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Yeter EÇ, Şahin S, Caglayan MO, Üstündağ Z. An electrochemical label-free DNA impedimetric sensor with AuNP-modified glass fiber/carbonaceous electrode for the detection of HIV-1 DNA. CHEMICKE ZVESTI 2020; 75:77-87. [PMID: 32836707 PMCID: PMC7354876 DOI: 10.1007/s11696-020-01280-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/06/2020] [Indexed: 11/17/2022]
Abstract
In this study, a highly sensitive, electrochemical, and label-free DNA impedimetric sensor was developed using carbonized glass fiber-coal tar pitch (GF-CTP) electrodes supported with gold nanoparticles (AuNPs) for the detection of HIV-1 gene. Thiol-modified GF-CTP electrodes were prepared using amine crosslinking chemistry and AuNPs were self-assembled obtaining highly conductive nanoelectrodes, GF-CTP-ATP-Au. All steps of electrode modifications were characterized using electrochemical, spectroscopic, and microscopic methods. GF-CTP-ATP-Au electrode was then modified with a capture DNA probe (C-ssDNA) and optimized with a target DNA probe in terms of hybridization time and temperature between 30 and 180 min and 20-50 °C, respectively. Finally, the analytic performance of the developed ssDNA biosensor was evaluated using electrochemical impedance spectroscopy. The calibration of the sensor was obtained between 0.1 pM and 10 nM analyte working range. The limit of detection was calculated using signal to noise ratio of 3 (S/N = 3) as 13 fM. Moreover, interference results for two noncomplementary DNA probes were also tested to demonstrate non-specific ssDNA interactions. An electrochemical label-free DNA impedimetric sensor was successfully developed using a novel GF-CTP-ATP-Au electrode. This study suggests that highly sensitive DNA-based biosensors can be developed using relatively low-cost carbonaceous materials.
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Affiliation(s)
- Ece Ç. Yeter
- Department of Chemistry, Kütahya Dumlupınar University, 43100 Kütahya, Turkey
| | - Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
| | - M. Oguzhan Caglayan
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
| | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, 43100 Kütahya, Turkey
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3
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Ali I, Ramage H, Boehm D, Dirk LMA, Sakane N, Hanada K, Pagans S, Kaehlcke K, Aull K, Weinberger L, Trievel R, Schnoelzer M, Kamada M, Houtz R, Ott M. The HIV-1 Tat Protein Is Monomethylated at Lysine 71 by the Lysine Methyltransferase KMT7. J Biol Chem 2016; 291:16240-8. [PMID: 27235396 DOI: 10.1074/jbc.m116.735415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 transactivator protein Tat is a critical regulator of HIV transcription primarily enabling efficient elongation of viral transcripts. Its interactions with RNA and various host factors are regulated by ordered, transient post-translational modifications. Here, we report a novel Tat modification, monomethylation at lysine 71 (K71). We found that Lys-71 monomethylation (K71me) is catalyzed by KMT7, a methyltransferase that also targets lysine 51 (K51) in Tat. Using mass spectrometry, in vitro enzymology, and modification-specific antibodies, we found that KMT7 monomethylates both Lys-71 and Lys-51 in Tat. K71me is important for full Tat transactivation, as KMT7 knockdown impaired the transcriptional activity of wild type (WT) Tat but not a Tat K71R mutant. These findings underscore the role of KMT7 as an important monomethyltransferase regulating HIV transcription through Tat.
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Affiliation(s)
- Ibraheem Ali
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Departments of Medicine and
| | - Holly Ramage
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Daniela Boehm
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Lynnette M A Dirk
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40508
| | - Naoki Sakane
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Kazuki Hanada
- Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Sara Pagans
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Katrin Kaehlcke
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Katherine Aull
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Leor Weinberger
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Raymond Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and
| | | | - Masafumi Kamada
- Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Robert Houtz
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40508
| | - Melanie Ott
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Departments of Medicine and
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4
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Fatin MF, Ruslinda AR, Md Arshad MK, Tee KK, Ayub RM, Hashim U, Kamarulzaman A, Gopinath SCB. HIV-1 Tat biosensor: Current development and trends for early detection strategies. Biosens Bioelectron 2015; 78:358-366. [PMID: 26655174 DOI: 10.1016/j.bios.2015.11.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/20/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus (HIV) has infected almost 35 million people worldwide. Various tests have been developed to detect the presence of HIV during the early stages of the disease in order to reduce the risk of transmission to other humans. The HIV-1 Tat protein is one of the proteins present in HIV that are released abundantly approximately 2-4 weeks after infection. In this review, we have outlined various strategies for detecting the Tat protein, which helps transcribe the virus and enhances replication. Detection strategies presented include immunoassays, biosensors and gene expression, which utilize antibodies or aptamers as common probes to sense the presence of Tat. Alternatively, measuring the levels of gene transcription is a direct method of analysing the HIV gene to confirm the presence of Tat. By detection of the Tat protein, virus transmission can be detected in high-risk individuals in the early stages of the disease to reduce the risk of an HIV pandemic.
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Affiliation(s)
- M F Fatin
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - A R Ruslinda
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia.
| | - M K Md Arshad
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - K K Tee
- Center of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - R M Ayub
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - A Kamarulzaman
- Center of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
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5
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Zhang X, Huang Y, Shi X. Emerging roles of lysine methylation on non-histone proteins. Cell Mol Life Sci 2015; 72:4257-72. [PMID: 26227335 PMCID: PMC11114002 DOI: 10.1007/s00018-015-2001-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 06/27/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Lysine methylation is a common posttranslational modification (PTM) of histones that is important for the epigenetic regulation of transcription and chromatin in eukaryotes. Increasing evidence demonstrates that in addition to histones, lysine methylation also occurs on various non-histone proteins, especially transcription- and chromatin-regulating proteins. In this review, we will briefly describe the histone lysine methyltransferases (KMTs) that have a broad spectrum of non-histone substrates. We will use p53 and nuclear receptors, especially estrogen receptor alpha, as examples to discuss the dynamic nature of non-histone protein lysine methylation, the writers, erasers, and readers of these modifications, and the crosstalk between lysine methylation and other PTMs in regulating the functions of the modified proteins. Understanding the roles of lysine methylation in normal cells and during development will shed light on the complex biology of diseases associated with the dysregulation of lysine methylation on both histones and non-histone proteins.
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Affiliation(s)
- Xi Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yaling Huang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Genes and Development and the Epigenetics and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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6
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Chesarino NM, McMichael TM, Yount JS. Regulation of the trafficking and antiviral activity of IFITM3 by post-translational modifications. Future Microbiol 2015; 9:1151-63. [PMID: 25405885 DOI: 10.2217/fmb.14.65] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IFITM3 restricts cellular infection by multiple important viral pathogens, and is particularly critical for the innate immune response against influenza virus. Expression of IFITM3 expands acidic endolysosomal compartments and prevents fusion of endocytosed viruses, leading to their degradation. This small, 133 amino acid, antiviral protein is controlled by at least four distinct post-translational modifications. Positive regulation of IFITM3 antiviral activity is provided by S-palmitoylation, while negative regulatory mechanisms include lysine ubiquitination, lysine methylation and tyrosine phosphorylation. Herein, we describe specific insights into IFITM3 trafficking and activity that were provided by studies of IFITM3 post-translational modifications, and discuss evidence suggesting that IFITM3 adopts multiple membrane topologies involving at least one intramembrane domain in its antivirally active conformation.
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Affiliation(s)
- Nicholas M Chesarino
- Department of Microbial Infection & Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210, USA
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Sargeant DP, Deverasetty S, Strong CL, Alaniz IJ, Bartlett A, Brandon NR, Brooks SB, Brown FA, Bufi F, Chakarova M, David RP, Dobritch KM, Guerra HP, Hedden MW, Kumra R, Levitt KS, Mathew KR, Matti R, Maza DQ, Mistry S, Novakovic N, Pomerantz A, Portillo J, Rafalski TF, Rathnayake VR, Rezapour N, Songao S, Tuggle SL, Yousif S, Dorsky DI, Schiller MR. The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. PLoS One 2014; 9:e98810. [PMID: 24886930 PMCID: PMC4041786 DOI: 10.1371/journal.pone.0098810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/06/2014] [Indexed: 12/15/2022] Open
Abstract
There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com].
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Affiliation(s)
- David P. Sargeant
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sandeep Deverasetty
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Christy L. Strong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Izua J. Alaniz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Alexandria Bartlett
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Nicholas R. Brandon
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Steven B. Brooks
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Frederick A. Brown
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Flaviona Bufi
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Monika Chakarova
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Roxanne P. David
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Karlyn M. Dobritch
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Horacio P. Guerra
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Michael W. Hedden
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Rma Kumra
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Kelvy S. Levitt
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Kiran R. Mathew
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Ray Matti
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Dorothea Q. Maza
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sabyasachy Mistry
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Nemanja Novakovic
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Austin Pomerantz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Josue Portillo
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Timothy F. Rafalski
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Viraj R. Rathnayake
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Noura Rezapour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sarah Songao
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sean L. Tuggle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sandy Yousif
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - David I. Dorsky
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Martin R. Schiller
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
- * E-mail:
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Lanouette S, Mongeon V, Figeys D, Couture JF. The functional diversity of protein lysine methylation. Mol Syst Biol 2014; 10:724. [PMID: 24714364 PMCID: PMC4023394 DOI: 10.1002/msb.134974] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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9
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Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell 2013; 52:314-24. [PMID: 24207025 PMCID: PMC3936344 DOI: 10.1016/j.molcel.2013.10.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/26/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022]
Abstract
Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA polymerase II, is subject to acetylation in mammalian cells. Acetylation occurs at eight lysines within the C-terminal domain (CTD) of the largest polymerase subunit and is mediated by p300/KAT3B. CTD acetylation is specifically enriched downstream of the transcription start sites of polymerase-occupied genes genome-wide, indicating a role in early stages of transcription initiation or elongation. Mutation of lysines or p300 inhibitor treatment causes the loss of epidermal growth-factor-induced expression of c-Fos and Egr2, immediate-early genes with promoter-proximally paused polymerases, but does not affect expression or polymerase occupancy at housekeeping genes. Our studies identify acetylation as a new modification of the mammalian RNA polymerase II required for the induction of growth factor response genes.
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Affiliation(s)
- Sebastian Schröder
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eva Herker
- Gladstone Institutes, San Francisco, CA 94158, USA
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Friederike Itzen
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Daniel He
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sean Thomas
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Gilchrist
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Katrin Kaehlcke
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungyoo Cho
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - John A. Capra
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Matthias Geyer
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
- Research Center Caesar, 53175 Bonn, Germany
| | - Benoit G. Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karen Adelman
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
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Catch and measure-mass spectrometry-based immunoassays in biomarker research. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:927-32. [PMID: 24060810 DOI: 10.1016/j.bbapap.2013.09.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/28/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022]
Abstract
Mass spectrometry-based (MS) methods are effective tools for discovering protein biomarker candidates that can differentiate between physiological and pathophysiological states. Promising candidates are validated in studies comprising large patient cohorts. Here, targeted protein analytics are used to increase sample throughput. Methods involving antibodies, such as sandwich immunoassays or Western blots, are commonly applied at this stage. Highly-specific and sensitive mass spectrometry-based immunoassays that have been established in recent years offer a suitable alternative to sandwich immunoassays for quantifying proteins. Mass Spectrometric ImmunoAssays (MSIA) and Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA/iMALDI) are two prominent types of MS-based immunoassays in which the capture is done either at the protein or the peptide level. We present an overview of these emerging types of immunoassays and discuss their suitability for the discovery and validation of protein biomarkers. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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11
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Protein methylation at the surface and buried deep: thinking outside the histone box. Trends Biochem Sci 2013; 38:243-52. [PMID: 23490039 DOI: 10.1016/j.tibs.2013.02.004] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 01/31/2013] [Accepted: 02/05/2013] [Indexed: 01/08/2023]
Abstract
Methylated lysine and arginine residues in histones represent a crucial part of the histone code, and recognition of these methylated residues by protein interaction domains modulates transcription. Although some methylating enzymes appear to be histone specific, many can modify histone and non-histone substrates and an increasing number are specific for non-histone substrates. Some of the non-histone substrates can also be involved in transcription, but a distinct subset of protein methylation reactions occurs at residues buried deeply in ribosomal proteins that may function in protein-RNA interactions rather than protein-protein interactions. Additionally, recent work has identified enzymes that catalyze protein methylation reactions at new sites in ribosomal and other proteins. These reactions include modifications of histidine and cysteine residues as well as the N terminus.
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Kakiya N, Saito T, Nilsson P, Matsuba Y, Tsubuki S, Takei N, Nawa H, Saido TC. Cell surface expression of the major amyloid-β peptide (Aβ)-degrading enzyme, neprilysin, depends on phosphorylation by mitogen-activated protein kinase/extracellular signal-regulated kinase kinase (MEK) and dephosphorylation by protein phosphatase 1a. J Biol Chem 2012; 287:29362-72. [PMID: 22767595 PMCID: PMC3436156 DOI: 10.1074/jbc.m112.340372] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neprilysin is one of the major amyloid-β peptide (Aβ)-degrading enzymes, the expression of which declines in the brain during aging. The decrease in neprilysin leads to a metabolic Aβ imbalance, which can induce the amyloidosis underlying Alzheimer disease. Pharmacological activation of neprilysin during aging therefore represents a potential strategy to prevent the development of Alzheimer disease. However, the regulatory mechanisms mediating neprilysin activity in the brain remain unclear. To address this issue, we screened for pharmacological regulators of neprilysin activity and found that the neurotrophic factors brain-derived neurotrophic factor, nerve growth factor, and neurotrophins 3 and 4 reduce cell surface neprilysin activity. This decrease was mediated by MEK/ERK signaling, which enhanced phosphorylation at serine 6 in the neprilysin intracellular domain (S6-NEP-ICD). Increased phosphorylation of S6-NEP-ICD in primary neurons reduced the levels of cell surface neprilysin and led to a subsequent increase in extracellular Aβ levels. Furthermore, a specific inhibitor of protein phosphatase-1a, tautomycetin, induced extensive phosphorylation of the S6-NEP-ICD, resulting in reduced cell surface neprilysin activity. In contrast, activation of protein phosphatase-1a increased cell surface neprilysin activity and lowered Aβ levels. Taken together, these results indicate that the phosphorylation status of S6-NEP-ICD influences the localization of neprilysin and affects extracellular Aβ levels. Therefore, maintaining S6-NEP-ICD in a dephosphorylated state, either by inhibition of protein kinases involved in its phosphorylation or by activation of phosphatases catalyzing its dephosphorylation, may represent a new approach to prevent reduction of cell surface neprilysin activity during aging and to maintain physiological levels of Aβ in the brain.
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Affiliation(s)
- Naomasa Kakiya
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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Kwon HS, Lim HW, Wu J, Schnölzer M, Verdin E, Ott M. Three novel acetylation sites in the Foxp3 transcription factor regulate the suppressive activity of regulatory T cells. THE JOURNAL OF IMMUNOLOGY 2012; 188:2712-21. [PMID: 22312127 DOI: 10.4049/jimmunol.1100903] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The Foxp3 transcription factor is the master regulator of regulatory T cell (Treg) differentiation and function. Its activity is regulated by reversible acetylation. Using mass spectrometry of immunoprecipitated proteins, we identify three novel acetylation sites in murine Foxp3 (K31, K262, and K267) and the corresponding sites in human FOXP3 proteins. Newly raised modification-specific Abs against acetylated K31 and K267 confirm acetylation of these residues in murine Tregs. Mutant Foxp3 proteins carrying arginine substitutions at the three acetylation sites (3KR) accumulate in T cells to higher levels than wild-type Foxp3 and exert better suppressive activity in coculture experiments. Acetylation and stability of wild-type, but not mutant, Foxp3 is enhanced when cells are treated with Ex-527, an inhibitor of the NAD(+)-dependent deacetylase SIRT1. Treatment with Ex-527 promotes Foxp3 expression during induced Treg differentiation, enhances Foxp3 levels in natural Tregs, and prevents loss of Foxp3 expression in adoptively transferred Tregs in mice. Our data identify SIRT1 as a negative regulator of Treg function via deacetylation of three novel target sites in Foxp3. SIRT1 inhibitors strengthen the suppressive activity of Tregs and may be useful in enhancing Treg-based therapeutic approaches to autoimmune diseases or graft rejections.
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Affiliation(s)
- Hye-Sook Kwon
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
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Sakane N, Kwon HS, Pagans S, Kaehlcke K, Mizusawa Y, Kamada M, Lassen KG, Chan J, Greene WC, Schnoelzer M, Ott M. Activation of HIV transcription by the viral Tat protein requires a demethylation step mediated by lysine-specific demethylase 1 (LSD1/KDM1). PLoS Pathog 2011; 7:e1002184. [PMID: 21876670 PMCID: PMC3158049 DOI: 10.1371/journal.ppat.1002184] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 06/14/2011] [Indexed: 12/11/2022] Open
Abstract
The essential transactivator function of the HIV Tat protein is regulated by multiple posttranslational modifications. Although individual modifications are well characterized, their crosstalk and dynamics of occurrence during the HIV transcription cycle remain unclear.We examine interactions between two critical modifications within the RNA-binding domain of Tat: monomethylation of lysine 51 (K51) mediated by Set7/9/KMT7, an early event in the Tat transactivation cycle that strengthens the interaction of Tat with TAR RNA, and acetylation of lysine 50 (K50) mediated by p300/KAT3B, a later process that dissociates the complex formed by Tat, TAR RNA and the cyclin T1 subunit of the positive transcription elongation factor b (P-TEFb). We find K51 monomethylation inhibited in synthetic Tat peptides carrying an acetyl group at K50 while acetylation can occur in methylated peptides, albeit at a reduced rate. To examine whether Tat is subject to sequential monomethylation and acetylation in cells, we performed mass spectrometry on immunoprecipitated Tat proteins and generated new modification-specific Tat antibodies against monomethylated/acetylated Tat. No bimodified Tat protein was detected in cells pointing to a demethylation step during the Tat transactivation cycle. We identify lysine-specific demethylase 1 (LSD1/KDM1) as a Tat K51-specific demethylase, which is required for the activation of HIV transcription in latently infected T cells. LSD1/KDM1 and its cofactor CoREST associates with the HIV promoter in vivo and activate Tat transcriptional activity in a K51-dependent manner. In addition, small hairpin RNAs directed against LSD1/KDM1 or inhibition of its activity with the monoamine oxidase inhibitor phenelzine suppresses the activation of HIV transcription in latently infected T cells.Our data support the model that a LSD1/KDM1/CoREST complex, normally known as a transcriptional suppressor, acts as a novel activator of HIV transcription through demethylation of K51 in Tat. Small molecule inhibitors of LSD1/KDM1 show therapeutic promise by enforcing HIV latency in infected T cells.
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Affiliation(s)
- Naoki Sakane
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
- Pharmaceutical Frontier Research Laboratory, Yokohama, Japan
| | - Hye-Sook Kwon
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Sara Pagans
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Katrin Kaehlcke
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | | | - Masafumi Kamada
- Pharmaceutical Frontier Research Laboratory, Yokohama, Japan
| | - Kara G. Lassen
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Jonathan Chan
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Warner C. Greene
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, United States of America
- Department of Microbiology and Immunology, University of California, San Francisco, United States of America
| | - Martina Schnoelzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, United States of America
- * E-mail:
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Ott M. HIV never ceases to surprise: Innovative methods in the quest for a cure. Methods 2011; 53:1-2. [PMID: 21251605 DOI: 10.1016/j.ymeth.2010.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2010] [Indexed: 11/16/2022] Open
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