Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction

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Abstract

The alarmone (p)ppGpp regulates diverse targets, yet its target specificity and evolution remain poorly understood. Here we elucidate the mechanism by which basal (p)ppGpp inhibits the purine salvage enzyme HPRT by sharing a conserved motif with its substrate PRPP. Intriguingly, HPRT regulation by (p)ppGpp varies across organisms and correlates with HPRT oligomeric forms. (p)ppGpp-sensitive HPRT exists as a PRPP-bound dimer or an apo- and (p)ppGpp-bound tetramer, where a dimer-dimer interface triggers allosteric structural rearrangements to enhance (p)ppGpp inhibition. Loss of this oligomeric interface results in weakened (p)ppGpp regulation. Our results reveal an evolutionary principle whereby protein oligomerization allows evolutionary change to accumulate away from a conserved binding pocket to allosterically alter specificity of ligand interaction. This principle also explains how another (p)ppGpp target GMK is variably regulated across species. Since most ligands bind near protein interfaces, we propose that this principle extends to many other protein-ligand interactions.

Data availability

Diffraction data have been deposited in PDB under the accession codes 6D9Q (https://www.rcsb.org/structure/6d9q), 6D9R (https://www.rcsb.org/structure/6d9r), and 6D9S (https://www.rcsb.org/structure/6D9S). All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Table 2.

The following data sets were generated

1. Satyshur KA
2. Dubiel K
3. Anderson B
4. Wolak C
5. Keck JL
(2019) The sulfate-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
Protein Data Bank, 6D9Q.

https://www.rcsb.org/structure/6D9Q
1. Satyshur KA
2. Dubiel K
3. Anderson B
4. Wolak C
5. Keck JL
(2019) The substrate-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
Protein Data Bank, 6D9R.

https://www.rcsb.org/structure/6D9R
1. Satyshur KA
2. Dubiel K
3. Anderson B
4. Wolak C
5. Keck JL
(2019) The (p)ppGpp-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
Protein Data Bank, 6D9S.

https://www.rcsb.org/structure/6D9S

The following previously published data sets were used

1. Zhang N
2. Gong X
3. Lu M
4. Chen X
5. Qin X
6. Ge H
(2016) Crystal structures of Apo and GMP bound hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila and the implications in gouty arthritis
Protein Data Bank, 5ESW.

https://www.rcsb.org/structure/5esw
1. Zhang N
2. Gong X
3. Lu M
4. Chen X
5. Qin X
6. Ge H
(2016) Crystal structures of Apo and GMP bound hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila and the implications in gouty arthritis
Protein Data Bank, 5ESX.

https://www.rcsb.org/structure/5esx
(2009) 2.06 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor'
Protein Data Bank, 3H83.

https://www.rcsb.org/structure/3h83

Article and author information

Author details

Brent W Anderson

Department of Bacteriology, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Kuanqing Liu

Department of Bacteriology, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Christine Wolak

Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Katarzyna Dubiel

Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Fukang She

Department of Bacteriology, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Kenneth A Satyshur

Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9371-2493
James L Keck

Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Jue D Wang

Department of Bacteriology, University of Wisconsin-Madison, Madison, United States

For correspondence
wang@bact.wisc.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1503-170X

Funding

National Institute of General Medical Sciences (R35 GM127088)

Jue D Wang

Howard Hughes Medical Institute (Faculty Scholar)

Jue D Wang

National Science Foundation (GRFP DGE-1256259)

Brent W Anderson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.