Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model

ABSTRACT Lsr2-like nucleoid-associated proteins play an important role as xenogeneic silencers (XS) of horizontally acquired genomic regions in actinobacteria. In this study, we systematically analyzed the in vivo constraints underlying silencing and counter-silencing of the Lsr2-like protein CgpS i...

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Autores principales:	Johanna Wiechert, Andrei Filipchyk, Max Hünnefeld, Cornelia Gätgens, Jannis Brehm, Ralf Heermann, Julia Frunzke
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	AT-rich DNA Lsr2 actinobacteria counter-silencing horizontal gene transfer regulatory networks Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/30c88609c7574dc3a1cde05ab12e5165
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spelling	oai:doaj.org-article:30c88609c7574dc3a1cde05ab12e51652021-11-15T15:56:58ZDeciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model10.1128/mBio.02273-192150-7511https://doaj.org/article/30c88609c7574dc3a1cde05ab12e51652020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02273-19https://doaj.org/toc/2150-7511ABSTRACT Lsr2-like nucleoid-associated proteins play an important role as xenogeneic silencers (XS) of horizontally acquired genomic regions in actinobacteria. In this study, we systematically analyzed the in vivo constraints underlying silencing and counter-silencing of the Lsr2-like protein CgpS in Corynebacterium glutamicum. Genome-wide analysis revealed binding of CgpS to regions featuring a distinct drop in GC profile close to the transcription start site (TSS) but also identified an overrepresented motif with multiple A/T steps at the nucleation site of the nucleoprotein complex. Binding of specific transcription factors (TFs) may oppose XS activity, leading to counter-silencing. Following a synthetic counter-silencing approach, target gene activation was realized by inserting operator sites of an effector-responsive TF within various CgpS target promoters, resulting in increased promoter activity upon TF binding. Analysis of reporter constructs revealed maximal counter-silencing when the TF operator site was inserted at the position of maximal CgpS coverage. This principle was implemented in a synthetic toggle switch, which features a robust and reversible response to effector availability, highlighting the potential for biotechnological applications. Together, our results provide comprehensive insights into how Lsr2 silencing and counter-silencing shape evolutionary network expansion in this medically and biotechnologically relevant bacterial phylum. IMPORTANCE In actinobacteria, Lsr2-like nucleoid-associated proteins function as xenogeneic silencers (XS) of horizontally acquired genomic regions, including viral elements, virulence gene clusters in Mycobacterium tuberculosis, and genes involved in cryptic specialized metabolism in Streptomyces species. Consequently, a detailed mechanistic understanding of Lsr2 binding in vivo is relevant as a potential drug target and for the identification of novel bioactive compounds. Here, we followed an in vivo approach to investigate the rules underlying xenogeneic silencing and counter-silencing of the Lsr2-like XS CgpS from Corynebacterium glutamicum. Our results demonstrated that CgpS distinguishes between self and foreign by recognizing a distinct drop in GC profile in combination with a short, sequence-specific motif at the nucleation site. Following a synthetic counter-silencer approach, we studied the potential and constraints of transcription factors to counteract CgpS silencing, thereby facilitating the integration of new genetic traits into host regulatory networks.Johanna WiechertAndrei FilipchykMax HünnefeldCornelia GätgensJannis BrehmRalf HeermannJulia FrunzkeAmerican Society for MicrobiologyarticleAT-rich DNALsr2actinobacteriacounter-silencinghorizontal gene transferregulatory networksMicrobiologyQR1-502ENmBio, Vol 11, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	AT-rich DNA Lsr2 actinobacteria counter-silencing horizontal gene transfer regulatory networks Microbiology QR1-502
spellingShingle	AT-rich DNA Lsr2 actinobacteria counter-silencing horizontal gene transfer regulatory networks Microbiology QR1-502 Johanna Wiechert Andrei Filipchyk Max Hünnefeld Cornelia Gätgens Jannis Brehm Ralf Heermann Julia Frunzke Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model
description	ABSTRACT Lsr2-like nucleoid-associated proteins play an important role as xenogeneic silencers (XS) of horizontally acquired genomic regions in actinobacteria. In this study, we systematically analyzed the in vivo constraints underlying silencing and counter-silencing of the Lsr2-like protein CgpS in Corynebacterium glutamicum. Genome-wide analysis revealed binding of CgpS to regions featuring a distinct drop in GC profile close to the transcription start site (TSS) but also identified an overrepresented motif with multiple A/T steps at the nucleation site of the nucleoprotein complex. Binding of specific transcription factors (TFs) may oppose XS activity, leading to counter-silencing. Following a synthetic counter-silencing approach, target gene activation was realized by inserting operator sites of an effector-responsive TF within various CgpS target promoters, resulting in increased promoter activity upon TF binding. Analysis of reporter constructs revealed maximal counter-silencing when the TF operator site was inserted at the position of maximal CgpS coverage. This principle was implemented in a synthetic toggle switch, which features a robust and reversible response to effector availability, highlighting the potential for biotechnological applications. Together, our results provide comprehensive insights into how Lsr2 silencing and counter-silencing shape evolutionary network expansion in this medically and biotechnologically relevant bacterial phylum. IMPORTANCE In actinobacteria, Lsr2-like nucleoid-associated proteins function as xenogeneic silencers (XS) of horizontally acquired genomic regions, including viral elements, virulence gene clusters in Mycobacterium tuberculosis, and genes involved in cryptic specialized metabolism in Streptomyces species. Consequently, a detailed mechanistic understanding of Lsr2 binding in vivo is relevant as a potential drug target and for the identification of novel bioactive compounds. Here, we followed an in vivo approach to investigate the rules underlying xenogeneic silencing and counter-silencing of the Lsr2-like XS CgpS from Corynebacterium glutamicum. Our results demonstrated that CgpS distinguishes between self and foreign by recognizing a distinct drop in GC profile in combination with a short, sequence-specific motif at the nucleation site. Following a synthetic counter-silencer approach, we studied the potential and constraints of transcription factors to counteract CgpS silencing, thereby facilitating the integration of new genetic traits into host regulatory networks.
format	article
author	Johanna Wiechert Andrei Filipchyk Max Hünnefeld Cornelia Gätgens Jannis Brehm Ralf Heermann Julia Frunzke
author_facet	Johanna Wiechert Andrei Filipchyk Max Hünnefeld Cornelia Gätgens Jannis Brehm Ralf Heermann Julia Frunzke
author_sort	Johanna Wiechert
title	Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model
title_short	Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model
title_full	Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model
title_fullStr	Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model
title_full_unstemmed	Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model
title_sort	deciphering the rules underlying xenogeneic silencing and counter-silencing of lsr2-like proteins using cgps of <named-content content-type="genus-species">corynebacterium glutamicum</named-content> as a model
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/30c88609c7574dc3a1cde05ab12e5165
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Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of <named-content content-type="genus-species">Corynebacterium glutamicum</named-content> as a Model

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