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Hagar M, Andersen RJ, Ryan KS. Prephenate decarboxylase: An unexplored branchpoint to unusual natural products. Cell Chem Biol 2024; 31:1610-1626. [PMID: 39059391 DOI: 10.1016/j.chembiol.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/03/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
Prephenate decarboxylases are a small family of enzymes which initiate a specialized divergence from the shikimate pathway, where prephenate (2) is decarboxylated without aromatization. In addition to effecting a challenging chemical transformation, prephenate decarboxylases have been implicated in the production of rare specialized metabolites, sometimes directly constructing bioactive warheads. Many of the biosynthetic steps to natural products derived from prephenate decarboxylases remain elusive. Here, we review prephenate decarboxylase research thus far and highlight natural products that may be derived from biosynthetic pathways involving prephenate decarboxylases. We also highlight commonly encountered challenges in the structure elucidation of these natural products. Prephenate decarboxylases are a gateway into understudied biosynthetic pathways which present a high potential for the discovery of novel and bioactive natural products, as well as new biosynthetic enzymes.
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Affiliation(s)
- Mostafa Hagar
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond J Andersen
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada; Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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2
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Kavakli S, Grammbitter GL, Bode HB. Biosynthesis of the multifunctional isopropylstilbene in Photorhabdus laumondii involves cross-talk between specialized and primary metabolism. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Lulamba TE, Green E, Serepa-Dlamini MH. Genome assembly and annotation of Photorhabdus heterorhabditis strain ETL reveals genetic features involved in pathogenicity with its associated entomopathogenic nematode and anti-host effectors with biocontrol potential applications. Gene 2021; 795:145780. [PMID: 34147570 DOI: 10.1016/j.gene.2021.145780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 11/28/2022]
Abstract
The genome sequences of entomopathogenic nematode (EPN) bacteria and their functional analyses can lead to the genetic engineering of the bacteria for use as biocontrol agents. The bacterial symbiont Photorhabdus heterorhabditis strain ETL isolated from an insect pathogenic nematode, Heterorhabditis zealandica strain ETL, collected in the northernmost region of South Africa was studied to reveal information that can be useful in the design of improvement strategies for both effective and liquid production method of EPN-based pesticides. The strain ETL genome was found closely related to the type strain genome of P. australis DSM 17,609 (~60 to 99.9% CDSs similarity), but closely related to the not yet genome-sequenced type strain, P. heterorhabditis. It has a genome size of 4,866,148 bp and G + C content of 42.4% similar to other Photorhabdus. It contains 4,351 protein coding genes (CDSs) of which, at least 84% are shared with the de facto type strain P. luminescens subsp. laumondii TTO1, and has 318 unknown CDSs and the genome has a higher degree of plasticity allowing it to adapt to different environmental conditions, and to be virulent against various insects; observed through genes acquired through horizontal gene transfer mechanisms, clustered regularly interspaced short palindromic repeats, non-determined polyketide- and non-ribosomal peptide- synthase gene clusters, and many genes associated with uncharacterized proteins; which also justify the strain ETL's genes differences (quantity and quality) compared to P. luminescens subsp. laumondii TTO1. The protein coding sequences contained genes with both bio-engineering and EPNs mass production importance, of which numerous are uncharacterized.
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Affiliation(s)
- Tshikala Eddie Lulamba
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Ezekiel Green
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa.
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4
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Hill V, Kuhnert P, Erb M, Machado RAR. Identification of Photorhabdus symbionts by MALDI-TOF MS. MICROBIOLOGY-SGM 2021; 166:522-530. [PMID: 32301690 DOI: 10.1099/mic.0.000905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Species of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.
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Affiliation(s)
- Virginia Hill
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland.,Institute of Plant Sciences, University of Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Switzerland
| | - Ricardo A R Machado
- Experimental Biology Research Group, University of Neuchatel, Switzerland.,Institute of Plant Sciences, University of Bern, Switzerland
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5
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Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family. Int J Mol Sci 2021; 22:ijms22041880. [PMID: 33668649 PMCID: PMC7918813 DOI: 10.3390/ijms22041880] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.
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6
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Symbiosis, virulence and natural-product biosynthesis in entomopathogenic bacteria are regulated by a small RNA. Nat Microbiol 2020; 5:1481-1489. [PMID: 33139881 DOI: 10.1038/s41564-020-00797-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/16/2020] [Indexed: 01/07/2023]
Abstract
Photorhabdus and Xenorhabdus species have mutualistic associations with nematodes and an entomopathogenic stage1,2 in their life cycles. In both stages, numerous specialized metabolites are produced that have roles in symbiosis and virulence3,4. Although regulators have been implicated in the regulation of these specialized metabolites3,4, how small regulatory RNAs (sRNAs) are involved in this process is not clear. Here, we show that the Hfq-dependent sRNA, ArcZ, is required for specialized metabolite production in Photorhabdus and Xenorhabdus. We discovered that ArcZ directly base-pairs with the mRNA encoding HexA, which represses the expression of specialized metabolite gene clusters. In addition to specialized metabolite genes, we show that the ArcZ regulon affects approximately 15% of all transcripts in Photorhabdus and Xenorhabdus. Thus, the ArcZ sRNA is crucial for specialized metabolite production in Photorhabdus and Xenorhabdus species and could become a useful tool for metabolic engineering and identification of commercially relevant natural products.
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7
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Park HB, Goddard TN, Oh J, Patel J, Wei Z, Perez CE, Mercado BQ, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. Bacterial Autoimmune Drug Metabolism Transforms an Immunomodulator into Structurally and Functionally Divergent Antibiotics. Angew Chem Int Ed Engl 2020; 59:7871-7880. [PMID: 32097515 PMCID: PMC7200298 DOI: 10.1002/anie.201916204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 01/01/2023]
Abstract
Tapinarof is a stilbene drug that is used to treat psoriasis and atopic dermatitis, and is thought to function through regulation of the AhR and Nrf2 signaling pathways, which have also been linked to inflammatory bowel diseases. It is produced by the gammaproteobacterial Photorhabdus genus, which thus represents a model to probe tapinarof structural and functional transformations. We show that Photorhabdus transforms tapinarof into novel drug metabolism products that kill inflammatory bacteria, and that a cupin enzyme contributes to the conversion of tapinarof and related dietary stilbenes into novel dimers. One dimer has activity against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE), and another undergoes spontaneous cyclizations to a cyclopropane-bridge-containing hexacyclic framework that exhibits activity against Mycobacterium. These dimers lack efficacy in a colitis mouse model, whereas the monomer reduces disease symptoms.
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Affiliation(s)
- Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- These authors contributed equally: Hyun Bong Park, Tyler N. Goddard
| | - Tyler N. Goddard
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- These authors contributed equally: Hyun Bong Park, Tyler N. Goddard
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jaymin Patel
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Zheng Wei
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Corey E. Perez
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical and Biophysical Instrumentation Center, Yale University, New Haven, CT 06520, USA
| | - Rurun Wang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Thomas P. Wyche
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
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8
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Chu L, Huang J, Muhammad M, Deng Z, Gao J. Genome mining as a biotechnological tool for the discovery of novel marine natural products. Crit Rev Biotechnol 2020; 40:571-589. [PMID: 32308042 DOI: 10.1080/07388551.2020.1751056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.
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Affiliation(s)
- Leixia Chu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinping Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mustafa Muhammad
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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9
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Abstract
Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus
Photorhabdus
comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore
Photorhabdus
has three distinct and obligate roles to play during this life-cycle: (1)
Photorhabdus
must kill the insect host; (2)
Photorhabdus
must be capable of supporting nematode growth and development; and (3)
Photorhabdus
must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between
Photorhabdus
and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.
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Affiliation(s)
- David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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10
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Park HB, Goddard TN, Oh J, Patel J, Wei Z, Perez CE, Mercado BQ, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. Bacterial Autoimmune Drug Metabolism Transforms an Immunomodulator into Structurally and Functionally Divergent Antibiotics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Hyun Bong Park
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Tyler N. Goddard
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Joonseok Oh
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Jaymin Patel
- Chemical Biology Institute Yale University West Haven CT 06516 USA
- Department of Molecular, Cellular, and Developmental Biology Yale University New Haven CT 06520 USA
| | - Zheng Wei
- Chemical Biology Institute Yale University West Haven CT 06516 USA
- Department of Immunobiology Yale University School of Medicine New Haven CT 06520 USA
| | - Corey E. Perez
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Brandon Q. Mercado
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical and Biophysical Instrumentation Center Yale University New Haven CT 06520 USA
| | - Rurun Wang
- Exploratory Science Center Merck & Co., Inc. Cambridge MA USA
| | - Thomas P. Wyche
- Exploratory Science Center Merck & Co., Inc. Cambridge MA USA
| | - Grazia Piizzi
- Exploratory Science Center Merck & Co., Inc. Cambridge MA USA
| | - Richard A. Flavell
- Department of Immunobiology Yale University School of Medicine New Haven CT 06520 USA
- Howard Hughes Medical Institute Yale University School of Medicine New Haven CT 06520 USA
| | - Jason M. Crawford
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
- Department of Microbial Pathogenesis Yale School of Medicine New Haven CT 06536 USA
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11
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Eckstein S, Heermann R. Regulation of Phenotypic Switching and Heterogeneity in Photorhabdus luminescens Cell Populations. J Mol Biol 2019; 431:4559-4568. [DOI: 10.1016/j.jmb.2019.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/22/2019] [Accepted: 04/12/2019] [Indexed: 11/26/2022]
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12
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Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
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Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
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13
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Hapeshi A, Benarroch JM, Clarke DJ, Waterfield NR. Iso-propyl stilbene: a life cycle signal? MICROBIOLOGY-SGM 2019; 165:516-526. [PMID: 30882293 DOI: 10.1099/mic.0.000790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Members of the Gram-negative bacterial genus Photorhabdus are all highly insect pathogenic and exist in an obligate symbiosis with the entomopathogenic nematode worm Heterorhabditis. All members of the genus produce the small-molecule 3,5-dihydroxy-4-isopropyl-trans-stilbene (IPS) as part of their secondary metabolism. IPS is a multi-potent compound that has antimicrobial, antifungal, immunomodulatory and anti-cancer activities and also plays an important role in symbiosis with the nematode. In this study we have examined the response of Photorhabdus itself to exogenous ectopic addition of IPS at physiologically relevant concentrations. We observed that the bacteria had a measureable phenotypic response, which included a decrease in bioluminescence and pigment production. This was reflected in changes in its transcriptomic response, in which we reveal a reduction in transcript levels of genes relating to many fundamental cellular processes, such as translation and oxidative phosphorylation. Our observations suggest that IPS plays an important role in the biology of Photorhabdus bacteria, fulfilling roles in quorum sensing, antibiotic-competition advantage and maintenance of the symbiotic developmental cycle.
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Affiliation(s)
- Alexia Hapeshi
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Jonatan Mimon Benarroch
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - David James Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nicholas Robin Waterfield
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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14
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Jahanshah G, Yan Q, Gerhardt H, Pataj Z, Lämmerhofer M, Pianet I, Josten M, Sahl HG, Silby MW, Loper JE, Gross H. Discovery of the Cyclic Lipopeptide Gacamide A by Genome Mining and Repair of the Defective GacA Regulator in Pseudomonas fluorescens Pf0-1. JOURNAL OF NATURAL PRODUCTS 2019; 82:301-308. [PMID: 30666877 DOI: 10.1021/acs.jnatprod.8b00747] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secondary metabolite gacamide A, a lipodepsipeptide that forms a new family of Pseudomonas lipopeptides. The compound has a moderate, narrow-spectrum antibiotic activity and facilitates bacterial surface motility.
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Affiliation(s)
- Gahzaleh Jahanshah
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Qing Yan
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Heike Gerhardt
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Zoltán Pataj
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Isabelle Pianet
- CESAMO-ISM, UMR 5255, CNRS , Université Bordeaux I , 351 Cours de la Libération , F-33405 Talence , France
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Mark W Silby
- Department of Biology , University of Massachusetts Dartmouth , North Dartmouth , Massachusetts 02747 , United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
- Agricultural Research Service , U.S. Department of Agriculture , Corvallis , Oregon 97331 , United States
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
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15
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Perez CE, Park HB, Crawford JM. Functional Characterization of a Condensation Domain That Links Nonribosomal Peptide and Pteridine Biosynthetic Machineries in Photorhabdus luminescens. Biochemistry 2018; 57:354-361. [PMID: 29111689 DOI: 10.1021/acs.biochem.7b00863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) produce a wide variety of biologically important small molecules. NRPSs can interface with other enzymes to form hybrid biosynthetic systems that expand the structural and functional diversity of their products. The pepteridines are metabolites encoded by an unprecedented pteridine-NRPS-type hybrid biosynthetic gene cluster in Photorhabdus luminescens, but how the distinct enzymatic systems interface to produce these molecules has not been examined at the biochemical level. By an unknown mechanism, the genetic locus can also affect the regulation of other enzymes involved in autoinducer and secondary metabolite biosynthesis. Here, through in vitro protein biochemical assays, we demonstrate that an atypical NRPS condensation (C) domain present in the pathway condenses acyl units derived from α-keto acids onto a free 5,6,7,8-tetrahydropterin core, producing the tertiary cis-amide-containing pepteridines. Solution studies of the chemically synthesized molecules led to the same amide regiochemistries that were observed in the natural products. The biochemical transformations mediated by the C domain destroy the radical scavenging activity of its redox active tetrahydropterin substrate. Secondary metabolite analyses revealed that the pepteridine locus affects select metabolic pathways associated with quorum sensing, antibiosis, and symbiosis. Taken together, the results suggest that the pathway likely regulates cellular redox and specialized metabolic pathways through engagement with the citric acid cycle.
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Affiliation(s)
- Corey E Perez
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Hyun Bong Park
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06510, United States
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16
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STOCK SPATRICIA, KUSAKABE AYAKO, OROZCO ROUSELA. Secondary Metabolites Produced by Heterorhabditis Symbionts and Their Application in Agriculture: What We Know and What to Do Next. J Nematol 2018. [DOI: 10.21307/jofnem-2017-084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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17
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Stock SP, Kusakabe A, Orozco RA. Secondary Metabolites Produced by Heterorhabditis Symbionts and Their Application in Agriculture: What We Know and What to Do Next. J Nematol 2017; 49:373-383. [PMID: 29353924 PMCID: PMC5770283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Indexed: 06/07/2023] Open
Abstract
Gram-negative Photorhabdus bacteria have a dual lifestyle: they are mutualists of Heterorhabditis nematodes and are pathogens of insects. Together, this nematode-bacterium partnership has been used to successfully control a wide range of agricultural insect pests. Photorhabdus produce a diverse array of small molecules that play key biological roles in regulating their dual roles. In particular, several secondary metabolites (SM) produced by this bacterium are known to play a critical role in the maintenance of a monoxenic infection in the insect host and are also known to prevent contamination of the cadaver from soil microbes and/or predation by arthropods. A few of the SM this bacteria produce have been isolated and identified, and their biological activities have also been tested in laboratory assays. Over the past two decades, analyses of the genomes of several Photorhabdus spp. have revealed the presence of SM numerous gene clusters that comprise more than 6% of these bacteria genomes. Furthermore, genome mining and characterization of biosynthetic pathways, have uncovered the richness of these compounds, which are predicted to vary across different Photorhabdus spp. and strains. Although progress has been made in the identification and function of SM genes and gene clusters, the targeted testing for the bioactivity of molecules has been scarce or mostly focused on medical applications. In this review, we summarize the current knowledge of Photorhabdus SM, emphasizing on their activity against plant pathogens and parasites. We further discuss their potential in the management of agricultural pests and the steps that need to be taken for the implementation of Photorhabdus SM in pest management.
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Affiliation(s)
- S Patricia Stock
- Department of Entomology, University of Arizona, Tucson, AZ 85721
- Entomology and Insect Science Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721
| | - Ayako Kusakabe
- Entomology and Insect Science Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721
| | - Rousel A Orozco
- Entomology and Insect Science Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721
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18
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Heinrich AK, Hirschmann M, Neubacher N, Bode HB. LuxS-dependent AI-2 production is not involved in global regulation of natural product biosynthesis in Photorhabdus and Xenorhabdus. PeerJ 2017; 5:e3471. [PMID: 28663937 PMCID: PMC5488855 DOI: 10.7717/peerj.3471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/26/2017] [Indexed: 01/06/2023] Open
Abstract
The Gram-negative bacteria Photorhabdus and Xenorhabdus are known to produce a variety of different natural products (NP). These compounds play different roles since the bacteria live in symbiosis with nematodes and are pathogenic to insect larvae in the soil. Thus, a fine tuned regulatory system controlling NP biosynthesis is indispensable. Global regulators such as Hfq, Lrp, LeuO and HexA have been shown to influence NP production of Photorhabdus and Xenorhabdus. Additionally, photopyrones as quorum sensing (QS) signals were demonstrated to be involved in the regulation of NP production in Photorhabdus. In this study, we investigated the role of another possible QS signal, autoinducer-2 (AI-2), in regulation of NP production. The AI-2 synthase (LuxS) is widely distributed within the bacterial kingdom and has a dual role as a part of the activated methyl cycle pathway, as well as being responsible for AI-2 precursor production. We deleted luxS in three different entomopathogenic bacteria and compared NP levels in the mutant strains to the wild type (WT) but observed no difference to the WT strains. Furthermore, the absence of the small regulatory RNA micA, which is encoded directly upstream of luxS, did not influence NP levels. Phenotypic differences between the P. luminescens luxS deletion mutant and an earlier described luxS deficient strain of P. luminescens suggested that two phenotypically different strains have evolved in different laboratories.
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Affiliation(s)
- Antje K. Heinrich
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Merle Hirschmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Nick Neubacher
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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19
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Langer A, Moldovan A, Harmath C, Joyce SA, Clarke DJ, Heermann R. HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens. PLoS One 2017; 12:e0176535. [PMID: 28448559 PMCID: PMC5407808 DOI: 10.1371/journal.pone.0176535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/12/2017] [Indexed: 12/04/2022] Open
Abstract
Phenotypic heterogeneity in microbial communities enables genetically identical organisms to behave differently even under the same environmental conditions. Photorhabdus luminescens, a bioluminescent Gram-negative bacterium, contains a complex life cycle, which involves a symbiotic interaction with nematodes as well as a pathogenic association with insect larvae. P. luminescens exists in two distinct phenotypic cell types, designated as the primary (1°) and secondary (2°) cells. The 1° cells are bioluminescent, pigmented and can support nematode growth and development. Individual 1° cells undergo phenotypic switching after prolonged cultivation and convert to 2° cells, which lack the 1° specific phenotypes. The LysR-type regulator HexA has been described as major regulator of this switching process. Here we show that HexA controls phenotypic heterogeneity in a versatile way, directly and indirectly. Expression of hexA is enhanced in 2° cells, and the corresponding regulator inhibits 1° specific traits in 2° cells. HexA does not directly affect bioluminescence, a predominant 1° specific phenotype. Since the respective luxCDABE operon is repressed at the post-transcriptional level and transcriptional levels of the RNA chaperone gene hfq are also enhanced in 2° cells, small regulatory RNAs are presumably involved that are under control of HexA. Another phenotypic trait that is specific for 1° cells is quorum sensing mediated cell clumping. The corresponding pcfABCDEF operon could be identified as the first direct target of HexA, since the regulator binds to the pcfA promoter region and thereby blocks expression of the target operon. In summary, our data show that HexA fulfills the task as repressor of 1° specific features in 2° cells in a versatile way and gives first insights into the complexity of regulating phenotypic heterogeneity in Photorhabdus bacteria.
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Affiliation(s)
- Angela Langer
- Bereich Mikrobiologie, Biozentrum Martinsried, Ludwig-Maximilians-Universität München, München, Germany
| | - Adriana Moldovan
- Bereich Mikrobiologie, Biozentrum Martinsried, Ludwig-Maximilians-Universität München, München, Germany
| | - Christian Harmath
- Bereich Mikrobiologie, Biozentrum Martinsried, Ludwig-Maximilians-Universität München, München, Germany
| | - Susan A. Joyce
- School of Microbiology and Microbiome Institute, University College Cork, Cork, Ireland
| | - David J. Clarke
- School of Microbiology and Microbiome Institute, University College Cork, Cork, Ireland
| | - Ralf Heermann
- Bereich Mikrobiologie, Biozentrum Martinsried, Ludwig-Maximilians-Universität München, München, Germany
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20
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Wesche F, He Y, Bode HB. Solid-phase enrichment and analysis of electrophilic natural products. Beilstein J Org Chem 2017; 13:405-409. [PMID: 28382178 PMCID: PMC5355884 DOI: 10.3762/bjoc.13.43] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/25/2022] Open
Abstract
In search for new natural products, which may lead to the development of new drugs for all kind of applications, novel methods are needed. Here we describe the identification of electrophilic natural products in crude extracts via their reactivity against azide as a nucleophile followed by their subsequent enrichment using a cleavable azide-reactive resin (CARR). Using this approach, natural products carrying epoxides and α,β-unsaturated enones as well as several unknown compounds were identified in crude extracts from entomopathogenic Photorhabdus bacteria.
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Affiliation(s)
- Frank Wesche
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Yue He
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany
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21
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Park HB, Perez CE, Barber KW, Rinehart J, Crawford JM. Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster. eLife 2017; 6. [PMID: 28431213 PMCID: PMC5384830 DOI: 10.7554/elife.25229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/28/2017] [Indexed: 01/03/2023] Open
Abstract
Nonribosomal peptides represent a large class of metabolites with pharmaceutical relevance. Pteridines, such as pterins, folates, and flavins, are heterocyclic metabolites that often serve as redox-active cofactors. The biosynthetic machineries for construction of these distinct classes of small molecules operate independently in the cell. Here, we discovered an unprecedented nonribosomal peptide synthetase-like-pteridine synthase hybrid biosynthetic gene cluster in Photorhabdus luminescens using genome synteny analysis. P. luminescens is a Gammaproteobacterium that undergoes phenotypic variation and can have both pathogenic and mutualistic roles. Through extensive gene deletion, pathway-targeted molecular networking, quantitative proteomic analysis, and NMR, we show that the genetic locus affects the regulation of quorum sensing and secondary metabolic enzymes and encodes new pteridine metabolites functionalized with cis-amide acyl-side chains, termed pepteridine A (1) and B (2). The pepteridines are produced in the pathogenic phenotypic variant and represent the first reported metabolites to be synthesized by a hybrid NRPS-pteridine pathway. These studies expand our view of the combinatorial biosynthetic potential available in bacteria.
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Affiliation(s)
- Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, United States.,Chemical Biology Institute, Yale University, West Haven, United States
| | - Corey E Perez
- Department of Chemistry, Yale University, New Haven, United States.,Chemical Biology Institute, Yale University, West Haven, United States
| | - Karl W Barber
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, United States.,Systems Biology Institute, Yale University, West Haven, United States
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, United States.,Systems Biology Institute, Yale University, West Haven, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, United States.,Chemical Biology Institute, Yale University, West Haven, United States.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, United States
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22
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Park HB, Sampathkumar P, Perez CE, Lee JH, Tran J, Bonanno JB, Hallem EA, Almo SC, Crawford JM. Stilbene epoxidation and detoxification in a Photorhabdus luminescens-nematode symbiosis. J Biol Chem 2017; 292:6680-6694. [PMID: 28246174 DOI: 10.1074/jbc.m116.762542] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/16/2017] [Indexed: 11/06/2022] Open
Abstract
Members of the gammaproteobacterial Photorhabdus genus share mutualistic relationships with Heterorhabditis nematodes, and the pairs infect a wide swath of insect larvae. Photorhabdus species produce a family of stilbenes, with two major components being 3,5-dihydroxy-4-isopropyl-trans-stilbene (compound 1) and its stilbene epoxide (compound 2). This family of molecules harbors antimicrobial and immunosuppressive activities, and its pathway is responsible for producing a nematode "food signal" involved in nematode development. However, stilbene epoxidation biosynthesis and its biological roles remain unknown. Here, we identified an orphan protein (Plu2236) from Photorhabdus luminescens that catalyzes stilbene epoxidation. Structural, mutational, and biochemical analyses confirmed the enzyme adopts a fold common to FAD-dependent monooxygenases, contains a tightly bound FAD prosthetic group, and is required for the stereoselective epoxidation of compounds 1 and 2. The epoxidase gene was dispensable in a nematode-infective juvenile recovery assay, indicating the oxidized compound is not required for the food signal. The epoxide exhibited reduced cytotoxicity toward its producer, suggesting this may be a natural route for intracellular detoxification. In an insect infection model, we also observed two stilbene-derived metabolites that were dependent on the epoxidase. NMR, computational, and chemical degradation studies established their structures as new stilbene-l-proline conjugates, prolbenes A (compound 3) and B (compound 4). The prolbenes lacked immunosuppressive and antimicrobial activities compared with their stilbene substrates, suggesting a metabolite attenuation mechanism in the animal model. Collectively, our studies provide a structural view for stereoselective stilbene epoxidation and functionalization in an invertebrate animal infection model and provide new insights into stilbene cellular detoxification.
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Affiliation(s)
- Hyun Bong Park
- From the Department of Chemistry, Yale University, New Haven, Connecticut 06520.,the Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | | | - Corey E Perez
- From the Department of Chemistry, Yale University, New Haven, Connecticut 06520.,the Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Joon Ha Lee
- the Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, California 90095, and
| | - Jeannie Tran
- the Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Jeffrey B Bonanno
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Elissa A Hallem
- the Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, California 90095, and
| | - Steven C Almo
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jason M Crawford
- From the Department of Chemistry, Yale University, New Haven, Connecticut 06520, .,the Chemical Biology Institute, Yale University, West Haven, Connecticut 06516.,the Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06510
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23
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Engel Y, Windhorst C, Lu X, Goodrich-Blair H, Bode HB. The Global Regulators Lrp, LeuO, and HexA Control Secondary Metabolism in Entomopathogenic Bacteria. Front Microbiol 2017; 8:209. [PMID: 28261170 PMCID: PMC5313471 DOI: 10.3389/fmicb.2017.00209] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/30/2017] [Indexed: 11/13/2022] Open
Abstract
Photorhabdus luminescens TTO1 and Xenorhabdus nematophila HGB081 are insect pathogenic bacteria and producers of various structurally diverse bioactive natural products. In these entomopathogenic bacteria we investigated the role of the global regulators Lrp, LeuO, and HexA in the production of natural products. Lrp is a general activator of natural product biosynthesis in X. nematophila and for most compounds in TTO1. Microarray analysis confirmed these results in X. nematophila and enabled the identification of additional biosynthesis gene clusters (BGC) regulated by Lrp. Moreover, when promoters of two X. nematophila BGC were analyzed, transcriptional activation by Lrp was observed. In contrast, LeuO in X. nematophila and P. luminescens has both repressing and activating features, depending on the natural product examined. Furthermore, heterologous overexpression of leuO from X. nematophila in the closely related Xenorhabdus szentirmaii resulted in overproduction of several natural products including novel compounds. The presented findings could be of importance for establishing a tool for overproduction of secondary metabolites and subsequent identification of novel compounds.
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Affiliation(s)
- Yvonne Engel
- Merck-Stiftungsprofessur Molekulare Biotechnologie, Molekulare Biowissenschaften, Goethe Universität Frankfurt Frankfurt am Main, Germany
| | - Carina Windhorst
- Merck-Stiftungsprofessur Molekulare Biotechnologie, Molekulare Biowissenschaften, Goethe Universität Frankfurt Frankfurt am Main, Germany
| | - Xiaojun Lu
- Department of Bacteriology, University of Wisconsin-Madison, Madison WI, USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, MadisonWI, USA; Department of Microbiology, University of Tennessee, Knoxville, KnoxvilleTN, USA
| | - Helge B Bode
- Merck-Stiftungsprofessur Molekulare Biotechnologie, Molekulare Biowissenschaften, Goethe Universität FrankfurtFrankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität FrankfurtFrankfurt am Main, Germany
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24
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Valverde C. Who's the boss here? The post‐transcriptional global regulator
H
fq takes over control of secondary metabolite production in the nematode symbiont
P
hotorhabdus luminiscens. Environ Microbiol 2017; 19:21-24. [DOI: 10.1111/1462-2920.13635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Claudio Valverde
- Departamento de Ciencia y Tecnología, LBMIBSUniversidad Nacional de Quilmes – CONICETBernalB1876BXD Argentina
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25
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Heinrich AK, Glaeser A, Tobias NJ, Heermann R, Bode HB. Heterogeneous regulation of bacterial natural product biosynthesis via a novel transcription factor. Heliyon 2016; 2:e00197. [PMID: 27957552 PMCID: PMC5133734 DOI: 10.1016/j.heliyon.2016.e00197] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/19/2016] [Accepted: 11/11/2016] [Indexed: 11/25/2022] Open
Abstract
Biological diversity arises among genetically equal subpopulations in the same environment, a phenomenon called phenotypic heterogeneity. The life cycle of the enteric bacterium Photorhabdus luminescens involves a symbiotic interaction with nematodes as well as a pathogenic association with insect larvae. P. luminescens exists in two distinct phenotypic forms designated as primary (1°) and secondary (2°). In contrast to 1° cells, 2° cells are non-pigmented due to the absence of natural compounds, especially anthraquinones (AQs). We identified a novel type of transcriptional regulator, AntJ, which activates expression of the antA-I operon responsible for AQ production. AntJ heterogeneously activates the AQ production in single P. luminescens 1° cells, and blocks AQ production in 2° cells. AntJ contains a proposed ligand-binding WYL-domain, which is widespread among bacteria. AntJ is one of the rare examples of regulators that mediate heterogeneous gene expression by altering activity rather than copy number in single cells.
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Affiliation(s)
- Antje K Heinrich
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Angela Glaeser
- Bereich Mikrobiologie, Biozentrum Martinsried, Ludwig-Maximilians-Universität München, München, Germany
| | - Nicholas J Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Ralf Heermann
- Bereich Mikrobiologie, Biozentrum Martinsried, Ludwig-Maximilians-Universität München, München, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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26
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Orozco RA, Molnár I, Bode H, Stock SP. Bioprospecting for secondary metabolites in the entomopathogenic bacterium Photorhabdus luminescens subsp. sonorensis. J Invertebr Pathol 2016; 141:45-52. [PMID: 27702563 DOI: 10.1016/j.jip.2016.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 10/20/2022]
Abstract
Crude extracts of in vitro and in vivo cultures of two strains of Photorhabdus l. sonorensis (Enterobacteriaceae) were analyzed by TLC, HPLC-UV and LC-MS. Nine unique compounds with mass/charge ratios (m/z) ranging from 331.3 to 713.5 were found in MS analyses. Bioactivity of extracts was assessed on a selection of plant pathogens/pests and non-target species. Caborca strain extracts showed the highest activity against Helicoverpa zea (Lepidoptera: Noctuidae) neonates at all concentrations tested. Mortality ranged from 11% (at 10μg/ml) to 37% (at 40μg/ml). Strain CH35 extracts showed the highest nematicidal activity on Meloidogyne incognita (Tylenchida: Meloidogynidae) at 40μg/ml. Low to no nematicidal activity was observed against the non-target species Steinernema carpocapsae (Rhabditida: Steinernematidae) and Caenorhabditis elegans (Rhabditida: Rhabditidae). Caborca extracts exhibited a strong antibiotic effect on Pseudomonas syringae (Pseudomonadales: Pseudomonadacedae) at 40μg/ml, while both Caborca and CH35 extracts inhibited the growth of Bacillus subitillis (Bacillales: Bacillaceae) at 40μg/ml. All extracts strongly inhibited the growth of the fungus Fusarium oxysporum (Hypocreales: Nectriceae) but not that of Alternaria alternata (Pleosporales: Pleosporaceae). Contrastingly, a moderate to high inhibitory effect was denoted on the non-target biocontrol fungus Beauveria bassiana (Hypocreales: Clavivipitaceae).
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Affiliation(s)
- Rousel A Orozco
- Department of Entomology, University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721-0036, United States
| | - István Molnár
- Natural Products Center, University of Arizona, 250 E. Valencia Road, Tucson, AZ 85706, United States
| | - Helge Bode
- Institut für Molekulare Biowissenschaften, Goethe Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - S Patricia Stock
- Department of Entomology, University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721-0036, United States.
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27
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Tobias NJ, Heinrich AK, Eresmann H, Wright PR, Neubacher N, Backofen R, Bode HB. Photorhabdus‐nematode symbiosis is dependent onhfq‐mediated regulation of secondary metabolites. Environ Microbiol 2016; 19:119-129. [DOI: 10.1111/1462-2920.13502] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas J. Tobias
- Fachbereich BiowissenschaftenMerck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität FrankfurtFrankfurt am Main Germany
| | - Antje K. Heinrich
- Fachbereich BiowissenschaftenMerck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität FrankfurtFrankfurt am Main Germany
| | - Helena Eresmann
- Fachbereich BiowissenschaftenMerck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität FrankfurtFrankfurt am Main Germany
| | - Patrick R. Wright
- Department of Computer ScienceBioinformatics Group, Albert Ludwigs University FreiburgFreiburg Germany
| | - Nick Neubacher
- Fachbereich BiowissenschaftenMerck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität FrankfurtFrankfurt am Main Germany
| | - Rolf Backofen
- Department of Computer ScienceBioinformatics Group, Albert Ludwigs University FreiburgFreiburg Germany
- BIOSS Centre for Biological Signaling Studies, University of FreiburgFreiburg Germany
| | - Helge B. Bode
- Fachbereich BiowissenschaftenMerck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität FrankfurtFrankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität FrankfurtFrankfurt am Main Germany
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Joyce SA, Lango L, Clarke DJ. The Regulation of Secondary Metabolism and Mutualism in the Insect Pathogenic Bacterium Photorhabdus luminescens. ADVANCES IN APPLIED MICROBIOLOGY 2016; 76:1-25. [PMID: 21924970 DOI: 10.1016/b978-0-12-387048-3.00001-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Photorhabdus is a genus of insect-pathogenic Gram-negative bacteria that also maintain a mutualistic interaction with nematodes from the family Heterorhabditis. This complex life cycle, involving different interactions with different invertebrate hosts, coupled with the amenability of the system to laboratory culture has resulted in the development of Photorhabdus as a model system for studying bacterial-host interactions. Photorhabdus is predicted to have an extensive secondary metabolism with the genetic potential to produce >20 different small secondary metabolites. Therefore, this system also presents us with a unique opportunity to study the contribution of secondary metabolism to the environmental fitness of the producing organism in its natural habitat (i.e., the insect and/or the nematode). In vivo and in vitro studies have revealed that the vast majority of the genetic loci in Photorhabdus predicted to be involved in the production of secondary metabolites appear to be cryptic and, to date, although several have been characterized, only three compounds have been studied in any great detail: 3,5-dihydroxy-4-isopropylstilbene, the β-lactam antibiotic carbapenem, and an anthraquinone pigment. In this chapter, we describe how these compounds are made and the role (if any) that they have during the interactions between Photorhabdus and its invertebrate hosts. We will also outline recent work on the regulation of secondary metabolism in Photorhabdus and comment on how this has led to an increased understanding of mutualism in this bacterium.
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Affiliation(s)
- Susan A Joyce
- Department of Microbiology, University College Cork, Cork, Ireland
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Abstract
Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics.
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Affiliation(s)
- Victoria L Challinor
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt am Main, Germany
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Bager R, Roghanian M, Gerdes K, Clarke DJ. Alarmone (p)ppGpp regulates the transition from pathogenicity to mutualism in Photorhabdus luminescens. Mol Microbiol 2016; 100:735-47. [PMID: 26845750 DOI: 10.1111/mmi.13345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2016] [Indexed: 01/21/2023]
Abstract
The enteric gamma-proteobacterium Photorhabdus luminescens kills a wide range of insects, whilst also maintaining a mutualistic relationship with soil nematodes from the family Heterorhabditis. Pathogenicity is associated with bacterial exponential growth, whilst mutualism is associated with post-exponential (stationary) phase. During post-exponential growth, P. luminescens also elaborates an extensive secondary metabolism, including production of bioluminescence, antibiotics and pigment. However, the regulatory network that controls the expression of this secondary metabolism is not well understood. The stringent response is a well-described global regulatory system in bacteria and mediated by the alarmone (p)ppGpp. In this study, we disrupted the genes relA and spoT, encoding the two predicted (p)ppGpp synthases of P. luminescens TTO1, and we showed that (p)ppGpp is required for secondary metabolism. Moreover, we found the (p)ppGpp is not required for pathogenicity of P. luminescens, but is required for bacterial survival within the insect cadaver. Finally, we showed that (p)ppGpp is required for P. luminescens to support normal nematode growth and development. Therefore, the regulatory network that controls the transition from pathogenicity to mutualism in P. luminescens requires (p)ppGpp. This is the first report outlining a role for (p)ppGpp in controlling the outcome of an interaction between a bacteria and its host.
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Affiliation(s)
- Ragnhild Bager
- Department of Biology, University of Copenhagen, DK-2200, Copenhagen, Denmark.,School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Mohammad Roghanian
- Department of Biology, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - David J Clarke
- School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland
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Bozhüyük KAJ, Zhou Q, Engel Y, Heinrich A, Pérez A, Bode HB. Natural Products from Photorhabdus and Other Entomopathogenic Bacteria. Curr Top Microbiol Immunol 2016; 402:55-79. [PMID: 28091935 DOI: 10.1007/82_2016_24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although the first natural products (NP) from Photorhabdus and Xenorhabdus bacteria have been known now for almost 30 years, a huge variety of new compounds have been identified in the last 5-10 years, mainly due to the application of modern mass spectrometry. Additionally, application of molecular methods that allow the activation of NP production in several different strains as well as efficient heterologous expression methods have led to the production and validation of many new compounds. In this chapter we discuss the benefit of using Photorhabdus as a model system for microbial chemical ecology. We also examine non-ribosomal peptide synthetases as the most important pathway for NP production. Finally, we discuss the origin and function of all currently known NPs and the development of the molecular and chemical tools used to identify these NPs faster.
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Affiliation(s)
- Kenan A J Bozhüyük
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Qiuqin Zhou
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Yvonne Engel
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Antje Heinrich
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Alexander Pérez
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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Reen FJ, Romano S, Dobson ADW, O'Gara F. The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms. Mar Drugs 2015; 13:4754-83. [PMID: 26264003 PMCID: PMC4557003 DOI: 10.3390/md13084754] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 06/05/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022] Open
Abstract
Unlocking the rich harvest of marine microbial ecosystems has the potential to both safeguard the existence of our species for the future, while also presenting significant lifestyle benefits for commercial gain. However, while significant advances have been made in the field of marine biodiscovery, leading to the introduction of new classes of therapeutics for clinical medicine, cosmetics and industrial products, much of what this natural ecosystem has to offer is locked in, and essentially hidden from our screening methods. Releasing this silent potential represents a significant technological challenge, the key to which is a comprehensive understanding of what controls these systems. Heterologous expression systems have been successful in awakening a number of these cryptic marine biosynthetic gene clusters (BGCs). However, this approach is limited by the typically large size of the encoding sequences. More recently, focus has shifted to the regulatory proteins associated with each BGC, many of which are signal responsive raising the possibility of exogenous activation. Abundant among these are the LysR-type family of transcriptional regulators, which are known to control production of microbial aromatic systems. Although the environmental signals that activate these regulatory systems remain unknown, it offers the exciting possibility of evoking mimic molecules and synthetic expression systems to drive production of potentially novel natural products in microorganisms. Success in this field has the potential to provide a quantum leap forward in medical and industrial bio-product development. To achieve these new endpoints, it is clear that the integrated efforts of bioinformaticians and natural product chemists will be required as we strive to uncover new and potentially unique structures from silent or cryptic marine gene clusters.
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Affiliation(s)
- F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Stefano Romano
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
- School of Biomedical Sciences, Curtin University, Perth WA 6845, Australia.
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Abstract
This Viewpoint article provides a brief and selective summary of research on the chemical ecology underlying symbioses between bacteria and animals. Animals engage in multiple highly specialized interactions with bacteria that reflect their long coevolutionary history. The article focuses on a few illustrative but hardly exhaustive examples in which bacterially produced small molecules initiate a developmental step with important implications for the evolution of animals, provide signals for the maturation of mammalian immune systems, and furnish chemical defenses against microbial pathogens.
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Affiliation(s)
- Alexandra M Cantley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Park HB, Crawford JM. Lumiquinone A, an α-Aminomalonate-Derived Aminobenzoquinone from Photorhabdus luminescens. JOURNAL OF NATURAL PRODUCTS 2015; 78:1437-41. [PMID: 25988621 PMCID: PMC5055755 DOI: 10.1021/np500974f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Lumiquinone A (1), an unusual aminobenzoquinone member within the phenylpropanoid class of natural products, together with the known compound 3,5-dihydroxy-4-isopropyl-trans-stilbene (2), was isolated from the entomopathogenic bacterium Photorhabdus luminescens TT01. On the basis of the analysis of extensive 2D NMR and high-resolution ESI-QTOF-MS spectral data, the structure of 1 was determined to be a 2-amino-5-hydroxy-1,4-benzoquinone substituted with (E)-2-phenylvinyl and isopropyl functional groups. Free α-aminomalonate medium supplementation significantly enhanced production of 1 relative to 2 in a dose-dependent manner, suggesting that promiscuous polyketide synthase processing of malonate- versus α-aminomalonate-derived substrates represents a competitive route for polyketide structural diversification. Metabolites 1 and 2 were active against Bacillus subtilis and Saccharomyces cerevisiae.
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Affiliation(s)
- Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
- Corresponding Author: Tel: +1 203 737 3966. Fax: +1 203 432 8726.
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Schimming O, Fleischhacker F, Nollmann FI, Bode HB. Yeast Homologous Recombination Cloning Leading to the Novel Peptides Ambactin and Xenolindicin. Chembiochem 2014; 15:1290-4. [DOI: 10.1002/cbic.201402065] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 12/12/2022]
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Vizcaino MI, Guo X, Crawford JM. Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. J Ind Microbiol Biotechnol 2014; 41:285-99. [PMID: 24127069 PMCID: PMC3946945 DOI: 10.1007/s10295-013-1356-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/23/2013] [Indexed: 12/24/2022]
Abstract
The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights into the upregulation of orphan biosynthetic pathways and the enhancement of the enzyme substrate supply can be obtained, leading to the discovery of new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe certain functional natural products produced by Xenorhabdus and Photorhabdus bacteria with experimentally linked biosynthetic gene clusters as illustrative examples of the synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects and, in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with their animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function for these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open up new avenues for investigating and exploiting microbial chemical signaling in host-bacteria interactions.
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Affiliation(s)
- Maria I. Vizcaino
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Xun Guo
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06510, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
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38
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The genetic basis of the symbiosis between Photorhabdus and its invertebrate hosts. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:1-29. [PMID: 24767424 DOI: 10.1016/b978-0-12-800260-5.00001-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photorhabdus is a pathogen of insects that also maintains a mutualistic association with nematodes from the family Heterorhabditis. Photorhabdus colonizes the gut of the infective juvenile (IJ) stage of the nematode. The IJ infects an insect and regurgitates the bacteria and the bacteria reproduce to kill the insect. The nematodes feed on the resulting bacterial biomass until a new generation of IJs emerges from the insect cadaver. Therefore, during its life cycle, Photorhabdus must (1) kill the insect host, (2) support nematode growth and development, and (3) be able to colonize the new generation of IJs. In this review, functional genomic studies that have been aimed at understanding the molecular mechanisms underpinning each of these roles will be discussed. These studies have begun to reveal that distinct gene sets may be required for each of these interactions, suggesting that there is only a minimal genetic overlap between pathogenicity and mutualism in Photorhabdus.
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Lango-Scholey L, Brachmann AO, Bode HB, Clarke DJ. The expression of stlA in Photorhabdus luminescens is controlled by nutrient limitation. PLoS One 2013; 8:e82152. [PMID: 24278476 PMCID: PMC3838401 DOI: 10.1371/journal.pone.0082152] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/24/2013] [Indexed: 11/22/2022] Open
Abstract
Photorhabdus is a genus of Gram-negative entomopathogenic bacteria that also maintain a mutualistic association with nematodes from the family Heterorhabditis. Photorhabdus has an extensive secondary metabolism that is required for the interaction between the bacteria and the nematode. A major component of this secondary metabolism is a stilbene molecule, called ST. The first step in ST biosynthesis is the non-oxidative deamination of phenylalanine resulting in the production of cinnamic acid. This reaction is catalyzed by phenylalanine-ammonium lyase, an enzyme encoded by the stlA gene. In this study we show, using a stlA-gfp transcriptional fusion, that the expression of stlA is regulated by nutrient limitation through a regulatory network that involves at least 3 regulators. We show that TyrR, a LysR-type transcriptional regulator that regulates gene expression in response to aromatic amino acids in E. coli, is absolutely required for stlA expression. We also show that stlA expression is modulated by σS and Lrp, regulators that are implicated in the regulation of the response to nutrient limitation in other bacteria. This work is the first that describes pathway-specific regulation of secondary metabolism in Photorhabdus and, therefore, our study provides an initial insight into the complex regulatory network that controls secondary metabolism, and therefore mutualism, in this model organism.
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Affiliation(s)
| | - Alexander O. Brachmann
- Molecular Biotechnology, Institute for Molecular Biosciences, Goethe University, Frankfurt, Frankfurt, Germany
| | - Helge B. Bode
- Molecular Biotechnology, Institute for Molecular Biosciences, Goethe University, Frankfurt, Frankfurt, Germany
| | - David J. Clarke
- Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail:
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Brachmann AO, Bode HB. Identification and bioanalysis of natural products from insect symbionts and pathogens. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 135:123-55. [PMID: 23657492 DOI: 10.1007/10_2013_192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
: With the development of several novel methods in genome sequencing, molecular biology, and analytical chemistry a new area of natural product chemistry is currently starting that allows the analysis of minute amounts of complex biological samples. The combination of these methods, as discussed in this review, also enables the analysis of bacteria living in symbiosis or being pathogenic to insects, which might be the largest reservoir for novel microbes associated with higher organisms due to the huge number of insect species.
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Affiliation(s)
- Alexander O Brachmann
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438, Frankfurt am Main, Germany
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41
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Statistical optimization of process variables for antibiotic activity of Xenorhabdus bovienii. PLoS One 2012; 7:e38421. [PMID: 22701637 PMCID: PMC3368850 DOI: 10.1371/journal.pone.0038421] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 05/09/2012] [Indexed: 11/19/2022] Open
Abstract
The production of secondary metabolites with antibiotic properties is a common characteristic to entomopathogenic bacteria Xenorhabdus spp. These metabolites not only have diverse chemical structures but also have a wide range of bioactivities of medicinal and agricultural interests. Culture variables are critical to the production of secondary metabolites of microorganisms. Manipulating culture process variables can promote secondary metabolite biosynthesis and thus facilitate the discovery of novel natural products. This work was conducted to evaluate the effects of five process variables (initial pH, medium volume, rotary speed, temperature, and inoculation volume) on the antibiotic production of Xenorhabdus bovienii YL002 using response surface methodology. A 25–1 factorial central composite design was chosen to determine the combined effects of the five variables, and to design a minimum number of experiments. The experimental and predicted antibiotic activity of X. bovienii YL002 was in close agreement. Statistical analysis of the results showed that initial pH, medium volume, rotary speed and temperature had a significant effect (P<0.05) on the antibiotic production of X. bovienii YL002 at their individual level; medium volume and rotary speed showed a significant effect at a combined level and was most significant at an individual level. The maximum antibiotic activity (287.5 U/mL) was achieved at the initial pH of 8.24, medium volume of 54 mL in 250 mL flask, rotary speed of 208 rpm, temperature of 32.0°C and inoculation volume of 13.8%. After optimization, the antibiotic activity was improved by 23.02% as compared with that of unoptimized conditions.
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Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. PLoS One 2012; 7:e33727. [PMID: 22470465 PMCID: PMC3312335 DOI: 10.1371/journal.pone.0033727] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/16/2012] [Indexed: 12/24/2022] Open
Abstract
Adaptation is normally viewed as the enemy of the antibiotic discovery and development process because adaptation among pathogens to antibiotic exposure leads to resistance. We present a method here that, in contrast, exploits the power of adaptation among antibiotic producers to accelerate the discovery of antibiotics. A competition-based adaptive laboratory evolution scheme is presented whereby an antibiotic-producing microorganism is competed against a target pathogen and serially passed over time until the producer evolves the ability to synthesize a chemical entity that inhibits growth of the pathogen. When multiple Streptomyces clavuligerus replicates were adaptively evolved against methicillin-resistant Staphylococcus aureus N315 in this manner, a strain emerged that acquired the ability to constitutively produce holomycin. In contrast, no holomycin could be detected from the unevolved wild-type strain. Moreover, genome re-sequencing revealed that the evolved strain had lost pSCL4, a large 1.8 Mbp plasmid, and acquired several single nucleotide polymorphisms in genes that have been shown to affect secondary metabolite biosynthesis. These results demonstrate that competition-based adaptive laboratory evolution can constitute a platform to create mutants that overproduce known antibiotics and possibly to discover new compounds as well.
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43
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Crawford JM, Mahlstedt SA, Malcolmson SJ, Clardy J, Walsh CT. Dihydrophenylalanine: a prephenate-derived Photorhabdus luminescens antibiotic and intermediate in dihydrostilbene biosynthesis. ACTA ACUST UNITED AC 2012; 18:1102-12. [PMID: 21944749 DOI: 10.1016/j.chembiol.2011.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/21/2011] [Accepted: 07/12/2011] [Indexed: 11/28/2022]
Abstract
2,5-Dihydrophenylalanine (H(2)Phe) is a multipotent nonproteinogenic amino acid produced by various Actinobacteria and Gammaproteobacteria. Although the metabolite was discovered over 40 years ago, details of its biosynthesis have remained largely unknown. We show here that L-H(2)Phe is a secreted metabolite in Photorhabdus luminescens cultures and a precursor of a recently described 2,5-dihydrostilbene. Bioinformatic analysis suggested a candidate gene cluster for the processing of prephenate to H(2)Phe, and gene knockouts validated that three adjacent genes plu3042-3044 were required for H(2)Phe production. Biochemical experiments validated Plu3043 as a nonaromatizing prephenate decarboxylase generating an endocyclic dihydro-hydroxyphenylpyruvate. Plu3042 acted next to transaminate the Plu3043 product, precluding spontaneous exocyclic double-bond isomerization and yielding 2,5-dihydrotyrosine. The enzymatic products most plausibly on path to H(2)Phe illustrate the versatile metabolic rerouting of prephenate from aromatic amino acid synthesis to antibiotic synthesis.
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Affiliation(s)
- Jason M Crawford
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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44
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Schmitt EK, Moore CM, Krastel P, Petersen F. Natural products as catalysts for innovation: a pharmaceutical industry perspective. Curr Opin Chem Biol 2011; 15:497-504. [DOI: 10.1016/j.cbpa.2011.05.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 05/11/2011] [Accepted: 05/23/2011] [Indexed: 12/21/2022]
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Abstract
The study of bacterial symbionts of eukaryotic hosts has become a powerful discovery engine for chemistry. This highlight looks at four case studies that exemplify the range of chemistry and biology involved in these symbioses: a bacterial symbiont of a fungus and a marine invertebrate that produce compounds with significant anticancer activity, and bacterial symbionts of insects and nematodes that produce compounds that regulate multilateral symbioses.
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Affiliation(s)
- Jason M Crawford
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Manipulation of pH shift to enhance the growth and antibiotic activity of Xenorhabdus nematophila. J Biomed Biotechnol 2011; 2011:672369. [PMID: 21660139 PMCID: PMC3110314 DOI: 10.1155/2011/672369] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 03/19/2011] [Indexed: 12/03/2022] Open
Abstract
To evaluate the effects of pH control strategy on cell growth and the production of antibiotic (cyclo(2-Me-BABA-Gly)) by Xenorhabdus nematophila and enhance the antibiotic activity. The effects of uncontrolled- (different initial pH) and controlled-pH (different constant pH and pH-shift) operations on cell growth and antibiotic activity of X. nematophila YL00I were examined. Experiments showed that the optimal initial pH for cell growth and antibiotic production of X. nematophila YL001 occurred at 7.0. Under different constant pH, a pH level of 7.5 was found to be optimal for biomass and antibiotic activity at 23.71 g/L and 100.0 U/mL, respectively. Based on the kinetic information relating to the different constant pH effects on the fermentation of X. nematophila YL001, a two-stage pH control strategy in which pH 6.5 was maintained for the first 24 h, and then switched to 7.5 after 24 h, was established to improve biomass production and antibiotic activity. By applying this pH-shift strategy, the maximal antibiotic activity and productivity were significantly improved and reaching 185.0 U/mL and 4.41 U/mL/h, respectively, compared to values obtained from constant pH operation (100.0 U/mL and 1.39 U/mL/h).
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47
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Danchin A. A path from predation to mutualism. Mol Microbiol 2010; 77:1346-50. [PMID: 20860087 DOI: 10.1111/j.1365-2958.2010.07341.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Luminescent bacteria and nematodes associate in a strategy where the bacteria act as virulent pathogens of insects, used as their food supply, while the nematodes graze on them. Upon reaching high density, the bacteria produce light and metabolites that turn the nematodes into hosts permitting them to be carried over to further nematode preys. In this issue of Molecular Microbiology, Lango and Clarke show that the corresponding shift in lifestyle is triggered by a metabolic switch closely linked to the tricarboxylic acid cycle, but apparently not by the well-known acetate switch that monitors entry of bacteria into the stationary phase of growth.
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Affiliation(s)
- Antoine Danchin
- AMAbiotics SAS, Genavenir 8, 5 rue Henri Desbruères, 91030 Evry Cedex, France.
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Mahlstedt S, Fielding EN, Moore BS, Walsh CT. Prephenate decarboxylases: a new prephenate-utilizing enzyme family that performs nonaromatizing decarboxylation en route to diverse secondary metabolites. Biochemistry 2010; 49:9021-3. [PMID: 20863139 DOI: 10.1021/bi101457h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Prephenate is the direct precursor of phenylpyruvate and 4-hydroxyphenylpyruvate in the biogenesis of phenylalanine and tyrosine by action of the decarboxylative, aromatizing enzymes prephenate dehydratase and dehydrogenase, respectively. The recent characterization of BacA in bacilysin biosynthesis as a nonaromatizing decarboxylase reveals a new route from prephenate in the biosynthesis of nonproteinogenic amino acids. This study describes two additional enzymes, AerD from Planktothrix agardhii and SalX from Salinispora tropica, that utilize the central building block prephenate for flux down distinct pathways to amino acid products, representing a new metabolic fate for prephenate and establishing a new family of nonaromatizing prephenate decarboxylases.
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Affiliation(s)
- Sarah Mahlstedt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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