Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction

Matthew Green; Louise Hatter; Emre Brookes; Panos Soultanas; David J. Scott

doi:10.1016/j.jmb.2015.12.007

Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction

Matthew Green
, Louise Hatter
, Emre Brookes
, Panos Soultanas
, David J. Scott

Chemistry and Biochemistry

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

The bacterial single-stranded DNA (ssDNA) binding protein SSB is a strictly conserved and essential protein involved in diverse functions of DNA metabolism, including replication and repair. SSB comprises a well-characterized tetrameric core of N-terminal oligonucleotide binding OB folds that bind ssDNA and four intrinsically disordered C-terminal domains of unknown structure that interact with partner proteins. The generally accepted, albeit speculative, mechanistic model in the field postulates that binding of ssDNA to the OB core induces the flexible, undefined C-terminal arms to expand outwards encouraging functional interactions with partner proteins. In this structural study, we show that the opposite is true. Combined small-angle scattering with X-rays and neutrons coupled to coarse-grained modeling reveal that the intrinsically disordered C-terminal arms are relatively collapsed around the tetrameric OB core and collapse further upon ssDNA binding. This implies a mechanism of action, in which the disordered C-terminal domain collapse traps the ssDNA and pulls functional partners onto the ssDNA.

Original language	English
Pages (from-to)	357-364
Number of pages	8
Journal	Journal of Molecular Biology
Volume	428
Issue number	2
DOIs	https://doi.org/10.1016/j.jmb.2015.12.007
State	Published - Jan 29 2016

Funding

We would like to acknowledge Luke Clifton (ISIS) who provided helpful guidance throughout. We are grateful to Dr. Neil Oldham's group for mass spectroscopy, especially to Dr. Matthew Jenner who measured per-deuterated SSB. SANS data were collected through a beam time award to D.J.S. Small-angle X-ray data were collected through the Midlands (UK) BAG allocation award. This work was supported by the Wellcome Trust grant WT091968 and the Biotechnology and Biological Sciences Research Council (UK) grant BB/K021540/1 to P.S. E.B. is supported by a National Institutes of Health grant (K25GM090154). This work benefitted from CCP-SAS software developed through the joint Engineering and Physical Sciences Research Council (UK) grant EP/K039121/1 and National Science Foundation (USA) grant CHE-126582 . D.J.S. is a Senior Molecular Biology and Neutron Fellow supported by the Science and Technology Facilities Council (UK). We would like to acknowledge Luke Clifton (ISIS) who provided helpful guidance throughout. We are grateful to Dr. Neil Oldham''s group for mass spectroscopy, especially to Dr. Matthew Jenner who measured per-deuterated SSB. SANS data were collected through a beam time award to D.J.S. Small-angle X-ray data were collected through the Midlands (UK) BAG allocation award. This work was supported by the Wellcome Trust grant WT091968 and the Biotechnology and Biological Sciences Research Council (UK) grant BB/K021540/1 to P.S. E.B. is supported by a National Institutes of Health grant (K25GM090154). This work benefitted fromCCP-SAS software developed through the joint Engineering and Physical Sciences Research Council (UK) grant EP/K039121/1 and National Science Foundation (USA) grant CHE-126582. D.J.S. is a Senior Molecular Biology and Neutron Fellow supported by the Science and Technology Facilities Council (UK).

Funders	Funder number
ISIS Foundation (USA)
CHE-126582
K25GM090154
Wellcome Trust	WT091968
Engineering and Physical Sciences Research Council	EP/K039121/1
BB/K021540/1
Science and Technology Facilities Council

Keywords

Bacillus subtilis
SANS
SASSIE
SAXS
intrinsic disorder

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10.1016/j.jmb.2015.12.007

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title = "Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction",

abstract = "The bacterial single-stranded DNA (ssDNA) binding protein SSB is a strictly conserved and essential protein involved in diverse functions of DNA metabolism, including replication and repair. SSB comprises a well-characterized tetrameric core of N-terminal oligonucleotide binding OB folds that bind ssDNA and four intrinsically disordered C-terminal domains of unknown structure that interact with partner proteins. The generally accepted, albeit speculative, mechanistic model in the field postulates that binding of ssDNA to the OB core induces the flexible, undefined C-terminal arms to expand outwards encouraging functional interactions with partner proteins. In this structural study, we show that the opposite is true. Combined small-angle scattering with X-rays and neutrons coupled to coarse-grained modeling reveal that the intrinsically disordered C-terminal arms are relatively collapsed around the tetrameric OB core and collapse further upon ssDNA binding. This implies a mechanism of action, in which the disordered C-terminal domain collapse traps the ssDNA and pulls functional partners onto the ssDNA.",

keywords = "Bacillus subtilis, SANS, SASSIE, SAXS, intrinsic disorder",

author = "Matthew Green and Louise Hatter and Emre Brookes and Panos Soultanas and Scott, \{David J.\}",

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T1 - Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction

AU - Green, Matthew

AU - Hatter, Louise

AU - Brookes, Emre

AU - Soultanas, Panos

AU - Scott, David J.

PY - 2016/1/29

Y1 - 2016/1/29

N2 - The bacterial single-stranded DNA (ssDNA) binding protein SSB is a strictly conserved and essential protein involved in diverse functions of DNA metabolism, including replication and repair. SSB comprises a well-characterized tetrameric core of N-terminal oligonucleotide binding OB folds that bind ssDNA and four intrinsically disordered C-terminal domains of unknown structure that interact with partner proteins. The generally accepted, albeit speculative, mechanistic model in the field postulates that binding of ssDNA to the OB core induces the flexible, undefined C-terminal arms to expand outwards encouraging functional interactions with partner proteins. In this structural study, we show that the opposite is true. Combined small-angle scattering with X-rays and neutrons coupled to coarse-grained modeling reveal that the intrinsically disordered C-terminal arms are relatively collapsed around the tetrameric OB core and collapse further upon ssDNA binding. This implies a mechanism of action, in which the disordered C-terminal domain collapse traps the ssDNA and pulls functional partners onto the ssDNA.

AB - The bacterial single-stranded DNA (ssDNA) binding protein SSB is a strictly conserved and essential protein involved in diverse functions of DNA metabolism, including replication and repair. SSB comprises a well-characterized tetrameric core of N-terminal oligonucleotide binding OB folds that bind ssDNA and four intrinsically disordered C-terminal domains of unknown structure that interact with partner proteins. The generally accepted, albeit speculative, mechanistic model in the field postulates that binding of ssDNA to the OB core induces the flexible, undefined C-terminal arms to expand outwards encouraging functional interactions with partner proteins. In this structural study, we show that the opposite is true. Combined small-angle scattering with X-rays and neutrons coupled to coarse-grained modeling reveal that the intrinsically disordered C-terminal arms are relatively collapsed around the tetrameric OB core and collapse further upon ssDNA binding. This implies a mechanism of action, in which the disordered C-terminal domain collapse traps the ssDNA and pulls functional partners onto the ssDNA.

KW - Bacillus subtilis

KW - SANS

KW - SASSIE

KW - SAXS

KW - intrinsic disorder

UR - https://www.scopus.com/pages/publications/84957442625

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DO - 10.1016/j.jmb.2015.12.007

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ER -

Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction

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