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Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular determinants and signaling effects of PKA RIα phase separation. Mol Cell 2024; 84:1570-1584.e7. [PMID: 38537638 PMCID: PMC11031308 DOI: 10.1016/j.molcel.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/07/2023] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures proper cellular function. Liquid-liquid phase separation (LLPS) of the ubiquitous PKA regulatory subunit RIα promotes cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces, combined with the cAMP-induced unleashing of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence, drive RIα condensate formation in the cytosol of mammalian cells, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in forming a non-canonical R:C complex, which recruits active PKA-C to RIα condensates to maintain low basal PKA activity in the cytosol. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
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Affiliation(s)
- Julia C Hardy
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily H Pool
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica G H Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingrong Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daojia R Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Max Palay
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gerald Tan
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lisa Chen
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jaclyn L C Choi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ha Neul Lee
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stefan Strack
- Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Dong Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular Determinants and Signaling Effects of PKA RIα Phase Separation. bioRxiv 2023:2023.12.10.570836. [PMID: 38168176 PMCID: PMC10760030 DOI: 10.1101/2023.12.10.570836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures the specific execution of various cellular functions. Liquid-liquid phase separation (LLPS) of the ubiquitously expressed PKA regulatory subunit RIα was recently identified as a major driver of cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces combined with the cAMP-induced release of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence are required to drive RIα condensate formation in cytosol, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in the formation of a non-canonical R:C complex, which serves to maintain low basal PKA activity in the cytosol by enabling the recruitment of active PKA-C to RIα condensates. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
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Schemenauer D, Pool EH, Raynor SN, Ruiz GP, Goehring LM, Koelper AJ, Wilson MA, Durand AJ, Kourtoglou EC, Larsen EM, Lavis LD, Esteb JJ, Hoops GC, Johnson RJ. Sequence and Structural Motifs Controlling the Broad Substrate Specificity of the Mycobacterial Hormone-Sensitive Lipase LipN. ACS Omega 2023; 8:13252-13264. [PMID: 37065048 PMCID: PMC10099132 DOI: 10.1021/acsomega.3c00534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Mycobacterium tuberculosis has a complex life cycle transitioning between active and dormant growth states depending on environmental conditions. LipN (Rv2970c) is a conserved mycobacterial serine hydrolase with regulated catalytic activity at the interface between active and dormant growth conditions. LipN also catalyzes the xenobiotic degradation of a tertiary ester substrate and contains multiple conserved motifs connected with the ability to catalyze the hydrolysis of difficult tertiary ester substrates. Herein, we expanded a library of fluorogenic ester substrates to include more tertiary and constrained esters and screened 33 fluorogenic substrates for activation by LipN, identifying its unique substrate signature. LipN preferred short, unbranched ester substrates, but had its second highest activity against a heteroaromatic five-membered oxazole ester. Oxazole esters are present in multiple mycobacterial serine hydrolase inhibitors but have not been tested widely as ester substrates. Combined structural modeling, kinetic measurements, and substitutional analysis of LipN showcased a fairly rigid binding pocket preorganized for catalysis of short ester substrates. Substitution of diverse amino acids across the binding pocket significantly impacted the folded stability and catalytic activity of LipN with two conserved motifs (HGGGW and GDSAG) playing interconnected, multidimensional roles in regulating its substrate specificity. Together this detailed substrate specificity profile of LipN illustrates the complex interplay between structure and function in mycobacterial hormone-sensitive lipase homologues and indicates oxazole esters as promising inhibitor and substrate scaffolds for mycobacterial hydrolases.
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Affiliation(s)
- Daniel
E. Schemenauer
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Emily H. Pool
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Stephanie N. Raynor
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Gabriela P. Ruiz
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Leah M. Goehring
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Andrew J. Koelper
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Madeleine A. Wilson
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Anthony J. Durand
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Elexi C. Kourtoglou
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Erik M. Larsen
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Luke D. Lavis
- Howard
Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - John J. Esteb
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Geoffrey C. Hoops
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - R. Jeremy Johnson
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
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Hardy JC, Zhang JZ, Pool EH, Choi JL, Taylor SS, Zhuo X, Zhang J. Non‐canonical Recruitment of PKA Catalytic Subunits to RIα‐driven Biomolecular Condensates. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julia C. Hardy
- BioengineeringUniversity of California, San DiegoLa JollaCA
| | - Jason Z. Zhang
- BioengineeringUniversity of California, San DiegoLa JollaCA
| | - Emily H. Pool
- Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCA
| | - Jaclyn L. Choi
- Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCA
| | - Susan S. Taylor
- Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCA
- PharmacologyUniversity of California, San DiegoLa JollaCA
| | - Xin Zhuo
- PharmacologyUniversity of California, San DiegoLa JollaCA
| | - Jin Zhang
- BioengineeringUniversity of California, San DiegoLa JollaCA
- Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCA
- PharmacologyUniversity of California, San DiegoLa JollaCA
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Bowles IE, Pool EH, Lancaster BS, Lawson EK, Savas CP, Kartje ZJ, Severinac L, Cho DH, Macbeth MR, Johnson RJ, Hoops GC. Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C. Protein Sci 2021; 30:1554-1565. [PMID: 33914998 DOI: 10.1002/pro.4089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/16/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis virulence is highly metal-dependent with metal availability modulating the shift from the dormant to active states of M. tuberculosis infection. Rv0045c from M. tuberculosis is a proposed metabolic serine hydrolase whose folded stability is dependent on divalent metal concentration. Herein, we measured the divalent metal inhibition profile of the enzymatic activity of Rv0045c and found specific divalent transition metal cations (Cu2+ ≥ Zn2+ > Ni2+ > Co2+ ) strongly inhibited its enzymatic activity. The metal cations bind allosterically, largely affecting values for kcat rather than KM . Removal of the artificial N-terminal 6xHis-tag did not change the metal-dependent inhibition, indicating that the allosteric inhibition site is native to Rv0045c. To isolate the site of this allosteric regulation in Rv0045c, the structures of Rv0045c were determined at 1.8 Å and 2.0 Å resolution in the presence and absence of Zn2+ with each structure containing a previously unresolved dynamic loop spanning the binding pocket. Through the combination of structural analysis with and without zinc and targeted mutagenesis, this metal-dependent inhibition was traced to multiple chelating residues (H202A/E204A) on a flexible loop, suggesting dynamic allosteric regulation of Rv0045c by divalent metals. Although serine hydrolases like Rv0045c are a large and diverse enzyme superfamily, this is the first structural confirmation of allosteric regulation of their enzymatic activity by divalent metals.
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Affiliation(s)
- Isobel E Bowles
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Emily H Pool
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Benjamin S Lancaster
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Emily K Lawson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Christopher P Savas
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Zach J Kartje
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Luke Severinac
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - David H Cho
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Mark R Macbeth
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - R Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Geoffrey C Hoops
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
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Meleney FL, Howes EL, Colp R, Grace RV, White WC, Heyd CG, Eggers C, Neuhof H, McCreery JA, Pool EH, Farr CE, Moschcowitz AV, Whipple AO, Harvey S, Bancroft FW, Gerster JC. DISRUPTION OF ABDOMINAL WOUNDS: Symposium at the Meeting of the New York Surgical Society, November 8, 1933. Ann Surg 2007; 99:5-46. [PMID: 17867126 PMCID: PMC1390012 DOI: 10.1097/00000658-193401000-00002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Pool EH. Recent Activities of the New York Academy of Medicine. Bull N Y Acad Med 1937; 13:110-117. [PMID: 19312014 PMCID: PMC1966102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Pool EH. Opening Remarks. Bull N Y Acad Med 1936; 12:593-596. [PMID: 19312002 PMCID: PMC1965831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Pool EH. The Relations of the Academy to the Public and the Profession. Bull N Y Acad Med 1936; 12:14-21. [PMID: 19311977 PMCID: PMC1965895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Pool EH. Address of the Incoming President: Problems Facing Medicine. Bull N Y Acad Med 1935; 11:9-18. [PMID: 19311947 PMCID: PMC1965737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Pool EH. Appendicitis. Bull N Y Acad Med 1931; 7:171-184. [PMID: 19311769 PMCID: PMC2096068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Pool EH. Francis Wisner Murray M.D. 1873-1929. Ann Surg 1930; 91:319-20. [PMID: 17866268 PMCID: PMC1398181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
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Pool EH, Jopson JH. TREATMENT OF RECENT WOUNDS OF THE KNEE-JOINT. Ann Surg 1919; 70:266-86. [PMID: 17864159 PMCID: PMC1410345 DOI: 10.1097/00000658-191909000-00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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