1
|
Akbar M, Ali N, Imran M, Hussain A, Hassan SW, Haroon U, Kamal A, Farhana, Chaudhary HJ, Munis MFH. Spherical Fe 2O 3 nanoparticles inhibit the production of aflatoxins (B 1 and B 2) and regulate total soluble solids and titratable acidity of peach fruit. Int J Food Microbiol 2024; 410:110508. [PMID: 38029662 DOI: 10.1016/j.ijfoodmicro.2023.110508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
Aflatoxin is a group I carcinogen and causes significant public health and food safety risks, throughout the world. This study was carried out to assess the levels of aflatoxin contamination in diseased peach (Prunus persica L.) fruit and their control using myco-synthesized iron oxide nanoparticles (Fe2O3 NPs). Diseased peach fruit were diagnosed to be infected with Aspergillus flavus. The isolated pathogen was cultured under UV light (365 nm) and exposed to ammonium hydroxide (31 %) vapors, which confirmed its ability to produce aflatoxin. For the control of this disease, Fe2O3 NPs were synthesized in the filtrate of a biocontrol fungus (Trichoderma harzianum) and characterized before analyzing their potential in disease control. FTIR spectrum described the presence of capping and reducing agents (secondary amines, alcohol, alkyne and aromatic compounds) on the surface of Fe2O3 NPs. X-ray Diffraction (XRD) described the crystalline size (7.78), while the spherical shape of Fe2O3 NPs was described by the SEM analysis. The EDX spectrum indicated the successful formation of Fe2O3 NPs by showing strong signals of iron (74.38 %). All concentrations displayed mycelial growth inhibition, in vitro and the greatest growth reduction (65.4 %) was observed at 1 mg/ml concentration of NPs. At the same concentration of Fe2O3 NPs, significant control of fruit rot of peach was also observed, in vivo. Treatment of Fe2O3 NPs maintained higher soluble solids, sucrose, total sugar, ascorbic acid, titratable acidity and firmness of peach fruit. Diseased fruit were further investigated for the presence and detection of aflatoxins. All three methods viz. thin layer chromatography (TLC), enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC) confirmed a higher production of aflatoxins in control plants, while this production was significantly reduced in Fe2O3 NPs-treated peach fruit.
Collapse
Affiliation(s)
- Mahnoor Akbar
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Naeem Ali
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Imran
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Arshad Hussain
- Department of Electronics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Waqas Hassan
- Department of Biosciences, University of Wah, Quaid Avenue, Wah Cantt., Pakistan
| | - Urooj Haroon
- Department of Plant Pathology, University of California, Davis 95616, USA
| | - Asif Kamal
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Farhana
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | | |
Collapse
|
2
|
Martín JF. Interaction of calcium responsive proteins and transcriptional factors with the PHO regulon in yeasts and fungi. Front Cell Dev Biol 2023; 11:1225774. [PMID: 37601111 PMCID: PMC10437122 DOI: 10.3389/fcell.2023.1225774] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Phosphate and calcium ions are nutrients that play key roles in growth, differentiation and the production of bioactive secondary metabolites in filamentous fungi. Phosphate concentration regulates the biosynthesis of hundreds of fungal metabolites. The central mechanisms of phosphate transport and regulation, mediated by the master Pho4 transcriptional factor are known, but many aspects of the control of gene expression need further research. High ATP concentration in the cells leads to inositol pyrophosphate molecules formation, such as IP3 and IP7, that act as phosphorylation status reporters. Calcium ions are intracellular messengers in eukaryotic organisms and calcium homeostasis follows elaborated patterns in response to different nutritional and environmental factors, including cross-talking with phosphate concentrations. A large part of the intracellular calcium is stored in vacuoles and other organelles forming complexes with polyphosphate. The free cytosolic calcium concentration is maintained by transport from the external medium or by release from the store organelles through calcium permeable transient receptor potential (TRP) ion channels. Calcium ions, particularly the free cytosolic calcium levels, control the biosynthesis of fungal metabolites by two mechanisms, 1) direct interaction of calcium-bound calmodulin with antibiotic synthesizing enzymes, and 2) by the calmodulin-calcineurin signaling cascade. Control of very different secondary metabolites, including pathogenicity determinants, are mediated by calcium through the Crz1 factor. Several interactions between calcium homeostasis and phosphate have been demonstrated in the last decade: 1) The inositol pyrophosphate IP3 triggers the release of calcium ions from internal stores into the cytosol, 2) Expression of the high affinity phosphate transporter Pho89, a Na+/phosphate symporter, is controlled by Crz1. Also, mutants defective in the calcium permeable TRPCa7-like of Saccharomyces cerevisiae shown impaired expression of Pho89. This information suggests that CrzA and Pho89 play key roles in the interaction of phosphate and calcium regulatory pathways, 3) Finally, acidocalcisomes organelles have been found in mycorrhiza and in some melanin producing fungi that show similar characteristics as protozoa calcisomes. In these organelles there is a close interaction between orthophosphate, pyrophosphate and polyphosphate and calcium ions that are absorbed in the polyanionic polyphosphate matrix. These advances open new perspectives for the control of fungal metabolism.
Collapse
Affiliation(s)
- Juan F. Martín
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, León, Spain
| |
Collapse
|
3
|
Barona-Gómez F, Chevrette MG, Hoskisson PA. On the evolution of natural product biosynthesis. Adv Microb Physiol 2023; 83:309-349. [PMID: 37507161 DOI: 10.1016/bs.ampbs.2023.05.001] [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] [Indexed: 07/30/2023]
Abstract
Natural products are the raw material for drug discovery programmes. Bioactive natural products are used extensively in medicine and agriculture and have found utility as antibiotics, immunosuppressives, anti-cancer drugs and anthelminthics. Remarkably, the natural role and what mechanisms drive evolution of these molecules is relatively poorly understood. The exponential increase in genome and chemical data in recent years, coupled with technical advances in bioinformatics and genetics have enabled progress to be made in understanding the evolution of biosynthetic gene clusters and the products of their enzymatic machinery. Here we discuss the diversity of natural products, incorporating the mechanisms that govern evolution of metabolic pathways and how this can be applied to biosynthetic gene clusters. We build on the nomenclature of natural products in terms of primary, integrated, secondary and specialised metabolism and place this within an ecology-evolutionary-developmental biology framework. This eco-evo-devo framework we believe will help to clarify the nature and use of the term specialised metabolites in the future.
Collapse
Affiliation(s)
| | - Marc G Chevrette
- Department of Microbiology and Cell Sciences, University of Florida, Museum Drive, Gainesville, FL, United States; University of Florida Genetics Institute, University of Florida, Mowry Road, Gainesville, FL, United States
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Cathedral Street, Glasgow, United Kingdom.
| |
Collapse
|
4
|
Pita T, Feliciano JR, Leitão JH. Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection. Appl Microbiol Biotechnol 2023; 107:3653-3671. [PMID: 37097504 PMCID: PMC10175445 DOI: 10.1007/s00253-023-12530-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Small non-coding RNAs (sRNAs) are key regulators of post-transcriptional gene expression in bacteria. Despite the identification of hundreds of bacterial sRNAs, their roles on bacterial physiology and virulence remain largely unknown, as is the case of bacteria of the Burkholderia cepacia complex (Bcc). Bcc is a group of opportunistic pathogens with relatively large genomes that can cause lethal lung infections amongst cystic fibrosis (CF) patients. To characterise sRNAs expressed by Bcc bacteria when infecting a host, the nematode Caenorhabditis elegans was used as an infection model by the epidemic CF strain B. cenocepacia J2315. A total of 108 new and 31 previously described sRNAs with a predicted Rho independent terminator were identified, most of them located on chromosome 1. RIT11b, a sRNA downregulated under C. elegans infection conditions, was shown to directly affect B. cenocepacia virulence, biofilm formation, and swimming motility. RIT11b overexpression reduced the expression of the direct targets dusA and pyrC, involved in biofilm formation, epithelial cell adherence, and chronic infections in other organisms. The in vitro direct interaction of RIT11b with the dusA and pyrC messengers was demonstrated by electrophoretic mobility shift assays. To the best of our knowledge this is the first report on the functional characterization of a sRNA directly involved in B. cenocepacia virulence. KEY POINTS: • 139 sRNAs expressed by B. cenocepacia during C. elegans infection were identified • The sRNA RIT11b affects B. cenocepacia virulence, biofilm formation, and motility • RIT11b directly binds to and regulates dusA and pyrC mRNAs.
Collapse
Affiliation(s)
- Tiago Pita
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, and Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Joana R Feliciano
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, and Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
| | - Jorge H Leitão
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, and Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
| |
Collapse
|
5
|
Transcriptomic analysis reveals the inhibition mechanism of pulsed light on fungal growth and ochratoxin A biosynthesis in Aspergillus carbonarius. Food Res Int 2023; 165:112501. [PMID: 36869509 DOI: 10.1016/j.foodres.2023.112501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/28/2022] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
Pulsed light (PL) technology has a good effect on the control of fungi in postharvest fruit. In this present work, PL inhibited the growth of Aspergillus carbonarius in a dose-dependent manner, the mycelial growth decreased by 4.83 %, 13.91 % and 30.01 % at a fluence of 4.5 J·cm-2 (PL5), 9 J·cm-2 (PL10) and 13.5 J·cm2 (PL15), respectively. When inoculated with PL15 treated A. carbonarius, the scab diameter of the pears, ergosterol and OTA content was reduced by 23.2 %, 27.9 % and 80.7 % after 7 days, respectively. The third-generation sequencing technique was applied to study the transcriptome response of A. carbonarius treated with PL. Compared with the blank control, a total number of 268 and 963 differentially expressed genes (DEGs) were discovered in the group of PL10 and PL15, respectively. To be specific, a large amount of DEGs involved in DNA metabolism were up-regulated, while most of DEGs related to cell integrity, energy and glucose metabolism, ochratoxin A (OTA) biosynthesis and transport were down-regulated. In addition, the stress response of A. carbonarius was imbalanced, including up-regulation of Catalase and PEX12 and down-regulation of taurine and subtaurine metabolism, alcohol dehydrogenase and glutathione metabolism. Meanwhile, the results of transmission electron microscopy, mycelium cellular leakage and DNA electrophoresis indicated that PL15 treatment caused mitochondrial swelling, the destroyed cell membrane permeability and imbalance of DNA metabolism. The expression of P450 and Hal involved in OTA biosynthesis pathway were down-regulated in PL treated samples detected by qRT-PCR. In conclusion, this study reveals the molecular mechanism of pulsed light on inhibiting the growth, development and toxin production of A. carbonarius.
Collapse
|
6
|
Nasiri A, Rashidi-Monfared S, Ebrahimi A, Falahi Charkhabi N, Moieni A. Metabolic engineering of the diosgenin biosynthesis pathway in Trigonella foenum-graceum hairy root cultures. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111410. [PMID: 35944746 DOI: 10.1016/j.plantsci.2022.111410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/04/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Diosgenin as a triterpene with numbers of pharmaceutical applications has been identified in Trigonella foenum-graceum. In this survey, in order to scale up the amount of diosgenin in Fenugreek as a promising alternative of yam, ∆24-reductase as a rate limiting enzyme in diosgenin biosynthesis pathway has been overexpressed by utilizing pBI121 expression plasmid in hairy roots culture platform. The recombinant binary vector pBI121-∆24-reductase was transformed into R. rhizogenes strain ATCC 15834 to induce transgenic hairy roots in "Hamedan" as a low-diosgenin production genotype. In the transgenic hairy roots, the ∆24-reductase expression level was significantly 8.15 times overexpressed comparing to the non-transgenic hairy roots, Nonetheless the Sterol-methyltransferase, as a competitive enzyme, was 6 times downregulated. Furthermore, the expression rate of Squalene synthase, Cycloartenol synthase, C26-Hydroxylase were also increased 1.5, 1.7, 2.9 times higher than those of the non-transgenic hairy roots, respectively. The diosgenin content in the transgenic hairy root was raised 3 times up comparing to the non-transgenic hairy roots, besides it was scaled up 25-fold comparing to the diosgenin amount in "Hamedan" Leaf. As a result, the first metabolic engineering on this pathway was clearly revealed the impact of ∆24 -reductase gene in diosgenin content enhancement.
Collapse
Affiliation(s)
- Ahmad Nasiri
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi-Monfared
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran.
| | - Nargues Falahi Charkhabi
- Department of Entomology and Plant Pathology, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Ahmad Moieni
- Genetics and Plant Breeding Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
7
|
Vélëz H, Gauchan DP, García-Gil MDR. Taxol and β-tubulins from endophytic fungi isolated from the Himalayan Yew, Taxus wallichiana Zucc. Front Microbiol 2022; 13:956855. [PMID: 36246258 PMCID: PMC9557061 DOI: 10.3389/fmicb.2022.956855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Paclitaxel, better known as the anticancer drug Taxol®, has been isolated from several plant species and has been shown to be produced by fungi, actinomycetes, and even bacteria isolated from marine macroalgae. Given its cytostatic effect, studies conducted in the 1990's showed that paclitaxel was toxic to many pathogenic fungi and oomycetes. Further studies led to the idea that the differences in paclitaxel sensitivity exhibited by different fungi were due to differences in the β-tubulin protein sequence. With the recent isolation of endophytic fungi from the leaves and bark of the Himalayan Yew, Taxus wallichiana Zucc., and the availability of genomes from paclitaxel-producing fungi, we decided to further explore the idea that endophytic fungi isolated from Yews should be well-adapted to their environment by encoding β-tubulin proteins that are insensitive to paclitaxel. Our results found evidence of episodic positive/diversifying selection at 10 sites (default p-value threshold of 0.1) in the β-tubulin sequences, corresponding to codon positions 33, 55, 172, 218, 279, 335, 359, 362, 379, and 406. Four of these positions (i.e., 172, 279, 359, and 362) have been implicated in the binding of paclitaxel by β-tubulin or formed part of the binding pocket. As expected, all the fungal endophytes grew in different media regardless of the paclitaxel concentration tested. Furthermore, our results also showed that Taxomyces andreanae CBS 279.92, the first fungus shown to produce paclitaxel, is a Basidiomycete fungus as the two beta tubulins encoded by the fungus clustered together with other Basidiomycete fungi.
Collapse
Affiliation(s)
- Heriberto Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Heriberto Vélëz
| | - Dhurva Prasad Gauchan
- Department of Biotechnology, School of Science, Kathmandu University, Dhulikhel, Nepal
| | - María del Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| |
Collapse
|
8
|
Gude F, Molloy EM, Horch T, Dell M, Dunbar KL, Krabbe J, Groll M, Hertweck C. A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria. Angew Chem Int Ed Engl 2022; 61:e202206168. [PMID: 35852818 PMCID: PMC9545259 DOI: 10.1002/anie.202206168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 12/04/2022]
Abstract
Understanding antibiotic resistance mechanisms is central to the development of anti‐infective therapies and genomics‐based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less‐explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self‐resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X‐ray crystallography revealed CtaZ as a founding member of a new group of GyrI‐like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand‐optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI‐like domain in self‐resistance and unprecedented thioamide binding, this work aids in uncovering related drug‐resistance mechanisms.
Collapse
Affiliation(s)
- Finn Gude
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Evelyn M. Molloy
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Therese Horch
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Maria Dell
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Kyle L. Dunbar
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Jana Krabbe
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Michael Groll
- Center for Protein AssembliesTechnical University of MunichErnst-Otto-Fischer-Straße 885747GarchingGermany
| | - Christian Hertweck
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| |
Collapse
|
9
|
Ramzan R, Virk MS, Chen F. The ABCT31 Transporter Regulates the Export System of Phenylacetic Acid as a Side-Chain Precursor of Penicillin G in Monascus ruber M7. Front Microbiol 2022; 13:915721. [PMID: 35966689 PMCID: PMC9370074 DOI: 10.3389/fmicb.2022.915721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The biosynthesis of penicillin G (PG) is compartmentalized, and the transportation of the end and intermediate products, and substrates (precursors) such as L-cysteine (L-Cys), L-valine (L-Val) and phenylacetic acid (PAA) requires traversing membrane barriers. However, the transportation system of PAA as a side chain of PG are unclear yet. To discover ABC transporters (ABCTs) involved in the transportation of PAA, the expression levels of 38 ABCT genes in the genome of Monascus ruber M7, culturing with and without PAA, were examined, and found that one abct gene, namely abct31, was considerably up-regulated with PAA, indicating that abct31 may be relative with PAA transportation. Furthermore the disruption of abct31 was carried out, and the effects of two PG substrate's amino acids (L-Cys and L-Val), PAA and some other weak acids on the morphologies and production of secondary metabolites (SMs) of Δabct31 and M. ruber M7, were performed through feeding experiments. The results revealed that L-Cys, L-Val and PAA substantially impacted the morphologies and SMs production of Δabct31 and M. ruber M7. The UPLC-MS/MS analysis findings demonstrated that Δabct31 did not interrupt the synthesis of PG in M. ruber M7. According to the results, it suggests that abct31 is involved in the resistance and detoxification of the weak acids, including the PAA in M. ruber M7.
Collapse
Affiliation(s)
- Rabia Ramzan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- Department of Food Science and Technology, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Safiullah Virk
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Fusheng Chen
| |
Collapse
|
10
|
Gude F, Molloy EM, Horch T, Dell M, Dunbar KL, Krabbe J, Groll M, Hertweck C. A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Finn Gude
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Evelyn M. Molloy
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Therese Horch
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Maria Dell
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Kyle L. Dunbar
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Jana Krabbe
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Michael Groll
- TU München: Technische Universitat Munchen Center for Protein Assemblies GERMANY
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Department of Biomolecular Chemistry Beutenbergstr. 11a 07745 Jena GERMANY
| |
Collapse
|
11
|
Gan Y, Bai M, Lin X, Liu K, Huang B, Jiang X, Liu Y, Gao C. Improvement of macrolactins production by the genetic adaptation of Bacillus siamensis A72 to saline stress via adaptive laboratory evolution. Microb Cell Fact 2022; 21:147. [PMID: 35854349 PMCID: PMC9294813 DOI: 10.1186/s12934-022-01871-9] [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: 05/01/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Macrolactins, a type of macrolide antibiotic, are toxic to the producer strains. As such, its level is usually maintained below the lethal concentration during the fermentation process. To improve the production of macrolactins, we applied adaptive laboratory evolution technology to engineer a saline-resistant mutant strain. The hypothesis that strains with saline resistance show improved macrolactins production was investigated. RESULTS Using saline stress as a selective pressure, we engineered a mutant strain with saline resistance coupled with enhanced macrolactins production within 60 days using a self-made device. As compared with the parental strain, the evolved strain produced macrolactins with 11.93% improvement in non-saline stress fermentation medium containing 50 g/L glucose, when the glucose concentration increased to 70 g/L, the evolved strain produced macrolactins with 71.04% improvement. RNA sequencing and metabolomics results revealed that amino acid metabolism was involved in the production of macrolactins in the evolved strain. Furthermore, genome sequencing of the evolved strain revealed a candidate mutation, hisDD41Y, that was causal for the improved MLNs production, it was 3.42 times higher than the control in the overexpression hisDD41Y strain. Results revealed that saline resistance protected the producer strain from feedback inhibition of end-product (macrolide antibiotic), resulting in enhanced MLNs production. CONCLUSIONS In the present work, we successfully engineered a mutant strain with enhanced macrolactins production by adaptive laboratory evolution using saline stress as a selective pressure. Based on physiological, transcriptomic and genetic analysis, amino acid metabolism was found to benefit macrolactins production improvement. Our strategy might be applicable to improve the production of other kinds of macrolide antibiotics and other toxic compounds. The identification of the hisD mutation will allow for the deduction of metabolic engineering strategies in future research.
Collapse
Affiliation(s)
- Yuman Gan
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China.
| | - Meng Bai
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China
| | - Xiao Lin
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China
| | - Kai Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China
| | - Bingyao Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China
| | - Xiaodong Jiang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China.
| | - Chenghai Gao
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Guangxi, 530001, People's Republic of China.
| |
Collapse
|
12
|
Zhong Q, Huang X, Zhang R, Zhang K, Liu B. Optical Sensing Strategies for Probing Single-Cell Secretion. ACS Sens 2022; 7:1779-1790. [PMID: 35709496 DOI: 10.1021/acssensors.2c00474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Measuring cell secretion events is crucial to understand the fundamental cell biology that underlies cell-cell communication, migration, proliferation, and differentiation. Although strategies targeting cell populations have provided significant information about live cell secretion, they yield ensemble profiles that obscure intrinsic cell-to-cell variations. Innovation in single-cell analysis has made breakthroughs allowing accurate sensing of a wide variety of secretions and their release dynamics with high spatiotemporal resolution. This perspective focuses on the power of single-cell protocols to revolutionize cell-secretion analysis by allowing real-time and real-space measurements on single live cell resolution. We begin by discussing recent progress on single-cell bioanalytical techniques, specifically optical sensing strategies such as fluorescence-, surface plasmon resonance-, and surface-enhanced Raman scattering-based strategies, capable of in situ real-time monitoring of single-cell released ions, metabolites, proteins, and vesicles. Single-cell sensing platforms which allow for high-throughput high-resolution analysis with enough accuracy are highlighted. Furthermore, we discuss remaining challenges that should be addressed to get a more comprehensive understanding of secretion biology. Finally, future opportunities and potential breakthroughs in secretome analysis that will arise as a result of further development of single-cell sensing approaches are discussed.
Collapse
Affiliation(s)
- Qingmei Zhong
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Rongrong Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Kun Zhang
- Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| |
Collapse
|
13
|
Mróz M, Gajęcka M, Brzuzan P, Lisieska-Żołnierczyk S, Leski D, Zielonka Ł, Gajęcki MT. Carry-Over of Zearalenone and Its Metabolites to Intestinal Tissues and the Expression of CYP1A1 and GSTπ1 in the Colon of Gilts before Puberty. Toxins (Basel) 2022; 14:354. [PMID: 35622600 PMCID: PMC9145504 DOI: 10.3390/toxins14050354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
The objective of this study was to evaluate whether low doses of zearalenone (ZEN) affect the carry-over of ZEN and its metabolites to intestinal tissues and the expression of CYP1A1 and GSTπ1 in the large intestine. Prepubertal gilts (with a BW of up to 14.5 kg) were exposed in group ZEN to daily ZEN5 doses of 5 μg/kg BW (n = 15); in group ZEN10, 10 μg/kg BW (n = 15); in group ZEN15, 15 μg/kg BW (n = 15); or were administered a placebo (group C, n = 15) throughout the experiment. After euthanasia, tissues were sampled on exposure days 7, 21, and 42 (D1, D2, and D3, respectively). The results confirmed that the administered ZEN doses (LOAEL, NOAEL, and MABEL) were appropriate to reliably assess the carry-over of ZEN. Based on the observations made during 42 days of exposure to pure ZEN, it can be hypothesized that all mycotoxins (ZEN, α-zearalenol, and β-zearalenol) contribute to a balance between intestinal cells and the expression of selected genes encoding enzymes that participate in biotransformation processes in the large intestine; modulate feminization processes in prepubertal gilts; and elicit flexible, adaptive responses of the macroorganism to mycotoxin exposure at the analyzed doses.
Collapse
Affiliation(s)
- Magdalena Mróz
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland; (M.M.); (Ł.Z.); (M.T.G.)
| | - Magdalena Gajęcka
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland; (M.M.); (Ł.Z.); (M.T.G.)
| | - Paweł Brzuzan
- Department of Environmental Biotechnology, Faculty of Environmental Sciences and Fisheries, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-719 Olsztyn, Poland;
| | - Sylwia Lisieska-Żołnierczyk
- Independent Public Health Care Centre of the Ministry of the Interior and Administration, and the Warmia and Mazury Oncology Centre in Olsztyn, Wojska Polskiego 37, 10-228 Olsztyn, Poland;
| | - Dawid Leski
- Research and Development Department, Wipasz S.A., Wadąg 9, 10-373 Wadąg, Poland;
| | - Łukasz Zielonka
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland; (M.M.); (Ł.Z.); (M.T.G.)
| | - Maciej T. Gajęcki
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland; (M.M.); (Ł.Z.); (M.T.G.)
| |
Collapse
|
14
|
Martin JF, Alvarez-Alvarez R, Liras P. Penicillin-Binding Proteins, β-Lactamases, and β-Lactamase Inhibitors in β-Lactam-Producing Actinobacteria: Self-Resistance Mechanisms. Int J Mol Sci 2022; 23:5662. [PMID: 35628478 PMCID: PMC9146315 DOI: 10.3390/ijms23105662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023] Open
Abstract
The human society faces a serious problem due to the widespread resistance to antibiotics in clinical practice. Most antibiotic biosynthesis gene clusters in actinobacteria contain genes for intrinsic self-resistance to the produced antibiotics, and it has been proposed that the antibiotic resistance genes in pathogenic bacteria originated in antibiotic-producing microorganisms. The model actinobacteria Streptomyces clavuligerus produces the β-lactam antibiotic cephamycin C, a class A β-lactamase, and the β lactamases inhibitor clavulanic acid, all of which are encoded in a gene supercluster; in addition, it synthesizes the β-lactamase inhibitory protein BLIP. The secreted clavulanic acid has a synergistic effect with the cephamycin produced by the same strain in the fight against competing microorganisms in its natural habitat. High levels of resistance to cephamycin/cephalosporin in actinobacteria are due to the presence (in their β-lactam clusters) of genes encoding PBPs which bind penicillins but not cephalosporins. We have revised the previously reported cephamycin C and clavulanic acid gene clusters and, in addition, we have searched for novel β-lactam gene clusters in protein databases. Notably, in S. clavuligerus and Nocardia lactamdurans, the β-lactamases are retained in the cell wall and do not affect the intracellular formation of isopenicillin N/penicillin N. The activity of the β-lactamase in S. clavuligerus may be modulated by the β-lactamase inhibitory protein BLIP at the cell-wall level. Analysis of the β-lactam cluster in actinobacteria suggests that these clusters have been moved by horizontal gene transfer between different actinobacteria and have culminated in S. clavuligerus with the organization of an elaborated set of genes designed for fine tuning of antibiotic resistance and cell wall remodeling for the survival of this Streptomyces species. This article is focused specifically on the enigmatic connection between β-lactam biosynthesis and β-lactam resistance mechanisms in the producer actinobacteria.
Collapse
Affiliation(s)
| | | | - Paloma Liras
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain; (J.F.M.); (R.A.-A.)
| |
Collapse
|
15
|
Perry EK, Meirelles LA, Newman DK. From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance. Nat Rev Microbiol 2022; 20:129-142. [PMID: 34531577 PMCID: PMC8857043 DOI: 10.1038/s41579-021-00620-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Secondary metabolites profoundly affect microbial physiology, metabolism and stress responses. Increasing evidence suggests that these molecules can modulate microbial susceptibility to commonly used antibiotics; however, secondary metabolites are typically excluded from standard antimicrobial susceptibility assays. This may in part account for why infections by diverse opportunistic bacteria that produce secondary metabolites often exhibit discrepancies between clinical antimicrobial susceptibility testing results and clinical treatment outcomes. In this Review, we explore which types of secondary metabolite alter antimicrobial susceptibility, as well as how and why this phenomenon occurs. We discuss examples of molecules that opportunistic and enteric pathogens either generate themselves or are exposed to from their neighbours, and the nuanced impacts these molecules can have on tolerance and resistance to certain antibiotics.
Collapse
Affiliation(s)
- Elena K Perry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lucas A Meirelles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
16
|
Claus S, Jezierska S, Elbourne LDH, Van Bogaert I. Exploring the transportome of the biosurfactant producing yeast Starmerella bombicola. BMC Genomics 2022; 23:22. [PMID: 34998388 PMCID: PMC8742932 DOI: 10.1186/s12864-021-08177-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
Starmerella bombicola is a non-conventional yeast mainly known for its capacity to produce high amounts of the glycolipids 'sophorolipids'. Although its product has been used as biological detergent for a couple of decades, the genetics of S. bombicola are still largely unknown. Computational analysis of the yeast's genome enabled us to identify 254 putative transporter genes that make up the entire transportome. For each of them, a potential substrate was predicted using homology analysis, subcellular localization prediction and RNA sequencing in different stages of growth. One transporter family is of exceptional importance to this yeast: the ATP Binding Cassette (ABC) transporter Superfamily, because it harbors the main driver behind the highly efficient sophorolipid export. Furthermore, members of this superfamily translocate a variety of compounds ranging from antibiotics to hydrophobic molecules. We conducted an analysis of this family by creating deletion mutants to understand their role in the export of hydrophobic compounds, antibiotics and sophorolipids. Doing this, we could experimentally confirm the transporters participating in the efflux of medium chain fatty alcohols, particularly decanol and undecanol, and identify a second sophorolipid transporter that is located outside the sophorolipid biosynthetic gene cluster.
Collapse
Affiliation(s)
- Silke Claus
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Sylwia Jezierska
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - Inge Van Bogaert
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| |
Collapse
|
17
|
Biosynthetic process and strain improvement approaches for industrial penicillin production. Biotechnol Lett 2022; 44:179-192. [PMID: 35000028 DOI: 10.1007/s10529-022-03222-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/01/2022] [Indexed: 11/02/2022]
Abstract
Penicillins and cephalosporins are the most important class of beta (β) lactam antibiotics, accounting for 65% total antibiotic market. Penicillins are produced by Penicillium rubens (popularly known as P. chrysogenum) were used to synthesize the active pharmaceutical intermediate (API), 6-aminopenicillinic acid (6-APA) employed in semisynthetic antibiotic production. The wild strains produce a negligible amount of penicillin (Pen). High antibiotic titre-producing P. chrysogenum strains are necessitating for industrial Pen production to meet global demand at lower prices. Classical strain improvement (CSI) approaches such as random mutagenesis, medium engineering, and fermentation are the cornerstones for high-titer Pen production. Since, Sir Alexander Fleming Discovery of Pen, great efforts are expanded to develop at a commercial scale antibiotics producing strains. Breakthroughs in genetic engineering, heterologous expression and CRISPR/Cas9 genome editing tools opened a new window for Pen production at a commercial scale to assure health crisis. The current state of knowledge, limitations of CSI and genetic engineering approaches to Pen production are discussed in this review.
Collapse
|
18
|
Genetic and evolutionary characterization of the Major Facilitator Superfamily transporters of the antibacterial, Pantoea Natural Product 3. Res Microbiol 2021; 173:103899. [PMID: 34774705 DOI: 10.1016/j.resmic.2021.103899] [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: 07/13/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022]
Abstract
Pantoea Natural Product 3 (PNP-3) is an antibiotic produced by Pantoea agglomerans that is effective against a broad range of multi-drug resistant bacteria. PNP-3 is encoded by a unique, eight-gene biosynthetic gene cluster composed of predicted enzymes (pnp3b, pnp3e-h), a regulator (pnp3d), and two Major Facilitator Superfamily transporters (pnp3a and pnp3c). To better characterize the role of the transporters, we generated pnp3a and pnp3c mutants and evaluated PNP-3 production. Disruption of pnp3a in Pantoea results in impaired growth and loss of antibiosis, suggesting a role in PNP-3 export and resistance. In contrast, pnp3c mutants display only reduced antibiotic production/export, suggesting a minor role for Pnp3c. Expression of pnp3a in susceptible Erwinia amylovora led to increased PNP-3 tolerance, while co-expression of pnp3a and pnp3e-h resulted in the production and export of PNP-3. Comparative genomic analyses identified pnp3a in 12 other Pantoea strains, eight of which carry a complete or nearly complete PNP-3 biosynthetic cluster. The four other Pantoea strains that carry pnp3a lack most of the PNP-3 cluster; however, they are PNP-3 tolerant. These results suggest Pnp3a plays an essential role in PNP-3 export and resistance in Pantoea.
Collapse
|
19
|
Seong J, Shin J, Kim K, Cho BK. Microbial production of nematicidal agents for controlling plant-parasitic nematodes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
20
|
Chu L, Li S, Dong Z, Zhang Y, Jin P, Ye L, Wang X, Xiang W. Mining and engineering exporters for titer improvement of macrolide biopesticides in Streptomyces. Microb Biotechnol 2021; 15:1120-1132. [PMID: 34437755 PMCID: PMC8966021 DOI: 10.1111/1751-7915.13883] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/21/2021] [Indexed: 11/27/2022] Open
Abstract
Exporter engineering is a promising strategy to construct high-yield Streptomyces for natural product pharmaceuticals in industrial biotechnology. However, available exporters are scarce, due to the limited knowledge of bacterial transporters. Here, we built a workflow for exporter mining and devised a tunable plug-and-play exporter (TuPPE) module to improve the production of macrolide biopesticides in Streptomyces. Combining genome analyses and experimental confirmations, we found three ATP-binding cassette transporters that contribute to milbemycin production in Streptomyces bingchenggensis. We then optimized the expression level of target exporters for milbemycin titer optimization by designing a TuPPE module with replaceable promoters and ribosome binding sites. Finally, broader applications of the TuPPE module were implemented in industrial S. bingchenggensis BC04, Streptomyces avermitilis NEAU12 and Streptomyces cyaneogriseus NMWT1, which led to optimal titer improvement of milbemycin A3/A4, avermectin B1a and nemadectin α by 24.2%, 53.0% and 41.0%, respectively. Our work provides useful exporters and a convenient TuPPE module for titer improvement of macrolide biopesticides in Streptomyces. More importantly, the feasible exporter mining workflow developed here might shed light on widespread applications of exporter engineering in Streptomyces to boost the production of other secondary metabolites.
Collapse
Affiliation(s)
- Liyang Chu
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhuoxu Dong
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Pinjiao Jin
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lan Ye
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangjing Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| |
Collapse
|
21
|
Breitling R, Avbelj M, Bilyk O, Carratore F, Filisetti A, Hanko EKR, Iorio M, Redondo RP, Reyes F, Rudden M, Severi E, Slemc L, Schmidt K, Whittall DR, Donadio S, García AR, Genilloud O, Kosec G, De Lucrezia D, Petković H, Thomas G, Takano E. Synthetic biology approaches to actinomycete strain improvement. FEMS Microbiol Lett 2021; 368:6289918. [PMID: 34057181 PMCID: PMC8195692 DOI: 10.1093/femsle/fnab060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022] Open
Abstract
Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete perspective and presents examples of their application to the rational improvement of industrially relevant strains.
Collapse
Affiliation(s)
- Rainer Breitling
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Martina Avbelj
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Oksana Bilyk
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Francesco Del Carratore
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | - Erik K R Hanko
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnologico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Michelle Rudden
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Lucija Slemc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Kamila Schmidt
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Dominic R Whittall
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnologico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnološki Park 21, 1000, Ljubljana, Slovenia
| | - Davide De Lucrezia
- Explora Biotech Srl, Doulix business unit, Via Torino 107, 30133 Venice, Italy
| | - Hrvoje Petković
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Gavin Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Eriko Takano
- Corresponding author: Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
| |
Collapse
|
22
|
Prasad JK, Pandey P, Anand R, Raghuwanshi R. Drought Exposed Burkholderia seminalis JRBHU6 Exhibits Antimicrobial Potential Through Pyrazine-1,4-Dione Derivatives Targeting Multiple Bacterial and Fungal Proteins. Front Microbiol 2021; 12:633036. [PMID: 33935993 PMCID: PMC8079638 DOI: 10.3389/fmicb.2021.633036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/22/2021] [Indexed: 01/29/2023] Open
Abstract
The present study aimed to explore the antimicrobial potentials of soil bacteria and identify the bioactive compounds and their likely targets through in silico studies. A total 53 bacterial isolates were screened for their antimicrobial potential of which the strain JRBHU6 showing highest antimicrobial activity was identified as Burkholderia seminalis (GenBank accession no. MK500868) based on 16S ribosomal RNA (rRNA) gene sequencing and phylogenetic analysis. B. seminalis JRBHU6 also produced hydrolytic enzymes chitinases and cellulase of significance in accrediting its antimicrobial nature. The bioactive metabolites produced by the isolate were extracted in different organic solvents among which methanolic extract showed best growth-suppressing activities toward multidrug resistant Staphylococcus aureus and fungal strains, viz Fusarium oxysporum, Aspergillus niger, Microsporum gypseum, Trichophyton mentagrophytes, and Trichoderma harzianum. The antimicrobial compounds were purified using silica gel thin layer chromatography and high-performance liquid chromatography (HPLC). On the basis of spectroscopic analysis, the bioactive metabolites were identified as pyrrolo(1,2-a)pyrazine-1,4-dione,hexahydro (PPDH) and pyrrolo(1,2-a)pyrazine-1,4-dione, hexahydro-3(2-methylpropyl) (PPDHMP). In silico molecular docking studies showed the bioactive compounds targeting fungal and bacterial proteins, among which PPDHMP was multitargeting in nature as reported for the first time through this study.
Collapse
Affiliation(s)
- Jay Kishor Prasad
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Priyanka Pandey
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Richa Anand
- Department of Applied Science, Indian Institute of Information Technology-Allahabad, Prayagraj, India
| | - Richa Raghuwanshi
- Department of Botany, MMV, Banaras Hindu University, Varanasi, India
| |
Collapse
|
23
|
Zhou Y, Yan P, Tang L. Self-protection of Streptomyces to ε-poly-l-lysine improves fermentation efficacy. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
24
|
The role of transport proteins in the production of microbial glycolipid biosurfactants. Appl Microbiol Biotechnol 2021; 105:1779-1793. [PMID: 33576882 DOI: 10.1007/s00253-021-11156-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 01/20/2023]
Abstract
Several microorganisms are currently being used as production platform for glycolipid biosurfactants, providing a greener alternative to chemical biosurfactants. One of the reasons why these processes are commercially competitive is the fact that microbial producers can efficiently export their product to the extracellular environment, reaching high product titers. Glycolipid biosynthetic genes are often found in a dedicated cluster, amidst which genes encoding a dedicated transporter committed to shuttle the glycolipid to the extracellular environment are often found, as is the case for many other secondary metabolites. Knowing this, one can rely on gene clustering features to screen for novel putative transporters, as described and performed in this review. The above strategy proves to be very powerful to identify glycolipid transporters in fungi but is less valid for bacterial systems. Indeed, the genetics of these export systems are currently largely unknown, but some hints are given. Apart from the direct export of the glycolipid, several other transport systems have an indirect effect on glycolipid production. Specific importers dictate which hydrophilic and hydrophobic substrates can be used for production and influence the final yields. In eukaryotes, cellular compartmentalization allows the assembly of glycolipid building blocks in a highly specialized and efficient way. Yet, this requires controlled transport across intracellular membranes. Next to the direct export of glycolipids, the current state of the art regarding this indirect involvement of transporter systems in microbial glycolipid synthesis is summarized in this review. KEY POINTS: • Transporters are directly and indirectly involved in microbial glycolipid synthesis. • Yeast glycolipid transporters are found in their biosynthetic gene cluster. • Hydrophilic and hydrophobic substrate uptake influence microbial glycolipid synthesis.
Collapse
|
25
|
Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res 2021; 31:239-250. [PMID: 33361114 PMCID: PMC7849407 DOI: 10.1101/gr.268169.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022]
Abstract
Biosynthetic gene clusters (BGCs) are operonic sets of microbial genes that synthesize specialized metabolites with diverse functions, including siderophores and antibiotics, which often require export to the extracellular environment. For this reason, genes for transport across cellular membranes are essential for the production of specialized metabolites and are often genomically colocalized with BGCs. Here, we conducted a comprehensive computational analysis of transporters associated with characterized BGCs. In addition to known exporters, in BGCs we found many importer-specific transmembrane domains that co-occur with substrate binding proteins possibly for uptake of siderophores or metabolic precursors. Machine learning models using transporter gene frequencies were predictive of known siderophore activity, molecular weights, and a measure of lipophilicity (log P) for corresponding BGC-synthesized metabolites. Transporter genes associated with BGCs were often equally or more predictive of metabolite features than biosynthetic genes. Given the importance of siderophores as pathogenicity factors, we used transporters specific for siderophore BGCs to identify both known and uncharacterized siderophore-like BGCs in genomes from metagenomes from the infant and adult gut microbiome. We find that 23% of microbial genomes from premature infant guts have siderophore-like BGCs, but only 3% of those assembled from adult gut microbiomes do. Although siderophore-like BGCs from the infant gut are predominantly associated with Enterobacteriaceae and Staphylococcus, siderophore-like BGCs can be identified from taxa in the adult gut microbiome that have rarely been recognized for siderophore production. Taken together, these results show that consideration of BGC-associated transporter genes can inform predictions of specialized metabolite structure and function.
Collapse
Affiliation(s)
- Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Nicholas Bhattacharya
- Department of Mathematics, University of California, Berkeley, California 94720, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University, California 94305, USA
| | - Yun S Song
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
- Department of Statistics, University of California, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, Berkeley, California 94720, USA
- Department of Microbiology and Immunology, Stanford University, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
26
|
Li X, Lv JM, Hu D, Abe I. Biosynthesis of alkyne-containing natural products. RSC Chem Biol 2021; 2:166-180. [PMID: 34458779 PMCID: PMC8341276 DOI: 10.1039/d0cb00190b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Alkyne-containing natural products are important molecules that are widely distributed in microbes and plants. Inspired by the advantages of acetylenic products used in the fields of medicinal chemistry, organic synthesis and material science, great efforts have focused on discovering the biosynthetic enzymes and pathways for alkyne formation. Here, we summarize the biosyntheses of alkyne-containing natural products and introduce de novo biosynthetic strategies for alkyne-tagged compound production.
Collapse
Affiliation(s)
- Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
| |
Collapse
|
27
|
Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria. Int J Mol Sci 2021; 22:ijms22031129. [PMID: 33498785 PMCID: PMC7866108 DOI: 10.3390/ijms22031129] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorous, in the form of phosphate, is a key element in the nutrition of all living beings. In nature, it is present in the form of phosphate salts, organophosphates, and phosphonates. Bacteria transport inorganic phosphate by the high affinity phosphate transport system PstSCAB, and the low affinity PitH transporters. The PstSCAB system consists of four components. PstS is the phosphate binding protein and discriminates between arsenate and phosphate. In the Streptomyces species, the PstS protein, attached to the outer side of the cell membrane, is glycosylated and released as a soluble protein that lacks its phosphate binding ability. Transport of phosphate by the PstSCAB system is drastically regulated by the inorganic phosphate concentration and mediated by binding of phosphorylated PhoP to the promoter of the PstSCAB operon. In Mycobacterium smegmatis, an additional high affinity transport system, PhnCDE, is also under PhoP regulation. Additionally, Streptomyces have a duplicated low affinity phosphate transport system encoded by the pitH1–pitH2 genes. In this system phosphate is transported as a metal-phosphate complex in simport with protons. Expression of pitH2, but not that of pitH1 in Streptomyces coelicolor, is regulated by PhoP. Interestingly, in many Streptomyces species, three gene clusters pitH1–pstSCAB–ppk (for a polyphosphate kinase), are linked in a supercluster formed by nine genes related to phosphate metabolism. Glycerol-3-phosphate may be transported by the actinobacteria Corynebacterium glutamicum that contains a ugp gene cluster for glycerol-3-P uptake, but the ugp cluster is not present in Streptomyces genomes. Sugar phosphates and nucleotides are used as phosphate source by the Streptomyces species, but there is no evidence of the uhp gene involved in the transport of sugar phosphates. Sugar phosphates and nucleotides are dephosphorylated by extracellular phosphatases and nucleotidases. An isolated uhpT gene for a hexose phosphate antiporter is present in several pathogenic corynebacteria, such as Corynebacterium diphtheriae, but not in non-pathogenic ones. Phosphonates are molecules that contains phosphate linked covalently to a carbon atom through a very stable C–P bond. Their utilization requires the phnCDE genes for phosphonates/phosphate transport and genes for degradation, including those for the subunits of the C–P lyase. Strains of the Arthrobacter and Streptomyces genera were reported to degrade simple phosphonates, but bioinformatic analysis reveals that whole sets of genes for putative phosphonate degradation are present only in three Arthrobacter species and a few Streptomyces species. Genes encoding the C–P lyase subunits occur in several Streptomyces species associated with plant roots or with mangroves, but not in the laboratory model Streptomyces species; however, the phnCDE genes that encode phosphonates/phosphate transport systems are frequent in Streptomyces species, suggesting that these genes, in the absence of C–P lyase genes, might be used as surrogate phosphate transporters. In summary, Streptomyces and related actinobacteria seem to be less versatile in phosphate transport systems than Enterobacteria.
Collapse
|
28
|
Qiu Z, Zhang J, Chen S, Liu Y, Wu Q, Yang H, Gao M, Li L. Preparation of Extracellular and Intracellular Water-Insoluble Monascus Pigments during Submerged Fermentaion. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
29
|
The Analysis of Estrogen-Degrading and Functional Metabolism Genes in Rhodococcus equi DSSKP-R-001. Int J Genomics 2020; 2020:9369182. [PMID: 32908857 PMCID: PMC7471831 DOI: 10.1155/2020/9369182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 11/17/2022] Open
Abstract
Estrogen contamination is recognized as one of the most serious environmental problems, causing widespread concern worldwide. Environmental estrogens are mainly derived from human and vertebrate excretion, drugs, and agricultural activities. The use of microorganisms is currently the most economical and effective method for biodegradation of environmental estrogens. Rhodococcus equi DSSKP-R-001 (R-001) has strong estrogen-degrading capabilities. Our study indicated that R-001 can use different types of estrogen as its sole carbon source for growth and metabolism, with final degradation rates above 90%. Transcriptome analysis showed that 720 (E1), 983 (E2), and 845 (EE2) genes were significantly upregulated in the estrogen-treated group compared with the control group, and 270 differentially expressed genes (DEGs) were upregulated across all treatment groups. These DEGs included ABC transporters; estrogen-degrading genes, including those that perform initial oxidation and dehydrogenation reactions and those that further degrade the resulting substrates into small molecules; and metabolism genes that complete the intracellular transformation and utilization of estrogen metabolites through biological processes such as amino acid metabolism, lipid metabolism, carbohydrate metabolism, and the tricarboxylic acid cycle. In summary, the biodegradation of estrogens is coordinated by a metabolic network of estrogen-degrading enzymes, transporters, metabolic enzymes, and other coenzymes. In this study, the metabolic mechanisms by which Rhodococcus equi R-001 degrades various estrogens were analyzed for the first time. A new pollutant metabolism system is outlined, providing a starting point for the construction of engineered estrogen-degrading bacteria.
Collapse
|
30
|
Bai C, Liu Y, Chen X, Qian Z, Liu H, Zhou X, Zhang Y, Cai M. Fungal statin pump protein improves monacolin J efflux and regulates its production in Komagataella phaffii. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Monacolin J (MJ) is a key intermediate for the synthesis of cholesterol-lowering drug simvastatin. Current industrial production of MJ involves complicated chemical hydrolysis of microbial fermented lovastatin. Recently, heterologous production of MJ has been achieved in yeast and bacteria, but the resulting metabolic stress and excessive accumulation of the compound adversely affect cell activity.
Results
Five genes, tapA, stapA, slovI, smokI and smlcE, coding for fungal statin pump proteins were expressed in an MJ producing yeast strain, Komagataella phaffii J#9. Overexpression of these genes facilitated MJ production. Among them, tapA from Aspergillus terreus highly improved MJ production and led to a titer increase of 108%. Exogenous MJ feeding study on an MJ non-producing strain GS-PGAP-TapA was then performed, and the results illustrated tough entry of MJ into cells and possible efflux action of TapA. Further, intracellular and extracellular MJ levels of J#9 and J#9-TapA were analyzed. The extracellular MJ level of J#9-TapA increased faster, but its intracellular MJ percentage kept lower as compared to J#9. The results proved that TapA effectively excreted MJ from cells. Then functions of TapA were evaluated in a high-production bioreactor fermentation. Differently, TapA expression caused a low MJ titer but high intracellular MJ accumulation in J#9-TapA compared with J#9.
Conclusions
Statin pump proteins improved MJ production in K. phaffii in a shake flask. Exogenous MJ feeding and endogenous MJ producing experiments demonstrated the efflux function of TapA. TapA improved MJ production at low MJ levels in a shake flask, but decreased it at high MJ levels in a bioreactor. This finding is useful for statin pump improvement and metabolic engineering for statin bioproduction.
Collapse
|
31
|
Mahdiyah D, Farida H, Riwanto I, Mustofa M, Wahjono H, Laksana Nugroho T, Reki W. Screening of Indonesian peat soil bacteria producing antimicrobial compounds. Saudi J Biol Sci 2020; 27:2604-2611. [PMID: 32994717 PMCID: PMC7499089 DOI: 10.1016/j.sjbs.2020.05.033] [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: 01/24/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 11/02/2022] Open
Abstract
The development and world-wide spread of multidrug-resistant (MDR) bacteria have a high concern in the medicine, especially the extended-spectrum of beta-lactamase (ESBL) producing Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA). There are currently very limited effective antibiotics to treat infections caused by MDR bacteria. Peat-soil is a unique environment in which bacteria have to compete each other to survive, for instance, by producing antimicrobial substances. This study aimed to isolate bacteria from peat soils from South Kalimantan Indonesia, which capable of inhibiting the growth of Gram-positive and Gram-negative bacteria. Isolates from peat soil were grown and identified phenotypically. The cell-free supernatant was obtained from broth culture by centrifugation and was tested by agar well-diffusion technique against non ESBL-producing E. coli ATCC 25922, ESBL-producing E. coli ATCC 35218, methicillin susceptible Staphylococcus aureus (MSSA) ATCC 29,213 and MRSA ATCC 43300. Putative antimicrobial compounds were separated using SDS-PAGE electrophoresis and purified using electroelution method. Antimicrobial properties of the purified compounds were confirmed by measuring the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). In total 28 isolated colonies were recovered; three (25PS, 26PS, and 27PS) isolates produced proteins with strong antimicrobial activities against both reference strains. The substance of proteins from three isolates exerted strong antimicrobial activity against ESBL-producing E. coli ATCC 35,218 (MIC = 2,80 µg/mL (25PS), 3,76 µg/mL (26PS), and 2,41 µg/mL (27PS), and MRSA ATCC 43,300 (MIC = 4,20 µg/mL (25PS), 5,65 µg/mL (26PS), and 3,62 µg/mL (27PS), and also had the ability bactericidal properties against the reference strains. There were isolates from Indonesian peat which were potentials sources of new antimicrobials.
Collapse
Affiliation(s)
- Dede Mahdiyah
- Department of Pharmacy, Faculty of Health, Sari Mulia University, Banjarmasin, Indonesia.,Post Graduate Program, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Helmia Farida
- Department of Clinical Microbiology, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Ignatius Riwanto
- Department of Surgery, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Mustofa Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Hendro Wahjono
- Department of Clinical Microbiology, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Tri Laksana Nugroho
- Department Pharmacology, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Winarto Reki
- Department of Clinical Microbiology, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| |
Collapse
|
32
|
Mechanisms of response to pH shock in microbial fermentation. Bioprocess Biosyst Eng 2019; 43:361-372. [PMID: 31650352 DOI: 10.1007/s00449-019-02232-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
Abstract
The following review highlights pH shock, a novel environmental factor, as a tool for the improvement of fermentation production. The aim of this review is to introduce some recent original studies on the enhancement of microbial fermentation production by pH shock. Another purpose of this review is to improve the understanding of the processes that underlie physiological and genetic differences, which will facilitate future research on the improvement of fermentation production and reveal the associated molecular mechanisms. This understanding will simultaneously promote the application of this strategy to other microbial fermentation systems. Furthermore, improvement of the cellular tolerance of genetically engineered bacteria can also be a new field of research in the future to enhance fermentation production.
Collapse
|
33
|
Characterization of the Noncanonical Regulatory and Transporter Genes in Atratumycin Biosynthesis and Production in a Heterologous Host. Mar Drugs 2019; 17:md17100560. [PMID: 31569487 PMCID: PMC6835768 DOI: 10.3390/md17100560] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/20/2022] Open
Abstract
Atratumycin is a cyclodepsipeptide with activity against Mycobacteria tuberculosis isolated from deep-sea derived Streptomyces atratus SCSIO ZH16NS-80S. Analysis of the atratumycin biosynthetic gene cluster (atr) revealed that its biosynthesis is regulated by multiple factors, including two LuxR regulatory genes (atr1 and atr2), two ABC transporter genes (atr29 and atr30) and one Streptomyces antibiotic regulatory gene (atr32). In this work, three regulatory and two transporter genes were unambiguously determined to provide positive, negative and self-protective roles during biosynthesis of atratumycin through bioinformatic analyses, gene inactivations and trans-complementation studies. Notably, an unusual Streptomyces antibiotic regulatory protein Atr32 was characterized as a negative regulator; the function of Atr32 is distinct from previous studies. Five over-expression mutant strains were constructed by rational application of the regulatory and transporter genes; the resulting strains produced significantly improved titers of atratumycin that were ca. 1.7-2.3 fold greater than wild-type (WT) producer. Furthermore, the atratumycin gene cluster was successfully expressed in Streptomyces coelicolor M1154, thus paving the way for the transfer and recombination of large DNA fragments. Overall, this finding sets the stage for understanding the unique biosynthesis of pharmaceutically important atratumycin and lays the foundation for generating anti-tuberculosis lead compounds possessing novel structures.
Collapse
|
34
|
Genetic Modification of mfsT Gene Stimulating the Putative Penicillin Production in Monascus ruber M7 and Exhibiting the Sensitivity towards Precursor Amino Acids of Penicillin Pathway. Microorganisms 2019; 7:microorganisms7100390. [PMID: 31554331 PMCID: PMC6843564 DOI: 10.3390/microorganisms7100390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/15/2019] [Accepted: 09/19/2019] [Indexed: 01/09/2023] Open
Abstract
The biosynthesis of penicillin G (PG) is compartmentalized, which forces penicillin and its intermediates to cross the membrane barriers. Although many aspects around the penicillin intermediates traffic system remain unclosed, the transmembrane transporter protein involvement has been only predicted. In the present work, detection of PG and isopenicillin N (IPN) in Monascus ruber M7 was performed and functions of mfst gene as a transporter were investigated by the combination of gene deletion (Δmfst) complementation (ΔmfsT::mfsT) and overexpression (M7::PtrpC-mfsT). While, the feeding of PG pathway precursor side chain and amino acids, i.e., phenylacetic acid, D-valine, and L-cysteine was performed for the interpretation of mfsT gene role as an intermediate transporter. The results showed that, the feeding of phenylacetic acid, D-valine, and L-cysteine possessed a significant effect on morphologies, secondary metabolites (SMs) production of all above-mentioned strains including M. ruber M7. The results of UPLC-MS/MS revealed that, ΔmfsT interrupt the penicillin G (PG) production in M. ruber M7 by blocking the IPN transportation, while PG and IPN produced by the ΔmfsT::mfsT have been recovered the similar levels to those of M. ruber M7. Conclusively, these findings suggest that the M. ruber M7 is, not only a PG producer, but also, indicate that the mfsT gene is supposed to play a key role in IPN intermediate compound transportation during the PG production in M. ruber M7.
Collapse
|
35
|
Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
Collapse
Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
| |
Collapse
|
36
|
Severi E, Thomas GH. Antibiotic export: transporters involved in the final step of natural product production. Microbiology (Reading) 2019; 165:805-818. [DOI: 10.1099/mic.0.000794] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Emmanuele Severi
- Department of Biology, University of York, Wentworth Way, York, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, Wentworth Way, York, UK
| |
Collapse
|
37
|
Hammerl R, Frank O, Schmittnägel T, Ehrmann MA, Hofmann T. Functional Metabolome Analysis of Penicillium roqueforti by Means of Differential Off-Line LC-NMR. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5135-5146. [PMID: 30950274 DOI: 10.1021/acs.jafc.9b00388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
UPLC-TOF/MS profiling, followed by the recently reported differential off-line LC-NMR (DOLC-NMR) and quantitative 1H NMR spectroscopy (qHNMR), led to the differential qualitative analysis and accurate quantitation of l-tryptophan-induced metabolome alterations of Penicillium roqueforti, which is typically used in making blue-mold cheese. Among the 24 metabolites identified, two tetrapeptides, namely, d-Phe-l-Val-d-Val-l-Tyr and d-Phe-l-Val-d-Val-l-Phe, as well as cis-bis(methylthio)silvatin, are reported for the first time as metabolites of P. roqueforti. Antimicrobial activity tests showed strong effects of the catabolic l-tryptophan metabolites 3-hydroxyanthranilic acid, anthranilic acid, and 3-indolacetic acid against Saccharomyces cerevisiae, with IC50 values between 15.6 and 24.0 μg/mL, while roquefortine C and cis-bis(methylthio)silvatin inhibited the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis with IC50 values between 30.0 and 62.5 μg/mL.
Collapse
Affiliation(s)
| | | | | | - Matthias A Ehrmann
- Chair of Technical Microbiology , Technische Universität München , Gregor-Mendel-Strasse 4 , D-85354 Freising-Weihenstephan , Germany
| | | |
Collapse
|
38
|
Baral B, Akhgari A, Metsä-Ketelä M. Activation of microbial secondary metabolic pathways: Avenues and challenges. Synth Syst Biotechnol 2018; 3:163-178. [PMID: 30345402 PMCID: PMC6190515 DOI: 10.1016/j.synbio.2018.09.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial natural products are a tremendous source of new bioactive chemical entities for drug discovery. Next generation sequencing has revealed an unprecedented genomic potential for production of secondary metabolites by diverse micro-organisms found in the environment and in the microbiota. Genome mining has further led to the discovery of numerous uncharacterized 'cryptic' metabolic pathways in the classical producers of natural products such as Actinobacteria and fungi. These biosynthetic gene clusters may code for improved biologically active metabolites, but harnessing the full genetic potential has been hindered by the observation that many of the pathways are 'silent' under laboratory conditions. Here we provide an overview of the various biotechnological methodologies, which can be divided to pleiotropic, biosynthetic gene cluster specific, and targeted genome-wide approaches that have been developed for the awakening of microbial secondary metabolic pathways.
Collapse
Affiliation(s)
| | | | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014, Turku, Finland
| |
Collapse
|
39
|
Liu Y, Bai C, Xu Q, Yu J, Zhou X, Zhang Y, Cai M. Improved methanol-derived lovastatin production through enhancement of the biosynthetic pathway and intracellular lovastatin efflux in methylotrophic yeast. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0202-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
40
|
Tkachenko AG. Stress Responses of Bacterial Cells as Mechanism of Development of Antibiotic Tolerance (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020114] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
41
|
Pinu FR, Granucci N, Daniell J, Han TL, Carneiro S, Rocha I, Nielsen J, Villas-Boas SG. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test. Metabolomics 2018; 14:43. [PMID: 30830324 DOI: 10.1007/s11306-018-1339-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/07/2018] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. MATERIALS AND METHODS The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow. CONCLUSIONS Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.
Collapse
Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
| | - Ninna Granucci
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - James Daniell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
- LanzaTech, Skokie, IL, 60077, USA
| | - Ting-Li Han
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Sonia Carneiro
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Rocha
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| |
Collapse
|
42
|
Fungal Cordycepin Biosynthesis Is Coupled with the Production of the Safeguard Molecule Pentostatin. Cell Chem Biol 2017; 24:1479-1489.e4. [DOI: 10.1016/j.chembiol.2017.09.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/05/2017] [Accepted: 09/01/2017] [Indexed: 12/31/2022]
|
43
|
Xie Y, Ma J, Qin X, Li Q, Ju J. Identification and utilization of two important transporters: SgvT1 and SgvT2, for griseoviridin and viridogrisein biosynthesis in Streptomyces griseoviridis. Microb Cell Fact 2017; 16:177. [PMID: 29065880 PMCID: PMC5655939 DOI: 10.1186/s12934-017-0792-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/14/2017] [Indexed: 01/08/2023] Open
Abstract
Background Griseoviridin (GV) and viridogrisein (VG, also referred as etamycin), both biosynthesized by a distinct 105 kb biosynthetic gene cluster (BGC) in Streptomyces griseoviridis NRRL 2427, are a pair of synergistic streptogramin antibiotics and very important in treating infections of many multi-drug resistant microorganisms. Three transporter genes, sgvT1–T3 have been discovered within the 105 kb GV/VG BGC, but the function of these efflux transporters have not been identified. Results In the present study, we have identified the different roles of these three transporters, SgvT1, SgvT2 and SgvT3. SgvT1 is a major facilitator superfamily (MFS) transporter whereas SgvT2 appears to serve as the sole ATP-binding cassette (ABC) transporter within the GV/VG BGC. Both proteins are necessary for efficient GV/VG biosynthesis although SgvT1 plays an especially critical role by averting undesired intracellular GV/VG accumulation during biosynthesis. SgvT3 is an alternative MFS-based transporter that appears to serve as a compensatory transporter in GV/VG biosynthesis. We also have identified the γ-butyrolactone (GBL) signaling pathway as a central regulator of sgvT1–T3 expression. Above all, overexpression of sgvT1 and sgvT2 enhances transmembrane transport leading to steady production of GV/VG in titers ≈ 3-fold greater than seen for the wild-type producer and without any notable disturbances to GV/VG biosynthetic gene expression or antibiotic control. Conclusions Our results shows that SgvT1–T2 are essential and useful in GV/VG biosynthesis and our effort highlight a new and effective strategy by which to better exploit streptogramin-based natural products of which GV and VG are prime examples with clinical potential. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0792-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yunchang Xie
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Research Network for Applied Microbiology Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Research Network for Applied Microbiology Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiangjing Qin
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Research Network for Applied Microbiology Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Research Network for Applied Microbiology Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Research Network for Applied Microbiology Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China.
| |
Collapse
|
44
|
Abstract
Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements. Nevertheless, despite long histories of antibiotic production and exposure, environmental bacteria are not resistant to all known antibiotics. This means that there are barriers to the acquisition of a complete resistance armamentarium. The sources, distribution, and movement of resistance mechanisms in different microbes and bacterial populations are mosaic features that act as barriers to slow this movement, thus moderating the emergence of bacterial pan-resistance. This is highly relevant to understanding the emergence of resistance in pathogenic bacteria that can inform better antibiotic management practices and influence new drug discovery.
Collapse
Affiliation(s)
- Nicholas Waglechner
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 4K1, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 4K1, Canada.
| |
Collapse
|
45
|
Rojas-Aedo JF, Gil-Durán C, Del-Cid A, Valdés N, Álamos P, Vaca I, García-Rico RO, Levicán G, Tello M, Chávez R. The Biosynthetic Gene Cluster for Andrastin A in Penicillium roqueforti. Front Microbiol 2017; 8:813. [PMID: 28529508 PMCID: PMC5418334 DOI: 10.3389/fmicb.2017.00813] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/20/2017] [Indexed: 02/02/2023] Open
Abstract
Penicillium roqueforti is a filamentous fungus involved in the ripening of several kinds of blue cheeses. In addition, this fungus produces several secondary metabolites, including the meroterpenoid compound andrastin A, a promising antitumoral compound. However, to date the genomic cluster responsible for the biosynthesis of this compound in P. roqueforti has not been described. In this work, we have sequenced and annotated a genomic region of approximately 29.4 kbp (named the adr gene cluster) that is involved in the biosynthesis of andrastin A in P. roqueforti. This region contains ten genes, named adrA, adrC, adrD, adrE, adrF, adrG, adrH, adrI, adrJ and adrK. Interestingly, the adrB gene previously found in the adr cluster from P. chrysogenum, was found as a residual pseudogene in the adr cluster from P. roqueforti. RNA-mediated gene silencing of each of the ten genes resulted in significant reductions in andrastin A production, confirming that all of them are involved in the biosynthesis of this compound. Of particular interest was the adrC gene, encoding for a major facilitator superfamily transporter. According to our results, this gene is required for the production of andrastin A but does not have any role in its secretion to the extracellular medium. The identification of the adr cluster in P. roqueforti will be important to understand the molecular basis of the production of andrastin A, and for the obtainment of strains of P. roqueforti overproducing andrastin A that might be of interest for the cheese industry.
Collapse
Affiliation(s)
- Juan F Rojas-Aedo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Abdiel Del-Cid
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Natalia Valdés
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Pamela Álamos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Ramón O García-Rico
- GIMBIO Group, Department of Microbiology, Faculty of Basic Sciences, Universidad de PamplonaPamplona, Colombia
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Mario Tello
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiago, Chile
| |
Collapse
|
46
|
Raghava Rao KV, Mani P, Satyanarayana B, Raghava Rao T. Purification and structural elucidation of three bioactive compounds isolated from Streptomyces coelicoflavus BC 01 and their biological activity. 3 Biotech 2017; 7:24. [PMID: 28401462 PMCID: PMC5388647 DOI: 10.1007/s13205-016-0581-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/01/2016] [Indexed: 01/17/2023] Open
Abstract
The strain Streptomyces coelicoflavus BC 01 was isolated from mangrove soil and used as inoculum for submerged fermentation. The fermented broth was extracted with ethyl acetate, the crude extract was subjected to silica gel column chromatography and the homogeneity of the isolated fractions was determined by TLC and then subjected to RP-HPLC for their purity. The purification steps led to the isolation of three pure bioactive compounds named as BC 01_C1, BC 01_C2 and BC 01_C3. The chemical structure of these three compounds was established on the basis of their spectroscopic studies like UV, IR, 1H and 13C NMR and GC–MS data by comparison with reference data from literature. The structure of the compound BC 01_C1 was established as 5-amino-2-(6-(2-hydroxyethyl)-3-oxononyl) cyclohex-2-enone. The compound BC 01_C2 was established as8-(aminomethyl)-7-hydroxy-1-(1-hydroxy-4-(hydroxylmethoxy)-2,3-dimethylbutyl)-2-methyl dodecahydro phenanthren-9(1H)-one and the compound BC 01_C3 was established as1-((E)-2-ethylhex-1-en-1-yl)2-((E)-2-ethylidenehexyl)cyclohexane-1,2-dicarboxylate. The MIC values of the three isolated compounds (BC 01_C1, BC 01_C2 and BC 01_C3) were found between 12.5–75 μg/ml for bacteria and 50–125 μg/ml for fungi used in this study. These compounds also possess in vitro antioxidant and anti-inflammatory activities.
Collapse
|
47
|
Nielsen JC, Nielsen J. Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism. Synth Syst Biotechnol 2017; 2:5-12. [PMID: 29062956 PMCID: PMC5625732 DOI: 10.1016/j.synbio.2017.02.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/01/2022] Open
Abstract
The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being identified. New computational tools are driven by genomics and metabolomics analysis, and enables rapid identification of novel secondary metabolites. To translate this increased discovery rate into industrial exploitation, it is necessary to integrate secondary metabolite pathways in the metabolic engineering process. In this review, we will describe the novel advances in discovery of secondary metabolites produced by filamentous fungi, highlight the utilization of genome-scale metabolic models (GEMs) in the design of fungal cell factories for the production of secondary metabolites and review strategies for optimizing secondary metabolite production through the construction of high yielding platform cell factories.
Collapse
Affiliation(s)
| | - Jens Nielsen
- Chalmers University of Technology, Kemivägen 10, Sweden
| |
Collapse
|
48
|
Kovalchuk A, Lee YH, Asiegbu FO. Diversity and evolution of ABC proteins in basidiomycetes. Mycologia 2017; 105:1456-70. [DOI: 10.3852/13-001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andriy Kovalchuk
- Department of Forest Sciences, P.O. Box 27, Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University Seoul 151-921, Korea
| | - Fred O. Asiegbu
- Department of Forest Sciences, P.O. Box 27, Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| |
Collapse
|
49
|
Wang TJ, Shan YM, Li H, Dou WW, Jiang XH, Mao XM, Liu SP, Guan WJ, Li YQ. Multiple transporters are involved in natamycin efflux in Streptomyces chattanoogensis L10. Mol Microbiol 2017; 103:713-728. [PMID: 27874224 DOI: 10.1111/mmi.13583] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/24/2022]
Abstract
Antibiotic-producing microorganisms have evolved several self-resistance mechanisms to prevent auto-toxicity. Overexpression of specific transporters to improve the efflux of toxic antibiotics has been found one of the most important and intrinsic resistance strategies used by many Streptomyces strains. In this work, two ATP-binding cassette (ABC) transporter-encoding genes located in the natamycin biosynthetic gene cluster, scnA and scnB, were identified as the primary exporter genes for natamycin efflux in Streptomyces chattanoogensis L10. Two other transporters located outside the cluster, a major facilitator superfamily transporter Mfs1 and an ABC transporter NepI/II were found to play a complementary role in natamycin efflux. ScnA/ScnB and Mfs1 also participate in exporting the immediate precursor of natamycin, 4,5-de-epoxynatamycin, which is more toxic to S. chattanoogensis L10 than natamycin. As the major complementary exporter for natamycin efflux, Mfs1 is up-regulated in response to intracellular accumulation of natamycin and 4,5-de-epoxynatamycin, suggesting a key role in the stress response for self-resistance. This article discusses a novel antibiotic-related efflux and response system in Streptomyces, as well as a self-resistance mechanism in antibiotic-producing strains.
Collapse
Affiliation(s)
- Tan-Jun Wang
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yi-Ming Shan
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Han Li
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Wei-Wang Dou
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xin-Hang Jiang
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolism Engineering, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Shui-Ping Liu
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Wen-Jun Guan
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolism Engineering, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolism Engineering, 866 Yuhangtang Road, Hangzhou, 310058, China
| |
Collapse
|
50
|
Ong KS, Aw YK, Lee LH, Yule CM, Cheow YL, Lee SM. Burkholderia paludis sp. nov., an Antibiotic-Siderophore Producing Novel Burkholderia cepacia Complex Species, Isolated from Malaysian Tropical Peat Swamp Soil. Front Microbiol 2016; 7:2046. [PMID: 28066367 PMCID: PMC5174137 DOI: 10.3389/fmicb.2016.02046] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022] Open
Abstract
A novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to be done.
Collapse
Affiliation(s)
- Kuan Shion Ong
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| | - Yoong Kit Aw
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| | - Learn Han Lee
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia
- Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University PhayaoPhayao, Thailand
| | - Catherine M. Yule
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| | - Yuen Lin Cheow
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University MalaysiaBandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University MalaysiaBandar Sunway, Malaysia
| |
Collapse
|