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van der Meij A, Elsayed SS, Du C, Willemse J, Wood TM, Martin NI, Raaijmakers JM, van Wezel GP. The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes. Appl Environ Microbiol 2023; 89:e0123923. [PMID: 37902333 PMCID: PMC10686085 DOI: 10.1128/aem.01239-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.
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Affiliation(s)
- Anne van der Meij
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Somayah S. Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Chao Du
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Thomas M. Wood
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Nathaniel I. Martin
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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BarA/UvrY differentially regulates prodigiosin biosynthesis and swarming motility in Serratia marcescens FS14. Res Microbiol 2023; 174:104010. [PMID: 36410584 DOI: 10.1016/j.resmic.2022.104010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
BarA/UvrY, a two-component system and global regulator that controls expression of more than a hundred of genes involved in virulence, motility, biofilm formation, and central carbon metabolism under various stress conditions. In this study, we investigated the function of BarA/UvrY system in Serratia marcescens FS14. The disruption of barA or/and uvrY results in the yield increase of secondary metabolite prodigiosin. We further demonstrated that BarA/UvrY system represses prodigiosin production by inhibiting the transcription level of pig gene cluster with direct binding to the pigA promoter. In addition, deletion of barA or/and uvrY abolished the swarming motility of FS14, but not the swimming motility. We revealed that BarA/UvrY activates swarming through directly upregulating the expression of the biosurfactant synthesis gene swrW rather than flagella system. We also observed that BarA/UvrY positively regulates the resistance to H2O2 same as in Escherichia coli highlighting the importance of BarA/UvrY on hydrogen peroxide resistance. Our results demonstrated that the BarA/UvrY system differentially regulates the biosynthesis of the secondary metabolite prodigiosin and swarming motility in S. marcescens FS14. Comparison of our results with those observed for Serratia sp. 39006 suggests that BarA/UvrY's role in regulation of secondary metabolite production is different among Serratia species.
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Structures, biosynthesis, and bioactivities of prodiginine natural products. Appl Microbiol Biotechnol 2022; 106:7721-7735. [DOI: 10.1007/s00253-022-12245-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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Richardson SM, Marchetti PM, Herrera MA, Campopiano DJ. Coupled Natural Fusion Enzymes in a Novel Biocatalytic Cascade Convert Fatty Acids to Amines. ACS Catal 2022; 12:12701-12710. [PMID: 36313522 PMCID: PMC9594044 DOI: 10.1021/acscatal.2c02954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/29/2022] [Indexed: 11/28/2022]
Abstract
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Tambjamine YP1 is a pyrrole-containing natural product.
Analysis
of the enzymes encoded in the Pseudoalteromonas tunicata “tam” biosynthetic gene cluster (BGC)
identified a unique di-domain biocatalyst (PtTamH).
Sequence and bioinformatic analysis predicts that PtTamH comprises an N-terminal, pyridoxal 5′-phosphate (PLP)-dependent
transaminase (TA) domain fused to a NADH-dependent C-terminal thioester
reductase (TR) domain. Spectroscopic and chemical analysis revealed
that the TA domain binds PLP, utilizes l-Glu as an amine
donor, accepts a range of fatty aldehydes (C7–C14 with a preference for C12), and produces the
corresponding amines. The previously characterized PtTamA from the “tam” BGC is an ATP-dependent, di-domain
enzyme comprising a class I adenylation domain fused to an acyl carrier
protein (ACP). Since recombinant PtTamA catalyzes
the activation and thioesterification of C12 acid to the holo-ACP domain, we hypothesized that C12 ACP
is the natural substrate for PtTamH. PtTamA and PtTamH were successfully coupled together
in a biocatalytic cascade that converts fatty acids (FAs) to amines
in one pot. Moreover, a structural model of PtTamH
provides insights into how the TA and TR domains are organized. This
work not only characterizes the formation of the tambjamine YP1 tail
but also suggests that PtTamA and PtTamH could be useful biocatalysts for FA to amine functional group
conversion.
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Affiliation(s)
- Shona M. Richardson
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Piera M. Marchetti
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Michael A. Herrera
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
| | - Dominic J. Campopiano
- School of Chemistry, The University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, U.K
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5
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Whole-genome sequencing and analysis of Streptomyces strains producing multiple antinematode drugs. BMC Genomics 2022; 23:610. [PMID: 35996099 PMCID: PMC9396898 DOI: 10.1186/s12864-022-08847-4] [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: 04/22/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background Nematodes are parasitic animals that cause over 100 billion US dollars loss in agricultural business. The whole-genomes of two Streptomyces strains, Streptomyces spectabilis KCTC9218T and Streptomyces sp. AN091965, were sequenced. Both strains produce spectinabilin, an antinematode drug. Its secondary metabolism was examined to aid the development of an efficient nematicidal drug-producing host strain. Results The whole-genome sequences of S. spectabilis KCTC9218T and Streptomyces sp. AN091965 were analyzed using PacBio and Illumina sequencing platforms, and assembled using hybrid methodology. The total contig lengths for KCTC9218T and AN091965 were 9.97 Mb and 9.84 Mb, respectively. A total of 8,374 and 8,054 protein-coding genes, as well as 39 and 45 secondary metabolite biosynthetic gene clusters were identified in KCTC9218T and AN091965, respectively. 18.4 ± 6.45 mg/L and 213.89 ± 21.30 mg/L of spectinabilin were produced by S. spectabilis KCTC9218T and Streptomyces sp. AN091965, respectively. Pine wilt disease caused by nematode was successfully prevented by lower concentration of spectinabilin injection than that of abamectin recommended by its manufacturer. Production of multiple antinematode drugs, including spectinabilin, streptorubin B, and undecylprodigiosin was observed in both strains using high-resolution liquid chromatography mass spectrometry (LC–MS) analysis. Conclusions Whole-genome sequencing of spectinabilin-producing strains, coupled with bioinformatics and mass spectrometry analyses, revealed the production of multiple nematicidal drugs in the KCTC9218T and AN091965 strains. Especially, Streptomyces sp. AN091965 showed high production level of spectinabilin, and this study provides crucial information for the development of potential nematicidal drug producers. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08847-4.
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Chen X, Li S, Zhang B, Sun H, Wang J, Zhang W, Meng W, Chen T, Dyson P, Liu G. A new bacterial tRNA enhances antibiotic production in Streptomyces by circumventing inefficient wobble base-pairing. Nucleic Acids Res 2022; 50:7084-7096. [PMID: 35699212 PMCID: PMC9262613 DOI: 10.1093/nar/gkac502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
We report the discovery and functional characterization of a new bacterial tRNA species. The tRNA-Asp-AUC, from a fast-growing desert streptomycete, decodes GAU codons. In the absence of queuosine tRNA anticodon modification in streptomycetes, the new tRNA circumvents inefficient wobble base-pairing during translation. The tRNA, which is constitutively expressed, greatly enhances synthesis of 4 different antibiotics in the model mesophilic species Streptomyces coelicolor, including the product of a so-called cryptic pathway, and increases yields of medically-important antibiotics in other species. This can be rationalised due to increased expression of both pleiotropic and pathway-specific transcriptional activators of antibiotic biosynthesis whose genes generally possess one or more GAT codons; the frequency of this codon in these gene sets is significantly higher than the average for streptomycete genes. In addition, the tRNA enhances production of cobalamin, a precursor of S-adenosyl methionine, itself an essential cofactor for synthesis of many antibiotics. The results establish a new paradigm of inefficient wobble base-pairing involving GAU codons as an evolved strategy to regulate gene expression and, in particular, antibiotic biosynthesis. Circumventing this by expression of the new cognate tRNA offers a generic strategy to increase antibiotic yields and to expand the repertoire of much-needed new bioactive metabolites produced by these valuable bacteria.
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Affiliation(s)
- Ximing Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, China,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, China
| | - Shuyan Li
- School of Medical Information and Engineering, Xuzhou Medical University, Jiangsu, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, China,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Haili Sun
- School of Chemistry and Environmental Science, Lanzhou City University, Lanzhou, Gansu, China
| | - Jinxiu Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, China,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, China,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, China
| | - Wenbo Meng
- Key Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province; The First Clinical Medical School of Lanzhou University, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, China,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Paul Dyson
- To whom correspondence should be addressed. Tel: +44 1792 295667;
| | - Guangxiu Liu
- Correspondence may also be addressed to Guangxiu Liu.
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Ramesh C, Anwesh M, Vinithkumar NV, Kirubagaran R, Dufossé L. Complete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive Applications. Microorganisms 2021; 9:microorganisms9112249. [PMID: 34835376 PMCID: PMC8618203 DOI: 10.3390/microorganisms9112249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/17/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023] Open
Abstract
Marine Streptomyces species are underexplored for their pigment molecules and genes. In this study, we report the genome of the undecylprodigiosin biosynthesizing gene cluster carrying Streptomyces sp. strain BSE6.1, displaying antioxidant, antimicrobial, and staining properties. This Gram-positive obligate aerobic bacterium was isolated from the coastal sediment of the Andaman and Nicobar Islands, India. Pink to reddish pigmented colonies with whitish powdery spores on both agar and broth media are the important morphological characteristics of this bacterium. Growth tolerance to NaCl concentrations was 2 to 7%. The assembled genome of Streptomyces sp. BSE6.1 contains one linear chromosome 8.02 Mb in length with 7157 protein-coding genes, 82 tRNAs, 3 rRNAs and at least 11 gene clusters related to the synthesis of various secondary metabolites, including undecylprodigiosin. This strain carries type I, type II, and type III polyketide synthases (PKS) genes. Type I PKS gene cluster is involved in the biosynthesis of red pigment undecylprodigiosin of BSE6.1, similar to the one found in the S. coelicolor A3(2). This red pigment was reported to have various applications in the food and pharmaceutical industries. The genome of Streptomyces sp. BSE6.1 was submitted to NCBI with a BioProject ID of PRJNA514840 (Sequence Read Archive ID: SRR10849367 and Genome accession ID: CP085300).
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Affiliation(s)
- Chatragadda Ramesh
- National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MOES), Government of India (GOI), Dollygunj, Port Blair 744103, Andaman and Nicobar Islands, India;
- Correspondence: (C.R.); (M.A.); (L.D.)
| | - Maile Anwesh
- Model Rural Health Research Unit (ICMR-MRHRU), Dahanu 401601, Maharashtra, India
- Correspondence: (C.R.); (M.A.); (L.D.)
| | - Nambali Valsalan Vinithkumar
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MOES), Government of India (GOI), Dollygunj, Port Blair 744103, Andaman and Nicobar Islands, India;
| | - Ramalingam Kirubagaran
- Marine Biotechnology Group, National Institute of Ocean Technology, MOES, GOI, Chennai 600100, Tamil Nadu, India;
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, ESIROI Agroalimentaire, 15 Avenue René Cassin, CEDEX 9, F-97744 Saint-Denis, France
- Correspondence: (C.R.); (M.A.); (L.D.)
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8
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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9
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Bioproduction of Prodigiosin from Fishery Processing Waste Shrimp Heads and Evaluation of Its Potential Bioactivities. FISHES 2021. [DOI: 10.3390/fishes6030030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aim of this work was to reuse a fish processing waste, shrimp head powder (SHP), for the production of prodigiosin (PG) via microbial technology and to assess its potential bioactivities. PG was produced in a 12 L-bioreactor system, and the highest PG productivity of 6310 mg L−1 was achieved when Serratia marcescens CC17 was used for fermentation in a novel designed medium (6.75 L) containing 1.5% C/N source (SHP/casein = 9/1), 0.02% K2SO4, ans 0.025% Ca3(PO4)2, with initial pH 7.0, and fermentation was performed at 28 °C for 8 h. The purified PG showed moderate antioxidants, efficient anti-NO (anti-nitric oxide), and acetylcholinesterase (AChE) inhibitory activities. In a docking study, PG showed better binding energy scores (−12.3 kcal/mol) and more interactions (6 linkages) with several prominent amino acids in the biding sites on AChE that were superior to those of Berberine chloride (−10.8 kcal/mol and one linkage). Notably, this is the first investigation using shrimp heads for the mass bioproduction of PG with high productivity, and Ca3(PO4)2 salt was also newly found to significantly enhance PG production by S. marcescens. This study also provided available data on the anti-NO and anti-AChE effects of PG, especially from the docking simulation PG towards AChE that was described for the first time in this study. The above results suggest that SHP is a good material for the cost-effective bioproduction of PG, which is a potential candidate for anti-NO and anti-Alzheimer drugs.
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Sharma V, Kaur R, Salwan R. Streptomyces: host for refactoring of diverse bioactive secondary metabolites. 3 Biotech 2021; 11:340. [PMID: 34221811 DOI: 10.1007/s13205-021-02872-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Microbial secondary metabolites are intensively explored due to their demands in pharmaceutical, agricultural and food industries. Streptomyces are one of the largest sources of secondary metabolites having diverse applications. In particular, the abundance of secondary metabolites encoding biosynthetic gene clusters and presence of wobble position in Streptomyces strains make it potential candidate as a native or heterologous host for secondary metabolite production including several cryptic gene clusters expression. Here, we have discussed the developments in Streptomyces strains genome mining, its exploration as a suitable host and application of synthetic biology for refactoring genetic systems for developing chassis for enhanced as well as novel secondary metabolites with reduced genome and cleaned background.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Randhir Kaur
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Richa Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture and Forestry, Neri, Hamirpur, Himachal Pradesh 177001 India
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Nguyen TH, Wang SL, Nguyen DN, Nguyen AD, Nguyen TH, Doan MD, Ngo VA, Doan CT, Kuo YH, Nguyen VB. Bioprocessing of Marine Chitinous Wastes for the Production of Bioactive Prodigiosin. Molecules 2021; 26:molecules26113138. [PMID: 34073944 PMCID: PMC8197340 DOI: 10.3390/molecules26113138] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
Recently, microbial prodigiosin (PG) has received much attention due to its numerous beneficial applications. The aim of this study was to establish the bioprocessing of marine chitinous wastes (MCWs) for the cost-effective preparation of PG. Of the MCWs, demineralized shrimp shell powders (de-SSP) were found to be a potential source of carbon/nitrogen (C/N) for PG production by bacterial fermentation using Serratia marcescens strains. Further, PG scale-up production was investigated in a 15 L bioreactor system, and the highest yield (6200 mg/L) was achieved during fermentation using 5 L of a novel-designed culture broth that included 1.60% C/N sources (a de-SSP/casein ratio of 7/3), 0.02% K2SO4, and 0.05% K2HPO4, with an initial pH of 6–7. Fermentation was conducted in the dark at 27.5 °C for 8.0 h. This study was the first to report on the utilization of shrimp wastes for cost-effective, large-scale (5 L/pilot) PG production with high productivity (6200 mg/L) in a short cultivation time. The combination of 0.02% K2SO4 and 0.05% K2HPO4 was also found to be a novel salt composition that significantly enhanced PG yield. The red compound was purified and confirmed as PG after analyzing its HPLC profile, mass, and UV/vis spectra. The purified PG was then tested for its bioactivities and showed effective anticancer activities, moderated antioxidant activities, and novel anti-NO effects.
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Affiliation(s)
- Thi-Hanh Nguyen
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.-H.N.); (D.-N.N.); (C.-T.D.)
| | - San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
- Correspondence: (S.-L.W.); (V.-B.N.); Tel.: +886-2-2621-5656 (S.-L.W.); Fax: +886-2-2620-9924 (S.-L.W.)
| | - Dai-Nam Nguyen
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.-H.N.); (D.-N.N.); (C.-T.D.)
| | - Anh-Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (A.-D.N.); (T.-H.N.); (M.-D.D.); (V.-A.N.)
| | - Thi-Huyen Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (A.-D.N.); (T.-H.N.); (M.-D.D.); (V.-A.N.)
| | - Manh-Dung Doan
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (A.-D.N.); (T.-H.N.); (M.-D.D.); (V.-A.N.)
| | - Van-Anh Ngo
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (A.-D.N.); (T.-H.N.); (M.-D.D.); (V.-A.N.)
| | - Chien-Thang Doan
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.-H.N.); (D.-N.N.); (C.-T.D.)
| | - Yao-Haur Kuo
- Division of Chinese Materia Medica Development, National Research Institute of Chinese Medicine, Taipei 11221, Taiwan;
| | - Van-Bon Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (A.-D.N.); (T.-H.N.); (M.-D.D.); (V.-A.N.)
- Correspondence: (S.-L.W.); (V.-B.N.); Tel.: +886-2-2621-5656 (S.-L.W.); Fax: +886-2-2620-9924 (S.-L.W.)
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12
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Genetic Network Architecture and Environmental Cues Drive Spatial Organization of Phenotypic Division of Labor in Streptomyces coelicolor. mBio 2021; 12:mBio.00794-21. [PMID: 34006658 PMCID: PMC8262882 DOI: 10.1128/mbio.00794-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of bacteria are known to differentiate into cells with distinct phenotypic traits during processes such as biofilm formation or the development of reproductive structures. These cell types, by virtue of their specialized functions, embody a division of labor. However, how bacteria build spatial patterns of differentiated cells is not well understood. Here, we examine the factors that drive spatial patterns in divisions of labor in colonies of Streptomyces coelicolor, a multicellular bacterium capable of synthesizing an array of antibiotics and forming complex reproductive structures (e.g., aerial hyphae and spores). Using fluorescent reporters, we demonstrate that the pathways for antibiotic biosynthesis and aerial hypha formation are activated in distinct waves of gene expression that radiate outwards in S. coelicolor colonies. We also show that the spatiotemporal separation of these cell types depends on a key activator in the developmental pathway, AdpA. Importantly, when we manipulated local gradients by growing competing microbes nearby, or through physical disruption, expression in these pathways could be decoupled and/or disordered, respectively. Finally, the normal spatial organization of these cell types was partially restored with the addition of a siderophore, a public good made by these organisms, to the growth medium. Together, these results indicate that spatial divisions of labor in S. coelicolor colonies are determined by a combination of physiological gradients and regulatory network architecture, key factors that also drive patterns of cellular differentiation in multicellular eukaryotic organisms.
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Han R, Xiang R, Li J, Wang F, Wang C. High-level production of microbial prodigiosin: A review. J Basic Microbiol 2021; 61:506-523. [PMID: 33955034 DOI: 10.1002/jobm.202100101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/06/2021] [Accepted: 04/18/2021] [Indexed: 12/11/2022]
Abstract
Prodigiosin is a natural red pigment derived primarily from secondary metabolites of microorganisms, especially Serratia marcescens. It can also be chemically synthesized. Prodigiosin has been proven to have antitumor, antibacterial, antimalaria, anti-insect, antialgae, and immunosuppressive activities, and is gaining increasing important in the global market because of its great potential application value in clinical medicine development, environmental treatment, preparation of food additives, and so on. Due to the low efficiency of prodigiosin chemical synthesis, high-level prodigiosin of production by microorganisms are necessary for prodigiosin applications. In this paper, the production of prodigiosin by microorganism in recent decades is reviewed. The methods and strategies for increasing the yield of prodigiosin are discussed from the aspects of medium composition, additives, factors affecting production conditions, strain modification, and fermentation methods.
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Affiliation(s)
- Rui Han
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Roujin Xiang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Jinglin Li
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Fengqing Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Chuan Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
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Bikash B, Vilja S, Mitchell L, Keith Y, Mikael I, Mikko MK, Jarmo N. Differential regulation of undecylprodigiosin biosynthesis in the yeast-scavenging Streptomyces strain MBK6. FEMS Microbiol Lett 2021; 368:6244240. [PMID: 33881506 PMCID: PMC8102152 DOI: 10.1093/femsle/fnab044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Streptomyces are efficient chemists with a capacity to generate diverse and potent chemical scaffolds. The secondary metabolism of these soil-dwelling prokaryotes is stimulated upon interaction with other microbes in their complex ecosystem. We observed such an interaction when a Streptomyces isolate was cultivated in a media supplemented with dead yeast cells. Whole-genome analysis revealed that Streptomyces sp. MBK6 harbors the red cluster that is cryptic under normal environmental conditions. An interactive culture of MBK6 with dead yeast triggered the production of the red pigments metacycloprodigiosin and undecylprodigiosin. Streptomyces sp. MBK6 scavenges dead-yeast cells and preferentially grows in aggregates of sequestered yeasts within its mycelial network. We identified that the activation depends on the cluster-situated regulator, mbkZ, which may act as a cross-regulator. Cloning of this master regulator mbkZ in S. coelicolor with a constitutive promoter and promoter-deprived conditions generated different production levels of the red pigments. These surprising results were further validated by DNA–protein binding assays. The presence of the red cluster in Streptomyces sp. MBK6 provides a vivid example of horizontal gene transfer of an entire metabolic pathway followed by differential adaptation to a new environment through mutations in the receiver domain of the key regulatory protein MbkZ.
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Affiliation(s)
- Baral Bikash
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Siitonen Vilja
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Laughlin Mitchell
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Yamada Keith
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Ilomäki Mikael
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Metsä-Ketelä Mikko
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
| | - Niemi Jarmo
- Department of Biotechnology, University of Turku, FIN-20014 Turku, Finland
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15
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Couturier M, Bhalara HD, Monson RE, Salmond GPC, Leeper FJ. Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate. RSC Chem Biol 2021; 2:551-555. [PMID: 34458798 PMCID: PMC8341465 DOI: 10.1039/d0cb00173b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/05/2021] [Indexed: 01/14/2023] Open
Abstract
A biosynthetic pathway for the red-antibiotic, prodigiosin, was proposed over a decade ago but not all the suggested intermediates could be detected experimentally. Here we show that a thioester that was not originally included in the pathway is an intermediate. In addition, the enzyme PigE was originally described as a transaminase but we present evidence that it also catalyses the reduction of the thioester intermediate to its aldehyde substrate. A revision is proposed to the biosynthetic pathway to the well-known red pigment prodigiosin via a new thioester intermediate.![]()
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Affiliation(s)
- Maxime Couturier
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Hiral D Bhalara
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Rita E Monson
- Dept. of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1QW UK
| | - George P C Salmond
- Dept. of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1QW UK
| | - Finian J Leeper
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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16
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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17
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Ferreira LC, Maul JE, Viana MVC, de Sousa TJ, de Carvalho Azevedo VA, Roberts DP, de Souza JT. Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact. Braz J Microbiol 2020; 52:245-250. [PMID: 32965626 DOI: 10.1007/s42770-020-00382-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022] Open
Abstract
Serratia marcescens are gram-negative bacteria found in several environmental niches, including the plant rhizosphere and patients in hospitals. Here, we present the genome of Serratia marcescens strain N4-5 (=NRRL B-65519), which has a size of 5,074,473 bp (664-fold coverage) and contains 4840 protein coding genes, 21 RNA genes, and an average G + C content of 59.7%. N4-5 harbours a plasmid of 11,089 bp and 43.5% G + C content that encodes six unique CDS repeated 2.5× times totalling 13 CDS. Our genome assembly and manual curation uncovered the insertion of two extra copies of the 5S rRNA gene in the assembled sequence, which was confirmed by PCR and Sanger sequencing to be a misassembly. This artefact was subsequently removed from the final assembly. The occurrence of extra copies of the 5S rRNA gene was also observed in most complete genomes of Serratia spp. deposited in public databases in our comparative analysis. These elements, which also occur naturally, can easily be confused with true genetic variation. Efforts to discover and correct assembly artefacts should be made in order to generate genome sequences that represent the biological truth underlying the studied organism. We present the genome of N4-5 and discuss genes potentially involved in biological control activity against plant pathogens and also the possible mechanisms responsible for the artefact we observed in our initial assembly. This report raises awareness about the extra copies of the 5S rRNA gene in sequenced bacterial genomes as they may represent misassemblies and therefore should be verified experimentally.
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Affiliation(s)
- Larissa Carvalho Ferreira
- Plant Pathology Department, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
| | | | - Thiago Jesus de Sousa
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Jorge Teodoro de Souza
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK.
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18
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Zhao Y, Tian J, Zheng G, Chen J, Sun C, Yang Z, Zimin AA, Jiang W, Deng Z, Wang Z, Lu Y. Multiplex genome editing using a dCas9-cytidine deaminase fusion in Streptomyces. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1053-1062. [PMID: 31872379 DOI: 10.1007/s11427-019-1559-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/27/2019] [Indexed: 01/19/2023]
Abstract
CRISPR/Cas-mediated genome editing has greatly facilitated the study of gene function in Streptomyces. However, it could not be efficiently employed in streptomycetes with low homologous recombination (HR) ability. Here, a deaminase-assisted base editor dCas9-CDA-ULstr was developed in Streptomyces, which comprises the nuclease-deficient Cas9 (dCas9), the cytidine deaminase from Petromyzon marinus (PmCDA1), the uracil DNA glycosylase inhibitor (UGI) and the protein degradation tag (LVA tag). Using dCas9-CDA-ULstr, we achieved single-, double- and triple-point mutations (cytosine-to-thymine substitutions) at target sites in Streptomyces coelicolor with efficiency up to 100%, 60% and 20%, respectively. This base editor was also demonstrated to be highly efficient for base editing in the industrial strain, Streptomyces rapamycinicus, which produces the immunosuppressive agent rapamycin. Compared with base editors derived from the cytidine deaminase rAPOBEC1, the PmCDA1-assisted base editor dCas9-CDA-ULstr could edit cytosines preceded by guanosines with high efficiency, which is a great advantage for editing Streptomyces genomes (with high GC content). Collectively, the base editor dCas9-CDA-ULstr could be employed for efficient multiplex genome editing in Streptomyces. Since the dCas9-CDA-ULstr-based genome editing is independent of HR-mediated DNA repair, we believe this technology will greatly facilitate functional genome research and metabolic engineering in Streptomyces strains with weak HR ability.
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Affiliation(s)
- Yawei Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinzhong Tian
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guosong Zheng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun Chen
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chuanwen Sun
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhongyi Yang
- School of Life Science, Taizhou University, Taizhou, 318000, China
| | - Andrei A Zimin
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China. .,Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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19
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Microbial Reclamation of Chitin and Protein-Containing Marine By-Products for the Production of Prodigiosin and the Evaluation of Its Bioactivities. Polymers (Basel) 2020; 12:polym12061328. [PMID: 32532124 PMCID: PMC7361997 DOI: 10.3390/polym12061328] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
Chitin and protein-containing marine by-products (CPCMBPs), including crab shells, squid pens, and shrimp shells, were investigated as the sole carbon/nitrogen (C/N) source for prodigiosin (PG) production by Serratia marcescens TNU01 in a 250 mL Erlenmeyer flask and a 10 L bioreactor system. Among the used C/N source of CPCMBPs, squid pens powder (SPP) showed the most optimum PG productivity. Different ratios of chitin/protein combination were also used as the C/N sources for PG production. With a similar chitin/protein ratio (4/6) of squid pens, a significant PG productivity was achieved when the chitin/protein ratios were controlled in the range of 3/7-4/6. Maximum PG yield (3450 mg/L) by S. marcescens TNU01 was achieved in the bioreactor system containing 3 L medium of 1.75% SPP, 0.03% K2HPO4, and 0.05% MgSO4 at 25 °C for 12 h in dark. The results of in vitro bioassays reveal that the purified PG possesses acetylcholinesterase inhibitory activity and antioxidant as well as anticancer activities. This study suggests that squid pens may have the potential to be used for cost effective production of bioactive PG at a large-scale.
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20
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Lapenda JCL, Alves VP, Adam ML, Rodrigues MD, Nascimento SC. Cytotoxic Effect of Prodigiosin, Natural Red Pigment, Isolated from Serratia marcescens UFPEDA 398. Indian J Microbiol 2020; 60:182-195. [PMID: 32255851 PMCID: PMC7105545 DOI: 10.1007/s12088-020-00859-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/14/2020] [Indexed: 11/30/2022] Open
Abstract
Prodigiosin is a secondary metabolite, with red pigmentation, produced by Serratia marcescens. Red pigment is a natural alkaloid whose chemical structure has three pyrrole rings. Prodigiosin has been described for several biological activities, including antitumor, inducing apotosis in T and B lymphocytes. This work aimed to evaluate the cytotoxic activity of prodigiosin in NCHI-292, HEp-2, MCF-7 and HL-60 tumor cell lines. The red pigment was isolated from Serratia marcescens UFPEDA 398 biomass whose fractions were previously separated by column chromatography, purified, identified and further characterized by GC-MS and compared with the computerized library of m/z values. The pigment corresponded to prodigiosin with maximum absorption at 534 nm, molecular weight 323 and structural formula C20H25N3O. During the prodigiosin purification process a purple absorbance fraction at 272.65 nm was also observed. Significant cytotoxic effects of prodigiosin were evidenced for NCHI-292, Hep-2, MCF-7 and HL-60 tumor cell lines. The isolated purple fraction had no cytotoxic effect (IC50 11.3 µg/mL) when compared to prodigiosin (IC50 3.4 µg/mL) for the tumor cell lines studied. The MCF-7 strain was slightly more pigment resistant (IC50 5.1 µg/mL). Therefore, further studies will be needed to elucidate the antitumor mechanisms of prodigiosin action against tumor strains from flow cytometry tests. However, although these data are preliminary, it was evidenced that prodigiosin showed cytotoxic activity in tumor cell lines suggesting promising antitumor properties. In this sense, future studies on the cytotoxic and genotoxic effects of prodigiosin produced by S. marcecsens UFPEDA 398 are suggested.
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Affiliation(s)
- J. C. L. Lapenda
- Department of Antibiotics, Federal University of Pernambuco, Recife, PE Brazil
| | - V. P. Alves
- Immunology Laboratory, Aggeu Magalhães Research Center, Recife, PE Brazil
| | - M. L. Adam
- Department of Biological Sciences, Federal University of Pernambuco, Academic Center of Vitória, Recife, PE Brazil
| | - M. D. Rodrigues
- Department of Antibiotics, Federal University of Pernambuco, Recife, PE Brazil
| | - S. C. Nascimento
- Department of Antibiotics, Federal University of Pernambuco, Recife, PE Brazil
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21
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Molecular dynamics of the membrane interaction and localisation of prodigiosin. J Mol Graph Model 2020; 98:107614. [PMID: 32289740 DOI: 10.1016/j.jmgm.2020.107614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 01/24/2023]
Abstract
The tripyrrolic antibiotic prodigiosin causes diverse reactions on its targets like energy spilling, membrane leakage, loss of motility and phototoxicity. It has bacteriostatic, bactericidal, anti-fungal, anti-cancer and immunosuppressive properties. Most of the functions suggest the role of prodigiosin in membrane disruption but the exact mechanism remains unknown. A molecular dynamics study was performed to understand the interactions of prodigiosin with the membrane. It was seen that prodigiosin from the solvent enters the membrane immediately either individually or as small clusters. Prodigiosin clusters with more than eight molecules do not appear to enter the membrane. Upon entry, the molecules orient themselves along the membrane-water interface with the pyrrole rings interacting with lipid head groups and with water. This orientation is stabilised by hydrogen bonding and hydrophobic interactions. The presence of prodigiosin molecules in the membrane changes the local lipid architecture and reduces the solvent accessibility of the membrane. The membrane fluidity, thickness or area per lipid head are largely unaffected. This suggests that prodigiosin could cause most damage in the vicinity of a membrane protein and thus could also explain the reason for varied effects on the targets.
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22
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Picott KJ, Deichert JA, deKemp EM, Snieckus V, Ross AC. Purification and Kinetic Characterization of the Essential Condensation Enzymes Involved in Prodiginine and Tambjamine Biosynthesis. Chembiochem 2020; 21:1036-1042. [DOI: 10.1002/cbic.201900503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/11/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Katherine J. Picott
- Department of ChemistryQueen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Julie A. Deichert
- Department of ChemistryQueen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Ella M. deKemp
- Department of ChemistryQueen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Victor Snieckus
- Department of ChemistryQueen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Avena C. Ross
- Department of ChemistryQueen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
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23
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Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep 2020; 37:355-379. [PMID: 31593192 PMCID: PMC7101270 DOI: 10.1039/c9np00047j] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 1990 to 2019 Many medicinally-relevant compounds are derived from non-ribosomal peptide synthetase (NRPS) products. Type I NRPSs are organized into large modular complexes, while type II NRPS systems contain standalone or minimal domains that often encompass specialized tailoring enzymes that produce bioactive metabolites. Protein-protein interactions and communication between the type II biosynthetic machinery and various downstream pathways are critical for efficient metabolite production. Importantly, the architecture of type II NRPS proteins makes them ideal targets for combinatorial biosynthesis and metabolic engineering. Future investigations exploring the molecular basis or protein-protein recognition in type II NRPS pathways will guide these engineering efforts. In this review, we consolidate the broad range of NRPS systems containing type II proteins and focus on structural investigations, enzymatic mechanisms, and protein-protein interactions important to unraveling pathways that produce unique metabolites, including dehydrogenated prolines, substituted benzoic acids, substituted amino acids, and cyclopropanes.
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Affiliation(s)
- Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
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24
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Couturier M, Bhalara HD, Chawrai SR, Monson R, Williamson NR, Salmond GPC, Leeper FJ. Substrate Flexibility of the Flavin-Dependent Dihydropyrrole Oxidases PigB and HapB Involved in Antibiotic Prodigiosin Biosynthesis. Chembiochem 2020; 21:523-530. [PMID: 31433555 PMCID: PMC7065143 DOI: 10.1002/cbic.201900424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Indexed: 11/28/2022]
Abstract
In the biosynthesis of the tripyrrolic pigment prodigiosin, PigB is a predicted flavin-dependent oxidase responsible for the formation of 2-methyl-3-amylpyrrole (MAP) from a dihydropyrrole. To prove which dihydropyrrole is the true intermediate, both possibilities, 5-methyl-4-pentyl-3,4-dihydro-2H-pyrrole (5 a, resulting from transamination of the aldehyde of 3-acetyloctanal) and 2-methyl-3-pentyl-3,4-dihydro-2H-pyrrole (6, resulting from transamination of the ketone), were synthesised. Only 5 a restored pigment production in a strain of Serratia sp. ATCC 39006 blocked earlier in MAP biosynthesis. PigB is membrane-associated and inactive when its transmembrane domain was deleted, but HapB, its homologue in Hahella chejuensis, lacks the transmembrane domain and is active in solution. Two colourimetric assays for PigB and HapB were developed, and the HapB-catalysed reaction was kinetically characterised. Ten analogues of 5 a were synthesised, varying in the C2 and C3 side chains, and tested as substrates of HapB in vitro and for restoration of pigment production in Serratia ΔpigD in vivo. All lengths of side chain tested at C3 were accepted, but only short side chains at C2 were accepted. The knowledge that 5 a is an intermediate in prodigiosin biosynthesis and the ease of synthesis of analogues of 5 a makes a range of prodigiosin analogues readily available by mutasynthesis.
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Affiliation(s)
- Maxime Couturier
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Hiral D. Bhalara
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Suresh R. Chawrai
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Rita Monson
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1QWUK
| | - Neil R. Williamson
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1QWUK
| | - George P. C. Salmond
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCambridgeCB2 1QWUK
| | - Finian J. Leeper
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
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25
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RedH and PigC Catalyze the Biosynthesis of Hybrubins via Phosphorylation of 4'-Methoxy-2,2'-Bipyrrole-5'-Carbaldehyde. Appl Environ Microbiol 2020; 86:AEM.02331-19. [PMID: 31704680 DOI: 10.1128/aem.02331-19] [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: 10/10/2019] [Accepted: 11/05/2019] [Indexed: 11/20/2022] Open
Abstract
Hybrubins are "unnatural" alkaloids with the same 4'-methoxy-2,2'-bipyrrole-5'-methine moiety found in prodiginines and a different ring derived from tetramic acids. Here, we demonstrated that RedH, a homologue of prodigiosin synthetase PigC, was responsible for the biosynthesis of hybrubins A and B in Streptomyces lividans In vitro reactions indicated that RedH and PigC catalyzed the intermolecular condensation between 4'-methoxy-2,2'-bipyrrole-5'-carbaldehyde (MBC) and (Z)-5-ethylidenetetramic acid (ETA) to produce hybrubin B. Moreover, we demonstrated that RedH and PigC activated MBC via phosphorylation of the aldehyde group to form an intermediate Pi-MBC and that the subsequent condensation between Pi-MBC and (Z)-5-ethylidenetetramic acid occurs in a nonenzymatic way.IMPORTANCE Hybrubins are an emerging class of prodiginines possessing a new C ring derived from 5'-substituted tetramic acids and the methylene bridge connecting the C ring at a different position. We have supposed that condensation between 4'-methoxy-2,2'-bipyrrole-5'-carbaldehyde (MBC) and 5-ethylidenetetramic acid (ETA) yields the hybrid natural products hybrubins, which was proposed to be catalyzed by the undecylprodigiosin synthetase RedH. However, it is doubted whether RedH is able to catalyze another type of condensation between MBC and tetramic acids. In this study, we have demonstrated that the MBC-ETA condensation proceeds through RedH/PigC-catalyzed enzymatic activation of MBC via phosphorylation and a nonenzymatic condensation of Pi-MBC with ETA. Since MBC analogues have been shown to be accepted by PigC, more hybrubin analogues might be produced by using combinations of MBC analogues and other tetramic acids in future studies.
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26
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Novel Efficient Bioprocessing of Marine Chitins into Active Anticancer Prodigiosin. Mar Drugs 2019; 18:md18010015. [PMID: 31878048 PMCID: PMC7024390 DOI: 10.3390/md18010015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Marine chitins (MC) have been utilized for the production of vast array of bioactive products, including chitooligomers, chitinase, chitosanase, antioxidants, anti-NO, and antidiabetic compounds. The aim of this study is the bioprocessing of MC into a potent anticancer compound, prodigiosin (PG), via microbial fermentation. This bioactive compound was produced by Serratia marcescens TKU011 with the highest yield of 4.62 mg/mL at the optimal conditions of liquid medium with initial pH of 5.65-6.15 containing 1% α-chitin, 0.6% casein, 0.05% K2HPO4, and 0.1% CaSO4. Fermentation was kept at 25 °C for 2 d. Notably, α-chitin was newly investigated as the major potential material for PG production via fermentation; the salt CaSO4 was also found to play the key role in the enhancement of PG yield of Serratia marcescens fermentation for the first time. PG was qualified and identified based on specific UV, MALDI-TOF MS analysis. In the biological activity tests, purified PG demonstrated potent anticancer activities against A549, Hep G2, MCF-7, and WiDr with the IC50 values of 0.06, 0.04, 0.04, and 0.2 µg/mL, respectively. Mytomycin C, a commercial anti-cancer compound was also tested for comparison purpose, showing weaker activity with the IC50 values of 0.11, 0.1, 0.14, and 0.15 µg/mL, respectively. As such, purified PG displayed higher 2.75-fold, 1.67-fold, and 3.25-fold efficacy than Mytomycin C against MCF-7, A549, and Hep G2, respectively. The results suggest that marine chitins are valuable sources for production of prodigiosin, a potential candidate for cancer drugs.
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Nappi J, Soldi E, Egan S. Diversity and Distribution of Bacteria Producing Known Secondary Metabolites. MICROBIAL ECOLOGY 2019; 78:885-894. [PMID: 31016338 DOI: 10.1007/s00248-019-01380-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.
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Affiliation(s)
- Jadranka Nappi
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Erika Soldi
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia.
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Liu X, Tang J, Wang L, Giesy JP. Al 2O 3 nanoparticles promote secretion of antibiotics in Streptomyces coelicolor by regulating gene expression through the nano effect. CHEMOSPHERE 2019; 226:687-695. [PMID: 30959453 DOI: 10.1016/j.chemosphere.2019.03.156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Toxic effects of nanoparticles (NPs) on microorganisms have attracted substantial attention; however, there are few reports on whether NPs can affect the secondary metabolism of microbes. To investigate the toxic effects of Al2O3 NPs on cell growth and antibiotic secretion, Streptomyces coelicolor M145 was exposed to Al2O3 NPs with diameters of 30 and 80 nm and bulk Al2O3 at concentrations up to 1000 mg/L. The results indicated that differences in the toxicity of Al2O3 NPs were related to the particle size. In treatment with Al2O3 NPs, the maximum yields of undecylprodigiosin (RED) and actinorhodin (ACT) were 3.7- and 4.6-fold greater than that of the control, respectively, and the initial time of antibiotic production was much shorter. ROS quenching experiment by N-acetylcysteine (NAC) confirmed that ROS were responsible for the increased RED production. From 0 to 72 h, ROS had a significant impact on ACT production; however, after 72 h, the ROS content began to decrease until it disappeared. During ongoing exposure (0-144 h), ACT production continued to increase, indicating that in addition to ROS, nano effect of Al2O3 NPs also played roles in this process. Transcriptional analysis demonstrated that Al2O3 NPs could increase the expression levels of antibiotic biosynthetic genes and two-component systems (TCSs) and inhibit the expression levels of primary metabolic pathways. This study provides a new perspective for understanding the mechanisms of antibiotic production in nature and reveals important implications for exploring other uses of NPs in biomedical applications or regulation of antibiotics in nature.
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Affiliation(s)
- Xiaomei Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
| | - Lan Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Sinha A, Phillips-Salemka S, Niraula TA, Short KA, Niraula NP. The complete genomic sequence of Streptomyces spectabilis NRRL-2792 and identification of secondary metabolite biosynthetic gene clusters. J Ind Microbiol Biotechnol 2019; 46:1217-1223. [PMID: 31197515 DOI: 10.1007/s10295-019-02172-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/03/2019] [Indexed: 10/26/2022]
Abstract
This is the first report of a fully annotated genomic sequence of Streptomyces spectabilis NRRL-2792, isolated and identified by The Upjohn Company in 1961. The genome was assembled into a single scaffold for annotation and analysis. The chromosome is linear, 9.5 Mb in size which is one of the largest Streptomyces genomes yet described, has a G+C content of 72%, and encodes for approximately 7943 genes. Antibiotic Secondary Metabolite Analysis Shell (antiSMASH) and Basic Local Alignment Search Tool (BLAST) bioinformatics analyses identified six complete secondary metabolite biosynthetic gene clusters for ectoine, melanin, albaflavenone, spectinomycin, 2-methylisoborneol and coelichelin. Additionally, biosynthetic clusters were identified that shared ≥ 90% gene content with complestatin, hopene, neoaureothin, or undecylprodigiosin. Thirty-one other likely secondary metabolite gene clusters were identified by antiSMASH. BLAST identified two subsets of undecylprodigiosin biosynthetic genes at polar opposites of the chromosome; their duplication was subsequently confirmed by primer walking.
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Affiliation(s)
- Arkadeep Sinha
- Bioprocess Development Group, Pfizer, 7000 Portage Rd, Kalamazoo, 49001, USA
| | | | | | - Kevin A Short
- Bioprocess Development Group, Pfizer, 7000 Portage Rd, Kalamazoo, 49001, USA
| | - Narayan P Niraula
- Bioprocess Development Group, Pfizer, 7000 Portage Rd, Kalamazoo, 49001, USA.
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Ravindran A, Sunderrajan S, Pennathur G. Phylogenetic Studies on the Prodigiosin Biosynthetic Operon. Curr Microbiol 2019; 76:597-606. [DOI: 10.1007/s00284-019-01665-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/01/2019] [Indexed: 11/30/2022]
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Lim Y, Jung ES, Lee JH, Kim EJ, Hong SJ, Lee YH, Lee CH. Non-targeted metabolomics unravels a media-dependent prodiginines production pathway in Streptomyces coelicolor A3(2). PLoS One 2018; 13:e0207541. [PMID: 30485320 PMCID: PMC6261592 DOI: 10.1371/journal.pone.0207541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
The genus Streptomyces is the best-known source of therapeutic secondary metabolites, especially antibiotics with pharmaceutical applications. Here, we performed a comparative study based on the time-resolved metabolic disparity in S. coelicolor A3(2) subjected to fermentative cultivation in two different types of media (R2YE and RSM3) in order to investigate secondary metabolite production pathways. The relative abundance of secondary metabolites, such as prodiginines, indoles, germicidins, and selected diketopiperazines, was increased in S. coelicolor A3(2) cultivated in R2YE medium compared to that in RSM3 medium, variably at the late-log and stationary phases of fermentative growth. Correlation analysis indicated that “antibiotic prodiginines” contributed maximally to the absorption maxima (A530) of culture supernatants, indicating their optimal production at 96 hours in R2YE medium. A higher abundance of L-proline (48–72 hours) followed by prodiginines (96 hours) was evident, substantiating the intertwined links between precursor and activated prodiginines pathway. Similarly, the higher abundance of indoles was concurrent with tryptophan levels in the shikimate pathway, whereas diketopiperazines were synchronously abundant along with the levels of phenylalanine, leucine, and proline. Additionally, acetyl-CoA induced the acetate pathway, resulting in the production of germicidins. Thus, our results demonstrate that S. coelicolor A3(2) produces specific secondary metabolites by enhancing the dedicated metabolic pathway responsible for their production. In conclusion, our results from this study provide insight into the metabolic pathways of S. coelicolor A3(2), and can be applied to further optimize the production of prodiginines.
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Affiliation(s)
- Yonghwan Lim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Eun Sung Jung
- Department of Systems Biotechnology, Konkuk University, Seoul, Korea
| | | | | | | | | | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
- Department of Systems Biotechnology, Konkuk University, Seoul, Korea
- * E-mail:
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Su L, Zhang R, Kyeremeh K, Deng Z, Deng H, Yu Y. Dissection of the neocarazostatin: a C 4 alkyl side chain biosynthesis by in vitro reconstitution. Org Biomol Chem 2018; 15:3843-3848. [PMID: 28406521 DOI: 10.1039/c7ob00617a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neocarazostatin A (1) is a potent free radical scavenger possessing an intriguing tricyclic carbazole nucleus with a C4 alkyl side chain attached to ring "A". Although the biosynthetic gene cluster of 1 (nzs) has been identified, and several key steps of the pathway have been well characterized, the enzyme(s) involved in the biosynthesis of the C4 unit still remains obscure. In this work, we demonstrate that three enzymes, including one (MA37-FabG) from primary fatty acid metabolism and two pathway-specific ones (NzsE and NzsF), are responsible for the formation of the side chain precursor. We show that NzsE is a free-standing acyl carrier protein (ACP), and NzsF, which is a homolog of β-ketoacyl-acyl carrier protein synthase III (KAS III, also called FabH), catalyzes a decarboxylative condensation between an acetyl-CoA and the NzsE bound malonyl thioester to generate acetoacetyl-NzsE. We also show that NzsF can only accept NzsE as its cognate ACP substrate, suggesting that NzsE and NzsF constitute pathway-specific KAS III enzyme pairs for the assembly line of 1. Furthermore, we have identified two FabG (the NADPH-dependent reductase) homologs from the fatty acid biosynthesis pathway that can reduce the 3-keto group of acetoacetyl-NzsE to generate a 3-hydroxybutyl-NzsE product, which is the putative intermediate for the following incorporation into 1. Therefore, our work successfully reconstitutes the biosynthetic pathway of the C4 alkyl side chain of 1in vitro, and sheds light on the potential of engineering NzsE/F for producing novel neocarazostatin analogues in the host strain.
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Affiliation(s)
- Li Su
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China.
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Zou X, Wang L, Li Z, Luo J, Wang Y, Deng Z, Du S, Chen S. Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics. Med Res Rev 2017; 38:229-260. [PMID: 28295439 DOI: 10.1002/med.21439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/06/2017] [Accepted: 01/14/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Xuan Zou
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Lianrong Wang
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Zhiqiang Li
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Jie Luo
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Yunfu Wang
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Zixin Deng
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Shiming Du
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Shi Chen
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
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Xu Z, Wang Y, Chater KF, Ou HY, Xu HH, Deng Z, Tao M. Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis. Appl Environ Microbiol 2017; 83:AEM.02889-16. [PMID: 28062460 PMCID: PMC5335527 DOI: 10.1128/aem.02889-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/28/2016] [Indexed: 01/16/2023] Open
Abstract
Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites, including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a hyperactive transposase-based Tn5 transposition system and employed it to mutagenize the model species Streptomyces coelicolor, leading to the identification of 51,443 transposition insertions. These insertions were distributed randomly along the chromosome except for some preferred regions associated with relatively low GC content in the chromosomal core. The base composition of the insertion site and its flanking sequences compiled from the 51,443 insertions implied a 19-bp expanded target site surrounding the insertion site, with a slight nucleic acid base preference in some positions, suggesting a relative randomness of Tn5 transposition targeting in the high-GC Streptomyces genome. From the mutagenesis library, 724 mutants involving 365 genes had altered levels of production of the tripyrrole antibiotic undecylprodigiosin (RED), including 17 genes in the RED biosynthetic gene cluster. Genetic complementation revealed that most of the insertions (more than two-thirds) were responsible for the changed antibiotic production. Genes associated with branched-chain amino acid biosynthesis, DNA metabolism, and protein modification affected RED production, and genes involved in signaling, stress, and transcriptional regulation were overrepresented. Some insertions caused dramatic changes in RED production, identifying future targets for strain improvement.IMPORTANCE High-GC Gram-positive streptomycetes and related actinomycetes have provided more than 100 clinical drugs used as antibiotics, immunosuppressants, and antitumor drugs. Their genomes harbor biosynthetic genes for many more unknown compounds with potential as future drugs. Here we developed a useful genome-wide mutagenesis tool based on the transposon Tn5 for the study of secondary metabolism and its regulation. Using Streptomyces coelicolor as a model strain, we found that chromosomal insertion was relatively random, except at some hot spots, though there was evidence of a slightly preferred 19-bp target site. We then used prodiginine production as a model to systematically survey genes affecting antibiotic biosynthesis, providing a global view of antibiotic regulation. The analysis revealed 348 genes that modulate antibiotic production, among which more than half act to reduce production. These might be valuable targets in future investigations of regulatory mechanisms, for strain improvement, and for the activation of silent biosynthetic gene clusters.
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Affiliation(s)
- Zhong Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - H Howard Xu
- Department of Biological Sciences, California State University, Los Angeles, California, USA
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Crystal structure of MBP-PigG fusion protein and the essential function of PigG in the prodigiosin biosynthetic pathway in Serratia marcescens FS14. Int J Biol Macromol 2017; 99:394-400. [PMID: 28258005 DOI: 10.1016/j.ijbiomac.2017.02.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 11/23/2022]
Abstract
Prodigiosin, a tripyrrole red pigment is synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway; MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. PigI, PigG and PigA have been shown to be involved in the first steps of MBC biosynthesis (proline incorporation). The crystal structure of PigG was resolved to elucidate its function and mechanism. PigG, an acyl carrier protein (ACP), features the ACP architecture:, a helical bundle fold containing three major helices and a minor distorted helix together with a conserved "S" motif. An in-frame deletion mutation of the pigG gene abolished the synthesis of prodigiosin in Serratia marcescens FS14. The production of prodigiosin was fully restored by complementation of intact pigG; however the S36A mutant was not able to restore function in the in-frame deletion pigG mutant, indicating that PigG and the conserved serine residue (S36) of PigG are essential for the synthesis of prodigiosin.
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Dozie-Nwachukwu S, Danyuo Y, Obayemi J, Odusanya O, Malatesta K, Soboyejo W. Extraction and encapsulation of prodigiosin in chitosan microspheres for targeted drug delivery. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 71:268-278. [DOI: 10.1016/j.msec.2016.09.078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/06/2016] [Accepted: 09/29/2016] [Indexed: 10/20/2022]
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Hu DX, Withall DM, Challis GL, Thomson RJ. Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products. Chem Rev 2016; 116:7818-53. [PMID: 27314508 PMCID: PMC5555159 DOI: 10.1021/acs.chemrev.6b00024] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The prodiginine family of bacterial alkaloids is a diverse set of heterocyclic natural products that have likely been known to man since antiquity. In more recent times, these alkaloids have been discovered to span a wide range of chemical structures that possess a number of interesting biological activities. This review provides a comprehensive overview of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, research toward chemical synthesis of the prodiginine alkaloids over the last several decades is extensively reviewed. Finally, the current, evidence-based understanding of the various biosynthetic pathways employed by bacteria to produce prodiginine alkaloids is summarized.
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Affiliation(s)
- Dennis X. Hu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - David M. Withall
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Fernández-García L, Blanco M, Blanco C, Álvarez P, Granda M, Santamaría R, Menéndez R. Graphene anchored palladium complex as efficient and recyclable catalyst in the Heck cross-coupling reaction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcata.2016.02.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1-43. [PMID: 26609051 PMCID: PMC4711186 DOI: 10.1128/mmbr.00019-15] [Citation(s) in RCA: 908] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
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Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
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Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
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Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
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41
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Tian H, Yang H, Zhu C, Fu H. Transition metal-free intramolecular regioselective couplings of aliphatic and aromatic C-H bonds. Sci Rep 2016; 6:19931. [PMID: 26822836 PMCID: PMC4731807 DOI: 10.1038/srep19931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/21/2015] [Indexed: 11/09/2022] Open
Abstract
Cross-dehydrogenative couplings of two different C-H bonds have emerged as an attractive goal in organic synthesis. However, achieving regioselective C-H activation is a great challenge because C-H bonds are ubiquitous in organic compounds. Actually, the regioselective couplings promoted by enzymes are a common occurrence in nature. Herein, we have developed simple, efficient and general transition metal-free intramolecular couplings of alphatic and aromatic C-H bonds. The protocol uses readily available aryl triazene as the radical initiator, cheap K2S2O8 as the oxidant, and the couplings were performed well with excellent tolerance of functional groups. Interestingly, α-carbon configuration of some amino acid residues in the substrates was kept after the reactions, and the couplings for substrates with substituted phenylalanine residues exhibited complete β-carbon diastereoselectivity for induction of the chiral α-carbon. Therefore, the present study should provide a novel strategy for regioselective cross-dehydrogenative couplings of two different C-H bonds.
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Affiliation(s)
- Hua Tian
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.,Department of Applied Chemistry, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Haijun Yang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Changjin Zhu
- Department of Applied Chemistry, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Hua Fu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.,Department of Applied Chemistry, Beijing Institute of Technology, Beijing 100081, P. R. China
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Singh R, Reynolds KA. Identification and Characterization of FabA from the Type II Fatty Acid Synthase of Streptomyces coelicolor. JOURNAL OF NATURAL PRODUCTS 2016; 79:240-243. [PMID: 26731437 DOI: 10.1021/acs.jnatprod.5b00560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
FabA is proposed to catalyze the dehydration step of chain elongation in fatty acid and undecylprodiginine biosynthesis in Streptomyces coelicolor. Analysis of the S. coelicolor genome has revealed a fabA gene (SCO4636-SCO4637, encoding a heterodimer 3-hydroxyacyl-ACP dehydratase). Herein, we report the identification and characterization of the corresponding gene products. Kinetic analysis has demonstrated that FabA is capable of utilizing various chain lengths of straight- and branched-chain 3-hydroxyacyl-NAC substrates. Additionally, FabA does not discriminate between acyl carrier proteins (ACPs) from primary and secondary metabolism. These data provide the first experimental evidence that FabA has 3-hydroxyacyl-ACP dehydratase activity and processes intermediates for both biosynthetic pathways.
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Affiliation(s)
- Renu Singh
- Department of Chemistry, Portland State University , Portland, Oregon 97201, United States
| | - Kevin A Reynolds
- Department of Chemistry, Portland State University , Portland, Oregon 97201, United States
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Zhao Z, Shi T, Xu M, Brock NL, Zhao YL, Wang Y, Deng Z, Pang X, Tao M. Hybrubins: Bipyrrole Tetramic Acids Obtained by Crosstalk between a Truncated Undecylprodigiosin Pathway and Heterologous Tetramic Acid Biosynthetic Genes. Org Lett 2016; 18:572-5. [DOI: 10.1021/acs.orglett.5b03609] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zhilong Zhao
- State
Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Min Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Nelson L. Brock
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiuhua Pang
- State
Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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Wu C, Zhu H, van Wezel GP, Choi YH. Metabolomics-guided analysis of isocoumarin production by Streptomyces species MBT76 and biotransformation of flavonoids and phenylpropanoids. Metabolomics 2016; 12:90. [PMID: 27073352 PMCID: PMC4819732 DOI: 10.1007/s11306-016-1025-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/18/2016] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Actinomycetes produce the majority of the antibiotics currently in clinical use. The efficiency of antibiotic production is affected by multiple factors such as nutrients, pH, temperature and growth phase. Finding the optimal harvesting time is crucial for successful isolation of the desired bioactive metabolites from actinomycetes, but for this conventional chemical analysis has limitations due to the metabolic complexity. OBJECTIVES This study explores the utility of NMR-based metabolomics for (1) optimizing fermentation time for the production of known and/or unknown bioactive compounds produced by actinomycetes; (2) elucidating the biosynthetic pathway for microbial natural products; and (3) facilitating the biotransformation of nature-abundant chemicals. METHOD The aqueous culture broth of actinomycete Streptomyces sp. MBT76 was harvested every 24 h for 5 days and each broth was extracted by ethyl acetate. The extracts were analyzed by 1H NMR spectroscopy and the data were compared with principal component analysis (PCA) and orthogonal projection to latent structures (OPLS) analysis. Antimicrobial test were performed by agar diffusion assay. RESULTS The secondary metabolites production by Streptomyces sp. MBT76 was growth phase-dependent. Isocoumarins (1-9), undecylprodiginine (10), streptorubin B (11), 1H-pyrrole-2-carboxamide (12), acetyltryptamine (13), and fervenulin (14) were identified, and their optimal production time was determined in crude extracts without tedious chromatographic fractionation. Of these compounds, 5,6,7,8-tetramethoxyl-3-methyl-isocoumarin (9) is as a novel compound, which was most likely synthesized by a type I iterative polyketide synthase (PKS) encoded by the icm gene cluster. Multivariate data analysis of the 1H NMR spectra showed that acetyltryptamine (13) and tri-methoxylated isocoumarins (7 and 8) were the major determinants of antibiotic activity during later time points. The methoxylation was exploited to allow bioconversion of exogenously added genistein into a suite of methoxylated isoflavones (15-18). Methoxylation increased the antimicrobial efficacy of isocoumarins, but decreased that of the isoflavones. CONCLUSION Our results show the applicability of NMR-based metabolic profiling to streamline microbial biotransformation and to determine the optimal harvesting time of actinomycetes for antibiotic production.
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Affiliation(s)
- Changsheng Wu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
| | - Hua Zhu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
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Li X, Wang J, Li S, Ji J, Wang W, Yang K. ScbR- and ScbR2-mediated signal transduction networks coordinate complex physiological responses in Streptomyces coelicolor. Sci Rep 2015; 5:14831. [PMID: 26442964 PMCID: PMC4595836 DOI: 10.1038/srep14831] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/07/2015] [Indexed: 12/21/2022] Open
Abstract
In model organism Streptomyces coelicolor, γ-butyrolactones (GBLs) and antibiotics were recognized as signalling molecules playing fundamental roles in intra- and interspecies communications. To dissect the GBL and antibiotic signalling networks systematically, the in vivo targets of their respective receptors ScbR and ScbR2 were identified on a genome scale by ChIP-seq. These identified targets encompass many that are known to play important roles in diverse cellular processes (e.g. gap1, pyk2, afsK, nagE2, cdaR, cprA, cprB, absA1, actII-orf4, redZ, atrA, rpsL and sigR), and they formed regulatory cascades, sub-networks and feedforward loops to elaborately control key metabolite processes, including primary and secondary metabolism, morphological differentiation and stress response. Moreover, interplay among ScbR, ScbR2 and other regulators revealed intricate cross talks between signalling pathways triggered by GBLs, antibiotics, nutrient availability and stress. Our work provides a global view on the specific responses that could be triggered by GBL and antibiotic signals in S. coelicolor, among which the main echo was the change of production profile of endogenous antibiotics and antibiotic signals manifested a role to enhance bacterial stress tolerance as well, shedding new light on GBL and antibiotic signalling networks widespread among streptomycetes.
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Affiliation(s)
- Xiao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Juan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shanshan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Junjie Ji
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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Darshan N, Manonmani HK. Prodigiosin and its potential applications. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2015; 52:5393-407. [PMID: 26344956 PMCID: PMC4554646 DOI: 10.1007/s13197-015-1740-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 10/24/2022]
Abstract
Since a decade, there has been a strong consumer demand for more natural products. This has augmented inclination towards substitution of synthetic colorants with natural pigments. Natural pigments not only have the capacity to increase the marketability of products, they also demonstrate valuable biological activities as antioxidants and anticancer agents. There is a long history of exploitation of natural products produced by bacteria as sources of pharmaceutically important, bioactive compounds. Among natural pigments, pigments from microbial sources are potentially suitable alternatives to synthetic pigments. The red pigment prodigiosin (PG) has unusual properties, which have long been documented. The red-pigmented prodiginines are bioactive secondary metabolites produced by both Gram-negative and Gram-positive bacteria. Prodigiosins are characterized by a common pyrrolyl pyrromethene skeleton, and the biological role of these pigments in the producer organisms remains unclear. Bacterial prodigiosins and their synthetic derivatives are effective proapoptotic agents against various cancer cell lines, with multiple cellular targets including multi-drug resistant cells with little or no toxicity towards normal cell lines. However, research into the biology of pigment production will stimulate interest in the bioengineering of strains to synthesize useful prodiginine derivatives. This review article highlights the characteristics and potential applications of prodigiosin pigment from Serratia as prodigiosins are real potential therapeutic drugs.
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Affiliation(s)
- N. Darshan
- />Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
- />Central Food Technological Research Institute (CSIR – CFTRI), Mysore, 570020 India
| | - H. K. Manonmani
- />Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
- />Central Food Technological Research Institute (CSIR – CFTRI), Mysore, 570020 India
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Cobb RE, Wang Y, Zhao H. High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 2015; 4:723-8. [PMID: 25458909 PMCID: PMC4459934 DOI: 10.1021/sb500351f] [Citation(s) in RCA: 393] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Actinobacteria,
particularly those of genus Streptomyces, remain
invaluable hosts for the discovery and engineering of natural
products and their cognate biosynthetic pathways. However, genetic
manipulation of these bacteria is often labor and time intensive.
Here, we present an engineered CRISPR/Cas system for rapid multiplex
genome editing of Streptomyces strains, demonstrating
targeted chromosomal deletions in three different Streptomyces species and of various sizes (ranging from 20 bp to 30 kb) with
efficiency ranging from 70 to 100%. The designed pCRISPomyces plasmids
are amenable to assembly of spacers and editing templates via Golden
Gate assembly and isothermal assembly (or traditional digestion/ligation),
respectively, allowing rapid plasmid construction to target any genomic
locus of interest. As such, the pCRISPomyces system represents a powerful
new tool for genome editing in Streptomyces.
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Affiliation(s)
- Ryan E. Cobb
- Department of Chemical and Biomolecular
Engineering, ‡Institute for Genomic Biology, §Departments of Chemistry,
Biochemistry and Bioengineering, Center for Biophysics and Computational
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yajie Wang
- Department of Chemical and Biomolecular
Engineering, ‡Institute for Genomic Biology, §Departments of Chemistry,
Biochemistry and Bioengineering, Center for Biophysics and Computational
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular
Engineering, ‡Institute for Genomic Biology, §Departments of Chemistry,
Biochemistry and Bioengineering, Center for Biophysics and Computational
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Morgenstern A, Paetz C, Behrend A, Spiteller D. Divalent transition-metal-ion stress induces prodigiosin biosynthesis in Streptomyces coelicolor M145: formation of coeligiosins. Chemistry 2015; 21:6027-32. [PMID: 25760402 DOI: 10.1002/chem.201405733] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/12/2022]
Abstract
The bacterium Streptomyces coelicolor M145 reacts to transition-metal-ion stress with myriad growth responses, leading to different phenotypes. In particular, in the presence of Co(2+) ions (0.7 mM) S. coelicolor consistently produced a red phenotype. This phenotype, when compared to the wild type, differed strongly in its production of volatile compounds as well as high molecular weight secondary metabolites. LC-MS analysis revealed that in the red phenotype the production of the prodigiosins, undecylprodigiosin and streptorubin B, was strongly induced and, in addition, several intense signals appeared in the LC-MS chromatogram. Using LC-MS/MS and NMR spectroscopy, two new prodigiosin derivatives were identified, that is, coeligiosin A and B, which contained an additional undecylpyrrolyl side chain attached to the central carbon of the tripyrrole ring system of undecylprodigiosin or streptorubin B. This example demonstrates that environmental factors such as heavy metal ion stress can not only induce the production of otherwise not observed metabolites from so called sleeping genes but alter the products from well-studied biosynthetic pathways.
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Affiliation(s)
- Anne Morgenstern
- Max Planck Institute for Chemical Ecology, Hans Knöll Strasse 8, 07745 Jena (Germany)
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Singh R, Reynolds KA. Characterization of FabG and FabI of theStreptomyces coelicolorDissociated Fatty Acid Synthase. Chembiochem 2015; 16:631-40. [DOI: 10.1002/cbic.201402670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 12/16/2022]
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Regulation of myo-inositol catabolism by a GntR-type repressor SCO6974 in Streptomyces coelicolor. Appl Microbiol Biotechnol 2015; 99:3141-53. [PMID: 25575890 DOI: 10.1007/s00253-014-6368-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 10/24/2022]
Abstract
Myo-inositol is important for Streptomyces growth and morphological differentiation. Genomic sequence analysis revealed a myo-inositol catabolic gene cluster in Streptomyces coelicolor. Disruption of the corresponding genes in this cluster abolished the bacterial growth on myo-inositol as a single carbon source. The transcriptions of these genes were remarkably enhanced by addition of myo-inositol in minimal medium. A putative regulatory gene SCO6974, encoding a GntR family protein, is situated in the cluster. Disruption of SCO6974 significantly enhanced the transcription of myo-inositol catabolic genes. SCO6974 was shown to interact with the promoter regions of myo-inositol catabolic genes using electrophoretic mobility shift assays. DNase I footprinting assays demonstrated that SCO6974 recognized a conserved palindromic sequence (A/T)TGT(A/C)N(G/T)(G/T)ACA(A/T). Base substitution of the conserved sequence completely abolished the binding of SCO6974 to the targets demonstrating that SCO6974 directly represses the transcriptions of myo-inositol catabolic genes. Furthermore, the disruption of SCO6974 was correlated with a reduced sporulation of S. coelicolor in mannitol soya flour medium and with the overproduction of actinorhodin and calcium-dependent antibiotic. The addition of myo-inositol suppressed the sporulation deficiency of the mutant, indicating that the effect could be related to a shortage in myo-inositol due to its enhanced catabolism in this strain. This enhanced myo-inositol catabolism likely yields dihydroxyacetone phosphate and acetyl-CoA that are indirect or direct precursors of the overproduced antibiotics.
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