Shewanella oneidensis
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ABSTRACT:
PROVIDER: PRJNA317508 | ENA |
REPOSITORIES: ENA
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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:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1
2012-07-19 | GSE39462 | GEO
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:Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. To gain insights into why MR-1 is incapable of fermentative growth, this study examined a hypothesis that this strain is programmed to repress the expression of some carbon metabolic genes in the absence of electron acceptors. Comparative transcriptomic analyses of the MR-1 derivative were conducted in the presence and absence of fumarate as an electron acceptor, and these found that the expression of many genes involved in carbon metabolism required for cell growth, including several tricarboxylic acid (TCA) cycle genes, was significantly downregulated in the absence of fumarate. This finding suggests a possibility that MR-1 is unable to grow fermentatively on glucose in minimal media owing to the shortage of nutrients essential for cell growth, such as amino acids. This idea was demonstrated in subsequent experiments that showed that the MR-1 derivative fermentatively grows in GMM containing tryptone or a defined mixture of amino acids. We suggest that gene regulatory circuits in MR-1 are tuned to minimize energy consumption under electron acceptor-depleted conditions, and that this results in defective fermentative growth in minimal media. IMPORTANCE It is an enigma why S. oneidensis MR-1 is incapable of fermentative growth despite having complete sets of genes for reconstructing fermentative pathways. Understanding the molecular mechanisms behind this defect will facilitate the development of novel fermentation technologies for the production of value-added chemicals from biomass feedstocks, such as electro-fermentation. The information provided in this study will also improve our understanding of the ecological strategies of bacteria living in redox-stratified environments.
2023-06-20 | GSE220284 | GEO
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: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.
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MODEL1507180036.
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2015-07-30 | MODEL1507180036 | BioModels
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:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain.
2013-11-01 | GSE44689 | GEO
Project description:High-resolution tiling analysis of the MR-1 transcriptome under diverse growth conditions The conditions include aerobic growth in Luria-Bertani broth (LB), aerobic growth in defined lactate minimal medium, anaerobic growth in defined lactate minimal medium with 20mM dimethyl sulfoxide as the electron acceptor, anaerobic growth in defined lactate minimal medium with 10mM iron (III) citrate as the electron acceptor, 10 minutes post heat shock at 42oC see GSE39468 for tiling data on lactate minimal media
2013-03-18 | GSE45217 | GEO
Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS. S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.
2014-06-12 | E-GEOD-58292 | biostudies-arrayexpress