High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters

2021 ◽  
Author(s):  
Jimin Park ◽  
Sung Sun Yim ◽  
Harris H. Wang
Keyword(s):  
High Throughput ◽  
Gene Clusters ◽  
Regulatory Sequences ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

scholarly journals Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

2019 ◽  
Vol 116 (40) ◽  
pp. 19805-19814 ◽  
Author(s):  
Zachary L. Reitz ◽  
Clifford D. Hardy ◽  
Jaewon Suk ◽  
Jean Bouvet ◽  
Alison Butler
Keyword(s):  
Predictive Power ◽  
Genome Mining ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Peptide Synthetase ◽  
Condensation Domain

Genome mining of biosynthetic pathways streamlines discovery of secondary metabolites but can leave ambiguities in the predicted structures, which must be rectified experimentally. Through coupling the reactivity predicted by biosynthetic gene clusters with verified structures, the origin of the β-hydroxyaspartic acid diastereomers in siderophores is reported herein. Two functional subtypes of nonheme Fe(II)/α-ketoglutarate–dependent aspartyl β-hydroxylases are identified in siderophore biosynthetic gene clusters, which differ in genomic organization—existing either as fused domains (IβHAsp) at the carboxyl terminus of a nonribosomal peptide synthetase (NRPS) or as stand-alone enzymes (TβHAsp)—and each directs opposite stereoselectivity of Asp β-hydroxylation. The predictive power of this subtype delineation is confirmed by the stereochemical characterization of β-OHAsp residues in pyoverdine GB-1, delftibactin, histicorrugatin, and cupriachelin. The l-threo (2S, 3S) β-OHAsp residues of alterobactin arise from hydroxylation by the β-hydroxylase domain integrated into NRPS AltH, while l-erythro (2S, 3R) β-OHAsp in delftibactin arises from the stand-alone β-hydroxylase DelD. Cupriachelin contains both l-threo and l-erythro β-OHAsp, consistent with the presence of both types of β-hydroxylases in the biosynthetic gene cluster. A third subtype of nonheme Fe(II)/α-ketoglutarate–dependent enzymes (IβHHis) hydroxylates histidyl residues with l-threo stereospecificity. A previously undescribed, noncanonical member of the NRPS condensation domain superfamily is identified, named the interface domain, which is proposed to position the β-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized β-OHAsp diastereomers to the phylogenetic tree of siderophore β-hydroxylases, methods to predict β-OHAsp stereochemistry in silico are realized.

scholarly journals Recent advances in the genome mining of Aspergillus secondary metabolites (covering 2012–2018)

MedChemComm ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 840-866 ◽  
Author(s):  
Jillian Romsdahl ◽  
Clay C. C. Wang
Keyword(s):  
Aspergillus Terreus ◽  
Genome Mining ◽  
Gene Clusters ◽  
Genetic Identification ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
The Past ◽  
Made In

This review covers advances made in genome mining SMs produced by Aspergillus nidulans, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus in the past six years (2012–2018). Genetic identification and molecular characterization of SM biosynthetic gene clusters, along with proposed biosynthetic pathways, is discussed in depth.

scholarly journals Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6580
Author(s):  
Charlotte Beck ◽  
Tetiana Gren ◽  
Francisco Javier Ortiz-López ◽  
Tue Sparholt Jørgensen ◽  
Daniel Carretero-Molina ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Gene Clusters ◽  
Transcriptional Regulators ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Heterologous Host ◽  
Streptomyces Sp ◽  
Identification And Characterization

Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that “silent” biosynthetic gene clusters (BGCs) can be activated by heterologously expressing transcriptional regulators from other BGCs. Here, we have activated a silent BGC in Streptomyces sp. CA-256286 by overexpression of a set of SARP family transcriptional regulators. The structure of the produced compound was elucidated by NMR and found to be an N-acetyl cysteine adduct of the pyranonaphtoquinone polyketide 3′-O-α-d-forosaminyl-(+)-griseusin A. Employing a combination of multi-omics and metabolic engineering techniques, we identified the responsible BGC. These methods include genome mining, proteomics and transcriptomics analyses, in combination with CRISPR induced gene inactivations and expression of the BGC in a heterologous host strain. This work demonstrates an easy-to-implement workflow of how silent BGCs can be activated, followed by the identification and characterization of the produced compound, the responsible BGC, and hints of its biosynthetic pathway.

Phylogeny of the Bacillus altitudinis Complex and Characterization of a Newly Isolated Strain with Antilisterial Activity

2021 ◽  
Author(s):  
Lauren Kathryn Hudson ◽  
Leticia A.G. Orellana ◽  
Daniel W Bryan ◽  
Andrew Moore ◽  
John P. Munafo ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Foodborne Pathogens ◽  
Food Industry ◽  
Gene Clusters ◽  
Single Species ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Bacillus Altitudinis ◽  
Biocontrol Potential

Here, a Bacillus strain, UTK D1-0055, is described that was isolated from a laboratory environment. It was of interest as it demonstrated antilisterial activity. The genome was sequenced, which identified the strain as Bacillus altitudinis, and a high-quality complete annotated genome was produced. Additionally, the taxonomy of this and related species was evaluated, including B. aerophilus, B. pumilus, B. safensis, B. stratosphericus, and B. xiamensis, which is unclear and contains errors in public databases such as NCBI. The included strains grouped into seven clusters based on average nucleotide identity (ANI). Strains designated as B. aerophilus, B. altitudinis, and B. stratosphericus grouped together in the cluster containing the B. altitudinis type strain, suggesting that they should be considered a single species, B. altitudinis. Furthermore, the antimicrobial activity of UTK D1-0055 was determined against a panel of 15 Listeria spp. strains (including nine L. monocytogenes serotypes, L. innocua, and L. marthii), other foodborne pathogens (six Salmonella enterica serotypes and Escherichia coli), and three representative fungi (Saccharomyces cerevisiae, Botrytis cinerea, and Hyperdermium pulvinatum). Antibacterial activity was observed against all Listeria spp. strains, but no antagonistic effects were observed against the other bacterial or fungal strains tested. Biosynthetic gene clusters were identified in silico that may be related to the observed antibacterial activity, which included clusters that putatively encode bacteriocins and nonribosomally synthesized peptides. The Bacillus altitudinis strain identified in the present investigation showed a broad range of antilisterial activity, suggesting that it and other related strains may potentially be evaluated for their biocontrol potential in the food industry.

scholarly journals Genome-Wide High-Throughput Mining of Natural-Product Biosynthetic Gene Clusters by Phage Display

2007 ◽  
Vol 14 (3) ◽  
pp. 303-312 ◽  
Author(s):  
Jun Yin ◽  
Paul D. Straight ◽  
Siniša Hrvatin ◽  
Pieter C. Dorrestein ◽  
Stefanie B. Bumpus ◽  
...  
Keyword(s):  
Phage Display ◽  
Natural Product ◽  
High Throughput ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Genome Wide

scholarly journals Uncharted biosynthetic potential of the ocean microbiome

2021 ◽  
Author(s):  
Lucas Paoli ◽  
Hans-Joachim Ruscheweyh ◽  
Clarissa C. Forneris ◽  
Satria Kautsar ◽  
Quentin Clayssen ◽  
...  
Keyword(s):  
Single Cells ◽  
Niche Partitioning ◽  
Natural Populations ◽  
Gene Clusters ◽  
Natural Environments ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Phylogenetic Groups ◽  
Globally Distributed

SummaryMicrobes are phylogenetically and metabolically diverse. Yet capturing this diversity, assigning functions to host organisms and exploring the biosynthetic potential in natural environments remains challenging. We reconstructed >25,000 draft genomes, including from >2,500 uncharacterized species, from globally-distributed ocean microbial communities, and combined them with ∼10,000 genomes from cultivated and single cells. Mining this resource revealed ∼40,000 putative biosynthetic gene clusters (BGCs), many from unknown phylogenetic groups. Among these, we discovered Candidatus Eudoremicrobiaceae as one of the most biosynthetically diverse microbes detected to date. Discrete transcriptional states structuring natural populations were associated with a potentially niche-partitioning role for BGC products. Together with the characterization of the first Eudoremicrobiaceae natural product, this study demonstrates how microbiomics enables prospecting for candidate bioactive compounds in underexplored microbes and environments.

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