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Title: A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein

Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e. bicarbonate and CO 2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and carbon dioxide, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but which has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. Finally, CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
Authors:
 [1] ;  [2] ;  [2] ;  [2] ;  [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [4]
  1. Univ. of California, Los Angeles, CA (United States). DOE Institute for Genomics and Proteomics
  2. Univ. of California, Los Angeles, CA (United States). Dept of Chemistry and Biochemistry
  3. Univ. of California, Los Angeles, CA (United States). Dept of Chemistry and Biochemistry; Univ. of California, Los Angeles, CA (United States). Jules Stein Eye Institute
  4. Univ. of California, Los Angeles, CA (United States). DOE Institute for Genomics and Proteomics; Univ. of California, Los Angeles, CA (United States). Dept of Chemistry and Biochemistry
Publication Date:
Grant/Contract Number:
AC02-06CH11357; AI081146; FC02-02ER63421; S10 RR029205
Type:
Accepted Manuscript
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 428; Journal Issue: 20; Journal ID: ISSN 0022-2836
Publisher:
Elsevier
Research Org:
Univ. of California, Los Angeles, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC); National Institutes of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; nitrogen regulatory PII proteins; bicarbonate; allostery; carbon concentrating mechanism; carboxysome; Rubisco; nucleotide-binding; CPII; DUF2309; NADH oxidoreductase subunit 5
OSTI Identifier:
1473840
Alternate Identifier(s):
OSTI ID: 1396659

Wheatley, Nicole M., Eden, Kevin D., Ngo, Joanna, Rosinski, Justin S., Sawaya, Michael R., Cascio, Duilio, Collazo, Michael, Hoveida, Hamidreza, Hubbell, Wayne L., and Yeates, Todd O.. A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. United States: N. p., Web. doi:10.1016/j.jmb.2016.07.015.
Wheatley, Nicole M., Eden, Kevin D., Ngo, Joanna, Rosinski, Justin S., Sawaya, Michael R., Cascio, Duilio, Collazo, Michael, Hoveida, Hamidreza, Hubbell, Wayne L., & Yeates, Todd O.. A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. United States. doi:10.1016/j.jmb.2016.07.015.
Wheatley, Nicole M., Eden, Kevin D., Ngo, Joanna, Rosinski, Justin S., Sawaya, Michael R., Cascio, Duilio, Collazo, Michael, Hoveida, Hamidreza, Hubbell, Wayne L., and Yeates, Todd O.. 2016. "A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein". United States. doi:10.1016/j.jmb.2016.07.015. https://www.osti.gov/servlets/purl/1473840.
@article{osti_1473840,
title = {A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein},
author = {Wheatley, Nicole M. and Eden, Kevin D. and Ngo, Joanna and Rosinski, Justin S. and Sawaya, Michael R. and Cascio, Duilio and Collazo, Michael and Hoveida, Hamidreza and Hubbell, Wayne L. and Yeates, Todd O.},
abstractNote = {Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e. bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and carbon dioxide, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but which has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. Finally, CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.},
doi = {10.1016/j.jmb.2016.07.015},
journal = {Journal of Molecular Biology},
number = 20,
volume = 428,
place = {United States},
year = {2016},
month = {7}
}