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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression analysis of Shewanellla oneidensis MR-1 to Fe nanoparticle decorated anodes in microbial electrolysis cells

ABSTRACT: 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 .

ORGANISM(S): Shewanella oneidensis MR-1

SUBMITTER: Shoutao Xu

PROVIDER: E-GEOD-31535 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression analysis of Shewanellla oneidensis MR-1 to Fe nanoparticle decorated anodes in microbial electrolysis cells

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.

2011-08-20 | GSE31535 | GEO

Transcriptome profiling of cells initially attached to different surfaces

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

Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

2012-07-19 | GSE39462 | GEO

Shewanella oneidensis MR-1

Project description:Expression analysis of Shewanellla oneidensis MR-1 to Fe nanoparticle decorated anodes in microbial electrolysis cells

| PRJNA145505 | ENA

Expression data from Shewanella oneidensis MR-1 in time series experiment

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

delta-arcS versus wild-type

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

Quantitative proteome of Shewanella oneidensis MR-1

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

Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

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

RNA-Seq of Fe-cycling microorganisms in monoculture versus co-culture

Project description:Comparative RNA-Seq profiling of Sideroxydans sp. CL21, a microaerophilic, Fe(II)-oxidizer, and the facultative anaerobe Shewanella oneidensis, an Fe(III) reducer. The microorganisms were grown in co-culture and monoculture batch incubations under microaerobic growth conditions. RNA-Seq profiling was used to compare the transcriptomes of both Sideroxydans sp. CL21 and S. oneidensis when grown in co-culture compared to growth in monoculture

2020-06-01 | E-MTAB-9015 | biostudies-arrayexpress

delta-uvrY versus wild-type

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

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