Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms

ABSTRACT To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GA...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jeffrey A. Freiberg, Yoann Le Breton, Bao Q. Tran, Alison J. Scott, Janette M. Harro, Robert K. Ernst, Young Ah Goo, Emmanuel F. Mongodin, David R. Goodlett, Kevin S. McIver, Mark E. Shirtliff
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	LC-MS/MS RNA-seq shotgun proteomics Streptococcus pyogenes transcriptomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/50dac4ebd33841f7a2835b84722aa5a8
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:50dac4ebd33841f7a2835b84722aa5a8
record_format	dspace
spelling	oai:doaj.org-article:50dac4ebd33841f7a2835b84722aa5a82021-12-02T19:48:49ZGlobal Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms10.1128/mSystems.00149-162379-5077https://doaj.org/article/50dac4ebd33841f7a2835b84722aa5a82016-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00149-16https://doaj.org/toc/2379-5077ABSTRACT To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points. However, there was little overlap between the genes and proteins on these two lists. In line with other studies comparing transcriptomic and proteomic data, the overall correlation between the two data sets was modest. Furthermore, correlation was poorest for biofilm samples. This suggests a high degree of regulation of protein expression by nontranscriptional mechanisms. This report illustrates the benefits and weaknesses of two different approaches to global expression profiling, and it also demonstrates the advantage of using proteomics in conjunction with transcriptomics to gain a more complete picture of global expression within biofilms. In addition, this report provides the fullest characterization of expression patterns in GAS biofilms currently available. IMPORTANCE Prokaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between transcription and translation becomes even more pronounced when microbes exist in a biofilm or a stationary planktonic state. Since the transcriptome level does not usually equal the proteome level, the validity attributed to gene expression studies as well as proteomic studies in microbial analyses must be brought into question. Therefore, the results attained by either approach, whether RNA-seq or shotgun proteomics, must be taken in context and evaluated with particular care since they are by no means interchangeable.Jeffrey A. FreibergYoann Le BretonBao Q. TranAlison J. ScottJanette M. HarroRobert K. ErnstYoung Ah GooEmmanuel F. MongodinDavid R. GoodlettKevin S. McIverMark E. ShirtliffAmerican Society for MicrobiologyarticleLC-MS/MSRNA-seqshotgun proteomicsStreptococcus pyogenestranscriptomicsMicrobiologyQR1-502ENmSystems, Vol 1, Iss 6 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	LC-MS/MS RNA-seq shotgun proteomics Streptococcus pyogenes transcriptomics Microbiology QR1-502
spellingShingle	LC-MS/MS RNA-seq shotgun proteomics Streptococcus pyogenes transcriptomics Microbiology QR1-502 Jeffrey A. Freiberg Yoann Le Breton Bao Q. Tran Alison J. Scott Janette M. Harro Robert K. Ernst Young Ah Goo Emmanuel F. Mongodin David R. Goodlett Kevin S. McIver Mark E. Shirtliff Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms
description	ABSTRACT To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points. However, there was little overlap between the genes and proteins on these two lists. In line with other studies comparing transcriptomic and proteomic data, the overall correlation between the two data sets was modest. Furthermore, correlation was poorest for biofilm samples. This suggests a high degree of regulation of protein expression by nontranscriptional mechanisms. This report illustrates the benefits and weaknesses of two different approaches to global expression profiling, and it also demonstrates the advantage of using proteomics in conjunction with transcriptomics to gain a more complete picture of global expression within biofilms. In addition, this report provides the fullest characterization of expression patterns in GAS biofilms currently available. IMPORTANCE Prokaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between transcription and translation becomes even more pronounced when microbes exist in a biofilm or a stationary planktonic state. Since the transcriptome level does not usually equal the proteome level, the validity attributed to gene expression studies as well as proteomic studies in microbial analyses must be brought into question. Therefore, the results attained by either approach, whether RNA-seq or shotgun proteomics, must be taken in context and evaluated with particular care since they are by no means interchangeable.
format	article
author	Jeffrey A. Freiberg Yoann Le Breton Bao Q. Tran Alison J. Scott Janette M. Harro Robert K. Ernst Young Ah Goo Emmanuel F. Mongodin David R. Goodlett Kevin S. McIver Mark E. Shirtliff
author_facet	Jeffrey A. Freiberg Yoann Le Breton Bao Q. Tran Alison J. Scott Janette M. Harro Robert K. Ernst Young Ah Goo Emmanuel F. Mongodin David R. Goodlett Kevin S. McIver Mark E. Shirtliff
author_sort	Jeffrey A. Freiberg
title	Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms
title_short	Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms
title_full	Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms
title_fullStr	Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms
title_full_unstemmed	Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms
title_sort	global analysis and comparison of the transcriptomes and proteomes of group a <italic toggle="yes">streptococcus</italic> biofilms
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/50dac4ebd33841f7a2835b84722aa5a8
work_keys_str_mv	AT jeffreyafreiberg globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT yoannlebreton globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT baoqtran globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT alisonjscott globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT janettemharro globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT robertkernst globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT youngahgoo globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT emmanuelfmongodin globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT davidrgoodlett globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT kevinsmciver globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms AT markeshirtliff globalanalysisandcomparisonofthetranscriptomesandproteomesofgroupaitalictoggleyesstreptococcusitalicbiofilms
_version_	1718375960172036096

Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <italic toggle="yes">Streptococcus</italic> Biofilms

Ejemplares similares