The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes

ABSTRACT Transposon insertion sequencing (TIS; also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of t...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Satoshi Kimura, Troy P. Hubbard, Brigid M. Davis, Matthew K. Waldor
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7085546dbfec4993a1c9bd93278f16fd
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:7085546dbfec4993a1c9bd93278f16fd
record_format	dspace
spelling	oai:doaj.org-article:7085546dbfec4993a1c9bd93278f16fd2021-11-15T15:50:19ZThe Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes10.1128/mBio.01351-162150-7511https://doaj.org/article/7085546dbfec4993a1c9bd93278f16fd2016-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01351-16https://doaj.org/toc/2150-7511ABSTRACT Transposon insertion sequencing (TIS; also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of transposon insertions contribute to fitness. However, it is not known whether factors such as nucleoid binding proteins can alter the frequency of transposon insertion and thus whether TIS output may systematically reflect factors that are independent of the role of the loci in fitness. Here, we investigated whether the histone-like nucleoid structuring (H-NS) protein, which preferentially associates with AT-rich sequences, modulates the frequency of Mariner transposon insertion in the Vibrio cholerae genome, using comparative analysis of TIS results from wild-type (wt) and Δhns V. cholerae strains. These analyses were overlaid on gene classification based on GC content as well as on extant genome-wide identification of H-NS binding loci. Our analyses revealed a significant dearth of insertions within AT-rich loci in wt V. cholerae that was not apparent in the Δhns insertion library. Additionally, we observed a striking correlation between genetic loci that are overrepresented in the Δhns insertion library relative to their insertion frequency in wt V. cholerae and loci previously found to physically interact with H-NS. Collectively, our findings reveal that factors other than genetic fitness can systematically modulate the frequency of transposon insertions in TIS studies and add a cautionary note to interpretation of TIS data, particularly for AT-rich sequences. IMPORTANCE Transposon insertion sequencing (TIS) is often used to assess the relative frequency with which genetic loci can be disrupted, which is taken as an indicator of their importance for bacterial fitness. Here, we report that biological factors other than the relative levels of fitness of insertion mutants can influence TIS output. We found that the presence of the DNA binding protein H-NS, which preferentially recognizes AT-rich sequences, is linked to significant underrepresentation of mutations within AT-rich loci in transposon insertion libraries. Furthermore, there is a marked correspondence between loci bound by H-NS and loci with an increased frequency of disruption in a Δhns insertion library relative to a wt library. Our data suggest that factors other than genetic fitness (e.g., DNA binding proteins such as H-NS) can systematically modulate the frequency of transposon insertions in TIS studies and add a note of caution for interpretation of TIS data.Satoshi KimuraTroy P. HubbardBrigid M. DavisMatthew K. WaldorAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 7, Iss 4 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Satoshi Kimura Troy P. Hubbard Brigid M. Davis Matthew K. Waldor The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
description	ABSTRACT Transposon insertion sequencing (TIS; also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of transposon insertions contribute to fitness. However, it is not known whether factors such as nucleoid binding proteins can alter the frequency of transposon insertion and thus whether TIS output may systematically reflect factors that are independent of the role of the loci in fitness. Here, we investigated whether the histone-like nucleoid structuring (H-NS) protein, which preferentially associates with AT-rich sequences, modulates the frequency of Mariner transposon insertion in the Vibrio cholerae genome, using comparative analysis of TIS results from wild-type (wt) and Δhns V. cholerae strains. These analyses were overlaid on gene classification based on GC content as well as on extant genome-wide identification of H-NS binding loci. Our analyses revealed a significant dearth of insertions within AT-rich loci in wt V. cholerae that was not apparent in the Δhns insertion library. Additionally, we observed a striking correlation between genetic loci that are overrepresented in the Δhns insertion library relative to their insertion frequency in wt V. cholerae and loci previously found to physically interact with H-NS. Collectively, our findings reveal that factors other than genetic fitness can systematically modulate the frequency of transposon insertions in TIS studies and add a cautionary note to interpretation of TIS data, particularly for AT-rich sequences. IMPORTANCE Transposon insertion sequencing (TIS) is often used to assess the relative frequency with which genetic loci can be disrupted, which is taken as an indicator of their importance for bacterial fitness. Here, we report that biological factors other than the relative levels of fitness of insertion mutants can influence TIS output. We found that the presence of the DNA binding protein H-NS, which preferentially recognizes AT-rich sequences, is linked to significant underrepresentation of mutations within AT-rich loci in transposon insertion libraries. Furthermore, there is a marked correspondence between loci bound by H-NS and loci with an increased frequency of disruption in a Δhns insertion library relative to a wt library. Our data suggest that factors other than genetic fitness (e.g., DNA binding proteins such as H-NS) can systematically modulate the frequency of transposon insertions in TIS studies and add a note of caution for interpretation of TIS data.
format	article
author	Satoshi Kimura Troy P. Hubbard Brigid M. Davis Matthew K. Waldor
author_facet	Satoshi Kimura Troy P. Hubbard Brigid M. Davis Matthew K. Waldor
author_sort	Satoshi Kimura
title	The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
title_short	The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
title_full	The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
title_fullStr	The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
title_full_unstemmed	The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
title_sort	nucleoid binding protein h-ns biases genome-wide transposon insertion landscapes
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/7085546dbfec4993a1c9bd93278f16fd
work_keys_str_mv	AT satoshikimura thenucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT troyphubbard thenucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT brigidmdavis thenucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT matthewkwaldor thenucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT satoshikimura nucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT troyphubbard nucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT brigidmdavis nucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes AT matthewkwaldor nucleoidbindingproteinhnsbiasesgenomewidetransposoninsertionlandscapes
_version_	1718427405106806784

The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes

Ejemplares similares