M.ruminantium B.proteoclasticus coculture vs monocultures
Ontology highlight
ABSTRACT:
ORGANISM(S): Butyrivibrio proteoclasticus B316 Methanobrevibacter ruminantium M1
PROVIDER: GSE18716 | GEO | 2010/01/28
SECONDARY ACCESSION(S): PRJNA121517
REPOSITORIES: GEO
Similar Datasets
Project description:This study was undertaken with two major goals in mind: i) To investigate the potential for interspecies hydrogen transfer between a hemicellulytic rumen bacterium (B. proteoclasticus) and a methanogenic achaea (M. ruminantium) Microscopic examination had previously shown B. proteoclasticus in co-culture with M. ruminantium rapidly formed cell to cell co-aggregates. ii) To examine the expression of genes involved in methanogenesis under more rumen-like conditions. Cells of M.ruminantium and B. proteoclasticus were grown in triplicate as mono- or co-cultures until a mid-exponential growth phase was reached. RNAs were extracted and purified. The relative quantities of RNAs contributed by each organism to the co-culture samples were determined by rt qPCR using genes previously shown to be constitutively expressed. The mono-culture RNAs were then combined in the determined proportions to normalise mRNA abundance with their co-culture replicates. cDNAs were synthesized and labelled and hybridised to the arrays. 3 biological replicates were used and the cDNA from each was divided in two to allow each to undergo a dyeswap (total of six arrays) giving technical replicates. Each gene was probed in triplicate adding further technical replication. Blanks and negative controls were also included. The log ratios for each probes replicates (biological and technical) were averaged prior to further analysis.
2010-01-27 | E-GEOD-18716 | biostudies-arrayexpress
Project description:Biogenic methane formation, methanogenesis, a key process in the global carbon cycle is the only energy metabolism known to sustain growth of the microorganisms employing it, the methanogenic archaea. All known methanogenic pathways converge at the methane-liberating step where also the terminal electron acceptor of methanogenic respiration, the heterodisulfide of coenzyme M and coenzyme B is formed. Carbon monoxide (CO) utilization of Methanosarcina acetivorans is unique in that the organism can shift from methanogenesis towards acetogenesis. Here, we show that M. acetivorans can dispense of methanogenesis for energy conservation completely. By disrupting the methanogenic pathway through targeted mutagenesis, followed by adaptive evolution, a strain capable of sustained growth by CO-dependent acetogenesis was created. Still, a minute flux through the methane-liberating reaction remained essential, which was attributed to the involvement of the heterodisulfide in at least one essential anabolic reaction. Genomic and proteomic analysis showed that substantial metabolic rewiring had occurred in the strain. Most notably, heterodisulfide reductase, the terminal respiratory oxidoreductase was eliminated to funnel the heterodisulfide towards anabolism. These results suggest that the metabolic flexibility of “methanogenic” archaea is much greater than anticipated and open avenues for probing the mechanism of energetic coupling and the crosstalk between catabolism and anabolism.
2021-10-05 | PXD022016 | Pride
Project description:M.ruminantium B.proteoclasticus coculture vs monocultures
| PRJNA121517 | ENA
Project description:BackgroundTo date silica nanoparticles (SNPs) play an important role in modern technology and nanomedicine. SNPs are present in various materials (tyres, electrical and thermal insulation material, photovoltaic facilities). They are also used in products that are directly exposed to humans such as cosmetics or toothpaste. For that reason it is of great concern to evaluate the possible hazards of these engineered particles for human health. Attention should primarily be focussed on SNP effects on biological barriers. Accidentally released SNP could, for example, encounter the alveolar-capillary barrier by inhalation. In this study we examined the inflammatory and cytotoxic responses of monodisperse amorphous silica nanoparticles (aSNPs) of 30 nm in size on an in vitro coculture model mimicking the alveolar-capillary barrier and compared these to conventional monocultures.MethodsThus, the epithelial cell line, H441, and the endothelial cell line, ISO-HAS-1, were used in monoculture and in coculture on opposite sides of a filter membrane. Cytotoxicity was evaluated by the MTS assay, detection of membrane integrity (LDH release), and TER (Transepithelial Electrical Resistance) measurement. Additionally, parameters of inflammation (sICAM-1, IL-6 and IL-8 release) and apoptosis markers were investigated.ResultsRegarding toxic effects (viability, membrane integrity, TER) the coculture model was less sensitive to apical aSNP exposure than the conventional monocultures of the appropriate cells. On the other hand, the in vitro coculture model responded with the release of inflammatory markers in a much more sensitive fashion than the conventional monoculture. At concentrations that were 10-100fold less than the toxic concentrations the apically exposed coculture showed a release of IL-6 and IL-8 to the basolateral side. This may mimic the early inflammatory events that take place in the pulmonary alveoli after aSNP inhalation. Furthermore, a number of apoptosis markers belonging to the intrinsic pathway were upregulated in the coculture following aSNP treatment. Analysis of the individual markers indicated that the cells suffered from DNA damage, hypoxia and ER-stress.ConclusionWe present evidence that our in vitro coculture model of the alveolar-capillary barrier is clearly advantageous compared to conventional monocultures in evaluating the extent of damage caused by hazardous material encountering the principle biological barrier in the lower respiratory tract.
| S-EPMC3040689 | biostudies-literature
Project description:Methane is a well-known factor in green house effect and also could be an alternative energy, which produced via methanogenesis by methanogenic archaea. Methanohalophilus portucalensis FDF1T is a halophilic methylotrophic methanogen and has been used as a model to study osmoadaptation in fluctuated abiotic environmental conditions. Here we report a genome-wide phosphoproteomic analysis of M. portucalensis FDF1T to uncover the possible phosphorylation-mediated regulations in methanogenesis and osmoadaptation. According to the biological function analysis revealed 20.6% of total 149 phosphoproteins were involved in the regulation of the single carbon metabolism for methanogenesis and osmoadaptation. Together with genome sequencing and phosphoproteomic analysis, we provided the first evidence to indicate protein phosphorylation networks in regulating the pyrrolysine (Pyl) mediated translation of methylotrophic methyltransferase. Furthermore, the functional assays of glycine sarcosine N-methyltransferase revealed that the enzymatic activity was modulated by threonine phosphorylation. Collectively, our results not only provide new insight into phosphorylation-mediated regulations in single carbon energy metabolism but also clearly demonstrate that phosphorylation plays a critical role in osmolyte betaine synthesis through a phospho-switch mechanism.
2016-07-05 | PXD002024 | Pride
Project description:Propionate accumulation is an important bottleneck for anaerobic degradation of organic matter. We hypothesized that propionate conversion by a novel coculture of Syntrophobacter fumaroxidans and Geobacter sulfurreducens can be an alternative strategy for propionate oxidation coupled to Fe(III) reduction. In this study, we successfully cocultured S. fumaroxidans and G. sulfurreducens on propionate and Fe(III). Proteomic analyses of this coculture provided insights into the underlying mechanisms of propionate metabolism pathway and interspecies electron transfer mechanism. Our study can be further useful in understanding syntrophic propionate degradation in bioelectrochemical and anaerobic digestion systems.
2022-02-17 | PXD027104 | Pride
Project description:Hong2004 - Genome-scale metabolic network of
Mannheimia succiniciproducens (iSH335)
This model is described in the article:
The genome sequence of the
capnophilic rumen bacterium Mannheimia succiniciproducens.
Hong SH, Kim JS, Lee SY, In YH, Choi
SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ.
Nat. Biotechnol. 2004 Oct; 22(10):
1275-1281
Abstract:
The rumen represents the first section of a ruminant
animal's stomach, where feed is collected and mixed with
microorganisms for initial digestion. The major gas produced in
the rumen is CO(2) (65.5 mol%), yet the metabolic
characteristics of capnophilic (CO(2)-loving) microorganisms
are not well understood. Here we report the 2,314,078 base pair
genome sequence of Mannheimia succiniciproducens MBEL55E, a
recently isolated capnophilic Gram-negative bacterium from
bovine rumen, and analyze its genome contents and metabolic
characteristics. The metabolism of M. succiniciproducens was
found to be well adapted to the oxygen-free rumen by using
fumarate as a major electron acceptor. Genome-scale metabolic
flux analysis indicated that CO(2) is important for the
carboxylation of phosphoenolpyruvate to oxaloacetate, which is
converted to succinic acid by the reductive tricarboxylic acid
cycle and menaquinone systems. This characteristic metabolism
allows highly efficient production of succinic acid, an
important four-carbon industrial chemical.
This model is hosted on
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MODEL1507180025.
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2015-07-30 | MODEL1507180025 | BioModels
Project description:Hydrogenotrophic methanogenic Archaea are defined by a H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. Hydrogenotrophs respond to H2 starvation both phenotypically and at the level of gene expression; however, the responses during growth on formate have not been characterized. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess, suggesting that energy spilling occurs. Using microarray analysis, we show that the expression of genes encoding F420-dependent steps of methanogenesis, including one of two formate dehydrogenases, increased with H2 starvation, but with formate occurred at high levels regardless of limitation or excess. One gene, encoding H2-dependent methylene-tetrahydromethanopterin dehydrogenase, decreased in expression with either H2 limitation or formate limitation. Expression of genes for the second formate dehydrogenase, molybdenum-dependent formylmethanofuran dehydrogenase, and molybdenum transport increased specifically with formate limitation. Of the two formate dehydrogenases, only the first could support growth on formate in batch culture where formate was in excess.
2013-05-03 | GSE42111 | GEO