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Balasubramanian I, Bandyopadhyay S, Flores J, Bianchi‐Smak J, Lin X, Liu H, Sun S, Golovchenko NB, Liu Y, Wang D, Patel R, Joseph I, Suntornsaratoon P, Vargas J, Green PHR, Bhagat G, Lagana SM, Ying W, Zhang Y, Wang Z, Li WV, Singh S, Zhou Z, Kollias G, Farr LA, Moonah SN, Yu S, Wei Z, Bonder EM, Zhang L, Kiela PR, Edelblum KL, Ferraris R, Liu T, Gao N. Infection and inflammation stimulate expansion of a CD74 + Paneth cell subset to regulate disease progression. EMBO J 2023; 42:e113975. [PMID: 37718683 PMCID: PMC10620768 DOI: 10.15252/embj.2023113975] [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: 03/08/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Paneth cells (PCs), a specialized secretory cell type in the small intestine, are increasingly recognized as having an essential role in host responses to microbiome and environmental stresses. Whether and how commensal and pathogenic microbes modify PC composition to modulate inflammation remain unclear. Using newly developed PC-reporter mice under conventional and gnotobiotic conditions, we determined PC transcriptomic heterogeneity in response to commensal and invasive microbes at single cell level. Infection expands the pool of CD74+ PCs, whose number correlates with auto or allogeneic inflammatory disease progressions in mice. Similar correlation was found in human inflammatory disease tissues. Infection-stimulated cytokines increase production of reactive oxygen species (ROS) and expression of a PC-specific mucosal pentraxin (Mptx2) in activated PCs. A PC-specific ablation of MyD88 reduced CD74+ PC population, thus ameliorating pathogen-induced systemic disease. A similar phenotype was also observed in mice lacking Mptx2. Thus, infection stimulates expansion of a PC subset that influences disease progression.
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Affiliation(s)
| | | | - Juan Flores
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | | | - Xiang Lin
- Department of Computer ScienceNew Jersey Institute of TechnologyNewarkNJUSA
| | - Haoran Liu
- Department of Computer ScienceNew Jersey Institute of TechnologyNewarkNJUSA
| | - Shengxiang Sun
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMOUSA
| | | | - Yue Liu
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Dahui Wang
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Radha Patel
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Ivor Joseph
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Panan Suntornsaratoon
- Department of Pharmacology, Physiology & NeuroscienceRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Justin Vargas
- Department of Medicine, Celiac Disease CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Peter HR Green
- Department of Medicine, Celiac Disease CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Govind Bhagat
- Department of Medicine, Celiac Disease CenterColumbia University Irving Medical CenterNew YorkNYUSA
- Department of Pathology and Cell BiologyColumbia University Irving Medical CenterNew YorkNYUSA
| | - Stephen M Lagana
- Department of Pathology and Cell BiologyColumbia University Irving Medical CenterNew YorkNYUSA
| | - Wang Ying
- Hackensack Meridian Health Center for Discovery and InnovationNutleyNJUSA
| | - Yi Zhang
- Hackensack Meridian Health Center for Discovery and InnovationNutleyNJUSA
| | - Zhihan Wang
- Department of StatisticsRutgers UniversityNew BrunswickNJUSA
| | - Wei Vivian Li
- Department of Biostatistics and EpidemiologyRutgers UniversityNew BrunswickNJUSA
| | - Sukhwinder Singh
- Department of PathologyRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Zhongren Zhou
- Department of Pathology & Laboratory Medicine, Robert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNJUSA
| | - George Kollias
- Biomedical Sciences Research Centre, “Alexander Fleming”VariGreece
| | - Laura A Farr
- Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVAUSA
| | - Shannon N Moonah
- Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVAUSA
| | - Shiyan Yu
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Zhi Wei
- Department of Computer ScienceNew Jersey Institute of TechnologyNewarkNJUSA
| | - Edward M Bonder
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Lanjing Zhang
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
- Department of PathologyPenn Medicine Princeton Medical CenterPlainsboroNJUSA
| | - Pawel R Kiela
- Departments of Pediatrics and Immunology, and Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children's Research CenterThe University of Arizona Health SciencesTucsonAZUSA
| | - Karen L Edelblum
- Center for Immunity and InflammationRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology & NeuroscienceRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Ta‐Chiang Liu
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMOUSA
| | - Nan Gao
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
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2
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Goyal S, Paspureddi A, Lu M, Chan H, Lyons SN, Wilson CN, Niere M, Ziegler M, Cambronne XA. Dynamics of SLC25A51 reveal preference for oxidized NAD + and substrate led transport. EMBO Rep 2023; 24:e56596. [PMID: 37575034 PMCID: PMC10561365 DOI: 10.15252/embr.202256596] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023] Open
Abstract
SLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that contribute to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+ across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we use Molecular Dynamics simulations to reconstitute SLC25A51 homology models into lipid bilayers and to generate hypotheses to test. We observe spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51's central pore and find that mutation of these sites impairs cardiolipin binding and transporter activity. We also observe that stable formation of the required matrix gate is controlled by a single salt bridge. We identify binding sites in SLC25A51 for NAD+ and show that its selectivity for NAD+ is guided by an electrostatic interaction between the charged nicotinamide ring in the ligand and a negatively charged patch in the pore. In turn, interaction of NAD+ with interior residue E132 guides the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport.
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Affiliation(s)
- Shivansh Goyal
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | | | - Mu‐Jie Lu
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Hsin‐Ru Chan
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Scott N Lyons
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Crystal N Wilson
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Marc Niere
- Department of BiomedicineUniversity of BergenBergenNorway
| | | | - Xiaolu A Cambronne
- Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
- Livestrong Cancer InstituteUniversity of Texas at AustinAustinTXUSA
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3
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Boegholm N, Petriman NA, Loureiro‐López M, Wang J, Vela MIS, Liu B, Kanie T, Ng R, Jackson PK, Andersen JS, Lorentzen E. The IFT81-IFT74 complex acts as an unconventional RabL2 GTPase-activating protein during intraflagellar transport. EMBO J 2023; 42:e111807. [PMID: 37606072 PMCID: PMC10505919 DOI: 10.15252/embj.2022111807] [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: 06/04/2022] [Revised: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Cilia are important cellular organelles for signaling and motility and are constructed via intraflagellar transport (IFT). RabL2 is a small GTPase that localizes to the basal body of cilia via an interaction with the centriolar protein CEP19 before downstream association with the IFT machinery, which is followed by initiation of IFT. We reconstituted and purified RabL2 with CEP19 or IFT proteins to show that a reconstituted pentameric IFT complex containing IFT81/74 enhances the GTP hydrolysis rate of RabL2. The binding site on IFT81/74 that promotes GTP hydrolysis in RabL2 was mapped to a 70-amino-acid-long coiled-coil region of IFT81/74. We present structural models for RabL2-containing IFT complexes that we validate in vitro and in cellulo and demonstrate that Chlamydomonas IFT81/74 enhances GTP hydrolysis of human RabL2, suggesting an ancient evolutionarily conserved activity. Our results provide an architectural understanding of how RabL2 is incorporated into the IFT complex and a molecular rationale for why RabL2 dissociates from anterograde IFT trains soon after departure from the ciliary base.
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Affiliation(s)
- Niels Boegholm
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Narcis A Petriman
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Marta Loureiro‐López
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Jiaolong Wang
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | | | - Beibei Liu
- Department of Cell BiologyUniversity of Oklahoma Health Science CenterOklahomaOKUSA
| | - Tomoharu Kanie
- Department of Cell BiologyUniversity of Oklahoma Health Science CenterOklahomaOKUSA
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
| | - Roy Ng
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Jens S Andersen
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Esben Lorentzen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
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4
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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5
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Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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6
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Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [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: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
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Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
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7
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Haase MAB, Ólafsson G, Flores RL, Boakye‐Ansah E, Zelter A, Dickinson MS, Lazar‐Stefanita L, Truong DM, Asbury CL, Davis TN, Boeke JD. DASH/Dam1 complex mutants stabilize ploidy in histone-humanized yeast by weakening kinetochore-microtubule attachments. EMBO J 2023; 42:e112600. [PMID: 36651597 PMCID: PMC10106983 DOI: 10.15252/embj.2022112600] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 09/14/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Forcing budding yeast to chromatinize their DNA with human histones manifests an abrupt fitness cost. We previously proposed chromosomal aneuploidy and missense mutations as two potential modes of adaptation to histone humanization. Here, we show that aneuploidy in histone-humanized yeasts is specific to a subset of chromosomes that are defined by their centromeric evolutionary origins but that these aneuploidies are not adaptive. Instead, we find that a set of missense mutations in outer kinetochore proteins drives adaptation to human histones. Furthermore, we characterize the molecular mechanism underlying adaptation in two mutants of the outer kinetochore DASH/Dam1 complex, which reduce aneuploidy by suppression of chromosome instability. Molecular modeling and biochemical experiments show that these two mutants likely disrupt a conserved oligomerization interface thereby weakening microtubule attachments. We propose a model through which weakened microtubule attachments promote increased kinetochore-microtubule turnover and thus suppress chromosome instability. In sum, our data show how a set of point mutations evolved in histone-humanized yeasts to counterbalance human histone-induced chromosomal instability through weakening microtubule interactions, eventually promoting a return to euploidy.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
- Vilcek Institute of Graduate Biomedical SciencesNYU School of MedicineNew YorkNYUSA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - Rachel L Flores
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Alex Zelter
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Luciana Lazar‐Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - David M Truong
- Department of Biomedical EngineeringNYU Tandon School of EngineeringBrooklynNYUSA
- Department of PathologyNYU Langone HealthNew YorkNYUSA
| | - Charles L Asbury
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
- Department of Physiology and BiophysicsUniversity of WashingtonSeattleWAUSA
| | - Trisha N Davis
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
- Department of Biomedical EngineeringNYU Tandon School of EngineeringBrooklynNYUSA
- Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
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8
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Corbet GA, Burke JM, Parker R. Nucleic acid-protein condensates in innate immune signaling. EMBO J 2023; 42:e111870. [PMID: 36178199 PMCID: PMC10068312 DOI: 10.15252/embj.2022111870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 06/14/2022] [Revised: 07/24/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
The presence of foreign nucleic acids in the cytosol is a marker of infection. Cells have sensors, also known as pattern recognition receptors (PRRs), in the cytosol that detect foreign nucleic acid and initiate an innate immune response. Recent studies have reported the condensation of multiple PRRs including PKR, NLRP6, and cGAS, with their nucleic acid activators into discrete nucleoprotein assemblies. Nucleic acid-protein condensates form due to multivalent interactions and can create high local concentrations of components. The formation of PRR-containing condensates may alter the magnitude or timing of PRR activation. In addition, unique condensates form following RNase L activation or during paracrine signaling from virally infected cells that may play roles in antiviral defense. These observations suggest that condensate formation may be a conserved mechanism that cells use to regulate activation of the innate immune response and open an avenue for further investigation into the composition and function of these condensates. Here we review the nucleic acid-protein granules that are implicated in the innate immune response, discuss general consequences of condensate formation and signal transduction, as well as what outstanding questions remain.
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Affiliation(s)
- Giulia A Corbet
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
| | - James M Burke
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
- Present address:
Department of Molecular MedicineUniversity of Florida Scripps Biomedical ResearchJupiterFLUSA
| | - Roy Parker
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
- Howard Hughes Medical InstituteChevy ChaseMDUSA
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9
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Bhaduri S, Aguayo A, Ohno Y, Proietto M, Jung J, Wang I, Kandel R, Singh N, Ibrahim I, Fulzele A, Bennett EJ, Kihara A, Neal SE. An ERAD-independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis. EMBO J 2023; 42:e112275. [PMID: 36350249 PMCID: PMC9929635 DOI: 10.15252/embj.2022112275] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Nearly one-third of nascent proteins are initially targeted to the endoplasmic reticulum (ER), where they are correctly folded and assembled before being delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) removes these client proteins from the ER membrane to the cytosol in a process known as retrotranslocation. Our previous work demonstrated that rhomboid pseudoprotease Dfm1 is involved in the retrotranslocation of ubiquitinated membrane integral ERAD substrates. Herein, we found that Dfm1 associates with the SPOTS complex, which is composed of serine palmitoyltransferase (SPT) enzymes and accessory components that are critical for catalyzing the first rate-limiting step of the sphingolipid biosynthesis pathway. Furthermore, Dfm1 employs an ERAD-independent role for facilitating the ER export and endosome- and Golgi-associated degradation (EGAD) of Orm2, which is a major antagonist of SPT activity. Given that the accumulation of human Orm2 homologs, ORMDLs, is associated with various pathologies, our study serves as a molecular foothold for understanding how dysregulation of sphingolipid metabolism leads to various diseases.
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Affiliation(s)
- Satarupa Bhaduri
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Analine Aguayo
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Yusuke Ohno
- Laboratory of Biochemistry, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Marco Proietto
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Jasmine Jung
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Isabel Wang
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Rachel Kandel
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Narinderbir Singh
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Ikran Ibrahim
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Amit Fulzele
- Present address:
Institute of Molecular BiologyMainzGermany
| | - Eric J Bennett
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Sonya E Neal
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
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10
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Li X, Zhuo S, Cho YS, Liu Y, Yang Y, Zhu J, Jiang J. YAP antagonizes TEAD-mediated AR signaling and prostate cancer growth. EMBO J 2023; 42:e112184. [PMID: 36588499 PMCID: PMC9929633 DOI: 10.15252/embj.2022112184] [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: 07/21/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/03/2023] Open
Abstract
Hippo signaling restricts tumor growth by inhibiting the oncogenic potential of YAP/TAZ-TEAD transcriptional complex. Here, we uncover a context-dependent tumor suppressor function of YAP in androgen receptor (AR) positive prostate cancer (PCa) and show that YAP impedes AR+ PCa growth by antagonizing TEAD-mediated AR signaling. TEAD forms a complex with AR to enhance its promoter/enhancer occupancy and transcriptional activity. YAP and AR compete for TEAD binding and consequently, elevated YAP in the nucleus disrupts AR-TEAD interaction and prevents TEAD from promoting AR signaling. Pharmacological inhibition of MST1/2 or LATS1/2, or transgenic activation of YAP suppressed the growth of PCa expressing therapy resistant AR splicing variants. Our study uncovers an unanticipated crosstalk between Hippo and AR signaling pathways, reveals an antagonistic relationship between YAP and TEAD in AR+ PCa, and suggests that targeting the Hippo signaling pathway may provide a therapeutical opportunity to treat PCa driven by therapy resistant AR variants.
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Affiliation(s)
- Xu Li
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Shu Zhuo
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Center for Cancer Targeted Therapies, Signet Therapeutics Inc.Research Institute of Tsinghua University in ShenzhenShenzhenChina
| | - Yong Suk Cho
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Yuchen Liu
- Department of Developmental BiologyHarvard School of Dental MedicineBostonMAUSA
- Harvard Stem Cell InstituteBostonMAUSA
- Dana‐Farber/Harvard Cancer CenterBostonMAUSA
| | - Yingzi Yang
- Department of Developmental BiologyHarvard School of Dental MedicineBostonMAUSA
- Harvard Stem Cell InstituteBostonMAUSA
- Dana‐Farber/Harvard Cancer CenterBostonMAUSA
| | - Jian Zhu
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of General Surgery, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Jin Jiang
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
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11
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Le LTM, Thompson JR, Dehghani‐Ghahnaviyeh S, Pant S, Dang PX, French JB, Kanikeyo T, Tajkhorshid E, Alam A. Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. EMBO J 2023; 42:e111065. [PMID: 36484366 PMCID: PMC9890230 DOI: 10.15252/embj.2022111065] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
Phospholipid extrusion by ABC subfamily A (ABCA) exporters is central to cellular physiology, although the specifics of the underlying substrate interactions and transport mechanisms remain poorly resolved at the molecular level. Here we report cryo-EM structures of lipid-embedded human ABCA7 in an open state and in a nucleotide-bound, closed state at resolutions between 3.6 and 4.0 Å. The former reveals an ordered patch of bilayer lipids traversing the transmembrane domain (TMD), while the latter reveals a lipid-free, closed TMD with a small extracellular opening. These structures offer a structural framework for both substrate entry and exit from the ABCA7 TMD and highlight conserved rigid-body motions that underlie the associated conformational transitions. Combined with functional analysis and molecular dynamics (MD) simulations, our data also shed light on lipid partitioning into the ABCA7 TMD and localized membrane perturbations that underlie ABCA7 function and have broader implications for other ABCA family transporters.
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Affiliation(s)
- Le Thi My Le
- The Hormel InstituteUniversity of MinnesotaAustinMNUSA
| | | | - Sepehr Dehghani‐Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
- Present address:
Loxo Oncology at LillyLouisvilleCOUSA
| | | | | | | | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Amer Alam
- The Hormel InstituteUniversity of MinnesotaAustinMNUSA
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12
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Fuller DM, Melia TJ. Closing the autophagosome is easy-PC. EMBO J 2023; 42:e113046. [PMID: 36478568 PMCID: PMC9841321 DOI: 10.15252/embj.2022113046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
In their recent article, Polyansky et al identify phosphatidylcholine (PC) as the most abundant lipid in the autophagosome membrane and demonstrate that eliminating de novo PC synthesis sharply impairs autophagic processing. In the absence of PC synthesis, open cup-like structures accumulate, implicating PC as a key component in the closure of autophagosomes.
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Affiliation(s)
- Devin M Fuller
- Department of Cell BiologyYale University School of MedicineNew HavenCTUSA
| | - Thomas J Melia
- Department of Cell BiologyYale University School of MedicineNew HavenCTUSA
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13
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Lau RK, Enustun E, Gu Y, Nguyen JV, Corbett KD. A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage. EMBO J 2022; 41:e111540. [PMID: 36156805 PMCID: PMC9670203 DOI: 10.15252/embj.2022111540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/27/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 01/13/2023] Open
Abstract
To protect themselves from the constant threat of bacteriophage (phage) infection, bacteria have evolved diverse immune systems including restriction-modification, CRISPR-Cas, and many others. Here, we describe the discovery of a two-protein transcriptional regulator module associated with hundreds of CBASS immune systems and demonstrate that this module drives the expression of its associated CBASS system in response to DNA damage. We show that the helix-turn-helix transcriptional repressor CapH binds the promoter region of its associated CBASS system to repress transcription until it is cleaved by the metallopeptidase CapP. CapP is activated in vitro by single-stranded DNA, and in cells by DNA-damaging drugs. Together, CapH and CapP drive increased expression of their associated CBASS system in response to DNA damage. We identify CapH- and CapP-related proteins associated with diverse known and putative bacterial immune systems including DISARM and Pycsar antiphage operons. Overall, our data highlight a mechanism by which bacterial immune systems can sense and respond to a universal signal of cell stress, potentially enabling multiple immune systems to mount a coordinated defensive response against an invading pathogen.
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Affiliation(s)
- Rebecca K Lau
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaCAUSA
| | - Eray Enustun
- Department of Molecular Biology, School of Biological SciencesUniversity of California, San DiegoLa JollaCAUSA
| | - Yajie Gu
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaCAUSA
| | - Justin V Nguyen
- Department of Molecular Biology, School of Biological SciencesUniversity of California, San DiegoLa JollaCAUSA
| | - Kevin D Corbett
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaCAUSA
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14
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Golloshi R, Playter C, Freeman TF, Das P, Raines TI, Garretson JH, Thurston D, McCord RP. Constricted migration is associated with stable 3D genome structure differences in cancer cells. EMBO Rep 2022; 23:e52149. [PMID: 35969179 PMCID: PMC9535800 DOI: 10.15252/embr.202052149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/22/2020] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation, and DNA repair, here, we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain features of the 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.
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Affiliation(s)
- Rosela Golloshi
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Christopher Playter
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Trevor F Freeman
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Priyojit Das
- UT‐ORNL Graduate School of Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
| | - Thomas Isaac Raines
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Joshua H Garretson
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Delaney Thurston
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Rachel Patton McCord
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
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15
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Gross S, Hooper R, Tomar D, Armstead AP, Shanas N, Mallu P, Joshi H, Ray S, Chong PL, Astsaturov I, Farma JM, Cai KQ, Chitrala KN, Elrod JW, Zaidi MR, Soboloff J. Suppression of Ca 2+ signaling enhances melanoma progression. EMBO J 2022; 41:e110046. [PMID: 36039850 PMCID: PMC9531303 DOI: 10.15252/embj.2021110046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/26/2021] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 01/18/2023] Open
Abstract
The role of store-operated Ca2+ entry (SOCE) in melanoma metastasis is highly controversial. To address this, we here examined UV-dependent metastasis, revealing a critical role for SOCE suppression in melanoma progression. UV-induced cholesterol biosynthesis was critical for UV-induced SOCE suppression and subsequent metastasis, although SOCE suppression alone was both necessary and sufficient for metastasis to occur. Further, SOCE suppression was responsible for UV-dependent differences in gene expression associated with both increased invasion and reduced glucose metabolism. Functional analyses further established that increased glucose uptake leads to a metabolic shift towards biosynthetic pathways critical for melanoma metastasis. Finally, examination of fresh surgically isolated human melanoma explants revealed cholesterol biosynthesis-dependent reduced SOCE. Invasiveness could be reversed with either cholesterol biosynthesis inhibitors or pharmacological SOCE potentiation. Collectively, we provide evidence that, contrary to current thinking, Ca2+ signals can block invasive behavior, and suppression of these signals promotes invasion and metastasis.
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Affiliation(s)
- Scott Gross
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Robert Hooper
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Dhanendra Tomar
- The Center for Translational MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Alexander P Armstead
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - No'ad Shanas
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Pranava Mallu
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
- Department of Cancer and Cellular BiologyThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Hinal Joshi
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
- Department of Cancer and Cellular BiologyThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Suravi Ray
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
- Department of Cancer and Cellular BiologyThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Parkson Lee‐Gau Chong
- Department of Cancer and Cellular BiologyThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Igor Astsaturov
- Department of Hematology/OncologyFox Chase Cancer CenterPhiladelphiaPAUSA
| | - Jeffrey M Farma
- Department of Surgical OncologyFox Chase Cancer CenterPhiladelphiaPAUSA
| | - Kathy Q Cai
- Department of Hematology/OncologyFox Chase Cancer CenterPhiladelphiaPAUSA
| | - Kumaraswamy Naidu Chitrala
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - John W Elrod
- The Center for Translational MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - M Raza Zaidi
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
- Department of Cancer and Cellular BiologyThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
| | - Jonathan Soboloff
- Fels Cancer Institute for Personalized MedicineThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
- Department of Cancer and Cellular BiologyThe Lewis Katz School of Medicine at Temple UniversityPhiladelphiaPAUSA
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