scholarly journals Whole-Genome Sequencing Reveals a New Genospecies ofMethylobacteriumsp. GXS13, Isolated fromVitis viniferaL. Xylem Sap

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Wan Xin Lai ◽  
Han Ming Gan ◽  
André O. Hudson ◽  
Michael A. Savka
Keyword(s):  
Xylem Sap ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Acyl Homoserine Lactone ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Cell Wall Modification ◽  
Cytokinin Synthesis

The whole-genome sequence of a new genospecies ofMethylobacteriumsp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.

scholarly journals Whole-genome sequence of a novel, mangrove-derived streptomycete, Streptomyces malaysiense strain MUSC 136T

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Learn-Han Lee
Keyword(s):  
Genome Sequence ◽  
Mangrove Forest ◽  
Streptomyces Griseus ◽  
Prediction Method ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Since the discovery of streptomycin from Streptomyces griseus in the early 1940s, streptomycetes from various environments have been studied thoroughly for the ability to produce bioactive compounds including antibacterial, antioxidant, anticancer, antifungal as well as immunomodulatory properties. Previously identified as a novel strain from a mangrove forest in Malaysia, Streptomyces malaysiense MUSC 136T was selected for genome sequencing to explore its genomic potential. The genomic size comprises of 7,963,326 bp with a G+C content of 72.2% and a total of 6,614 proteincoding genes. As an attempt to investigate the types of biosynthetic gene cluster present in the MUSC 136T, the whole genome sequence was analyzed with a bioinformatics tool, antibiotics & Secondary Metabolite Analysis Shell (antiSMASH). Using the “strict” prediction method, a total of seven biosynthetic gene clusters which displayed similarity of more than 80% to known gene clusters including ectoine, geosmin as well as desferrioxamine. Apart from emphasizing the importance of streptomycetes from unique environments like mangrove forest, the current study serves as a foundation for future studies on the role of specific genes present in biosynthetic gene clusters which enables the exploitation of MUSC 136T to synthesize important and valuable compounds.

scholarly journals Draft Genome Sequence of Streptomyces albidoflavus 09MW18-IS, Cultivated from the Atlantic Ocean off the Coast of Virginia

2022 ◽  
Author(s):  
Indu Sharma ◽  
Masuud Washington ◽  
Jeremy Chen See ◽  
Rola Suleiman ◽  
Regina Lamendella
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Streptomyces Albidoflavus

We report a draft genome sequence for Streptomyces albidoflavus strain 09MW18-IS, isolated from the Atlantic slope off the coast of Virginia. The whole-genome sequence will provide novel insights into biosynthetic gene clusters and ecological adaptation in an oligotrophic environment.

scholarly journals Whole-genome sequence of bioactive streptomycete derived from mangrove forest in Malaysia, Streptomyces sp. MUSC 14

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Loh Teng-Hern Tan ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan
Keyword(s):  
East Coast ◽  
Genetic Manipulation ◽  
Genome Mining ◽  
Gene Clusters ◽  
Peninsular Malaysia ◽  
Whole Genome Sequence ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Streptomyces Sp ◽  
A Genome

The contribution of streptomycetes to human health is undeniably important and significant, given that these filamentous microbes can produce interesting compounds that can be used to cure deadly infections and even cancer. Isolated from the east coast of Peninsular Malaysia, Streptomyces sp. MUSC 14 has shown significant antioxidant capacity. The current study explores the genomic potential of MUSC 14 via a genome mining approach. The genome size of MUSC 14 is 10,274,825 bp with G + C content of 71.3 %. AntiSMASH analysis revealed a total of nine biosynthetic gene clusters (with more than 80 % similarities to known gene clusters). This information serves as an important foundation for subsequent studies, particularly the purification and isolation of bioactive compounds by genetic manipulation techniques.

scholarly journals Whole genome sequence of Streptomyces humi strain MUSC 119T isolated from intertidal soil

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Nurul Syakima Ab Mutalib ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biosynthetic Gene Clusters ◽  
Streptomyces Species ◽  
Genus Streptomyces ◽  
The Past ◽  
Mangrove Soil ◽  
Natural Product Research ◽  
Biochemical Assays

Over the past few decades, microorganisms have made major contribution in natural product research, particularly those from the genus Streptomyces. Streptomyces humi MUSC 119T was previously isolated as novel streptomycete from mangrove soil in Malaysia. During the screening programme for bioactive strains, this strain was discovered to possess antioxidant activity – scavenging and reducing accumulation of free radicals in biochemical assays. Consequently, whole genome sequencing was performed to evaluate genomic potential of the strain. Based on our analysis, the genome size of MUSC 119T is described to be 10.01 Mbps with G + C content of 71.80%. Based on antiSMASH analysis, the strain possess great genomic potential, having nine biosynthetic gene clusters displaying high similarities to known gene clusters. These findings indicates that mangrove Streptomyces species like MUSC 119T may potentially play an important role in drug development process, while the availability of its whole genome sequences allows further manipulation to isolate and identify compound of interest.

scholarly journals Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Camila R. Paludo ◽  
Antonio C. Ruzzini ◽  
Eduardo A. Silva-Junior ◽  
Gleb Pishchany ◽  
Cameron R. Currie ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Clusters ◽  
Stingless Bee ◽  
Whole Genome Sequence ◽  
Antimicrobial Compounds ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Circular Chromosome ◽  
The Social ◽  
Social Bee

We announce the complete genome sequence of Bacillus sp. strain SDLI1, isolated from larval gut of the stingless bee Scaptotrigona depilis . The 4.13-Mb circular chromosome harbors biosynthetic gene clusters for the production of antimicrobial compounds.

scholarly journals Synergistic activity of cosecreted natural products from amoebae-associated bacteria

2018 ◽  
Vol 115 (15) ◽  
pp. 3758-3763 ◽  
Author(s):  
Johannes Arp ◽  
Sebastian Götze ◽  
Ruchira Mukherji ◽  
Derek J. Mattern ◽  
María García-Altares ◽  
...  
Keyword(s):  
Natural Products ◽  
Polyketide Synthase ◽  
Bacterial Genome ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Microbial Interactions ◽  
Signal Molecules ◽  
Synergistic Activity ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Microbial predator–prey interactions in particular rely on natural products as signal or defense molecules. In this context, we identified a grazing-resistant Pseudomonas strain, isolated from the bacterivorous amoeba Dictyostelium discoideum. Genome analysis of this bacterium revealed the presence of two biosynthetic gene clusters that were found adjacent to each other on a contiguous stretch of the bacterial genome. Although one cluster codes for the polyketide synthase producing the known antibiotic mupirocin, the other cluster encodes a nonribosomal peptide synthetase leading to the unreported cyclic lipopeptide jessenipeptin. We describe its complete structure elucidation, as well as its synergistic activity against methicillin-resistant Staphylococcus aureus, when in combination with mupirocin. Both biosynthetic gene clusters are regulated by quorum-sensing systems, with 3-oxo-decanoyl homoserine lactone (3-oxo-C10-AHL) and hexanoyl homoserine lactone (C6-AHL) being the respective signal molecules. This study highlights the regulation, richness, and complex interplay of bacterial natural products that emerge in the context of microbial competition.

scholarly journals Draft genome sequence of Marssonina coronaria, causal agent of apple blotch, and comparisons with the Marssonina brunnea and Marssonina rosae genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246666
Author(s):  
Qiang Cheng ◽  
Junxiang Chen ◽  
Lijuan Zhao
Keyword(s):  
Secondary Metabolite ◽  
Gene Clusters ◽  
Secreted Proteins ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Marssonina Coronaria ◽  
Marssonina Brunnea ◽  
Species Specific ◽  
Small Secreted Proteins

Marssonina coronaria Ellis & Davis is a filamentous fungus in the class Leotiomycetes that causes apple blotch, an economically important disease of apples worldwide. Here, we sequenced the whole genome of M. coronaria strain NL1. The genome contained 50.3 Mb with 589 scaffolds and 9,622 protein-coding genes. A phylogenetic analysis using multiple loci and a whole-genome alignment revealed that M. coronaria is closely related to Marssonina rosae and Marssonina brunnea. A comparison of the three genomes revealed 90 species-specific carbohydrate-active enzymes, 19 of which showed atypical distributions, and 12 species-specific secondary metabolite biosynthetic gene clusters, two of which have the potential to synthesize products analogous to PR toxin and swainsonine, respectively. We identified 796 genes encoding for small secreted proteins in Marssonina spp., many encoding for unknown hypothetical proteins. In addition, we revealed the genetic architecture of the MAT1-1 and MAT1-2 mating-type loci of M. coronaria, as well as 16 tested isolates carrying either MAT1-1 idiomorph (3) or MAT1-2 idiomorph (13). Our results showed a series of species-specific carbohydrate-active enzyme, secondary metabolite biosynthetic gene clusters and small-secreted proteins that may be involved in the adaptation of Marssonina spp. to their distinct hosts. We also confirmed that M. coronaria possesses a heterothallic mating system and has outcrossing potential in nature.

scholarly journals Secondary metabolites from hypocrealean entomopathogenic fungi: genomics as a tool to elucidate the encoded parvome

2020 ◽  
Vol 37 (9) ◽  
pp. 1164-1180 ◽  
Author(s):  
Liwen Zhang ◽  
Qun Yue ◽  
Chen Wang ◽  
Yuquan Xu ◽  
István Molnár
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bioactive Compounds ◽  
Entomopathogenic Fungi ◽  
Gene Clusters ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Whole genome sequencing allows the cataloguing of the parvome (secondary metabolome) of hypocrealean entomopathogenic fungi, uncovering biosynthetic gene clusters for known and novel bioactive compounds with ecological and pharmaceutical significance.

scholarly journals Comparative Genomics and Transcriptomics Depict Marine Algicolous Arthrinium Species as Endosymbionts That Help Regulate Oxidative Stress in Brown Algae

2021 ◽  
Vol 8 ◽  
Author(s):  
Young Mok Heo ◽  
Seung-Yoon Oh ◽  
Kyeongwon Kim ◽  
Sang-Il Han ◽  
Sun Lul Kwon ◽  
...  
Keyword(s):  
Brown Algae ◽  
Plant Pathogens ◽  
Gene Clusters ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Rna Seq ◽  
Interspecies Interactions ◽  
Biosynthetic Gene Clusters ◽  
Alcohol Production ◽  
Fungal Secondary Metabolite

The whole genome and transcriptome analyses were performed for prediction of the ecological characteristics of Arthrinium and the genes involved in gentisyl alcohol biosynthesis. Whole genome sequences of A. koreanum KUC21332 and A. saccharicola KUC21221 were analyzed, and the genes involved in interspecies interaction, carbohydrate-active enzymes, and secondary metabolites were investigated. Three of the seven genes associated with interspecies interactions shared by four Arthrinium spp. were involved in pathogenesis. A. koreanum and A. saccharicola exhibit the enzyme profiles similar to those observed in plant pathogens and endophytes rather than saprobes. Furthermore, six of the seven metabolites of known clusters identified in the genomes of the four Arthrinium spp. are associated with plant virulence. These results indicate that Arthrinium spp. are potentially pathogenic to plants. Subsequently, different conditions for gentisyl alcohol production in A. koreanum were established, and mRNA extracted from cultures of each condition was subjected to RNA-Seq to analyze the differentially-expressed genes. The gentisyl alcohol biosynthetic pathway and related biosynthetic gene clusters were identified, and gentisyl alcohol biosynthesis was significantly downregulated in the mannitol-supplemented group where remarkably low antioxidant activity was observed. These results indicate that gentisyl alcohol production in algicolous Arthrinium spp. is influenced by mannitol. It was suggested that the algicolous Arthrinium spp. form a symbiotic relationship that provides antioxidants when the photosynthetic activity of brown algae decreases in exchange for receiving mannitol. This is the first study to analyze the lifestyle of marine algicolous Arthrinium spp. at the molecular level and suggests a symbiotic mechanism with brown algae. It also improves the understanding of fungal secondary metabolite production via identification of the gentisyl alcohol biosynthetic gene clusters in Arthrinium spp.

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