scholarly journals Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Hongyan Zhao ◽  
Kejian Tian ◽  
Qing Qiu ◽  
Yu Wang ◽  
Hongyan Zhang ◽  
...  
Keyword(s):  
Sole Source ◽  
Rhodococcus Opacus ◽  
Whole Genome ◽  
Metabolic Potential ◽  
Protein Coding ◽  
Degrading Enzymes ◽  
Degrading Bacterium ◽  
Rhodococcus Jostii Rha1 ◽  
Multiple Strains ◽  
Rhodococcus Sp

We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4 Mbp with G + C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.

scholarly journals Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07

2020 ◽  
Vol 21 (24) ◽  
pp. 9363
Author(s):  
Gillian Li Yin Lee ◽  
Nur Nadhirah Zakaria ◽  
Peter Convey ◽  
Hiroyuki Futamata ◽  
Azham Zulkharnain ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Sequence ◽  
Phenol Degradation ◽  
Draft Genome ◽  
South Shetland Islands ◽  
Whole Genome ◽  
Metabolic Potential ◽  
Rhodococcus Sp ◽  
Dioxygenase Activity

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.

scholarly journals Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Ya He ◽  
Kangfei Wei ◽  
Kaiwei Si ◽  
Jacques Mathieu ◽  
Mengyan Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Metabolic Pathway ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sole Source ◽  
Molecular Biomarkers ◽  
Whole Genome Sequence ◽  
Contaminated Sites ◽  
Whole Genome ◽  
Degrading Bacterium

ABSTRACT We report here the complete genome sequence of Mycobacterium dioxanotrophicus PH-06, which is capable of using 1,4-dioxane as a sole source of carbon and energy. The reported sequence will enable the elucidation of this novel metabolic pathway and the development of molecular biomarkers to assess bioremediation potential at contaminated sites.

scholarly journals A toolkit enabling efficient, scalable and reproducible gene tagging in trypanosomatids

Open Biology ◽  
2015 ◽  
Vol 5 (1) ◽  
pp. 140197 ◽  
Author(s):  
Samuel Dean ◽  
Jack Sunter ◽  
Richard J. Wheeler ◽  
Ian Hodkinson ◽  
Eva Gluenz ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Large Datasets ◽  
Gene Tagging ◽  
Deletion Mutants ◽  
Whole Genome ◽  
Leishmania Mexicana ◽  
Protein Coding ◽  
Achievable Goal ◽  
Endogenous Loci ◽  
Pcr Conditions

One of the first steps in understanding a protein's function is to determine its localization; however, the methods for localizing proteins in some systems have not kept pace with the developments in other fields, creating a bottleneck in the analysis of the large datasets that are generated in the post-genomic era. To address this, we developed tools for tagging proteins in trypanosomatids. We made a plasmid that, when coupled with long primer PCR, can be used to produce transgenes at their endogenous loci encoding proteins tagged at either terminus or within the protein coding sequence. This system can also be used to generate deletion mutants to investigate the function of different protein domains. We show that the length of homology required for successful integration precluded long primer PCR tagging in Leishmania mexicana . Hence, we developed plasmids and a fusion PCR approach to create gene tagging amplicons with sufficiently long homologous regions for targeted integration, suitable for use in trypanosomatids with less efficient homologous recombination than Trypanosoma brucei . Importantly, we have automated the primer design, developed universal PCR conditions and optimized the workflow to make this system reliable, efficient and scalable such that whole genome tagging is now an achievable goal.

scholarly journals Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Fenghua Tian ◽  
Changtian Li ◽  
Yu Li
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Genomic Analysis ◽  
Single Copy ◽  
Whole Genome Sequence ◽  
Type I ◽  
Whole Genome ◽  
Uridine Diphosphate ◽  
Protein Coding ◽  
Medicinal Value

Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.

scholarly journals Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10343
Author(s):  
Pattsarun Cheawchanlertfa ◽  
Sawannee Sutheeworapong ◽  
Piroon Jenjaroenpun ◽  
Thidathip Wongsurawat ◽  
Intawat Nookaew ◽  
...  
Keyword(s):  
Related Species ◽  
Anaerobic Bacterium ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Circular Chromosome ◽  
Closely Related Species ◽  
Degrading Enzymes ◽  
Cassava Pulp ◽  
Pectinolytic Enzymes ◽  
Genes Encoding

Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

scholarly journals Quorum sensing and genomic studies of a marine bacterium Vibrio variabilis strain T01

2015 ◽  
Author(s):  
Kok-Gan Chan ◽  
Nur Izzati Mohamad
Keyword(s):  
Quorum Sensing ◽  
Coastal Waters ◽  
Marine Bacterium ◽  
Cell Communication ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Protein Coding ◽  
Signalling Molecule ◽  
Genomic Studies ◽  
Rna Genes

Vibrio variabilis strain T01 was isolated from the coastal waters in Hulu Selangor, Malaysia and its genome sequenced. This curved gram-negative bacterium shows cell-to-cell communication properties. The characteristics of the sequenced genome and its annotation processes are described here. The finished assembled whole genome of T01T exhibits genome size of 4,529,728 bp in 83 contigs with 46.22% G+C content, 4053 protein coding genes and 94 RNA genes. The whole genome analysis revealed the presence of quorum sensing signalling molecule synthase gene (luxM) which is crucial to understand the quorum sensing dependent phenotypes in this isolate.

scholarly journals Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Hikaru Suenaga ◽  
Mamoru Oshiki ◽  
Shuichi Kawano ◽  
Toshikazu Fukushima
Keyword(s):  
Activated Sludge ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Coke Oven ◽  
Rrna Genes ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

scholarly journals Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT

2019 ◽  
Vol 202 (2) ◽  
pp. 421-426 ◽  
Author(s):  
András Táncsics ◽  
Milán Farkas ◽  
Balázs Horváth ◽  
Gergely Maróti ◽  
Lauren M. Bradford ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mobile Element ◽  
Sole Source ◽  
Degradation Pathway ◽  
Whole Genome Sequence ◽  
Toluene Degradation ◽  
Extradiol Dioxygenase ◽  
Protein Coding ◽  
Microaerobic Conditions ◽  
Rna Genes

Abstract Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain BucT was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z .  oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions.

scholarly journals Biodesulfurization of Naphthothiophene and Benzothiophene through Selective Cleavage of Carbon-Sulfur Bonds by Rhodococcus sp. Strain WU-K2R

2002 ◽  
Vol 68 (8) ◽  
pp. 3867-3872 ◽  
Author(s):  
Kohtaro Kirimura ◽  
Toshiki Furuya ◽  
Rika Sato ◽  
Yoshitaka Ishii ◽  
Kuniki Kino ◽  
...  
Keyword(s):  
Sole Source ◽  
Diesel Oil ◽  
The Other ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Structural Isomer ◽  
Degradation Pathways ◽  
Spectrometry Analysis ◽  
Specific Degradation ◽  
Rhodococcus Sp

ABSTRACT Naphtho[2,1-b]thiophene (NTH) is an asymmetric structural isomer of dibenzothiophene (DBT), and in addition to DBT derivatives, NTH derivatives can also be detected in diesel oil following hydrodesulfurization treatment. Rhodococcus sp. strain WU-K2R was newly isolated from soil for its ability to grow in a medium with NTH as the sole source of sulfur, and growing cells of WU-K2R degraded 0.27 mM NTH within 7 days. WU-K2R could also grow in the medium with NTH sulfone, benzothiophene (BTH), 3-methyl-BTH, or 5-methyl-BTH as the sole source of sulfur but could not utilize DBT, DBT sulfone, or 4,6-dimethyl-DBT. On the other hand, WU-K2R did not utilize NTH or BTH as the sole source of carbon. By gas chromatography-mass spectrometry analysis, desulfurized NTH metabolites were identified as NTH sulfone, 2′-hydroxynaphthylethene, and naphtho[2,1-b]furan. Moreover, since desulfurized BTH metabolites were identified as BTH sulfone, benzo[c][1,2]oxathiin S-oxide, benzo[c][1,2]oxathiin S,S-dioxide, o-hydroxystyrene, 2-(2′-hydroxyphenyl)ethan-1-al, and benzofuran, it was concluded that WU-K2R desulfurized NTH and BTH through the sulfur-specific degradation pathways with the selective cleavage of carbon-sulfur bonds. Therefore, Rhodococcus sp. strain WU-K2R, which could preferentially desulfurize asymmetric heterocyclic sulfur compounds such as NTH and BTH through the sulfur-specific degradation pathways, is a unique desulfurizing biocatalyst showing properties different from those of DBT-desulfurizing bacteria.

scholarly journals Whole-Genome Sequencing of Sphingobium sp. Strain RSMS, a Highly Efficient Tributyl Phosphate-Degrading Bacterium

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Shyam Sunder Rangu ◽  
Ashish Beck ◽  
Mohak Sharda ◽  
Rita Mukhopadhyaya ◽  
Aswin Sai Narain Seshasayee ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Tributyl Phosphate ◽  
Organic Pollutant ◽  
Whole Genome ◽  
Future Studies ◽  
Genetic Elements ◽  
Highly Efficient ◽  
Degrading Bacterium

ABSTRACT Sphingobium sp. strain RSMS was described earlier as an efficient degrader of tributyl phosphate, an organic pollutant. This report describes the generation and annotation of the genome sequence of Sphingobium sp. strain RSMS, which will facilitate future studies to identify genetic elements responsible for the degradation of tributyl phosphate.

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