Genome-Wide Analysis of Secondary Metabolite Gene Clusters in Ophiostoma ulmi and Ophiostoma novo-ulmi Reveals a Fujikurin-Like Gene Cluster with a Putative Role in Infection

ABSTRACT Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.

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A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

BMC Genomics ◽

10.1186/1471-2164-10-396 ◽

2009 ◽

Vol 10 (1) ◽

pp. 396 ◽

Cited By ~ 63

Author(s):

Trine B Rounge ◽

Thomas Rohrlack ◽

Alexander J Nederbragt ◽

Tom Kristensen ◽

Kjetill S Jakobsen

Keyword(s):

Gene Clusters ◽

Nonribosomal Peptide Synthetase ◽

Nonribosomal Peptide ◽

Genome Wide Analysis ◽

Planktothrix Rubescens ◽

Genome Wide ◽

A Genome ◽

Peptide Synthetase

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A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1

Genome Biology and Evolution ◽

10.1093/gbe/evz267 ◽

2019 ◽

Vol 11 (12) ◽

pp. 3529-3533

Author(s):

Pavelas Sazinas ◽

Morten Lindqvist Hansen ◽

May Iren Aune ◽

Marie Højmark Fischer ◽

Lars Jelsbak

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Plant Pathogens ◽

Gene Clusters ◽

Fungal Species ◽

Antagonistic Activity ◽

Evolutionary Origins

Abstract Many of the soil-dwelling Pseudomonas species are known to produce secondary metabolite compounds, which can have antagonistic activity against other microorganisms, including important plant pathogens. It is thus of importance to isolate new strains of Pseudomonas and discover novel or rare gene clusters encoding bioactive products. In an effort to accomplish this, we have isolated a bioactive Pseudomonas strain DTU12.1 from leaf-covered soil in Denmark. Following genome sequencing with Illumina and Oxford Nanopore technologies, we generated a complete genome sequence with the length of 5,943,629 base pairs. The DTU12.1 strain contained a complete gene cluster for a rare thioquinolobactin siderophore, which was previously described as possessing bioactivity against oomycetes and several fungal species. We placed the DTU12.1 strain within Pseudomonas gessardii subgroup of fluorescent pseudomonads, where it formed a distinct clade with other Pseudomonas strains, most of which also contained a complete thioquinolobactin gene cluster. Only two other Pseudomonas strains were found to contain the gene cluster, though they were present in a different phylogenetic clade and were missing a transcriptional regulator of the whole cluster. We show that having the complete genome sequence and establishing phylogenetic relationships with other strains can enable us to start evaluating the distribution and evolutionary origins of secondary metabolite clusters.

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Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea

Biology ◽

10.3390/biology10010017 ◽

2020 ◽

Vol 10 (1) ◽

pp. 17

Author(s):

Hua Yang ◽

Philipp E. Bayer ◽

Soodeh Tirnaz ◽

David Edwards ◽

Jacqueline Batley

Keyword(s):

Brassica Juncea ◽

Agronomic Traits ◽

Gene Clusters ◽

Gene Duplications ◽

Genome Wide Analysis ◽

Germplasm Resource ◽

Genome Wide ◽

Receptor Like Kinase ◽

Development Processes ◽

Allotetraploid Species

Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.

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Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

10.1101/149856 ◽

2017 ◽

Cited By ~ 1

Author(s):

Abigail L. Lind ◽

Jennifer H. Wisecaver ◽

Catarina Lameiras ◽

Philipp Wiemann ◽

Jonathan M. Palmer ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Cluster ◽

Metabolic Pathways ◽

Point Mutations ◽

Gene Clusters ◽

Fungal Species ◽

Species Variation ◽

Gene Gain ◽

Genome Wide ◽

Gain And Loss

SummaryFilamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed five general types of variation in SM gene clusters: non-functional gene polymorphisms, gene gain and loss polymorphisms, whole cluster gain and loss polymorphisms, allelic polymorphisms where different alleles corresponded to distinct, non-homologous clusters, and location polymorphisms in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid, as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms whose detection requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and non-homologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, genomic deletion and insertion events, as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.

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Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400694 ◽

2019 ◽

Vol 10 (1) ◽

pp. 23-35 ◽

Cited By ~ 1

Author(s):

Xiyi Ren ◽

Yongxiang Liu ◽

Yumei Tan ◽

Yonghui Huang ◽

Zuoyi Liu ◽

...

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Functional Annotation ◽

Gene Clusters ◽

Secreted Proteins ◽

Regulation Mechanism ◽

Whole Genome ◽

Genomic Information ◽

Shiraia Bambusicola ◽

Metabolite Synthesis

Shiraia bambusicola is a rare medicinal fungus found in China that causes bamboo plants to decay and die with severe infection. Hypocrellin, its main active ingredient, is widely used in several fields, such as medicine, agriculture, and food industry. In this study, to clarify the genomic components, taxonomic status, pathogenic genes, secondary metabolite synthesis pathways, and regulatory mechanisms of S. bambusicola, whole-genome sequencing, assembly, and functional annotation were performed using high-throughput sequencing and bioinformatics approaches. It was observed that S. bambusicola has 33 Mb genome size, 48.89% GC content, 333 scaffolds, 2590 contigs, 10,703 genes, 82 tRNAs, and 21 rRNAs. The total length of the repeat sequence is 2,151,640 bp. The annotation of 5945 proteins was obtained from InterProScan hits based on the Gene Ontology database. Phylogenetic analysis showed that S. bambusicola belongs to Shiraiaceae, a new family of Pleosporales. It was speculated that there are more than two species or genus in Shiraiaceae. According to the annotation, 777 secreted proteins were associated with virulence or detoxification, including 777 predicted by the PHI database, 776 by the CAZY and Fungal CytochromeP450 database, and 441 by the Proteases database. The 252 genes associated with the secondary metabolism of S. bambusicola were screened and enriched into 28 pathways, among which the terpenoids, staurosporine, aflatoxin, and folate synthesis pathways have not been reported in S. bambusicola. The T1PKS was the main gene cluster among the 28 secondary metabolite synthesis gene clusters in S. bambusicola. The analysis of the T3PKS gene cluster related to the synthesis of hypocrellin showed that there was some similarity between S. bambusicola and 10 other species of fungi; however, the similarity was very low wherein the highest similarity was 17%. The genomic information of S. bambusicola obtained in this study was valuable to understand its genetic function and pathogenicity. The genomic information revealed that several enzyme genes and secreted proteins might be related to their host interactions and pathogenicity. The annotation and analysis of its secondary metabolite synthesis genes and gene clusters will be an important reference for future studies on the biosynthesis and regulation mechanism of the secondary metabolites, contributing to the discovery of new metabolites and accelerating drug development and application.

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Automating Assessment of the Undiscovered Biosynthetic Potential of Actinobacteria

10.1101/036087 ◽

2016 ◽

Cited By ~ 3

Author(s):

Bogdan Tokovenko ◽

Yuriy Rebets ◽

Andriy Luzhetskyy

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Gene Clusters ◽

Command Line ◽

Computational Pipeline ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

The Subject ◽

Similarity Thresholds ◽

Similar Gene

Background. Biosynthetic potential of Actinobacteria has long been the subject of theoretical estimates. Such an estimate is indeed important as a test of further exploitability of a taxon or group of taxa for new therapeutics. As neither a set of available genomes nor a set of bacterial cultivation methods are static, it makes sense to simplify as much as possible and to improve reproducibility of biosynthetic gene clusters similarity, diversity, and abundance estimations. Results. We have developed a command-line computational pipeline (available at https://bitbucket.org/qmentis/clusterscluster/) that assists in performing empirical (genome-based) assessment of microbial secondary metabolite gene clusters similarity and abundance, and applied it to a set of 208 complete and de-duplicated Actinobacteria genomes. After a brief overview of Actinobacteria biosynthetic potential as compared to other bacterial taxa, we use similarity thresholds derived from 4 pairs of known similar gene clusters to identify up to 40-48% of 3247 gene clusters in our set of genomes as unique. There is no saturation of the cumulative unique gene clusters curve within the examined dataset, and Heap's alpha is 0.129, suggesting an open pan-clustome. We identify and highlight pitfalls and possible improvements of genome-based gene cluster similarity measurements.

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Activation of a Silent Fungal Polyketide Biosynthesis Pathway through Regulatory Cross Talk with a Cryptic Nonribosomal Peptide Synthetase Gene Cluster

Applied and Environmental Microbiology ◽

10.1128/aem.00683-10 ◽

2010 ◽

Vol 76 (24) ◽

pp. 8143-8149 ◽

Cited By ~ 96

Author(s):

Sebastian Bergmann ◽

Alexander N. Funk ◽

Kirstin Scherlach ◽

Volker Schroeckh ◽

Ekaterina Shelest ◽

...

Keyword(s):

Natural Products ◽

Gene Cluster ◽

Secondary Metabolite ◽

Cross Talk ◽

Regulatory Gene ◽

Gene Clusters ◽

Nonribosomal Peptide Synthetase ◽

Nonribosomal Peptide ◽

Peptide Synthetase ◽

Biosynthesis Gene

ABSTRACT Filamentous fungi produce numerous natural products that constitute a consistent source of potential drug leads, yet it seems that the majority of natural products are overlooked since most biosynthesis gene clusters are silent under standard cultivation conditions. Screening secondary metabolite genes of the model fungus Aspergillus nidulans, we noted a silent gene cluster on chromosome II comprising two nonribosomal peptide synthetase (NRPS) genes, inpA and inpB, flanked by a regulatory gene that we named scpR for secondary metabolism cross-pathway regulator. The induced expression of the scpR gene using the promoter of the alcohol dehydrogenase AlcA led to the transcriptional activation of both the endogenous scpR gene and the NRPS genes. Surprisingly, metabolic profiling of the supernatant of mycelia overexpressing scpR revealed the production of the polyketide asperfuranone. Through transcriptome analysis we found that another silent secondary metabolite gene cluster located on chromosome VIII coding for asperfuranone biosynthesis was specifically induced. Quantitative reverse transcription-PCR proved the transcription not only of the corresponding polyketide synthase (PKS) biosynthesis genes, afoE and afoG, but also of their activator, afoA, under alcAp-scpR-inducing conditions. To exclude the possibility that the product of the inp cluster induced the asperfuranone gene cluster, a strain carrying a deletion of the NRPS gene inpB and, in addition, the alcAp-scpR overexpression cassette was generated. In this strain, under inducing conditions, transcripts of the biosynthesis genes of both the NRPS-containing gene cluster inp and the asperfuranone gene cluster except gene inpB were detected. Moreover, the existence of the polyketide product asperfuranone indicates that the transcription factor ScpR controls the expression of the asperfuranone biosynthesis gene cluster. This expression as well as the biosynthesis of asperfuranone was abolished after the deletion of the asperfuranone activator gene afoA, indicating that ScpR binds to the afoA promoter. To the best of our knowledge, this is the first report of regulatory cross talk between two biosynthesis gene clusters located on different chromosomes.

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Genome-wide Identification and Analysis of CCT Genes in Wheat (Triticum Aestivum L.)

10.21203/rs.3.rs-104841/v1 ◽

2020 ◽

Author(s):

Hongwei Zhang ◽

Xinxia Liang ◽

Shuo Zhou ◽

Haibo Wang

Keyword(s):

Gene Clusters ◽

Triticum Aestivum L ◽

Suppressor Gene ◽

Pcr Analysis ◽

Genome Wide Analysis ◽

Real Time Quantitative Pcr ◽

Genome Wide ◽

A Genome ◽

Mads Box Gene ◽

And Function

Abstract Background: The vernalization, in which the plants must undergo a prolonged winter cold exposure to flower, is mainly controlled by a suppressive MADS-box gene FLC in Arabidopsis. However, different from Arabidopsis, the CCT-domain containing gene VRN2 is the critical vernalization-related suppressor gene in cereals. Based on this apparent diversity of vernalization in different plants, and involvement of VRN2 with vernalization in cereals, we conducted a genome-wide analysis of CCT genes in wheat, and the relationship between vernalization and these genes were also revealed.Results: A genome-wide analysis of the CCT genes in common wheat was performed by employing a hidden Markov model-based method, and 127 sequences, which assigned to 40 clusters, were obtained in three subgenomes. Specially, two of the gene clusters are duplicated, and distinguishingly located near telomere. Furthermore, these sequences were classified into eight groups by a phylogenetic analysis procedure using the UPGMA method, and this taxonomy is concordant to the classification based on CCT interruptions and domain organization which roughly divided the proteins into four divergently related subfamilies. Moreover, the expression of several CCT genes is continually downregulated during and after vernalization, but no continually upregulated CCT genes were revealed, as indicated by transcriptome sequencing and real-time quantitative PCR analysis.Conclusion: This study improves our understanding of the structure and function of CCT genes, suggests many vernalization-related CCT genes, and may guide future investigations on CCT genes and vernalization in wheat.

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Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds

mBio ◽

10.1128/mbio.01691-20 ◽

2020 ◽

Vol 11 (4) ◽

Cited By ~ 2

Author(s):

Lindsay K. Caesar ◽

Matthew T. Robey ◽

Michael Swyers ◽

Md N. Islam ◽

Rosa Ye ◽

...

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Heterologous Gene Expression ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Metabolic Enzyme ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Artificial Chromosomes ◽

Indoleamine 2,3 Dioxygenase

ABSTRACT Advances in genome sequencing have revitalized natural product discovery efforts, revealing the untapped biosynthetic potential of fungi. While the volume of genomic data continues to expand, discovery efforts are slowed due to the time-consuming nature of experiments required to characterize new molecules. To direct efforts toward uncharacterized biosynthetic gene clusters most likely to encode novel chemical scaffolds, we took advantage of comparative metabolomics and heterologous gene expression using fungal artificial chromosomes (FACs). By linking mass spectral profiles with structural clues provided by FAC-encoded gene clusters, we targeted a compound originating from an unusual gene cluster containing an indoleamine 2,3-dioxygenase (IDO). With this approach, we isolate and characterize R and S forms of the new molecule terreazepine, which contains a novel chemical scaffold resulting from cyclization of the IDO-supplied kynurenine. The discovery of terreazepine illustrates that FAC-based approaches targeting unusual biosynthetic machinery provide a promising avenue forward for targeted discovery of novel scaffolds and their biosynthetic enzymes, and it also represents another example of a biosynthetic gene cluster “repurposing” a primary metabolic enzyme to diversify its secondary metabolite arsenal. IMPORTANCE Here, we provide evidence that Aspergillus terreus encodes a biosynthetic gene cluster containing a repurposed indoleamine 2,3-dioxygenase (IDO) dedicated to secondary metabolite synthesis. The discovery of this neofunctionalized IDO not only enabled discovery of a new compound with an unusual chemical scaffold but also provided insight into the numerous strategies fungi employ for diversifying and protecting themselves against secondary metabolites. The observations in this study set the stage for further in-depth studies into the function of duplicated IDOs present in fungal biosynthetic gene clusters and presents a strategy for accessing the biosynthetic potential of gene clusters containing duplicated primary metabolic genes.

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