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Chamcha V, Reddy PBJ, Kannanganat S, Wilkins C, Gangadhara S, Velu V, Green R, Law GL, Chang J, Bowen JR, Kozlowski PA, Lifton M, Santra S, Legere T, Chea LS, Chennareddi L, Yu T, Suthar MS, Silvestri G, Derdeyn CA, Gale M, Villinger F, Hunter E, Amara RR. Strong T H1-biased CD4 T cell responses are associated with diminished SIV vaccine efficacy. Sci Transl Med 2020; 11:11/519/eaav1800. [PMID: 31748228 DOI: 10.1126/scitranslmed.aav1800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/07/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022]
Abstract
Activated CD4 T cells are a major target of HIV infection. Results from the STEP HIV vaccine trial highlighted a potential role for total activated CD4 T cells in promoting HIV acquisition. However, the influence of vaccine insert-specific CD4 T cell responses on HIV acquisition is not known. Here, using the data obtained from four macaque studies, we show that the DNA prime/modified vaccinia Ankara boost vaccine induced interferon γ (IFNγ+) CD4 T cells [T helper 1 (TH1) cells] rapidly migrate to multiple tissues including colon, cervix, and vaginal mucosa. These mucosal TH1 cells persisted at higher frequencies and expressed higher density of CCR5, a viral coreceptor, compared to cells in blood. After intravaginal or intrarectal simian immunodeficiency virus (SIV)/simian-human immunodeficiency virus (SHIV) challenges, strong vaccine protection was evident only in animals that had lower frequencies of vaccine-specific TH1 cells but not in animals that had higher frequencies of TH1 cells, despite comparable vaccine-induced humoral and CD8 T cell immunity in both groups. An RNA transcriptome signature in blood at 7 days after priming immunization from one study was associated with induction of fewer TH1-type CD4 cells and enhanced protection. These results demonstrate that high and persisting frequencies of HIV vaccine-induced TH1-biased CD4 T cells in the intestinal and genital mucosa can mitigate beneficial effects of protective antibodies and CD8 T cells, highlighting a critical role of priming immunization and vaccine adjuvants in modulating HIV vaccine efficacy.
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Affiliation(s)
- Venkateswarlu Chamcha
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Pradeep B J Reddy
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sunil Kannanganat
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Courtney Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Vijayakumar Velu
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - G Lynn Law
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Jean Chang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - James R Bowen
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lifton
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Sampa Santra
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Traci Legere
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Lynette S Chea
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Lakshmi Chennareddi
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Francois Villinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA. .,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
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2
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Korth MJ, Law GL. Systems Virology. Viral Pathogenesis 2016. [PMCID: PMC7149947 DOI: 10.1016/b978-0-12-800964-2.00011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Selinger C, Tisoncik-Go J, Menachery VD, Agnihothram S, Law GL, Chang J, Kelly SM, Sova P, Baric RS, Katze MG. Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates. BMC Genomics 2014; 15:1161. [PMID: 25534508 PMCID: PMC4522970 DOI: 10.1186/1471-2164-15-1161] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 12/12/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic and pathogenic potential of emerging coronaviruses in humans. Clinical features of Middle East respiratory syndrome (MERS) include atypical pneumonia and progressive respiratory failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV. The host response is a key component of highly pathogenic respiratory virus infection. Here, we computationally analyzed gene expression changes in a human airway epithelial cell line infected with two genetically distinct MERS-CoV strains obtained from human patients, MERS-CoV SA 1 and MERS-CoV Eng 1. RESULTS Using topological techniques, including persistence homology and filtered clustering, we performed a comparative transcriptional analysis of human Calu-3 cell host responses to the different MERS-CoV strains, with MERS-CoV Eng 1 inducing early kinetic changes, between 3 and 12 hours post infection, compared to MERS-CoV SA 1. Robust transcriptional changes distinguished the two MERS-CoV strains predominantly at the late time points. Combining statistical analysis of infection and cytokine-stimulated Calu-3 transcriptomics, we identified differential innate responses, including up-regulation of extracellular remodeling genes following MERS-CoV Eng 1 infection and differential pro-inflammatory responses. CONCLUSIONS Through our genomics-based approach, we found topological differences in the kinetics and magnitude of the host response to MERS-CoV SA 1 and MERS-CoV Eng 1, with differential expression of innate immune and pro-inflammatory responsive genes as a result of IFN, TNF and IL-1α signaling. Predicted activation for STAT3 mediating gene expression relevant for epithelial cell-to-cell adherens and junction signaling in MERS-CoV Eng 1 infection suggest that these transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity during MERS-CoV infection.
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Affiliation(s)
- Christian Selinger
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
| | - Jennifer Tisoncik-Go
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA.
| | - G Lynn Law
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
| | - Jean Chang
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
| | - Sara M Kelly
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
| | - Pavel Sova
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Michael G Katze
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
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4
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Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TRW, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data 2014; 1:140033. [PMID: 25977790 PMCID: PMC4410982 DOI: 10.1038/sdata.2014.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022] Open
Abstract
The Systems Biology for Infectious Diseases Research program was established by
the U.S. National Institute of Allergy and Infectious Diseases to investigate
host-pathogen interactions at a systems level. This program generated 47
transcriptomic and proteomic datasets from 30 studies that investigate
in vivo and in vitro host responses to
viral infections. Human pathogens in the Orthomyxoviridae and
Coronaviridae families, especially pandemic H1N1 and avian
H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus
(SARS-CoV), were investigated. Study validation was demonstrated via
experimental quality control measures and meta-analysis of independent
experiments performed under similar conditions. Primary assay results are
archived at the GEO and PeptideAtlas public repositories, while processed
statistical results together with standardized metadata are publically available
at the Influenza Research Database (www.fludb.org) and the Virus Pathogen
Resource (www.viprbrc.org). By comparing data from mutant versus wild-type
virus and host strains, RNA versus protein differential expression, and
infection with genetically similar strains, these data can be used to further
investigate genetic and physiological determinants of host responses to viral
infection.
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Affiliation(s)
| | | | - Sanjeev Kumar
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Edward B Klem
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | | | - Armand Bankhead
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Meagen Bolles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Victoria Carter
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Jean Chang
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Therese R W Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Alan H Diercks
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Amy Ellis
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Shufang Fan
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Richard R Green
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Masato Hatta
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Robert A Heegel
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Sophia Jeng
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA
| | - Laurence Josset
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Shari M Kaiser
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Sara Kelly
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - G Lynn Law
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Chengjun Li
- Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China
| | - Jiangning Li
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Casey Long
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Maria L Luna
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Melissa Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jason McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Vineet Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Hugh Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Garnet Navarro
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | | | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA
| | | | - Catherine J Sanders
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Amy Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Pavel Sova
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Vincent C Tam
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Nicolas Tchitchek
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Allison Totura
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Jing Wang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | | | - Ji Wen
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Shannon McWeeney
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Alan Aderem
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA
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Law GL, Tisoncik-Go J, Korth MJ, Katze MG. Drug repurposing: a better approach for infectious disease drug discovery? Curr Opin Immunol 2013; 25:588-92. [PMID: 24011665 PMCID: PMC4015799 DOI: 10.1016/j.coi.2013.08.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/22/2013] [Indexed: 11/23/2022]
Abstract
Infectious disease investigators need to embrace new drug repurposing approaches. Key components include public databases and predictive computational methods. This approach could significantly reduce cost and time for drug development. Support for large scale drug and disease phenotype screening is essential.
The advent of publicly available databases containing system-wide phenotypic data of the host response to both drugs and pathogens, in conjunction with bioinformatics and computational methods now allows for in silico predictions of FDA-approved drugs as treatments against infection diseases. This systems biology approach captures the complexity of both the pathogen and drug host response in the form of expression patterns or molecular interaction networks without having to understand the underlying mechanisms of action. These drug repurposing techniques have been successful in identifying new drug candidates for several types of cancers and were recently used to identify potential therapeutics against influenza, the newly discovered Middle Eastern Respiratory Syndrome coronavirus and several parasitic diseases. These new approaches have the potential to significantly reduce both the time and cost for infectious diseases drug discovery.
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Affiliation(s)
- G Lynn Law
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Abstract
The nucleosome-scanning assay (NuSA) couples isolation of mononucleosomal DNA after micrococcal nuclease (MNase) digestion with quantitative real-time PCR (qPCR) to map nucleosome positions in chromatin. It is a relatively simple, rapid procedure that can produce a high-resolution map of nucleosome location and occupancy and thus is suitable for analyzing individual promoters in great detail. The analysis can also quantify the protection of DNA sequences due to interaction with proteins other than nucleosomes and show how this protection varies when conditions change. When coupled with chromatin immunoprecipitation (ChIP), NuSA can identify histone variants and modifications associated with specific nucleosomes.
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Affiliation(s)
- Juan Jose Infante
- Department of Microbiology, University of Washington, Seattle, WA, USA
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7
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Abstract
Transcriptional regulation of Snf1-dependent genes occurs in part by histone-acetylation-dependent binding of the transcription factor Adr1. Analysis of previously published microarray data indicated unscheduled transcription of a large number of Snf1- and Adr1-dependent genes when either the histone H3 or H4 tail was deleted. Quantitative real-time PCR confirmed that the tails were important to preserve stringent transcriptional repression of Snf1-dependent genes when glucose was present. The absence of the tails allowed Adr1 and RNA Polymerase II to bind promoters in normally inhibitory conditions. The promoters escaped glucose repression to a limited extent and the weak constitutive ADH2 transcription induced by deletion of the histone tails was transcription factor- and Snf1-independent. These effects were apparently due to a permissive chromatin structure that allowed transcription in the absence of repression mediated by the histone tails. Deleting REG1, and thus activating Snf1 in the H3 tail mutant enhanced transcription in repressing conditions, indicating that Snf1 and the H3 tail influence transcription independently. Deleting REG1 in the histone H4 tail mutant appeared to be lethal, even in the absence of Snf1, suggesting that Reg1 and the H4 tail have redundant functions that are important for cell viability.
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Affiliation(s)
- Juan J Infante
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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8
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Young ET, Yen K, Dombek KM, Law GL, Chang E, Arms E. Snf1-independent, glucose-resistant transcription of Adr1-dependent genes in a mediator mutant of Saccharomyces cerevisiae. Mol Microbiol 2009; 74:364-83. [PMID: 19732343 DOI: 10.1111/j.1365-2958.2009.06866.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glucose represses transcription of a network of co-regulated genes in Saccharomyces cerevisiae, ensuring that it is utilized before poorer carbon sources are metabolized. Adr1 is a glucose-regulated transcription factor whose promoter binding and activity require Snf1, the yeast homologue of the AMP-activated protein kinase in higher eukaryotes. In this study we found that a temperature-sensitive allele of MED14, a Mediator middle subunit that tethers the tail to the body, allowed a low level of Adr1-independent ADH2 expression that can be enhanced by Adr1 in a dose-dependent manner. A low level of TATA-independent ADH2 expression was observed in the med14-truncated strain and transcription of ADH2 and other Adr1-dependent genes occurred in the absence of Snf1 and chromatin remodeling coactivators. Loss of ADH2 promoter nucleosomes had occurred in the med14 strain in repressing conditions and did not require ADR1. A global analysis of transcription revealed that loss of Med14 function was associated with both up- and down- regulation of several groups of co-regulated genes, with ADR1-dependent genes being the most highly represented in the upregulated class. Expression of most genes was not significantly affected by the loss of Med14 function.
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Affiliation(s)
- Elton T Young
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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Biddick RK, Law GL, Chin KKB, Young ET. The transcriptional coactivators SAGA, SWI/SNF, and mediator make distinct contributions to activation of glucose-repressed genes. J Biol Chem 2008; 283:33101-9. [PMID: 18826948 DOI: 10.1074/jbc.m805258200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The paradigm of activation via ordered recruitment has evolved into a complicated picture as the influence of coactivators and chromatin structures on gene regulation becomes understood. We present here a comprehensive study of many elements of activation of ADH2 and FBP1, two glucose-regulated genes. We identify SWI/SNF as the major chromatin-remodeling complex at these genes, whereas SAGA (Spt-Ada-Gcn5-acetyltransferase complex) is required for stable recruitment of other coactivators. Mediator plays a crucial role in expression of both genes but does not affect chromatin remodeling. We found that Adr1 bound unaided by coactivators to ADH2, but Cat8 binding depended on coactivators at FBP1. Taken together, our results suggest that commonly regulated genes share many aspects of activation, but that gene-specific regulators or elements of promoter architecture may account for small differences in the mechanism of activation. Finally, we found that activator overexpression can compensate for the loss of SWI/SNF but not for the loss of SAGA.
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Affiliation(s)
- Rhiannon K Biddick
- Department of Biochemistry, University of Washington, Seattle, Washington 98105, USA
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10
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Biddick RK, Law GL, Young ET. Adr1 and Cat8 mediate coactivator recruitment and chromatin remodeling at glucose-regulated genes. PLoS One 2008; 3:e1436. [PMID: 18197247 PMCID: PMC2175534 DOI: 10.1371/journal.pone.0001436] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 12/17/2007] [Indexed: 11/18/2022] Open
Abstract
Background Adr1 and Cat8 co-regulate numerous glucose-repressed genes in S. cerevisiae, presenting a unique opportunity to explore their individual roles in coactivator recruitment, chromatin remodeling, and transcription. Methodology/Principal Findings We determined the individual contributions of Cat8 and Adr1 on the expression of a cohort of glucose-repressed genes and found three broad categories: genes that need both activators for full derepression, genes that rely mostly on Cat8 and genes that require only Adr1. Through combined expression and recruitment data, along with analysis of chromatin remodeling at two of these genes, ADH2 and FBP1, we clarified how these activators achieve this wide range of co-regulation. We find that Adr1 and Cat8 are not intrinsically different in their abilities to recruit coactivators but rather, promoter context appears to dictate which activator is responsible for recruitment to specific genes. These promoter-specific contributions are also apparent in the chromatin remodeling that accompanies derepression: ADH2 requires both Adr1 and Cat8, whereas, at FBP1, significant remodeling occurs with Cat8 alone. Although over-expression of Adr1 can compensate for loss of Cat8 at many genes in terms of both activation and chromatin remodeling, this over-expression cannot complement all of the cat8Δ phenotypes. Conclusions/Significance Thus, at many of the glucose-repressed genes, Cat8 and Adr1 appear to have interchangeable roles and promoter architecture may dictate the roles of these activators.
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Affiliation(s)
- Rhiannon K. Biddick
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - G. Lynn Law
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Elton T. Young
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
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11
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Abstract
Snf1, the yeast AMP kinase homolog, is essential for derepression of glucose-repressed genes that are activated by Adr1. Although required for Adr1 DNA binding, the precise role of Snf1 is unknown. Deletion of histone deacetylase genes allowed constitutive promoter binding of Adr1 and Cat8, another activator of glucose-repressed genes. In repressed conditions, at the Adr1-and Cat8-dependent ADH2 promoter, partial chromatin remodeling had occurred, and the activators recruited a partial preinitiation complex that included RNA polymerase II. Transcription did not occur, however, unless Snf1 was activated, suggesting a Snf1-dependent event that occurs after RNA polymerase II recruitment. Glucose regulation persisted because shifting to low glucose increased expression. Glucose repression could be completely relieved by combining the three elements of 1) chromatin perturbation by mutation of histone deacetylases, 2) activation of Snf1, and 3) the addition of an Adr1 mutant that by itself confers only weak constitutive activity.
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Affiliation(s)
- Christine Tachibana
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Fox R, Nhan TQ, Law GL, Morris DR, Liles WC, Schwartz SM. PSGL-1 and mTOR regulate translation of ROCK-1 and physiological functions of macrophages. EMBO J 2007. [DOI: 10.1038/sj.emboj.7601713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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13
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Fox R, Nhan TQ, Law GL, Morris DR, Liles WC, Schwartz SM. PSGL-1 and mTOR regulate translation of ROCK-1 and physiological functions of macrophages. EMBO J 2007; 26:505-15. [PMID: 17245434 PMCID: PMC1783463 DOI: 10.1038/sj.emboj.7601522] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 11/30/2006] [Indexed: 10/23/2022] Open
Abstract
Rho-associated kinases (ROCKs) are critical molecules involved in the physiological functions of macrophages, such as chemotaxis and phagocytosis. We demonstrate that macrophage adherence promotes rapid changes in physiological functions that depend on translational upregulation of preformed ROCK-1 mRNA, but not ROCK-2 mRNA. Before adherence, both ROCK mRNAs were present in the cytoplasm of macrophages, whereas ROCK proteins were undetectable. Macrophage adherence promoted signaling through P-selectin glycoprotein ligand-1 (PSGL-1)/Akt/mTOR that resulted in synthesis of ROCK-1, but not ROCK-2. Following synthesis, ROCK-1 was catalytically active. In addition, there was a rapamycin/sirolimus-sensitive enhanced loading of ribosomes on preformed ROCK-1 mRNAs. Inhibition of mTOR by rapamycin abolished ROCK-1 synthesis in macrophages resulting in an inhibition of chemotaxis and phagocytosis. Macrophages from PSGL-1-deficient mice recapitulated pharmacological inhibitor studies. These results indicate that receptor-mediated regulation at the level of translation is a component of a rapid set of mechanisms required to direct the macrophage phenotype upon adherence and suggest a mechanism for the immunosuppressive and anti-inflammatory effects of rapamycin/sirolimus.
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Affiliation(s)
- Richard Fox
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, 815 Mercer Street, Seattle, WA 98109, USA. Tel.: +1 206 390 2997; Fax: +1 206 897 1540; E-mail:
| | - Thomas Q Nhan
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - G Lynn Law
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - W Conrad Liles
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Toronto/University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Stephen M Schwartz
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, 815 Mercer Street, Room 421, Seattle, WA 98109-4714, USA. Tel.: +1 206 543 0258; Fax: +1 206 897 1540; E-mail:
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14
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Law GL, Bickel KS, MacKay VL, Morris DR. The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders. Genome Biol 2006; 6:R111. [PMID: 16420678 PMCID: PMC1414110 DOI: 10.1186/gb-2005-6-13-r111] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 10/17/2005] [Accepted: 11/21/2005] [Indexed: 11/21/2022] Open
Abstract
Eight per cent of yeast transcripts, mostly involved in responses to stress or external stimuli, were found to be under-loaded with ribosomes, and most of them exhibited structural changes in their 5’ transcript leaders in response to the environmental signal. Background Translational efficiencies in Saccharomyces cerevisiae vary from transcript to transcript by approximately two orders of magnitude. Many of the poorly translated transcripts were found to respond to the appropriate external stimulus by recruiting ribosomes. Unexpectedly, a high frequency of these transcripts showed the appearance of altered 5' leaders that coincide with increased ribosome loading. Results Of the detectable transcripts in S. cerevisiae, 8% were found to be underloaded with ribosomes. Gene ontology categories of responses to stress or external stimuli were overrepresented in this population of transcripts. Seventeen poorly loaded transcripts involved in responses to pheromone, nitrogen starvation, and osmotic stress were selected for detailed study and were found to respond to the appropriate environmental signal with increased ribosome loading. Twelve of these regulated transcripts exhibited structural changes in their 5' transcript leaders in response to the environmental signal. In many of these the coding region remained intact, whereas regulated shortening of the 5' end truncated the open reading frame in others. Colinearity between the gene and transcript sequences eliminated regulated splicing as a mechanism for these alterations in structure. Conclusion Frequent occurrence of coordinated changes in transcript structure and translation efficiency, in at least three different gene regulatory networks, suggests a widespread phenomenon. It is likely that many of these altered 5' leaders arose from changes in promoter usage. We speculate that production of translationally silenced transcripts may be one mechanism for allowing low-level transcription activity necessary for maintaining an open chromatin structure while not allowing inappropriate protein production.
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Affiliation(s)
- G Lynn Law
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kellie S Bickel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Vivian L MacKay
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR. Gene Expression Analyzed by High-resolution State Array Analysis and Quantitative Proteomics. Mol Cell Proteomics 2004; 3:478-89. [PMID: 14766929 DOI: 10.1074/mcp.m300129-mcp200] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The transcriptome provides the database from which a cell assembles its collection of proteins. Translation of individual mRNA species into their encoded proteins is regulated, producing discrepancies between mRNA and protein levels. Using a new modeling approach to data analysis, a striking diversity is revealed in association of the transcriptome with the translational machinery. Each mRNA has its own pattern of ribosome loading, a circumstance that provides an extraordinary dynamic range of regulation, above and beyond actual transcript levels. Using this approach together with quantitative proteomics, we explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone. Interestingly, in 26% of those transcripts where the predicted protein synthesis rate changed by at least 3-fold, more than half of these changes resulted from altered translational efficiencies. These observations underscore that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions.
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Affiliation(s)
- Vivian L MacKay
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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16
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Serikawa KA, Xu XL, MacKay VL, Law GL, Zong Q, Zhao LP, Bumgarner R, Morris DR. The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Mol Cell Proteomics 2003; 2:191-204. [PMID: 12684541 DOI: 10.1074/mcp.d200002-mcp200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complete genome sequences together with high throughput technologies have made comprehensive characterizations of gene expression patterns possible. While genome-wide measurement of mRNA levels was one of the first applications of these advances, other important aspects of gene expression are also amenable to a genomic approach, for example, the translation of message into protein. Earlier we reported a high throughput technology for simultaneously studying mRNA level and translation, which we termed translation state array analysis, or TSAA. The current studies test the proposition that TSAA can identify novel instances of translation regulation at the genome-wide level. As a biological model, cultures of Saccharomyces cerevisiae were cell cycle-arrested using either alpha-factor or the temperature-sensitive cdc15-2 allele. Forty-eight mRNAs were found to change significantly in translation state following release from alpha-factor arrest, including genes involved in pheromone response and cell cycle arrest such as BAR1, SST2, and FAR1. After the shift of the cdc15-2 strain from 37 degrees C to 25 degrees C, 54 mRNAs were altered in translation state, including the products of the stress genes HSP82, HSC82, and SSA2. Thus, regulation at the translational level seems to play a significant role in the response of yeast cells to external physical or biological cues. In contrast, surprisingly few genes were found to be translationally controlled as cells progressed through the cell cycle. Additional refinements of TSAA should allow characterization of both transcriptional and translational regulatory networks on a genomic scale, providing an additional layer of information that can be integrated into models of system biology and function.
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Affiliation(s)
- Kyle A Serikawa
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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17
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Raney A, Law GL, Mize GJ, Morris DR. Regulated translation termination at the upstream open reading frame in s-adenosylmethionine decarboxylase mRNA. J Biol Chem 2002; 277:5988-94. [PMID: 11741992 DOI: 10.1074/jbc.m108375200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The upstream open reading frame (uORF) in the mRNA encoding S-adenosylmethionine decarboxylase is a cis-acting element that confers feedback control by cellular polyamines on translation of this message. Recent studies demonstrated that elevated polyamines inhibit synthesis of the peptide encoded by the uORF by stabilizing a ribosome paused in the vicinity of the termination codon. These studies suggested that polyamines act at the termination step of uORF translation. In this paper, we demonstrate that elevated polyamines stabilize an intermediate in the termination process, the complete nascent peptide linked to the tRNA that decodes the final codon. The peptidyl-tRNA molecule is found associated with the ribosome fraction, and decay of this molecule correlated with release of the paused ribosome from the message. Furthermore, the stability of this complex is influenced by the same parameters that influence regulation by the uORF in vivo, namely the concentration of polyamines and the sequence of the uORF-encoded peptide. These results suggest that the regulated step in uORF translation is after formation of the peptidyl-tRNA molecule but before hydrolysis of the peptidyl-tRNA bond. This regulation may involve an interaction between the peptide, polyamines, and a target in the translational apparatus.
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Affiliation(s)
- Alexa Raney
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA
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18
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Law GL, Raney A, Heusner C, Morris DR. Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase. J Biol Chem 2001; 276:38036-43. [PMID: 11489903 DOI: 10.1074/jbc.m105944200] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synthesis of S-adenosylmethionine decarboxylase (AdoMetDC), a key regulated enzyme in the pathway of polyamine biosynthesis, is feedback-controlled at the level of translation by spermidine and spermine. The peptide product of an upstream open reading frame (uORF) in the mRNA is solely responsible for polyamine regulation of AdoMetDC translation. Using a primer extension inhibition assay and in vitro protein synthesis reactions, we found ribosomes paused at or close to the termination codon of the uORF. This pause was greatly diminished with the altered uORFs' sequences that abolish uORF regulation in vivo. The half-life of the ribosome pause was related to the concentration of polyamines present but was unaffected by magnesium concentration. Furthermore, inhibition of translation initiation at a reporter gene placed downstream of the AdoMetDC uORF directly correlated with the stability of the ribosome pause at the uORF. These observations are consistent with a model in which regulation of ribosome pausing at the uORF by polyamines controls ribosome access to the downstream AdoMetDC reading frame.
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Affiliation(s)
- G L Law
- Department of Biochemistry, University of Washington, Seattle, 98195-7350, USA
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Raney A, Baron AC, Mize GJ, Law GL, Morris DR. In vitro translation of the upstream open reading frame in the mammalian mRNA encoding S-adenosylmethionine decarboxylase. J Biol Chem 2000; 275:24444-50. [PMID: 10829027 DOI: 10.1074/jbc.m003364200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The upstream open reading frame (uORF) in the mRNA encoding S-adenosylmethionine decarboxylase is a polyamine-responsive element that suppresses translation of the associated downstream cistron in vivo. In this paper, we provide the first direct evidence of peptide synthesis from the S-adenosylmethionine decarboxylase uORF using an in vitro translation system. We examine both the influence of cation concentration on peptide synthesis and the effect of altering the uORF sequence on peptide synthesis. Synthesis of wild type and altered peptides was similar at all concentrations of magnesium tested. In contrast, synthesis of the wild type peptide was more sensitive than that of altered peptides to elevated concentrations of the naturally occurring polyamines, spermidine and spermine, as well as several polyamine analogs. The sensitivity of in vitro synthesis to spermidine was influenced by both the amino acid sequence and the length of the peptide product of the uORF. Findings from the present study correlate with the effects of the uORF and polyamines on translation of a downstream cistron in vivo and support the hypothesis that polyamines and the structure of the nascent peptide create a rate-limiting step in uORF translation, perhaps through a ribosome stalling mechanism.
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Affiliation(s)
- A Raney
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA
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Law DJ, Du M, Law GL, Merchant JL. ZBP-99 defines a conserved family of transcription factors and regulates ornithine decarboxylase gene expression. Biochem Biophys Res Commun 1999; 262:113-20. [PMID: 10448078 DOI: 10.1006/bbrc.1999.1180] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Among transcription factors that regulate ornithine decarboxylase (ODC) gene expression are those that interact with GC-rich promoters, including Sp1 and ZBP-89. Sp1 functions as a transactivator and ZBP-89 as a transrepressor of both the ODC and gastrin promoters. This study reports the cloning and characterization of a second member of the ZBP family that also binds GC boxes. ZBP-99 contains four Krüppel-type zinc fingers that collectively share 91% amino acid sequence similarity and 79% sequence identity with those found in ZBP-89. In addition, there are highly conserved amino acid sequences in the carboxy-terminal segments of the two genes. In spite of their structural similarities, the two proteins are encoded at distinct loci, ZBP-89 on chromosome 3q21 and ZBP-99 on 1q32.1. The predicted open reading frame of ZBP-99 cDNA encodes a 99-kDa protein. Electrophoretic mobility shift assays showed that ZBP-99 protein specifically binds to the GC-rich promoter elements of gastrin and ODC genes. Northern blot analysis showed that a major ZBP-99 transcript of 5.6 kb is expressed ubiquitously at low levels, with elevated expression levels in placenta and in adult kidney, liver, and lymphocytes. Cotransfection of AGS gastric adenocarcinoma and HT-29 colon adenocarcinoma cells with a ZBP-99 expression construct and with an ODC reporter construct show that ZBP-99 repressed basal expression in the two cell lines by 80 and 60%, respectively. Collectively, the data suggest that ZBP-99 binds GC-rich promoters and may complement the activities mediated by ZBP-89.
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Affiliation(s)
- D J Law
- Department of Internal Medicine, Department of Physiology, University of Michigan, Michigan, Ann Arbor 48109-0650, USA
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Abstract
The product of the Wilm's tumor suppressor gene, WT1, is a zinc-finger DNA-binding protein, which is thought to be a transcription factor. Two genes, those encoding epidermal growth factor receptor and syndecan-1, are known to be endogenous targets of WT1. Previous studies had identified binding sites for WT1 in the promoter of the ornithine decarboxylase (ODC) gene. In this paper, we tested whether the endogenous ODC gene might be a target of WT1 by establishing lines of baby hamster kidney (BHK) cells that expressed WT1 isoform A under control of a tetracycline-regulated expression system. When expression of WT1 was activated in BHK cells, the cellular level of ODC mRNA declined, with kinetics that correlated with the increase in WT1 level, demonstrating that the endogenous ODC gene was indeed responsive to cellular level of WT1. WT1 isoforms A and B inhibited the activity of the ODC promoter by approximately fivefold in transiently transfected BHK cells, while isoforms C and D, which have altered DNA binding domains, had no significant effect. The sequence CTCCCCCGC, located at nucleotides -106 to -98 relative to the site of transcriptional initiation in the ODC gene, interacted with the zinc-finger domain of isoforms A and B of WT1 with high affinity and specificity. A mutation in the binding site that disrupted this interaction partially removed the inhibition of ODC promoter activity by WT1, as did mutation of the two E-box sequences in intron I of the ODC gene. Simultaneous mutation of the WT1-binding motif and the two E-boxes completely abolished inhibition by WT1 of ODC promoter activity. These results, taken together, implicate the ODC gene as a downstream target of the tumor suppressor WT1.
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Affiliation(s)
- R S Li
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA
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Law GL, Itoh H, Law DJ, Mize GJ, Merchant JL, Morris DR. Transcription factor ZBP-89 regulates the activity of the ornithine decarboxylase promoter. J Biol Chem 1998; 273:19955-64. [PMID: 9685330 DOI: 10.1074/jbc.273.32.19955] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Appropriate cellular levels of polyamines are required for cell growth and differentiation. Ornithine decarboxylase is a key regulatory enzyme in the biosynthesis of polyamines, and precise regulation of the expression of this enzyme is required, according to cellular growth state. A variety of mitogens increase the level of ornithine decarboxylase activity, and, in most cases, this elevation is due to increased levels of mRNA. A GC box in the proximal promoter of the ornithine decarboxylase gene is required for basal and induced transcriptional activity, and two proteins, Sp1 and NF-ODC1, bind to this region in a mutually exclusive manner. Using a yeast one-hybrid screening method, ZBP-89, a DNA-binding protein, was identified as a candidate for the protein responsible for NF-ODC1 binding activity. Three lines of evidence verified this identification; ZBP-89 copurified with NF-ODC1 binding activity, ZBP-89 antibodies specifically abolished NF-ODC1 binding to the GC box, and binding affinities of 12 different double-stranded oligonucleotides were indistinguishable between NF-ODC1, in nuclear extract, and in vitro translated ZBP-89. ZBP-89 inhibited the activation of the ornithine decarboxylase promoter by Sp1 in Schneider's Drosophila line 2, consistent with properties previously attributed to NF-ODC1.
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Affiliation(s)
- G L Law
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Law GL, McGuinness MP, Linder CC, Griswold MD. Expression of apolipoprotein E mRNA in the epithelium and interstitium of the testis and the epididymis. J Androl 1997; 18:32-42. [PMID: 9089066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Apolipoprotein E (apo E) is an important constituent of plasma lipoproteins and is believed to be involved in the regulation of lipid transport and distribution between tissues. The production of this apolipoprotein in extra-hepatic tissues such as the testis and epididymis could facilitate specific local functions. Apo E mRNA was detected in testis, epididymis, seminal vesicles, and prostate. In the epididymis, apo E was detected using in situ hybridization in epithelial cells and in some cells in the interstitium throughout the organ (i.e., caput, corpus, and cauda). Northern blot analysis showed that apo E mRNA is present in Sertoli cells and germ cells, but not peritubular myoid cells. Interstitial cells of the testis displayed the most intense signal for apo E message using in situ hybridization. Messenger RNA for apo E was also detected in the interstitium of rat testes at 3 and 6 days after animals were treated with ethylene dimethanesulfonate (EDS) to eliminate Leydig cells. Thus, in addition to Leydig cells, other cell types within the interstitium are capable of producing apo E message. Levels of testicular apo E mRNA increased between 30 and 60 days pc during which the germ cell population is increasing. As determined by northern blot analysis of RNA from stage synchronized testes, the levels of apo E mRNA fluctuate in relation to the cycle of the seminiferous epithelium. The cells responsible for this stage-specific variation in message could not be identified by in situ hybridization. Apolipoprotein Al (apo Al) mRNA was also found to be expressed in the epididymis but not in the testis of adult rats. The role of apolipoproteins in spermatogenesis and sperm maturation has not been elucidated. The results of this study demonstrate the specific tissues and cells types which play a role in the production and possible regulation of apo E mRNA in the male reproductive tract. These data will help in the elucidation of the function of apo E in spermatogenesis and sperm maturation.
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Affiliation(s)
- G L Law
- Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660, USA
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Abstract
Sulfated glycoprotein 2 (SGP 2) is a 73-kDa highly glycosylated disulfide-linked heterodimer. It is a major secreted protein of Sertoli cells, is found in high abundance within the seminiferous tubule fluid (STF) and epididymal fluid (EPF), and can be found on the surface of spermatozoa. Due to its high abundance and location it is believed to play a major role in the development of spermatozoa; however, its specific function(s) within the reproductive tract is not known. Purified and renatured SGP 2 were found to have the ability to inhibit complement activity with a mean concentration of 66 mg/ml for 50% inhibition. Extraction of epididymal sperm with various reagents showed that a major fraction of the SGP 2 in EPF was free or was loosely associated with the spermatozoa whereas a smaller fraction was more tightly associated and disruption of the lipid bilayer was required for its complete removal. Ultracentrifugation techniques and gel permeation chromatography revealed that SGP 2 in plasma, STF, and EPF formed complexes with other proteins and/or lipids but was not specifically associated with the apolipoprotein-like particles containing apolipoprotein A1 (apo A1).
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Affiliation(s)
- G L Law
- Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660
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