Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in <i>Streptomyces</i> sp. CC0208

Zhang, Hong Yu; Dong, Shihua; Lou, Tingting; Wang, Suying

doi:10.1002/jobm.201800563

Cited by 10 publications

(7 citation statements)

References 55 publications

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“…Out of the total genes, a total of 406 genes were involved in metabolism of cofactors, vitamins, terpenoids, polyketides and other secondary metabolites (Table 2). Moreover, the previous study by Zhang et al (2019) reports the similar scenario in Streptomyces sp. CC0208 contains 439 genes which involved in the metabolism of cofactors, vitamins, terpenoids, glycan, polyketides and other secondary metabolites.…”

Section: Resultssupporting

confidence: 62%

The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

Veilumuthu

Nagarajan

Sasikumar

et al. 2021

Preprint

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Streptomyces species is one among the dominant group of bacteria in the family Actinobacteria with a rich repertoire of secondary metabolites. Secondary metabolites with antimicrobial activity and plant growth promotor have been isolated from various Streptomyces sp. Here in this investigation, we present the draft genome of a new species, Streptomyces sp. VITGV156 isolated from healthy tomato plant (Lycopersicon esculentum) which has some rare antimicrobial secondary metabolites, like coelichelin, fluostatins, vicenistatin, nystatin, sipanmycin, and informatipeptin. The genome is 8.18 Mb in size with 6,259 protein coding genes. The average GC content of the genome is 72.61 %. Preliminary analysis with antiSMASH 6.0 revealed the presence of 29 biosynthetic gene clusters for the synthesis of potential secondary metabolites. These includes 4 NRPS (non – ribosomal peptide synthetase), 7 PKS (Polyketide Synthases), 2 RiPP (Ribosomally synthesized and post-translationally modified peptides) clusters. When we look into genes associated with secondary metabolites, 406 genes are present which includes 184 genes for cofactor and vitamins, 72 genes for terpenoids and polyketides, 70 genes for xenobiotics and 80 genes for other metabolites are present. Comparative genome analysis of VITGV156 with its closest neighbor Streptomyces luteus strain TRM45540 revealed ANI 91.22% and dDDH value 44.00%.

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Section: Resultssupporting

confidence: 62%

The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

Veilumuthu

Nagarajan

Sasikumar

et al. 2021

Preprint

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“…AIIW2. GIs can carry through "horizontal gene transfer" among the genetically adjacent species which can be recognized through phylogenetic analysis [40,41]. In this comparative study, AIIW2 shared the highest genomic islands with B. paralicheniformis followed by B. sonorensis and displayed lesser shared GIs with B. haynesii ( Figure 5).…”

Section: Discussionmentioning

confidence: 83%

Draft genome sequence of plastic degrading Bacillus sp. AIIW2 isolated from the Arabian ocean

et al. 2020

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The endemic spread of plastic in the environment requires urgent need of a sustainable approach. Marine microbes found to have vast bioactivity and play a central role in biogeochemical cycling in the ocean; however, very few of them had been explored for biochemical cycling or plastic degradation. In the present study, we report the draft genome sequence of marine Bacillus sp. AIIW2 which was found to utilize plastic as a carbon source. The Bacillus sonorensis SRCM101395 was used as a reference genome for mapping the reads. The genome size of strain AIIW2 was approximately 4.4 Mb and composed of 4737 coding sequences with 45.7% G + C contents. The whole genome comparison of strain AIIW2 with three closest Bacillus strains showed strain specificity, the 16S ribosomal RNA sequence shows 99.93% similarity with Bacillus paralicheniformis KJ‐16T (KY694465). This genome data would provide the genetic basis in developing plastic bioremediation approaches and discover the enzymes pertinent in the biodegradation processes.

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“…Depending on the Kyoto Encyclopedia of Genes and Genomes (KEGG) (Galperin et al 2014;Zhang et al 2019) with BLASTP, several databases were utilized for genome annotation and gene function prediction, including Gene Ontology, Clusters of Orthologous Groups (COG), and "shn." Java version 1.8.0_152 ( 2019), which is the OS version for Java 10.0 (http://java.sun.com), was used for accessing most databases.…”

Section: Genome Data Analysismentioning

confidence: 99%

Genomic analysis of a functional haloacid-degrading gene of Bacillus megaterium strain BHS1 isolated from Blue Lake (Mavi Gölü, Turkey)

Wahhab

Samsulrizal

Edbeib³

et al. 2021

Ann Microbiol

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Purpose Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level. Methods The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with strain BHS1. Next, genome data were analyzed to demarcate DNA regions containing protein-coding genes and determine the function of certain BHS1 genes. Finally, results from a colorimetric chloride ion–release assay demonstrated that strain BHS1 produces dehalogenase. Results De novo assembly of the BHS1 genomic sequence revealed a genome size of ~ 5.37 Mb with an average G+C content of 38%. The predicted nuclear genome harbors 5509 protein-coding genes, 1353 tRNA genes, 67 rRNA genes, and 6 non-coding (mRNA) genes. Genomic mapping of strain BHS1 revealed its amenability to synthesize two families of dehalogenases (Cof-type haloacid dehalogenase IIB family hydrolase and haloacid dehalogenase type II), suggesting that these enzymes can participate in the catabolism of halogenated organic acids. The mapping identified seven Na+/H+ antiporter subunits that are vital for adaptation of the bacterium to an alkaline environment. Apart from a pairwise analysis to the well-established L-2-haloacid dehalogenases, whole-cell analysis strongly suggested that the haloacid dehalogenase type II might act stereospecifically on L-2-chloropropionic acid, D,L-2-chloropropionic acid, and 2,2-dichloropropionic acid. Whole-cell studies confirmed the utilization of these three substrates and the gene’s role in dehalogenation. Conclusions To our knowledge, this is the first report of the full genome sequence for strain BHS1, which enabled the characterization of selected genes having specific metabolic activities and their roles in the biodegradation of halogenated compounds.

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Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208

Cited by 10 publications

References 55 publications

The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

Draft genome sequence of plastic degrading Bacillus sp. AIIW2 isolated from the Arabian ocean

Genomic analysis of a functional haloacid-degrading gene of Bacillus megaterium strain BHS1 isolated from Blue Lake (Mavi Gölü, Turkey)

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