Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Caldicoprobacter oshimai

ABSTRACT: Caldicoprobacter oshimai overview

PROVIDER: PRJNA195994 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	JAGB01.dat.gz	Other
	JAGB01.fasta.gz	Fasta.gz
	JAGB01.master.dat	Other
	SRR1801171_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Caldicoprobacter oshimai DSM 21659

Project description:Caldicoprobacter oshimai DSM 21659 Genome sequencing and assembly

| PRJNA195830 | ENA

Thermus oshimai

Project description:Thermus oshimai overview

| PRJNA63235 | ENA

Thermus oshimai JL-2

Project description:Thermus oshimai JL-2 genome sequencing

| PRJNA63181 | ENA

Thermus oshimai DSM 12092

Project description:Thermus oshimai DSM 12092 Genome sequencing and assembly

| PRJNA169715 | ENA

Caldicoprobacter algeriensis strain:TH7C1

Project description:Caldicoprobacter algeriensis strain:TH7C1 Genome sequencing and assembly

| PRJNA743054 | ENA

Caldicoprobacter guelmensis strain:DSM 24605 | isolate:DSM 24605

Project description:Caldicoprobacter guelmensis DSM 24605 genome sequencing

| PRJNA695631 | ENA

Caldicoprobacter faecalis strain:DSM 20678 | isolate:DSM 20678

Project description:Caldicoprobacter faecalis DSM 20678 genome sequencing

| PRJNA335206 | ENA

Project description:Caldicoprobacter faecalis DSM 20678

| PRJEB17439 | ENA

Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.

Project description:G-quadruplexes (G4s) are unusual stable DNA structures that cause genomic instability. To overcome the potential barriers formed by G4s, cells have evolved different families of proteins that unfold G4s. Pif1 is a DNA helicase from superfamily 1 (SF1) conserved from bacteria to humans with high G4-unwinding activity. Here, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B which constitute a G4-Recognizing Surface (GRS). The overall structure of the G4 maintains its three-layered propeller-type G4 topology, without significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 are recognized by GRS residues mainly through electrostatic, ionic interactions, and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Compared with previously solved structures of SF2 helicases in complex with G4, our structure reveals how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.

| S-EPMC9253758 | biostudies-literature

Genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of the thermophilic Caldicoprobacter algeriensis TH7C1<sup>T</sup>.

Project description:BackgroundOmics approaches are widely applied in the field of biology for the discovery of potential CAZymes including whole genome sequencing. The aim of this study was to identify protein encoding genes including CAZymes in order to understand glycans-degrading machinery in the thermophilic Caldicoprobacter algeriensis TH7C1T strain.ResultsCaldicoprobacter algeriensis TH7C1T is a thermophilic anaerobic bacterium belonging to the Firmicutes phylum, which grows between the temperatures of 55 °C and 75 °C. Next generation sequencing using Illumina technology was performed on the C. algeriensis strain resulting in 45 contigs with an average GC content of 44.9% and a total length of 2,535,023 bp. Genome annotation reveals 2425 protein-coding genes with 97 ORFs coding CAZymes. Many glycoside hydrolases, carbohydrate esterases and glycosyltransferases genes were found linked to genes encoding oligosaccharide transporters and transcriptional regulators; suggesting that CAZyme encoding genes are organized in clusters involved in polysaccharides degradation and transport. In depth analysis of CAZomes content in C. algeriensis genome unveiled 33 CAZyme gene clusters uncovering new enzyme combinations targeting specific substrates.ConclusionsThis study is the first targeting CAZymes repertoire of C. algeriensis, it provides insight to the high potential of identified enzymes for plant biomass degradation and their biotechnological applications.

| S-EPMC9124407 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data