Cargando…

A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT

Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have bee...

Descripción completa

Detalles Bibliográficos
Autores principales: Ding, Pengfei, McFarland, Kirsty A., Jin, Shujuan, Tong, Grace, Duan, Bo, Yang, Ally, Hughes, Timothy R., Liu, Jun, Dove, Simon L., Navarre, William Wiley, Xia, Bin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466236/
https://www.ncbi.nlm.nih.gov/pubmed/26068099
http://dx.doi.org/10.1371/journal.ppat.1004967
_version_ 1782376169568468992
author Ding, Pengfei
McFarland, Kirsty A.
Jin, Shujuan
Tong, Grace
Duan, Bo
Yang, Ally
Hughes, Timothy R.
Liu, Jun
Dove, Simon L.
Navarre, William Wiley
Xia, Bin
author_facet Ding, Pengfei
McFarland, Kirsty A.
Jin, Shujuan
Tong, Grace
Duan, Bo
Yang, Ally
Hughes, Timothy R.
Liu, Jun
Dove, Simon L.
Navarre, William Wiley
Xia, Bin
author_sort Ding, Pengfei
collection PubMed
description Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an “AT-pincer” motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.
format Online
Article
Text
id pubmed-4466236
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-44662362015-06-25 A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT Ding, Pengfei McFarland, Kirsty A. Jin, Shujuan Tong, Grace Duan, Bo Yang, Ally Hughes, Timothy R. Liu, Jun Dove, Simon L. Navarre, William Wiley Xia, Bin PLoS Pathog Research Article Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an “AT-pincer” motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA. Public Library of Science 2015-06-11 /pmc/articles/PMC4466236/ /pubmed/26068099 http://dx.doi.org/10.1371/journal.ppat.1004967 Text en © 2015 Ding et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ding, Pengfei
McFarland, Kirsty A.
Jin, Shujuan
Tong, Grace
Duan, Bo
Yang, Ally
Hughes, Timothy R.
Liu, Jun
Dove, Simon L.
Navarre, William Wiley
Xia, Bin
A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
title A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
title_full A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
title_fullStr A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
title_full_unstemmed A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
title_short A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
title_sort novel at-rich dna recognition mechanism for bacterial xenogeneic silencer mvat
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466236/
https://www.ncbi.nlm.nih.gov/pubmed/26068099
http://dx.doi.org/10.1371/journal.ppat.1004967
work_keys_str_mv AT dingpengfei anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT mcfarlandkirstya anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT jinshujuan anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT tonggrace anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT duanbo anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT yangally anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT hughestimothyr anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT liujun anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT dovesimonl anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT navarrewilliamwiley anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT xiabin anovelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT dingpengfei novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT mcfarlandkirstya novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT jinshujuan novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT tonggrace novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT duanbo novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT yangally novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT hughestimothyr novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT liujun novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT dovesimonl novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT navarrewilliamwiley novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat
AT xiabin novelatrichdnarecognitionmechanismforbacterialxenogeneicsilencermvat