Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1165503 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30805189_1.fastq.gz | Fastqsanger.gz | |||
| SRR30805189_2.fastq.gz | Fastqsanger.gz | |||
| SRR30805190_1.fastq.gz | Fastqsanger.gz | |||
| SRR30805190_2.fastq.gz | Fastqsanger.gz | |||
| SRR30805191_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. In fact, Shewanella species have been demonstrated to adhere to various surfaces and form biofilms. Global transcriptome profiling was performed on cells in the transition to surface-associated growth using different surfaces and conditions to understand molecular mechanisms underlying the initiation of microbe-surface interactions and the switch from planktonic to sessile life style. In the study presented, expression profiles of two independent replicates of Shewanella oneidensis MR-1 wild type cells attached to glass for 0.25 h and 1 h, respectively, under hydrodynamic conditions were compared to two independent replicates of planktonic grown Shewanella oneidensis MR-1 wild type cells. Furthermore, expression profiles of two independent replicates of Shewanella oneidensis MR-1 wild type cells attached for 1 h to iron surface under hydrodynamic conditions were compared to two independent replicates of Shewanella oneidensis MR-1 wild type cells attached to glass for 1 h. All samples were obtained from aerobically grown cells in LM.
2010-12-07 | E-GEOD-25865 | biostudies-arrayexpress
Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1
2012-07-19 | GSE39462 | GEO
Project description:Investigation of whole genome gene expression level changes in a Shewanella oneidensis MR-1 to Fe nanoparticle decorated anodes, compared to the carbon plate anodes in microbial electrolysis cells. Whole genome microarray analysis of the gene expression showed that the encoding biofilm formation genes were significantly up-regulated as response to nanoparticle decorated anodes which indicated thickness improvements contributed to enhance current density. The increased expression genes related to nanowire, flavins and c-type cytochromes also have partially contributed to enhance current density by Fe nanoparticle decorated anode. The majority of additional differentially expressed genes associated with electron transport, anaerobic metabolism in response to the nanostructured anodes possibly play roles in current density enhancement. A six chip study using total RNA recovered from three separate replicates of biofilm on Fe Nanoparticle decorated anode of Shewanella oneidensis MR-1 and three separate replicates of carbon plate control. Each chip measures the expression level of 4,295 genes .
2011-08-19 | E-GEOD-31535 | biostudies-arrayexpress
Project description:Pinchuck2010 - Genome-scale metabolic network
of Shewanella oneidensis (iSO783)
This model is described in the article:
Constraint-based model of
Shewanella oneidensis MR-1 metabolism: a tool for data analysis
and hypothesis generation.
Pinchuk GE, Hill EA, Geydebrekht OV,
De Ingeniis J, Zhang X, Osterman A, Scott JH, Reed SB, Romine MF,
Konopka AE, Beliaev AS, Fredrickson JK, Reed JL.
PLoS Comput. Biol. 2010 Jun; 6(6):
e1000822
Abstract:
Shewanellae are gram-negative facultatively anaerobic
metal-reducing bacteria commonly found in chemically (i.e.,
redox) stratified environments. Occupying such niches requires
the ability to rapidly acclimate to changes in electron
donor/acceptor type and availability; hence, the ability to
compete and thrive in such environments must ultimately be
reflected in the organization and utilization of electron
transfer networks, as well as central and peripheral carbon
metabolism. To understand how Shewanella oneidensis MR-1
utilizes its resources, the metabolic network was
reconstructed. The resulting network consists of 774 reactions,
783 genes, and 634 unique metabolites and contains biosynthesis
pathways for all cell constituents. Using constraint-based
modeling, we investigated aerobic growth of S. oneidensis MR-1
on numerous carbon sources. To achieve this, we (i) used
experimental data to formulate a biomass equation and estimate
cellular ATP requirements, (ii) developed an approach to
identify cycles (such as futile cycles and circulations), (iii)
classified how reaction usage affects cellular growth, (iv)
predicted cellular biomass yields on different carbon sources
and compared model predictions to experimental measurements,
and (v) used experimental results to refine metabolic fluxes
for growth on lactate. The results revealed that aerobic
lactate-grown cells of S. oneidensis MR-1 used less efficient
enzymes to couple electron transport to proton motive force
generation, and possibly operated at least one futile cycle
involving malic enzymes. Several examples are provided whereby
model predictions were validated by experimental data, in
particular the role of serine hydroxymethyltransferase and
glycine cleavage system in the metabolism of one-carbon units,
and growth on different sources of carbon and energy. This work
illustrates how integration of computational and experimental
efforts facilitates the understanding of microbial metabolism
at a systems level.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180036.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180036 | BioModels
Project description:The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium) To explore the effect of various growth phases in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles growth in two sets media was compared to each other. Strain was grown in chemostat at 20% O2 in batch culture. Samples were collected in duplicate from both experiments.
2012-04-30 | E-GEOD-25821 | biostudies-arrayexpress
Project description:The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria, such as Shewanella species, which thrive in redox-stratified environments. One of the best studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in E. coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in S. oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analysis suggests that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organization. Thus, we speculate ArcS might have adopted the role of ArcB after loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment. In the study presented, expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB
2010-06-05 | E-GEOD-21044 | biostudies-arrayexpress
Project description:We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive ammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture.
2016-12-08 | PXD004090 | Pride
Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1 Expression data for 15 growth conditions in mid-exponential phase and expression data across growth phases for 3 of those conditions
2012-07-18 | E-GEOD-39462 | biostudies-arrayexpress
Project description:In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA-Seq analysis was employed to determine differential gene expression over time from cultures maintained in a chemostat and limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression. The coordinated increased expression of heme biosynthesis, cytochrome maturation, and transport pathways indicates that S. oneidensis MR-1 increases cytochrome production, including transcription of genes encoding MtrA, MtrC and OmcA, and properly positions these decaheme cytochromes in or near the outer membrane during nanowire formation. In contrast, the expression of the mtrA and mtrC homologs mtrF and mtrD either remain unaffected or decrease during nanowire formation. The ompW gene, encoding a small outer membrane porin, has 50-fold higher expression during oxygen limitation, and it is proposed that OmpW plays a role in cation transport to maintain electrical neutrality during electron transfer. The genes encoding the anaerobic respiration regulator CRP and the extracytoplasmic function sigma factor RpoE are among transcription factor genes with increased expression. RpoE could function by signaling the initial response to oxygen limitation. Our results show that RpoE activates transcription from promoters upstream of mtrC and omcA. The transcriptome and mutant analysis of S. oneidensis MR-1 nanowire production are consistent with independent regulatory mechanisms for extending the outer membrane into tubular structures and for ensuring the electron transfer function of the nanowires.
2016-07-13 | GSE79964 | GEO
Project description:The BarA/UvrY two-component system is well conserved in numerous species of the γ-proteobacteria. However, the regulatory output of this system differs significantly between the species. In this study, we characterized the BarA/UvrY two-component system in Shewanella oneidensis MR-1. Sensor kinase BarA and the cognate response regulator UvrY were identified by bioinformatic analysis and subsequent in vivo interaction and phosphotransfer studies. The expression of two putative small regulatory RNAs (sRNAs), CsrB1 and CsrB2, was demonstrated to be dependent on UvrY. In contrast, a third predicted sRNA, CsrC, was expressed independently of UvrY. Transcriptomic analysis by microarrays revealed that UvrY is a global regulator and affects transcription of key enzymes of carbon metabolism such as ackA, aceAB, and pflAB. Subsequent growth experiments demonstrated that mutants lacking UvrY have a significant growth advantage over the wild type during aerobic growth on N-acetylglucosamine while under under anaerobic conditions the mutant grew more slowly. This effect was absent during growth with lactate as carbon source or in complex medium. Based on these results, we conclude that, in S.oneidensis MR-1, the global BarA/UvrY regulatory system is involved in central carbon metabolism processes. In the study presented, expression profiles of three independent replicates of Shewanella oneidensis MR-1 ∆uvrY were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB to stationary phase (OD600nm=4.0)
2011-01-01 | E-GEOD-24994 | biostudies-arrayexpress