scholarly journals Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Nora Khaldi ◽  
Kenneth H. Wolfe
Keyword(s):  
Comparative Genomics ◽  
Aspergillus Niger ◽  
Gene Cluster ◽  
Secondary Metabolite ◽  
Horizontal Transfer ◽  
Fusarium Verticillioides ◽  
Gene Clusters ◽  
Evolutionary Origins ◽  
Species Specific ◽  
Secondary Metabolite Gene Cluster

The secondary metabolite gene clusters of euascomycete fungi are among the largest known clusters of functionally related genes in eukaryotes. Most of these clusters are species specific or genus specific, and little is known about how they are formed during evolution. We used a comparative genomics approach to study the evolutionary origins of a secondary metabolite cluster that synthesizes a polyketide derivative, namely, the fumonisin (FUM) cluster of Fusarium verticillioides, and that of Aspergillus niger another fumonisin (fumonisin B) producing species. We identified homologs in other euascomycetes of the Fusarium verticillioides FUM genes and their flanking genes. We discuss four models for the origin of the FUM cluster in Fusarium verticillioides and argue that two of these are plausible: (i) assembly by relocation of initially scattered genes in a recent Fusarium verticillioides; or (ii) horizontal transfer of the FUM cluster from a distantly related Sordariomycete species. We also propose that the FUM cluster was horizontally transferred into Aspergillus niger, most probably from a Sordariomycete species.

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

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.

scholarly journals Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi

2008 ◽  
Vol 9 (1) ◽  
pp. R18 ◽  
Author(s):  
Nora Khaldi ◽  
Jérôme Collemare ◽  
Marc-Henri Lebrun ◽  
Kenneth H Wolfe
Keyword(s):  
Gene Cluster ◽  
Secondary Metabolite ◽  
Horizontal Transfer ◽  
Secondary Metabolite Gene Cluster

Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator

2021 ◽  
Vol 85 (3) ◽  
pp. 714-721
Author(s):  
Risa Takao ◽  
Katsuyuki Sakai ◽  
Hiroyuki Koshino ◽  
Hiroyuki Osada ◽  
Shunji Takahashi
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Secondary Metabolite ◽  
Response Regulator ◽  
Bac Library ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Gene Organization ◽  
Biosynthetic Gene ◽  
Streptomyces Sp

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.

scholarly journals The Fusarium verticillioides FUM Gene Cluster Encodes a Zn(II)2Cys6 Protein That Affects FUM Gene Expression and Fumonisin Production

2007 ◽  
Vol 6 (7) ◽  
pp. 1210-1218 ◽  
Author(s):  
Daren W. Brown ◽  
Robert A. E. Butchko ◽  
Mark Busman ◽  
Robert H. Proctor
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Fusarium Verticillioides ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Regulatory Proteins ◽  
Wild Type ◽  
Polyketide Synthase Gene ◽  
Splice Forms ◽  
Self Protection

ABSTRACT Fumonisins are mycotoxins produced by some Fusarium species and can contaminate maize or maize products. Ingestion of fumonisins is associated with diseases, including cancer and neural tube defects, in humans and animals. In fungi, genes involved in the synthesis of mycotoxins and other secondary metabolites are often located adjacent to each other in gene clusters. Such genes can encode structural enzymes, regulatory proteins, and/or proteins that provide self-protection. The fumonisin biosynthetic gene cluster includes 16 genes, none of which appear to play a role in regulation. In this study, we identified a previously undescribed gene (FUM21) located adjacent to the fumonisin polyketide synthase gene, FUM1. The presence of a Zn(II)2Cys6 DNA-binding domain in the predicted protein suggested that FUM21 was involved in transcriptional regulation. FUM21 deletion (Δfum21) mutants produce little to no fumonisin in cracked maize cultures but some FUM1 and FUM8 transcripts in a liquid GYAM medium. Complementation of a Δfum21 mutant with a wild-type copy of the gene restored fumonisin production. Analysis of FUM21 cDNAs identified four alternative splice forms (ASFs), and microarray analysis indicated the ASFs were differentially expressed. Based on these data, we present a model for how FUM21 ASFs may regulate fumonisin biosynthesis.

scholarly journals Apicidin F: Characterization and Genetic Manipulation of a New Secondary Metabolite Gene Cluster in the Rice Pathogen Fusarium fujikuroi

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e103336 ◽  
Author(s):  
Eva-Maria Niehaus ◽  
Slavica Janevska ◽  
Katharina W. von Bargen ◽  
Christian M. K. Sieber ◽  
Henning Harrer ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Secondary Metabolite ◽  
Genetic Manipulation ◽  
Fusarium Fujikuroi ◽  
Secondary Metabolite Gene Cluster

scholarly journals Genome Sequences of Serratia Strains Revealed Common Genes in Both Serratomolides Gene Clusters

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 482
Author(s):  
Catarina Marques-Pereira ◽  
Diogo Neves Proença ◽  
Paula V. Morais
Keyword(s):  
Comparative Genomics ◽  
Gene Cluster ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Biosynthetic Gene Clusters ◽  
Bacteria And Fungi ◽  
Different Strains ◽  
First Time

Serratia strains are ubiquitous microorganisms with the ability to produce serratomolides, such as serrawettins. These extracellular lipopeptides are described as biocides against many bacteria and fungi and may have a nematicidal activity against phytopathogenic nematodes. Serrawettins W1 and W2 from different strains have different structures that might be correlated with distinct genomic organizations. This work used comparative genomics to determine the distribution and the organization of the serrawettins biosynthetic gene clusters in all the 84 publicly available genomes of the Serratia genus. The serrawettin W1 and W2 gene clusters’ organization was established using antiSMASH software and compared with single and short data previously described for YD25TSerratia. Here, the serrawettin W1 gene clusters’ organization is reported for the first time. The serrawettin W1 biosynthetic gene swrW was present in 17 Serratia genomes. Eighty different coding sequence (CDS) were assigned to the W1 gene cluster, 13 being common to all clusters. The serrawettin W2 swrA gene was present in 11 Serratia genomes. The W2 gene clusters included 68 CDS with 24 present in all the clusters. The genomic analysis showed the swrA gene constitutes five modules, four with three domains and one with four domains, while the swrW gene constitutes one module with four domains. This work identified four genes common to all serrawettin gene clusters, highlighting their essential potential in the serrawettins biosynthetic process.

scholarly journals Lae1 regulates expression of multiple secondary metabolite gene clusters in Fusarium verticillioides

2012 ◽  
Vol 49 (8) ◽  
pp. 602-612 ◽  
Author(s):  
Robert A.E. Butchko ◽  
Daren W. Brown ◽  
Mark Busman ◽  
Bettina Tudzynski ◽  
Philipp Wiemann
Keyword(s):  
Secondary Metabolite ◽  
Fusarium Verticillioides ◽  
Gene Clusters

scholarly journals Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola

2019 ◽  
Vol 10 (1) ◽  
pp. 23-35 ◽  
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.

Sign in / Sign up

Export Citation Format

Share Document