1
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Yang W, Meyer AN, Jiang Z, Jiang X, Donoghue DJ. Critical domains for NACC2-NTRK2 fusion protein activation. PLoS One 2024; 19:e0301730. [PMID: 38935636 PMCID: PMC11210774 DOI: 10.1371/journal.pone.0301730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 03/20/2024] [Indexed: 06/29/2024] Open
Abstract
Neurotrophic receptor tyrosine kinases (NTRKs) belong to the receptor tyrosine kinase (RTK) family. NTRKs are responsible for the activation of multiple downstream signaling pathways that regulate cell growth, proliferation, differentiation, and apoptosis. NTRK-associated mutations often result in oncogenesis and lead to aberrant activation of downstream signaling pathways including MAPK, JAK/STAT, and PLCγ1. This study characterizes the NACC2-NTRK2 oncogenic fusion protein that leads to pilocytic astrocytoma and pediatric glioblastoma. This fusion joins the BTB domain (Broad-complex, Tramtrack, and Bric-a-brac) domain of NACC2 (Nucleus Accumbens-associated protein 2) with the transmembrane helix and tyrosine kinase domain of NTRK2. We focus on identifying critical domains for the biological activity of the fusion protein. Mutations were introduced in the charged pocket of the BTB domain or in the monomer core, based on a structural comparison of the NACC2 BTB domain with that of PLZF, another BTB-containing protein. Mutations were also introduced into the NTRK2-derived portion to allow comparison of two different breakpoints that have been clinically reported. We show that activation of the NTRK2 kinase domain relies on multimerization of the BTB domain in NACC2-NTRK2. Mutations which disrupt BTB-mediated multimerization significantly reduce kinase activity and downstream signaling. The ability of these mutations to abrogate biological activity suggests that BTB domain inhibition could be a potential treatment for NACC2-NTRK2-induced cancers. Removal of the transmembrane helix leads to enhanced stability of the fusion protein and increased activity of the NACC2-NTRK2 fusion, suggesting a mechanism for the oncogenicity of a distinct NACC2-NTRK2 isoform observed in pediatric glioblastoma.
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Affiliation(s)
- Wei Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - April N. Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Zian Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Xuan Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Daniel J. Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- UCSD Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
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2
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Komives EA. The multifunctional role of intrinsic disorder in NF-κB signaling. Biochem Soc Trans 2023; 51:2085-2092. [PMID: 38095058 PMCID: PMC10754279 DOI: 10.1042/bst20230035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The nuclear factor-κB (NF-κB) transcription activation system involves disordered regions of both the NF-κB dimers and their inhibitors, the IκBs. The system is well-studied both at the cellular and biophysical levels affording a unique opportunity to compare and contrast the conclusions from both types of experiments. Through a combination of both experiments and theory, we have discovered that the RelA/p50 heterodimer and its inhibitor IκBα operate under kinetic control. Intrinsically disordered parts of both proteins are directly involved in temporal control and their folding and unfolding determines the rates of various processes. In this review, we show how the dynamic state of the intrinsically disordered sequences define the rates of intracellular processes.
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Affiliation(s)
- Elizabeth A. Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92161, U.S.A
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3
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Oliveira AS, Aredes-Riguetti LM, Pereira BAS, Alves CR, Souza-Silva F. Degron Pathways and Leishmaniasis: Debating Potential Roles of Leishmania spp. Proteases Activity on Guiding Hosts Immune Response and Their Relevance to the Development of Vaccines. Vaccines (Basel) 2023; 11:1015. [PMID: 37376405 DOI: 10.3390/vaccines11061015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 06/29/2023] Open
Abstract
Degrons are short peptide sequences that signalize target sites for protein degradation by proteases. Herein, we bring forth the discussion on degrons present in proteins related to the immune system of Mus musculus that are potential targets for cysteine and serine proteases of Leishmania spp. and their possible roles on host immune regulation by parasites. The Merops database was used to identify protease substrates and proteases sequence motifs, while MAST/MEME Suite was applied to find degron motifs in murine cytokines (IFN-y, IL-4, IL-5, IL-13, IL-17) and transcription factors (NF-kappaB, STAT-1, AP-1, CREB, and BACH2). STRING tool was used to construct an interaction network for the immune factors and SWISS-MODEL server to generate three-dimensional models of proteins. In silico assays confirm the occurrence of degrons in the selected immune response factors. Further analyses were conducted only in those with resolved three-dimensional structures. The predicted interaction network of degron-containing M. musculus proteins shows the possibility that the specific activity of parasite proteases could interfere with the trend of Th1/Th2 immune responses. Data suggest that degrons may play a role in the immune responses in leishmaniases as targets for parasite proteases activity, directing the degradation of specific immune-related factors.
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Affiliation(s)
- Adriane Silva Oliveira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
| | - Lara Mata Aredes-Riguetti
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
| | | | - Carlos Roberto Alves
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
| | - Franklin Souza-Silva
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
- Faculdade de Ciências Biológicas e da Saúde, Universidade Iguaçu, Avenida Abílio Augusto Távora, 2134, Dom Rodrigo, Nova Iguaçu 26260-100, RJ, Brazil
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4
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Liu Y, Trnka MJ, He L, Burlingame AL, Correia MA. In-Cell Chemical Crosslinking Identifies Hotspots for SQSTM-1/p62-IκBα Interaction That Underscore a Critical Role of p62 in Limiting NF-κB Activation Through IκBα Stabilization. Mol Cell Proteomics 2023; 22:100495. [PMID: 36634736 PMCID: PMC9947424 DOI: 10.1016/j.mcpro.2023.100495] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
We have previously documented that in liver cells, the multifunctional protein scaffold p62/SQSTM1 is closely associated with IκBα, an inhibitor of the transcriptional activator NF-κB. Such an intimate p62-IκBα association we now document leads to a marked 18-fold proteolytic IκBα-stabilization, enabling its nuclear entry and termination of the NF-κB-activation cycle. In p62-/--cells, such termination is abrogated resulting in the nuclear persistence and prolonged activation of NF-κB following inflammatory stimuli. Utilizing various approaches both classic (structural deletion, site-directed mutagenesis) as well as novel (in-cell chemical crosslinking), coupled with proteomic analyses, we have defined the precise structural hotspots of p62-IκBα association. Accordingly, we have identified such IκBα hotspots to reside around N-terminal (K38, K47, and K67) and C-terminal (K238/C239) residues in its fifth ankyrin repeat domain. These sites interact with two hotspots in p62: One in its PB-1 subdomain around K13, and the other comprised of a positively charged patch (R183/R186/K187/K189) between its ZZ- and TB-subdomains. APEX proximity analyses upon IκBα-cotransfection of cells with and without p62 have enabled the characterization of the p62 influence on IκBα-protein-protein interactions. Interestingly, consistent with p62's capacity to proteolytically stabilize IκBα, its presence greatly impaired IκBα's interactions with various 20S/26S proteasomal subunits. Furthermore, consistent with p62 interaction with IκBα on an interface opposite to that of its NF-κB-interacting interface, p62 failed to significantly affect IκBα-NF-κB interactions. These collective findings together with the known dynamic p62 nucleocytoplasmic shuttling leads us to speculate that it may be involved in "piggy-back" nuclear transport of IκBα following its NF-κB-elicited transcriptional activation and de novo synthesis, required for termination of the NF-κB-activation cycle. Consequently, mice carrying a liver-specific deletion of p62-residues 68 to 252 reveal age-dependent-enhanced liver inflammation. Our findings reveal yet another mode of p62-mediated pathophysiologically relevant regulation of NF-κB.
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Affiliation(s)
- Yi Liu
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Liang He
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - A L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Maria Almira Correia
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA; The Liver Center, University of California San Francisco, San Francisco, California, USA.
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5
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Nagati JS, Kobeissy PH, Nguyen MQ, Xu M, Garcia T, Comerford SA, Hammer RE, Garcia JA. Mammalian acetate-dependent acetyl CoA synthetase 2 contains multiple protein destabilization and masking elements. J Biol Chem 2021; 297:101037. [PMID: 34343565 PMCID: PMC8405932 DOI: 10.1016/j.jbc.2021.101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/13/2021] [Accepted: 07/30/2021] [Indexed: 11/05/2022] Open
Abstract
Besides contributing to anabolism, cellular metabolites serve as substrates or cofactors for enzymes and may also have signaling functions. Given these roles, multiple control mechanisms likely ensure fidelity of metabolite-generating enzymes. Acetate-dependent acetyl CoA synthetases (ACS) are de novo sources of acetyl CoA, a building block for fatty acids and a substrate for acetyltransferases. Eukaryotic acetate-dependent acetyl CoA synthetase 2 (Acss2) is predominantly cytosolic, but is also found in the nucleus following oxygen or glucose deprivation, or upon acetate exposure. Acss2-generated acetyl CoA is used in acetylation of Hypoxia-Inducible Factor 2 (HIF-2), a stress-responsive transcription factor. Mutation of a putative nuclear localization signal in endogenous Acss2 abrogates HIF-2 acetylation and signaling, but surprisingly also results in reduced Acss2 protein levels due to unmasking of two protein destabilization elements (PDE) in the Acss2 hinge region. In the current study, we identify up to four additional PDE in the Acss2 hinge region and determine that a previously identified PDE, the ABC domain, consists of two functional PDE. We show that the ABC domain and other PDE are likely masked by intramolecular interactions with other domains in the Acss2 hinge region. We also characterize mice with a prematurely truncated Acss2 that exposes a putative ABC domain PDE, which exhibits reduced Acss2 protein stability and impaired HIF-2 signaling. Finally, using primary mouse embryonic fibroblasts, we demonstrate that the reduced stability of select Acss2 mutant proteins is due to a shortened half-life, which is a result of enhanced degradation via a nonproteasome, nonautophagy pathway.
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Affiliation(s)
- Jason S Nagati
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Philippe H Kobeissy
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Minh Q Nguyen
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Min Xu
- Department of Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Trent Garcia
- Department of Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sarah A Comerford
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert E Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph A Garcia
- Department of Medicine, Columbia University Medical Center, New York, New York, USA; Department of Research, James J. Peters VA Medical Center, New York, New York, USA.
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6
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Johnson SL, Blount JR, Libohova K, Ranxhi B, Paulson HL, Tsou WL, Todi SV. Differential toxicity of ataxin-3 isoforms in Drosophila models of Spinocerebellar Ataxia Type 3. Neurobiol Dis 2019; 132:104535. [PMID: 31310802 DOI: 10.1016/j.nbd.2019.104535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/28/2022] Open
Abstract
The most commonly inherited dominant ataxia, Spinocerebellar Ataxia Type 3 (SCA3), is caused by a CAG repeat expansion that encodes an abnormally long polyglutamine (polyQ) repeat in the disease protein ataxin-3, a deubiquitinase. Two major full-length isoforms of ataxin-3 exist, both of which contain the same N-terminal portion and polyQ repeat, but differ in their C-termini; one (denoted here as isoform 1) contains a motif that binds ataxin-3's substrate, ubiquitin, whereas the other (denoted here as isoform 2) has a hydrophobic tail. Most SCA3 studies have focused on isoform 1, the predominant version in mammalian brain, yet both isoforms are present in brain and a better understanding of their relative pathogenicity in vivo is needed. We took advantage of the fruit fly, Drosophila melanogaster to model SCA3 and to examine the toxicity of each ataxin-3 isoform. Our assays reveal isoform 1 to be markedly more toxic than isoform 2 in all fly tissues. Reduced toxicity from isoform 2 is due to much lower protein levels as a result of its expedited degradation. Additional studies indicate that isoform 1 is more aggregation-prone than isoform 2 and that the C-terminus of isoform 2 is critical for its enhanced proteasomal degradation. According to our results, although both full-length, pathogenic ataxin-3 isoforms are toxic, isoform 1 is likely the primary contributor to SCA3 due to its presence at higher levels. Isoform 2, as a result of rapid degradation that is dictated by its tail, is unlikely to be a key player in this disease. Our findings provide new insight into the biology of this ataxia and the cellular processing of the underlying disease protein.
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Affiliation(s)
- Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bedri Ranxhi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA.
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7
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Adelaja A, Hoffmann A. Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB. Front Immunol 2019; 10:433. [PMID: 31312197 PMCID: PMC6614373 DOI: 10.3389/fimmu.2019.00433] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/19/2019] [Indexed: 01/14/2023] Open
Abstract
Precise control of inflammatory gene expression is critical for effective host defense without excessive tissue damage. The principal regulator of inflammatory gene expression is nuclear factor kappa B (NFκB), a transcription factor. Nuclear NFκB activity is controlled by IκB proteins, whose stimulus-responsive degradation and re-synthesis provide for transient or dynamic regulation. The IκB-NFκB signaling module receives input signals from a variety of pathogen sensors, such as toll-like receptors (TLRs). The molecular components and mechanisms of NFκB signaling are well-understood and have been reviewed elsewhere in detail. Here we review the molecular mechanisms that mediate cross-regulation of TLR-IκB-NFκB signal transduction by signaling pathways that do not activate NFκB themselves, such as interferon signaling pathways. We distinguish between potential regulatory crosstalk mechanisms that (i) occur proximal to TLRs and thus may have stimulus-specific effects, (ii) affect the core IκB-NFκB signaling module to modulate NFκB activation in response to several stimuli. We review some well-documented examples of molecular crosstalk mechanisms and indicate other potential mechanisms whose physiological roles require further study.
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Affiliation(s)
- Adewunmi Adelaja
- UCLA-Caltech Medical Scientist Training Program, Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
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8
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Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A. An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Front Immunol 2019; 10:1425. [PMID: 31293585 PMCID: PMC6604663 DOI: 10.3389/fimmu.2019.01425] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/05/2019] [Indexed: 01/22/2023] Open
Abstract
Nuclear factor kappa B (NFκB) is a transcription factor that controls inflammation and cell survival. In clinical histology, elevated NFκB activity is a hallmark of poor prognosis in inflammatory disease and cancer, and may be the result of a combination of diverse micro-environmental constituents. While previous quantitative studies of NFκB focused on its signaling dynamics in single cells, we address here how multiple stimuli may combine to control tissue level NFκB activity. We present a novel, simplified model of NFκB (SiMoN) that functions as an NFκB activity calculator. We demonstrate its utility by exploring how type I and type II interferons modulate NFκB activity in macrophages. Whereas, type I IFNs potentiate NFκB activity by inhibiting translation of IκBα and by elevating viral RNA sensor (RIG-I) expression, type II IFN amplifies NFκB activity by increasing the degradation of free IκB through transcriptional induction of proteasomal cap components (PA28). Both cross-regulatory mechanisms amplify NFκB activation in response to weaker (viral) inducers, while responses to stronger (bacterial or cytokine) inducers remain largely unaffected. Our work demonstrates how the NFκB calculator can reveal distinct mechanisms of crosstalk on NFκB activity in interferon-containing microenvironments.
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Affiliation(s)
- Simon Mitchell
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States
| | - Ellen L Mercado
- Signaling Systems Laboratory, San Diego Center for Systems Biology, La Jolla, CA, United States
| | - Adewunmi Adelaja
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States
| | - Jessica Q Ho
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Quen J Cheng
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States.,Signaling Systems Laboratory, San Diego Center for Systems Biology, La Jolla, CA, United States
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9
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Baudier J, Jenkins ZA, Robertson SP. The filamin-B–refilin axis – spatiotemporal regulators of the actin-cytoskeleton in development and disease. J Cell Sci 2018; 131:131/8/jcs213959. [DOI: 10.1242/jcs.213959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT
During development, cycles of spatiotemporal remodeling of higher-order networks of actin filaments contribute to control cell fate specification and differentiation. Programs for controlling these dynamics are hard-wired into actin-regulatory proteins. The filamin family of actin-binding proteins exert crucial mechanotransduction and signaling functions in tissue morphogenesis. Filamin-B (FLNB) is a key player in chondrocyte progenitor differentiation for endochondral ossification. Biallelic loss-of-function mutations or gain-of-function mutations in FLNB cause two groups of skeletal disorders that can be attributed to either the loss of repressive function on TGF-β signaling or a disruption in mechanosensory properties, respectively. In this Review, we highlight a unique family of vertebrate-specific short-lived filamin-binding proteins, the refilins (refilin-A and refilin-B), that modulate filamin-dependent actin crosslinking properties. Refilins are downstream TGF-β effectors in epithelial cells. Double knockout of both refilin-A and refilin-B in mice results in precocious ossification of some axial skeletal elements, leading to malformations that are similar to those seen in FLNB-deficient mice. Based on these findings, we present a model summarizing the role of refilins in regulating the mechanosensory functions of FLNB during skeletal development. We also discuss the possible contribution of refilins to FLNB-related skeletal pathologies that are associated with gain-of-function mutations.
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Affiliation(s)
- Jacques Baudier
- Aix Marseille Université, CNRS, IBDM, 13284 Marseille Cedex 07, France
- Institut de Biologie du Développement de Marseille-UMR CNRS 7288, Campus de Luminy-Case 907, 13288 Marseille Cedex 9, France
| | - Zandra A. Jenkins
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Stephen P. Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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10
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Ramirez-Sarmiento CA, Komives EA. Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions. Methods 2018; 144:43-52. [PMID: 29627358 DOI: 10.1016/j.ymeth.2018.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 11/29/2022] Open
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDXMS) has emerged as a powerful approach for revealing folding and allostery in protein-protein interactions. The advent of higher resolution mass spectrometers combined with ion mobility separation and ultra performance liquid chromatographic separations have allowed the complete coverage of large protein sequences and multi-protein complexes. Liquid-handling robots have improved the reproducibility and accurate temperature control of the sample preparation. Many researchers are also appreciating the power of combining biophysical approaches such as stopped-flow fluorescence, single molecule FRET, and molecular dynamics simulations with HDXMS. In this review, we focus on studies that have used a combination of approaches to reveal (re)folding of proteins as well as on long-distance allosteric changes upon interaction.
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Affiliation(s)
- Cesar A Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, United States.
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11
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Eldridge MJG, Sanchez-Garrido J, Hoben GF, Goddard PJ, Shenoy AR. The Atypical Ubiquitin E2 Conjugase UBE2L3 Is an Indirect Caspase-1 Target and Controls IL-1β Secretion by Inflammasomes. Cell Rep 2017; 18:1285-1297. [PMID: 28147281 PMCID: PMC5300903 DOI: 10.1016/j.celrep.2017.01.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
Caspase-1 activation by inflammasome signaling scaffolds initiates inflammation and antimicrobial responses. Caspase-1 proteolytically converts newly induced pro-interleukin 1 beta (IL-1β) into its mature form and directs its secretion, triggering pyroptosis and release of non-substrate alarmins such as interleukin 1 alpha (IL-1α) and HMGB1. While some caspase-1 substrates involved in these events are known, the identities and roles of non-proteolytic targets remain unknown. Here, we use unbiased proteomics to show that the UBE2L3 ubiquitin conjugase is an indirect target of caspase-1. Caspase-1, but not caspase-4, controls pyroptosis- and ubiquitin-independent proteasomal degradation of UBE2L3 upon canonical and non-canonical inflammasome activation by sterile danger signals and bacterial infection. Mechanistically, UBE2L3 acts post-translationally to promote K48-ubiquitylation and turnover of pro-IL-1β and dampen mature-IL-1β production. UBE2L3 depletion increases pro-IL-1β levels and mature-IL-1β secretion by inflammasomes. These findings regarding UBE2L3 as a molecular rheostat have implications for IL-1-driven pathology in hereditary fever syndromes and in autoinflammatory conditions associated with UBE2L3 polymorphisms. Caspase-1 inflammasomes induce loss of UBE2L3 in macrophages and dendritic cells UBE2L3 loss is proteasome-dependent, ubiquitin- and pyroptosis-independent UBE2L3 participates in K48 ubiquitylation and proteasomal turnover of pro-IL-1β UBE2L3 modulates levels of pro-IL-1β available for processing by caspase-1
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Affiliation(s)
- Matthew J G Eldridge
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gil Ferreira Hoben
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Philippa J Goddard
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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12
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Functional importance of stripping in NFκB signaling revealed by a stripping-impaired IκBα mutant. Proc Natl Acad Sci U S A 2017; 114:1916-1921. [PMID: 28167786 DOI: 10.1073/pnas.1610192114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stress-response transcription factors such as NFκB turn on hundreds of genes and must have a mechanism for rapid cessation of transcriptional activation. We recently showed that the inhibitor of NFκB signaling, IκBα, dramatically accelerates the dissociation of NFκB from transcription sites, a process we have called "stripping." To test the role of the IκBα C-terminal PEST (rich in proline, glutamic acid, serine, and threonine residues) sequence in NFκB stripping, a mutant IκBα was generated in which five acidic PEST residues were mutated to their neutral analogs. This IκBα(5xPEST) mutant was impaired in stripping NFκB from DNA and formed a more stable intermediate ternary complex than that formed from IκBα(WT) because DNA dissociated more slowly. NMR and amide hydrogen-deuterium exchange mass spectrometry showed that the IκBα(5xPEST) appears to be "caught in the act of stripping" because it is not yet completely in the folded and NFκB-bound state. When the mutant was introduced into cells, the rate of postinduction IκBα-mediated export of NFκB from the nucleus decreased markedly.
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Cohen-Kaplan V, Livneh I, Avni N, Cohen-Rosenzweig C, Ciechanover A. The ubiquitin-proteasome system and autophagy: Coordinated and independent activities. Int J Biochem Cell Biol 2016; 79:403-418. [DOI: 10.1016/j.biocel.2016.07.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 01/10/2023]
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Mitchell S, Vargas J, Hoffmann A. Signaling via the NFκB system. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:227-41. [PMID: 26990581 DOI: 10.1002/wsbm.1331] [Citation(s) in RCA: 670] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 12/25/2022]
Abstract
The nuclear factor kappa B (NFκB) family of transcription factors is a key regulator of immune development, immune responses, inflammation, and cancer. The NFκB signaling system (defined by the interactions between NFκB dimers, IκB regulators, and IKK complexes) is responsive to a number of stimuli, and upon ligand-receptor engagement, distinct cellular outcomes, appropriate to the specific signal received, are set into motion. After almost three decades of study, many signaling mechanisms are well understood, rendering them amenable to mathematical modeling, which can reveal deeper insights about the regulatory design principles. While other reviews have focused on upstream, receptor proximal signaling (Hayden MS, Ghosh S. Signaling to NF-κB. Genes Dev 2004, 18:2195-2224; Verstrepen L, Bekaert T, Chau TL, Tavernier J, Chariot A, Beyaert R. TLR-4, IL-1R and TNF-R signaling to NF-κB: variations on a common theme. Cell Mol Life Sci 2008, 65:2964-2978), and advances through computational modeling (Basak S, Behar M, Hoffmann A. Lessons from mathematically modeling the NF-κB pathway. Immunol Rev 2012, 246:221-238; Williams R, Timmis J, Qwarnstrom E. Computational models of the NF-KB signalling pathway. Computation 2014, 2:131), in this review we aim to summarize the current understanding of the NFκB signaling system itself, the molecular mechanisms, and systems properties that are key to its diverse biological functions, and we discuss remaining questions in the field. WIREs Syst Biol Med 2016, 8:227-241. doi: 10.1002/wsbm.1331 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Simon Mitchell
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jesse Vargas
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
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