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Microbial Genomics and Biosynthesis

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 7832

Special Issue Editor


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Guest Editor
Department of Biology and Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON, Canada
Interests: biosynthesis; antibiotics; gene regulation; non-coding RNA; streptomyces; strain prioritization; genetic engineering
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Special Issue Information

Dear Colleagues,

Microbial small molecules often have potent biological activities, e.g., anti-infective, anticancer, immunosuppressive activities, and mediator substances during microbe–microbe or host–microbe interactions. The increasing number of genome sequences has virtually advanced any microbial research area, including (i) the discovery of novel biosynthetic gene clusters and their products, (ii) new biosynthetic pathways and enzymatic mechanism, intricate and fascinating regulatory elements, (iii) novel mechanisms of resistance to anti-infectives, (iv) new approaches to the yield improvement of microbial products, and (v) microbial ecology. 

Published genomes have also opened the door to strain prioritization. Researchers were previously limited to one or two strains for biosynthetic studies. Now, alternative strains can be found by genomic comparative analysis and be further investigated to establish a better model system. Interestingly, we could look for a better system in nature (by strain isolation, screening, and genome sequencing). Coupled with the continuous development of bioinformatic tools and biosynthetic knowledge, strain prioritization is on an upward trajectory to the discovery of molecular analogues with more potent bioactivities and/or more stable during isolation.

To contribute to the research areas mentioned above, this Special Issue will cover (but not be limited to) the following topics:

  • Novel microbial strains as producers of bioactive small molecules;
  • Microbial genomes as a source of inspiration in synthetic biology;
  • Hidden treasures of molecular sciences unveiled by genome mining;
  • Method development in genome sequencing and analysis;
  • Microbial genomes as an essential tool for microbe–microbe or host–microbe interaction studies.

We look forward to your manuscript submission in the form of original research articles or reviews.

Dr. Hindra Hindra
Guest Editor

Manuscript Submission Information

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Keywords

  • secondary metabolism
  • biosynthetic genes
  • phylogenetic
  • fermentation
  • titer or yield
  • specialized metabolites
  • signaling molecules
  • long-read sequencing
  • heterologous expression
  • induction/stimulation/activation

Published Papers (3 papers)

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Research

22 pages, 38576 KiB  
Article
Polyenic Antibiotics and Other Antifungal Compounds Produced by Hemolytic Streptomyces Species
by Jan Bobek, Eliška Filipová, Natalie Bergman, Matouš Čihák, Miroslav Petříček, Ana Catalina Lara, Vaclav Kristufek, Melinda Megyes, Theresa Wurzer, Alica Chroňáková and Kateřina Petříčková
Int. J. Mol. Sci. 2022, 23(23), 15045; https://doi.org/10.3390/ijms232315045 - 30 Nov 2022
Cited by 1 | Viewed by 2643
Abstract
Streptomyces are of great interest in the pharmaceutical industry as they produce a plethora of secondary metabolites that act as antibacterial and antifungal agents. They may thrive on their own in the soil, or associate with other organisms, such as plants or invertebrates. [...] Read more.
Streptomyces are of great interest in the pharmaceutical industry as they produce a plethora of secondary metabolites that act as antibacterial and antifungal agents. They may thrive on their own in the soil, or associate with other organisms, such as plants or invertebrates. Some soil-derived strains exhibit hemolytic properties when cultivated on blood agar, raising the question of whether hemolysis could be a virulence factor of the bacteria. In this work we examined hemolytic compound production in 23 β-hemolytic Streptomyces isolates; of these 12 were soil-derived, 10 were arthropod-associated, and 1 was plant-associated. An additional human-associated S. sp. TR1341 served as a control. Mass spectrometry analysis suggested synthesis of polyene molecules responsible for the hemolysis: candicidins, filipins, strevertene A, tetrafungin, and tetrin A, as well as four novel polyene compounds (denoted here as polyene A, B, C, and D) in individual liquid cultures or paired co-cultures. The non-polyene antifungal compounds actiphenol and surugamide A were also identified. The findings indicate that the ability of Streptomyces to produce cytolytic compounds (here manifested by hemolysis on blood agar) is an intrinsic feature of the bacteria in the soil environment and could even serve as a virulence factor when colonizing available host organisms. Additionally, a literature review of polyenes and non-polyene hemolytic metabolites produced by Streptomyces is presented. Full article
(This article belongs to the Special Issue Microbial Genomics and Biosynthesis)
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12 pages, 2966 KiB  
Article
Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T
by Jun Ho Lee, Seong-Rae Lee, Sejong Han and Pyung Cheon Lee
Int. J. Mol. Sci. 2022, 23(18), 10884; https://doi.org/10.3390/ijms231810884 - 17 Sep 2022
Cited by 3 | Viewed by 1821
Abstract
Flavobacteria are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of Flavobacterium faecale WV33T, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of F. faecale WV33 [...] Read more.
Flavobacteria are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of Flavobacterium faecale WV33T, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of F. faecale WV33T represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of F. faecale WV33T contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 Flavobacterium type strains, including F. faecale WV33T, tend to be very plastic, and Flavobacterium strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 Flavobacterium-type strains showed that F. faecale WV33T was positioned in a unique clade in the evolutionary tree. Full article
(This article belongs to the Special Issue Microbial Genomics and Biosynthesis)
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13 pages, 1448 KiB  
Article
Combination Strategy of Genetic Dereplication and Manipulation of Epigenetic Regulators Reveals a Novel Compound from Plant Endophytic Fungus
by Lu Yang, Guangwei Wu, Fanyue Meng, Huomiao Ran, Wenbing Yin, Wei Li and Xiaoqing Liu
Int. J. Mol. Sci. 2022, 23(7), 3686; https://doi.org/10.3390/ijms23073686 - 28 Mar 2022
Viewed by 2119
Abstract
The strategies of genetic dereplication and manipulation of epigenetic regulators to activate the cryptic gene clusters are effective to discover natural products with novel structure in filamentous fungi. In this study, a combination of genetic dereplication (deletion of pesthetic acid biosynthetic gene, PfptaA [...] Read more.
The strategies of genetic dereplication and manipulation of epigenetic regulators to activate the cryptic gene clusters are effective to discover natural products with novel structure in filamentous fungi. In this study, a combination of genetic dereplication (deletion of pesthetic acid biosynthetic gene, PfptaA) and manipulation of epigenetic regulators (deletion of histone methyltransferase gene PfcclA and histone deacetylase gene PfhdaA) was developed in plant endophytic fungus Pestalotiopsis fici. The deletion of PfptaA with PfcclA and/or PfhdaA led to isolation of 1 novel compound, pestaloficiol X (1), as well as another 11 known compounds with obvious yield changes. The proposed biosynthesis pathway of pestaloficiol X was speculated using comparative analysis of homologous biosynthetic gene clusters. Moreover, phenotypic effects on the conidial development and response to oxidative stressors in the mutants were explored. Our results revealed that the new strain with deletion of PfcclA or PfhdaA in ΔPfptaA background host can neutralise the hyperformation of conidia in the PfptaA mutant, and that the ΔPfptaA ΔPfhdaA mutant was generally not sensitive to oxidative stressors as much as the ΔPfptaA ΔcclA mutant in comparison with the single mutant ΔPfptaA or the parental strains. This combinatorial approach can be applied to discover new natural products in filamentous fungi. Full article
(This article belongs to the Special Issue Microbial Genomics and Biosynthesis)
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