Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-Genome Sequence of Rhizobacterium Sphingomonas sp. Strain 7/4-4, Isolated from the Root Nodule of Astragalus tugarinovii Basil Growing in the Russian Arctic.

ABSTRACT: The complete genome sequence of Sphingomonas sp. strain 7/4-4, which was isolated from the root nodule of the circumpolar legume Astragalus tugarinovii Basil, is reported. The assembly contains 4,423,370 bp in 1 circular chromosome, with a GC content of 65.94%. The genome sequence of strain 7/4-4 could provide insights into the metabolic potential of Arctic rhizobacteria.

SUBMITTER: Guro P

PROVIDER: S-EPMC10281104 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Whole-Genome Sequence of Rhizobacterium Sphingomonas sp. Strain 7/4-4, Isolated from the Root Nodule of Astragalus tugarinovii Basil Growing in the Russian Arctic.

Guro Polina P Karlov Denis D Kuznetsova Irina I Sazanova Anna A Alekhina Irina I Belimov Andrey A Safronova Vera V

Microbiology resource announcements 20230515 6

The complete genome sequence of Sphingomonas sp. strain 7/4-4, which was isolated from the root nodule of the circumpolar legume Astragalus tugarinovii Basil, is reported. The assembly contains 4,423,370 bp in 1 circular chromosome, with a GC content of 65.94%. The genome sequence of strain 7/4-4 could provide insights into the metabolic potential of Arctic rhizobacteria. ...[more]

PMID: 37184420

Similar Datasets

Draft genome sequence of a Sphingomonas sp., an endosymbiotic bacterium isolated from an arctic lichen Umbilicaria sp.

Project description:Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on the Svalbard Islands. Here we present the draft genome sequence of this strain, which represents a valuable resource for understanding the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in extreme environments.

| S-EPMC3370618 | biostudies-literature

Biotransformation of chromium by root nodule bacteria Sinorhizobium sp. SAR1.

Project description:The present study aims to address the problem of chromium (Cr) toxicity by providing important insights into the mechanisms involved in its bioremediation. Among the 22 Rhizobium and Sinorhizobium isolates obtained from Sesbania sesban root nodules, Sinorhizobium sp. SAR1 (JX174035.1) tolerated the maximum Cr concentration (1mM) and hence was used for further studies. The excess secretion of extra polymeric substances, as seen from scanning electron micrographs, could be a probable mechanism of adaptation to the Cr stress. The Energy dispersive X-ray spectroscopy data did not show any peaks of Cr. The biosorption studies done on the isolate gave maximum adsorption capacity as 285.71mg/g. The isotherm studies showed a better fit to Langmuir isotherm. The Weber and Morris plot established that the phenomenon of adsorption was governed by film diffusion mechanism. The FTIR analysis suggested the role of cell wall components and extracellular polymeric substances in Cr adsorption to the biomass of Sinorhizobium. On the basis of these results a compiled mechanism of Cr (VI) adsorption and its biotransformation into Cr (III) by Sinorhizobium sp. SAR1 is explained. This work outlines a comprehensive detail for the exact phenomenon of Cr biotransformation by Sinorhizobium sp. SAR1. These results may further help in developing and enhancing effective bioremediation approaches.

| S-EPMC6667149 | biostudies-literature

Nocardioides astragali sp. nov., isolated from a nodule of wild Astragalus chrysopterus in northwestern China.

Project description:A Gram-positive, non-motile, rod-shaped bacterial strain, designated HH06T, was isolated from a nodule of Astragalus chrysopterus in northwestern China. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides alpinus Cr7-14T and Nocardioides furvisabuli DSM 18445T with 98.5 and 98.1% similiarity, respectively. Growth was observed at 4-28 °C in R2A medium (optimum at 25 °C), at 10-30 °C in YMA and LB medium (optimum in both at 28 °C) and at pH 5.0-10.0 in R2A medium (optimum at pH 7.0-8.0). The cell wall peptidoglycan was found to contain LL-diaminopimelic acid as the principal diamino acid and MK-8(H4) was identified as the predominant menaquinone. The major polar lipids were identified as phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, two unidentified glycolipids and two unidentified polar lipids. The major fatty acids were identified as iso-C16:0 (32.8%) and C18:1 ω9c (15.1%). The DNA G+C content of strain HH06T was determined to be 71.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic properties and DNA-DNA relatedness, it is concluded that strain HH06T represents a novel species of the genus Nocardioides, for which the name Nocardioides astragali sp. nov. is proposed. The type strain is HH06T (= CGMCC 4.7327T = NBRC 112322T).

| S-EPMC5999194 | biostudies-literature

Genome sequence of Sphingomonas sp. strain PAMC 26621, an Arctic-lichen-associated bacterium isolated from a Cetraria sp.

Project description:The lichen-associated bacterial strain Sphingomonas sp. PAMC 26621 was isolated from an Arctic lichen Cetraria sp. on Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide novel insights into the molecular principles of lichen-microbe interactions.

| S-EPMC3370613 | biostudies-literature

Draft Genome Sequence of Rhizobium sp. Strain 32-5/1, Isolated from Vicia cracca L. Root Nodules in the Russian Arctic.

Project description:This study reports the whole-genome sequence of an endosymbiotic bacterium, Rhizobium sp. strain 32-5/1, isolated from root nodules of the legume Vicia cracca L. in the Arctic region of Russia. The genome consists of two plasmids and one chromosome, with a total length of 5,621,108 bp and 59.5% GC content.

| S-EPMC10281122 | biostudies-literature

Nocaviogua A and B: two lipolanthines from root-nodule-associated Nocardia sp.

Project description:Nocaviogua A (1) and B (2), two lipolanthines featuring a non-canonical avionin (Avi)-containing macrocycle and a long acyl chain, were identified from the mutualistic actinomycete Nocardia sp. XZ19_369, which was isolated from the nodules of sea buckthorn collected in Tibet. Their planar structures were elucidated via extensive analyses of 1D and 2D NMR, as well as HRMS data. The absolute configurations were fully elucidated by advanced Marfey’s analysis and GIAO NMR calculations, representing the first time that the configurations of this family of lipolanthines have been determined. Nocaviogua A (1) exhibited weak cytotoxicity against human chronic uveal melanoma cells (UM92-1), non-small cell lung cancer (NCI-H2170), and breast cancer (MDA-MB-231). Our work provides valuable information on this burgeoning class of lipolanthines for further investigations.

| S-EPMC10435860 | biostudies-literature

Essential roles of buried phenylalanine in the structural stability of thioredoxin from a psychrophilic Arctic bacterium Sphingomonas sp.

Project description:Thioredoxin (Trx), a small redox protein, exhibits thermal stability at high temperatures regardless of its origin, including psychrophiles. Trxs have a common structure consisting of the central β-sheet flanked by an aliphatic cluster on one side and an aromatic cluster on the other side. Although the roles of aromatic amino acids in the folding and stability of proteins have been studied extensively, the contributions of aromatic residues to the stability and function of Trx, particularly Trxs from cold-adapted organisms, have not been fully elucidated. This study examined the roles of aromatic amino acids in the aromatic cluster of a Trx from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621 (SpTrx). The aromatic cluster of SpTrx was comprised of W11, F26, F69, and F80, in which F26 at the β2 terminus was buried inside. The substitution of tyrosine for F26 changed the SpTrx conformation substantially compared to that of F69 and F80. Further biochemical and spectroscopic investigations on F26 showed that the F26Y, F26W, and F26A mutants resulted in structural instability of SpTrx in both urea- and temperature-induced unfolding and lower insulin reduction activities. The Trx reductase (SpTR) showed lower catalytic efficiencies against F26 mutants compared to the wild-type SpTrx. These results suggest that buried F26 is essential for maintaining the active-site conformation of SpTrx as an oxidoreductase and its structural stability for interactions with SpTR at colder temperatures.

| S-EPMC8673628 | biostudies-literature

nar nodule vs root transcriptome-analysis of symbiotic root nodule development

Project description:12plex_medicago_2014_02 - nar nodule vs root transcriptome - which are the genes differentially expressed in alfalfa spontaneous (non rhizobium-infected) nodules vs. control roots? - biological material: aeroponically grown cuttings of a Medicago sativa (alfalfa) accession that produces empty nodules when nitrogen-starved. Samples for transcriptome comparison: isolated NAR nodules (10 days post N-starvation) vs. roots of the same plants (pools of 3 roots).

2018-11-01 | GSE121571 | GEO

Chemical diversity in basil (Ocimum sp.) germplasm.

Project description:The present study aimed to chemically characterize 31 accessions and seven cultivars of basil. The percentage composition of the essential oils of the accessions and cultivars was based on the 14 most abundant constituents: 1,8-cineole, linalool, methyl chavicol, neral, nerol, geraniol, geranial, methyl cinnamate, β-bourbonene, methyl eugenol, α-trans-bergamotene, germacrene-D, epi-α-cadinol, and δ-cadinene. The genetic materials were classified into eight clusters according to the chemical composition of the essential oils: Cluster 1--mostly linalool and 1,8-cineole; Cluster 2--mostly linalool, geraniol, and α-trans-bergamotene; Cluster 3--mostly linalool, methyl chavicol, methyl cinnamate, and β-bourbonene; Cluster 4--mostly linalool, methyl chavicol, epi-α-cadinol, and α-trans-bergamotene; Cluster 5--mainly linalool, methyl eugenol, α-trans-bergamotene, and epi-α-cadinol; Cluster 6--mainly linalool, geraniol, and epi-α-cadinol; Cluster 7--mostly linalool and methyl chavicol; Cluster 8--mainly geranial and neral.

| S-EPMC4299303 | biostudies-other