Candidatus Cyclonatronum proteinivorum strain:Omega
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ABSTRACT:
PROVIDER: PRJNA392178 | ENA |
REPOSITORIES: ENA
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Project description:The catalytic core of the RNA polymerase of most eubacteria is composed of two α subunits and β, β’ and ω subunits. In Escherichia coli, the ω subunit (encoded by the rpoZ gene) has been suggested to assist β’ during RNA polymerase core assembly. The function of the ω subunit is particularly interesting in cyanobacteria because the cyanobacterial β’ is split to N-terminal γ and C-terminal β’ subunits. The ∆rpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions although the mutant cells showed low light-saturated photosynthetic activity, low Rubisco content and accumulated high quantities of protective carotenoids and α-tocopherol. The ∆rpoZ strain contained 15% less of the primary σ factor, SigA, than the control strain, and recruitment of SigA to the RNA polymerase core was inefficient in ∆rpoZ. Thus, a cyanobacterial RNA polymerase holoenzyme lacking the ω subunit contains less frequently the primary σ factor. A DNA microarray analysis revealed that this leads to specific down-regulation of highly expressed genes, like genes encoding subunits for Rubisco, ATP synthase, NADH-dehydrogenase and carbon concentrating mechanisms. On the contrary, many genes showing only low or moderate expression in the control strain were up-regulated in ∆rpoZ. A conserved -10 region was detected in promoters showing up or down-regulation in ∆rpoZ, but -35 regions of down-regulated genes completely differed from -35 regions of up-regulated genes.
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Project description:The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids, and to characterize the biological mechanisms related to PUFA metabolism. Polish Landrace pigs (n =12) were fed diet enriched with linoleic acid (LA, omega-6) and alpha-linolenic acid (ALA, omega-3 family) or standard diet as a control. The fatty acids profiling was assayed in order to verify how feeding influenced the fatty acids content in liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified by analysis in DAVID and Cytoscape tools. Fatty acids profile analysis indicated a higher contribution of PUFAs in liver for LA and ALA-enriched diet group, particularly for the omega-3 fatty acids family, but not omega-6. Next-generation sequencing identified 3,565 DEG, 1,484 of which were induced and 2,081 were suppressed by PUFA supplemenation. Low ratio of omega-6/-3 fatty acids resulted in modulation of fatty acids metabolism pathways and over-representation of genes involved in membrane composition, signal transduction and immune response pathways. In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and affected a set of genes involved in metabolic pathways important to animal health status. Hepatic mRNA profiles of Polish Landrace pig breed fed two different diets, were generated by deep sequencing, using Illumina MiSeq. Experimental diet was enriched with polyunsaturated fatty acids (omega-6 and omega-3), while standard diet remain as a cotrol. 2 pooled samples each containing RNA extracts from 6 individuals livers were analyzed.
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