Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>

ABSTRACT Regulatory small RNAs (sRNAs) are known to play important roles in the Gram-positive bacterial pathogen Staphylococcus aureus; however, their existence is often overlooked, primarily because sRNA genes are absent from genome annotation files. Consequently, transcriptome sequencing (RNA-Seq)...

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Autores principales:	Hailee M. Sorensen, Rebecca A. Keogh, Marcus A. Wittekind, Andrew R. Caillet, Richard E. Wiemels, Elizabeth A. Laner, Ronan K. Carroll
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	RNA stability RNA-Seq Staphylococcus aureus genome annotation regulatory RNA sRNA Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/50b22a5b492c42afbc54cf851a2c42bc
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spelling	oai:doaj.org-article:50b22a5b492c42afbc54cf851a2c42bc2021-11-15T15:30:51ZReading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>10.1128/mSphere.00439-202379-5042https://doaj.org/article/50b22a5b492c42afbc54cf851a2c42bc2020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00439-20https://doaj.org/toc/2379-5042ABSTRACT Regulatory small RNAs (sRNAs) are known to play important roles in the Gram-positive bacterial pathogen Staphylococcus aureus; however, their existence is often overlooked, primarily because sRNA genes are absent from genome annotation files. Consequently, transcriptome sequencing (RNA-Seq)-based experimental approaches, performed using standard genome annotation files as a reference, have likely overlooked data for sRNAs. Previously, we created an updated S. aureus genome annotation file, which included annotations for 303 known sRNAs in USA300. Here, we utilized this updated reference file to reexamine publicly available RNA-Seq data sets in an attempt to recover lost information on sRNA expression, stability, and potential to encode peptides. First, we used transcriptomic data from 22 studies to identify how the expression of 303 sRNAs changed under 64 different experimental conditions. Next, we used RNA-Seq data from an RNA stability assay to identify highly stable/unstable sRNAs. We went on to reanalyze a ribosome profiling (Ribo-seq) data set to identify sRNAs that have the potential to encode peptides and to experimentally confirm the presence of three of these peptides in the USA300 background. Interestingly, one of these sRNAs/peptides, encoded at the tsr37 locus, influences the ability of S. aureus cells to autoaggregate. Finally, we reexamined two recently published in vivo RNA-Seq data sets, from the cystic fibrosis (CF) lung and a murine vaginal colonization study, and identified 29 sRNAs that may play a role in vivo. Collectively, these results can help inform future studies of these important regulatory elements in S. aureus and highlight the need for ongoing curating and updating of genome annotation files. IMPORTANCE Regulatory small RNAs (sRNAs) are a class of RNA molecules that are produced in bacterial cells but that typically do not encode proteins. Instead, they perform a variety of critical functions within the cell as RNA. Most bacterial genomes do not include annotations for sRNA genes, and any type of analysis that is performed using a bacterial genome as a reference will therefore overlook data for sRNAs. In this study, we reexamined hundreds of previously generated S. aureus RNA-Seq data sets and reanalyzed them to generate data for sRNAs. To do so, we utilized an updated S. aureus genome annotation file, previously generated by our group, which contains annotations for 303 sRNAs. The data generated (which were previously discarded) shed new light on sRNAs in S. aureus, most of which are unstudied, and highlight certain sRNAs that are likely to play important roles in the cell.Hailee M. SorensenRebecca A. KeoghMarcus A. WittekindAndrew R. CailletRichard E. WiemelsElizabeth A. LanerRonan K. CarrollAmerican Society for MicrobiologyarticleRNA stabilityRNA-SeqStaphylococcus aureusgenome annotationregulatory RNAsRNAMicrobiologyQR1-502ENmSphere, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA stability RNA-Seq Staphylococcus aureus genome annotation regulatory RNA sRNA Microbiology QR1-502
spellingShingle	RNA stability RNA-Seq Staphylococcus aureus genome annotation regulatory RNA sRNA Microbiology QR1-502 Hailee M. Sorensen Rebecca A. Keogh Marcus A. Wittekind Andrew R. Caillet Richard E. Wiemels Elizabeth A. Laner Ronan K. Carroll Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>
description	ABSTRACT Regulatory small RNAs (sRNAs) are known to play important roles in the Gram-positive bacterial pathogen Staphylococcus aureus; however, their existence is often overlooked, primarily because sRNA genes are absent from genome annotation files. Consequently, transcriptome sequencing (RNA-Seq)-based experimental approaches, performed using standard genome annotation files as a reference, have likely overlooked data for sRNAs. Previously, we created an updated S. aureus genome annotation file, which included annotations for 303 known sRNAs in USA300. Here, we utilized this updated reference file to reexamine publicly available RNA-Seq data sets in an attempt to recover lost information on sRNA expression, stability, and potential to encode peptides. First, we used transcriptomic data from 22 studies to identify how the expression of 303 sRNAs changed under 64 different experimental conditions. Next, we used RNA-Seq data from an RNA stability assay to identify highly stable/unstable sRNAs. We went on to reanalyze a ribosome profiling (Ribo-seq) data set to identify sRNAs that have the potential to encode peptides and to experimentally confirm the presence of three of these peptides in the USA300 background. Interestingly, one of these sRNAs/peptides, encoded at the tsr37 locus, influences the ability of S. aureus cells to autoaggregate. Finally, we reexamined two recently published in vivo RNA-Seq data sets, from the cystic fibrosis (CF) lung and a murine vaginal colonization study, and identified 29 sRNAs that may play a role in vivo. Collectively, these results can help inform future studies of these important regulatory elements in S. aureus and highlight the need for ongoing curating and updating of genome annotation files. IMPORTANCE Regulatory small RNAs (sRNAs) are a class of RNA molecules that are produced in bacterial cells but that typically do not encode proteins. Instead, they perform a variety of critical functions within the cell as RNA. Most bacterial genomes do not include annotations for sRNA genes, and any type of analysis that is performed using a bacterial genome as a reference will therefore overlook data for sRNAs. In this study, we reexamined hundreds of previously generated S. aureus RNA-Seq data sets and reanalyzed them to generate data for sRNAs. To do so, we utilized an updated S. aureus genome annotation file, previously generated by our group, which contains annotations for 303 sRNAs. The data generated (which were previously discarded) shed new light on sRNAs in S. aureus, most of which are unstudied, and highlight certain sRNAs that are likely to play important roles in the cell.
format	article
author	Hailee M. Sorensen Rebecca A. Keogh Marcus A. Wittekind Andrew R. Caillet Richard E. Wiemels Elizabeth A. Laner Ronan K. Carroll
author_facet	Hailee M. Sorensen Rebecca A. Keogh Marcus A. Wittekind Andrew R. Caillet Richard E. Wiemels Elizabeth A. Laner Ronan K. Carroll
author_sort	Hailee M. Sorensen
title	Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>
title_short	Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>
title_full	Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>
title_fullStr	Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>
title_full_unstemmed	Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>
title_sort	reading between the lines: utilizing rna-seq data for global analysis of srnas in <named-content content-type="genus-species">staphylococcus aureus</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/50b22a5b492c42afbc54cf851a2c42bc
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Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <named-content content-type="genus-species">Staphylococcus aureus</named-content>

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