scholarly journals Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Li ◽  
Meng Wang ◽  
Zhen Ren ◽  
Yang Ji ◽  
Min Yin ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Complete Genome ◽  
Type Strain ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Antitumor Agent ◽  
Northwest China ◽  
Rrna Gene ◽  
Circular Chromosome ◽  
Nocardicin A

A novel actinobacterium, strain YIM 96748T, was isolated from a saline soil sample collected from the south bank of Aiding Lake in Xinjiang Province, Northwest China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 96748T is closely related to Amycolatopsis cihanbeyliensis BNT52T (98.9%) and Amycolatopsis jiangsuensis KLBMP 1262T (97.2%). The DNA–DNA relatedness between strain YIM 96748T and its closest type strain A. cihanbeyliensis BNT52T was 59.6%. The average nucleotide identity between strain YIM 96748T and its neighbor strain was 88.97%. Based on the genotypic and phenotypic characteristics, it is concluded that strain YIM 96748T represents a novel species of the genus Amycolatopsis, whose name was proposed as Amycolatopsis aidingensis sp. nov. The type strain is YIM 96748T. To investigate the biosynthetic potential of producing secondary metabolites, the complete genome of YIM 96748T was sequenced and analyzed. The complete genome sequence of YIM 96748T consists of a 7,657,695-bp circular chromosome, comprising 7,162 predicted genes with a DNA G + C content of 70.21 mol%. Fifty-one putative biosynthetic gene clusters of secondary metabolites were found, including the antibacterial/antitumor agent TLN-05220, the antibacterial agent nocardicin A, the antifungal agent nystatin A1, and the osmolyte ectoine. The investigation of the secondary metabolites of A. aidingensis YIM96748T led to the discovery of two new phenylpropyl acetate enantiomers, amycoletates A (1) and B (2), and five known compounds: 4-hydroxy phenethyl acetate (3), 2-p-acetoxyphenylethanol (4), (S)-ethyl indole-3-lactate (5), (R)-ethyl indole-3-lactate (6), and p-hydroxybenzoic acid (7). One of the gene clusters 14, 36, and 43, which contain a single module of polyketide synthase, might be responsible for the biosynthesis of compounds 1 and 2 from compound 7 as a precursor. Further studies, including the one strain many compounds approach (OSMAC) and genetic modification, are needed to explore novel compounds from this talented halophilic Amycolatopsis strain.

scholarly journals Complete Genome Sequences of Three Bacillus amyloliquefaciens Strains That Inhibit the Growth of Listeria monocytogenes In Vitro

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Thao D. Tran ◽  
Steven Huynh ◽  
Craig T. Parker ◽  
Robert Hnasko ◽  
Lisa Gorski ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Secondary Metabolites ◽  
Growth Inhibition ◽  
Complete Genome ◽  
Bacillus Amyloliquefaciens ◽  
Gene Clusters ◽  
Genome Sequences ◽  
Multiple Gene ◽  
Content Type

ABSTRACT Here, we report the complete genome sequences of three Bacillus amyloliquefaciens strains isolated from alfalfa, almond drupes, and grapes that inhibited the growth of Listeria monocytogenes strain 2011L-2857 in vitro. We also report multiple gene clusters encoding secondary metabolites that may be responsible for the growth inhibition of L. monocytogenes.

scholarly journals Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 257
Author(s):  
Hisayuki Komaki ◽  
Tomohiko Tamura
Keyword(s):  
Secondary Metabolites ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Nrps Gene ◽  
Nonribosomal Peptide ◽  
Rare Actinomycetes ◽  
Whole Genomes ◽  
Peptide Synthetase ◽  
Established Genus

(1) Background: Phytohabitans is a recently established genus belonging to rare actinomycetes. It has been unclear if its members have the capacity to synthesize diverse secondary metabolites. Polyketide and nonribosomal peptide compounds are major secondary metabolites in actinomycetes and expected as a potential source for novel pharmaceuticals. (2) Methods: Whole genomes of Phytohabitans flavus NBRC 107702T, Phytohabitans rumicis NBRC 108638T, Phytohabitans houttuyneae NBRC 108639T, and Phytohabitans suffuscus NBRC 105367T were sequenced by PacBio. Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters were bioinformatically analyzed in the genome sequences. (3) Results: These four strains harbored 10, 14, 18 and 14 PKS and NRPS gene clusters, respectively. Most of the gene clusters were annotated to synthesis unknown chemistries. (4) Conclusions: Members of the genus Phytohabitans are a possible source for novel and diverse polyketides and nonribosomal peptides.

scholarly journals Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Sohaib Sarfraz ◽  
Saïd Oulghazi ◽  
Jérémy Cigna ◽  
Shahbaz Talib Sahi ◽  
Kashif Riaz ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Gc Content ◽  
Illumina Miseq ◽  
Blackleg Disease ◽  
Circular Chromosome ◽  
Content Type ◽  
Potato Plants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

scholarly journals Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Jun Kong ◽  
Hongshan Jiang ◽  
Baiyun Li ◽  
Wenjun Zhao ◽  
Zhihong Li ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Strain Atcc ◽  
Circular Chromosome ◽  
Coding Sequences

Pseudomonas syringae pv. lapsa is a pathovar of Pseudomonas syringae that can infect wheat. The complete genome of P. syringae pv. lapsa strain ATCC 10859 contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16 rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome revealed several gene clusters that are related to pathogenesis and virulence.

scholarly journals Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis

2016 ◽  
Vol 82 (6) ◽  
pp. 1945-1957 ◽  
Author(s):  
Nestor Zaburannyi ◽  
Boyke Bunk ◽  
Josef Maier ◽  
Jörg Overmann ◽  
Rolf Müller
Keyword(s):  
Fruiting Body ◽  
Type Strain ◽  
Prokaryotic Genome ◽  
Gene Clusters ◽  
Trna Genes ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Reduced Pressure ◽  
Circular Chromosome ◽  
Content Type

ABSTRACTHere, we report the complete genome sequence of the type strain of the myxobacterial genusChondromyces,Chondromyces crocatusCm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr−) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family,Sorangium cellulosum, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.

scholarly journals Complete Genome Sequence of the Cytokinin-Producing Biocontrol Strain Pseudomonas fluorescens G20-18

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Tue K. Nielsen ◽  
Mengistu F. Mekureyaw ◽  
Lars H. Hansen ◽  
Mette H. Nicolaisen ◽  
Thomas G. Roitsch ◽  
...  
Keyword(s):  
Plant Growth ◽  
Pseudomonas Fluorescens ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Circular Chromosome ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

Here, we report the complete genome sequence of the cytokinin-producing plant growth-promoting strain Pseudomonas fluorescens G20-18. The complete genome assembly resulted in a single, circular chromosome of 6.48 Mbp and harbors several secondary metabolite biosynthesis gene clusters that are potentially involved in its plant growth-promoting function.

scholarly journals Desulfovibrio africanus subsp. uniflagellum subsp. nov., a sulfate-reducing bacterium from a uranium-contaminated subsurface aquifer

2010 ◽  
Vol 60 (4) ◽  
pp. 880-886 ◽  
Author(s):  
I. Nydia Castañeda-Carrión ◽  
Cody S. Sheik ◽  
Lee R. Krumholz
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Type Strain ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Contaminated Site ◽  
Amino Acid Sequence Similarity ◽  
Trna Genes ◽  
Rrna Gene ◽  
Small Plasmid

The bacterial strain SR-1T was isolated from subsurface sediments of a uranium-contaminated site in Shiprock, New Mexico, USA. Cells are vibrioid and motile by means of a single polar flagellum. Strain SR-1T grows on sulfate, oxidizing formate, lactate and H2, but not malate, and ferments pyruvate. The DNA sequences of the 16S rRNA gene and the 16S–23S internal transcribed spacer of strain SR-1T showed 99.9 and 99.4 % similarity, respectively, to those of the type strain Desulfovibrio africanus DSM 2603T. The DNA sequence of the ITS region is 300 bases in length and contains two tRNA genes (tRNAIle, tRNAAla). The partial DNA sequence of the dsrAB gene showed 94.6 % amino acid sequence similarity to that of D. africanus. The DNA G+C content of strain SR-1T was 62.4 mol% and it showed 72 % DNA–DNA similarity to D. africanus. DNA typing methods that target gene clusters and whole genomes revealed characteristic genomic fingerprints for strain SR-1T. A small plasmid was detected by gel electrophoresis. On the basis of distinct phenotypic and genotypic characteristics, strain SR-1T represents a novel subspecies of D. africanus, for which the name Desulfovibrio africanus subsp. uniflagellum subsp. nov. is proposed. The type strain is SR-1T (=JCM 15510T =LS KCTC 5649T).

scholarly journals Complete Genome Sequence of Pseudomonas otitidis Strain MrB4, Isolated from Lake Biwa in Japan

2020 ◽  
Vol 9 (16) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Erina Hase ◽  
Tomomasa Maruya
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Lake Biwa ◽  
Draft Genome ◽  
Circular Chromosome ◽  
Content Type ◽  
Near Shore ◽  
Single Circular Chromosome

We isolated Pseudomonas otitidis strain MrB4 from the near-shore area of Lake Biwa in Japan and generated its complete genome sequence. MrB4 possesses a single circular chromosome of 6,089,454 bp, with ∼97% average nucleotide identity to the P. otitidis type strain MCC10330 (draft genome).

scholarly journals Complete Genome Sequence of Mycobacterium sp. MS1601, a Bacterium Performing Selective Oxidation of Polyols

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Mahmoud Sayed ◽  
Waiel F. Sayed ◽  
Rajni Hatti-Kaul ◽  
Sang-Hyun Pyo
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rrna Gene ◽  
Total Size ◽  
Circular Chromosome ◽  
Genome Sequence Analysis ◽  
Hydroxycarboxylic Acids ◽  
Complete Genome Sequence Analysis

ABSTRACT Corynebacterium sp. (ATCC 21245) is reclassified here as Mycobacterium sp. MS1601 based on 16S rRNA gene and complete-genome sequence analysis. It is able to oxidize branched polyols to corresponding hydroxycarboxylic acids. The total size of the genome sequence was 6,829,132 bp, including one circular chromosome of 6,407,860 bp.

scholarly journals Complete Genome Sequence of the Type Strain of the Acetogenic BacteriumMoorella thermoaceticaDSM 521T

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Anja Poehlein ◽  
Frank R. Bengelsdorf ◽  
Carola Esser ◽  
Bettina Schiel-Bengelsdorf ◽  
Rolf Daniel ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Circular Chromosome ◽  
Moorella Thermoacetica ◽  
Acetogenic Bacterium

Here we report the closed genome sequence of the type strainMoorella thermoaceticaDSM 521T, an acetogenic bacterium, which is able to grow autotrophically on H2+ CO2and/or CO, using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.53 Mb).

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