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Microorganisms
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Secondary Metabolism of Microorganisms
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Secondary Metabolism of Microorganisms

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 75187

Special Issue Editors

Dr. Carlos García-Estrada

E-Mail Website
Guest Editor
1. Instituto de Biotecnología de León (INBIOTEC), León, Spain
2. Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Campus de Vegazana, Universidad de León, 24071 León, Spain
Interests: fungal secondary metabolism; molecular biology; biotechnology; genetic engineering; omics
Special Issues, Collections and Topics in MDPI journals
Dr. Carlos Barreiro

E-Mail Website
Guest Editor
Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain
Interests: secondary metabolites; microorganisms; proteomics; plastics; actinobacteria; fungi; carotenoids; steroids; immunosuppressors; antibiotics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial secondary metabolism represents a very interesting research field. On the one hand, secondary metabolism is considered nonessential for microbial growth and development, but it results in the biosynthesis of an impressive array of compounds relevant for i) human and animal health (e.g., antibiotics, receptor antagonists and agonists, immunosuppressants), ii) food and feed (e.g., pigments), iii) agriculture (e.g., pheromones, plant protectants), and iv) farming (e.g., toxins). This industrially relevant group of compounds is produced by certain taxonomic clades of organisms such as bacteria, mainly Actinobacteria, and fungi. Since metabolite formation is usually repressed during the logarithmic phase of growth and boosted along the stationary growth phase, a regulatory fine-tuning of nutrients (e.g., phosphate, nitrogen), precursors, and energy molecules is needed. The understanding of this strictly controlled process opens the door to synthetic biology to redirect metabolic pathways, avoiding nutrient sinks and by-products generation.

On the other hand, secondary metabolism plays a significant ecological role in the communication among different microorganisms in nature. At present, mixed fermentation or co-cultivation is a trending manner in order to study, understand, and harness the microbial competition and communication when the appropriate physiological conditions are provided.

This Special Issue of Microorganisms invites researchers to contribute research articles, reviews, and opinions addressing the latest knowledge on the secondary metabolism of microorganisms, including molecular biology, omics, synthetic biology, industrial microbiology, genome editing, metabolites production, downstream processing, gene control and regulation, etc., both in fundamental research and its applications. This Special Issue is divided into three blocks: i) microbial secondary metabolites; ii) regulation of secondary metabolism; and iii) communication of microbial communities. Manuscripts covering these areas of knowledge, and others related to microbial secondary metabolism, are of interest for this Special Issue.

Dr. Carlos García-Estrada
Dr. Carlos Barreiro
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • secondary metabolites
  • industrial microbiology
  • microbial communication
  • metabolism regulation
  • genome editing
  • human and animal health
  • food and feed additives
  • biocontrol

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Published Papers (23 papers)

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13 pages, 3110 KiB  
Article
Overexpression of llm1 Affects the Synthesis of Secondary Metabolites of Aspergillus cristatus
by Yunsheng Wang, Yincui Chen, Jin Zhang and Chuanbo Zhang
Microorganisms 2022, 10(9), 1707; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10091707 - 24 Aug 2022
Cited by 2 | Viewed by 1568
Abstract
Putative methyltransferases are thought to be involved in the regulation of secondary metabolites in filamentous fungi. Here, we report the effects of overexpression of a predicted LaeA-like methyltransferase gene llm1 on the synthesis of secondary metabolites in Aspergillus cristatus. Our results revealed [...] Read more.
Putative methyltransferases are thought to be involved in the regulation of secondary metabolites in filamentous fungi. Here, we report the effects of overexpression of a predicted LaeA-like methyltransferase gene llm1 on the synthesis of secondary metabolites in Aspergillus cristatus. Our results revealed that overexpression of the gene llm1 in A. cristatus significantly hindered the production of conidia and enhanced sexual development, and reduced oxidative tolerance to hydrogen peroxide. Compared with the wild-type, the metabolic profile of the overexpression transformant was distinct, and the contents of multiple secondary metabolites were markedly increased, mainly including terpenoids and flavonoids, such as (S)-olEuropeic acid, gibberellin A62, gibberellin A95, ovalitenone, PD 98059, and 1-isomangostin. A total of 600 significantly differentially expressed genes (DEGs) were identified utilizing transcriptome sequencing, and the DEGs were predominantly enriched in transmembrane transport and secondary metabolism-related biological processes. In summary, the strategy of overexpressing global secondary metabolite regulators successfully activated the expression of secondary metabolite gene clusters, and the numerous secondary metabolites were greatly strengthened in A. cristatus. This study provides new insights into the in-depth exploitation and utilization of novel secondary metabolites of A. cristatus. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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14 pages, 3771 KiB  
Article
Comparative Analysis of Catabolic and Anabolic Dehydroshikimate Dehydratases for 3,4-DHBA Production in Escherichia coli
by Ekaterina A. Shmonova, Ekaterina A. Savrasova, Elizaveta N. Fedorova and Vera G. Doroshenko
Microorganisms 2022, 10(7), 1357; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071357 - 05 Jul 2022
Viewed by 1800
Abstract
The production of 3,4-dihydroxybenzoic acid (3,4-DHBA or protocatechuate) is a relevant task owing to 3,4-DHBA’s pharmaceutical properties and its use as a precursor for subsequent synthesis of high value-added chemicals. The microbial production of 3,4-DHBA using dehydroshikimate dehydratase (DSD) (EC: 4.2.1.118) has been [...] Read more.
The production of 3,4-dihydroxybenzoic acid (3,4-DHBA or protocatechuate) is a relevant task owing to 3,4-DHBA’s pharmaceutical properties and its use as a precursor for subsequent synthesis of high value-added chemicals. The microbial production of 3,4-DHBA using dehydroshikimate dehydratase (DSD) (EC: 4.2.1.118) has been demonstrated previously. DSDs from soil-dwelling organisms (where DSD is involved in quinate/shikimate degradation) and from Bacillus spp. (synthesizing the 3,4-DHBA-containing siderophore) were compared in terms of the kinetic properties and their ability to produce 3,4-DHBA. Catabolic DSDs from Corynebacterium glutamicum (QsuB) and Neurospora crassa (Qa-4) had higher Km (1 and 0.6 mM, respectively) and kcat (61 and 220 s−1, respectively) than biosynthetic AsbF from Bacillus thuringiensis (Km~0.04 mM, kcat~1 s−1). Product inhibition was found to be a crucial factor when choosing DSD for strain development. AsbF was more inhibited by 3,4-DHBA (IC50~0.08 mM), and Escherichia coli MG1655 ΔaroE PlacUV5-asbFattφ80 strain provided only 0.2 g/L 3,4-DHBA in test-tube fermentation. Isogenic strains MG1655 ΔaroE PlacUV5-qsuBattφ80 and MG1655 ΔaroE PlacUV5-qa-4attφ80 expressing QsuB and Qa-4 with IC50 ~0.35 mM and ~0.64 mM, respectively, accumulated 2.7 g/L 3,4-DHBA under the same conditions. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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17 pages, 3356 KiB  
Article
Identification of Nematicidal Metabolites from Purpureocillium lavendulum
by Rui Liu, Zheng-Xue Bao, Guo-Hong Li, Chun-Qiang Li, Shao-Lin Wang, Xue-Rong Pan, Ke-Qin Zhang and Pei-Ji Zhao
Microorganisms 2022, 10(7), 1343; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071343 - 02 Jul 2022
Cited by 7 | Viewed by 1758
Abstract
Purpureocillium lavendulum is a fungus with promising biocontrol applications. Here, transcriptome data acquired during the infection of Caenorhabditis elegans by Purpureocillium lavendulum showed that the transcription of metabolite synthesis genes was significantly up-regulated after 24 and 48 h of the fungus-nematode interaction. Then, [...] Read more.
Purpureocillium lavendulum is a fungus with promising biocontrol applications. Here, transcriptome data acquired during the infection of Caenorhabditis elegans by Purpureocillium lavendulum showed that the transcription of metabolite synthesis genes was significantly up-regulated after 24 and 48 h of the fungus-nematode interaction. Then, the up-regulated transcription level of lipoxygenase was confirmed by RT-qPCR. The ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis of differential metabolites revealed that this interaction resulted in the emergence of new metabolites or enhanced the production of metabolites. The results of the UPLC-MS analysis and the nematicidal assay were used to establish optimal culturing conditions under which 12 metabolites, including 3 hydroxylated C18 fatty acids and 9 steroids, were isolated and identified. Among them, hydroxylated fatty acids showed pronounced nematicidal activity against Meloidogyne incognita, and two degradative sterols showed chemotaxis activity to M. incognita. This study lays a foundation for the function of lipoxygenase and its products during the infection of Purpureocillium lavendulum. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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21 pages, 4624 KiB  
Article
Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms
by Óscar Velasco-Rodríguez, Mariana Fil, Tonje M. B. Heggeset, Kristin F. Degnes, David Becerro-Recio, Katarina Kolsaková, Tone Haugen, Malene Jønsson, Macarena Toral-Martínez, Carlos García-Estrada, Alberto Sola-Landa, Kjell D. Josefsen, Håvard Sletta and Carlos Barreiro
Microorganisms 2022, 10(6), 1249; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061249 - 18 Jun 2022
Cited by 6 | Viewed by 2119
Abstract
Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a [...] Read more.
Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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17 pages, 8386 KiB  
Article
Improved Neomycin Sulfate Potency in Streptomyces fradiae Using Atmospheric and Room Temperature Plasma (ARTP) Mutagenesis and Fermentation Medium Optimization
by Fei Yu, Min Zhang, Junfeng Sun, Fang Wang, Xiangfei Li, Yan Liu, Zhou Wang, Xinrui Zhao, Jianghua Li, Jian Chen, Guocheng Du and Zhenglian Xue
Microorganisms 2022, 10(1), 94; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010094 - 01 Jan 2022
Cited by 18 | Viewed by 2858
Abstract
To improve the screening efficiency of high-yield neomycin sulfate (NM) Streptomyces fradiae strains after mutagenesis, a high-throughput screening method using streptomycin resistance prescreening (8 μg/mL) and a 24-deep well plates/microplate reader (trypan blue spectrophotometry) rescreening strategy was developed. Using this approach, we identified [...] Read more.
To improve the screening efficiency of high-yield neomycin sulfate (NM) Streptomyces fradiae strains after mutagenesis, a high-throughput screening method using streptomycin resistance prescreening (8 μg/mL) and a 24-deep well plates/microplate reader (trypan blue spectrophotometry) rescreening strategy was developed. Using this approach, we identified a high-producing NM mutant strain, Sf6-2, via six rounds of atmospheric and room temperature plasma (ARTP) mutagenesis and screening. The mutant displayed a NM potency of 7780 ± 110 U/mL and remarkably stable genetic properties over six generations. Furthermore, the key components (soluble starch, peptone, and (NH4)2SO4) affecting NM potency in fermentation medium were selected using Plackett-Burman and optimized by Box-Behnken designs. Finally, the NM potency of Sf6-2 was increased to 10,849 ± 141 U/mL at the optimal concentration of each factor (73.98 g/L, 9.23 g/L, and 5.99 g/L, respectively), and it exhibited about a 40% and 100% enhancement when compared with before optimization conditions and the wild-type strain, respectively. In this study, we provide a new S. fradiae NM production strategy and generate valuable insights for the breeding and screening of other microorganisms. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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15 pages, 2351 KiB  
Article
Characterization of the Gene Encoding S-adenosyl-L-methionine (AdoMet) Synthetase in Penicillium chrysogenum; Role in Secondary Metabolism and Penicillin Production
by Rebeca Domínguez-Santos, Katarina Kosalková, Isabel-Clara Sánchez-Orejas, Carlos Barreiro, Yolanda Pérez-Pertejo, Rosa M. Reguera, Rafael Balaña-Fouce and Carlos García-Estrada
Microorganisms 2022, 10(1), 78; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010078 - 30 Dec 2021
Cited by 2 | Viewed by 1888
Abstract
The filamentous fungus Penicillium chrysogenum (recently reidentified as Penicillium rubens) is used in the industrial production of the β-lactam antibiotic penicillin. There are several mechanisms regulating the production of this antibiotic, acting both at the genetic and epigenetic levels, the latter including [...] Read more.
The filamentous fungus Penicillium chrysogenum (recently reidentified as Penicillium rubens) is used in the industrial production of the β-lactam antibiotic penicillin. There are several mechanisms regulating the production of this antibiotic, acting both at the genetic and epigenetic levels, the latter including the modification of chromatin by methyltransferases. S-adenosyl-L-methionine (AdoMet) is the main donor of methyl groups for methyltransferases. In addition, it also acts as a donor of aminopropyl groups during the biosynthesis of polyamines. AdoMet is synthesized from L-methionine and ATP by AdoMet-synthetase. In silico analysis of the P. chrysogenum genome revealed the presence of a single gene (Pc16g04380) encoding a putative protein with high similarity to well-known AdoMet-synthetases. Due to the essential nature of this gene, functional analysis was carried out using RNAi-mediated silencing techniques. Knock-down transformants exhibited a decrease in AdoMet, S-adenosyl-L-homocysteine (AdoHcy), spermidine and benzylpenicillin levels, whereas they accumulated a yellow-orange pigment in submerged cultures. On the other hand, overexpression led to reduced levels of benzylpenicillin, thereby suggesting that the AdoMet synthetase, in addition to participate in primary metabolism, also controls secondary metabolism in P. chrysogenum. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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9 pages, 1639 KiB  
Article
Pathogenicity and Volatile Nematicidal Metabolites from Duddingtonia flagrans against Meloidogyne incognita
by Xiaoyu Mei, Xin Wang and Guohong Li
Microorganisms 2021, 9(11), 2268; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112268 - 31 Oct 2021
Cited by 14 | Viewed by 2124
Abstract
Plant parasitic nematodes, especially parasitic root-knot nematodes, are one of the most destructive plant pathogens worldwide. The control of plant root-knot nematodes is extremely challenging. Duddingtonia flagrans is a type of nematode-trapping fungi (NTF), which produces three-dimensional adhesive networks to trap nematodes. In [...] Read more.
Plant parasitic nematodes, especially parasitic root-knot nematodes, are one of the most destructive plant pathogens worldwide. The control of plant root-knot nematodes is extremely challenging. Duddingtonia flagrans is a type of nematode-trapping fungi (NTF), which produces three-dimensional adhesive networks to trap nematodes. In this study, the pathogenicity and volatile organic compounds (VOCs) of the NTF D. flagrans against the plant root-knot nematode, Meloidogyne incognita, were investigated. The predatory process of D. flagrans trapping M. incognita was observed using scanning electron microscopy. Gas chromatography-mass spectrometry analysis of the VOCs from D. flagrans led to the identification of 52 metabolites, of which 11 main compounds were tested individually for their activity against M. incognita. Three compounds, cyclohexanamine, cyclohexanone, and cyclohexanol, were toxic to M. incognita. Furthermore, these three VOCs inhibited egg hatching of M. incognita. Cyclohexanamine showed the highest nematicidal activity, which can cause 97.93% mortality of M. incognita at 8.71 µM within 12 h. The number of hatched juveniles per egg mass after 3 days was just 8.44 when treated with 26.14 µM cyclohexanamine. This study is the first to demonstrate the nematicidal activity of VOCs produced by D. flagrans against M. incognita, which indicates that D. flagrans has the potential to biocontrol plant root-knot nematodes. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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15 pages, 4171 KiB  
Article
A Multidisciplinary Approach to Unraveling the Natural Product Biosynthetic Potential of a Streptomyces Strain Collection Isolated from Leaf-Cutting Ants
by Ana Ceniceros, Lorena Cuervo, Carmen Méndez, José A. Salas, Carlos Olano and Mónica G. Malmierca
Microorganisms 2021, 9(11), 2225; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112225 - 26 Oct 2021
Cited by 7 | Viewed by 1698
Abstract
The rapid emergence of bacterial resistance to antibiotics has urged the need to find novel bioactive compounds against resistant microorganisms. For that purpose, different strategies are being followed, one of them being exploring secondary metabolite production in microorganisms from uncommon sources. In this [...] Read more.
The rapid emergence of bacterial resistance to antibiotics has urged the need to find novel bioactive compounds against resistant microorganisms. For that purpose, different strategies are being followed, one of them being exploring secondary metabolite production in microorganisms from uncommon sources. In this work, we have analyzed the genome of 12 Streptomyces sp. strains of the CS collection isolated from the surface of leaf-cutting ants of the Attini tribe and compared them to four Streptomyces model species and Pseudonocardia sp. Ae150A_Ps1, which shares the ecological niche with those of the CS collection. We used a combination of phylogenetics, bioinformatics and dereplication analysis to study the biosynthetic potential of our strains. 51.5% of the biosynthetic gene clusters (BGCs) predicted by antiSMASH were unknown and over half of them were strain-specific, making this strain collection an interesting source of putative novel compounds. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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15 pages, 1918 KiB  
Article
Activation of Secondary Metabolism in Red Soil-Derived Streptomycetes via Co-Culture with Mycolic Acid-Containing Bacteria
by Kairui Wang, Ning Liu, Fei Shang, Jiao Huang, Bingfa Yan, Minghao Liu and Ying Huang
Microorganisms 2021, 9(11), 2187; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112187 - 20 Oct 2021
Cited by 1 | Viewed by 2168
Abstract
Our previous research has demonstrated a promising capacity of streptomycetes isolated from red soils to produce novel secondary metabolites, most of which, however, remain to be explored. Co-culturing with mycolic acid-containing bacteria (MACB) has been used successfully in activating the secondary metabolism in [...] Read more.
Our previous research has demonstrated a promising capacity of streptomycetes isolated from red soils to produce novel secondary metabolites, most of which, however, remain to be explored. Co-culturing with mycolic acid-containing bacteria (MACB) has been used successfully in activating the secondary metabolism in Streptomyces. Here, we co-cultured 44 strains of red soil-derived streptomycetes with four MACB of different species in a pairwise manner and analyzed the secondary metabolites. The results revealed that each of the MACB strains induced changes in the metabolite profiles of 35–40 streptomycetes tested, of which 12–14 streptomycetes produced “new” metabolites that were not detected in the pure cultures. Moreover, some of the co-cultures showed additional or enhanced antimicrobial activity compared to the pure cultures, indicating that co-culture may activate the production of bioactive compounds. From the co-culture-induced metabolites, we identified 49 putative new compounds. Taking the co-culture of Streptomyces sp. FXJ1.264 and Mycobacterium sp. HX09-1 as a case, we further explored the underlying mechanism of co-culture activation and found that it most likely relied on direct physical contact between the two living bacteria. Overall, our results verify co-culture with MACB as an effective approach to discover novel natural products from red soil-derived streptomycetes. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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17 pages, 4421 KiB  
Article
Secreted Secondary Metabolites Reduce Bacterial Wilt Severity of Tomato in Bacterial–Fungal Co-Infections
by Nandhitha Venkatesh, Max J. Koss, Claudio Greco, Grant Nickles, Philipp Wiemann and Nancy P. Keller
Microorganisms 2021, 9(10), 2123; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102123 - 09 Oct 2021
Cited by 5 | Viewed by 2272
Abstract
In order to gain a comprehensive understanding of plant disease in natural and agricultural ecosystems, it is essential to examine plant disease in multi-pathogen–host systems. Ralstonia solanacearum and Fusarium oxysporum f. sp. lycopersici are vascular wilt pathogens that can result in heavy [...] Read more.
In order to gain a comprehensive understanding of plant disease in natural and agricultural ecosystems, it is essential to examine plant disease in multi-pathogen–host systems. Ralstonia solanacearum and Fusarium oxysporum f. sp. lycopersici are vascular wilt pathogens that can result in heavy yield losses in susceptible hosts such as tomato. Although both pathogens occupy the xylem, the costs of mixed infections on wilt disease are unknown. Here, we characterize the consequences of co-infection with R. solanacearum and F. oxysporum using tomato as the model host. Our results demonstrate that bacterial wilt severity is reduced in co-infections, that bikaverin synthesis by Fusarium contributes to bacterial wilt reduction, and that the arrival time of each microbe at the infection court is important in driving the severity of wilt disease. Further, analysis of the co-infection root secretome identified previously uncharacterized secreted metabolites that reduce R. solanacearum growth in vitro and provide protection to tomato seedlings against bacterial wilt disease. Taken together, these results highlight the need to understand the consequences of mixed infections in plant disease. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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18 pages, 28085 KiB  
Article
6S-Like scr3559 RNA Affects Development and Antibiotic Production in Streptomyces coelicolor
by Jan Bobek, Adéla Mikulová, Dita Šetinová, Marie Elliot and Matouš Čihák
Microorganisms 2021, 9(10), 2004; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102004 - 22 Sep 2021
Cited by 6 | Viewed by 2123
Abstract
Regulatory RNAs control a number of physiological processes in bacterial cells. Here we report on a 6S-like RNA transcript (scr3559) that affects both development and antibiotic production in Streptomyces coelicolor. Its expression is enhanced during the transition to stationary phase. [...] Read more.
Regulatory RNAs control a number of physiological processes in bacterial cells. Here we report on a 6S-like RNA transcript (scr3559) that affects both development and antibiotic production in Streptomyces coelicolor. Its expression is enhanced during the transition to stationary phase. Strains that over-expressed the scr3559 gene region exhibited a shortened exponential growth phase in comparison with a control strain; accelerated aerial mycelium formation and spore maturation; alongside an elevated production of actinorhodin and undecylprodigiosin. These observations were supported by LC-MS analyses of other produced metabolites, including: germicidins, desferrioxamines, and coelimycin. A subsequent microarray differential analysis revealed increased expression of genes associated with the described morphological and physiological changes. Structural and functional similarities between the scr3559 transcript and 6S RNA, and its possible employment in regulating secondary metabolite production are discussed. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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15 pages, 2188 KiB  
Article
Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces
by Jin-Soo Park, Da-Eun Kim, Sung-Chul Hong, Seung-Young Kim, Hak Cheol Kwon, Chang-Gu Hyun and Jaeyoung Choi
Microorganisms 2021, 9(9), 1802; https://doi.org/10.3390/microorganisms9091802 - 25 Aug 2021
Cited by 4 | Viewed by 3209
Abstract
Streptomyces spp. have been major contributors of novel natural products that are used in many application areas. We found that the nojirimycin (NJ) producer JCM 3382 has antimicrobial activity against Staphylococcus aureus via cellular degradation. Genome analysis revealed 30 biosynthetic gene clusters, including [...] Read more.
Streptomyces spp. have been major contributors of novel natural products that are used in many application areas. We found that the nojirimycin (NJ) producer JCM 3382 has antimicrobial activity against Staphylococcus aureus via cellular degradation. Genome analysis revealed 30 biosynthetic gene clusters, including those responsible for producing antibiotics, including an azasugar NJ. In-depth MS/MS analysis confirmed the production of 1-deoxynojirimycin (DNJ) along with NJ. In addition, the production of tambromycins, setomimycin, and linearmycins was verified by spectroscopic analyses, including LC-MS and NMR. The distribution of the clusters of genes coding for antibiotics in 2061 Streptomyces genomes suggested potential producers of tambromycin, setomimycin, and linearmycin. For a DNJ gene cluster, homologs of gabT1 and gutB1 were commonly found; however, yktC1 was identified in only 112 genomes. The presence of several types of clusters suggests that different strains may produce different types of azasugars. Chemical-profile-inspired comparative genome analysis may facilitate a more accurate assessment of the biosynthetic potential to produce secondary metabolites. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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11 pages, 5453 KiB  
Article
Pathogenicity and Metabolites of Endoparasitic Nematophagous Fungus Drechmeria coniospora YMF1.01759 against Nematodes
by Juan Wan, Zebao Dai, Keqin Zhang, Guohong Li and Peiji Zhao
Microorganisms 2021, 9(8), 1735; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081735 - 14 Aug 2021
Cited by 11 | Viewed by 3081
Abstract
Plant parasitic nematodes cause severe damage to crops. Endoparasitic nematophagous fungi (ENF) are a type of important biocontrol fungi, which can cause disease or kill nematodes by producing various spores. As a major ENF, Drechmeria coniospora displays certain potential for controlling plant-parasitic nematodes. [...] Read more.
Plant parasitic nematodes cause severe damage to crops. Endoparasitic nematophagous fungi (ENF) are a type of important biocontrol fungi, which can cause disease or kill nematodes by producing various spores. As a major ENF, Drechmeria coniospora displays certain potential for controlling plant-parasitic nematodes. In this study, the pathogenicity and secondary metabolites of the endoparasitic fungus D. coniospora YMF1.01759 were investigated. The strain D. coniospora YMF1.01759 had high infection efficiency against nematodes. The process of infecting nematodes by the strain was observed under an electron microscope. Here, 13 metabolites including one new compound 4(S)-butoxy-3-(butoxymethyl)-2-hydroxycyclopent-2-en-1-one (2) were isolated and identified from the fermentation products of D. coniospora YMF1.01759 cultured in a SDAY solid medium. Furthermore, a bioassay showed that 5-hydroxymethylfuran-2-carboxylic acid (1) is toxic to the root knot nematode Meloidogyne incognita and affects the hatching of its egg. Thereby, the nematicidal mortality attained 81.50% at 100 μg/mL for 48 h. Furthermore, egg hatching was inhibited at the tested concentrations, compared with water control eggs. This is the first report on the secondary metabolites of the ENF D. coniospora. The results indicated that D. coniospora could infect nematodes by spores and produce active metabolites to kill nematodes. The biological control potential of D. coniospora against nematodes was expounded further. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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15 pages, 948 KiB  
Article
Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
by Dingrong Kang, Saeed Shoaie, Samuel Jacquiod, Søren J. Sørensen and Rodrigo Ledesma-Amaro
Microorganisms 2021, 9(5), 1042; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051042 - 12 May 2021
Cited by 7 | Viewed by 3268
Abstract
A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species [...] Read more.
A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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18 pages, 1772 KiB  
Article
Sustainable Production of N-methylphenylalanine by Reductive Methylamination of Phenylpyruvate Using Engineered Corynebacterium glutamicum
by Anastasia Kerbs, Melanie Mindt, Lynn Schwardmann and Volker F. Wendisch
Microorganisms 2021, 9(4), 824; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040824 - 13 Apr 2021
Cited by 11 | Viewed by 3196
Abstract
N-alkylated amino acids occur widely in nature and can also be found in bioactive secondary metabolites such as the glycopeptide antibiotic vancomycin and the immunosuppressant cyclosporine A. To meet the demand for N-alkylated amino acids, they are currently produced chemically; however, [...] Read more.
N-alkylated amino acids occur widely in nature and can also be found in bioactive secondary metabolites such as the glycopeptide antibiotic vancomycin and the immunosuppressant cyclosporine A. To meet the demand for N-alkylated amino acids, they are currently produced chemically; however, these approaches often lack enantiopurity, show low product yields and require toxic reagents. Fermentative routes to N-alkylated amino acids like N-methyl-l-alanine or N-methylantranilate, a precursor of acridone alkaloids, have been established using engineered Corynebacterium glutamicum, which has been used for the industrial production of amino acids for decades. Here, we describe metabolic engineering of C. glutamicum for de novo production of N-methylphenylalanine based on reductive methylamination of phenylpyruvate. Pseudomonas putida Δ-1-piperideine-2-carboxylate reductase DpkA containing the amino acid exchanges P262A and M141L showed comparable catalytic efficiencies with phenylpyruvate and pyruvate, whereas the wild-type enzyme preferred the latter substrate over the former. Deletion of the anthranilate synthase genes trpEG and of the genes encoding branched-chain amino acid aminotransferase IlvE and phenylalanine aminotransferase AroT in a strain engineered to overproduce anthranilate abolished biosynthesis of l-tryptophan and l-phenylalanine to accumulate phenylpyruvate. Upon heterologous expression of DpkAP262A,M141L, N-methylphenylalanine production resulted upon addition of monomethylamine to the medium. In glucose-based minimal medium, an N-methylphenylalanine titer of 0.73 ± 0.05 g L−1, a volumetric productivity of 0.01 g L−1 h−1 and a yield of 0.052 g g−1 glucose were reached. When xylose isomerase gene xylA from Xanthomonas campestris and the endogenous xylulokinase gene xylB were expressed in addition, xylose as sole carbon source supported production of N-methylphenylalanine to a titer of 0.6 ± 0.04 g L−1 with a volumetric productivity of 0.008 g L−1 h−1 and a yield of 0.05 g g−1 xylose. Thus, a fermentative route to sustainable production of N-methylphenylalanine by recombinant C. glutamicum has been established. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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Review

Jump to: Research

20 pages, 3155 KiB  
Review
Metabolites and Their Bioactivities from the Genus Cordyceps
by Shuai-Ling Qu, Su-Su Li, Dong Li and Pei-Ji Zhao
Microorganisms 2022, 10(8), 1489; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081489 - 24 Jul 2022
Cited by 4 | Viewed by 3534
Abstract
The Cordyceps genus is a group of ascomycete parasitic fungi, and all known species of this genus are endoparasites; they mainly feed on insects or arthropods and a few feed on other fungi. Fungi of this genus have evolved highly specific and complex [...] Read more.
The Cordyceps genus is a group of ascomycete parasitic fungi, and all known species of this genus are endoparasites; they mainly feed on insects or arthropods and a few feed on other fungi. Fungi of this genus have evolved highly specific and complex mechanisms to escape their host’s immune system and coordinate their life cycle coefficients with those of their hosts for survival and reproduction; this mechanism has led to the production of distinctive metabolites in response to the host’s defenses. Herein, we review approximately 131 metabolites discovered in the genus Cordyceps (including mycelium, fruiting bodies and fungal complexes) in the past 15 years, which can be used as an important source for new drug research and development. We summarize chemical structures, bioactivity and the potential application of these natural metabolites. We have excluded some reports that originally belonged to Cordyceps, but whose taxonomic attribution is no longer the Cordyceps genus. This can and will serve as a resource for drug discovery. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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16 pages, 1377 KiB  
Review
Mycelium vs. Fruiting Bodies of Edible Fungi—A Comparison of Metabolites
by Ralf G. Berger, Sven Bordewick, Nina-Katharina Krahe and Franziska Ersoy
Microorganisms 2022, 10(7), 1379; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071379 - 08 Jul 2022
Cited by 24 | Viewed by 5485
Abstract
Edible mushrooms are widely appreciated for their appealing flavours, low caloric values and high content of presumably health-protecting metabolites. Their long history of safe use together with the looming worldwide food crisis have revived the idea of generating meat analogues and protein isolates [...] Read more.
Edible mushrooms are widely appreciated for their appealing flavours, low caloric values and high content of presumably health-protecting metabolites. Their long history of safe use together with the looming worldwide food crisis have revived the idea of generating meat analogues and protein isolates by the controlled fermentation of mycelia of these edible fungi as a dietary option. The occurrence of proteins, polysaccharides, smaller metabolites, metal ions and toxins in mycelia and fruiting bodies is compared among the three most popular species, Agaricus bisporus (button mushroom), Pleurotus ostreatus (oyster mushroom), Lentinus edodes (shiitake) and some closely related species. Large effects of substrate chemistry, strain, developmental stage and ecological interactions result in a wide variation of the concentrations of some metabolites in both mycelial cells and fruiting bodies. This is obviously a result of the high adaptation abilities required to survive in natural habitats. Fungal bioprocesses are decoupled from agricultural production and can be operated anytime, anywhere, and on any scale according to demand. It is concluded that fungal biomass, if produced under food-grade conditions and on an industrial scale, could provide a safe and nutritious meat substitute and protein isolates with a high biological value for future vegan foods. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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14 pages, 320 KiB  
Review
Nematicidal Effects of Volatile Organic Compounds from Microorganisms and Plants on Plant-Parasitic Nematodes
by Xiaotong Deng, Xin Wang and Guohong Li
Microorganisms 2022, 10(6), 1201; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061201 - 12 Jun 2022
Cited by 13 | Viewed by 2735
Abstract
Plant-parasitic nematodes (PPNs) are one of the most destructive plant pathogens worldwide, and controlling them is extremely challenging. Volatile organic compounds (VOCs), which naturally exist in plants and microorganisms, play an important role in the biological control of PPNs and are considered potential [...] Read more.
Plant-parasitic nematodes (PPNs) are one of the most destructive plant pathogens worldwide, and controlling them is extremely challenging. Volatile organic compounds (VOCs), which naturally exist in plants and microorganisms, play an important role in the biological control of PPNs and are considered potential substances for the development of commercial nematicides. This paper summarizes the VOCs produced by microorganisms and plants as well as their toxic effects on PPNs. VOCs from 26 microbial strains and 51 plants that are active against nematodes from over the last decade were reviewed. Furthermore, the mechanisms of toxicity of some VOCs against PPNs are also illustrated. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
58 pages, 3014 KiB  
Review
Penicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology
by Francisco Fierro, Inmaculada Vaca, Nancy I. Castillo, Ramón Ovidio García-Rico and Renato Chávez
Microorganisms 2022, 10(3), 573; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030573 - 06 Mar 2022
Cited by 25 | Viewed by 9187
Abstract
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since [...] Read more.
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since the forties of the past century; industrial biotechnology developed hand in hand with it, and currently P. chrysogenum is a thoroughly studied model for secondary metabolite production and regulation. In addition to its role as penicillin producer, recent synthetic biology advances have put P. chrysogenum on the path to become a cell factory for the production of metabolites with biotechnological interest. In this review, we tell the history of P. chrysogenum, from the discovery of penicillin and the first isolation of strains with high production capacity to the most recent research advances with the fungus. We will describe how classical strain improvement programs achieved the goal of increasing production and how the development of different molecular tools allowed further improvements. The discovery of the penicillin gene cluster, the origin of the penicillin genes, the regulation of penicillin production, and a compilation of other P. chrysogenum secondary metabolites will also be covered and updated in this work. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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22 pages, 876 KiB  
Review
Endophytic Fungal Terpenoids: Natural Role and Bioactivities
by Juan M. Galindo-Solís and Francisco J. Fernández
Microorganisms 2022, 10(2), 339; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020339 - 01 Feb 2022
Cited by 18 | Viewed by 4753
Abstract
Endophytic fungi are a highly diverse group of fungi that intermittently colonize all plants without causing symptoms of the disease. They sense and respond to physiological and environmental changes of their host plant and microbiome. The inter-organism interactions are largely driven by chemical [...] Read more.
Endophytic fungi are a highly diverse group of fungi that intermittently colonize all plants without causing symptoms of the disease. They sense and respond to physiological and environmental changes of their host plant and microbiome. The inter-organism interactions are largely driven by chemical networks mediated by specialized metabolites. The balance of these complex interactions leads to healthy and strong host plants. Endophytic strains have particular machinery to produce a plethora of secondary metabolites with a variety of bioactivities and unknown functions in an ecological niche. Terpenoids play a key role in endophytism and represent an important source of bioactive molecules for human health and agriculture. In this review, we describe the role of endophytic fungi in plant health, fungal terpenoids in multiple interactions, and bioactive fungal terpenoids recently reported from endophytes, mainly from plants used in traditional medicine, as well as from algae and mangroves. Additionally, we highlight endophytic fungi as producers of important chemotherapeutic terpenoids, initially discovered in plants. Despite advances in understanding endophytism, we still have much to learn in this field. The study of the role, the evolution of interactions of endophytic fungi and their terpenoids provide an opportunity for better applications in human health and agriculture. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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16 pages, 504 KiB  
Review
An Overview of Bioprocesses Employing Specifically Selected Microbial Catalysts for γ-Aminobutyric Acid Production
by Divakar Dahiya, Jemima V. Manuel and Poonam Singh Nigam
Microorganisms 2021, 9(12), 2457; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122457 - 28 Nov 2021
Cited by 24 | Viewed by 2340
Abstract
Gamma-aminobutyric acid (GABA) is an important chemical compound in the human brain. GABA acts as an inhibitory neurotransmitter by inducing hyperpolarization of cellular membranes. Usually, this pharmaceutically important compound is synthesized using a chemical process, but in this short overview we have only [...] Read more.
Gamma-aminobutyric acid (GABA) is an important chemical compound in the human brain. GABA acts as an inhibitory neurotransmitter by inducing hyperpolarization of cellular membranes. Usually, this pharmaceutically important compound is synthesized using a chemical process, but in this short overview we have only analysed microbial processes, which have been studied for the biosynthesis of this commercially important compound. The content of this article includes the following summarised information: the search for biological processes showed a number of lactic acid bacteria and certain species of fungi, which could be effectively used for the production of GABA. Strains found to possess GABA-producing pathways include Lactobacillus brevis CRL 1942, L. plantarum FNCC 260, Streptococcus salivarius subsp. thermophilus Y2, Bifidobacterium strains, Monascus spp., and Rhizopus spp. Each of these strains required specific growth conditions. However, several factors were common among these strains, such as the use of two main supplements in their fermentation medium—monosodium glutamate and pyridoxal phosphate—and maintaining an acidic pH. Optimization studies of GABA production were comprised of altering the media constituents, modifying growth conditions, types of cultivation system, and genetic manipulation. Some strains increased the production of GABA under anaerobic conditions. Genetic manipulation focused on silencing some genes or overexpression of gadB and gadC. The conclusion, based on the review of information available in published research, is that the targeted manipulation of selected microorganisms, as well as the culture conditions for an optimised bioprocess, should be adopted for an increased production of GABA to meet its increasing demand for food and pharmaceutical applications. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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17 pages, 2179 KiB  
Review
In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens
by Sami Khabthani, Jean-Marc Rolain and Vicky Merhej
Microorganisms 2021, 9(11), 2297; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112297 - 05 Nov 2021
Cited by 12 | Viewed by 3643
Abstract
Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new [...] Read more.
Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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50 pages, 7711 KiB  
Review
Bioactive Secondary Metabolites of the Genus Diaporthe and Anamorph Phomopsis from Terrestrial and Marine Habitats and Endophytes: 2010–2019
by Tang-Chang Xu, Yi-Han Lu, Jun-Fei Wang, Zhi-Qiang Song, Ya-Ge Hou, Si-Si Liu, Chuan-Sheng Liu and Shao-Hua Wu
Microorganisms 2021, 9(2), 217; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020217 - 21 Jan 2021
Cited by 44 | Viewed by 4449
Abstract
The genus Diaporthe and its anamorph Phomopsis are distributed worldwide in many ecosystems. They are regarded as potential sources for producing diverse bioactive metabolites. Most species are attributed to plant pathogens, non-pathogenic endophytes, or saprobes in terrestrial host plants. They colonize in the [...] Read more.
The genus Diaporthe and its anamorph Phomopsis are distributed worldwide in many ecosystems. They are regarded as potential sources for producing diverse bioactive metabolites. Most species are attributed to plant pathogens, non-pathogenic endophytes, or saprobes in terrestrial host plants. They colonize in the early parasitic tissue of plants, provide a variety of nutrients in the cycle of parasitism and saprophytism, and participate in the basic metabolic process of plants. In the past ten years, many studies have been focused on the discovery of new species and biological secondary metabolites from this genus. In this review, we summarize a total of 335 bioactive secondary metabolites isolated from 26 known species and various unidentified species of Diaporthe and Phomopsis during 2010–2019. Overall, there are 106 bioactive compounds derived from Diaporthe and 246 from Phomopsis, while 17 compounds are found in both of them. They are classified into polyketides, terpenoids, steroids, macrolides, ten-membered lactones, alkaloids, flavonoids, and fatty acids. Polyketides constitute the main chemical population, accounting for 64%. Meanwhile, their bioactivities mainly involve cytotoxic, antifungal, antibacterial, antiviral, antioxidant, anti-inflammatory, anti-algae, phytotoxic, and enzyme inhibitory activities. Diaporthe and Phomopsis exhibit their potent talents in the discovery of small molecules for drug candidates. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)
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