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Polyakov NE, Focsan AL, Gao Y, Kispert LD. The Endless World of Carotenoids-Structural, Chemical and Biological Aspects of Some Rare Carotenoids. Int J Mol Sci 2023; 24:9885. [PMID: 37373031 DOI: 10.3390/ijms24129885] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Carotenoids are a large and diverse group of compounds that have been shown to have a wide range of potential health benefits. While some carotenoids have been extensively studied, many others have not received as much attention. Studying the physicochemical properties of carotenoids using electron paramagnetic resonance (EPR) and density functional theory (DFT) helped us understand their chemical structure and how they interact with other molecules in different environments. Ultimately, this can provide insights into their potential biological activity and how they might be used to promote health. In particular, some rare carotenoids, such as sioxanthin, siphonaxanthin and crocin, that are described here contain more functional groups than the conventional carotenoids, or have similar groups but with some situated outside of the rings, such as sapronaxanthin, myxol, deinoxanthin and sarcinaxanthin. By careful design or self-assembly, these rare carotenoids can form multiple H-bonds and coordination bonds in host molecules. The stability, oxidation potentials and antioxidant activity of the carotenoids can be improved in host molecules, and the photo-oxidation efficiency of the carotenoids can also be controlled. The photostability of the carotenoids can be increased if the carotenoids are embedded in a nonpolar environment when no bonds are formed. In addition, the application of nanosized supramolecular systems for carotenoid delivery can improve the stability and biological activity of rare carotenoids.
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Affiliation(s)
- Nikolay E Polyakov
- Institute of Chemical Kinetics & Combustion, Institutskaya Str. 3, 630090 Novosibirsk, Russia
| | - A Ligia Focsan
- Department of Chemistry, Valdosta State University, Valdosta, GA 31698, USA
| | - Yunlong Gao
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lowell D Kispert
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
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2
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Ezeobiora CE, Igbokwe NH, Amin DH, Enwuru NV, Okpalanwa CF, Mendie UE. Uncovering the biodiversity and biosynthetic potentials of rare actinomycetes. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022. [DOI: 10.1186/s43094-022-00410-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
Antibiotic resistance is on the rise, and new antibiotic research has slowed in recent years, necessitating the discovery of possibly novel microbial resources capable of producing bioactive compounds. Microbial infections are gaining resistance to existing antibiotics, emphasizing the need for novel medicinal molecules to be discovered as soon as possible. Because the possibilities of isolating undiscovered actinomycetes strains have decreased, the quest for novel products has shifted to rare actinomycetes genera from regular environments or the identification of new species identified in unusual habitats.
Main body of the abstract
The non-streptomyces actinobacteria are known as rare actinomycetes that are extremely difficult to cultivate. Rare actinomycetes are known to produce a variety of secondary metabolites with varying medicinal value. In this review, we reported the diversity of rare actinomycetes in several habitat including soil, plants, aquatic environment, caves, insects and extreme environments. We also reported some isolation methods to easily recover rare Actinobacteria from various sources guided with some procedures to identify the rare Actinobacteria isolates. Finally, we reported the biosynthetic potential of rare actinomycetes and its role in the production of unique secondary metabolites that could be used in medicine, agriculture, and industry. These microbial resources will be of interest to humanity, as antibiotics, insecticides, anticancer, antioxidants, to mention but a few.
Short conclusion
Rare actinomycetes are increasingly being investigated for new medicinal compounds that could help to address existing human health challenges such as newly emerging infectious illnesses, antibiotic resistance, and metabolic disorders. The bioactive secondary metabolites from uncommon actinomycetes are the subject of this review, which focuses on their diversity in different habitats, isolation, identification and biosynthetic potentials.
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Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites. mBio 2021; 12:e0270021. [PMID: 34809466 PMCID: PMC8609351 DOI: 10.1128/mbio.02700-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography–high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames.
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Specialized Metabolite Mediated Predation Defense in the Marine Actinobacterium Salinispora. Appl Environ Microbiol 2021; 88:e0117621. [PMID: 34669450 DOI: 10.1128/aem.01176-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate marine actinobacterial genus Salinispora has become a model organism for natural product discovery, yet little is known about the ecological functions of the compounds produced by this taxon. The aims of this study were to assess the effects of live cultures and culture extracts from two Salinispora species on invertebrate predators. In choice-based feeding experiments using the bacterivorous nematode Caenorhabditis elegans, live cultures of both Salinispora species were less preferred than E. coli. When given a choice between the two species, C. elegans preferred S. areniolca over S. tropica. Culture extracts from S. tropica deterred C. elegans while those from S. arenicola did not, suggesting that compounds produced by S. tropica may account for the feeding deterrence. Bioactivity guided isolation linked compounds in the lomaiviticin series to the deterrent activity. Additional assays using the marine polychaete Ophryotrocha siberti and marine nematodes further support the deterrent activity of S. tropica against potential predators. These results provide evidence that Salinispora natural products may function as a defense against predation and that the strategies of predation defense differ between closely related species. Importance Bacteria inhabiting marine sediments are subject to predation by bacterivorous eukaryotes. Here we test the hypothesis that sediment-derived bacteria in the genus Salinispora produce biologically active natural products that function as a defense against predation. The results reveal that cultures and culture extracts of S. tropica deter feeding by Caenorhabditis elegans and negatively affect the habitat preference of a marine annelid (Ophryotrocha siberti). These activities were linked to the lomaiviticins, a series of cytotoxic compounds produced by S. tropica. Microbial natural products that function as a defense against predation represent a poorly understood trait that can influence community structure in marine sediments.
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5
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Worsley SF, Innocent TM, Holmes NA, Al-Bassam MM, Schiøtt M, Wilkinson B, Murrell JC, Boomsma JJ, Yu DW, Hutchings MI. Competition-based screening helps to secure the evolutionary stability of a defensive microbiome. BMC Biol 2021; 19:205. [PMID: 34526023 PMCID: PMC8444595 DOI: 10.1186/s12915-021-01142-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, which contributes to the control of Escovopsis fungus garden disease, is never compromised by the secondary acquisition of other bacterial strains. Game theory suggests that competition-based screening can allow the selective recruitment of antibiotic-producing bacteria from the environment, by providing abundant resources to foment interference competition between bacterial species and by using Pseudonocardia to bias the outcome of competition in favour of antibiotic producers. RESULTS Here, we use RNA-stable isotope probing (RNA-SIP) to confirm that Acromyrmex ants can maintain a range of microbial symbionts on their cuticle by supplying public resources. We then used RNA sequencing, bioassays, and competition experiments to show that vertically transmitted Pseudonocardia strains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately biassing the bacterial competition to allow the selective establishment of secondary antibiotic-producing strains while excluding non-antibiotic-producing strains that would parasitise the symbiosis. CONCLUSIONS Our findings are consistent with the hypothesis that competition-based screening is a plausible mechanism for maintaining the integrity of the co-adapted mutualism between the leaf-cutting ant farming symbiosis and its defensive microbiome. Our results have broader implications for explaining the stability of other complex symbioses involving horizontal acquisition.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Neil A Holmes
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Mahmoud M Al-Bassam
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Morten Schiøtt
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - J Colin Murrell
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Douglas W Yu
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Matthew I Hutchings
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK.
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Influence of Cultivation Conditions on the Sioxanthin Content and Antioxidative Protection Effect of a Crude Extract from the Vegetative Mycelium of Salinispora tropica. Mar Drugs 2021; 19:md19090509. [PMID: 34564171 PMCID: PMC8469146 DOI: 10.3390/md19090509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Due to their bioavailability, glycosylated carotenoids may have interesting biological effects. Sioxanthin, as a representative of this type of carotenoid, has been identified in marine actinomycetes of the genus Salinispora. This study evaluates, for the first time, the effect of cultivation temperature (T) and light intensity (LI) on the total cellular carotenoid content (TC), antioxidant activity (AA) and sioxanthin content (SX) of a crude extract (CE) from Salinispora tropica biomass in its vegetative state. Treatment-related differences in TC and SX values were statistically significantly and positively affected by T and LI, while AA was most significantly affected by T. In the S. tropica CE, TC correlated well (R2 = 0.823) with SX and somewhat less with AA (R2 = 0.777). A correlation between AA and SX was found to be less significant (R2 = 0.731). The most significant protective effect against oxidative stress was identified in the CE extracted from S. tropica biomass grown at the highest T and LI (CE-C), as was demonstrated using LNCaP and KYSE-30 human cell lines. The CE showed no cytotoxicity against LNCaP and KYSE-30 cell lines.
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7
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Chen X, Lim X, Bouin A, Lautier T, Zhang C. High-level de novo biosynthesis of glycosylated zeaxanthin and astaxanthin in Escherichia coli. BIORESOUR BIOPROCESS 2021; 8:67. [PMID: 38650269 PMCID: PMC10992962 DOI: 10.1186/s40643-021-00415-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/05/2021] [Indexed: 11/10/2022] Open
Abstract
Because of wide applications in food, feed, pharmaceutical and cosmetic industries, the carotenoid market is growing rapidly. Most carotenoids are hydrophobic, which limits their bioavailability. Glycosylation is a natural route that substantially increases the water solubility, as well as the bioavailability, photostability and biological activities of carotenoids. Here, we report metabolic engineering efforts (e.g., promoter and RBS engineering, optimization of carbon sources and supplementation of bottleneck genes) to produce glycosylated carotenoids in Escherichia coli. By fine-tuning the carotenoid-biosynthetic genes (crtX, crtZ and crtY), our strain produced up to 47.2 mg/L (~ 11,670 ppm) of zeaxanthin glucosides, ~ 78% of the total carotenoids produced. In another construct with mevalonate, astaxanthin pathway and crtX genes, the strain produced a mixture of carotenoid glucosides including astaxanthin and adonixanthin glucosides with a total yield of 8.1 mg/L (1774 ppm). Our work demonstrated a proof-of-concept study for the microbial biosynthesis of glycosylated carotenoids.
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Affiliation(s)
- Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Proteos level 4, Nanos, 138673, Singapore
| | - Xiaohui Lim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Proteos level 4, Nanos, 138673, Singapore
| | - Aurélie Bouin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Proteos level 4, Nanos, 138673, Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Thomas Lautier
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Proteos level 4, Nanos, 138673, Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Proteos level 4, Nanos, 138673, Singapore.
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8
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Jezkova Z, Binda E, Potocar T, Marinelli F, Halecky M, Branyik T. Laboratory scale cultivation of Salinispora tropica in shake flasks and mechanically stirred bioreactors. Biotechnol Lett 2021; 43:1715-1722. [PMID: 34003399 DOI: 10.1007/s10529-021-03121-1] [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: 11/04/2020] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE Marine actinomycetes from the genus Salinispora have an unexploited biotechnological potential. To accurately estimate their application potential however, data on their cultivation, including biomass growth kinetics, are needed but only incomplete information is currently available. RESULTS This work provides some insight into the effect of temperature, salinity, nitrogen source, glucose concentration and oxygen supply on growth rate, biomass productivity and yield of Salinispora tropica CBN-440T. The experiments were carried out in unbaffled shake flasks and agitated laboratory-scale bioreactors. The results show that the optimum growth temperature lies within the range 28-30 °C, salinity is close to sea water and the initial glucose concentration is around 10 g/L. Among tested nitrogen sources, yeast extract and soy peptone proved to be the most suitable. The change from unbaffled to baffled flasks increased the volumetric oxygen transfer coefficient (kLa) as did the use of agitated bioreactors. The highest specific growth rate (0.0986 h-1) and biomass productivity (1.11 g/L/day) were obtained at kLa = 28.3 h-1. A further increase in kLa was achieved by increasing stirrer speed, but this led to a deterioration in kinetic parameters. CONCLUSIONS Improvement of S. tropica biomass growth kinetics of was achieved mainly by identifying the most suitable nitrogen sources and optimizing kLa in baffled flasks and agitated bioreactors.
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Affiliation(s)
- Zuzana Jezkova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Via JH Dunant 3, 21100, Varèse, Italy
| | - Tomas Potocar
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Via JH Dunant 3, 21100, Varèse, Italy
| | - Martin Halecky
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Tomas Branyik
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic. .,Research Institute of Brewing and Malting, Lipova 15, 120 44, Prague, Czech Republic.
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9
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Hughes CC. Chemical labeling strategies for small molecule natural product detection and isolation. Nat Prod Rep 2021; 38:1684-1705. [PMID: 33629087 DOI: 10.1039/d0np00034e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: Up to 2020.It is widely accepted that small molecule natural products (NPs) evolved to carry out a particular ecological function and that these finely-tuned molecules can sometimes be appropriated for the treatment of disease in humans. Unfortunately, for the natural products chemist, NPs did not evolve to possess favorable physicochemical properties needed for HPLC-MS analysis. The process known as derivatization, whereby an NP in a complex mixture is decorated with a nonnatural moiety using a derivatizing agent (DA), arose from this sad state of affairs. Here, NPs are freed from the limitations of natural functionality and endowed, usually with some degree of chemoselectivity, with additional structural features that make HPLC-MS analysis more informative. DAs that selectively label amines, carboxylic acids, alcohols, phenols, thiols, ketones, and aldehydes, terminal alkynes, electrophiles, conjugated alkenes, and isocyanides have been developed and will be discussed here in detail. Although usually employed for targeted metabolomics, chemical labeling strategies have been effectively applied to uncharacterized NP extracts and may play an increasing role in the detection and isolation of certain classes of NPs in the future.
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Affiliation(s)
- Chambers C Hughes
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany 72076.
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10
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Sandmann G. Carotenoid Biosynthesis in the Phylum Actinobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1261:175-181. [PMID: 33783739 DOI: 10.1007/978-981-15-7360-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Actinobacteria is the phylum that has the biggest genome in the Bacteria domain and includes many colored species. Their pigment analysis revealed that structurally diverse carotenoids are responsible for their pigmentation. This chapter reviews the biosynthesis of the diverse carotenoids of Actinobacteria. Its carotenoids belong to three different types: 1) carotenoid of C50 chain length, 2) carotenoids with aromatic end groups, and 3) keto carotenoid like canthaxanthin (β,β-carotene-4,4'-dione) or monocyclic keto-γ-carotene derivatives. Species from the genus Rhodococcus are the only known Actinobacteria with a simultaneous pathway to aromatic and to keto carotenoids.
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Affiliation(s)
- Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, Goethe Universität, Frankfurt, Germany.
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11
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Chhun A, Sousoni D, Aguiló‐Ferretjans MDM, Song L, Corre C, Christie‐Oleza JA. Phytoplankton trigger the production of cryptic metabolites in the marine actinobacterium Salinispora tropica. Microb Biotechnol 2021; 14:291-306. [PMID: 33280260 PMCID: PMC7888443 DOI: 10.1111/1751-7915.13722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022] Open
Abstract
Filamentous members of the phylum Actinobacteria are a remarkable source of natural products with pharmaceutical potential. The discovery of novel molecules from these organisms is, however, hindered because most of the biosynthetic gene clusters (BGCs) encoding these secondary metabolites are cryptic or silent and are referred to as orphan BGCs. While co-culture has proven to be a promising approach to unlock the biosynthetic potential of many microorganisms by activating the expression of these orphan BGCs, it still remains an underexplored technique. The marine actinobacterium Salinispora tropica, for instance, produces valuable compounds such as the anti-cancer molecule salinosporamide but half of its putative BGCs are still orphan. Although previous studies have used marine heterotrophs to induce orphan BGCs in Salinispora, its co-culture with marine phototrophs has yet to be investigated. Following the observation of an antimicrobial activity against a range of phytoplankton by S. tropica, we here report that the photosynthate released by photosynthetic primary producers influences its biosynthetic capacities with production of cryptic molecules and the activation of orphan BGCs. Our work, using an approach combining metabolomics and proteomics, pioneers the use of phototrophs as a promising strategy to accelerate the discovery of novel natural products from marine actinobacteria.
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Affiliation(s)
- Audam Chhun
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | | | - Lijiang Song
- Department of ChemistryUniversity of WarwickCoventryUK
| | - Christophe Corre
- School of Life SciencesUniversity of WarwickCoventryUK
- Department of ChemistryUniversity of WarwickCoventryUK
| | - Joseph A. Christie‐Oleza
- School of Life SciencesUniversity of WarwickCoventryUK
- University of the Balearic IslandsPalmaSpain
- IMEDEA (CSIC‐UIB)EsporlesSpain
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12
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Kim H, Kim S, Kim M, Lee C, Yang I, Nam SJ. Bioactive natural products from the genus Salinospora: a review. Arch Pharm Res 2020; 43:1230-1258. [PMID: 33237436 DOI: 10.1007/s12272-020-01288-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/13/2020] [Indexed: 12/29/2022]
Abstract
Actinomycetes are an important source for bioactive secondary metabolites. Among them, the genus Salinispora is one of the first salt obligatory marine species worldwide and is typically found in various types of substrates in tropical and subtropical marine environments including sediments and marine organisms. This genus produces a wide range of chemical scaffolds and bioactive compounds such as lomaiviticins, cyclomarins, rifamycins, salinaphthoquinones, and salinosporamides. This review arranged Salinispora derived secondary metabolites according to the three species that comprise the genus. Moreover, muta- and semi-synthesis analogs derived from salinosporamide were also described in this review.
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Affiliation(s)
- Haerin Kim
- The Graduate School of Industrial Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea
| | - Sohee Kim
- The Graduate School of Industrial Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea
| | - Minju Kim
- The Graduate School of Industrial Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea
| | - Chaeyoung Lee
- The Graduate School of Industrial Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea
| | - Inho Yang
- Department of Convergence Study on the Ocean Science and Technology, Korea Maritime and Ocean University, Pusan, 49112, Korea.
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Korea.
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13
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Männle D, McKinnie SMK, Mantri SS, Steinke K, Lu Z, Moore BS, Ziemert N, Kaysser L. Comparative Genomics and Metabolomics in the Genus Nocardia. mSystems 2020; 5:e00125-20. [PMID: 32487740 PMCID: PMC7413640 DOI: 10.1128/msystems.00125-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/13/2020] [Indexed: 01/22/2023] Open
Abstract
Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic potential of Nocardia, an underinvestigated actinobacterial genus that is known to comprise opportunistic human pathogens. Our analysis revealed a plethora of putative biosynthetic gene clusters of various classes, including polyketide, nonribosomal peptide, and terpenoid pathways. Furthermore, we used the highly conserved biosynthetic pathway for nocobactin-like siderophores to investigate how gene cluster differences correlate to structural differences in the produced compounds. Sequence similarity networks generated by BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) showed the presence of several distinct gene cluster families. Metabolic profiling of selected Nocardia strains using liquid chromatography-mass spectrometry (LC-MS) metabolomics data, nuclear magnetic resonance (NMR) spectroscopy, and GNPS (Global Natural Product Social molecular networking) revealed that nocobactin-like biosynthetic gene cluster (BGC) families above a BiG-SCAPE threshold of 70% can be assigned to distinct structural types of nocobactin-like siderophores.IMPORTANCE Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug discovery campaigns.
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Affiliation(s)
- Daniel Männle
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Shaun M K McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA
| | - Shrikant S Mantri
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katharina Steinke
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Zeyin Lu
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California, San Diego, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
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14
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Mo XH, Zhang H, Wang TM, Zhang C, Zhang C, Xing XH, Yang S. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl Microbiol Biotechnol 2020; 104:4515-4532. [PMID: 32215707 DOI: 10.1007/s00253-020-10543-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023]
Abstract
The methylotrophic bacterium Methylorubrum extorquens AM1 holds a great potential of a microbial cell factory in producing high value chemicals with methanol as the sole carbon and energy source. However, many gene functions remain unknown, hampering further rewiring of metabolic networks. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been demonstrated to be a robust tool for gene knockdown in diverse organisms. In this study, we developed an efficient CRISPRi system through optimizing the promoter strength of Streptococcus pyogenes-derived deactivated cas9 (dcas9). When the dcas9 and sgRNA were respectively controlled by medium PR/tetO and strong PmxaF-g promoters, dynamic repression efficacy of cell growth through disturbing a central metabolism gene glyA was achieved from 41.9 to 96.6% dependent on the sgRNA targeting sites. Furthermore, the optimized CRISPRi system was shown to effectively decrease the abundance of exogenous fluorescent protein gene mCherry over 50% and to reduce the expression of phytoene desaturase gene crtI by 97.7%. We then used CRISPRi technology combined with 26 sgRNAs pool to rapidly discover a new phytoene desaturase gene META1_3670 from 2470 recombinant mutants. The gene function was further verified through gene deletion and complementation as well as phylogenetic tree analysis. In addition, we applied CRISPRi to repress the transcriptional level of squalene-hopene cyclase gene shc involved in hopanoid biosynthesis by 64.9%, which resulted in enhancing 1.9-fold higher of carotenoid production without defective cell growth. Thus, the CRISPRi system developed here provides a useful tool in mining functional gene of M. extorquens as well as in biotechnology for producing high-valued chemicals from methanol. KEY POINTS: Developing an efficient CRISPRi to knockdown gene expression in C1-utilizing bacteria CRISPRi combined with sgRNAs pool to rapidly discover a new phytoene desaturase gene Improvement of carotenoid production by repressing a competitive pathway.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Tian-Min Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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15
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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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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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Kuncharoen N, Kudo T, Yuki M, Okuma M, Booncharoen A, Tanasupawat S. Micromonospora musae sp. nov., an endophytic actinomycete isolated from roots of Musa species. Syst Appl Microbiol 2019; 42:126020. [DOI: 10.1016/j.syapm.2019.126020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 10/25/2022]
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18
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Fidan O, Zhan J. Discovery and engineering of an endophytic Pseudomonas strain from Taxus chinensis for efficient production of zeaxanthin diglucoside. J Biol Eng 2019; 13:66. [PMID: 31388354 PMCID: PMC6676639 DOI: 10.1186/s13036-019-0196-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Endophytic microorganisms are a rich source of bioactive natural products. They are considered as promising biofertilizers and biocontrol agents due to their growth-promoting interactions with the host plants and their bioactive secondary metabolites that can help manage plant pathogens. Identification of new endophytes may lead to the discovery of novel molecules or provide new strains for production of valuable compounds. RESULTS In this study, we isolated an endophytic bacterium from the leaves of Taxus chinensis, which was identified as Pseudomonas sp. 102515 based on the 16S rRNA gene sequence and physiological characteristics. Analysis of its secondary metabolites revealed that this endophytic strain produces a major product zeaxanthin diglucoside, a promising antioxidant natural product that belongs to the family of carotenoids. A carotenoid (Pscrt) biosynthetic gene cluster was amplified from this strain, and the functions of PsCrtI and PsCrtY in the biosynthesis of zeaxanthin diglucoside were characterized in Escherichia coli BL21(DE3). The entire Pscrt biosynthetic gene cluster was successfully reconstituted in E. coli BL21(DE3) and Pseudomonas putida KT2440. The production of zeaxanthin diglucoside in Pseudomonas sp. 102515 was improved through the optimization of fermentation conditions such as medium, cultivation temperature and culture time. The highest yield under the optimized conditions reached 206 mg/L. The engineered strain of P. putida KT2440 produced zeaxanthin diglucoside at 121 mg/L in SOC medium supplemented with 0.5% glycerol at 18 °C, while the yield of zeaxanthin diglucoside in E. coli BL21(DE3) was only 2 mg/L. To further enhance the production, we introduced an expression plasmid harboring the Pscrt biosynthetic gene cluster into Pseudomonas sp. 102515. The yield in this engineered strain reached 380 mg/L, 85% higher than the wild type. Through PCR, we also discovered the presence of a turnerbactin biosynthetic gene cluster in Pseudomonas sp. 102515. Because turnerbactin is involved in nitrogen fixation, this endophytic strain might have a role in promoting growth of the host plant. CONCLUSIONS We isolated and identified an endophytic strain of Pseudomonas from T. chinensis. A zeaxanthin diglucoside biosynthetic gene cluster was discovered and characterized in this bacterium. Through fermentation and genetic engineering, the engineered strain produced zeaxanthin diglucoside at 380 ± 12 mg/L, representing a promising strain for the production of this antioxidant natural product. Additionally, Pseudomonas sp. 102515 might also be utilized as a plant-promoting strain for agricultural applications.
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Affiliation(s)
- Ozkan Fidan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA
- TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
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Kuncharoen N, Kudo T, Yuki M, Okuma M, Pittayakhajonwut P, Tanasupawat S. Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov. Int J Syst Evol Microbiol 2019; 69:2884-2891. [PMID: 31310194 DOI: 10.1099/ijsem.0.003574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinomycete strain AZ1-13T was isolated from roots of Azadirachta indica, and its taxonomic position was investigated using a polyphasic approach. Pairwise 16S rRNA gene sequence similarities of strain AZ1-13T and its closest species, Jishegella zingiberis PLAI1-1T and Micromonospora endophytica 202201T, were 99.7 and 99.2 %, respectively. Phylogenetic analyses of the family Micromonosporaceae based on 16S rRNA gene sequences indicated strains AZ1-13T and J. zingiberis PLAI1-1Tare located within the genus Micromonospora. The approximate genome size of the strain was 5.96 Mb with 71.9 mol% of G+C content. The strain AZ1-13T exhibited ANIb values of 87.4 % with J. zingiberis PLAI1-1T and 85.1 % with M. endophytica 202201T. Chemotaxonomic characteristics of strain AZ1-13T were consistent within the genus Micromonospora: cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid; glucose, mannose, ribose and xylose are presented as the whole-cell sugars; the predominant menaquinones were MK-9(H4) and MK-9(H6); major cellular fatty acids were iso-C15 : 0, 10-methyl C17 : 0, C17 : 0, anteiso-C17 : 0 and iso-C17 : 1ω8c; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were detected as distinguished phospholipids. Based on phenotypic properties, phylogeny and genomic data, the strain AZ1-13T could be distinguished from its closest neighbours, representing a novel species of the genus Micromonospora, for which the name Micromonospora radicis sp. nov. is proposed. The type strain is AZ1-13T (=KCTC 39786T=NBRC 112324T=JCM 32147T = TISTR 2404T). This study also proposed that J. zingiberisis transferred to the genus Micromonospora as Micromonospora zingiberis comb. nov. (type strain PLAI1-1T=TBRC 7644T=NBRC 113144T=JCM 32592T).
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Affiliation(s)
- Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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Discovery of 16-Demethylrifamycins by Removing the Predominant Polyketide Biosynthesis Pathway in Micromonospora sp. Strain TP-A0468. Appl Environ Microbiol 2019; 85:AEM.02597-18. [PMID: 30530711 DOI: 10.1128/aem.02597-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
A number of strategies have been developed to mine novel natural products based on biosynthetic gene clusters and there have been dozens of successful cases facilitated by the development of genomic sequencing. During our study on biosynthesis of the antitumor polyketide kosinostatin (KST), we found that the genome of Micromonospora sp. strain TP-A0468, the producer of KST, contains other potential polyketide gene clusters, with no encoded products detected. Deletion of kst cluster led to abolishment of KST and the enrichment of several new compounds, which were isolated and characterized as 16-demethylrifamycins (referred to here as compounds 3 to 6). Transcriptional analysis demonstrated that the expression of the essential genes related to the biosynthesis of compounds 3 to 6 was comparable to the level in the wild-type and in the kst cluster deletion strain. This indicates that the accumulation of these compounds was due to the redirection of metabolic flux rather than transcriptional activation. Genetic disruption, chemical complementation, and bioinformatic analysis revealed that the production of compounds 3 to 6 was accomplished by cross talk between the two distantly placed polyketide gene clusters pks3 and M-rif This finding not only enriches the analogue pool and the biosynthetic diversity of rifamycins but also provides an auxiliary strategy for natural product discovery through genome mining in polyketide-producing microorganisms.IMPORTANCE Natural products are essential in the development of novel clinically used drugs. Discovering new natural products and modifying known compounds are still the two main ways to generate new candidates. Here, we have discovered several rifamycins with varied skeleton structures by redirecting the metabolic flux from the predominant polyketide biosynthetic pathway to the rifamycin pathway in the marine actinomycetes species Micromonospora sp. strain TP-A0468. Rifamycins are indispensable chemotherapeutics in the treatment of various diseases such as tuberculosis, leprosy, and AIDS-related mycobacterial infections. This study exemplifies a useful method for the discovery of cryptic natural products in genome-sequenced microbes. Moreover, the 16-demethylrifamycins and their genetically manipulable producer provide a new opportunity in the construction of novel rifamycin derivates to aid in the defense against the ever-growing drug resistance of Mycobacterium tuberculosis.
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Nahurira R, Wang J, Yan Y, Jia Y, Fan S, Khokhar I, Eltoukhy A. In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2. AMB Express 2019; 9:21. [PMID: 30715639 PMCID: PMC6362181 DOI: 10.1186/s13568-019-0733-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 01/03/2019] [Indexed: 12/29/2022] Open
Abstract
Members of genus Gordonia are known to degrade various xenobitics and produce secondary metabolites. The genome of a halotorelant phthalic acid ester (PAEs) degrading actinobacterium Gordonia alkanivorans strain YC-RL2 was sequenced using Biosciences RS II platform and Single Molecular Real-Time (SMRT) technology. The reads were assembled de novo by hierarchical genome assembly process (HGAP) algorithm version 2. Genes were annotated by NCBI Prokaryotic Genome Annotation Pipeline. The generated genome sequence was 4,979,656 bp with an average G+C content of 67.45%. Calculation of ANI confirmed previous classification that strain YC-RL2 is G. alkanivorans. The sequences were searched against KEGG and COG databases; 3132 CDSs were assigned to COG families and 1808 CDSs were predicted to be involved in 111 pathways. 95 of the KEGG annotated genes were predicted to be involved in the degradation of xenobiotics. A phthalate degradation operon could not be identified in the genome indicating that strain YC-RL2 possesses a novel way of phthalate degradation. A total of 203 and 22 CDSs were annotated as esterase/hydrolase and dioxygenase genes respectively. A total of 53 biosynthetic gene clusters (BGCs) were predicted by antiSMASH (antibiotics & Secondary Metabolite Analysis Shell) bacterial version 4.0. The genome also contained putative genes for heavy metal metabolism. The strain could tolerate 1 mM of Cd2+, Co2+, Cu2+, Ni2+, Zn2+, Mn2+ and Pb2+ ions. These results show that strain YC-RL2 has a great potential to degrade various xenobiotics in different environments and will provide a rich genetic resource for further biotechnological and remediation studies.
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Contador CA, Rodríguez V, Andrews BA, Asenjo JA. Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora. BMC SYSTEMS BIOLOGY 2019; 13:11. [PMID: 30665399 PMCID: PMC6341766 DOI: 10.1186/s12918-019-0683-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/11/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified species of Salinispora using constraints-based modeling. At present, only one manually curated genome-scale metabolic model (GSM) for Salinispora tropica strain CNB-440T has been built despite the role of Salinispora strains in drug discovery. RESULTS Here, we updated, and expanded the scope of the model of Salinispora tropica CNB-440T, and GSMs were constructed for two sequenced type strains covering the three-identified species. We also constructed a Salinispora core model that contains the genes shared by 93 sequenced strains and a few non-conserved genes associated with essential reactions. The models predicted no auxotrophies for essential amino acids, which was corroborated experimentally using a defined minimal medium (DMM). Experimental observations suggest possible sulfur accumulation. The Core metabolic content shows that the biosynthesis of specialised metabolites is the less conserved subsystem. Sets of reactions were analyzed to explore the differences between the reconstructions. Unique reactions associated to each GSM were mainly due to genome sequence data except for the ST-CNB440 reconstruction. In this case, additional reactions were added from experimental evidence. This reveals that by reaction content the ST-CNB440 model is different from the other species models. The differences identified in reaction content between models gave rise to different functional predictions of essential nutrient usage by each species in DMM. Furthermore, models were used to evaluate in silico single gene knockouts under DMM and complex medium. Cluster analysis of these results shows that ST-CNB440, and SP-CNR114 models are more similar when considering predicted essential genes. CONCLUSIONS Models were built for each of the three currently identified Salinispora species, and a core model representing the conserved metabolic capabilities of Salinispora was constructed. Models will allow in silico metabolism studies of Salinispora strains, and help researchers to guide and increase the production of specialised metabolites. Also, models can be used as templates to build GSMs models of closely related organisms with high biotechnology potential.
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Affiliation(s)
- Carolina A. Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Vida Rodríguez
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
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Draft Genome Sequence of Micromonospora sp. Strain MW-13, a Bacterial Strain with Antibacterial Properties and Plant Growth Promotion Potential Isolated from the Rhizosphere of Wheat in Iran. Microbiol Resour Announc 2019; 8:MRA01375-18. [PMID: 30643882 PMCID: PMC6328655 DOI: 10.1128/mra.01375-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/26/2018] [Indexed: 01/27/2023] Open
Abstract
Strain MW13 exhibited broad-spectrum antibacterial activity toward Gram-positive and Gram-negative pathogens. The 7.1-Mb draft genome gives insight into the complete secondary metabolite production capacity and reveals genes putatively responsible for its antibacterial activity, as well as genes which contribute to plant growth promotion.
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25
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Braesel J, Crnkovic CM, Kunstman KJ, Green SJ, Maienschein-Cline M, Orjala J, Murphy BT, Eustáquio AS. Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete. JOURNAL OF NATURAL PRODUCTS 2018; 81:2057-2068. [PMID: 30110167 PMCID: PMC6174880 DOI: 10.1021/acs.jnatprod.8b00394] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Actinomycete bacteria isolated from freshwater environments are an unexplored source of natural products. Here we report the complete genome of the Great Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to close remaining gaps. All identified biosynthetic gene clusters (BGCs) were manually curated. Five known BGCs were identified encoding desferrioxamine, alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and diazepinomicin, which is currently in phase II clinical trials to treat Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006 is indeed a producer of diazepinomicin and at yields higher than previously reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were transcriptionally active under the culture condition tested. Orphan BGCs include an enediyne polyketide synthase and an uncharacteristically large, 36-module polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in the future. This study is one of the few attempts to report the biosynthetic capacity of a freshwater-derived actinomycete and highlights this resource as a potential reservoir for new natural products.
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Affiliation(s)
- Jana Braesel
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Camila M. Crnkovic
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
| | - Kevin J. Kunstman
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, IL 60615, USA
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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26
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Torregrosa-Crespo J, Montero Z, Fuentes JL, Reig García-Galbis M, Garbayo I, Vílchez C, Martínez-Espinosa RM. Exploring the Valuable Carotenoids for the Large-Scale Production by Marine Microorganisms. Mar Drugs 2018; 16:E203. [PMID: 29890662 PMCID: PMC6025630 DOI: 10.3390/md16060203] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Abstract
Carotenoids are among the most abundant natural pigments available in nature. These pigments have received considerable attention because of their biotechnological applications and, more importantly, due to their potential beneficial uses in human healthcare, food processing, pharmaceuticals and cosmetics. These bioactive compounds are in high demand throughout the world; Europe and the USA are the markets where the demand for carotenoids is the highest. The in vitro synthesis of carotenoids has sustained their large-scale production so far. However, the emerging modern standards for a healthy lifestyle and environment-friendly practices have given rise to a search for natural biocompounds as alternatives to synthetic ones. Therefore, nowadays, biomass (vegetables, fruits, yeast and microorganisms) is being used to obtain naturally-available carotenoids with high antioxidant capacity and strong color, on a large scale. This is an alternative to the in vitro synthesis of carotenoids, which is expensive and generates a large number of residues, and the compounds synthesized are sometimes not active biologically. In this context, marine biomass has recently emerged as a natural source for both common and uncommon valuable carotenoids. Besides, the cultivation of marine microorganisms, as well as the downstream processes, which are used to isolate the carotenoids from these microorganisms, offer several advantages over the other approaches that have been explored previously. This review summarizes the general properties of the most-abundant carotenoids produced by marine microorganisms, focusing on the genuine/rare carotenoids that exhibit interesting features useful for potential applications in biotechnology, pharmaceuticals, cosmetics and medicine.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry, Biochemistry and Molecular Biology division, Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
| | - Zaida Montero
- Algal Biotechnology Group, University of Huelva, CIDERTA and Faculty of Science, Marine International Campus of Excellence (CEIMAR), Parque Huelva Empresarial S/N, 21007 Huelva, Spain.
| | - Juan Luis Fuentes
- Algal Biotechnology Group, University of Huelva, CIDERTA and Faculty of Science, Marine International Campus of Excellence (CEIMAR), Parque Huelva Empresarial S/N, 21007 Huelva, Spain.
| | - Manuel Reig García-Galbis
- Department of Nutrition and Dietetics, Faculty of Health Sciences, University of Atacama, Copayapu 2862, CP 1530000 Copiapó, Chile.
| | - Inés Garbayo
- Algal Biotechnology Group, University of Huelva, CIDERTA and Faculty of Science, Marine International Campus of Excellence (CEIMAR), Parque Huelva Empresarial S/N, 21007 Huelva, Spain.
| | - Carlos Vílchez
- Algal Biotechnology Group, University of Huelva, CIDERTA and Faculty of Science, Marine International Campus of Excellence (CEIMAR), Parque Huelva Empresarial S/N, 21007 Huelva, Spain.
| | - Rosa María Martínez-Espinosa
- Department of Agrochemistry and Biochemistry, Biochemistry and Molecular Biology division, Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
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27
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Patin NV, Floros DJ, Hughes CC, Dorrestein PC, Jensen PR. The role of inter-species interactions in Salinispora specialized metabolism. MICROBIOLOGY-SGM 2018; 164:946-955. [PMID: 29877785 DOI: 10.1099/mic.0.000679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Bacterial genome sequences consistently contain many more biosynthetic gene clusters encoding specialized metabolites than predicted by the compounds discovered from the respective strains. One hypothesis invoked to explain the cryptic nature of these gene clusters is that standard laboratory conditions do not provide the environmental cues needed to trigger gene expression. A potential source of such cues is other members of the bacterial community, which are logical targets for competitive interactions. In this study, we examined the effects of such interactions on specialized metabolism in the marine actinomycete Salinispora tropica. The results show that antibiotic activities and the concentration of some small molecules increase in the presence of co-occurring bacterial strains relative to monocultures. Some increases in antibiotic activity could be linked to nutrient depletion by the competitor as opposed to the production of a chemical cue. Other increases were correlated with the production of specific compounds by S. tropica. In particular, one interaction with a Vibrio sp. consistently induced antibiotic activity and was associated with parent ions that were unique to this interaction, although the associated compound could not be identified. This study provides insight into the metabolomic complexities of bacterial interactions and baseline information for future genome mining efforts.
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Affiliation(s)
- Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
- Present address: School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Dimitrios J Floros
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA
| | - Chambers C Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Pieter C Dorrestein
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA
- Center for Microbiome Innovation, University of California, San Diego, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
- Center for Microbiome Innovation, University of California, San Diego, USA
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28
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Abdel-Mawgoud AM, Stephanopoulos G. Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering. Synth Syst Biotechnol 2018; 3:3-19. [PMID: 29911195 PMCID: PMC5884252 DOI: 10.1016/j.synbio.2017.12.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/14/2017] [Accepted: 12/04/2017] [Indexed: 01/15/2023] Open
Abstract
Glycosylated lipids (GLs) are added-value lipid derivatives of great potential. Besides their interesting surface activities that qualify many of them to act as excellent ecological detergents, they have diverse biological activities with promising biomedical and cosmeceutical applications. Glycolipids, especially those of microbial origin, have interesting antimicrobial, anticancer, antiparasitic as well as immunomodulatory activities. Nonetheless, GLs are hardly accessing the market because of their high cost of production. We believe that experience of metabolic engineering (ME) of microbial lipids for biofuel production can now be harnessed towards a successful synthesis of microbial GLs for biomedical and other applications. This review presents chemical groups of bacterial and fungal GLs, their biological activities, their general biosynthetic pathways and an insight on ME strategies for their production.
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Affiliation(s)
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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29
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Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Göker M, Goodfellow M. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525. [PMID: 29323202 PMCID: PMC5765111 DOI: 10.1038/s41598-017-17392-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022] Open
Abstract
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Vartul Sangal
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiologia y Genetica, Lab 214, Universidad de Salamanca, Salamanca, Spain
| | | | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Kurupelit-Samsun, Turkey
| | - Darren Lee Smith
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Kristi E Kim
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | - Paul Peluso
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
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30
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Abstract
The small molecules produced by environmental bacteria have been mainstays of both chemical and biological research for decades, and some have led to important therapeutic interventions. These small molecules have been shaped by natural selection as they evolved to fulfill changing functional roles in their native environments. This minireview describes some recent systematic studies providing illustrative examples that involve the acquisition and alteration of genetic information for molecular innovation by bacteria in well-defined environments. Two different bacterial genera are featured, Pseudonocardia and Salinispora, and, although the small-molecule repertoires of both have benefited from horizontal gene transfer, Pseudonocardia spp. have relied on plasmid-based tactics while Salinispora spp. have relied on chromosomally integrated genomic islands.
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Affiliation(s)
- Antonio C Ruzzini
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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31
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Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality. Proc Natl Acad Sci U S A 2017; 114:E11121-E11130. [PMID: 29229817 DOI: 10.1073/pnas.1714381115] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown from Salinispora pacifica.
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32
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Ron EYC, Plaza M, Kristjansdottir T, Sardari RRR, Bjornsdottir SH, Gudmundsson S, Hreggvidsson GO, Turner C, van Niel EWJ, Nordberg-Karlsson E. Characterization of carotenoids in Rhodothermus marinus. Microbiologyopen 2017; 7. [PMID: 29045010 PMCID: PMC5822342 DOI: 10.1002/mbo3.536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/13/2022] Open
Abstract
Rhodothermus marinus, a marine aerobic thermophile, was first isolated from an intertidal hot spring in Iceland. In recent years, the R. marinus strain PRI 493 has been genetically modified, which opens up possibilities for targeted metabolic engineering of the species, such as of the carotenoid biosynthetic pathway. In this study, the carotenoids of the R. marinus type‐strain DSM 4252T, strain DSM 4253, and strain PRI 493 were characterized. Bioreactor cultivations were used for pressurized liquid extraction and analyzed by ultra‐high performance supercritical fluid chromatography with diode array and quadropole time‐of‐flight mass spectrometry detection (UHPSFC‐DAD‐QTOF/MS). Salinixanthin, a carotenoid originally found in Salinibacter ruber and previously detected in strain DSM 4253, was identified in all three R. marinus strains, both in the hydroxylated and nonhydroxylated form. Furthermore, an additional and structurally distinct carotenoid was detected in the three strains. MS/MS fragmentation implied that the mass difference between salinixanthin and the novel carotenoid structure corresponded to the absence of a 4‐keto group on the ß‐ionone ring. The study confirmed the lack of carotenoids for the strain SB‐71 (ΔtrpBΔpurAcrtBI’::trpB) in which genes encoding two enzymes of the proposed pathway are partially deleted. Moreover, antioxidant capacity was detected in extracts of all the examined R. marinus strains and found to be 2–4 times lower for the knock‐out strain SB‐71. A gene cluster with 11 genes in two operons in the R. marinusDSM 4252T genome was identified and analyzed, in which several genes were matched with carotenoid biosynthetic pathway genes in other organisms.
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Affiliation(s)
- Emanuel Y C Ron
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Merichel Plaza
- Division of Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | - Charlotta Turner
- Division of Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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33
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Chen R, Zhang Q, Tan B, Zheng L, Li H, Zhu Y, Zhang C. Genome Mining and Activation of a Silent PKS/NRPS Gene Cluster Direct the Production of Totopotensamides. Org Lett 2017; 19:5697-5700. [PMID: 29019409 DOI: 10.1021/acs.orglett.7b02878] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 92 kb silent hybrid polyketide and nonribosomal peptide gene cluster in marine-derived Streptomyces pactum SCSIO 02999 was activated by genetically manipulating the regulatory genes, including the knockout of two negative regulators (totR5 and totR3) and overexpression of a positive regulator totR1, to direct the production of the known totopotensamides (TPMs) A (1) and B (3) and a novel sulfonate-containing analogue TPM C (2). Inactivation of totG led to accumulation of TPM B (3) lacking the glycosyl moiety, which indicated TotG as a dedicated glycosyltransferase in the biosynthesis of 1 and 2.
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Affiliation(s)
- Ruidong Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Liujuan Zheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Huixian Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
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34
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Letzel AC, Li J, Amos GCA, Millán-Aguiñaga N, Ginigini J, Abdelmohsen UR, Gaudêncio SP, Ziemert N, Moore BS, Jensen PR. Genomic insights into specialized metabolism in the marine actinomycete Salinispora. Environ Microbiol 2017; 19:3660-3673. [PMID: 28752948 DOI: 10.1111/1462-2920.13867] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 11/28/2022]
Abstract
Comparative genomics is providing new opportunities to address the diversity and distributions of genes encoding the biosynthesis of specialized metabolites. An analysis of 119 genome sequences representing three closely related species of the marine actinomycete genus Salinispora reveals extraordinary biosynthetic diversity in the form of 176 distinct biosynthetic gene clusters (BGCs) of which only 24 have been linked to their products. Remarkably, more than half of the BGCs were observed in only one or two strains, suggesting they were acquired relatively recently in the evolutionary history of the genus. These acquired gene clusters are concentrated in specific genomic islands, which represent hot spots for BGC acquisition. While most BGCs are stable in terms of their chromosomal position, others migrated to different locations or were exchanged with unrelated gene clusters suggesting a plug and play type model of evolution that provides a mechanism to test the relative fitness effects of specialized metabolites. Transcriptome analyses were used to address the relationships between BGC abundance, chromosomal position and product discovery. The results indicate that recently acquired BGCs can be functional and that complex evolutionary processes shape the micro-diversity of specialized metabolism observed in closely related environmental bacteria.
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Affiliation(s)
- Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jing Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Gregory C A Amos
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California 22800, Mexico
| | - Joape Ginigini
- Institute of Applied Sciences, Faculty of Science, Technology and Environment, University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Fiji
| | - Usama R Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Germany.,Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Susana P Gaudêncio
- Department of Chemistry, REQUIMTE, LAQV and UCIBIO, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica 2529-516, Portugal
| | - Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Interfaculty Institute of Microbiology and Infection Medicine Tuübingen, University of Tuübingen, Auf der Morgenstelle 28, Tuübingen 72076, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
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35
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Dhakal D, Pokhrel AR, Shrestha B, Sohng JK. Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds. Front Microbiol 2017; 8:1106. [PMID: 28663748 PMCID: PMC5471306 DOI: 10.3389/fmicb.2017.01106] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/31/2017] [Indexed: 12/28/2022] Open
Abstract
Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications.
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Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Anaya Raj Pokhrel
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University Asan-siSouth Korea
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36
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Wolf T, Schneiker-Bekel S, Neshat A, Ortseifen V, Wibberg D, Zemke T, Pühler A, Kalinowski J. Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis. J Biotechnol 2017; 251:112-123. [PMID: 28427920 DOI: 10.1016/j.jbiotec.2017.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 12/16/2022]
Abstract
Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis are only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data. A whole transcriptome RNA-seq library as well as an RNA-seq library enriched for primary 5'-ends were used for the detection of transcription start sites, to correct tRNA predictions, to identify novel transcripts like small RNAs and to improve the annotation through the correction of falsely annotated translation start sites. The transcriptome data sets were also applied to identify 31 cis-regulatory RNA structures, such as riboswitches or RNA thermometers as well as three leaderless transcribed short peptides found in putative attenuators upstream of genes for amino acid biosynthesis. The transcriptional organization of the acarbose biosynthetic gene cluster was elucidated in detail and fourteen novel biosynthetic gene clusters were suggested. The accurate genome sequence and precise annotation of the Actinoplanes sp. SE50/110 genome will be the foundation for future genetic engineering and systems biology studies.
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Affiliation(s)
- Timo Wolf
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Susanne Schneiker-Bekel
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Vera Ortseifen
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Till Zemke
- Product Supply, Bayer Pharma AG, Friedrich Ebert Str. 217-475, 42117 Wuppertal, Germany
| | - Alfred Pühler
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
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Holmes NA, Innocent TM, Heine D, Bassam MA, Worsley SF, Trottmann F, Patrick EH, Yu DW, Murrell JC, Schiøtt M, Wilkinson B, Boomsma JJ, Hutchings MI. Genome Analysis of Two Pseudonocardia Phylotypes Associated with Acromyrmex Leafcutter Ants Reveals Their Biosynthetic Potential. Front Microbiol 2016; 7:2073. [PMID: 28082956 PMCID: PMC5183585 DOI: 10.3389/fmicb.2016.02073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
The attine ants of South and Central America are ancient farmers, having evolved a symbiosis with a fungal food crop >50 million years ago. The most evolutionarily derived attines are the Atta and Acromyrmex leafcutter ants, which harvest fresh leaves to feed their fungus. Acromyrmex and many other attines vertically transmit a mutualistic strain of Pseudonocardia and use antifungal compounds made by these bacteria to protect their fungal partner against co-evolved fungal pathogens of the genus Escovopsis. Pseudonocardia mutualists associated with the attines Apterostigma dentigerum and Trachymyrmex cornetzi make novel cyclic depsipeptide compounds called gerumycins, while a mutualist strain isolated from derived Acromyrmex octospinosus makes an unusual polyene antifungal called nystatin P1. The novelty of these antimicrobials suggests there is merit in exploring secondary metabolites of Pseudonocardia on a genome-wide scale. Here, we report a genomic analysis of the Pseudonocardia phylotypes Ps1 and Ps2 that are consistently associated with Acromyrmex ants collected in Gamboa, Panama. These were previously distinguished solely on the basis of 16S rRNA gene sequencing but genome sequencing of five Ps1 and five Ps2 strains revealed that the phylotypes are distinct species and each encodes between 11 and 15 secondary metabolite biosynthetic gene clusters (BGCs). There are signature BGCs for Ps1 and Ps2 strains and some that are conserved in both. Ps1 strains all contain BGCs encoding nystatin P1-like antifungals, while the Ps2 strains encode novel nystatin-like molecules. Strains show variations in the arrangement of these BGCs that resemble those seen in gerumycin gene clusters. Genome analyses and invasion assays support our hypothesis that vertically transmitted Ps1 and Ps2 strains have antibacterial activity that could help shape the cuticular microbiome. Thus, our work defines the Pseudonocardia species associated with Acromyrmex ants and supports the hypothesis that Pseudonocardia species could provide a valuable source of new antimicrobials.
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Affiliation(s)
- Neil A Holmes
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Mahmoud Al Bassam
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Felix Trottmann
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Elaine H Patrick
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia (UEA)Norwich, UK; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyKunming, China
| | - J C Murrell
- School of Environmental Sciences, University of East Anglia (UEA) Norwich, UK
| | - Morten Schiøtt
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
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Zhang W, Lu L, Lai Q, Zhu B, Li Z, Xu Y, Shao Z, Herrup K, Moore BS, Ross AC, Qian PY. Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria. J Biol Chem 2016; 291:27228-27238. [PMID: 27875306 DOI: 10.1074/jbc.m116.756858] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
The thalassospiramide lipopeptides have great potential for therapeutic applications; however, their structural and functional diversity and biosynthesis are poorly understood. Here, by cultivating 130 Rhodospirillaceae strains sampled from oceans worldwide, we discovered 21 new thalassospiramide analogues and demonstrated their neuroprotective effects. To investigate the diversity of biosynthetic gene cluster (BGC) architectures, we sequenced the draft genomes of 28 Rhodospirillaceae strains. Our family-wide genomic analysis revealed three types of dysfunctional BGCs and four functional BGCs whose architectures correspond to four production patterns. This correlation allowed us to reassess the "diversity-oriented biosynthesis" proposed for the microbial production of thalassospiramides, which involves iteration of several key modules. Preliminary evolutionary investigation suggested that the functional BGCs could have arisen through module/domain loss, whereas the dysfunctional BGCs arose through horizontal gene transfer. Further comparative genomics indicated that thalassospiramide production is likely to be attendant on particular genes/pathways for amino acid metabolism, signaling transduction, and compound efflux. Our findings provide a systematic understanding of thalassospiramide production and new insights into the underlying mechanism.
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Affiliation(s)
- Weipeng Zhang
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Liang Lu
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Qiliang Lai
- the Third Institute of Oceanography, State Oceanic Administration, Xiamen 361000, China
| | - Beika Zhu
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Zhongrui Li
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Ying Xu
- the School of Life Science, Shenzhen University, Shenzhen, Guangdong Province 518060, China
| | - Zongze Shao
- the Third Institute of Oceanography, State Oceanic Administration, Xiamen 361000, China
| | - Karl Herrup
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Bradley S Moore
- the Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, and
| | - Avena C Ross
- the Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Pei-Yuan Qian
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong,
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Zhang L, Hoshino S, Awakawa T, Wakimoto T, Abe I. Structural Diversification of Lyngbyatoxin A by Host-Dependent Heterologous Expression of thetleABCBiosynthetic Gene Cluster. Chembiochem 2016; 17:1407-11. [DOI: 10.1002/cbic.201600229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Pharmaceutical Sciences; Hokkaido University; Kita 12 Nishi 6 Kita-ku Sapporo 060-0812 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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Anti-MRSA and anti-TB metabolites from marine-derived Verrucosispora sp. MS100047. Appl Microbiol Biotechnol 2016; 100:7437-47. [PMID: 26975378 DOI: 10.1007/s00253-016-7406-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/31/2016] [Accepted: 02/18/2016] [Indexed: 02/05/2023]
Abstract
Microbes belonging to the genus Verrucosispora possess significant chemical diversity and biological properties. They have attracted the interests of many researchers and are becoming promising resources in the marine natural product research field. A bioassay-guided isolation from the crude extract of Verrucosispora sp. strain MS100047, isolated from sediments collected from the South China Sea, has led to the identification of a new salicylic derivative, glycerol 1-hydroxy-2,5-dimethyl benzoate (1), along with three known compounds, brevianamide F (2), abyssomicin B (3), and proximicin B (4). Compound 1 showed selective activity against methicillin-resistant Staphylococcus aureus (MRSA) with a minimum inhibitory concentration (MIC) value of 12.5 μg/mL. Brevianamide F (2), which was isolated from actinomycete for the first time, showed a good anti-BCG activity with a MIC value of 12.5 μg/mL that has not been reported previously in literatures. Proximicin B (4) showed significant anti-MRSA (MIC = 3.125 μg/mL), anti-BCG (MIC = 6.25 μg/mL), and anti-tuberculosis (TB) (MIC = 25 μg/mL) activities. This is the first report on the anti-tubercular activities of proximicins. In addition, Verrucosispora sp. strain MS100047 was found to harbor 18 putative secondary metabolite gene clusters based on genomic sequence analysis. These include the biosynthetic loci encoding polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) consistent with abyssomicins and proximicins, respectively. The biosynthetic pathways of these isolated compounds have been proposed. These results indicate that MS100047 possesses a great potential as a source of active secondary metabolites.
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Tang MC, Lin HC, Li D, Zou Y, Li J, Xu W, Cacho RA, Hillenmeyer ME, Garg NK, Tang Y. Discovery of Unclustered Fungal Indole Diterpene Biosynthetic Pathways through Combinatorial Pathway Reassembly in Engineered Yeast. J Am Chem Soc 2015; 137:13724-7. [PMID: 26469304 DOI: 10.1021/jacs.5b06108] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structural diversity and biological activities of fungal indole diterpenes (IDTs) are generated in large part by the IDT cyclases (IDTCs). Identifying different IDTCs from IDT biosynthetic pathways is therefore important toward understanding how these enzymes introduce chemical diversity from a common linear precursor. However, IDTCs involved in the cyclization of the well-known aflavinine subgroup of IDTs have not been discovered. Here, using Saccharomyces cerevisiae as a heterologous host and a phylogenetically guided enzyme mining approach, we combinatorially assembled IDT biosynthetic pathways using IDTCs homologues identified from different fungal hosts. We identified the genetically standalone IDTCs involved in the cyclization of aflavinine and anominine and produced new IDTs not previously isolated. The cyclization mechanisms of the new IDTCs were proposed based on the yeast reconstitution results. Our studies demonstrate heterologous pathway assembly is a useful tool in the reconstitution of unclustered biosynthetic pathways.
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Affiliation(s)
| | | | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao, Shandong 266003, P. R. China
| | | | - Jian Li
- Stanford Genome Technology Center, Stanford University , Palo Alto, California 94304, United States
| | | | | | - Maureen E Hillenmeyer
- Stanford Genome Technology Center, Stanford University , Palo Alto, California 94304, United States
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Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. Nat Prod Rep 2015; 32:738-51. [PMID: 25730728 PMCID: PMC4414829 DOI: 10.1039/c4np00167b] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review covers the initial discovery of the marine actinomycete genus Salinispora through its development as a model for natural product research. A focus is placed on the novel chemical structures reported with reference to their biological activities and the synthetic and biosynthetic studies they have inspired. The time line of discoveries progresses from more traditional bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target the products of specific biosynthetic gene clusters. This overview exemplifies the extraordinary biosynthetic diversity that can emanate from a narrowly defined genus and supports future efforts to explore marine taxa in the search for novel natural products.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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