Project description:To identify transcriptional adaptations associated with increased alkane production in Nostoc punctiforme, we performed comparative transcriptomic analysis of an alkane overproduction strain. RNA-seq data identified a large number of highly up-regulated genes in the overproduction strain potentially involved in rRNA processing, mycosporine-glycine production, and synthesis of non-ribosomal peptides including nostopeptolide A. Other up-regulated genes encoding helical carotenoid proteins, stress-induced proteins, and those for microviridin synthesis were also up-regulated. The presence of several up-regulated genes or operons on multi-copy plasmids resulted in reduced alkane production, indicating possible targets for mutagenesis that might limit lipid droplet and alkane production.
Project description:A significant part of the heavier petroleum fraction resulting from offshore oil-spills sinks to the deep-sea. Its fate and biodegradation by microbial communities is unclear. In particular, the physiological and metabolic features of hydrostatic pressure (HP) adapted oil-degraders have been neglected. In this study, hydrocarbon-free sediment from 1km below surface water (bsl) was incubated at 0.1, 10 and 20MPa (equivalent to surface waters, 1 and 2km bsl) using triacontane (C30) as sole carbon source for a 3-month enrichment period. HP strongly impacted biodegration, as it selected for microbial communities with small cells, high O2 respiration and nutrients requirements, but low biomass and C30-degradation yields. The alkane-degrading metaproteome linked to β-oxidation was detected but its expression was reduced under HP contrary to several housekeeping genes. This was reflected in the enriched communities, as atmospheric pressure was dominated by hydrocarbonoclastic bacteria while non-specialized or previously unrecognized oil-degrading genera were enriched under HP.
Project description:Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel-oxygenates methyl-tert-butyl ether and ethanol High-density whole genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of TBA to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Based on the expression data, hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, alkane monooxygenase as well as propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The global transcriptome response revealed the link between metabolism of MTBE and aromatic compounds (e.g. benzene, toluene) present in gasoline mixtures. The expression data aids our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment. Keywords: bacterial metabolism
Project description:In this study we compare the transcriptome of the strain Dietzia sp. DQ12-45-1b grown in octacosane , hexadecane and glucose for the characterization distinct adaption mechanisms under different alkane substrates
