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REPOSITORIES: ENA
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Project description:Acetate is a simple carboxylic acid that is synthesized in various microorganisms. Although acetate toxicity and tolerance have been studied in many microorganisms, little is known about the effects of exogenous acetate on the cell growth of acetogenic bacteria. In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution under acetate challenge. When compared with the wild-type strain, the acetate-adapted strain displayed a tolerance to acetate up to 10 g L-1 and higher biomass yields in batch cultures, although the metabolite profiles greatly varied depending on culture conditions. Interestingly, genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase, which is crucial to its autotrophic growth on CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed the global change in the gene expression profile of the acetate-adapted strain. Strikingly, most genes involved in CO2-fixing Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated. In addition, we observed that a couple of metabolic pathways associated with dissimilation of nucleosides and carbohydrates were significantly up-regulated in the acetate-adapted strain as well as several amino acid biosynthetic pathways, indicating that the strain might increase its fitness by utilizing organic substrates in response to the down-regulation of carbon fixation. Further investigation into the carbon fixation degeneration of the acetate-adapted strain will provide practical implications in CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation. The transcriptome profiles of the wild-type Clostridium sp. AWRP and its acetate-tolerant derivative 46T-a were compared.
2022-06-26 | GSE206757 | GEO
Project description:Acetogenic bacteria utilize cellular redox energy to convert CO2 to acetate using the Wood-Ljungdahl (WL) pathway. Such redox energy can be derived from electrons generated from H2 as well as inorganic materials such as photo-responsive semiconductors. To reveal how acetogenic bacteria utilize electrons generated from external energy sources to reduce CO2, we developed a nanoparticle-microbe hybrid system and generated RNA-seq results.
2020-09-09 | GSE157613 | GEO
Project description:Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degrading Paenarthrobacter spp. (Paenarthrobacter nitrojuajacolis LG01 and Paenarthrobacter histidinolovorans LG02) that were isolated by metabolic enrichment on levoglucosan as sole carbon source. Genome sequencing and proteomics analysis revealed expression of a series of gene clusters encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan b-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident. The expressed gene clusters contained a range of putative sugar phosphate isomerase/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbors revealed that homologues of LgdA, LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One sugar phosphate isomerase/xylose isomerase cluster (LgdB3) was identified with limited distribution mutually exclusive with LgdB2. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight the diversity within the LGDH pathway through which bacteria utilize levoglucosan as a nutrient source.
2023-05-10 | PXD039086 | Pride
Project description:We constructed the electroautotrophic bacteria, i.e., Sporomusa ovata together with CdS for artificial photosynthesis that achieved the conversion of carbon dioxide to the acetate. The proteomic analysis in S.ovata-CdS biohybrids and S.ovata-only groups was conducted to propose the working mechanisms including carbon dioxide fixation, electron transfer, energy metabolism and redox oxygen damage repair.
2021-08-18 | PXD027986 |
Project description:The identification and characterization of the transcriptional regulatory networks governing the physiological behaviour and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. This system has been investigated in bacteria, yeast and filamentous fungi. In the latter, the C2H2 zinc finger protein has been shown to act as the central transcriptional repressor in this process. Here, we deciphered the CRE1 regulon by profiling transcription in a wild-type and delta-cre1 mutant strains on glucose in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) at constant growth rates known to per se repress and derepress CCR-affected genes.
2011-06-01 | GSE21072 | GEO
Project description:Pesticide degrading bacteria genome sequencing
| PRJNA1006520 | ENA