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Alterations in the accumulation of adenylylated nucleotides in heavy-metal-ion-stressed and heat-stressed Synechococcus sp. strain PCC 6301, a cyanobacterium, in light and dark.

ABSTRACT: Heavy-metal-ion- (Cd2+, Cu2+, Pb2+, Hg2+ and Zn2+) or heat (50 degrees C)-stress treatments of the unicellular cyanobacterium Synechococcus sp., strain PCC 6301, under both light and dark conditions led to the accumulation of bis(5'-nucleosidyl)oligophosphates: Ap4A, Ap4G, Ap3A, Ap3G and Ap3Gp2. Under light regimens, the accumulation of Ap4A and Ap4G is more characteristic of heavy-metal-ion-stressed cells, whereas the accumulation of Ap3A, Ap3G and Ap3Gp2 is the dominant feature of heavy-metal-ion or heat-shock treatment during energy deprivation (i.e. in the dark). This accumulation of bisnucleoside oligophosphates supports a model whereby the adenylylated nucleotides are synthesized by the backward reaction of tRNA-aminoacyl synthetases. These nucleotides may also act to switch or modulate cyanobacterial responses under various environmental stress conditions.

SUBMITTER: Palfi Z

PROVIDER: S-EPMC1151117 | biostudies-other | 1991 Jun

REPOSITORIES: biostudies-other

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Project description:RNA degradation is an important process that influences the ultimate concentration of individual proteins inside cells. While the main enzymes that facilitate this process have been identified, global maps of RNA turnover are available for only a few species. Even in these cases, there are few sequence elements that are known to enhance or destabilize a native transcript; even fewer confer the same effect when added to a heterologous transcript. To address this knowledge gap, we assayed genome-wide RNA degradation in the cyanobacterium Synechococcus sp. strain PCC 7002 by collecting total RNA samples after stopping nascent transcription with rifampin. We quantified the abundance of each position in the transcriptome as a function of time using RNA-sequencing data and later analyzed the global mRNA decay map using machine learning principles. Half-lives, calculated on a per-ORF (open reading frame) basis, were extremely short, with a median half-life of only 0.97 min. Despite extremely rapid turnover of most mRNA, transcripts encoding proteins involved in photosynthesis were both highly expressed and highly stable. Upon inspection of these stable transcripts, we identified an enriched motif in the 3' untranslated region (UTR) that had similarity to Rho-independent terminators. We built statistical models for half-life prediction and used them to systematically identify sequence motifs in both 5' and 3' UTRs that correlate with stabilized transcripts. We found that transcripts linked to a terminator containing a poly(U) tract had a longer half-life than both those without a poly(U) tract and those without a terminator.IMPORTANCE RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used these sequences to guide tool design. This study probes global RNA turnover in a cyanobacterium, Synechococcus sp. strain PCC 7002, that both has a unique array of RNases that facilitate RNA degradation and is an industrially relevant strain that could be used to convert CO2 and sunlight into useful products.

Dataset Information

Alterations in the accumulation of adenylylated nucleotides in heavy-metal-ion-stressed and heat-stressed Synechococcus sp. strain PCC 6301, a cyanobacterium, in light and dark.

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