Dataset Information

Genome Sequences of Synechococcus sp. Strain MIT S9220 and Cocultured Cyanophage SynMITS9220M01.

ABSTRACT: Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture.

SUBMITTER: Belisle BS

PROVIDER: S-EPMC7378029 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Publications

Genome Sequences of Synechococcus sp. Strain MIT S9220 and Cocultured Cyanophage SynMITS9220M01.

Belisle B Shafer BS Avila Paz Andres A AA Carpenter Angelina R AR Cormier Tayla C TC Lewis Adam J AJ Menin Linnea S LS Oliveira Daniel R DR Song BuKyung B Szeto Amy A Tchantouridze Elizabeth I EI Watson Kayleigh A KA Yohannes Mary T MT Ahlgren Nathan A NA

Microbiology resource announcements 20200723 30

Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture. ...[more]

PMID: 32703830

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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

Genome Sequences of Synechococcus sp. Strain MIT S9220 and Cocultured Cyanophage SynMITS9220M01.

Publications

Genome Sequences of <i>Synechococcus</i> sp. Strain MIT S9220 and Cocultured Cyanophage SynMITS9220M01.

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