51
|
Kung CP, Cottrell KA, Ryu S, Bramel ER, Kladney RD, Bao EA, Freeman EC, Sabloak T, Maggi L, Weber JD. Evaluating the therapeutic potential of ADAR1 inhibition for triple-negative breast cancer. Oncogene 2021; 40:189-202. [PMID: 33110236 PMCID: PMC7796950 DOI: 10.1038/s41388-020-01515-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 11/09/2022]
Abstract
Triple-negative breast cancer (TNBC) is the deadliest form of breast cancer. Unlike other types of breast cancer that can be effectively treated by targeted therapies, no such targeted therapy exists for all TNBC patients. The ADAR1 enzyme carries out A-to-I editing of RNA to prevent sensing of endogenous double-stranded RNAs. ADAR1 is highly expressed in breast cancer including TNBC. Here, we demonstrate that expression of ADAR1, specifically its p150 isoform, is required for the survival of TNBC cell lines. In TNBC cells, knockdown of ADAR1 attenuates proliferation and tumorigenesis. Moreover, ADAR1 knockdown leads to robust translational repression. ADAR1-dependent TNBC cell lines also exhibit elevated IFN stimulated gene expression. IFNAR1 reduction significantly rescued the proliferative defects of ADAR1 loss. These findings establish ADAR1 as a novel therapeutic target for TNBC tumors.
Collapse
Affiliation(s)
- Che-Pei Kung
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kyle A Cottrell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sua Ryu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Emily R Bramel
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Raleigh D Kladney
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Emily A Bao
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eric C Freeman
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Thwisha Sabloak
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Leonard Maggi
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jason D Weber
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO, USA.
| |
Collapse
|
52
|
Higher-order phosphatase-substrate contacts terminate the integrated stress response. Nat Struct Mol Biol 2021; 28:835-846. [PMID: 34625748 PMCID: PMC8500838 DOI: 10.1038/s41594-021-00666-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023]
Abstract
Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally affecting flexible access of the phosphopeptide to the active site. However, catalytic efficiency of holophosphatases towards their phosphoprotein substrates remains unexplained. Here we present a cryo-EM structure of the tripartite PP1c-PPP1R15A-G-actin holophosphatase that terminates signaling in the mammalian integrated stress response (ISR) in the pre-dephosphorylation complex with its substrate, translation initiation factor 2α (eIF2α). G-actin, whose essential role in eIF2α dephosphorylation is supported crystallographically, biochemically and genetically, aligns the catalytic and regulatory subunits, creating a composite surface that engages the N-terminal domain of eIF2α to position the distant phosphoserine-51 at the active site. Substrate residues that mediate affinity for the holophosphatase also make critical contacts with eIF2α kinases. Thus, a convergent process of higher-order substrate recognition specifies functionally antagonistic phosphorylation and dephosphorylation in the ISR.
Collapse
|
53
|
Yang Y, Xie L, Zhong Y, Zhong X, Meng R, Xue Q, Liang F, Zhao K, Tang Y. Double-Stranded RNA Dependent Kinase R Regulates Antibacterial Immunity in Sepsis. J Innate Immun 2020; 13:26-37. [PMID: 33333514 DOI: 10.1159/000507932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Double-stranded RNA dependent kinase R (PKR) is originally identified as an intracellular sensor of viral infection, but its role in bacterial infection remains largely unknown. Here we report that PKR was an important regulator of antibacterial immunity in sepsis. Genetic deletion of PKR or pharmacological inhibition of its kinase activity markedly increased bacterial loads, organ injury, and mortality in polymicrobial infection induced by cecal ligation and puncture (CLP). In contrast, PKR deficiency or inhibition did not affect bacterial loads, organ injury, or mortality when mice were systemically challenged with Escherichia coli, an abundant microbe in the gastrointestinal tract. PKR deficiency or inhibition markedly decreased the release of interleukin (IL)-1β after CLP. Defect in IL-1 signaling phenocopied PKR deficiency or inhibition in CLP-induced bacterial sepsis. Taken together, these findings identified a critical role of the PKR signaling pathway in antibacterial immunity.
Collapse
Affiliation(s)
- Yanliang Yang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Lingli Xie
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China.,Department of Pathophysiology, Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Yanjun Zhong
- The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoli Zhong
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Ran Meng
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Qianqian Xue
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Fang Liang
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Kai Zhao
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Yiting Tang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China,
| |
Collapse
|
54
|
Teoh PJ, Koh MY, Chng WJ. ADARs, RNA editing and more in hematological malignancies. Leukemia 2020; 35:346-359. [PMID: 33139858 DOI: 10.1038/s41375-020-01076-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/21/2020] [Accepted: 10/20/2020] [Indexed: 02/08/2023]
Abstract
Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in humans, mediated by the adenosine deaminases acting on RNA (ADARs). Physiologically, these enzymes are present in the nucleus and/or the cytoplasm, where they catalyze the conversion of adenosines (A) to inosines (I) on double-stranded mRNA molecules. Aberrant ADAR-mediated-editing is a prominent feature in a variety of cancers. Importantly, the biological functions of ADARs and its functional implications in hematological malignancies have recently been unraveled. In this review, we will highlight the functions of ADARs and their involvements in cancer, specifically in hematological malignancies. RNA editing-independent function of cellular processes by ADARs and the potential of developing novel therapeutic approaches revolving RNA editing will also be discussed.
Collapse
Affiliation(s)
- Phaik Ju Teoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, Singapore, Singapore
| | - Mun Yee Koh
- Cancer Science Institute of Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Cancer Science Institute of Singapore, Singapore, Singapore. .,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.
| |
Collapse
|
55
|
El-Asmi F, McManus FP, Thibault P, Chelbi-Alix MK. Interferon, restriction factors and SUMO pathways. Cytokine Growth Factor Rev 2020; 55:37-47. [DOI: 10.1016/j.cytogfr.2020.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/18/2020] [Indexed: 12/21/2022]
|
56
|
Riad S, Xiang Y, AlDaif B, Mercer AA, Fleming SB. Rescue of a Vaccinia Virus Mutant Lacking IFN Resistance Genes K1L and C7L by the Parapoxvirus Orf Virus. Front Microbiol 2020; 11:1797. [PMID: 32903701 PMCID: PMC7438785 DOI: 10.3389/fmicb.2020.01797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Type 1 interferons induce the upregulation of hundreds of interferon-stimulated genes (ISGs) that combat viral replication. The parapoxvirus orf virus (ORFV) induces acute pustular skin lesions in sheep and goats and can reinfect its host, however, little is known of its ability to resist IFN. Vaccinia virus (VACV) encodes a number of factors that modulate the IFN response including the host-range genes C7L and K1L. A recombinant VACV-Western Reserve (WR) strain in which the K1L and C7L genes have been deleted does not replicate in cells treated with IFN-β nor in HeLa cells in which the IFN response is constitutive and is inhibited at the level of intermediate gene expression. Furthermore C7L is conserved in almost all poxviruses. We provide evidence that shows that although ORFV is more sensitive to IFN-β compared with VACV, and lacks homologues of KIL and C7L, it nevertheless has the ability to rescue a VACV KIL- C7L- gfp+ mutant in which gfp is expressed from a late promoter. Co-infection of HeLa cells with the mutant and ORFV demonstrated that ORFV was able to overcome the block in translation of intermediate transcripts in the mutant virus, allowing it to progress to late gene expression and new viral particles. Our findings strongly suggest that ORFV encodes a factor(s) that, although different in structure to C7L or KIL, targets an anti-viral cellular mechanism that is a highly potent at killing poxviruses.
Collapse
Affiliation(s)
- Sherief Riad
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Basheer AlDaif
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Andrew A Mercer
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Stephen B Fleming
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| |
Collapse
|
57
|
Eiermann N, Haneke K, Sun Z, Stoecklin G, Ruggieri A. Dance with the Devil: Stress Granules and Signaling in Antiviral Responses. Viruses 2020; 12:v12090984. [PMID: 32899736 PMCID: PMC7552005 DOI: 10.3390/v12090984] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating mRNAs rapidly condensate by phase separation into cytosolic stress granules, together with numerous RNA-binding proteins and components of signal transduction pathways. Growing evidence suggests that the integrated stress response, and stress granules in particular, contribute to antiviral defense. This review summarizes the current understanding of how stress and innate immune signaling act in concert to mount an effective response against virus infection, with a particular focus on the potential role of stress granules in the coordination of antiviral signaling cascades.
Collapse
Affiliation(s)
- Nina Eiermann
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Katharina Haneke
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Zhaozhi Sun
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
- Correspondence:
| |
Collapse
|
58
|
Medina GN, de los Santos T, Diaz-San Segundo F. Use of IFN-Based Biotherapeutics to Harness the Host Against Foot-And-Mouth Disease. Front Vet Sci 2020; 7:465. [PMID: 32851039 PMCID: PMC7431487 DOI: 10.3389/fvets.2020.00465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious vesicular disease of cloven-hoofed animals that severely constrains international trade of livestock and animal products. Currently, disease control measures include broad surveillance, enforcement of sanitary policy, and use of an inactivated vaccine. While use of these measures has contributed to eliminating foot-and-mouth disease virus (FMDV) from a vast area of the world, the disease remains endemic in three continents, and outbreaks occasionally appear in previously declared FMD-free zones, causing economic and social devastation. Among others, a very fast rate of viral replication and the need for 7 days to achieve vaccine-induced protection are the main limitations in controlling the disease. New fast-acting antiviral strategies targeted to boost the innate immunity of the host to block viral replication are needed. Here we review the knowledge on the multiple strategies FMDV has evolved to block the host innate immunity, with particularly focus on the past and current research toward the development of interferon (IFN)-based biotherapeutics in relevant livestock species.
Collapse
Affiliation(s)
- Gisselle N. Medina
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Orient Point, NY, United States
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Teresa de los Santos
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Orient Point, NY, United States
| | | |
Collapse
|
59
|
Abstract
Protein-RNA interactions have crucial roles in various cellular activities, which, when dysregulated, can lead to a range of human diseases. The identification of small molecules that target the interaction between RNA-binding proteins (RBPs) and RNA is progressing rapidly and represents a novel strategy for the discovery of chemical probes that facilitate understanding of the cellular functions of RBPs and of therapeutic agents with new mechanisms of action. In this Review, I present a current overview of targeting emerging RBPs using small-molecule inhibitors and recent progress in this burgeoning field. Small-molecule inhibitors that were reported for three representative emerging classes of RBPs, the microRNA-binding protein LIN28, the single-stranded or double-stranded RNA-binding Toll-like receptors and the CRISPR-associated (Cas) proteins, are highlighted from a medicinal-chemistry and chemical-biology perspective. However, although this field is burgeoning, challenges remain in the discovery and characterization of small-molecule inhibitors of RBPs.
Collapse
|
60
|
The structure of human GCN2 reveals a parallel, back-to-back kinase dimer with a plastic DFG activation loop motif. Biochem J 2020; 477:275-284. [PMID: 31868900 DOI: 10.1042/bcj20190196] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 12/10/2019] [Accepted: 12/23/2019] [Indexed: 11/17/2022]
Abstract
When activated by amino acid starvation, the stress sensing protein kinase GCN2 phosphorylates the eukaryotic initiation factor 2 alpha, inhibiting translation to conserve energy and facilitate cell survival. Amino acid starvation, particularly of tryptophan and arginine, affects immune tolerance by suppressing differentiation and proliferation of T-cells via activation of GCN2 kinase. In addition, the GCN2 pathway mediates cancer survival directly within the context of metabolic stress. Here, we report the first crystal structures of the human GCN2 kinase domain (KD) in complex with two inhibitors of different size, shape, and chemical scaffold. Three novel activation loop conformations representative of different activation states of the kinase are described. In addition, a novel dimerization organization for GCN2 is observed. This arrangement is consistent with the hypothesis that the GCN2 KD forms an antiparallel inactive dimer until uncharged tRNA binds to it and triggers conformational changes that shift the equilibrium to the active parallel dimer.
Collapse
|
61
|
Rodriguez S, Cao L, Rickenbacher GT, Benz EG, Magdamo C, Gomez LR, Holbrook EH, Albers AD, Gallagher R, Westover MB, Evans KE, Tatar DJ, Mukerji S, Zafonte R, Boyer EW, Yu CR, Albers MW. Innate immune signaling in the olfactory epithelium reduces odorant receptor levels: modeling transient smell loss in COVID-19 patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.06.14.20131128. [PMID: 32587994 PMCID: PMC7310652 DOI: 10.1101/2020.06.14.20131128] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Post-infectious anosmias typically follow death of olfactory sensory neurons (OSNs) with a months-long recovery phase associated with parosmias. While profound anosmia is the leading symptom associated with COVID-19 infection, many patients regain olfactory function within days to weeks without distortions. Here, we demonstrate that sterile induction of anti-viral type I interferon signaling in the mouse olfactory epithelium is associated with diminished odor discrimination and reduced odor-evoked local field potentials. RNA levels of all class I, class II, and TAAR odorant receptors are markedly reduced in OSNs in a non-cell autonomous manner. We find that people infected with COVID-19 rate odors with lower intensities and have odor discrimination deficits relative to people that tested negative for COVID-19. Taken together, we propose that inflammatory-mediated loss of odorant receptor expression with preserved circuit integrity accounts for the profound anosmia and rapid recovery of olfactory function without parosmias caused by COVID-19.
Collapse
Affiliation(s)
- Steven Rodriguez
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | - Luxiang Cao
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | | | - Eric G. Benz
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | - Colin Magdamo
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | | | - Eric H. Holbrook
- Dept. of Otolaryngology—Head and Neck Surgery, Mass. Eye and Ear, Boston, MA 02114
| | - Alefiya D. Albers
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
- Dept. of Psychology, Endicott College, Beverly, MA 01915
| | - Rose Gallagher
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | | | - Kyle E. Evans
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | | | - Shibani Mukerji
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| | - Ross Zafonte
- Dept. of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Boston, MA 02129
| | - Edward W Boyer
- Dept. of Emergency Medicine, Brigham and Women’s Hospital, Boston, MA 02115
| | - C. Ron Yu
- Stowers Institute of Medical Research, Kansas City, MO 64110
| | - Mark W. Albers
- Dept. of Neurology, Massachusetts General Hospital, Boston, MA 02129
| |
Collapse
|
62
|
Horvath A, Miskei M, Ambrus V, Vendruscolo M, Fuxreiter M. Sequence-based prediction of protein binding mode landscapes. PLoS Comput Biol 2020; 16:e1007864. [PMID: 32453748 PMCID: PMC7304629 DOI: 10.1371/journal.pcbi.1007864] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/19/2020] [Accepted: 04/09/2020] [Indexed: 02/04/2023] Open
Abstract
Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred (http://protdyn-fuzpred.org) algorithm to predict the range of context-dependent binding modes of proteins from their amino acid sequences. As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways. Great advances have been made in the last several decades in deciphering how the behavior of proteins is encoded in their amino acid sequences. A variety of sequence-based prediction methods have been developed to estimate a wide range of properties of proteins, including secondary structure propensity, native state structures, preference for being disordered and tendency to aggregate. Much less is known, however, about the rules that regulate the conformational changes of proteins upon binding. In particular, many proteins change their binding modes upon interacting with different partners, or as a consequence of post-translational modifications or changes in the cellular milieu. Here we address the problem of how amino acid sequences can encode different binding modes depending on their binding partners, and describe the FuzPred method of predicting context-dependent binding modes.
Collapse
Affiliation(s)
- Attila Horvath
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Marton Miskei
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Viktor Ambrus
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (MV); (MF)
| | - Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
- * E-mail: (MV); (MF)
| |
Collapse
|
63
|
Subramanian G, Popli S, Chakravarty S, Taylor RT, Chakravarti R, Chattopadhyay S. The interferon-inducible protein TDRD7 inhibits AMP-activated protein kinase and thereby restricts autophagy-independent virus replication. J Biol Chem 2020; 295:6811-6822. [PMID: 32273341 DOI: 10.1074/jbc.ra120.013533] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/03/2020] [Indexed: 12/25/2022] Open
Abstract
The interferon system is the first line of defense against virus infection. Recently, using a high-throughput genetic screen of a human interferon-stimulated gene short-hairpin RNA library, we identified a viral restriction factor, TDRD7 (Tudor domain-containing 7). TDRD7 inhibits the paramyxo-/pneumoviruses (e.g. Sendai virus and respiratory syncytial virus) by interfering with the virus-induced cellular autophagy pathway, which these viruses use for their replication. Here, we report that TDRD7 is a viral restriction factor against herpes simplex virus (HSV-1). Using knockdown, knockout, and ectopic expression systems, we demonstrate the anti-HSV-1 activity of TDRD7 in multiple human and mouse cell types. TDRD7 inhibited the virus-activated AMP-activated protein kinase (AMPK), which was essential for HSV-1 replication. Genetic ablation or chemical inhibition of AMPK activity suppressed HSV-1 replication in multiple human and mouse cells. Mechanistically, HSV-1 replication after viral entry depended on AMPK but not on its function in autophagy. The antiviral activity of TDRD7 depended on its ability to inhibit virus-activated AMPK. In summary, our results indicate that the newly identified viral restriction factor TDRD7 inhibits AMPK and thereby blocks HSV-1 replication independently of the autophagy pathway. These findings suggest that AMPK inhibition represents a potential strategy to manage HSV-1 infections.
Collapse
Affiliation(s)
- Gayatri Subramanian
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - Sonam Popli
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - Sukanya Chakravarty
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - R Travis Taylor
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - Ritu Chakravarti
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| |
Collapse
|
64
|
Yeung W, Ruan Z, Kannan N. Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease. IUBMB Life 2020; 72:1189-1202. [PMID: 32101380 DOI: 10.1002/iub.2253] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
The faithful propagation of cellular signals in most organisms relies on the coordinated functions of a large family of protein kinases that share a conserved catalytic domain. The catalytic domain is a dynamic scaffold that undergoes large conformational changes upon activation. Most of these conformational changes, such as movement of the regulatory αC-helix from an "out" to "in" conformation, hinge on a conserved, but understudied, loop termed the αC-β4 loop, which mediates conserved interactions to tether flexible structural elements to the kinase core. We previously showed that the αC-β4 loop is a unique feature of eukaryotic protein kinases. Here, we review the emerging roles of this loop in kinase structure, function, regulation, and diseases. Through a kinome-wide analysis, we define the boundaries of the loop for the first time and show that sequence and structural variation in the loop correlate with conformational and regulatory variation. Many recurrent disease mutations map to the αC-β4 loop and contribute to drug resistance and abnormal kinase activation by relieving key auto-inhibitory interactions associated with αC-helix and inter-lobe movement. The αC-β4 loop is a hotspot for post-translational modifications, protein-protein interaction, and Hsp90 mediated folding. Our kinome-wide analysis provides insights for hypothesis-driven characterization of understudied kinases and the development of allosteric protein kinase inhibitors.
Collapse
Affiliation(s)
- Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia
| |
Collapse
|
65
|
Avian Pattern Recognition Receptor Sensing and Signaling. Vet Sci 2020; 7:vetsci7010014. [PMID: 32012730 PMCID: PMC7157566 DOI: 10.3390/vetsci7010014] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/16/2020] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
Pattern recognition receptors (PRRs) are a class of immune sensors that play a critical role in detecting and responding to several conserved patterns of microorganisms. As such, they play a major role in the maintenance of immune homeostasis and anti-microbial defense. Fundamental knowledge pertaining to the discovery of PRR functions and their ligands continue to advance the understanding of immune system and disease resistance, which led to the rational design and/or application of various PRR ligands as vaccine adjuvants. In addition, the conserved nature of many PRRs throughout the animal kingdom has enabled the utilization of the comparative genomics approach in PRR identification and the study of evolution, structural features, and functions in many animal species including avian. In the present review, we focused on PRR sensing and signaling functions in the avian species, domestic chicken, mallard, and domestic goose. In addition to summarizing recent advances in the understanding of avian PRR functions, the present review utilized a comparative biology approach to identify additional PRRs, whose functions have been well studied in mammalians but await functional characterization in avian.
Collapse
|
66
|
Poxvirus encoded eIF2α homolog, K3 family proteins, is a key determinant of poxvirus host species specificity. Virology 2019; 541:101-112. [PMID: 32056708 DOI: 10.1016/j.virol.2019.12.008] [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: 10/04/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/24/2022]
Abstract
Protein kinase R plays a key role in innate antiviral immune responses of vertebrate animals. Most mammalian poxviruses encode two PKR antagonists, E3 (dsRNA binding) and K3 (eIF2α homolog) proteins. In this study, the role of K3 family proteins from poxviruses with distinct host tropisms in determining the virus host range was examined in a vaccinia E3L deletion mutant virus. It was found that K3 orthologs from the species-specific poxviruses (taterapox virus, sheeppox virus, myxoma virus, swinepox virus and yaba monkey tumor virus) restored the virus replication competency in cells derived from their natural hosts or related animal species. Further, it was found that the residues located in the helix insert region of the protein, K45 of vaccinia K3 and Y47 of the sheep poxvirus ortholog 011, are critical for the virus host species specificity. These observations demonstrate that poxvirus K3 proteins are major determinants of the virus host specificity.
Collapse
|
67
|
Kashiwagi K, Yokoyama T, Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Shirouzu M, Ito T. Structural basis for eIF2B inhibition in integrated stress response. Science 2019; 364:495-499. [PMID: 31048492 DOI: 10.1126/science.aaw4104] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/05/2019] [Indexed: 01/02/2023]
Abstract
A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5'-triphosphate-dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo-electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B.
Collapse
Affiliation(s)
- Kazuhiro Kashiwagi
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takeshi Yokoyama
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Madoka Nishimoto
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mari Takahashi
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Ayako Sakamoto
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mayumi Yonemochi
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuhiro Ito
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| |
Collapse
|
68
|
Niehl A, Heinlein M. Perception of double-stranded RNA in plant antiviral immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:1203-1210. [PMID: 30942534 PMCID: PMC6715784 DOI: 10.1111/mpp.12798] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
RNA silencing and antiviral pattern-triggered immunity (PTI) both rely on recognition of double-stranded (ds)RNAs as defence-inducing signals. While dsRNA recognition by dicer-like proteins during antiviral RNA silencing is thoroughly investigated, the molecular mechanisms involved in dsRNA perception leading to antiviral PTI are just about to be untangled. Parallels to antimicrobial PTI thereby only partially facilitate our view on antiviral PTI. PTI against microbial pathogens involves plasma membrane bound receptors; however, dsRNAs produced during virus infection occur intracellularly. Hence, how dsRNA may be perceived during this immune response is still an open question. In this short review, we describe recent discoveries in PTI signalling upon sensing of microbial patterns and endogenous 'danger' molecules with emphasis on immune signalling-associated subcellular trafficking processes in plants. Based on these studies, we develop different scenarios how dsRNAs could be sensed during antiviral PTI.
Collapse
Affiliation(s)
- Annette Niehl
- Julius Kühn‐Institute, Institute for Epidemiology and Pathogen DiagnosticsMesseweg 11‐12D‐38104BraunschweigGermany
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR235712 rue du Général ZimmerF‐67000StrasbourgFrance
| |
Collapse
|
69
|
Lamers MM, van den Hoogen BG, Haagmans BL. ADAR1: "Editor-in-Chief" of Cytoplasmic Innate Immunity. Front Immunol 2019; 10:1763. [PMID: 31404141 PMCID: PMC6669771 DOI: 10.3389/fimmu.2019.01763] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Specialized receptors that recognize molecular patterns such as double stranded RNA duplexes-indicative of viral replication-are potent triggers of the innate immune system. Although their activation is beneficial during viral infection, RNA transcribed from endogenous mobile genetic elements may also act as ligands potentially causing autoimmunity. Recent advances indicate that the adenosine deaminase ADAR1 through RNA editing is involved in dampening the canonical antiviral RIG-I-like receptor-, PKR-, and OAS-RNAse L pathways to prevent autoimmunity. However, this inhibitory effect must be overcome during viral infections. In this review we discuss ADAR1's critical role in balancing immune activation and self-tolerance.
Collapse
|
70
|
Ahuja LG, Aoto PC, Kornev AP, Veglia G, Taylor SS. Dynamic allostery-based molecular workings of kinase:peptide complexes. Proc Natl Acad Sci U S A 2019; 116:15052-15061. [PMID: 31285328 PMCID: PMC6660753 DOI: 10.1073/pnas.1900163116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A dense interplay between structure and dynamics underlies the working of proteins, especially enzymes. Protein kinases are molecular switches that are optimized for their regulation rather than catalytic turnover rates. Using long-simulations dynamic allostery analysis, this study describes an exploration of the dynamic kinase:peptide complex. We have used protein kinase A (PKA) as a model system as a generic prototype of the protein kinase superfamily of signaling enzymes. Our results explain the role of dynamic coupling of active-site residues that must work in coherence to provide for a successful activation or inhibition response from the kinase. Amino acid networks-based community analysis allows us to ponder the conformational entropy of the kinase:nucleotide:peptide ternary complex. We use a combination of 7 peptides that include 3 types of PKA-binding partners: Substrates, products, and inhibitors. The substrate peptides provide for dynamic insights into the enzyme:substrate complex, while the product phospho-peptide allows for accessing modes of enzyme:product release. Mapping of allosteric communities onto the PKA structure allows us to locate the more unvarying and flexible dynamic regions of the kinase. These distributions, when correlated with the structural elements of the kinase core, allow for a detailed exploration of key dynamics-based signatures that could affect peptide recognition and binding at the kinase active site. These studies provide a unique dynamic allostery-based perspective to kinase:peptide complexes that have previously been explored only in a structural or thermodynamic context.
Collapse
Affiliation(s)
- Lalima G Ahuja
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093;
| | - Phillip C Aoto
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Alexandr P Kornev
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Susan S Taylor
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093;
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| |
Collapse
|
71
|
Mayo CB, Erlandsen H, Mouser DJ, Feinstein AG, Robinson VL, May ER, Cole JL. Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry 2019; 58:2967-2977. [PMID: 31246429 DOI: 10.1021/acs.biochem.9b00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The RNA-activated protein kinase, PKR, is a key mediator of the innate immunity response to viral infection. Viral double-stranded RNAs induce PKR dimerization and autophosphorylation. The PKR kinase domain forms a back-to-back dimer. However, intermolecular ( trans) autophosphorylation is not feasible in this arrangement. We have obtained PKR kinase structures that resolves this dilemma. The kinase protomers interact via the known back-to-back interface as well as a front-to-front interface that is formed by exchange of activation segments. Mutational analysis of the front-to-front interface support a functional role in PKR activation. Molecular dynamics simulations reveal that the activation segment is highly dynamic in the front-to-front dimer and can adopt conformations conducive to phosphoryl transfer. We propose a mechanism where back-to-back dimerization induces a conformational change that activates PKR to phosphorylate a "substrate" kinase docked in a front-to-front geometry. This mechanism may be relevant to related kinases that phosphorylate the eukaryotic initiation factor eIF2α.
Collapse
|
72
|
Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome. Nature 2019; 570:338-343. [PMID: 31189953 PMCID: PMC6774351 DOI: 10.1038/s41586-019-1295-z] [Citation(s) in RCA: 462] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/16/2019] [Indexed: 01/01/2023]
Abstract
The NLRP3 inflammasome can be activated by diverse stimuli, including nigericin, uric acid crystals, amyloid-β fibrils, and extracellular ATP. The mitotic kinase NEK7 licenses NLRP3 inflammasome assembly and activation in the interphase. Here we report a 3.8-Å cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7. The earring-shaped NLRP3 consists of curved leucine-rich repeat (LRR) and globular NACHT domains, whereas the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations on this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7KO or NLRP3KO cells. Taken together, these data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate NLRP3 inflammasome activation.
Collapse
|
73
|
Pereira CM, Filev R, Dubiela FP, Brandão BB, Queiroz CM, Ludwig RG, Hipolide D, Longo BM, Mello LE, Mori MA, Castilho BA. The GCN2 inhibitor IMPACT contributes to diet-induced obesity and body temperature control. PLoS One 2019; 14:e0217287. [PMID: 31166980 PMCID: PMC6550387 DOI: 10.1371/journal.pone.0217287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/08/2019] [Indexed: 12/20/2022] Open
Abstract
IMPACT, a highly conserved protein, is an inhibitor of the eIF2α kinase GCN2. In mammals, it is preferentially expressed in neurons. Knock-down of IMPACT expression in neuronal cells increases basal GCN2 activation and eIF2α phosphorylation and decreases translation initiation. In the mouse brain, IMPACT is particularly abundant in the hypothalamus. Here we describe that the lack of IMPACT in mice affects hypothalamic functions. Impact-/- mice (Imp-KO) are viable and have no apparent major phenotypic defect. The hypothalamus in these animals shows increased levels of eIF2α phosphorylation, as expected from the described role of IMPACT in inhibiting GCN2 and from its abundance in this brain region. When fed a normal chow, animals lacking IMPACT weight slightly less than wild-type mice. When fed a high-fat diet, Imp-KO animals gain substantially less weight due to lower food intake when compared to wild-type mice. STAT3 signaling was depressed in Imp-KO animals even though leptin levels were identical to the wild-type mice. This finding supports the observation that Imp-KO mice have defective thermoregulation upon fasting. This phenotype was partially dependent on GCN2, whereas the lean phenotype was independent of GCN2. Taken together, our results indicate that IMPACT contributes to GCN2-dependent and -independent mechanisms involved in the regulation of autonomic functions in response to energy availability.
Collapse
Affiliation(s)
- Catia M. Pereira
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renato Filev
- Department of Physiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Francisco P. Dubiela
- Department of Psychobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bruna B. Brandão
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudio M. Queiroz
- Brain Institute, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Raissa G. Ludwig
- Department of Biochemistry and Tissue Biology, UNICAMP, Campinas, Brazil
| | - Debora Hipolide
- Department of Psychobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Beatriz M. Longo
- Department of Physiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Luiz E. Mello
- Department of Physiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marcelo A. Mori
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Beatriz A. Castilho
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- * E-mail:
| |
Collapse
|
74
|
The structural basis of translational control by eIF2 phosphorylation. Nat Commun 2019; 10:2136. [PMID: 31086188 PMCID: PMC6513899 DOI: 10.1038/s41467-019-10167-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/23/2019] [Indexed: 12/17/2022] Open
Abstract
Protein synthesis in eukaryotes is controlled by signals and stresses via a common pathway, called the integrated stress response (ISR). Phosphorylation of the translation initiation factor eIF2 alpha at a conserved serine residue mediates translational control at the ISR core. To provide insight into the mechanism of translational control we have determined the structures of eIF2 both in phosphorylated and unphosphorylated forms bound with its nucleotide exchange factor eIF2B by electron cryomicroscopy. The structures reveal that eIF2 undergoes large rearrangements to promote binding of eIF2α to the regulatory core of eIF2B comprised of the eIF2B alpha, beta and delta subunits. Only minor differences are observed between eIF2 and eIF2αP binding to eIF2B, suggesting that the higher affinity of eIF2αP for eIF2B drives translational control. We present a model for controlled nucleotide exchange and initiator tRNA binding to the eIF2/eIF2B complex. During the integrated stress response, translation is modulated through the phosphorylation of translation initiation factor eIF2 and the formation of a complex with eIF2B. Here the authors present structures of the eIF2:eIF2B complex with and without phosphorylation, shedding light on how eIF2 phosphorylation regulates translation.
Collapse
|
75
|
Bou-Nader C, Gordon JM, Henderson FE, Zhang J. The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA (NEW YORK, N.Y.) 2019; 25:539-556. [PMID: 30770398 PMCID: PMC6467004 DOI: 10.1261/rna.070169.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The interferon-inducible protein kinase R (PKR) is a key component of host innate immunity that restricts viral replication and propagation. As one of the four eIF2α kinases that sense diverse stresses and direct the integrated stress response (ISR) crucial for cell survival and proliferation, PKR's versatile roles extend well beyond antiviral defense. Targeted by numerous host and viral regulators made of RNA and proteins, PKR is subject to multiple layers of endogenous control and external manipulation, driving its rapid evolution. These versatile regulators include not only the canonical double-stranded RNA (dsRNA) that activates the kinase activity of PKR, but also highly structured viral, host, and artificial RNAs that exert a full spectrum of effects. In this review, we discuss our deepening understanding of the allosteric mechanism that connects the regulatory and effector domains of PKR, with an emphasis on diverse structured RNA regulators in comparison to their protein counterparts. Through this analysis, we conclude that much of the mechanistic details that underlie this RNA-regulated kinase await structural and functional elucidation, upon which we can then describe a "PKR code," a set of structural and chemical features of RNA that are both descriptive and predictive for their effects on PKR.
Collapse
Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| |
Collapse
|
76
|
Wong AW, Urisman A, Burlingame AL, Shokat KM. Chemically reprogramming the phospho-transfer reaction to crosslink protein kinases to their substrates. Protein Sci 2019; 28:654-662. [PMID: 30636329 PMCID: PMC6371225 DOI: 10.1002/pro.3570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022]
Abstract
The proteomic mapping of enzyme-substrate interactions is challenged by their transient nature. A method to capture interacting protein kinases in complexes with a single substrate of interest would provide a new tool for mapping kinase signaling networks. Here, we describe a nucleotide-based substrate analog capable of reprogramming the wild-type phosphoryl-transfer reaction to produce a kinase-acrylamide-based thioether crosslink to mutant substrates with a cysteine nucleophile substituted at the native phosphorylation site. A previously reported ATP-based methacrylate crosslinker (ATP-MA) was capable of mediating kinase crosslinking to short peptides but not protein substrates. Exploration of structural variants of ATP-MA to enable crosslinking of protein substrates to kinases led to the discovery that an ADP-based methacrylate (ADP-MA) crosslinker was superior to the ATP scaffold at crosslinking in vitro. The improved efficiency of ADP-MA over ATP-MA is due to reduced inhibition of the second step of the kinase-substrate crosslinking reaction by the product of the first step of the reaction. The new probe, ADP-MA, demonstrated enhanced in vitro crosslinking between the Src tyrosine kinase and its substrate Cortactin in a phosphorylation site-specific manner. The kinase-substrate crosslinking reaction can be carried out in a complex mammalian cell lysate setting, although the low abundance of endogenous kinases remains a significant challenge for efficient capture.
Collapse
Affiliation(s)
- Allison W. Wong
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCalifornia
| | - Anatoly Urisman
- Department of PathologyUniversity of California San FranciscoSan FranciscoCalifornia
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCalifornia
| | - Alma L. Burlingame
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCalifornia
| | - Kevan M. Shokat
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCalifornia
- Howard Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCalifornia
| |
Collapse
|
77
|
Bober P, Tomková Z, Alexovič M, Ropovik I, Sabo J. The unfolded protein response controls endoplasmic reticulum stress-induced apoptosis of MCF-7 cells via a high dose of vitamin C treatment. Mol Biol Rep 2019; 46:1275-1284. [PMID: 30694453 DOI: 10.1007/s11033-019-04598-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/07/2019] [Indexed: 12/11/2022]
Abstract
Recent in vitro studies have shown that vitamin C (Vit C) with pro-oxidative properties causes cytotoxicity of breast cancer cells by selective oxidative stress. However, the effect of Vit C in itself at different concentration levels on MCF-7 breast cancer cell line after 24 h, has not yet been described. We aimed to examine the effect of Vit C on the viability and signalling response of MCF-7/WT (MCF-7 wild-type) cells that were exposed to various concentrations (0.125-4 mM) of Vit C during 24 h. The cytotoxic effect of Vit C on MCF-7/VitC (MCF-7/WT after added 2 mM Vit C) was observed, resulting in a decrease of cell index after 12 h. Also, the cytotoxicity of Vit C (2 mM) after 24 h was confirmed by flow cytometry, i.e., increase of dead, late apoptotic, and depolarized dead MCF-7/VitC cells compared to MCF-7/WT cells. Moreover, changes in proteomic profile of MCF-7/VitC cells compared to the control group were investigated via label-free quantitative mass spectrometry and post-translational modification. Using bioinformatics assessment (i.e., iPathwayGuide and SPIA R packages), a significantly impacted pathway in MCF-7/VitC was identified, namely the protein processing in endoplasmic reticulum. The semi-quantitative change (log2fold change = 4.5) and autophosphorylation at Thr-446 of protein kinase (PKR) (involved in this pathway) indicates that PKR protein could be responsible for the unfolded protein response and inhibition of the cell translation during endoplasmic reticulum stress, and eventually, for cell apoptosis. These results suggest that increased activity of PKR (Thr-446 autophosphorylation) related to cytotoxic effect of Vit C (2 mM) may cause the MCF-7 cells death.
Collapse
Affiliation(s)
- Peter Bober
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Trieda SNP 1, 04011, Košice, Slovakia.
| | - Zuzana Tomková
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Trieda SNP 1, 04011, Košice, Slovakia
| | - Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Trieda SNP 1, 04011, Košice, Slovakia
| | - Ivan Ropovik
- Department of Pre-school and Elementary Education and Psychology, Faculty of Education, University of Presov, 17. novembra 15, 08001, Presov, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Trieda SNP 1, 04011, Košice, Slovakia
| |
Collapse
|
78
|
Abstract
Detection of double-stranded RNAs (dsRNAs) is a central mechanism of innate immune defense in many organisms. We here discuss several families of dsRNA-binding proteins involved in mammalian antiviral innate immunity. These include RIG-I-like receptors, protein kinase R, oligoadenylate synthases, adenosine deaminases acting on RNA, RNA interference systems, and other proteins containing dsRNA-binding domains and helicase domains. Studies suggest that their functions are highly interdependent and that their interdependence could offer keys to understanding the complex regulatory mechanisms for cellular dsRNA homeostasis and antiviral immunity. This review aims to highlight their interconnectivity, as well as their commonalities and differences in their dsRNA recognition mechanisms.
Collapse
Affiliation(s)
- Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| |
Collapse
|
79
|
Real-time 2-5A kinetics suggest that interferons β and λ evade global arrest of translation by RNase L. Proc Natl Acad Sci U S A 2019; 116:2103-2111. [PMID: 30655338 DOI: 10.1073/pnas.1818363116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cells of all mammals recognize double-stranded RNA (dsRNA) as a foreign material. In response, they release interferons (IFNs) and activate a ubiquitously expressed pseudokinase/endoribonuclease RNase L. RNase L executes regulated RNA decay and halts global translation. Here, we developed a biosensor for 2',5'-oligoadenylate (2-5A), the natural activator of RNase L. Using this biosensor, we found that 2-5A was acutely synthesized by cells in response to dsRNA sensing, which immediately triggered cellular RNA cleavage by RNase L and arrested host protein synthesis. However, translation-arrested cells still transcribed IFN-stimulated genes and secreted IFNs of types I and III (IFN-β and IFN-λ). Our data suggest that IFNs escape from the action of RNase L on translation. We propose that the 2-5A/RNase L pathway serves to rapidly and accurately suppress basal protein synthesis, preserving privileged production of defense proteins of the innate immune system.
Collapse
|
80
|
Park C, Peng C, Brennan G, Rothenburg S. Species-specific inhibition of antiviral protein kinase R by capripoxviruses and vaccinia virus. Ann N Y Acad Sci 2019; 1438:18-29. [PMID: 30644558 DOI: 10.1111/nyas.14000] [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: 11/09/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
Abstract
Double-stranded RNA-activated protein kinase R (PKR) is an important and rapidly evolving antiviral kinase. Most poxviruses contain two distinct PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), the prototypic orthopoxvirus. E3 prevents PKR homodimerization by binding double-stranded RNA, while K3 acts as a pseudosubstrate inhibitor by binding directly to activated PKR and thereby inhibiting interaction with its substrate eIF2α. In our study here, we analyzed E3 and K3 orthologs from the phylogenetically distinct capripoxviruses (CaPVs), which include lumpy skin disease virus, sheeppox virus, and goatpox virus. Whereas the sheeppox virus E3 ortholog did not substantially inhibit PKR, all three CaPV K3 orthologs showed species-specific inhibition of PKR, with strong inhibition of sheep, goat, and human PKR but only weak inhibition of cow and mouse PKR. In contrast, VACV K3 strongly inhibited cow and mouse PKR but not sheep, goat, or human PKR. Infection of cell lines from the respective species with engineered VACV strains that contained different K3 orthologs showed a good correlation of PKR inhibition with virus replication and eIF2α phosphorylation. Our results show that K3 orthologs can have dramatically different effects on PKR of different species and indicate that effective PKR inhibition by K3 orthologs is crucial for virus replication.
Collapse
Affiliation(s)
- Chorong Park
- School of Medicine, Department of Medial Microbiology and Immunology, University of California Davis, Davis, California
| | - Chen Peng
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Greg Brennan
- School of Medicine, Department of Medial Microbiology and Immunology, University of California Davis, Davis, California
| | - Stefan Rothenburg
- School of Medicine, Department of Medial Microbiology and Immunology, University of California Davis, Davis, California
| |
Collapse
|
81
|
Gal-Ben-Ari S, Barrera I, Ehrlich M, Rosenblum K. PKR: A Kinase to Remember. Front Mol Neurosci 2019; 11:480. [PMID: 30686999 PMCID: PMC6333748 DOI: 10.3389/fnmol.2018.00480] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/10/2018] [Indexed: 12/26/2022] Open
Abstract
Aging is a major risk factor for many diseases including metabolic syndrome, cancer, inflammation, and neurodegeneration. Identifying mechanistic common denominators underlying the impact of aging is essential for our fundamental understanding of age-related diseases and the possibility to propose new ways to fight them. One can define aging biochemically as prolonged metabolic stress, the innate cellular and molecular programs responding to it, and the new stable or unstable state of equilibrium between the two. A candidate to play a role in the process is protein kinase R (PKR), first identified as a cellular protector against viral infection and today known as a major regulator of central cellular processes including mRNA translation, transcriptional control, regulation of apoptosis, and cell proliferation. Prolonged imbalance in PKR activation is both affected by biochemical and metabolic parameters and affects them in turn to create a feedforward loop. Here, we portray the central role of PKR in transferring metabolic information and regulating cellular function with a focus on cancer, inflammation, and brain function. Later, we integrate information from open data sources and discuss current knowledge and gaps in the literature about the signaling cascades upstream and downstream of PKR in different cell types and function. Finally, we summarize current major points and biological means to manipulate PKR expression and/or activation and propose PKR as a therapeutic target to shift age/metabolic-dependent undesired steady states.
Collapse
Affiliation(s)
- Shunit Gal-Ben-Ari
- Laboratory of Molecular and Cellular Mechanisms Underlying Learning and Memory, Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Iliana Barrera
- Laboratory of Molecular and Cellular Mechanisms Underlying Learning and Memory, Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Marcelo Ehrlich
- Laboratory of Intracellular Trafficking and Signaling, School of Molecular Cell Biology & Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kobi Rosenblum
- Laboratory of Molecular and Cellular Mechanisms Underlying Learning and Memory, Sagol Department of Neurobiology, University of Haifa, Haifa, Israel.,Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel
| |
Collapse
|
82
|
Kalaivani R, Narwani TJ, de Brevern AG, Srinivasan N. Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms. Protein Sci 2018; 28:543-560. [PMID: 30468265 DOI: 10.1002/pro.3556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/11/2018] [Accepted: 11/18/2018] [Indexed: 12/24/2022]
Abstract
Many protein kinases are characterized by at least two structural forms corresponding to the highest level of activity (active) and low or no activity, (inactive). Further, protein dynamics is an important consideration in understanding the molecular and mechanistic basis of enzyme function. In this work, we use protein kinase A (PKA) as the model system and perform microsecond range molecular dynamics (MD) simulations on six variants which differ from one another in terms of active and inactive form, with or without bound ligands, C-terminal tail and phosphorylation at the activation loop. We find that the root mean square fluctuations in the MD simulations are generally higher for the inactive forms than the active forms. This difference is statistically significant. The higher dynamics of inactive states has significant contributions from ATP binding loop, catalytic loop, and αG helix. Simulations with and without C-terminal tail show this differential dynamics as well, with lower dynamics both in the active and inactive forms if C-terminal tail is present. Similarly, the dynamics associated with the inactive form is higher irrespective of the phosphorylation status of Thr 197. A relatively stable stature of active kinases may be better suited for binding of substrates and detachment of the product. Also, phosphoryl group transfer from ATP to the phosphosite on the substrate requires precise transient coordination of chemical entities from three different molecules, which may be facilitated by the higher stability of the active state.
Collapse
Affiliation(s)
- R Kalaivani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - T J Narwani
- INSERM, U 1134, DSIMB, F-75739, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739, Paris, France.,Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.,Laboratoire d'Excellence GR-Ex, F-75739, Paris, France
| | - A G de Brevern
- INSERM, U 1134, DSIMB, F-75739, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739, Paris, France.,Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.,Laboratoire d'Excellence GR-Ex, F-75739, Paris, France
| | - N Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| |
Collapse
|
83
|
Shibazaki C, Arai S, Shimizu R, Saeki M, Kinoshita T, Ostermann A, Schrader TE, Kurosaki Y, Sunami T, Kuroki R, Adachi M. Hydration Structures of the Human Protein Kinase CK2α Clarified by Joint Neutron and X-ray Crystallography. J Mol Biol 2018; 430:5094-5104. [DOI: 10.1016/j.jmb.2018.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
|
84
|
Binding of eEF1A2 to the RNA-dependent protein kinase PKR modulates its activity and promotes tumour cell survival. Br J Cancer 2018; 119:1410-1420. [PMID: 30420615 PMCID: PMC6265344 DOI: 10.1038/s41416-018-0336-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022] Open
Abstract
Background Through several not-fully-characterised moonlighting functions, translation elongation factor eEF1A2 is known to provide a fitness boost to cancer cells. Furthermore, eEF1A2 has been demonstrated to confer neoplastic characteristics on preneoplastic, nontumourigenic precursor cells. We have previously shown that eEF1A2 is the target of plitidepsin, a marine drug currently in development for cancer treatment. Herein, we characterised a new signalling pathway through which eEF1A2 promotes tumour cell survival. Methods Previously unknown binding partners of eEF1A2 were identified through co-immunoprecipitation, high-performance liquid chromatography-mass spectrometry and proximity ligation assay. Using plitidepsin to release eEF1A2 from those protein complexes, their effects on cancer cell survival were analysed in vitro. Results We uncovered that double-stranded RNA-activated protein kinase (PKR) is a novel eEF1A2-interacting partner whose pro-apoptotic effect is hindered by the translation factor, most likely through sequestration and inhibition of its kinase activity. Targeting eEF1A2 with plitidepsin releases PKR from the complex, facilitating its activation and triggering a mitogen-activated protein kinase signalling cascade together with a nuclear factor-κB-dependent activation of the extrinsic apoptotic pathway, which lead to tumour cell death. Conclusions Through its binding to PKR, eEF1A2 provides a survival boost to cancer cells, constituting an Achilles heel that can be exploited in anticancer therapy.
Collapse
|
85
|
Uppala JK, Ghosh C, Sathe L, Dey M. Phosphorylation of translation initiation factor eIF2α at Ser51 depends on site- and context-specific information. FEBS Lett 2018; 592:3116-3125. [PMID: 30070006 DOI: 10.1002/1873-3468.13214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/09/2018] [Accepted: 07/27/2018] [Indexed: 01/29/2023]
Abstract
Protein kinases phosphorylate specific amino acid residues of substrate proteins and regulate many cellular processes. Specificity for phosphorylation depends on the accessibility of these residues, and more importantly, kinases have preferences for certain residues flanking the phospho-acceptor site. Translation initiation factor 2α [eukaryotic translation initiation factor 2α (eIF2α)] kinase phosphorylates serine51 (Ser51) of eIF2α and downregulates cellular protein synthesis. Structural information on eIF2α reveals that Ser51 is located within a flexible loop, referred to as the Ser51 loop. Recently, we have shown that conformational change of the Ser51 loop increases the accessibility of Ser51 to the kinase active site for phosphorylation. Here, we show that the specificity of Ser51 phosphorylation depends largely on its relative position in the Ser51 loop and minimally on the flanking residues.
Collapse
Affiliation(s)
| | - Chandrima Ghosh
- Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Leena Sathe
- Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
| |
Collapse
|
86
|
Xiong S, Lorenzen K, Couzens AL, Templeton CM, Rajendran D, Mao DYL, Juang YC, Chiovitti D, Kurinov I, Guettler S, Gingras AC, Sicheri F. Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment. Structure 2018; 26:1101-1115.e6. [PMID: 29983373 PMCID: PMC6087429 DOI: 10.1016/j.str.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 05/17/2018] [Indexed: 11/27/2022]
Abstract
The human NDR family kinases control diverse aspects of cell growth, and are regulated through phosphorylation and association with scaffolds such as MOB1. Here, we report the crystal structure of the human NDR1 kinase domain in its non-phosphorylated state, revealing a fully resolved atypically long activation segment that blocks substrate binding and stabilizes a non-productive position of helix αC. Consistent with an auto-inhibitory function, mutations within the activation segment of NDR1 dramatically enhance in vitro kinase activity. Interestingly, NDR1 catalytic activity is further potentiated by MOB1 binding, suggesting that regulation through modulation of the activation segment and by MOB1 binding are mechanistically distinct. Lastly, deleting the auto-inhibitory activation segment of NDR1 causes a marked increase in the association with upstream Hippo pathway components and the Furry scaffold. These findings provide a point of departure for future efforts to explore the cellular functions and the mechanism of NDR1.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Binding Sites
- Cell Cycle Proteins
- Cell Line, Tumor
- Cloning, Molecular
- Crystallography, X-Ray
- Epithelial Cells/cytology
- Epithelial Cells/enzymology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Hepatocyte Growth Factor/chemistry
- Hepatocyte Growth Factor/genetics
- Hepatocyte Growth Factor/metabolism
- Humans
- Kinetics
- Microtubule-Associated Proteins/chemistry
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Serine-Threonine Kinases/chemistry
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Serine-Threonine Kinase 3
- Signal Transduction
- Substrate Specificity
Collapse
Affiliation(s)
- Shawn Xiong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristina Lorenzen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Catherine M Templeton
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Daniel Y L Mao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Yu-Chi Juang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - David Chiovitti
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, NE-CAT, Advanced Photon Source, Bldg. 436E, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
87
|
Gu L, Ge Z, Wang Y, Shen M, Zhao P, Chen W. Double-stranded RNA-dependent kinase PKR activates NF-κB pathway in acute pancreatitis. Biochem Biophys Res Commun 2018; 503:1563-1569. [PMID: 30031606 DOI: 10.1016/j.bbrc.2018.07.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/04/2023]
Abstract
The activation of transcription factor nuclear factor kappa B (NF-κB) occurs early in acute pancreatitis (AP) simultaneously with intracellular trypsinogen activation. Double-stranded RNA-dependent kinase (PKR) promotes the activation of NF-κB and the production of pro-inflammatory factors including tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). The rat and rat pancreatic AR42J cells were treated by cerulein to establish AP models, showing PKR increased. TNF-α, IL-6 and lactate dehydrogenase (LDH) in AP pancreatic tissues and cerulein-treated AR42J cells increased, while PKR knockdown in AR42J cells reversed cerulein-induced inflammatory response and pancreatic cell injury. In addition, inhibitor of kappa B kinase α (IKKα), phosphorylated P65 (p-P65), P65 increased in cerulein-treated AR42J cells. Meanwhile, in cerulein-treated AR42J cells, interaction between PKR and IKKα, as well as the co-localization and nuclear accumulation of PKR and P65, were detected. Furthermore, cerulein induced the phosphorylation and nuclear translocation of P65, which indicated the activation of NF-κB, while PKR knockdown hindered NF-κB activation to alleviate pancreatic cell injury. In summary, PKR might promote NF-κB activation via facilitating its phosphorylation and nuclear translocation, thus accelerated inflammatory response and pancreatic cell injury in AP, implying a novel molecular target for the treatment of AP.
Collapse
Affiliation(s)
- Liugen Gu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China; Department of Gastroenterology, The Second Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Zhenming Ge
- Department of Gastroenterology, The Second Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Yamin Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Meiqin Shen
- Department of Gastroenterology, The Second Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Ping Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Weichang Chen
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
| |
Collapse
|
88
|
Pavitt GD. Regulation of translation initiation factor eIF2B at the hub of the integrated stress response. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1491. [PMID: 29989343 DOI: 10.1002/wrna.1491] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/08/2018] [Accepted: 05/22/2018] [Indexed: 12/29/2022]
Abstract
Phosphorylation of the translation initiation factor eIF2 is one of the most widely used and well-studied mechanisms cells use to respond to diverse cellular stresses. Known as the integrated stress response (ISR), the control pathway uses modulation of protein synthesis to reprogram gene expression and restore homeostasis. Here the current knowledge of the molecular mechanisms of eIF2 activation and its control by phosphorylation at a single-conserved phosphorylation site, serine 51 are discussed with a major focus on the regulatory roles of eIF2B and eIF5 where a current molecular view of ISR control of eIF2B activity is presented. How genetic disorders affect eIF2 or eIF2B is discussed, as are syndromes where excess signaling through the ISR is a component. Finally, studies into the action of recently identified compounds that modulate the ISR in experimental systems are discussed; these suggest that eIF2B is a potential therapeutic target for a wide range of conditions. This article is categorized under: Translation > Translation Regulation.
Collapse
Affiliation(s)
- Graham D Pavitt
- Division Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| |
Collapse
|
89
|
Melzer AM, Palanisamy N. Deleterious single nucleotide polymorphisms of protein kinase R identified by the computational approach. Mol Immunol 2018; 101:65-73. [PMID: 29879548 DOI: 10.1016/j.molimm.2018.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/14/2018] [Accepted: 05/28/2018] [Indexed: 10/14/2022]
Abstract
The human protein kinase R (PKR) recognizes invading RNA viruses and mediates the antiviral immune response by phosphorylating the eukaryotic translation initiation factor 2α (eIF-2α), thus blocking protein translation in infected cells and thus preventing viral replication. The observation that individuals show different degrees of susceptibility to viral infections gives rise to the hypothesis that single nucleotide polymorphisms (SNPs) in the protein kinase R may alter the response to an infection. Using different available servers (e.g. SIFT, PROVEAN, Polyphen2, SNAP2, SNP&GOs, SNP-PhD, I-Mutant Suite), 14 SNPs were identified that were predicted to have deleterious effects on the protein kinase R. Five SNPs, namely D266Y, Y323D, I398 K, Y465C and Y472C, were selected for homology modeling and the generated models were investigated with regard to their secondary structure, residue fluctuations and eIF-2α binding. Analysis with computational tools POLYVIEW-MM, SAAPdap, SRIDE, CMView, elNémo, NMsim and PatchDock revealed structural changes in all mutants yielding a more stable structure at the cost of reduced flexibility (except Y465C) and less conformational freedom compared to the native protein. The conformational changes in the mutant protein structures and the displacement of functional residues from their strategic positions are predicted to affect the functionality of PKR, and consequently will affect the efficiency of the individual's antiviral immune response negatively. This study will aid the physicians in precision medicine field to tailor optimal treatment for the patients.
Collapse
Affiliation(s)
- Anna Maria Melzer
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Navaneethan Palanisamy
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany; HBIGS, University of Heidelberg, Heidelberg, Germany; Institute of Biology II, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
90
|
Dzananovic E, McKenna SA, Patel TR. Viral proteins targeting host protein kinase R to evade an innate immune response: a mini review. Biotechnol Genet Eng Rev 2018; 34:33-59. [PMID: 29716441 DOI: 10.1080/02648725.2018.1467151] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The innate immune system offers a first line of defense by neutralizing foreign pathogens such as bacteria, fungi, and viruses. These pathogens express molecules (RNA and proteins) that have discrete structures, known as the pathogen-associated molecular patterns that are recognized by a highly specialized class of host proteins called pattern recognition receptors to facilitate the host's immune response against infection. The RNA-dependent Protein Kinase R (PKR) is one of the host's pattern recognition receptors that is a key component of an innate immune system. PKR recognizes imperfectly double-stranded non-coding viral RNA molecules via its N-terminal double-stranded RNA binding motifs, undergoes phosphorylation of the C-terminal kinase domain, ultimately resulting in inhibition of viral protein translation by inhibiting the guanine nucleotide exchange activity of eukaryotic initiation factor 2α. Not surprisingly, viruses have evolved mechanisms by which viral non-coding RNA or protein molecules inhibit PKR's activation and/or its downstream activity to allow viral replication. In this review, we will highlight the role of viral proteins in inhibiting PKR's activity and summarize currently known mechanisms by which viral proteins execute such inhibitory activity.
Collapse
Affiliation(s)
- Edis Dzananovic
- a Plant Pathology, Plant Protection and Molecular Biology , Agriculture and Agri-Food Canada , Saskatoon , Canada
| | - Sean A McKenna
- b Department of Chemistry, Manitoba Institute for Materials, Department of Biochemistry and Medical Genetics , University of Manitoba , Winnipeg , Canada
| | - Trushar R Patel
- c Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada.,d DiscoveryLab, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada.,e Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada
| |
Collapse
|
91
|
Shen K, Johnson DW, Vesey DA, McGuckin MA, Gobe GC. Role of the unfolded protein response in determining the fate of tumor cells and the promise of multi-targeted therapies. Cell Stress Chaperones 2018; 23:317-334. [PMID: 28952072 PMCID: PMC5904077 DOI: 10.1007/s12192-017-0844-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
Although there have been advances in our understanding of carcinogenesis and development of new treatments, cancer remains a common cause of death. Many regulatory pathways are incompletely understood in cancer development and progression, with a prime example being those related to the endoplasmic reticulum (ER). The pathological sequelae that arise from disruption of ER homeostasis are not well defined. The ER is an organelle that is responsible for secretory protein biosynthesis and the quality control of protein folding. The ER triggers an unfolded protein response (UPR) when misfolded proteins accumulate, and while the UPR acts to restore protein folding and ER homeostasis, this response can work as a switch to determine the death or survival of cells. The treatment of cancer with agents that target the UPR has shown promising outcomes. The UPR has wide crosstalk with other signaling pathways. Multi-targeted cancer therapies which target the intersections within signaling networks have shown synergistic tumoricidal effects. In the present review, the basic cellular and signaling pathways of the ER and UPR are introduced; then the crosstalk between the ER and other signaling pathways is summarized; and ultimately, the evidence that the UPR is a potential target for cancer therapy is discussed. Regulation of the UPR downstream signaling is a common therapeutic target for different tumor types. Tumoricidal effects achieved from modulating the UPR downstream signaling could be enhanced by phosphodiesterase 5 (PDE5) inhibitors. Largely untapped by Western medicine for cancer therapies are Chinese herbal medicines. This review explores and discusses the value of some Chinese herbal extracts as PDE5 inhibitors.
Collapse
Affiliation(s)
- Kunyu Shen
- Kidney Disease Research Group, UQ Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, Brisbane, 4102, Australia
| | - David W Johnson
- Kidney Disease Research Group, UQ Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, Brisbane, 4102, Australia
- Department of Nephrology, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - David A Vesey
- Department of Nephrology, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Michael A McGuckin
- Mucosal Disease Inflammatory Disease Biology and Therapeutics Group, UQ Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Glenda C Gobe
- Kidney Disease Research Group, UQ Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent Street, Woolloongabba, Brisbane, 4102, Australia.
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.
| |
Collapse
|
92
|
Stroehlein AJ, Young ND, Gasser RB. Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes. Biotechnol Adv 2018; 36:915-934. [PMID: 29477756 DOI: 10.1016/j.biotechadv.2018.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Protein kinases are enzymes that play essential roles in the regulation of many cellular processes. Despite expansions in the fields of genomics, transcriptomics and bioinformatics, there is limited information on the kinase complements (kinomes) of most eukaryotic organisms, including parasitic worms that cause serious diseases of humans and animals. The biological uniqueness of these worms and the draft status of their genomes pose challenges for the identification and classification of protein kinases using established tools. In this article, we provide an account of kinase biology, the roles of kinases in diseases and their importance as drug targets, and drug discovery efforts in key socioeconomically important parasitic worms. In this context, we summarise methods and resources commonly used for the curation, identification, classification and functional annotation of protein kinase sequences from draft genomes; review recent advances made in the characterisation of the worm kinomes; and discuss the implications of these advances for investigating kinase signalling and developing small-molecule inhibitors as new anti-parasitic drugs.
Collapse
Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
93
|
Krishna KH, Kumar MS. Molecular evolution and functional divergence of eukaryotic translation initiation factor 2-alpha kinases. PLoS One 2018. [PMID: 29538447 PMCID: PMC5851622 DOI: 10.1371/journal.pone.0194335] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic translation initiation factor 2-alpha kinase (EIF2AK) proteins inhibit protein synthesis at translation initiation level, in response to various stress conditions, including oxidative stress, heme deficiency, osmotic shock, and heat shock. Origin and functional diversification of EIF2AK sequences remain ambiguous. Here we determine the origin and molecular evolution of EIF2AK proteins in lower eukaryotes and studied the molecular basis of divergence among sub-family sequences. Present work emphasized primitive origin of EIF2AK4 sub-family gene in lower eukaryotes of protozoan lineage. Phylogenetic analysis supported common origin and sub-family based classification of EIF2AKs. Functional divergence studies across sub-families revealed several putative amino acid sites, which assist in altered protein interactions of kinase domains. The data can facilitate designing site-directed experimental studies aiming at elucidating diverse functional aspects of kinase domains regarding down-regulation of protein synthesis.
Collapse
Affiliation(s)
- K. Hari Krishna
- Centre for Bioinformatics, Pondicherry University, Kalapet, Pondicherry, India
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (VFSTR) University, Vadlamudi, Andhra Pradesh, India
| | - Muthuvel Suresh Kumar
- Centre for Bioinformatics, Pondicherry University, Kalapet, Pondicherry, India
- * E-mail:
| |
Collapse
|
94
|
Miller CJ, Turk BE. Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends Biochem Sci 2018; 43:380-394. [PMID: 29544874 DOI: 10.1016/j.tibs.2018.02.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/21/2023]
Abstract
Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks.
Collapse
Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
95
|
Subramanian G, Kuzmanovic T, Zhang Y, Peter CB, Veleeparambil M, Chakravarti R, Sen GC, Chattopadhyay S. A new mechanism of interferon's antiviral action: Induction of autophagy, essential for paramyxovirus replication, is inhibited by the interferon stimulated gene, TDRD7. PLoS Pathog 2018; 14:e1006877. [PMID: 29381763 PMCID: PMC5806901 DOI: 10.1371/journal.ppat.1006877] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/09/2018] [Accepted: 01/12/2018] [Indexed: 12/14/2022] Open
Abstract
The interferon (IFN) system represents the first line of defense against a wide range of viruses. Virus infection rapidly triggers the transcriptional induction of IFN-β and IFN Stimulated Genes (ISGs), whose protein products act as viral restriction factors by interfering with specific stages of virus life cycle, such as entry, transcription, translation, genome replication, assembly and egress. Here, we report a new mode of action of an ISG, IFN-induced TDRD7 (tudor domain containing 7) inhibited paramyxovirus replication by inhibiting autophagy. TDRD7 was identified as an antiviral gene by a high throughput screen of an ISG shRNA library for blocking IFN’s protective effect against Sendai virus (SeV) replication. The antiviral activity of TDRD7 against SeV, human parainfluenza virus 3 and respiratory syncytial virus was confirmed by its genetic ablation or ectopic expression in several types of mouse and human cells. TDRD7’s antiviral action was mediated by its ability to inhibit autophagy, a cellular catabolic process which was robustly induced by SeV infection and required for its replication. Mechanistic investigation revealed that TDRD7 interfered with the activation of AMP-dependent kinase (AMPK), an enzyme required for initiating autophagy. AMPK activity was required for efficient replication of several paramyxoviruses, as demonstrated by its genetic ablation or inhibition of its activity by TDRD7 or chemical inhibitors. Therefore, our study has identified a new antiviral ISG with a new mode of action. The antiviral functions of interferons (IFNs) are mediated by the IFN-induced proteins, encoded by the IFN Stimulated Genes (ISGs). Because ISGs are virus-specific, we performed a high throughput genetic screen to identify novel antiviral ISGs against Sendai virus (SeV), a respirovirus of the Paramyxoviridae family. Our screen isolated a small subset of anti-SeV ISGs, among which we focused on a novel ISG, Tudor domain containing 7 (TDRD7). The antiviral activity of TDRD7 was confirmed by genetic ablation of the endogenous, and the ectopic expression of the exogenous, TDRD7 in human and mouse cell types. Investigation of the mechanism of antiviral action revealed that TDRD7 inhibited ‘virus-induced autophagy’, which was required for the replication of SeV. Autophagy, a cellular catabolic process, was robustly induced by SeV infection, and was inhibited by TDRD7. TDRD7 interfered with the ‘induction’ step of autophagy by inhibiting the activation of AMP-dependent Kinase (AMPK). AMPK is a multifunctional metabolic kinase, which was activated by SeV infection, and its activity was required for virus replication. Genetic ablation and inhibition of AMPK activity by physiological (TDRD7) or chemical (Compound C) inhibitors strongly attenuated SeV replication. The anti-AMPK activity of TDRD7 was capable of inhibiting other members of Paramyxoviridae family, human parainfluenza virus type 3 and respiratory syncytial virus. Therefore, our study uncovered a new antiviral mechanism of IFN by inhibiting the activation of autophagy-inducing kinase AMPK.
Collapse
Affiliation(s)
- Gayatri Subramanian
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine, Toledo, OH, United States of America
| | - Teodora Kuzmanovic
- Department of Immunology, Lerner Research Institute, Cleveland, OH, United States of America
| | - Ying Zhang
- Department of Immunology, Lerner Research Institute, Cleveland, OH, United States of America
| | - Cara Beate Peter
- Department of Surgery, University of Toledo College of Medicine, Toledo, OH, United States of America
| | - Manoj Veleeparambil
- Department of Immunology, Lerner Research Institute, Cleveland, OH, United States of America
| | - Ritu Chakravarti
- Department of Surgery, University of Toledo College of Medicine, Toledo, OH, United States of America
| | - Ganes C. Sen
- Department of Immunology, Lerner Research Institute, Cleveland, OH, United States of America
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine, Toledo, OH, United States of America
- Department of Immunology, Lerner Research Institute, Cleveland, OH, United States of America
- * E-mail:
| |
Collapse
|
96
|
Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018; 20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery.
Collapse
Affiliation(s)
- Inês C. M. Simões
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - João T. S. Coimbra
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Rui P. P. Neves
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Inês P. D. Costa
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Maria J. Ramos
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Pedro A. Fernandes
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| |
Collapse
|
97
|
Schubert AF, Gladkova C, Pardon E, Wagstaff JL, Freund SM, Steyaert J, Maslen SL, Komander D. Structure of PINK1 in complex with its substrate ubiquitin. Nature 2017; 552:51-56. [PMID: 29160309 PMCID: PMC6020998 DOI: 10.1038/nature24645] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022]
Abstract
Autosomal-recessive juvenile Parkinsonism (AR-JP) is caused by mutations in a number of PARK genes, in particular the genes encoding the E3 ubiquitin ligase Parkin (PARK2, also known as PRKN) and its upstream protein kinase PINK1 (also known as PARK6). PINK1 phosphorylates both ubiquitin and the ubiquitin-like domain of Parkin on structurally protected Ser65 residues, triggering mitophagy. Here we report a crystal structure of a nanobody-stabilized complex containing Pediculus humanus corporis (Ph)PINK1 bound to ubiquitin in the 'C-terminally retracted' (Ub-CR) conformation. The structure reveals many peculiarities of PINK1, including the architecture of the C-terminal region, and reveals how the N lobe of PINK1 binds ubiquitin via a unique insertion. The flexible Ser65 loop in the Ub-CR conformation contacts the activation segment, facilitating placement of Ser65 in a phosphate-accepting position. The structure also explains how autophosphorylation in the N lobe stabilizes structurally and functionally important insertions, and reveals the molecular basis of AR-JP-causing mutations, some of which disrupt ubiquitin binding.
Collapse
Affiliation(s)
- Alexander F. Schubert
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christina Gladkova
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Jane L. Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stefan M.V. Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sarah L. Maslen
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| |
Collapse
|
98
|
Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition. PLoS One 2017; 12:e0186849. [PMID: 29053745 PMCID: PMC5650172 DOI: 10.1371/journal.pone.0186849] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/09/2017] [Indexed: 02/06/2023] Open
Abstract
Highly structured RNA derived from viral genomes is a key cellular indicator of viral infection. In response, cells produce the interferon inducible RNA-dependent protein kinase (PKR) that, when bound to viral dsRNA, phosphorylates eukaryotic initiation factor 2α and attenuates viral protein translation. Adenovirus can evade this line of defence through transcription of a non-coding RNA, VAI, an inhibitor of PKR. VAI consists of three base-paired regions that meet at a three-way junction; an apical stem responsible for the interaction with PKR, a central stem required for inhibition, and a terminal stem. Recent studies have highlighted the potential importance of the tertiary structure of the three-way junction to PKR inhibition by enabling interaction between regions of the central and terminal stems. To further investigate the role of the three-way junction, we characterized the binding affinity and inhibitory potential of central stem mutants designed to introduce subtle alterations. These results were then correlated with small-angle X-ray scattering solution studies and computational tertiary structural models. Our results demonstrate that while mutations to the central stem have no observable effect on binding affinity to PKR, mutations that appear to disrupt the structure of the three-way junction prevent inhibition of PKR. Therefore, we propose that instead of simply sequestering PKR, a specific structural conformation of the PKR-VAI complex may be required for inhibition.
Collapse
|
99
|
Bhavnani V, Kaviraj S, Panigrahi P, Suresh CG, Yapara S, Pal J. Elucidation of molecular mechanism of stability of the heme-regulated eIF2α kinase upon binding of its ligand, hemin in its catalytic kinase domain. J Biomol Struct Dyn 2017; 36:2845-2861. [PMID: 28814160 DOI: 10.1080/07391102.2017.1368417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understanding its mechanism of functionality. In the present study, we report the thermostability achieved by the catalytic kinase domain of HRI (HRI.CKD) upon ligand (heme) binding. Our CD data demonstrates that the HRI.CKD retains its secondary structure at higher temperatures when it is in ligand bound state. HRI.CKD when incubated with hemin loses its monomeric state and attains a higher order oligomeric form resulting in its stability. The HRI.CKD fails to refold into its native conformation upon mutation of H377A/H381A, thereby confirming the necessity of these His residues for correct folding, stability, and activity of the kinase. Though our in silico study demonstrated these His being the ligand binding sites in the kinase insert region, the spectra-based study did not show significant difference in heme affinity for the wild type and His mutant HRI.CKD.
Collapse
Affiliation(s)
- Varsha Bhavnani
- a Department of Biotechnology , Savitribai Phule Pune University , Pune , Maharashtra 411007 , India
| | - Swarnendu Kaviraj
- b Vaccine Formulation & Research Centre , Gennova Biopharmaceuticals Limited , Pune , Maharashtra 411057 , India
| | - Priyabrata Panigrahi
- c Division of Biochemical Sciences , CSIR-National Chemical Laboratory , Pune 411008 , India
| | - C G Suresh
- c Division of Biochemical Sciences , CSIR-National Chemical Laboratory , Pune 411008 , India
| | - SuneelShekar Yapara
- b Vaccine Formulation & Research Centre , Gennova Biopharmaceuticals Limited , Pune , Maharashtra 411057 , India
| | - Jayanta Pal
- a Department of Biotechnology , Savitribai Phule Pune University , Pune , Maharashtra 411007 , India
| |
Collapse
|
100
|
Li X, Wu Z, An X, Mei Q, Bai M, Hanski L, Li X, Ahola T, Han W. Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy. eLife 2017; 6:27301. [PMID: 28820388 PMCID: PMC5562444 DOI: 10.7554/elife.27301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022] Open
Abstract
Acquired therapeutic resistance by tumors is a substantial impediment to reducing the morbidity and mortality that are attributable to human malignancies. The mechanisms responsible for the dramatic shift between chemosensitivity and chemoresistance in colorectal carcinoma have not been defined. Here, we report that LRP16 selectively interacts and activates double-stranded RNA-dependent kinase (PKR), and also acts as scaffolds to assist the formation of a ternary complex of PKR and IKKβ, prolonging the polymers of ADP-ribose (PAR)-dependent nuclear factor kappa B (NF-κB) transactivation caused by DNA-damaging agents and confers acquired chemoresistance. We also identified a small molecule, MRS2578, which strikingly abrogated the binding of LRP16 to PKR and IKKβ, converting LRP16 into a death molecule and forestalling colon tumorigenesis. Inclusion of MRS2578 with etoposide, versus each drug alone, exhibited synergistic antitumor cytotoxicity in xenografts. Our combinatorial approach introduces a strategy to enhance the efficacy of genotoxicity therapies for the treatment of tumors.
Collapse
Affiliation(s)
- Xiaolei Li
- Department of Molecular Biology, Immunological and Bio-therapeutic, Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| | - Zhiqiang Wu
- Department of Molecular Biology, Immunological and Bio-therapeutic, Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| | - Xiaojing An
- Department of Pathology, Chinese PLA General Hospital, Beijing, China.,Department of Pathology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qian Mei
- Department of Molecular Biology, Immunological and Bio-therapeutic, Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| | - Miaomiao Bai
- Department of Molecular Biology, Immunological and Bio-therapeutic, Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| | - Leena Hanski
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Xiang Li
- Department of Molecular Biology, Immunological and Bio-therapeutic, Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| | - Tero Ahola
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Weidong Han
- Department of Molecular Biology, Immunological and Bio-therapeutic, Institute of Basic Medicine, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|