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Muslimov A, Tereshchenko V, Shevyrev D, Rogova A, Lepik K, Reshetnikov V, Ivanov R. The Dual Role of the Innate Immune System in the Effectiveness of mRNA Therapeutics. Int J Mol Sci 2023; 24:14820. [PMID: 37834268 PMCID: PMC10573212 DOI: 10.3390/ijms241914820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Advances in molecular biology have revolutionized the use of messenger RNA (mRNA) as a therapeutic. The concept of nucleic acid therapy with mRNA originated in 1990 when Wolff et al. reported successful expression of proteins in target organs by direct injection of either plasmid DNA or mRNA. It took decades to bring the transfection efficiency of mRNA closer to that of DNA. The next few decades were dedicated to turning in vitro-transcribed (IVT) mRNA from a promising delivery tool for gene therapy into a full-blown therapeutic modality, which changed the biotech market rapidly. Hundreds of clinical trials are currently underway using mRNA for prophylaxis and therapy of infectious diseases and cancers, in regenerative medicine, and genome editing. The potential of IVT mRNA to induce an innate immune response favors its use for vaccination and immunotherapy. Nonetheless, in non-immunotherapy applications, the intrinsic immunostimulatory activity of mRNA directly hinders the desired therapeutic effect since it can seriously impair the target protein expression. Targeting the same innate immune factors can increase the effectiveness of mRNA therapeutics for some indications and decrease it for others, and vice versa. The review aims to present the innate immunity-related 'barriers' or 'springboards' that may affect the development of immunotherapies and non-immunotherapy applications of mRNA medicines.
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Affiliation(s)
- Albert Muslimov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
- Laboratory of Nano- and Microencapsulation of Biologically Active Substances, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia;
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia;
| | - Valeriy Tereshchenko
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
| | - Daniil Shevyrev
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
| | - Anna Rogova
- Laboratory of Nano- and Microencapsulation of Biologically Active Substances, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia;
- Saint-Petersburg Chemical-Pharmaceutical University, Professora Popova 14, 197376 St. Petersburg, Russia
- School of Physics and Engineering, ITMO University, Lomonosova 9, 191002 St. Petersburg, Russia
| | - Kirill Lepik
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia;
| | - Vasiliy Reshetnikov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Prospekt Akad. Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Roman Ivanov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
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Zhao K, Zhang S, Liu X, Guo X, Guo Z, Zhang X, Yuan W. The game between host antiviral innate immunity and immune evasion strategies of senecavirus A - A cell biological perspective. Front Immunol 2022; 13:1107173. [PMID: 36618383 PMCID: PMC9813683 DOI: 10.3389/fimmu.2022.1107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Innate immunity is the first line of the cellular host to defend against viral infection. Upon infection, viruses can be sensed by the cellular host's pattern recognition receptors (PRRs), leading to the activation of the signaling cascade and the robust production of interferons (IFNs) to restrict the infection and replication of the viruses. However, numerous cunning viruses have evolved strategies to evade host innate immunity. The senecavirus A (SVA) is a newly identified member of the Picornaviridae family, causing severe vesicular or ulcerative lesions on the oral mucosa, snout, coronary bands, and hooves of pigs of different ages. During SVA infection, the cellular host will launch the innate immune response and various physiological processes to restrict SVA. In contrast, SVA has evolved several strategies to evade the porcine innate immune responses. This review focus on the underlying mechanisms employed by SVA to evade pattern recognition receptor signaling pathways, type I interferon (IFN-α/β) receptor (IFNAR) signaling pathway, interferon-stimulated genes (ISGs) and autophagy, and stress granules. Deciphering the antiviral immune evasion mechanisms by SVA will enhance our understanding of SVA's pathogenesis and provide insights into developing antiviral strategies and improving vaccines.
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Affiliation(s)
- Kuan Zhao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China,Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding, China
| | - Shixia Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xiaona Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xiaoran Guo
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Zhaomeng Guo
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xiaozhan Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China,*Correspondence: Wanzhe Yuan, ; Xiaozhan Zhang,
| | - Wanzhe Yuan
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China,Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding, China,*Correspondence: Wanzhe Yuan, ; Xiaozhan Zhang,
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Chen K, Chen J, Tang T, Jiang H, Han Z, Wang L, Alradi MF, Lu S, Wei X, Liu X, Wei Y, Feng C. Characterization and functional analysis of a Relish gene from the Asian corn borer, Ostrinia furnacalis (Guenée). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 108:e21841. [PMID: 34468040 PMCID: PMC8453101 DOI: 10.1002/arch.21841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/02/2021] [Accepted: 08/19/2021] [Indexed: 05/21/2023]
Abstract
Pathogen-induced host immune responses reduce the efficacy of pathogens used to control pests. However, compared to the well-deciphered immunity system of Drosophila melanogaster, the immunity system of agricultural pests is largely unconfirmed through functional analysis. Beginning to unveil mechanisms of transcription regulation of immune genes in the Asian corn borer, Ostrinia furnacalis, we cloned the complementary DNA (cDNA) of a transcription factor Relish by rapid amplification of cDNA ends. The 3164 bp cDNA, designated Of-Relish, encodes a 956-residue protein. Bioinformatic analysis showed that Of-Relish had a Rel homology domain, a predicted cleavage site between Q409 and L410 , six ankyrin repeats, and a death domain. The response of Of-Relish expression to the Gram-negative bacteria Pseudomonas aeruginosa was sooner and stronger than to the Gram-positive Micrococcus luteus. The antimicrobial peptide genes Attacin and Gloverin had similar expression patterns in response to the infections. Knockdown of Of-Relish led to a decrease in Attacin and Gloverin messenger RNA levels, suggesting that Attacin and Gloverin were regulated by Of-Relish. Together, the results suggested that Of-Relish is a key component of the IMD pathway in O. furnacalis, involved in defense against P. aeruginosa through activation of Attacin and Gloverin.
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Affiliation(s)
- Kangkang Chen
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiaqian Chen
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tai Tang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zhaoyang Han
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Libao Wang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Mohamed F. Alradi
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shiqi Lu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiangyi Wei
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xu Liu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youheng Wei
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Congjing Feng
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Corresponding author Congjing Feng,
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Kashif H, Shah D, Sukumari-Ramesh S. Dysregulation of microRNA and Intracerebral Hemorrhage: Roles in Neuroinflammation. Int J Mol Sci 2021; 22:8115. [PMID: 34360881 PMCID: PMC8347974 DOI: 10.3390/ijms22158115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 12/23/2022] Open
Abstract
Intracerebral hemorrhage (ICH) is a major public health problem and devastating subtype of stroke with high morbidity and mortality. Notably, there is no effective treatment for ICH. Neuroinflammation, a pathological hallmark of ICH, contributes to both brain injury and repair and hence, it is regarded as a potential target for therapeutic intervention. Recent studies document that microRNAs, small non-coding RNA molecules, can regulate inflammatory brain response after ICH and are viable molecular targets to alter brain function. Therefore, there is an escalating interest in studying the role of microRNAs in the pathophysiology of ICH. Herein, we provide, for the first time, an overview of the microRNAs that play roles in ICH-induced neuroinflammation and identify the critical knowledge gap in the field, as it would help design future studies.
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Affiliation(s)
| | | | - Sangeetha Sukumari-Ramesh
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (H.K.); (D.S.)
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Dorrington MG, Fraser IDC. NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration. Front Immunol 2019; 10:705. [PMID: 31024544 PMCID: PMC6465568 DOI: 10.3389/fimmu.2019.00705] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/14/2019] [Indexed: 12/12/2022] Open
Abstract
The nuclear factor-κB (NF-κB) signaling pathway is one of the best understood immune-related pathways thanks to almost four decades of intense research. NF-κB signaling is activated by numerous discrete stimuli and is a master regulator of the inflammatory response to pathogens and cancerous cells, as well as a key regulator of autoimmune diseases. In this regard, the role of NF-κB signaling in immunity is not unlike that of the macrophage. The dynamics by which NF-κB proteins shuttle between the cytoplasm and the nucleus to initiate transcription have been studied rigorously in fibroblasts and other non-hematopoietic cells, but many questions remain as to how current models of NF-κB signaling and dynamics can be translated to innate immune cells such as macrophages. In this review, we will present recent research on the dynamics of NF-κB signaling and focus especially on how these dynamics vary in different cell types, while discussing why these characteristics may be important. We will end by looking ahead to how new techniques and technologies should allow us to analyze these signaling processes with greater clarity, bringing us closer to a more complete understanding of inflammatory transcription factor dynamics and how different cellular contexts might allow for appropriate control of innate immune responses.
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Affiliation(s)
- Michael G Dorrington
- Signaling Systems Section, Laboratory of Immune System Biology, NIAID, DIR, NIH, Bethesda, MD, United States
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Immune System Biology, NIAID, DIR, NIH, Bethesda, MD, United States
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IkappaB, NF-kappaB regulation model: simulation analysis of small number of molecules. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2008:25250. [PMID: 18301714 DOI: 10.1155/2007/25250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 08/27/2007] [Accepted: 11/08/2007] [Indexed: 11/17/2022]
Abstract
The regulation of IkappaB, NF-kappaB is of foremost interest in biology as the transcription factor NF-kappaB has multiple target genes. We have modeled a previously published model by Hoffmann et al. (2002) of IkappaB, NF-kappaB mathematically as discrete reaction systems. We have used stochastic algorithm to compare the results when there are large and small numbers of molecules available in a finite volume for each protein. Our results for small number of molecules show that with continuous presence of stimulation, nuclear NF-kappaB oscillates continuously in every individual cell rather than damping, which was observed in cell population results. This characteristic of the system is missed when averaged behavior is studied.
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Yao LC, Blitz IL, Peiffer DA, Phin S, Wang Y, Ogata S, Cho KWY, Arora K, Warrior R. Schnurri transcription factors fromDrosophilaand vertebrates can mediate Bmp signaling through a phylogenetically conserved mechanism. Development 2006; 133:4025-34. [PMID: 17008448 DOI: 10.1242/dev.02561] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Bone Morphogenetic Proteins (Bmps) are secreted growth factors that play crucial roles in animal development across the phylogenetic spectrum. Bmp signaling results in the phosphorylation and nuclear translocation of Smads,downstream signal transducers that bind DNA. In Drosophila, the zinc finger protein Schnurri (Shn) plays a key role in signaling by the Bmp2/Bmp4 homolog Decapentaplegic (Dpp), by forming a Shn/Smad repression complex on defined promoter elements in the brinker (brk) gene. Brk is a transcriptional repressor that downregulates Dpp target genes. Thus, brk inhibition by Shn results in the upregulation of Dpp-responsive genes. We present evidence that vertebrate Shn homologs can also mediate Bmp responsiveness through a mechanism similar to Drosophila Shn. We find that a Bmp response element (BRE) from the Xenopus Vent2 promoter drives Dpp-dependent expression in Drosophila. However, in sharp contrast to its activating role in vertebrates, the frog BRE mediates repression in Drosophila. Remarkably, despite these opposite transcriptional polarities, sequence changes that abolish cis-element activity in Drosophila also affect BRE function in Xenopus. These similar cis requirements reflect conservation of trans-acting factors, as human Shn1 (hShn1; HIVEP1) can interact with Smad1/Smad4 and assemble an hShn1/Smad complex on the BRE. Furthermore, both Shn and hShn1 activate the BRE in Xenopus embryos, and both repress brk and rescue embryonic patterning defects in shn mutants. Our results suggest that vertebrate Shn proteins function in Bmp signal transduction, and that Shn proteins recruit coactivators and co-repressors in a context-dependent manner,rather than acting as dedicated activators or repressors.
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Affiliation(s)
- Li-Chin Yao
- Department of Developmental and Cell Biology, and the Developmental Biology Center, University of California Irvine, Irvine, CA 92697, USA
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Prothmann C, Armstrong NJ, Roth S, Rupp RAW. Vertebrate rel proteins exhibit dorsal-like activities in earlyDrosophila embryogenesis. Dev Dyn 2006; 235:949-57. [PMID: 16493693 DOI: 10.1002/dvdy.20713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Drosophila, the Toll/Dorsal pathway triggers the nuclear entry of the Rel protein Dorsal, which controls dorsoventral patterning in early embryogenesis and plays an important role in innate immunity of the adult fly. In vertebrates, the homologous Toll/IL-1 receptor signaling pathway directs the nuclear localization of Rel/NF-kappaB complexes, which activate genes involved in proliferation, apoptosis, and immune response. Recently, first evidence has been reported for the activity of vertebrate Rel proteins and a Toll-like signaling pathway in the dorsoventral patterning process of Xenopus laevis embryos. Given the evolutionary divergence of the fly and frog model organisms, these findings raise the question, to what extent the effector functions of this pathway have been conserved? Here, we report the ability of two Xenopus Rel proteins to partially substitute for several, but not all, functions of the Dorsal protein in Drosophila embryos. Our results suggest the interaction between Rel proteins and their cytoplasmic inhibitors as an important interface of evolutionary adaptation.
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Affiliation(s)
- Christian Prothmann
- Adolf-Butenandt-Institut, Ludwif-Maximilians-Universität München, Schillerstrasse 44, D-80336 Munich, Germany
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Schooley K, Zhu P, Dower SK, Qwarnström EE. Regulation of nuclear translocation of nuclear factor-kappaB relA: evidence for complex dynamics at the single-cell level. Biochem J 2003; 369:331-9. [PMID: 12350227 PMCID: PMC1223076 DOI: 10.1042/bj20020253] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2002] [Revised: 09/17/2002] [Accepted: 09/26/2002] [Indexed: 01/14/2023]
Abstract
We have analysed activation of nuclear factor-kappaB (NF-kappaB) in response to interleukin-1 (IL-1) in human fibroblasts by tracking intracellular distribution and levels of endogenous relA, NF-kappaB1 and inhibitor of kappaB (I-kappaB) alpha using semi-quantitative confocal microscopy. Nuclear translocation of endogenous relA correlated with I-kappaBalpha degradation during stimulation with IL-1, whereas no effects were seen on levels or localization of NF-kappaB1. During pathway activation, relA was transported up a concentration gradient, resulting in a 3-4-fold increase in nuclear levels, but without any significant decrease in cytoplasmic concentration. IL-1 stimulation caused translocation of only 20% of the relA, but resulted in degradation of up to 70% of the cytoplasmic I-kappaBalpha. RelA nuclear translocation in fibroblasts correlated with DNA-binding activity measured by electrophoretic mobility shift assay (EMSA), both with respect to kinetics and IL-1 concentration-dependence. Clonal populations of cells demonstrated a marked degree of heterogeneity in the response to IL-1. The single-cell assay revealed the presence of responder and non-responder subpopulations, with an enhanced proportion of responder cells, and prolonged responses at higher concentrations of IL-1. Comparing different cell types demonstrated that whereas HepG2 cells, as fibroblasts, showed good correlation between nuclear translocation of relA and activation of DNA binding by relA-containing dimers, EL4 thymoma cells showed no effect on relA localization, even during induction of significant levels NF-kappaB activity, as measured by EMSA. The analysis shows that stimulation by IL-1 results in transient perturbation of the NF-kappaB system, which cycles between the resting and active states with net redistribution of a minor proportion of its DNA-binding component. In addition, it demonstrates significant cell-to-cell variations, as well as cell-type-specific differences in net relA nuclear transport in response to stimuli. The data are consistent with NF-kappaB constituting a dynamic and versatile system, regulated to a significant degree by binary events involving bidirectional trafficking between the cytoplasmic and nuclear compartments during pathway activation.
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Affiliation(s)
- Kenneth Schooley
- Department of Biochemistry, Immunex Research and Development Corporation, 51 University Street, Seattle, Washington 98101, U.S.A
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Abstract
Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution.
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Affiliation(s)
- Douglas H Erwin
- Department of Paleobiology, National Museum of Natural History, Washington, D.C. 20560, USA.
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Cheng H, Cenciarelli C, Tao M, Parks WP, Cheng-Mayer C. HTLV-1 Tax-associated hTid-1, a human DnaJ protein, is a repressor of Ikappa B kinase beta subunit. J Biol Chem 2002; 277:20605-10. [PMID: 11927590 DOI: 10.1074/jbc.m201204200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
hTid-1, a human DnaJ protein, is a novel cellular target for HTLV-1 Tax. Here, we show that hTid-1 represses NF-kappaB activity induced by Tax as well as other activators such as tumor necrosis factor alpha (TNFalpha) and Bcl10. hTid-1 specifically suppresses serine phosphorylation of IkappaBalpha by activated IkappaB kinase beta (IKKbeta), but the activities of other serine kinases including p38, ERK2, and JNK1 are not affected. The suppressive activity of hTid-1 on IKKbeta requires a functional J domain that mediates association with heat shock proteins and results in prolonging the half-life of the NF-kappaB inhibitors IkappaBalpha and IkappaBbeta. Collectively, our data suggest that hTid-1, in association with heat shock proteins, exerts a negative regulatory effect on the NF-kappaB activity induced by various extracellular and intracellular activators including HTLV-1 Tax.
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Affiliation(s)
- Hua Cheng
- Aaron Diamond AIDS Research Center, Rockefeller University, New York, New York 10021, USA.
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Ackerman H, Udalova I, Hull J, Kwiatkowski D. Evolution of a polymorphic regulatory element in interferon-gamma through transposition and mutation. Mol Biol Evol 2002; 19:884-90. [PMID: 12032244 DOI: 10.1093/oxfordjournals.molbev.a004145] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mammalian transposable elements have intrinsic regulatory elements that can activate neighboring genes, and it is speculated that they can also carry extrinsic transactivating DNA sequences to new genomic locations. We have identified a polymorphic segment of the human interferon-gamma promoter region where two adjacent binding sites for NF-kappaB and NFAT originated from the insertion of an Alu element approximately 22-34 MYA. Both binding sites lie outside the Alu consensus sequence but within the boundaries of the insertion, suggesting that this segment of DNA was comobilized when the Alu element moved from another part of the genome. Sequence comparisons and examination of DNA-protein interactions across nine different primate species indicate that the inserted sequence contained the intact NFAT binding site, whereas the ability to bind NF-kappaB evolved through a series of mutations after the insertion. These observations are consistent with the notion that retropseudogenes can comobilize intact regulatory sequences to new locations and thereby influence the evolution of gene regulatory networks; however, the extent to which such events have shaped the evolution of gene regulation remains unknown.
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Affiliation(s)
- Hans Ackerman
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom. University Department of Paediatrics, Oxford, United Kingdom.
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Cramer P, Varrot A, Barillas-Mury C, Kafatos FC, Müller CW. Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA. Structure 1999; 7:841-52. [PMID: 10425685 DOI: 10.1016/s0969-2126(99)80107-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND NF-kappa B/Rel transcription factors play important roles in immunity and development in mammals and insects. Their activity is regulated by their cellular localization, homo- and heterodimerization and association with other factors on their target gene promoters. Gambif1 from Anopheles gambiae is a member of the Rel family and a close homologue of the morphogen Dorsal, which establishes dorsoventral polarity in the Drosophila embryo. RESULTS We present the crystal structure of the N-terminal specificity domain of Gambif1 bound to DNA. This first structure of an insect Rel protein-DNA complex shows that Gambif1 binds a GGG half-site element using a stack of three arginine sidechains. Differences in affinity to Dorsal binding sites in target gene promoters are predicted to arise from base changes in these GGG elements. An arginine that is conserved in class II Rel proteins (members of which contain a transcription activation domain) contacts the outermost guanines of the DNA site. This previously unseen specific contact contributes strongly to the DNA-binding affinity and might be responsible for differences in specificity between Rel proteins of class I and II. CONCLUSIONS The Gambif1-DNA complex structure illustrates how differences in Dorsal affinity to binding sites in developmental gene promoters are achieved. Comparison with other Rel-DNA complex structures leads to a general model for DNA recognition by Rel proteins.
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Affiliation(s)
- P Cramer
- European Molecular Biology Laboratory, Grenoble Outstation, France
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Valentine JW, Jablonski D, Erwin DH. Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 1999; 126:851-9. [PMID: 9927587 DOI: 10.1242/dev.126.5.851] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Cambrian explosion is named for the geologically sudden appearance of numerous metazoan body plans (many of living phyla) between about 530 and 520 million years ago, only 1.7% of the duration of the fossil record of animals. Earlier indications of metazoans are found in the Neoproterozic; minute trails suggesting bilaterian activity date from about 600 million years ago. Larger and more elaborate fossil burrows appear near 543 million years ago, the beginning of the Cambrian Period. Evidence of metazoan activity in both trace and body fossils then increased during the 13 million years leading to the explosion. All living phyla may have originated by the end of the explosion. Molecular divergences among lineages leading to phyla record speciation events that have been earlier than the origins of the new body plans, which can arise many tens of millions of years after an initial branching. Various attempts to date those branchings by using molecular clocks have disagreed widely. While the timing of the evolution of the developmental systems of living metazoan body plans is still uncertain, the distribution of Hox and other developmental control genes among metazoans indicates that an extensive patterning system was in place prior to the Cambrian. However, it is likely that much genomic repatterning occurred during the Early Cambrian, involving both key control genes and regulators within their downstream cascades, as novel body plans evolved.
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Affiliation(s)
- J W Valentine
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94720, USA.
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16
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Vincenti MP, Coon CI, Brinckerhoff CE. Nuclear factor kappaB/p50 activates an element in the distal matrix metalloproteinase 1 promoter in interleukin-1beta-stimulated synovial fibroblasts. ARTHRITIS AND RHEUMATISM 1998; 41:1987-94. [PMID: 9811054 DOI: 10.1002/1529-0131(199811)41:11<1987::aid-art14>3.0.co;2-8] [Citation(s) in RCA: 160] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To determine how interleukin-1 (IL-1), through activation of collagenase 1 (matrix metalloproteinase 1 [MMP-1]) transcription in synovial fibroblasts, contributes to cartilage degradation in rheumatoid arthritis. METHODS Primary rabbit synovial fibroblasts were transiently transfected with MMP-1 promoter/ luciferase constructs, and promoter activity in response to IL-1 was assessed. A minimal IL-1-response element was defined and used to evaluate DNA binding proteins by electrophoretic mobility shift assay and in situ ultraviolet crosslinking assay. RESULTS Transcriptional activation of the MMP-1 gene by IL-1 in rabbit synovial fibroblasts required a dorsal-like element, which was located at nucleotide (nt) -3,029, as well as an activator protein 1 site at nt -77. Importantly, an IL-1-induced DNA binding activity that was specific for the dorsal-like element contained the p50 subunit of nuclear factor kappaB (NF-kappaB). CONCLUSION These studies demonstrate, for the first time, a role for NF-kappaB in the induction of MMP-1, and suggest a mechanism of NF-kappaB-mediated cartilage degradation in rheumatoid arthritis.
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Affiliation(s)
- M P Vincenti
- Department of Medicine, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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17
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Abstract
Recent studies suggest that lineage commitment steps, which occur during T-cell differentiation, follow principles in common with fate specification in simple invertebrates. Here we review T-cell development from the perspective of developmental biology. We present models for alpha beta vs gamma delta and CD4 vs CD8 lineage commitment that are consistent with previously published and newly presented experiments.
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Affiliation(s)
- S M Hedrick
- Department of Biology, University of California, San Diego, La Jolla, USA.
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18
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Ghosh S, May MJ, Kopp EB. NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses. Annu Rev Immunol 1998; 16:225-60. [PMID: 9597130 DOI: 10.1146/annurev.immunol.16.1.225] [Citation(s) in RCA: 4097] [Impact Index Per Article: 157.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The transcription factor NF-kappa B, more than a decade after its discovery, remains an exciting and active area of study. The involvement of NF-kappa B in the expression of numerous cytokines and adhesion molecules has supported its role as an evolutionarily conserved coordinating element in the organism's response to situations of infection, stress, and injury. Recently, significant advances have been made in elucidating the details of the pathways through which signals are transmitted to the NF-kappa B:I kappa B complex in the cytosol. The field now awaits the discovery and characterization of the kinase responsible for the inducible phosphorylation of I kappa B proteins. Another exciting development has been the demonstration that in certain situations NF-kappa B acts as an anti-apoptotic protein; therefore, elucidation of the mechanism by which NF-kappa B protects against cell death is an important goal. Finally, the generation of knockouts of members of the NF-kappa B/I kappa B family has allowed the study of the roles of these proteins in normal development and physiology. In this review, we discuss some of these recent findings and their implications for the study of NF-kappa B.
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Affiliation(s)
- S Ghosh
- Section of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
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19
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Bird TA, Schooley K, Dower SK, Hagen H, Virca GD. Activation of nuclear transcription factor NF-kappaB by interleukin-1 is accompanied by casein kinase II-mediated phosphorylation of the p65 subunit. J Biol Chem 1997; 272:32606-12. [PMID: 9405476 DOI: 10.1074/jbc.272.51.32606] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In fibroblasts and hepatoma cells, interleukin-1 (IL-1) treatment results in the rapid nuclear accumulation of the transcription factor NF-kappaB, present largely as p65 (RelA)/p50 heterodimers. It is well established that this process is dependent in large part upon the phosphorylation and subsequent degradation of the cytosolic inhibitor IkappaB. We looked for other IL-1-induced modifications of NF-kappaB components and found that, in both cell types, IL-1 stimulation led, within minutes, to phosphorylation of both NF-kappaB p65 and p50. Phosphorylation of p65 was sustained for at least 30 min after addition of the cytokine and occurred principally upon serine residues. Immunoprecipitates of NF-kappaB complexes contained an associated protein kinase, the biochemical characteristics of which were indistinguishable from casein kinase II (CKII). Purified CKII efficiently phosphorylated p65 in vitro, apparently on the same major sites that became phosphorylated in intact IL-1-treated cells. Although IL-1 treatment caused little apparent stimulation of total cellular CKII activity, the fraction that was specifically associated with NF-kappaB complexes was markedly elevated by the cytokine. The association of CKII with NF-kappaB occurred in the cytoplasm, suggesting that this phosphorylation might be involved either in control of translocation of the activated complex or in modulation of its DNA binding properties.
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Affiliation(s)
- T A Bird
- Department of Biochemistry, Immunex Corporation, Seattle, Washington 98101, USA.
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20
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Shirokawa JM, Courey AJ. A direct contact between the dorsal rel homology domain and Twist may mediate transcriptional synergy. Mol Cell Biol 1997; 17:3345-55. [PMID: 9154833 PMCID: PMC232187 DOI: 10.1128/mcb.17.6.3345] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The establishment of mesoderm and neuroectoderm in the early Drosophila embryo relies on interactions between the Dorsal morphogen and basic-helix-loop-helix (bHLH) activators. Here we show that Dorsal and the bHLH activator Twist synergistically activate transcription in cell culture and in vitro from a promoter containing binding sites for both factors. Somewhat surprisingly, a region of Twist outside the conserved bHLH domain is required for the synergy. In Dorsal, the rel homology domain appears to be sufficient for synergy. Protein-protein interaction assays show that Twist and Dorsal bind to one another in vitro. However, this interaction does not appear to be of sufficient strength to yield cooperative binding to DNA. Nonetheless, the regions of Twist and Dorsal required for the binding interaction are also required for synergistic transcriptional activation.
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Affiliation(s)
- J M Shirokawa
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095-1569, USA
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21
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Thanos D, Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 1995; 83:1091-100. [PMID: 8548797 DOI: 10.1016/0092-8674(95)90136-1] [Citation(s) in RCA: 803] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present evidence that transcriptional activation of the human interferon-beta (IFN beta) gene requires the assembly of a higher order transcription enhancer complex (enhanceosome). This multicomponent complex includes at least three distinct transcription factors and the high mobility group protein HMG I(Y). Both the in vitro assembly and in vivo transcriptional activity of this complex require a precise helical relationship between individual transcription factor-binding sites. In addition, HMG I(Y), which binds specifically to three sites within the enhancer, promotes cooperative binding of transcriptional factors in vitro and is required for transcriptional synergy between these factors in vivo. Thus, HMG I(Y) plays an essential role in the assembly and function of the IFN beta gene enhanceosome.
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Affiliation(s)
- D Thanos
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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22
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Shadan FF, Villarreal LP. The evolution of small DNA viruses of eukaryotes: past and present considerations. Virus Genes 1995; 11:239-57. [PMID: 8828150 DOI: 10.1007/bf01728663] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Historically, viral evolution has often been considered from the perspective of the ability of the virus to maintain viral pathogenic fitness by causing disease. A predator-prey model has been successfully applied to explain genetically variable quasi-species of viruses, such as influenza virus and human immunodeficiency virus (HIV), which evolve much faster rates than the host. In contrast, small DNA viruses (polyomaviruses, papillomaviruses, and parvoviruses) are species specific but are stable genetically, and appear to have co-evolved with their host species. Genetic stability is attributable primarily to the ability to establish and maintain a benign persistent state in vivo and not to the host DNA proofreading mechanisms. The persistent state often involves a cell cycle-regulated episomal state and a tight linkage of DNA amplification mechanisms to cellular differentiation. This linkage requires conserved features among viral regulatory proteins, with characteristic host-interactive domains needed to recruit and utilize host machinery, thus imposing mechanistic constrains on possible evolutionary options. Sequence similarities within these domains are seen amongst all small mammalian DNA viruses and most of the parvo-like viruses, including those that span the entire spectrum of evolution of organisms from E. coli to humans that replicate via a rolling circle-like mechanism among the entire spectrum of organisms throughout evolution from E. coli to humans. To achieve benign inapparent viral persistence, small DNA viruses are proposed to circumvent the host acute phase reaction (characterized by minimal inflammation) by mechanisms that are evolutionarily adapted to the immune system and the related cytokine communication networks. A striking example of this is the relationship of hymenoptera to polydnaviruses, in which the crucial to the recognition of self, development, and maintenance of genetic identity of both the host and virus. These observations in aggregate suggest that viral replicons are not recent "escapies" of host replication, but rather provide relentless pressure in driving the evolution of the host through cospeciation.
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Affiliation(s)
- F F Shadan
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717, USA
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23
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Li S, Rosen JM. Nuclear factor I and mammary gland factor (STAT5) play a critical role in regulating rat whey acidic protein gene expression in transgenic mice. Mol Cell Biol 1995; 15:2063-70. [PMID: 7891701 PMCID: PMC230433 DOI: 10.1128/mcb.15.4.2063] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The rat whey acidic protein (WAP) gene contains a mammary gland-specific and hormonally regulated DNase I-hypersensitive site 830 to 720 bp 5' to the site of transcription initiation. We have reported previously that nuclear factor I (NFI) binding at a palindromic site and binding at a half-site are the major DNA-protein interactions detected within this tissue-specific nuclease-hypersensitive region. We now show that point mutations introduced into these NFI-binding sites dramatically affect WAP gene expression in transgenic mice. Transgene expression was totally abrogated when the palindromic NFI site or both binding sites were mutated, suggesting that NFI is a key regulator of WAP gene expression. In addition, a recognition site for mammary gland factor (STAT5), which mediates prolactin induction of milk protein gene expression, was also identified immediately proximal to the NFI-binding sites. Mutation of this site reduced transgene expression by approximately 90% per gene copy, but did not alter tissue specificity. These results suggest that regulation of WAP gene expression is determined by the cooperative interactions among several enhancers that constitute a composite response element.
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Affiliation(s)
- S Li
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030
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24
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Davidson EH. Molecular biology of embryonic development: how far have we come in the last ten years? Bioessays 1994; 16:603-15. [PMID: 7980484 DOI: 10.1002/bies.950160903] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The successes of molecular developmental biology over the last ten years have been particularly impressive in those directions favored by its major paradigms. New technologies have both guided and been guided by the progress of the field. I review briefly some of the major insights into embryonic development that have derived from research in four specific areas: early embryogenesis of various forms; 'pattern formation'; evolutionary conservation of regulatory elements; and spatial mechanisms of gene regulation. There remain many major problem areas, some of which may require new orientations to solve.
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Affiliation(s)
- E H Davidson
- Division of Biology, California Institute of Technology, Pasadena 91125
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