Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002

ABSTRACT 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...

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Autores principales:	Gina C. Gordon, Jeffrey C. Cameron, Sanjan T. P. Gupta, Michael D. Engstrom, Jennifer L. Reed, Brian F. Pfleger
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	cyanobacteria mRNA decay photosynthesis termination gene expression machine learning Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/229c2e06c1fd4e0fa6fab9a8e8683513
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spelling	oai:doaj.org-article:229c2e06c1fd4e0fa6fab9a8e86835132021-12-02T19:46:20ZGenome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 700210.1128/mSystems.00224-202379-5077https://doaj.org/article/229c2e06c1fd4e0fa6fab9a8e86835132020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00224-20https://doaj.org/toc/2379-5077ABSTRACT 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.Gina C. GordonJeffrey C. CameronSanjan T. P. GuptaMichael D. EngstromJennifer L. ReedBrian F. PflegerAmerican Society for MicrobiologyarticlecyanobacteriamRNA decayphotosynthesisterminationgene expressionmachine learningMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	cyanobacteria mRNA decay photosynthesis termination gene expression machine learning Microbiology QR1-502
spellingShingle	cyanobacteria mRNA decay photosynthesis termination gene expression machine learning Microbiology QR1-502 Gina C. Gordon Jeffrey C. Cameron Sanjan T. P. Gupta Michael D. Engstrom Jennifer L. Reed Brian F. Pfleger Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002
description	ABSTRACT 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.
format	article
author	Gina C. Gordon Jeffrey C. Cameron Sanjan T. P. Gupta Michael D. Engstrom Jennifer L. Reed Brian F. Pfleger
author_facet	Gina C. Gordon Jeffrey C. Cameron Sanjan T. P. Gupta Michael D. Engstrom Jennifer L. Reed Brian F. Pfleger
author_sort	Gina C. Gordon
title	Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002
title_short	Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002
title_full	Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002
title_fullStr	Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002
title_full_unstemmed	Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002
title_sort	genome-wide analysis of rna decay in the cyanobacterium <italic toggle="yes">synechococcus</italic> sp. strain pcc 7002
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/229c2e06c1fd4e0fa6fab9a8e8683513
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Genome-Wide Analysis of RNA Decay in the Cyanobacterium <italic toggle="yes">Synechococcus</italic> sp. Strain PCC 7002

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