Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unbalancing FurB (Zur)-mediated homeostasis in Anabaena sp. PCC7120: Consequences on heterocyst development and biofilm formation

ABSTRACT: Here, we report the comparison of transcriptomes of Anabaena sp. PCC7120 and the FurB(Zur) deletion derivative strain (MN38). Anabaena sp PCC7120 is a cyanobacterium that differentiates specialized nitrogen-fixing cells called heterocysts and that is capable of forming biofilms. Our data showed that the deletion of FurB negativily affected the heterocyst development and the biofilm formation. In addition, the RNA-seq data together with gel retardation assays unveiled that FurB is directly involved in the regulation of several genes related to heterocyst development and biofilm formation and other novel functions different from the ones related to the canonical Zur regulon.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Anabaena ambigua

SUBMITTER: Cristina Sarasa-Buisan

PROVIDER: E-MTAB-12347 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Characterization of a cyanobacterial exoproteome reveals a novel zinc acquisition system used by primitive bacteria

Project description:Zinc can be limiting in many environments and bacteria have developed acclimation responses to counteract this deficiency. In most bacteria, the acclimation response to zinc limitation is controlled by Zur, a transcriptional regulator of the FUR family. Several proteins that take part in this response are present in the cytoplasm and the cell envelope. However, little is known about the involvement of proteins present in the extracellular space in the response to Zn limitation and whether the protein composition of this space might be also regulated by Zur. Therefore, in order to get an insight into these issues, a comparative analysis of the exoproteomes of the cyanobacterium Anabaena sp. PCC7120 (WT) and its Δzur derivative strain (referred as "MN" in the present dataset) was carried out using SWATH-MS analysis.

2024-02-15 | PXD036795 | Pride

RNA-seq of Nostoc sp. PCC 7120 (Anabaena sp. PCC 7120) wild-type strain compared to a FurC-overexpressing derivative strain grown in BG11 and after 48 hours of nitrogen-step down.

Project description:Here, we report the comparison of transcriptomes of Anabaena sp. PCC7120 and a FurC-overexpressing derivative strain grown under standard conditions (BG11) and after 48 hours of nitrogen step-down (BG110). Anabaena sp PCC7120 is a cyanobacterium that differentiates specialized nitrogen-fixing cells called heterocysts. Our data suggests that FurC directly controls the regulation of heterocyst differentiation and nitrogen fixation in this cyanobacterium. In addition, we found that FurC is also clearly involved in the regulation of several genes belonging to different functional categories, such as iron metabolism, photosynthesis and regulatory functions.

2020-04-28 | E-MTAB-8996 | biostudies-arrayexpress

RNA-seq of Nostoc sp. PCC 7120 (Anabaena sp. PCC 7120) wild-type strain, hetZ mutant and hetP mutant

Project description:Total RNA was extracted from Anabaena 7120, hetZ mutant and hetP mutant at 24 h after nitrogen stepdown with two independent biological replicates. To maintain the integrity of coding RNAs, total RNA were sequenced without ribosomal RNA elimination. Strand-specific RNA-Seq libraries were prepared and sequenced using the Illumina HiSeq 2500 sequencing instrument to generate paired-end reads with length of 125 bp.

2018-02-19 | E-MTAB-6459 | biostudies-arrayexpress

Exoproteome of a furC-overexpressing strain: FurC tunes peptidoglycan remodeling and intercell transfer

Project description:To study the effect of FurC overexpression in the exoproteome composition of Anabaena, sp. PCC120, SWATH-MS analyses have been carried out with the isolated exoproteome of the FurC overexpressing strain, EB2770FurC (named in the present dataset "EB") comparing to the one of the wild-type strain (WT). This data togheter combined with physiological and functional studies of FurC protein revealed a potential role of this regulator in the modulation of general cell-wall biogenesis and recycling processes, as well as and in intercellular transfer.

2024-02-07 | PXD043659 | Pride

RNA-seq of Synechococcus sp. WH8102 zur knockout mutant

Project description:Identification of Zur-regulated genes in Synechococcus sp. WH8102

2022-05-31 | E-MTAB-10194 | biostudies-arrayexpress

ChIP analysis unravels an exceptionally wide distribution of binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium.

Project description:The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. NtcA-activated canonical promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. In this study, we have used chromatin immunoprecipitation followed by high-throughput sequencing to identify the whole regulon of NtcA in cells of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 after the withdrawal of combined N. NtcA has been found to bind to 2,424 target regions in the genome of Anabaena, which have been ascribed to 2,153 genes. Interestingly, only a small proportion of those are involved in N assimilation and metabolism, and 65 % of the target regions were located intragenically. The NtcA regulon identified here constitutes the largest bacterial regulon described to date. Our results show that NtcA has a much wider role in the physiology of the cell than it has been previously thought, acting both as a global transcriptional regulator and possibly also as a factor influencing the superstructure of chromosome (and plasmids). Cells of Anabaena sp. PCC 7120 subjected to N-withdrawal for 3 h were used to perform chromatin immunoprecipitation with anti-NtcA antibody. The immunoprecipitated material was sequenced. Three ChIPs were performed from two independent sets of Anabaena cells. A sample of total DNA (not subjected to immunoprecipitation) was used as a control (Input sample).

2014-01-28 | E-GEOD-51865 | biostudies-arrayexpress

Transcriptional Regulation of Anabaena 7120 response to Nitrogen Deprivation

Project description:Here, we report the transcriptome of Anabaena sp. strain 7120, a cyanobacterium that forms specialized nitrogen-fixing cells called heterocysts. Our data suggests that cyanobacteria frequently have more complex transcripts than thought, with large 5' UTRs, numerous antisense transcripts, and multiple transcriptional start sites or processing sites. Four samples of total filament RNA were sequenced with Illumina 40bp reads using directional RNA sequencing (see the Illumina small RNA prep protocol). The samples are 0hr (vegetative cells grown in the presence of ammonia) and 6hr, 12hr, and 21hr cells (after nitrogen step down).

2011-06-22 | E-GEOD-26633 | biostudies-arrayexpress

Genome-wide identification of Bacillus subtilis Zur-binding sites.

Project description:The transcriptional factor Zur plays a key role in regulating zinc homeostasis in Bacillus subtilis. The genomic sites bound by Zur were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 80 inter- and intragenic chromosomal sites bound by Zur. This data set contains 2 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis BSAS36 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Zur protein) were extracted from bacterial cells in the exponential growth phase. IP and whole-cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were anlyzed.

2015-01-06 | E-GEOD-64671 | biostudies-arrayexpress

RNA-seq performed on Brassica oleracea var. italica (broccoli) control and blindness-affected plants, sampled from both leaves and roots.

Project description:Blindness, characterized by apical abortion, is a physiological condition that affects the Brassica family. While exposure to low temperatures during early development has been associated with blindness, the underlying causes and their impact on proper development remain unknown. This study aims to investigate the mechanisms involved in blindness occurrence in broccoli plants.

2023-07-18 | E-MTAB-13076 | biostudies-arrayexpress

Characterization of Zur-dependent genes and direct Zur targets in Yersinia pestis

Project description:The zinc uptake regulator Zur is a Zn2+-sensing metalloregulatory protein involved in the maintenance of bacterial zinc homeostasis. Up to now, regulation of zinc homeostasis by Zur is poorly understood in Y. pestis. We constructed a zur null mutant of Y. pestis biovar microtus strain 201. Microarray expression analysis disclosed a set of 154 Zur-dependent genes of Y. pestis under zinc rich condition. Real-time reverse transcription (RT)-PCR was subsequently used to validate the microarray data. Based on the 154 Zur-dependent genes, predicted regulatory Zur motifs were used to screen for potential direct Zur targets including three putative operons znuA, znuCB and ykgM-RpmJ2. The LacZ reporter fusion analysis verified that Zur greatly repressed the promoter activity of the above three operons. The subsequent electrophoretic mobility shift assay (EMSA) demonstrated that a purified Zur protein was able to bind to the promoter regions of the above three operons. The DNase I footprinting was used to identify the Zur binding sites for the above three operons, verifying the Zur box sequence as predicted previously in γ-Proteobacteria. The primer extension assay was further used to determine the transcription start sites for the above three operons and to localize the -10 and -35 elements. Zur binding sites overlapped the -10 sequence of its target promoters, which was consistent with the previous observation that Zur binding would block the entry of the RNA polymerase to repress the transcription of its target genes. Zur as a repressor directly controls the transcription of znuA, znuCB and ykgM-RpmJ2 in Y. pestis by employing a conserved mechanism of Zur-promoter DNA association as observed in γ-Proteobacteria. Zur contributes to zinc homeostasis in Y. pestis likely through transcriptional repression of the high-affinity zinc uptake system ZnuACB and two alternative ribosomal proteins YkgM and RpmJ2.

2009-06-01 | GSE15183 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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