University, Turabah, Taif, Saudi Arabia
| | - Hamada H. Amer
- Department of Chemistry, Turabah University College, Taif University, Turabah, Taif, Saudi Arabia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
- Unité de Culture Cellulaire, CVMIT, HMI Med V, Rabat, Morocco
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Turabah, Taif, Saudi Arabia
| | - Mohamed M. Soliman
- Department of Clinical Laboratory Sciences, Turabah University College, Taif University, Turabah, Taif, Saudi Arabia
| | - Yasser H. Zaki
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
- Department of Chemistry, Faculty of Science and Humanity Studies at Al-Quwayiyah, Shaqra University, Al Quwayiyah, Saudi Arabia
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Sinner E, Marous DR, Townsend CA. Evolution of Methods for the Study of Cobalamin-Dependent Radical SAM Enzymes. ACS BIO & MED CHEM AU 2022; 2:4-10. [PMID: 35341020 PMCID: PMC8950095 DOI: 10.1021/acsbiomedchemau.1c00032] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While bioinformatic evidence of cobalamin-dependent radical S-adenosylmethionine (SAM) enzymes has existed since the naming of the radical SAM superfamily in 2001, none were biochemically characterized until 2011. In the past decade, the field has flourished as methodological advances have facilitated study of the subfamily. Because of the ingenuity and perseverance of researchers in this field, we now have functional, mechanistic, and structural insight into how this class of enzymes harnesses the power of both the cobalamin and radical SAM cofactors to achieve catalysis. All of the early characterized enzymes in this subfamily were methylases, but the activity of these enzymes has recently been expanded beyond methylation. We anticipate that the characterized functions of these enzymes will become both better understood and increasingly diverse with continued study.
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Affiliation(s)
- Erica
K. Sinner
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| | - Daniel R. Marous
- Department
of Chemistry, Wittenberg University, 200 W Ward St., Springfield, Ohio 45504, United States
| | - Craig A. Townsend
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
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Structure of a B 12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 2022; 602:343-348. [PMID: 35110734 DOI: 10.1038/s41586-021-04392-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022]
Abstract
Carbapenems are antibiotics of last resort in the clinic. Owing to their potency and broad-spectrum activity, they are an important part of the antibiotic arsenal. The vital role of carbapenems is exemplified by the approval acquired by Merck from the US Food and Drug Administration (FDA) for the use of an imipenem combination therapy to treat the increased levels of hospital-acquired and ventilator-associated bacterial pneumonia that have occurred during the COVID-19 pandemic1. The C6 hydroxyethyl side chain distinguishes the clinically used carbapenems from the other classes of β-lactam antibiotics and is responsible for their low susceptibility to inactivation by occluding water from the β-lactamase active site2. The construction of the C6 hydroxyethyl side chain is mediated by cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes3. These radical SAM methylases (RSMTs) assemble the alkyl backbone by sequential methylation reactions, and thereby underlie the therapeutic usefulness of clinically used carbapenems. Here we present X-ray crystal structures of TokK, a B12-dependent RSMT that catalyses three-sequential methylations during the biosynthesis of asparenomycin A. These structures, which contain the two metallocofactors of the enzyme and were determined in the presence and absence of a carbapenam substrate, provide a visualization of a B12-dependent RSMT that uses the radical mechanism that is shared by most of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggest that substrate positioning governs the rate of each methylation event.
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Wang D, Xu P, Sun J, Yuan J, Zhao J. Effects of ethanol stress on epsilon-poly-l-lysine (ε-PL) biosynthesis in Streptomyces albulus X-18. Enzyme Microb Technol 2021; 153:109907. [PMID: 34670188 DOI: 10.1016/j.enzmictec.2021.109907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 01/10/2023]
Abstract
The aim of the study was to reveal the effects of ethanol stress on the production of epsilon-poly-l-lysine (ε-PL) in Streptomyces albulus X-18. The results showed that biomass and the utilization of glucose were respectively increased by ethanol stress. The ε-PL yield was increased by 41.42 % in the shake flask and 37.02 % in 10 L fermenter with 1% (v/v) ethanol. The morphology of colonies and mycelia showed significant differences. The intracellular reactive oxygen species level was increased by about 100 %. The ratio of unsaturated fatty acids to saturated fatty acids in the cell membrane was increased by ethanol stress. Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) proteomic profile showed that 265 identified proteins were differentially expressed. The differentially expressed proteins (DEPs) were mainly involved in biological processes. The up-regulated DEPs were mainly involved in the redox reaction and stress response. The metabolic flux of l-Asp was shifted to l-Lys biosynthesis, and the DAP pathway was strengthened. Protein-protein interaction analysis showed that 30 DEPs interacted with l-Lys biosynthesis. The changes of ten proteins by Parallel Reaction Monitoring (PRM) were consistent with those by iTRAQ. The study provided valuable clues to better understand the mechanism of ε-PL biosynthesis improvement by ethanol stress.
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Affiliation(s)
- Dahong Wang
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China; Henan Engineering Research Center of Food Microbiology, Luoyang, China.
| | - Peng Xu
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China
| | - Jianrui Sun
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China
| | - Jiangfeng Yuan
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, China
| | - Junfeng Zhao
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China
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De Simeis D, Serra S. Actinomycetes: A Never-Ending Source of Bioactive Compounds-An Overview on Antibiotics Production. Antibiotics (Basel) 2021; 10:antibiotics10050483. [PMID: 33922100 PMCID: PMC8143475 DOI: 10.3390/antibiotics10050483] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
The discovery of penicillin by Sir Alexander Fleming in 1928 provided us with access to a new class of compounds useful at fighting bacterial infections: antibiotics. Ever since, a number of studies were carried out to find new molecules with the same activity. Microorganisms belonging to Actinobacteria phylum, the Actinomycetes, were the most important sources of antibiotics. Bioactive compounds isolated from this order were also an important inspiration reservoir for pharmaceutical chemists who realized the synthesis of new molecules with antibiotic activity. According to the World Health Organization (WHO), antibiotic resistance is currently one of the biggest threats to global health, food security, and development. The world urgently needs to adopt measures to reduce this risk by finding new antibiotics and changing the way they are used. In this review, we describe the primary role of Actinomycetes in the history of antibiotics. Antibiotics produced by these microorganisms, their bioactivities, and how their chemical structures have inspired generations of scientists working in the synthesis of new drugs are described thoroughly.
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Lautenschläger N, Popp PF, Mascher T. Development of a novel heterologous β-lactam-specific whole-cell biosensor in Bacillus subtilis. J Biol Eng 2020; 14:21. [PMID: 32765644 PMCID: PMC7394692 DOI: 10.1186/s13036-020-00243-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background Whole-cell biosensors are a powerful and easy-to-use screening tool for the fast and sensitive detection of chemical compounds, such as antibiotics. β-Lactams still represent one of the most important antibiotic groups in therapeutic use. They interfere with late stages of the bacterial cell wall biosynthesis and result in irreversible perturbations of cell division and growth, ultimately leading to cell lysis. In order to simplify the detection of these antibiotics from solutions, solid media or directly from producing organisms, we aimed at developing a novel heterologous whole-cell biosensor in Bacillus subtilis, based on the β-lactam-induced regulatory system BlaR1/BlaI from Staphylococcus aureus. Results The BlaR1/BlaI system was heterologously expressed in B. subtilis and combined with the luxABCDE operon of Photorhabdus luminescens under control of the BlaR1/BlaI target promoter to measure the output of the biosensor. A combination of codon adaptation, constitutive expression of blaR1 and blaI and the allelic replacement of penP increased the inducer spectrum and dynamic range of the biosensor. β-Lactams from all four classes induced the target promoter PblaZ in a concentration-dependent manner, with a dynamic range of 7- to 53-fold. We applied our biosensor to a set of Streptomycetes soil isolates and demonstrated its potential to screen for the production of β-lactams. In addition to the successful implementation of a highly sensitive β-lactam biosensor, our results also provide the first experimental evidence to support previous suggestions that PenP functions as a β-lactamase in B. subtilis. Conclusion We have successfully established a novel heterologous whole-cell biosensor in B. subtilis that is highly sensitive for a broad spectrum of β-lactams from all four chemical classes. Therefore, it increases the detectable spectrum of compounds with respect to previous biosensor designs. Our biosensor can readily be applied for identifying β-lactams in liquid or on solid media, as well as for identifying potential β-lactam producers.
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Affiliation(s)
- Nina Lautenschläger
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Philipp F Popp
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
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Sinner EK, Lichstrahl MS, Li R, Marous DR, Townsend CA. Methylations in complex carbapenem biosynthesis are catalyzed by a single cobalamin-dependent radical S-adenosylmethionine enzyme. Chem Commun (Camb) 2019; 55:14934-14937. [PMID: 31774078 DOI: 10.1039/c9cc07197k] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complex carbapenem β-lactam antibiotics contain diverse C6 alkyl substituents constructed by cobalamin-dependent radical SAM enzymes. TokK installs the C6 isopropyl chain found in asparenomycin. Time-course analyses of TokK and its ortholog ThnK, which forms the C6 ethyl chain of thienamycin, indicate that catalysis occurs through a sequence of discrete, non-processive methyl transfers.
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Affiliation(s)
- Erica K Sinner
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, USA.
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12
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Hamed RB, Gomez-Castellanos JR, Henry L, Warhaut S, Claridge TDW, Schofield CJ. Biocatalytic production of bicyclic β-lactams with three contiguous chiral centres using engineered crotonases. Commun Chem 2019; 2. [PMID: 31157308 PMCID: PMC6542682 DOI: 10.1038/s42004-018-0106-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
There is a need to develop asymmetric routes to functionalised β-lactams, which remain the most important group of antibacterials. Here we describe biocatalytic and protein engineering studies concerning carbapenem biosynthesis enzymes, aiming to enable stereoselective production of functionalised carbapenams with three contiguous chiral centres. Structurally-guided substitutions of wildtype carboxymethylproline synthases enable tuning of their C-N and C-C bond forming capacity to produce 5-carboxymethylproline derivatives substituted at C-4 and C-6, from amino acid aldehyde and malonyl-CoA derivatives. Use of tandem enzyme incubations comprising an engineered carboxymethylproline synthase and an alkylmalonyl-CoA forming enzyme (i.e. malonyl-CoA synthetase or crotonyl-CoA carboxylase reductase) can improve stereocontrol and expand the product range. Some of the prepared 4,6-disubstituted-5-carboxymethylproline derivatives are converted to bicyclic β-lactams by carbapenam synthetase catalysis. The results illustrate the utility of tandem enzyme systems involving engineered crotonases for asymmetric bicyclic β-lactam synthesis. Beta-lactams are important antiobiotics but synthesising functionalised derivatives in high enantiomeric purity can be challenging. Here malonyl-CoA derivatives are applied in an enantioselective multi-enzyme cascade, yielding beta-lactams bearing three contiguous chiral centres in high diastereomeric purity.
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Affiliation(s)
- Refaat B Hamed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - J Ruben Gomez-Castellanos
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Luc Henry
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Sven Warhaut
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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14
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Rabe P, Kamps JJAG, Schofield CJ, Lohans CT. Roles of 2-oxoglutarate oxygenases and isopenicillin N synthase in β-lactam biosynthesis. Nat Prod Rep 2018; 35:735-756. [PMID: 29808887 PMCID: PMC6097109 DOI: 10.1039/c8np00002f] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/01/2023]
Abstract
Covering: up to 2017 2-Oxoglutarate (2OG) dependent oxygenases and the homologous oxidase isopenicillin N synthase (IPNS) play crucial roles in the biosynthesis of β-lactam ring containing natural products. IPNS catalyses formation of the bicyclic penicillin nucleus from a tripeptide. 2OG oxygenases catalyse reactions that diversify the chemistry of β-lactams formed by both IPNS and non-oxidative enzymes. Reactions catalysed by the 2OG oxygenases of β-lactam biosynthesis not only involve their typical hydroxylation reactions, but also desaturation, epimerisation, rearrangement, and ring-forming reactions. Some of the enzymes involved in β-lactam biosynthesis exhibit remarkable substrate and product selectivities. We review the roles of 2OG oxygenases and IPNS in β-lactam biosynthesis, highlighting opportunities for application of knowledge of their roles, structures, and mechanisms.
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Affiliation(s)
- Patrick Rabe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Jos J A G Kamps
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher T Lohans
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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16
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Lanz ND, Blaszczyk AJ, McCarthy EL, Wang B, Wang RX, Jones BS, Booker SJ. Enhanced Solubilization of Class B Radical S-Adenosylmethionine Methylases by Improved Cobalamin Uptake in Escherichia coli. Biochemistry 2018; 57:1475-1490. [PMID: 29298049 DOI: 10.1021/acs.biochem.7b01205] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The methylation of unactivated carbon and phosphorus centers is a burgeoning area of biological chemistry, especially given that such reactions constitute key steps in the biosynthesis of numerous enzyme cofactors, antibiotics, and other natural products of clinical value. These kinetically challenging reactions are catalyzed exclusively by enzymes in the radical S-adenosylmethionine (SAM) superfamily and have been grouped into four classes (A-D). Class B radical SAM (RS) methylases require a cobalamin cofactor in addition to the [4Fe-4S] cluster that is characteristic of RS enzymes. However, their poor solubility upon overexpression and their generally poor turnover has hampered detailed in vitro studies of these enzymes. It has been suggested that improper folding, possibly caused by insufficient cobalamin during their overproduction in Escherichia coli, leads to formation of inclusion bodies. Herein, we report our efforts to improve the overproduction of class B RS methylases in a soluble form by engineering a strain of E. coli to take in more cobalamin. We cloned five genes ( btuC, btuE, btuD, btuF, and btuB) that encode proteins that are responsible for cobalamin uptake and transport in E. coli and co-expressed these genes with those that encode TsrM, Fom3, PhpK, and ThnK, four class B RS methylases that suffer from poor solubility during overproduction. This strategy markedly enhances the uptake of cobalamin into the cytoplasm and improves the solubility of the target enzymes significantly.
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17
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Zhang Z, Mahanta N, Hudson GA, Mitchell DA, van der Donk WA. Mechanism of a Class C Radical S-Adenosyl-l-methionine Thiazole Methyl Transferase. J Am Chem Soc 2017; 139:18623-18631. [PMID: 29190095 PMCID: PMC5748327 DOI: 10.1021/jacs.7b10203] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The past decade has seen the discovery of four different classes of radical S-adenosylmethionine (rSAM) methyltransferases that methylate unactivated carbon centers. Whereas the mechanism of class A is well understood, the molecular details of methylation by classes B-D are not. In this study, we present detailed mechanistic investigations of the class C rSAM methyltransferase TbtI involved in the biosynthesis of the potent thiopeptide antibiotic thiomuracin. TbtI C-methylates a Cys-derived thiazole during posttranslational maturation. Product analysis demonstrates that two SAM molecules are required for methylation and that one SAM (SAM1) is converted to 5'-deoxyadenosine and the second SAM (SAM2) is converted to S-adenosyl-l-homocysteine (SAH). Isotope labeling studies show that a hydrogen is transferred from the methyl group of SAM2 to the 5'-deoxyadenosine of SAM1 and the other two hydrogens of the methyl group of SAM2 appear in the methylated product. In addition, a hydrogen appears to be transferred from the β-position of the thiazole to the methyl group in the product. We also show that the methyl protons in the product can exchange with solvent. A mechanism consistent with these observations is presented that differs from other characterized radical SAM methyltransferases.
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Affiliation(s)
- Zhengan Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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18
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TsrM as a Model for Purifying and Characterizing Cobalamin-Dependent Radical S-Adenosylmethionine Methylases. Methods Enzymol 2017; 595:303-329. [PMID: 28882204 DOI: 10.1016/bs.mie.2017.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (SAM) methylases play vital roles in the de novo biosynthesis of many antibiotics, cofactors, and other important natural products, yet remain an understudied subclass of radical SAM enzymes. In addition to a [4Fe-4S] cluster that is ligated by three cysteine residues, these enzymes also contain an N-terminal cobalamin-binding domain. In vitro studies of these enzymes have been severely limited because many are insoluble or sparingly soluble upon their overproduction in Escherichia coli. This solubility issue has led a number of groups either to purify the protein from inclusion bodies or to purify soluble protein that often lacks proper cofactor incorporation. Herein, we use TsrM as a model to describe methods that we have used to generate soluble protein that is purified in an active form with both cobalamin and [4Fe-4S] cluster cofactors bound. Additionally, we highlight the methods that we developed to characterize the enzyme following purification.
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19
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Kim J, Lee PG, Jung EO, Kim BG. In vitro characterization of CYP102G4 from Streptomyces cattleya: A self-sufficient P450 naturally producing indigo. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:60-67. [PMID: 28821467 DOI: 10.1016/j.bbapap.2017.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023]
Abstract
Self-sufficient CYP102As possess outstanding hydroxylating activity to fatty acids such as myristic acid. Other CYP102 subfamily members share substrate specificity of CYP102As, but, occasionally, unusual characteristics of its own subfamily have been found. In this study, only one self-sufficient cytochrome P450 from Streptomyces cattleya was renamed from CYP102A_scat to CYP102G4, purified and characterized. UV-Vis spectrometry pattern, FAD/FMN analysis, and protein sequence comparison among CYP102s have shown that CYP102 from Streptomyces cattleya belongs to CYP102G subfamily. It showed hydroxylation activity toward fatty acids generating ω-1, ω-2, and ω-3-hydroxyfatty acids, which is similar to the general substrate specificity of CYP102 family. Unexpectedly, however, expression of CYP102G4 showed indigo production in LB medium batch flask culture, and high catalytic activity (kcat/Km) for indole was measured as 6.14±0.10min-1mM-1. Besides indole, CYP102G4 was able to hydroxylate aromatic compounds such as flavone, benzophenone, and chloroindoles. Homology model has shown such ability to accept aromatic compounds is due to its bigger active site cavity. Unlike other CYP102s, CYP102G4 did not have biased cofactor dependency, which was possibly determined by difference in NAD(P)H binding residues (Ala984, Val990, and Tyr1064) compared to CYP102A1 (Arg966, Lys972 and Trp1046). Overall, a self-sufficient CYP within CYP102G subfamily was characterized using purified enzymes, which appears to possess unique properties such as an only prokaryotic CYP naturally producing indigo.
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Affiliation(s)
- Joonwon Kim
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Pyung-Gang Lee
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun-Ok Jung
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byung-Gee Kim
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
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20
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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21
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Hamed RB, Henry L, Claridge TDW, Schofield CJ. Stereoselective Production of Dimethyl-Substituted Carbapenams via Engineered Carbapenem Biosynthesis Enzymes. ACS Catal 2017. [DOI: 10.1021/acscatal.6b02509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Refaat B. Hamed
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Luc Henry
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy D. W. Claridge
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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22
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Townsend CA. Convergent biosynthetic pathways to β-lactam antibiotics. Curr Opin Chem Biol 2016; 35:97-108. [PMID: 27693891 DOI: 10.1016/j.cbpa.2016.09.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 02/05/2023]
Abstract
Five naturally-occurring families of β-lactams have inspired a class of drugs that constitute >60% of the antimicrobials used in human medicine. Their biosynthetic pathways reveal highly individualized synthetic strategies that yet converge on a common azetidinone ring assembled in structural contexts that confer selective binding and inhibition of d,d-transpeptidases that play essential roles in bacterial cell wall (peptidoglycan) biosynthesis. These enzymes belong to a single 'clan' of evolutionarily distinct serine hydrolases whose active site geometry and mechanism of action is specifically matched by these antibiotics for inactivation that is kinetically competitive with their native function. Unusual enzyme-mediated reactions and catalytic multitasking in these pathways are discussed with particular attention to the diverse ways the β-lactam itself is generated, and more broadly how the intrinsic reactivity of this core structural element is modulated in natural systems through the introduction of ring strain and electronic effects.
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Affiliation(s)
- Craig A Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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23
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Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:73-79. [PMID: 27632683 DOI: 10.1016/j.cbpa.2016.08.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 01/06/2023]
Abstract
Class B radical S-adenosylmethionine (SAM) methylases are notable for their ability to catalyse methylation reactions in the biosynthesis of a wide variety of natural products, including polyketides, ribosomally biosynthesised and post-translationally modified peptides (RiPPs), nonribosomal peptides (NRPs), aminoglycosides, β-lactams, phosphonates, enediynes, aminocoumarins and terpenes. Here, we discuss the diversity of substrates and catalytic mechanism utilised by such enzymes, highlighting the stereochemical course of methylation reactions at un-activated carbon centres and the ability of some members of the family to catalyse multiple methylations.
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24
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Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF. A Combinatorial Algorithm for Microbial Consortia Synthetic Design. Sci Rep 2016; 6:29182. [PMID: 27373593 PMCID: PMC4931573 DOI: 10.1038/srep29182] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology has boomed since the early 2000s when it started being shown that it was possible to efficiently synthetize compounds of interest in a much more rapid and effective way by using other organisms than those naturally producing them. However, to thus engineer a single organism, often a microbe, to optimise one or a collection of metabolic tasks may lead to difficulties when attempting to obtain a production system that is efficient, or to avoid toxic effects for the recruited microorganism. The idea of using instead a microbial consortium has thus started being developed in the last decade. This was motivated by the fact that such consortia may perform more complicated functions than could single populations and be more robust to environmental fluctuations. Success is however not always guaranteed. In particular, establishing which consortium is best for the production of a given compound or set thereof remains a great challenge. This is the problem we address in this paper. We thus introduce an initial model and a method that enable to propose a consortium to synthetically produce compounds that are either exogenous to it, or are endogenous but where interaction among the species in the consortium could improve the production line.
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Affiliation(s)
- Alice Julien-Laferrière
- Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I’Europe, 38330 Montbonnot-Saint-Martin, France
- University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France
| | - Laurent Bulteau
- Université Paris-Est, LIGM (UMR 8049), CNRS, UPEM, ESIEE Paris, ENPC, F-77454, Marne-la-Vallée, France
| | - Delphine Parrot
- Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I’Europe, 38330 Montbonnot-Saint-Martin, France
- University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France
| | - Alberto Marchetti-Spaccamela
- Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I’Europe, 38330 Montbonnot-Saint-Martin, France
- Sapienza University of Rome, Italy
| | - Leen Stougie
- Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I’Europe, 38330 Montbonnot-Saint-Martin, France
- VU University and CWI, Amsterdam, The Netherlands
| | - Susana Vinga
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Arnaud Mary
- Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I’Europe, 38330 Montbonnot-Saint-Martin, France
- University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France
| | - Marie-France Sagot
- Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I’Europe, 38330 Montbonnot-Saint-Martin, France
- University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France
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25
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Pang B, Wang M, Liu W. Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines. Nat Prod Rep 2016; 33:162-73. [PMID: 26604034 DOI: 10.1039/c5np00095e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are multifunctional megaenzymes that serve as templates to program the assembly of short carboxylic acids and amino acids in a primarily co-linear manner. The variation, combination, permutation and evolution of their functional units (e.g., modules, domains and proteins) along with their association with external enzymes have resulted in the generation of numerous versions of templates, the roles of which have not been fully recognized in the structural diversification of polyketides, non-ribosomal peptides and their hybrids present in nature. In this Highlight, we focus on the assembly-line enzymology and associated chemistry by providing examples of some newly characterized cyclization reactions that occur on and off the assembly lines during and after chain elongation for the purpose of elucidating the template effects of PKSs and NRPSs. A fundamental understanding of the underlying biosynthetic logic would facilitate the elucidation of chemical information contained within the PKS or NRPS templates and benefit the development of strategies for genome mining, biosynthesis-inspired chemical synthesis and combinatorial biosynthesis.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Min Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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26
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Blaszczyk AJ, Silakov A, Zhang B, Maiocco SJ, Lanz ND, Kelly WL, Elliott SJ, Krebs C, Booker SJ. Spectroscopic and Electrochemical Characterization of the Iron-Sulfur and Cobalamin Cofactors of TsrM, an Unusual Radical S-Adenosylmethionine Methylase. J Am Chem Soc 2016; 138:3416-26. [PMID: 26841310 DOI: 10.1021/jacs.5b12592] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
TsrM, an annotated radical S-adenosylmethionine (SAM) enzyme, catalyzes the methylation of carbon 2 of the indole ring of L-tryptophan. Its reaction is the first step in the biosynthesis of the unique quinaldic acid moiety of thiostrepton A, a thiopeptide antibiotic. The appended methyl group derives from SAM; however, the enzyme also requires cobalamin and iron-sulfur cluster cofactors for turnover. In this work we report the overproduction and purification of TsrM and the characterization of its metallocofactors by UV-visible, electron paramagnetic resonance, hyperfine sublevel correlation (HYSCORE), and Mössbauer spectroscopies as well as protein-film electrochemistry (PFE). The enzyme contains 1 equiv of its cobalamin cofactor in its as-isolated state and can be reconstituted with iron and sulfide to contain one [4Fe-4S] cluster with a site-differentiated Fe(2+)/Fe(3+) pair. Our spectroscopic studies suggest that TsrM binds cobalamin in an uncharacteristic five-coordinate base-off/His-off conformation, whereby the dimethylbenzimidazole group is replaced by a non-nitrogenous ligand, which is likely a water molecule. Electrochemical analysis of the protein by PFE indicates a one-electron redox feature with a midpoint potential of -550 mV, which is assigned to a [4Fe-4S](2+)/[4Fe-4S](+) redox couple. Analysis of TsrM by Mössbauer and HYSCORE spectroscopies suggests that SAM does not bind to the unique iron site of the cluster in the same manner as in other radical SAM (RS) enzymes, yet its binding still perturbs the electronic configuration of both the Fe/S cluster and the cob(II)alamin cofactors. These biophysical studies suggest that TsrM is an atypical RS enzyme, consistent with its reported inability to catalyze formation of a 5'-deoxyadenosyl 5'-radical.
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Affiliation(s)
| | | | | | - Stephanie J Maiocco
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | | | - Wendy L Kelly
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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27
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Doroghazi JR, Buckley DH. Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin. BMC Genomics 2014; 15:970. [PMID: 25399205 PMCID: PMC4239341 DOI: 10.1186/1471-2164-15-970] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/29/2014] [Indexed: 01/23/2023] Open
Abstract
Background Streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. While interspecific genomic diversity has been investigated among Streptomyces, information is lacking on intraspecific genomic diversity. Streptomyces pratensis has high rates of homologous recombination but the impact of such gene exchange on genome evolution and the evolution of natural product gene clusters remains uncharacterized. Results We report draft genome sequences of four S. pratensis strains and compare to the complete genome of Streptomyces flavogriseus IAF-45-CD (=ATCC 33331), a strain recently reclassified to S. pratensis. Despite disparate geographic origins, the genomes are highly similar with 85.9% of genes present in the core genome and conservation of all natural product gene clusters. Natural products include a novel combination of carbapenem and beta-lactamase inhibitor gene clusters. While high intraspecies recombination rates abolish the phylogenetic signal across the genome, intraspecies recombination is suppressed in two genomic regions. The first region is centered on an insertion/deletion polymorphism and the second on a hybrid NRPS-PKS gene. Finally, two gene families accounted for over 25% of the divergent genes in the core genome. The first includes homologs of bldB (required for spore development and antibiotic production) while the second includes homologs of an uncharacterized protein with a helix-turn-helix motif (hpb). Genes from these families co-occur with fifteen pairs spread across the genome. These genes have evidence for co-evolution of co-localized pairs, supporting previous assertions that these genes may function akin to a toxin-antitoxin system. Conclusions S. pratensis genomes are highly similar with exceptional levels of recombination which erase phylogenetic signal among strains of the species. This species has a large core genome and variable terminal regions that are smaller than those found in interspecies comparisons. There is no geographic differentiation between these strains, but there is evidence for local linkage disequilibrium affecting two genomic regions. We have also shown further observational evidence that the DUF397-HTH (bldB and hpb) are a novel toxin-antitoxin pair.
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Affiliation(s)
| | - Daniel H Buckley
- Department of Crop and Soil Sciences, Cornell University, Ithaca, USA.
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28
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Penicillin-binding proteins in Actinobacteria. J Antibiot (Tokyo) 2014; 68:223-45. [DOI: 10.1038/ja.2014.148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/24/2014] [Accepted: 09/30/2014] [Indexed: 11/09/2022]
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29
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Braña AF, Rodríguez M, Pahari P, Rohr J, García LA, Blanco G. Activation and silencing of secondary metabolites in Streptomyces albus and Streptomyces lividans after transformation with cosmids containing the thienamycin gene cluster from Streptomyces cattleya. Arch Microbiol 2014; 196:345-55. [PMID: 24633227 DOI: 10.1007/s00203-014-0977-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 02/17/2014] [Accepted: 03/04/2014] [Indexed: 01/09/2023]
Abstract
Activation and silencing of antibiotic production was achieved in Streptomyces albus J1074 and Streptomyces lividans TK21 after introduction of genes within the thienamycin cluster from S. cattleya. Dramatic phenotypic and metabolic changes, involving activation of multiple silent secondary metabolites and silencing of others normally produced, were found in recombinant strains harbouring the thienamycin cluster in comparison to the parental strains. In S. albus, ultra-performance liquid chromatography purification and NMR structural elucidation revealed the identity of four structurally related activated compounds: the antibiotics paulomycins A, B and the paulomenols A and B. Four volatile compounds whose biosynthesis was switched off were identified by gas chromatography-mass spectrometry analyses and databases comparison as pyrazines; including tetramethylpyrazine, a compound with important clinical applications to our knowledge never reported to be produced by Streptomyces. In addition, this work revealed the potential of S. albus to produce many others secondary metabolites normally obtained from plants, including compounds of medical relevance as dihydro-β-agarofuran and of interest in perfume industry as β-patchoulene, suggesting that it might be an alternative model for their industrial production. In S. lividans, actinorhodins production was strongly activated in the recombinant strains whereas undecylprodigiosins were significantly reduced. Activation of cryptic metabolites in Streptomyces species might represent an alternative approach for pharmaceutical drug discovery.
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Affiliation(s)
- Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain
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30
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Li R, Lloyd EP, Moshos KA, Townsend CA. Identification and characterization of the carbapenem MM 4550 and its gene cluster in Streptomyces argenteolus ATCC 11009. Chembiochem 2014; 15:320-31. [PMID: 24420617 PMCID: PMC3972073 DOI: 10.1002/cbic.201300319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 10/25/2013] [Indexed: 11/11/2022]
Abstract
Nearly 50 naturally occurring carbapenem β-lactam antibiotics, most produced by Streptomyces, have been identified. The structural diversity of these compounds is limited to variance of the C-2 and C-6 side chains as well as the stereochemistry at C-5/C-6. These structural motifs are of interest both for their antibiotic effects and their biosynthesis. Although the thienamycin gene cluster is the only active gene cluster publically available in this group, more comparative information is needed to understand the genetic basis of these structural differences. We report here the identification of MM 4550, a member of the olivanic acids, as the major carbapenem produced by Streptomyces argenteolus ATCC 11009. Its gene cluster was also identified by degenerate PCR and targeted gene inactivation. Sequence analysis revealed that the genes encoding the biosynthesis of the bicyclic core and the C-6 and C-2 side chains are well conserved in the MM 4550 and thienamycin gene clusters. Three new genes, cmmSu, cmm17 and cmmPah were found in the new cluster, and their putative functions in the sulfonation and epimerization of MM 4550 are proposed. Gene inactivation showed that, in addition to cmmI, two new genes, cmm22 and -23, encode a two-component response system thought to regulate the production of MM 4550. Overexpression of cmmI, cmm22 and cmm23 promoted MM 4550 production in an engineered strain. Finally, the involvement and putative roles of all genes in the MM 4550 cluster are proposed based on the results of bioinformatics analysis, gene inactivation, and analysis of disruption mutants. Overall, the differences between the thienamycin and MM 4550 gene clusters are reflected in characteristic structural elements and provide new insights into the biosynthesis of the complex carbapenems.
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Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 (USA)
| | - Evan P. Lloyd
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 (USA)
| | | | - Craig. A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 (USA)
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31
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Fujimori DG. Radical SAM-mediated methylation reactions. Curr Opin Chem Biol 2013; 17:597-604. [PMID: 23835516 DOI: 10.1016/j.cbpa.2013.05.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
A subset of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily is able to catalyze methylation reactions. Substrates of these enzymes are distinct from the nucleophilic substrates that undergo methylation by a polar mechanism. Recently, activities of several radical SAM methylating enzymes have been reconstituted in vitro and their mechanisms of catalysis investigated. The RNA modifying enzymes RlmN and Cfr catalyze methylation via a methyl synthase mechanism. These enzymes use SAM in two distinct roles: as a source of a methyl group transferred to a conserved cysteine and as a source of 5'-deoxyadenosyl radical (5'-dA). Hydrogen atom abstraction by this species generates a thiomethylene radical which adds into the RNA substrate, forming an enzyme-substrate covalent adduct. In another recent study, methylation of the indole moiety of tryptophan by the radical SAM and cobalamin-binding domain enzyme TsrM has been reconstituted. Methylcobalamin serves as an intermediate methyl donor in TsrM, and is proposed to transfer the methyl group as a methyl radical. Interestingly, despite the presence of the radical SAM motif, no reductive cleavage of SAM has been observed in this methylation. These important reconstitutions set the stage for further studies on mechanisms of radical methylation.
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Affiliation(s)
- Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-2280, USA.
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32
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Origins of the β-lactam rings in natural products. J Antibiot (Tokyo) 2013; 66:401-10. [DOI: 10.1038/ja.2013.24] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 02/26/2013] [Accepted: 03/05/2013] [Indexed: 11/08/2022]
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Hamed RB, Henry L, Gomez-Castellanos JR, Asghar A, Brem J, Claridge TDW, Schofield CJ. Stereoselective preparation of lipidated carboxymethyl-proline/pipecolic acid derivatives via coupling of engineered crotonases with an alkylmalonyl-CoA synthetase. Org Biomol Chem 2013; 11:8191-6. [DOI: 10.1039/c3ob41525b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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36
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Abstract
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Methylation is an essential and ubiquitous reaction that plays an important role in a wide range of biological processes. Most biological methylations use S-adenosylmethionine (SAM) as the methyl donor and proceed via an SN2 displacement mechanism. However, researchers have discovered an increasing number of methylations that involve radical chemistry. The enzymes known to catalyze these reactions all belong to the radical SAM superfamily. This family of enzymes utilizes a specialized [4Fe-4S] cluster for reductive cleavage of SAM to yield a highly reactive 5'-deoxyadenosyl (dAdo) radical. Radical chemistry is then imposed on a variety of organic substrates, leading to a diverse array of transformations. Until recently, researchers had not fully understood how these enzymes employ radical chemistry to mediate a methyl transfer reaction. Sequence analyses reveal that the currently identified radical SAM methyltransferases (RSMTs) can be grouped into three classes, which appear distinct in protein architecture and mechanism. Class A RSMTs mainly include the rRNA methyltransferases RlmN and Cfr from various origins. As exemplified by Escherichia coli RlmN, these proteins have a single canonical radical SAM core domain that includes an (βα)6 partial barrel most similar to that of pyruvate formate lyase-activase. The exciting recent studies on RlmN and Cfr are beginning to provide insights into the intriguing chemistry of class A RSMTs. These enzymes utilize a methylene radical generated on a unique methylated cysteine residue. However, based on the variety of substrates used by the other classes of RSMTs, alternative mechanisms are likely to be discovered. Class B RSMTs contain a proposed N-terminal cobalamin binding domain in addition to a radical SAM domain at the C-terminus. This class of proteins methylates diverse substrates at inert sp3 carbons, aromatic heterocycles, and phosphinates, possibly involving a cobalamin-mediated methyl transfer process. Class C RSMTs share significant sequence similarity with coproporphyrinogen III oxidase HemN. Despite methylating similar substrates (aromatic heterocycles), class C RSMTs likely employ a mechanism distinct from that of class A because two conserved cysteines that are required for class A are typically not found in class C RSMTs. Class A and class B enzymes probably share the use of two molecules of SAM: one to generate a dAdo radical and one to provide the methyl group to the substrate. In class A, a cysteine would act as a conduit of the methyl group whereas in class B cobalamin may serve this purpose. Currently no clues are available regarding the mechanism of class C RSMTs, but the sequence similarities between its members and HemN and the observation that HemN binds two SAM molecules suggest that class C enzymes could use two SAM molecules for catalysis. The diverse strategies for using two SAM molecules reflect the rich chemistry of radical-mediated methylation reactions and the remarkable versatility of the radical SAM superfamily.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | | | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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37
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Hamed RB, Henry L, Gomez-Castellanos JR, Mecinović J, Ducho C, Sorensen JL, Claridge TDW, Schofield CJ. Crotonase Catalysis Enables Flexible Production of Functionalized Prolines and Carbapenams. J Am Chem Soc 2011; 134:471-9. [DOI: 10.1021/ja208318d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Refaat B. Hamed
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Luc Henry
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | | | - Jasmin Mecinović
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christian Ducho
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - John L. Sorensen
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy D. W. Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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38
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Papp-Wallace KM, Endimiani A, Taracila MA, Bonomo RA. Carbapenems: past, present, and future. Antimicrob Agents Chemother 2011; 55:4943-60. [PMID: 21859938 PMCID: PMC3195018 DOI: 10.1128/aac.00296-11] [Citation(s) in RCA: 860] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In this review, we summarize the current "state of the art" of carbapenem antibiotics and their role in our antimicrobial armamentarium. Among the β-lactams currently available, carbapenems are unique because they are relatively resistant to hydrolysis by most β-lactamases, in some cases act as "slow substrates" or inhibitors of β-lactamases, and still target penicillin binding proteins. This "value-added feature" of inhibiting β-lactamases serves as a major rationale for expansion of this class of β-lactams. We describe the initial discovery and development of the carbapenem family of β-lactams. Of the early carbapenems evaluated, thienamycin demonstrated the greatest antimicrobial activity and became the parent compound for all subsequent carbapenems. To date, more than 80 compounds with mostly improved antimicrobial properties, compared to those of thienamycin, are described in the literature. We also highlight important features of the carbapenems that are presently in clinical use: imipenem-cilastatin, meropenem, ertapenem, doripenem, panipenem-betamipron, and biapenem. In closing, we emphasize some major challenges and urge the medicinal chemist to continue development of these versatile and potent compounds, as they have served us well for more than 3 decades.
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Affiliation(s)
- Krisztina M. Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
- Departments of Medicine
| | - Andrea Endimiani
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
- Institute for Infectious Diseases, University of Bern 3010, Bern, Switzerland
- Departments of Medicine
| | | | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
- Departments of Medicine
- Pharmacology
- Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106
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39
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Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites. J Bacteriol 2011; 193:5055-6. [PMID: 21868806 DOI: 10.1128/jb.05583-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of the rare bacteria known to synthesize fluorinated metabolites. The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons.
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40
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Bodner MJ, Li R, Phelan RM, Freeman MF, Moshos KA, Lloyd EP, Townsend CA. Definition of the common and divergent steps in carbapenem β-lactam antibiotic biosynthesis. Chembiochem 2011; 12:2159-65. [PMID: 21913298 PMCID: PMC3281309 DOI: 10.1002/cbic.201100366] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Indexed: 11/11/2022]
Abstract
Approximately 50 naturally occurring carbapenem β-lactam antibiotics are known. All but one of these have been isolated from Streptomyces species and are disubstituted structural variants of a simple core that is synthesized by Pectobacterium carotovorum (Erwinia carotovora), a phylogenetically distant plant pathogen. While the biosynthesis of the simple carbapenem, (5R)-carbapen-2-em-3-carboxylic acid, is impressively efficient requiring only three enzymes, CarA, CarB and CarC, the formation of thienamycin, one of the former group of metabolites from Streptomyces, is markedly more complex. Despite their phylogenetic separation, bioinformatic analysis of the encoding gene clusters suggests that the two pathways could be related. Here we demonstrate with gene swapping, stereochemical and kinetics experiments that CarB and CarA and their S. cattleya orthologues, ThnE and ThnM, respectively, are functionally and stereochemically equivalent, although their catalytic efficiencies differ. The biosynthetic pathways, therefore, to thienamycin, and likely to the other disubstituted carbapenems, and to the simplest carbapenem, (5R)-carbapen-2-em-3-carboxylic acid, are initiated in the same manner, but share only two common steps before diverging.
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Affiliation(s)
- Micah J. Bodner
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Rongfeng Li
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Ryan M. Phelan
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Michael F. Freeman
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Kristos A. Moshos
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Evan P. Lloyd
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
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41
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Challand MR, Driesener RC, Roach PL. Radical S-adenosylmethionine enzymes: mechanism, control and function. Nat Prod Rep 2011; 28:1696-721. [PMID: 21779595 DOI: 10.1039/c1np00036e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Martin R Challand
- School of Cellular and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS81TD, USA
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42
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Rodríguez M, Núñez LE, Braña AF, Méndez C, Salas JA, Blanco G. Mutational analysis of the thienamycin biosynthetic gene cluster from Streptomyces cattleya. Antimicrob Agents Chemother 2011; 55:1638-49. [PMID: 21263049 PMCID: PMC3067130 DOI: 10.1128/aac.01366-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/09/2010] [Accepted: 01/14/2011] [Indexed: 11/20/2022] Open
Abstract
The generation of non-thienamycin-producing mutants with mutations in the thnL, thnN, thnO, and thnI genes within the thn gene cluster from Streptomyces cattleya and their involvement in thienamycin biosynthesis and regulation were previously reported. Four additional mutations were independently generated in the thnP, thnG, thnR, and thnT genes by insertional inactivation. Only the first two genes were found to play a role in thienamycin biosynthesis, since these mutations negatively or positively affect antibiotic production. A mutation of thnP results in the absence of thienamycin production, whereas a 2- to 3-fold increase in thienamycin production was observed for the thnG mutant. On the other hand, mutations in thnR and thnT showed that although these genes were previously reported to participate in this pathway, they seem to be nonessential for thienamycin biosynthesis, as thienamycin production was not affected in these mutants. High-performance liquid chromatography (HPLC)-mass spectrometry (MS) analysis of all available mutants revealed some putative intermediates in the thienamycin biosynthetic pathway. A compound with a mass corresponding to carbapenam-3-carboxylic acid was detected in some of the mutants, suggesting that the assembly of the bicyclic nucleus of thienamycin might proceed in a way analogous to that of the simplest natural carbapenem, 1-carbapen-2-em-3-carboxylic acid biosynthesis. The accumulation of a compound with a mass corresponding to 2,3-dihydrothienamycin in the thnG mutant suggests that it might be the last intermediate in the biosynthetic pathway. These data, together with the establishment of cross-feeding relationships by the cosynthesis analysis of the non-thienamycin-producing mutants, lead to a proposal for some enzymatic steps during thienamycin assembly.
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Affiliation(s)
- Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Luz Elena Núñez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Alfredo F. Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Gloria Blanco
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
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43
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Blasiak LC, Clardy J. Discovery of 3-formyl-tyrosine metabolites from Pseudoalteromonas tunicata through heterologous expression. J Am Chem Soc 2010; 132:926-7. [PMID: 20041686 PMCID: PMC2808729 DOI: 10.1021/ja9097862] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (NRPS) or polyketide synthase (PKS) domains. Recently, other condensation enzymes, such as the ATP-grasp ligases, have been recognized as important players in natural product biosynthesis. In this study, sequence based searching for homologues of DdaF, the ATP-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously unannotated biosynthetic gene cluster in Pseudoalteromonas tunicata. Heterologous expression of the cluster in Escherichia coli allowed for the production and structure determination of two new 3-formyl tyrosine metabolites.
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Affiliation(s)
- Leah C Blasiak
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, Massachusetts 02115, USA
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44
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Raber ML, Castillo A, Greer A, Townsend CA. A conserved lysine in beta-lactam synthetase assists ring cyclization: Implications for clavam and carbapenem biosynthesis. Chembiochem 2010; 10:2904-12. [PMID: 19882698 DOI: 10.1002/cbic.200900389] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
beta-Lactam synthetase (beta-LS) is the paradigm of a growing class of enzymes that form the critical beta-lactam ring in the clavam and carbapenem antibiotics. beta-LS catalyzes a two-stage reaction in which N(2)-(2-carboxyethyl)-L-arginine is first adenylated, and then undergoes intramolecular ring closure. It was previously shown that the forward kinetic commitment to beta-lactam formation is high, and that the overall rate of reaction is partially limited to a protein conformational change rather than to the chemical step alone of closing the strained ring. beta-Lactam formation was evaluated on the basis of X-ray crystal structures, site-specific mutation, and kinetic and computational studies. The combined evidence clearly points to a reaction coordinate involving the formation of a tetrahedral transition state/intermediate stabilized by a conserved Lys. The combination of substrate preorganization, a well-stabilized transition state and an excellent leaving group facilitates this acyl substitution to account for the strong forward commitment to catalysis and to lower the barrier of four-membered ring formation to the magnitude of a protein conformational change.
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Affiliation(s)
- Mary L Raber
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
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45
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Rodríguez M, Méndez C, Salas JA, Blanco G. Transcriptional organization of ThnI-regulated thienamycin biosynthetic genes in Streptomyces cattleya. J Antibiot (Tokyo) 2010; 63:135-8. [DOI: 10.1038/ja.2009.133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Bodner MJ, Phelan RM, Freeman MF, Li R, Townsend CA. Non-heme iron oxygenases generate natural structural diversity in carbapenem antibiotics. J Am Chem Soc 2010; 132:12-3. [PMID: 20017478 PMCID: PMC2821876 DOI: 10.1021/ja907320n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Carbapenems are a clinically important antibiotic family. More than 50 naturally occurring carbapenam/ems are known and are distinguished primarily by their C-2/C-6 side chains where many are only differentiated by the oxidation states of these substituents. With a limited palette of variations the carbapenem family comprises a natural combinatorial library, and C-2/C-6 oxidation is associated with increased efficacy. We demonstrate that ThnG and ThnQ encoded by the thienamycin gene cluster in Streptomyces cattleya oxidize the C-2 and C-6 moieties of carbapenems, respectively. ThnQ stereospecifically hydroxylates PS-5 (5) giving N-acetyl thienamycin (2). ThnG catalyzes sequential desaturation and sulfoxidation of PS-5 (5), giving PS-7 (7) and its sulfoxide (9). The enzymes are relatively substrate selective but are proposed to give rise to the oxidative diversity of carbapenems produced by S. cattleya, and orthologues likely function similarly in allied streptomyces. Elucidating the roles of ThnG and ThnQ will focus further investigations of carbapenem antibiotic biosynthesis.
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Affiliation(s)
- Micah J. Bodner
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Ryan M. Phelan
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Michael F. Freeman
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
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47
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Hamed RB, Mecinović J, Ducho C, Claridge TDW, Schofield CJ. Carboxymethylproline synthase catalysed syntheses of functionalised N-heterocycles. Chem Commun (Camb) 2010; 46:1413-5. [PMID: 20162132 DOI: 10.1039/b924519g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The utility of wild-type and variant carboxymethylproline synthases for biocatalysis was demonstrated by preparing functionalised 5-, 6- and 7-membered N-heterocycles from amino acid aldehydes and (alkylated) malonyl-coenzyme A derivatives; the N-heterocycles produced were converted to the corresponding bicyclic beta-lactams by a carbapenem synthetase.
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Affiliation(s)
- Refaat B Hamed
- University of Oxford, Department of Chemistry, Chemistry Research Laboratory, Mansfield Road, Oxford, UK OX1 3TA
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48
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Ostash B, Doud EH, Lin C, Ostash I, Perlstein DL, Fuse S, Wolpert M, Kahne D, Walker S. Complete characterization of the seventeen step moenomycin biosynthetic pathway. Biochemistry 2009; 48:8830-41. [PMID: 19640006 DOI: 10.1021/bi901018q] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The moenomycins are phosphoglycolipid antibiotics produced by Streptomyces ghanaensis and related organisms. The phosphoglycolipids are the only known active site inhibitors of the peptidoglycan glycosyltransferases, an important family of enzymes involved in the biosynthesis of the bacterial cell wall. Although these natural products have exceptionally potent antibiotic activity, pharmacokinetic limitations have precluded their clinical use. We previously identified the moenomycin biosynthetic gene cluster in order to facilitate biosynthetic approaches to new derivatives. Here, we report a comprehensive set of genetic and enzymatic experiments that establish functions for the 17 moenomycin biosynthetic genes involved in the synthesis of moenomycin and variants. These studies reveal the order of assembly of the full molecular scaffold and define a subset of seven genes involved in the synthesis of bioactive analogues. This work will enable both in vitro and fermentation-based reconstitution of phosphoglycolipid scaffolds so that chemoenzymatic approaches to novel analogues can be explored.
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Affiliation(s)
- Bohdan Ostash
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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49
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Antibiotics from microbes: converging to kill. Curr Opin Microbiol 2009; 12:520-7. [PMID: 19695947 DOI: 10.1016/j.mib.2009.07.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/06/2009] [Accepted: 07/08/2009] [Indexed: 11/20/2022]
Abstract
As genetically encoded small molecules, antibiotics are phenotypes that have resulted from mutation and natural selection. Advances in genetics, biochemistry, and bioinformatics have connected hundreds of antibiotics to the gene clusters that encode them, allowing these molecules to be analyzed using the tools of evolutionary biology. This review surveys examples of convergent evolution from microbially produced antibiotics, including the convergence of distinct gene clusters on similar phenotypes and the merger of distinct gene clusters into a single functional unit. Examining antibiotics through an evolutionary lens highlights the versatility of biosynthetic pathways, reveals lessons for combating antibiotic resistance, and provides an entry point for studying the natural roles of these natural products.
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50
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Abstract
Investigations of antibiotic resistance from an environmental prospective shed new light on a problem that was traditionally confined to a subset of clinically relevant antibiotic-resistant bacterial pathogens. It is clear that the environmental microbiota, even in apparently antibiotic-free environments, possess an enormous number and diversity of antibiotic resistance genes, some of which are very similar to the genes circulating in pathogenic microbiota. It is difficult to explain the role of antibiotics and antibiotic resistance in natural environments from an anthropocentric point of view, which is focused on clinical aspects such as the efficiency of antibiotics in clearing infections and pathogens that are resistant to antibiotic treatment. A broader overview of the role of antibiotics and antibiotic resistance in nature from the evolutionary and ecological prospective suggests that antibiotics have evolved as another way of intra- and inter-domain communication in various ecosystems. This signalling by non-clinical concentrations of antibiotics in the environment results in adaptive phenotypic and genotypic responses of microbiota and other members of the community. Understanding the complex picture of evolution and ecology of antibiotics and antibiotic resistance may help to understand the processes leading to the emergence and dissemination of antibiotic resistance and also help to control it, at least in relation to the newer antibiotics now entering clinical practice.
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Affiliation(s)
- Rustam I Aminov
- University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Aberdeen AB21 9SB, UK.
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