Evolutionary age of genes can assist in genome mining

Cyanobacteria are prolific producers of natural products and genome mining has shown that many orphan biosynthetic gene clusters can be found in sequenced cyanobacterial genomes. New tools and methodologies are required to investigate these biosynthetic gene clusters and here we present the use of <i>Anabaena </i>sp. strain PCC 7120 as a host for combinatorial biosynthesis of natural products using the indolactam natural products (lyngbyatoxin A, pendolmycin, and teleocidin B-4) as a test case. We were able to successfully produce all three compounds using codon optimized genes from Actinobacteria. We also introduce a new plasmid backbone based on the native <i>Anabaena</i>7120 plasmid pCC7120ζ and show that production of teleocidin B-4 can be accomplished using a two-plasmid system, which can be introduced by co-conjugation.

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Faculty Opinions recommendation of Epigenetic genome mining of an endophytic fungus leads to the pleiotropic biosynthesis of natural products.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725516668.793507634 ◽

2015 ◽

Author(s):

Leo Eberl

Keyword(s):

Natural Products ◽

Endophytic Fungus ◽

Genome Mining

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Faculty Opinions recommendation of Epigenetic genome mining of an endophytic fungus leads to the pleiotropic biosynthesis of natural products.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725516668.793507166 ◽

2015 ◽

Author(s):

Gavin Williams ◽

Sean Lund

Keyword(s):

Natural Products ◽

Endophytic Fungus ◽

Genome Mining

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Faculty Opinions recommendation of Genome Mining Reveals High Topological Diversity of ω-Ester-Containing Peptides and Divergent Evolution of ATP-Grasp Macrocyclases.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.737245209.793579708 ◽

2020 ◽

Author(s):

Hiroaki Suga

Keyword(s):

Genome Mining ◽

Divergent Evolution

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Recent Advances in Discovery, Biosynthesis and Genome Mining of Medicinally Relevant Polycyclic Tetramate Macrolactams

Current Topics in Medicinal Chemistry ◽

10.2174/1568026616666151012112818 ◽

2016 ◽

Vol 16 (15) ◽

pp. 1727-1739 ◽

Cited By ~ 21

Author(s):

Guangtao Zhang ◽

Wenjun Zhang ◽

Subhasish Saha ◽

Changsheng Zhang

Keyword(s):

Genome Mining ◽

Recent Advances

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Genome Mining and Evaluation of the Biocontrol Potential of Pseudomonas fluorescens BRZ63, a New Endophyte of Oilseed Rape (Brassica napus L.) against Fungal Pathogens

International Journal of Molecular Sciences ◽

10.3390/ijms21228740 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8740

Author(s):

Daria Chlebek ◽

Artur Pinski ◽

Joanna Żur ◽

Justyna Michalska ◽

Katarzyna Hupert-Kocurek

Keyword(s):

Brassica Napus ◽

Plant Growth ◽

Pseudomonas Fluorescens ◽

Oilseed Rape ◽

Plant Growth Promotion ◽

Fungal Pathogens ◽

Growth Promotion ◽

Genome Mining ◽

Plant Colonization ◽

Brassica Napus L

Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion.

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An FYVE-Domain-Containing Protein, PsFP1, Is Involved in Vegetative Growth, Oxidative Stress Response and Virulence of Phytophthora sojae

International Journal of Molecular Sciences ◽

10.3390/ijms22126601 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6601

Author(s):

Jinhui Zhang ◽

Xiaoran Du ◽

Xin Zhou ◽

Duo Jin ◽

Jianqiang Miao ◽

...

Keyword(s):

Oxidative Stress ◽

Membrane Trafficking ◽

Vegetative Growth ◽

Genome Mining ◽

Gene Replacement ◽

Wide Distribution ◽

Stress Sensitivity ◽

Phytophthora Sojae ◽

Knock Out ◽

Fyve Domain

Proteins that contain the FYVE zinc-finger domain are recruited to PtdIns3P-containing membranes, participating in numerous biological processes such as membrane trafficking, cytoskeletal regulation, and receptor signaling. However, the genome-wide distribution, evolution, and biological functions of FYVE-containing proteins are rarely reported for oomycetes. By genome mining of Phytophthora sojae, two proteins (PsFP1 and PsFP2) with a combination of the FYVE domain and the PX domain (a major phosphoinositide binding module) were found. To clarify the functions of PsFP1 and PsFP2, the CRISPR/Cas9-mediated gene replacement system was used to knock out the two genes respectively. Only heterozygous deletion mutants of PsFP1 were recovered, and the expression level of PsFP1 in the heterozygous knockout transformants was significantly down-regulated. These PsFP1 mutants showed a decrease in mycelial growth and pathogenicity and were more sensitive to hydrogen peroxide. These phenotypes were recovered to the level of wild-type by overexpression PsFP1 gene in the PsFP1 heterozygous knockout transformant. In contrast, deletion of PsFP2 had no significant effect on vegetative growth, asexual and sexual reproduction, pathogenicity, or oxidative stress sensitivity. PsFP1 was primarily localized in vesicle-like structures and both the FYVE and PX domains are important for its localization. Overall, our results indicate that PsFP1 plays an important role in the vegetative growth and virulence of P. sojae.

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