Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry

Yusra Al-Eryani, Morten Ib Rasmussen, Sven Kjellström, Peter Højrup, Cecilia Emanuelsson, Claes von Wachenfeldt

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Adaptor proteins assist proteases in degrading specific proteins under appropriate conditions. The adaptor protein YjbH promotes the degradation of an important global transcriptional regulator Spx, which controls the expression of hundreds of genes and operons in response to thiol-specific oxidative stress in Bacillus subtilis. Under normal growth conditions, the transcription factor is bound to the adaptor protein and therefore degraded by the AAA+ protease ClpXP. If this binding is alleviated during stress, the transcription factor accumulates and turns on genes encoding stress-alleviating proteins. The adaptor protein YjbH is thus a key player involved in these interactions but its structure is unknown. To gain insight into its structure and interactions we have used chemical crosslinking mass spectrometry. Distance constraints obtained from the crosslinked monomer were used to select and validate a structure model of YjbH and then to probe its interactions with other proteins. The core structure of YjbH is reminiscent of DsbA family proteins. One lysine residue in YjbH (K177), located in one of the α-helices outside the thioredoxin fold, crosslinked to both Spx K99 and Spx K117, thereby suggesting one side of the YjbH for the interaction with Spx. Another lysine residue that crosslinked to Spx was YjbH K5, located in the long and presumably very flexible N-terminal arm of YjbH. Our crosslinking data lend support to a model proposed based on site-directed mutagenesis where the YjbH interaction with Spx can stabilize and present the C-terminal region of Spx for protease recognition and proteolysis. Proteins 2016; 84:1234-1245. © 2016 Wiley Periodicals, Inc.

Original languageEnglish
JournalProteins
Volume84
Issue number9
Pages (from-to)1234-1245
ISSN0887-3585
DOIs
Publication statusPublished - Sep 2016

Fingerprint

Crosslinking
Mass spectrometry
Proteins
Peptide Hydrolases
Lysine
Transcription Factors
Proteolysis
Mutagenesis
Thioredoxins
Gene encoding
Oxidative stress
Bacterial Proteins
Bacilli
Heat-Shock Proteins
Model structures
Site-Directed Mutagenesis
Sulfhydryl Compounds
Genes
Monomers
Degradation

Keywords

  • Journal Article

Cite this

Al-Eryani, Y., Ib Rasmussen, M., Kjellström, S., Højrup, P., Emanuelsson, C., & von Wachenfeldt, C. (2016). Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry. Proteins, 84(9), 1234-1245. https://doi.org/10.1002/prot.25072
Al-Eryani, Yusra ; Ib Rasmussen, Morten ; Kjellström, Sven ; Højrup, Peter ; Emanuelsson, Cecilia ; von Wachenfeldt, Claes. / Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry. In: Proteins. 2016 ; Vol. 84, No. 9. pp. 1234-1245.
@article{eecba065376c405ba4119fd4a1e684f2,
title = "Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry",
abstract = "Adaptor proteins assist proteases in degrading specific proteins under appropriate conditions. The adaptor protein YjbH promotes the degradation of an important global transcriptional regulator Spx, which controls the expression of hundreds of genes and operons in response to thiol-specific oxidative stress in Bacillus subtilis. Under normal growth conditions, the transcription factor is bound to the adaptor protein and therefore degraded by the AAA+ protease ClpXP. If this binding is alleviated during stress, the transcription factor accumulates and turns on genes encoding stress-alleviating proteins. The adaptor protein YjbH is thus a key player involved in these interactions but its structure is unknown. To gain insight into its structure and interactions we have used chemical crosslinking mass spectrometry. Distance constraints obtained from the crosslinked monomer were used to select and validate a structure model of YjbH and then to probe its interactions with other proteins. The core structure of YjbH is reminiscent of DsbA family proteins. One lysine residue in YjbH (K177), located in one of the α-helices outside the thioredoxin fold, crosslinked to both Spx K99 and Spx K117, thereby suggesting one side of the YjbH for the interaction with Spx. Another lysine residue that crosslinked to Spx was YjbH K5, located in the long and presumably very flexible N-terminal arm of YjbH. Our crosslinking data lend support to a model proposed based on site-directed mutagenesis where the YjbH interaction with Spx can stabilize and present the C-terminal region of Spx for protease recognition and proteolysis. Proteins 2016; 84:1234-1245. {\circledC} 2016 Wiley Periodicals, Inc.",
keywords = "Journal Article",
author = "Yusra Al-Eryani and {Ib Rasmussen}, Morten and Sven Kjellstr{\"o}m and Peter H{\o}jrup and Cecilia Emanuelsson and {von Wachenfeldt}, Claes",
note = "{\circledC} 2016 Wiley Periodicals, Inc.",
year = "2016",
month = "9",
doi = "10.1002/prot.25072",
language = "English",
volume = "84",
pages = "1234--1245",
journal = "Proteins: Structure, Function, and Bioinformatics",
issn = "0887-3585",
publisher = "JohnWiley & Sons, Inc.",
number = "9",

}

Al-Eryani, Y, Ib Rasmussen, M, Kjellström, S, Højrup, P, Emanuelsson, C & von Wachenfeldt, C 2016, 'Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry', Proteins, vol. 84, no. 9, pp. 1234-1245. https://doi.org/10.1002/prot.25072

Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry. / Al-Eryani, Yusra; Ib Rasmussen, Morten; Kjellström, Sven; Højrup, Peter; Emanuelsson, Cecilia; von Wachenfeldt, Claes.

In: Proteins, Vol. 84, No. 9, 09.2016, p. 1234-1245.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry

AU - Al-Eryani, Yusra

AU - Ib Rasmussen, Morten

AU - Kjellström, Sven

AU - Højrup, Peter

AU - Emanuelsson, Cecilia

AU - von Wachenfeldt, Claes

N1 - © 2016 Wiley Periodicals, Inc.

PY - 2016/9

Y1 - 2016/9

N2 - Adaptor proteins assist proteases in degrading specific proteins under appropriate conditions. The adaptor protein YjbH promotes the degradation of an important global transcriptional regulator Spx, which controls the expression of hundreds of genes and operons in response to thiol-specific oxidative stress in Bacillus subtilis. Under normal growth conditions, the transcription factor is bound to the adaptor protein and therefore degraded by the AAA+ protease ClpXP. If this binding is alleviated during stress, the transcription factor accumulates and turns on genes encoding stress-alleviating proteins. The adaptor protein YjbH is thus a key player involved in these interactions but its structure is unknown. To gain insight into its structure and interactions we have used chemical crosslinking mass spectrometry. Distance constraints obtained from the crosslinked monomer were used to select and validate a structure model of YjbH and then to probe its interactions with other proteins. The core structure of YjbH is reminiscent of DsbA family proteins. One lysine residue in YjbH (K177), located in one of the α-helices outside the thioredoxin fold, crosslinked to both Spx K99 and Spx K117, thereby suggesting one side of the YjbH for the interaction with Spx. Another lysine residue that crosslinked to Spx was YjbH K5, located in the long and presumably very flexible N-terminal arm of YjbH. Our crosslinking data lend support to a model proposed based on site-directed mutagenesis where the YjbH interaction with Spx can stabilize and present the C-terminal region of Spx for protease recognition and proteolysis. Proteins 2016; 84:1234-1245. © 2016 Wiley Periodicals, Inc.

AB - Adaptor proteins assist proteases in degrading specific proteins under appropriate conditions. The adaptor protein YjbH promotes the degradation of an important global transcriptional regulator Spx, which controls the expression of hundreds of genes and operons in response to thiol-specific oxidative stress in Bacillus subtilis. Under normal growth conditions, the transcription factor is bound to the adaptor protein and therefore degraded by the AAA+ protease ClpXP. If this binding is alleviated during stress, the transcription factor accumulates and turns on genes encoding stress-alleviating proteins. The adaptor protein YjbH is thus a key player involved in these interactions but its structure is unknown. To gain insight into its structure and interactions we have used chemical crosslinking mass spectrometry. Distance constraints obtained from the crosslinked monomer were used to select and validate a structure model of YjbH and then to probe its interactions with other proteins. The core structure of YjbH is reminiscent of DsbA family proteins. One lysine residue in YjbH (K177), located in one of the α-helices outside the thioredoxin fold, crosslinked to both Spx K99 and Spx K117, thereby suggesting one side of the YjbH for the interaction with Spx. Another lysine residue that crosslinked to Spx was YjbH K5, located in the long and presumably very flexible N-terminal arm of YjbH. Our crosslinking data lend support to a model proposed based on site-directed mutagenesis where the YjbH interaction with Spx can stabilize and present the C-terminal region of Spx for protease recognition and proteolysis. Proteins 2016; 84:1234-1245. © 2016 Wiley Periodicals, Inc.

KW - Journal Article

U2 - 10.1002/prot.25072

DO - 10.1002/prot.25072

M3 - Journal article

C2 - 27191337

VL - 84

SP - 1234

EP - 1245

JO - Proteins: Structure, Function, and Bioinformatics

JF - Proteins: Structure, Function, and Bioinformatics

SN - 0887-3585

IS - 9

ER -

Al-Eryani Y, Ib Rasmussen M, Kjellström S, Højrup P, Emanuelsson C, von Wachenfeldt C. Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry. Proteins. 2016 Sep;84(9):1234-1245. https://doi.org/10.1002/prot.25072