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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:Moorella glycerini strain:DSM 11254 Genome sequencing and assembly
| PRJNA580183 | ENA
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:Autotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and translational regulation of the corresponding genes is highly demanded. Here, we complete a genome sequence of Eubacterium limosum ATCC8466 in a circular form of 4.4 Mb, followed by integrating genome-scale measurements of its transcriptome and translatome. Interestingly, the transcriptionally abundant genes encoding the Wood-Ljungdahl pathway were regulated at translational level with decreased translation efficiency (TE). To understand the regulation, the primary transcriptome was augmented, which determined 1,458 transcription start sites (TSS) and 1,253 5’-untranslated regions (5′UTR). The data supports that under the autotrophic condition the TE of genes for the Wood-Ljungdahl pathway and the energy conservation system were regulated by 5′UTR secondary structure. In addition, it was illustrated that the strain reallocates protein synthesis and energy economically, focusing more on translation of energy conservation system rather than on carbon metabolism under autotrophic growth. Thus, our results provide potential route for strain engineering to enhance syngas fermenting capacity.
2018-07-16 | GSE97613 | GEO
Project description:The oxalate-carbonate Pathway (OCP) refers to the biotransformation process of soil Oxalate degradation and coupled Carbonate formation. It is of great significance to explore this complex biotransformation process to improve the suitable rhizosphere environment and promote soil carbon cycle. A strain of oxalate degrading bacteria, Spirillum OX-1, was isolated from soil.
2023-04-17 | PXD041599 |
Project description:Efflux of antimicrobial compounds from bacterial cells is one of the important mechanisms responsible for multi-drug resistance (MDR). Inhibiting the activity of efflux pumps using chemosensitizers like 1-(1-naphthylmethyl)-piperazine (NMP) is currently considered as a promising strategy to overcome MDR. However, additional effects of NMP other than inhibition are rarely if ever considered. Here, using phenotypic, phenotypic microarray and transcriptomic assays we show that NMP plays a role in membrane destabilization in MDR Klebsiella pneumoniae MGH 78578 strain. The observation of membrane destabilization was supported by RNA-seq data which showed that many up-regulated genes were either directly involved in responses to envelope stress or bacterial repair systems which are essential to maintain viability in an environment containing NMP. Membrane destabilization happens as early as 15 minutes post-NMP treatment. We postulate that the early membrane disruption leads to destabilization of inner membrane potential, impairing ATP production and consequently resulting in efflux pump inhibition.
2018-12-06 | GSE122651 | 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:Draft Genome Sequences of Two Hydrogenogenic Thermophilic Carbon Monoxide-Oxidizing Bacteria Moorella spp.
| PRJDB8248 | ENA