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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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3
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Unnikrishnan A, Guan YF, Huang Y, Beck D, Thoms JAI, Peirs S, Knezevic K, Ma S, de Walle IV, de Jong I, Ali Z, Zhong L, Raftery MJ, Taghon T, Larsson J, MacKenzie KL, Van Vlierberghe P, Wong JWH, Pimanda JE. A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network. Nucleic Acids Res 2016; 44:10644-10661. [PMID: 27604872 PMCID: PMC5159545 DOI: 10.1093/nar/gkw804] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022] Open
Abstract
Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.
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MESH Headings
- Base Sequence
- Binding Sites
- Cell Line, Tumor
- Consensus Sequence
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Humans
- Ikaros Transcription Factor/physiology
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Prognosis
- Proportional Hazards Models
- Protein Binding
- Proteome
- Proteomics
- Proto-Oncogene Proteins c-ets/physiology
- Repressor Proteins/physiology
- Transcription, Genetic
- Transcriptional Regulator ERG/physiology
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Ashwin Unnikrishnan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yi F Guan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yizhou Huang
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Dominik Beck
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Center for Medical Genetics, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Julie A I Thoms
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Sofie Peirs
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Kathy Knezevic
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Shiyong Ma
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Inge V de Walle
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Ineke de Jong
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Zara Ali
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Tom Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Pieter Van Vlierberghe
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Jason W H Wong
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - John E Pimanda
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Department of Haematology, Prince of Wales Hospital, Sydney, 2031, Australia
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Abstract
Y. pestis exhibits dramatically different traits of pathogenicity and transmission, albeit their close genetic relationship with its ancestor-Y. pseudotuberculosis, a self-limiting gastroenteric pathogen. Y. pestis is evolved into a deadly pathogen and transmitted to mammals and/or human beings by infected flea biting or directly contacting with the infected animals. Various kinds of environmental changes are implicated into its complex life cycle and pathogenesis. Dynamic regulation of gene expression is critical for environmental adaptation or survival, primarily reflected by genetic regulation mediated by transcriptional factors and small regulatory RNAs at the transcriptional and posttranscriptional level, respectively. The effects of genetic regulation have been shown to profoundly influence Y. pestis physiology and pathogenesis such as stress resistance, biofilm formation, intracellular survival, and replication. In this chapter, we mainly summarize the progresses on popular methods of genetic regulation and on regulatory patterns and consequences of many key transcriptional and posttranscriptional regulators, with a particular emphasis on how genetic regulation influences the biofilm and virulence of Y. pestis.
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Massah S, Hollebakken R, Labrecque MP, Kolybaba AM, Beischlag TV, Prefontaine GG. Epigenetic characterization of the growth hormone gene identifies SmcHD1 as a regulator of autosomal gene clusters. PLoS One 2014; 9:e97535. [PMID: 24818964 PMCID: PMC4018343 DOI: 10.1371/journal.pone.0097535] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 04/21/2014] [Indexed: 12/31/2022] Open
Abstract
Regulatory elements for the mouse growth hormone (GH) gene are located distally in a putative locus control region (LCR) in addition to key elements in the promoter proximal region. The role of promoter DNA methylation for GH gene regulation is not well understood. Pit-1 is a POU transcription factor required for normal pituitary development and obligatory for GH gene expression. In mammals, Pit-1 mutations eliminate GH production resulting in a dwarf phenotype. In this study, dwarf mice illustrated that Pit-1 function was obligatory for GH promoter hypomethylation. By monitoring promoter methylation levels during developmental GH expression we found that the GH promoter became hypomethylated coincident with gene expression. We identified a promoter differentially methylated region (DMR) that was used to characterize a methylation-dependent DNA binding activity. Upon DNA affinity purification using the DMR and nuclear extracts, we identified structural maintenance of chromosomes hinge domain containing -1 (SmcHD1). To better understand the role of SmcHD1 in genome-wide gene expression, we performed microarray analysis and compared changes in gene expression upon reduced levels of SmcHD1 in human cells. Knock-down of SmcHD1 in human embryonic kidney (HEK293) cells revealed a disproportionate number of up-regulated genes were located on the X-chromosome, but also suggested regulation of genes on non-sex chromosomes. Among those, we identified several genes located in the protocadherin β cluster. In addition, we found that imprinted genes in the H19/Igf2 cluster associated with Beckwith-Wiedemann and Silver-Russell syndromes (BWS & SRS) were dysregulated. For the first time using human cells, we showed that SmcHD1 is an important regulator of imprinted and clustered genes.
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Affiliation(s)
- Shabnam Massah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Robert Hollebakken
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Mark P. Labrecque
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Addie M. Kolybaba
- Faculty of Biology, Ludwig Maximilians University Munich, Martinsried, Germany
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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7
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Nagore LI, Nadeau RJ, Guo Q, Jadhav YLA, Jarrett HW, Haskins WE. Purification and characterization of transcription factors. MASS SPECTROMETRY REVIEWS 2013; 32:386-398. [PMID: 23832591 PMCID: PMC3758410 DOI: 10.1002/mas.21369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 11/19/2012] [Accepted: 11/19/2012] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA-protein complex on solid supports. Additional methods for improving dynamic range include two- and three-dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome.
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Affiliation(s)
- LI Nagore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
| | - RJ Nadeau
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Q Guo
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - YLA Jadhav
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - HW Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
| | - WE Haskins
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Biology, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
- Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
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Tacheny A, Michel S, Dieu M, Payen L, Arnould T, Renard P. Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis. Nucleic Acids Res 2012; 40:e168. [PMID: 22904091 PMCID: PMC3505963 DOI: 10.1093/nar/gks733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To depict the largest picture of a core promoter interactome, we developed a one-step DNA-affinity capture method coupled with an improved mass spectrometry analysis process focused on the identification of low abundance proteins. As a proof of concept, this method was developed through the analysis of 230 bp contained in the 5′long terminal repeat (LTR) of the human immunodeficiency virus 1 (HIV-1). Beside many expected interactions, many new transcriptional regulators were identified, either transcription factors (TFs) or co-regulators, which interact directly or indirectly with the HIV-1 5′LTR. Among them, the homeodomain-containing TF myeloid ectopic viral integration site was confirmed to functionally interact with a specific binding site in the HIV-1 5′LTR and to act as a transcriptional repressor, probably through recruitment of the repressive Sin3A complex. This powerful and validated DNA-affinity approach could also be used as an efficient screening tool to identify a large set of proteins that physically interact, directly or indirectly, with a DNA sequence of interest. Combined with an in silico analysis of the DNA sequence of interest, this approach provides a powerful approach to select the interacting candidates to validate functionally by classical approaches.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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Jiang D, Jia Y, Jarrett HW. Transcription factor proteomics: identification by a novel gel mobility shift-three-dimensional electrophoresis method coupled with southwestern blot and high-performance liquid chromatography-electrospray-mass spectrometry analysis. J Chromatogr A 2011; 1218:7003-15. [PMID: 21880322 PMCID: PMC3174475 DOI: 10.1016/j.chroma.2011.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/05/2011] [Accepted: 08/09/2011] [Indexed: 11/15/2022]
Abstract
Transcription factor (TF) purification and identification is an important step in elucidating gene regulatory mechanisms. In this study, we present two new electrophoretic mobility shift assay (EMSA)-based multi-dimensional electrophoresis approaches to isolate and characterize TFs, using detection with either southwestern or western blotting and HPLC-nanoESI-MS/MS analysis for identification. These new techniques involve several major steps. First, EMSA is performed with agents that diminish non-specific DNA-binding and the DNA-protein complex is separated by native PAGE gel. The gel is then electrotransferred to PVDF membrane and visualized by autoradiography. Next, the DNA-protein complex, which has been transferred onto the blot, is extracted using a detergent-containing elution buffer. Following detergent removal, concentrated extract is separated by SDS-PAGE (EMSA-2DE), followed by in-gel trypsin digestion and HPLC-nanoESI-MS/MS analysis, or the concentrated extract is separated by two-dimensional gel electrophoresis (EMSA-3DE), followed by southwestern or western blot analysis to localize DNA binding proteins on blot which are further identified by on-blot trypsin digestion and HPLC-nanoESI-MS/MS analysis. Finally, the identified DNA binding proteins are further validated by EMSA-immunoblotting or EMSA antibody supershift assay. This approach is used to purify and identify GFP-C/EBP fusion protein from bacterial crude extract, as well as purifying AP1 and CEBP DNA binding proteins from a human embryonic kidney cell line (HEK293) nuclear extract. AP1 components, c-Jun, Jun-D, c-Fos, CREB, ATF1 and ATF2 were successfully identified from 1.5 mg of nuclear extract (equivalent to 3×10(7) HEK293 cells) with AP1 binding activity of 750 fmol. In conclusion, this new strategy of combining EMSA with additional dimensions of electrophoresis and using southwestern blotting for detection proves to be a valuable approach in the identification of transcriptional complexes by proteomic methods.
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Affiliation(s)
- Daifeng Jiang
- Department of Chemistry, University of Texas San Antonio, San Antonio, TX 28249
| | - Yinshan Jia
- Department of Chemistry, University of Texas San Antonio, San Antonio, TX 28249
| | - Harry W. Jarrett
- Department of Chemistry, University of Texas San Antonio, San Antonio, TX 28249
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van Wezel GP, McDowall KJ. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 2011; 28:1311-33. [PMID: 21611665 DOI: 10.1039/c1np00003a] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Streptomycetes and other actinobacteria are renowned as a rich source of natural products of clinical, agricultural and biotechnological value. They are being mined with renewed vigour, supported by genome sequencing efforts, which have revealed a coding capacity for secondary metabolites in vast excess of expectations that were based on the detection of antibiotic activities under standard laboratory conditions. Here we review what is known about the control of production of so-called secondary metabolites in streptomycetes, with an emphasis on examples where details of the underlying regulatory mechanisms are known. Intriguing links between nutritional regulators, primary and secondary metabolism and morphological development are discussed, and new data are included on the carbon control of development and antibiotic production, and on aspects of the regulation of the biosynthesis of microbial hormones. Given the tide of antibiotic resistance emerging in pathogens, this review is peppered with approaches that may expand the screening of streptomycetes for new antibiotics by awakening expression of cryptic antibiotic biosynthetic genes. New technologies are also described that have potential to greatly further our understanding of gene regulation in what is an area fertile for discovery and exploitation
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Chiron S, Wei Z, Chen Y, Zhang K, Wen G, Fischer WH, Mahata SK, O'Connor DT. Proteomic analysis yields an unexpected trans-acting point in control of the human sympathochromaffin phenotype. ACTA ACUST UNITED AC 2011; 4:437-45. [PMID: 21551321 DOI: 10.1161/circgenetics.110.957886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The secretory protein chromogranin A (CHGA) plays a necessary role in formation of catecholamine storage vesicles and gives rise to a catecholamine release-inhibitory fragment. Because genetic variation in the proximal human CHGA promoter predicts autonomic function and blood pressure, we explored how a common genetic variant alters transcription of the gene. METHODS AND RESULTS Bioinformatic analysis suggested that the common G-462A promoter variant (rs9658634) may disrupt as many as 3 transcriptional control motifs: LEF1, COUP-TF, and PPARγ-RXRα. During electrophoretic mobility shifts, chromaffin cell nuclear proteins bound specifically to the A (though not G) allele of CHGA promoter G-462A. On oligonucleotide affinity chromatography followed by electrospray ionization followed by 2-dimensional (tandem) mass spectrometry analysis of A allele eluates, the transcription factor LEF1 (lymphoid enhancer-binding factor-1) was identified. Interaction of LEF1 with the A allele at G-462A was confirmed by supershift. On cotransfection, LEF1 discriminated between the allelic variants, especially in chromaffin cells. Allele specificity of trans-activation by LEF1 was transferable to an isolated G-462A element fused to a heterologous (SV40) promoter. Because β-catenin (CTNNB1) can heterodimerize with LEF1, we tested the effect of cotransfection of this factor and again found A allele-specific perturbation of CHGA transcription. CONCLUSIONS Common genetic variation within the human CHGA promoter alters the interaction of specific factors in trans with the promoter, with LEF1 identified by proteomic analysis and confirmed by supershift. Coexpression experiments show functional effects of LEF1 and CTNNB1 on CHGA promoter. The findings document a novel role for components of the immune and WNT pathways in control of human sympathochromaffin phenotypes.
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Affiliation(s)
- Stéphane Chiron
- Department of Medicine and Institute for Genomic Medicine, University of California at San Diego, La Jolla, 92093–0838, USA
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Khodyreva SN, Lavrik OI. Affinity modification in a proteomic study of DNA repair ensembles. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:91-107. [DOI: 10.1134/s1068162011010109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Simicevic J, Deplancke B. DNA-centered approaches to characterize regulatory protein-DNA interaction complexes. MOLECULAR BIOSYSTEMS 2009; 6:462-8. [PMID: 20174675 DOI: 10.1039/b916137f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene regulation is mediated by site-specific DNA-binding proteins or transcription factors (TFs), which form protein complexes at regulatory loci either to activate or repress the expression of a target gene. The study of the dynamic properties of these regulatory DNA-binding complexes has so far been dominated by protein-centered methodologies, aiming to characterize the DNA-binding behavior of one specific protein at a time. With the emerging evidence for a role of DNA in allosterically influencing DNA-binding protein complex formation, there is renewed interest in DNA-centered approaches to capture protein complexes on defined regulatory loci and to correlate changes in their composition with alterations in target gene expression. In this review, we present the current state-of-the-art in such DNA-centered approaches and evaluate recent technological improvements in the purification as well as in the identification of regulatory DNA-binding protein complexes within or outside their biological context. Finally, we suggest possible areas of improvement and assess the putative impact of DNA-centered methodologies on the gene regulation field for the forthcoming years.
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Affiliation(s)
- Jovan Simicevic
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Station 15, 1015 Lausanne, Switzerland.
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Jiang D, Jarrett HW, Haskins WE. Methods for proteomic analysis of transcription factors. J Chromatogr A 2009; 1216:6881-9. [PMID: 19726046 PMCID: PMC2778203 DOI: 10.1016/j.chroma.2009.08.044] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 08/12/2009] [Accepted: 08/17/2009] [Indexed: 02/08/2023]
Abstract
Investigation of the transcription factor (TF) proteome presents challenges including the large number of low abundance and post-translationally modified proteins involved. Specialized purification and analysis methods have been developed over the last decades which facilitate the study of the TF proteome and these are reviewed here. Generally applicable proteomics methods that have been successfully applied are also discussed. TFs are selectively purified by affinity techniques using the DNA response element (RE) as the basis for highly specific binding, and several agents have been discovered that either enhance binding or diminish non-specific binding. One such affinity method called "trapping" enables purification of TFs bound to nM concentrations and recovery of TF complexes in a highly purified state. The electrophoretic mobility shift assay (EMSA) is the most important assay of TFs because it provides both measures of the affinity and amount of the TF present. Southwestern (SW) blotting and DNA-protein crosslinking (DPC) allow in vitro estimates of DNA-binding-protein mass, while chromatin immunoprecipitation (ChIP) allows confirmation of promoter binding in vivo. Two-dimensional gel electrophoresis methods (2-DE), and 3-DE methods which combines EMSA with 2-DE, allow further resolution of TFs. The synergy of highly selective purification and analytical strategies has led to an explosion of knowledge about the TF proteome and the proteomes of other DNA- and RNA-binding proteins.
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Affiliation(s)
- Daifeng Jiang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249 USA
| | - Harry W. Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249 USA
| | - William E. Haskins
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249 USA
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249 USA
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249 USA
- Department of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229 USA
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Qin H, Wang Y. Exploring DNA-binding proteins with in vivo chemical cross-linking and mass spectrometry. J Proteome Res 2009; 8:1983-91. [PMID: 19714816 DOI: 10.1021/pr8009319] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-binding proteins are very important constituents of proteomes of all species and play crucial roles in transcription, DNA replication, recombination, repair, and other activities associated with DNA. Although a number of DNA-binding proteins have been identified, many proteins involved in gene regulation and DNA repair are likely still unknown because of their dynamic and/or weak interactions with DNA. In this report, we described an approach for the comprehensive identification of DNA-binding proteins with in vivo formaldehyde cross-linking and LC-MS/MS. DNA-binding proteins could be purified via the isolation of DNA-protein complexes and released from the complexes by reversing the cross-linking. By using this method, we were able to identify more than one hundred DNA-binding proteins, such as proteins involved in transcription, gene regulation, DNA replication and repair, and a large number of proteins that are potentially associated with DNA and DNA-binding proteins. This method should be generally applicable to the investigation of other nucleic acid-binding proteins, and hold great potential in the comprehensive study of gene regulation, DNA damage response and repair, as well as many other critical biological processes at proteomic level.
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Affiliation(s)
- Haibo Qin
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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16
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Ku WC, Chiu SK, Chen YJ, Huang HH, Wu WG, Chen YJ. Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2. Mol Cell Proteomics 2009; 8:2034-50. [PMID: 19505873 PMCID: PMC2742435 DOI: 10.1074/mcp.m900013-mcp200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2009] [Revised: 05/26/2009] [Indexed: 01/13/2023] Open
Abstract
Transcription factor activating enhancer-binding protein 4 (AP-4) is a basic helix-loop-helix protein that binds to E-box elements. AP-4 has received increasing attention for its regulatory role in cell growth and development, including transcriptional repression of the human homolog of murine double minute 2 (HDM2), an important oncoprotein controlling cell growth and survival, by an unknown mechanism. Here we demonstrate that AP-4 binds to an E-box located in the HDM2-P2 promoter and represses HDM2 transcription in a p53-independent manner. Incremental truncations of AP-4 revealed that the C-terminal Gln/Pro-rich domain was essential for transcriptional repression of HDM2. To further delineate the molecular mechanism(s) of AP-4 transcriptional control and its potential implications, we used DNA-affinity purification followed by complementary quantitative proteomics, cICAT and iTRAQ labeling methods, to identify a previously unknown E-box-bound AP-4 protein complex containing 75 putative components. The two labeling methods complementarily quantified differentially AP-4-enriched proteins, including the most significant recruitment of DNA damage response proteins, followed by transcription factors, transcriptional repressors/corepressors, and histone-modifying proteins. Specific interaction of AP-4 with CCCTC binding factor, stimulatory protein 1, and histone deacetylase 1 (an AP-4 corepressor) was validated using AP-4 truncation mutants. Importantly, inclusion of trichostatin A did not alleviate AP-4-mediated repression of HDM2 transcription, suggesting a previously unidentified histone deacetylase-independent repression mechanism. In contrast, the complementary quantitative proteomics study suggested that transcription repression occurs via coordination of AP-4 with other transcription factors, histone methyltransferases, and/or a nucleosome remodeling SWI.SNF complex. In addition to previously known functions of AP-4, our data suggest that AP-4 participates in a transcriptional-regulating complex at the HDM2-P2 promoter in response to DNA damage.
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Affiliation(s)
- Wei-Chi Ku
- From the ‡Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- §Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sung-Kay Chiu
- ¶Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Yi-Ju Chen
- ‖Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Hung Huang
- ‖Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Wen-Guey Wu
- From the ‡Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- §Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yu-Ju Chen
- From the ‡Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- **Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, and
- ‡‡Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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17
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Deplancke B. Experimental advances in the characterization of metazoan gene regulatory networks. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:12-27. [PMID: 19324929 DOI: 10.1093/bfgp/elp001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene regulatory networks (GRNs) play a vital role in metazoan development and function, and deregulation of these networks is often implicated in disease. GRNs depict the dynamic interactions between genomic and regulatory state components. The genomic components comprise genes and their associated cis-regulatory elements. The regulatory state components consist primarily of transcriptional complexes that bind the latter elements. With the availability of complete genome sequences, several approaches have recently been developed which promise to significantly enhance our ability to identify either the genomic or regulatory state components, or the interactions between these two. In this review, I provide an in-depth overview of these approaches and detail how each contributes to a more comprehensive understanding of GRN composition and function.
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Affiliation(s)
- Bart Deplancke
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.
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18
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Mittler G, Butter F, Mann M. A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genes Dev 2009; 19:284-93. [PMID: 19015324 PMCID: PMC2652210 DOI: 10.1101/gr.081711.108] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 11/04/2008] [Indexed: 12/15/2022]
Abstract
Determining the underlying logic that governs the networks of gene expression in higher eukaryotes is an important task in the post-genome era. Sequence-specific transcription factors (TFs) that can read the genetic regulatory information and proteins that interpret the information provided by CpG methylation are crucial components of the system that controls the transcription of protein-coding genes by RNA polymerase II. We have previously described Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for the quantitative comparison of proteomes and the determination of protein-protein interactions. Here, we report a generic and scalable strategy to uncover such DNA protein interactions by SILAC that uses a fast and simple one-step affinity capture of TFs from crude nuclear extracts. Employing mutated or nonmethylated control oligonucleotides, specific TFs binding to their wild-type or methyl-CpG bait are distinguished from the vast excess of copurifying background proteins by their peptide isotope ratios that are determined by mass spectrometry. Our proof of principle screen identifies several proteins that have not been previously reported to be present on the fully methylated CpG island upstream of the human metastasis associated 1 family, member 2 gene promoter. The approach is robust, sensitive, and specific and offers the potential for high-throughput determination of TF binding profiles.
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Affiliation(s)
- Gerhard Mittler
- Center for Experimental Bioinformatics, University of Southern Denmark, DK-5230 Odense M, Denmark
- BIOSS—Center of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
| | - Falk Butter
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany
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19
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Hégarat N, François JC, Praseuth D. Modern tools for identification of nucleic acid-binding proteins. Biochimie 2008; 90:1265-72. [PMID: 18452716 DOI: 10.1016/j.biochi.2008.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 03/21/2008] [Indexed: 11/25/2022]
Abstract
Numerous biological mechanisms depend on nucleic acid--protein interactions. The first step to the understanding of these mechanisms is to identify interacting molecules. Knowing one partner, the identification of other associated molecular species can be carried out using affinity-based purification procedures. When the nucleic acid-binding protein is known, the nucleic acid can be isolated and identified by sensitive techniques such as polymerase chain reaction followed by DNA sequencing or hybridization on chips. The reverse identification procedure is less straightforward in part because interesting nucleic acid-binding proteins are generally of low abundance and there are no methods to amplify amino acid sequences. In this article, we will review the strategies that have been developed to identify nucleic acid-binding proteins. We will focus on methods permitting the identification of these proteins without a priori knowledge of protein candidates.
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Affiliation(s)
- Nadia Hégarat
- INSERM, U565 Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
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20
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Stead JA, McDowall KJ. Two-dimensional gel electrophoresis for identifying proteins that bind DNA or RNA. Nat Protoc 2007; 2:1839-48. [PMID: 17703194 DOI: 10.1038/nprot.2007.248] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electrophoretic mobility shift assays (EMSAs) are commonly used to analyze nucleic acid-protein interactions. When nucleic acid is bound by protein, its mobility during gel electrophoresis is reduced. Similarly, the final position of protein within a complex is shifted when compared to its free state. Here we provide a protocol for a simple approach that uses these mobility differences to identify nucleic acid-binding proteins. Following EMSA, denaturing gel electrophoresis is implemented to provide a second dimension of separation. Protein that binds a specific nucleic acid is identified as a spot(s) whose presence at a particular position(s) is dependent on nucleic acid within the initial binding reaction. The polypeptide in a spot can be subsequently identified by mass spectrometry. As EMSAs can be performed using partially purified or cell extracts, this approach substantially reduces the need for protein purification. It should facilitate the identification of a nucleic acid-binding protein within approximately 4 d.
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Affiliation(s)
- Jonathan A Stead
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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21
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Hégarat N, Cardoso GM, Rusconi F, François JC, Praseuth D. Analytical biochemistry of DNA--protein assemblies from crude cell extracts. Nucleic Acids Res 2007; 35:e92. [PMID: 17617645 PMCID: PMC1935021 DOI: 10.1093/nar/gkm490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purification of specific DNA-protein complexes is a challenging task, as the involved interactions can be both electrostatic/H-bond and hydrophobic. The chromatographic stringency needed to obtain reasonable purifications uses salts and detergents. However, these components elicit the removal of proteins unspecifically bound to the chromatographic support itself, thus contaminating the purification products. In this work, a photocleavable linker connected the target oligonucleotidic sequence to the chromatographic beads so as to allow the irradiation-based release of the purified DNA-protein complexes off the beads. Our bioanalytical conditions were validated by purifying the tetracycline repressor protein onto a specific oligonucleotide. The purification factor was unprecedented, with a single contaminant. The robustness of our method was challenged by applying it to the purification of multiprotein assemblies forming onto DNA damage-mimicking oligonucleotides. The purified components were identified as well-known DNA repair proteins, and were shown to retain their enzymatic activities, as seen by monitoring DNA ligation products. Remarkably, kinase activities, also monitored, were found to be distinct on the beads and on the purified DNA-protein complexes, showing the benefits to uncouple the DNA-protein assemblies from the beads for a proper understanding of biochemical regulatory mechanisms involved in the DNA-protein assemblies.
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Affiliation(s)
- Nadia Hégarat
- INSERM, U565 and MNHN, USM503, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France
| | - Gildas Mouta Cardoso
- INSERM, U565 and MNHN, USM503, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France
| | - Filippo Rusconi
- INSERM, U565 and MNHN, USM503, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France
| | - Jean-Christophe François
- INSERM, U565 and MNHN, USM503, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France
| | - Danièle Praseuth
- INSERM, U565 and MNHN, USM503, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France
- *To whom correspondence should be addressed. +33 1 40 79 37 10+33 1 40 79 37 05 Correspondence may also be addressed to Dr. Jean-Christophe François, +33 1 40 79 38 01+33 1 40 79 37 05
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22
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Wen G, Wessel J, Zhou W, Ehret GB, Rao F, Stridsberg M, Mahata SK, Gent PM, Das M, Cooper RS, Chakravarti A, Zhou H, Schork NJ, O’Connor DT, Hamilton BA. An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension. Hum Mol Genet 2007; 16:1752-64. [PMID: 17584765 PMCID: PMC2695823 DOI: 10.1093/hmg/ddm123] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Granins regulate secretory vesicle formation in neuroendocrine cells and granin-derived peptides are co-released with neurotransmitters as modulatory signals at sympathetic sites. We report evidence for association between a regulatory polymorphism in Secretogranin II (SCG2) and hypertension in African-American subjects. The minor allele is ancestral in the human lineage and is associated with disease risk in two case-control studies and with elevated blood pressure in a separate familial study. Mechanistically, the ancestral allele acts as a transcriptional enhancer in cells that express endogenous Scg2, whereas the derived allele does not. ARIX (PHOX2A) and PHOX2B are identified as potential transactivating factors by oligonucleotide affinity chromatography and mass spectrometry and confirmed by chromatin immunoprecipitation. Each of these transcription factors preferentially binds the risk allele, both in vitro and in vivo. Population genetic considerations suggest positive selection of the protective allele within the human lineage. These results identify a common regulatory variation in SCG2 and implicate granin gene expression in the control of human blood pressure and susceptibility to hypertension.
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Affiliation(s)
- Gen Wen
- Department of Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Jennifer Wessel
- Department of Psychiatry, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Department of Family and Preventive Medicine, UCSD and Graduate School of Public Health, San Diego State University Joint Doctoral Program in Public Health Epidemiology
- Scripps Genomic Medicine and The Scripps Research Institute, La Jolla, CA
| | - Weidong Zhou
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Georg B. Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Fangwen Rao
- Department of Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Mats Stridsberg
- Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Sushil K. Mahata
- Department of Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- VA San Diego Healthcare System
| | - Peter M. Gent
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Madhusudan Das
- Department of Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Richard S. Cooper
- Department of Preventive Medicine and Epidemiology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois 60153
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Huilin Zhou
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Moores UCSD Cancer Center, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Nicholas J. Schork
- Department of Psychiatry, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Center for Human Genetics and Genomics, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Scripps Genomic Medicine and The Scripps Research Institute, La Jolla, CA
| | - Daniel T. O’Connor
- Department of Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Center for Human Genetics and Genomics, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Moores UCSD Cancer Center, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
| | - Bruce A. Hamilton
- Department of Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- Moores UCSD Cancer Center, University of California, San Diego School of Medicine 9500 Gilman Drive, La Jolla, California 92093
- author for correspondence Telephone: (858) 822-1055
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23
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Abstract
Acute myeloid leukemia (AML) is a frequent hematological malignancy. Despite enormous therapeutic efforts that range from various cytotoxic agents to allogeneic stem cell transplantation, overall survival of patients with AML remains unsatisfying. The poor survival rates are mainly due to therapy-related mortality, failure of induction chemotherapy and early relapses. Therefore, novel therapeutic agents that are more efficient and better tolerated are eagerly sought after. For existing therapeutic strategies, there is a lack of markers that are capable of reliably predicting prognosis or the therapeutic response prior to treatment. There is hope that elucidation of the AML-specific proteome will prompt the discovery of novel therapeutic targets and biomarkers in AML. Modern mass-spectrometry instrumentation has achieved excellent performance in terms of sensitivity, resolution and mass accuracy; however, so far, the contribution of proteomics to the care of patients with AML is virtually zero. This might be partly because mass spectrometry instrumentation and protein fractionation still lack true high-throughput capabilities with highest levels of reproducibility, thus hampering large-scale translational studies with clinical samples. Since mass-spectrometry instruments are very intricate devices, their successful operation will hinge on the willingness and ability of mass-spectrometry experts and clinical researchers to adopt new views, learn from each other and cooperate in order to ultimately benefit the patient suffering from AML. This review highlights some clinical problems circumventing the treatment of patients with AML. Furthermore, it provides a brief overview of the technical background of standard proteomics approaches and describes opportunities, challenges and pitfalls of proteomic studies with regards to AML.
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Affiliation(s)
- Akos Czibere
- Heinrich Heine University, Department of Hematology, Oncology and Clinical Immunlogy, Moorenstr. 5, 40225 Düsseldorf, Germany.
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24
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Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
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Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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25
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Dirksen EHC, Pinkse MWH, Rijkers DTS, Cloos J, Liskamp RMJ, Slijper M, Heck AJR. Investigating the Dynamic Nature of the Interactions between Nuclear Proteins and Histones upon DNA Damage Using an Immobilized Peptide Chemical Proteomics Approach. J Proteome Res 2006; 5:2380-8. [PMID: 16944950 DOI: 10.1021/pr060278b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a result of the complexity and dynamic range of the cellular proteome, including mutual interactions and interactions with other molecules, focused proteomic approaches are important to study subsets of physiologically important proteins. In one such approach, a small molecule or part of a protein is immobilized on a solid phase and used as bait to fish out interacting proteins from complex mixtures such as cellular lysates. Here, such a chemical proteomics experiment is presented to explore the range of proteins that interact with the N-terminal tail of core histones. Therefore, a core histone consensus N-terminal tail (NTT) peptide was synthesized and immobilized on agarose. Interactions between histone NTTs and proteins are extremely important as they regulate chromatin structure, which is important in many DNA-related processes, like transcription and DNA repair. Induction of DNA damage, like DNA double strand breaks, is known to trigger chromatin remodeling events through interactions between histone NTTs and so-called histone chaperones. Therefore, we set out to investigate specific changes in interactions of nuclear proteins before and shortly after DNA double strand break induction. Over 700 proteins were found to bind specifically to the NTT peptide, which makes our study the most comprehensive proteomic survey of the broad spectrum of nuclear proteins interacting with the NTT of core histones in nucleosomes. Apart from a few exceptions, the abundance of the majority of NTT binding proteins was found to be unchanged following DNA damage. However, an in-depth analysis of protein phosphorylation (we detected more than 90 unique sites in about 60 proteins) revealed that the phosphorylation status of several proteins involved in chromatin remodeling changes upon DNA damage. We observed that in these differentially phosphorylated chaperones are part of closely interacting protein complexes involved in regulatory mechanisms at the crossroads of nucleosome assembly, DNA replication, transcription, and the early onset of DNA damage repair.
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Affiliation(s)
- Eef H C Dirksen
- Department of Biomolecular Mass Spectrometry, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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26
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Stead JA, Keen JN, McDowall KJ. The identification of nucleic acid-interacting proteins using a simple proteomics-based approach that directly incorporates the electrophoretic mobility shift assay. Mol Cell Proteomics 2006; 5:1697-702. [PMID: 16845145 DOI: 10.1074/mcp.t600027-mcp200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins that interact with nucleic acids are central to numerous cellular processes, and their continuing characterization represents one of the foremost challenges in the postgenomic era. Here we describe a simple proteomics-based approach for the identification by mass spectrometry of proteins in crude extracts that interact with nucleic acids. It incorporates the electrophoretic mobility shift assay and is based on the finding that when a protein forms a complex with nucleic acid its electrophoretic mobility is affected as well as that of the nucleic acid. Our method should greatly reduce and in some cases may even eliminate the need for extensive protein purification and as such should contribute significantly to the functional annotation of the proteome. Furthermore it requires no prior knowledge of the molecular mass, quaternary structure, or pI of the interacting protein. Proof of principle is demonstrated using a recently discovered transcription factor; however, the approach should also have application in the identification of proteins that interact with RNA.
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Affiliation(s)
- Jonathan A Stead
- Astbury Centre for Structural Molecular Biology and Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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27
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Vanderpuije BNY, Han G, Rotello VM, Vachet RW. Mixed Monolayer-Protected Gold Nanoclusters as Selective Peptide Extraction Agents for MALDI-MS Analysis. Anal Chem 2006; 78:5491-6. [PMID: 16878887 DOI: 10.1021/ac0604181] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cationic and anionic nanoparticles selectively target peptides with low and high isoelectric points, respectively. Additionally, their high surface area-to-volume ratios make these nanoparticles (approximately 2-nm core diameter) very efficient extraction and concentration agents. Upon extraction, the peptide-bound nanoparticles can be analyzed by MALDI-MS to provide highly sensitive detection of the targeted peptides. We demonstrate that MALDI-MS can detect peptide concentrations as low as 500 pM from 250-microL solutions using these nanoparticle scaffolds as extraction and concentration agents.
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28
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Petti F, Thomson S, Haley JD. Peptide, domain, and DNA affinity selection in the identification and quantitation of proteins from complex biological samples. Anal Biochem 2006; 356:1-11. [PMID: 16797468 DOI: 10.1016/j.ab.2006.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 05/24/2006] [Accepted: 05/25/2006] [Indexed: 12/22/2022]
Affiliation(s)
- Filippo Petti
- Translational Research, OSI Oncology, Farmingdale, NY 11735, USA
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Yaneva M, Kippenberger S, Wang N, Su Q, McGarvey M, Nazarian A, Lacomis L, Erdjument-Bromage H, Tempst P. PU.1 and a TTTAAA Element in the MyeloidDefensin-1Promoter Create an Operational TATA Box That Can Impose Cell Specificity onto TFIID Function. THE JOURNAL OF IMMUNOLOGY 2006; 176:6906-17. [PMID: 16709851 DOI: 10.4049/jimmunol.176.11.6906] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Defensins are major components of a peptide-based, antimicrobial system in human neutrophils. While packed with peptide, circulating cells contain no defensin-1 (def1) transcripts, except in some leukemia patients and in derivative promyelocytic leukemia cell lines. Expression is modulated by serum factors, mediators of inflammation, and kinase activators and inhibitors, but the underlying mechanisms are not fully understood. A minimal def1 promoter drives transcription in HL-60 cells under control of PU.1 and a def1-binding protein ("D1BP"), acting through, respectively, proximal (-22/-19) and distal (-62/-59) GGAA elements. In this study, we identify D1BP, biochemically and functionally, as GA-binding protein (GABP)alpha/GABPbeta. Whereas GABP operates as an essential upstream activator, PU.1 assists the flanking "TTTAAA" element (-32/-27), a "weak" but essential TATA box, to bring TBP/TFIID to the transcription start site. PU.1 thus imparts a degree of cell specificity to the minimal promoter and provides a potential link between a number of signaling pathways and TFIID. However, a "strong" TATA box ("TATAAA") eliminates the need for the PU.1 binding site and for PU.1, but not for GABP. As GABP is widely expressed, a strong TATA box thus alleviates promyelocytic cell specificity of the def1 promoter. These findings suggest how the myeloid def1 promoter may have evolutionarily acquired its current properties.
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Affiliation(s)
- Mariana Yaneva
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, and Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA
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Park SS, Ko BJ, Kim BG. Mass spectrometric screening of transcriptional regulators using DNA affinity capture assay. Anal Biochem 2005; 344:152-4. [PMID: 16005423 DOI: 10.1016/j.ab.2005.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Revised: 05/09/2005] [Accepted: 05/16/2005] [Indexed: 01/08/2023]
Affiliation(s)
- Sung-Soo Park
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, Seoul National University, Kwanak-gu, Seoul 151-742, Republic of Korea
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31
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Chou PH, Chen SH, Liao HK, Lin PC, Her GR, Lai ACY, Chen JH, Lin CC, Chen YJ. Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma. Anal Chem 2005; 77:5990-7. [PMID: 16159132 DOI: 10.1021/ac050655o] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In recent decades, magnetic nanoparticles have emerged as a promising new platform in biomedical applications, particularly bioseparations. We have developed an immunoassay using antibody-conjugated magnetic nanoparticles as an efficient affinity probe to simultaneously preconcentrate and isolate targeted antigens from biological media. We combined this probe with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI MS) to profile proteins in diluted human plasma. The nanoparticles were designed to detect several disease-associated proteins and could be used directly in MALDI MS without an elution step, thereby facilitating multiple antigen screening and the characterization of antigen variants. Plasma antigens bound rapidly (approximately 10 min) to the antibody-conjugated nanoparticles, allowing the assay to be performed within 20 min. With sensitivity of detection in the femtomole range, the nanoscale immunoassay is superior to assays using microscale particles. We applied our method to comparative protein profiling of patients with gastric cancer and healthy individuals and found differential protein expression levels associated with the disease as well as individuals. Given the flexibility of manipulating functional groups on the nanoprobes, their low cost, robustness, and simplicity of the assay, our approach shows promise for targeted proteome profiling in clinical settings.
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Affiliation(s)
- Po-Hung Chou
- Institute of Chemistry and Genomic Research Center, Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
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Safarik I, Safarikova M. Magnetic techniques for the isolation and purification of proteins and peptides. BIOMAGNETIC RESEARCH AND TECHNOLOGY 2004; 2:7. [PMID: 15566570 PMCID: PMC544596 DOI: 10.1186/1477-044x-2-7] [Citation(s) in RCA: 286] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Accepted: 11/26/2004] [Indexed: 11/29/2022]
Abstract
Isolation and separation of specific molecules is used in almost all areas of biosciences and biotechnology. Diverse procedures can be used to achieve this goal. Recently, increased attention has been paid to the development and application of magnetic separation techniques, which employ small magnetic particles. The purpose of this review paper is to summarize various methodologies, strategies and materials which can be used for the isolation and purification of target proteins and peptides with the help of magnetic field. An extensive list of realised purification procedures documents the efficiency of magnetic separation techniques.
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Affiliation(s)
- Ivo Safarik
- Laboratory of Biochemistry and Microbiology, Institute of Landscape Ecology, Academy of Sciences, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
- Department of General Biology, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
| | - Mirka Safarikova
- Laboratory of Biochemistry and Microbiology, Institute of Landscape Ecology, Academy of Sciences, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
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Turney K, Drake TJ, Smith JE, Tan W, Harrison WW. Functionalized nanoparticles for liquid atmospheric pressure matrix-assisted laser desorption/ionization peptide analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2004; 18:2367-2374. [PMID: 15386634 DOI: 10.1002/rcm.1634] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanoparticles for the extraction of peptides and subsequent analysis using atmospheric pressure matrix-assisted laser desorption/ionization (APMALDI) have been evaluated. The atmospheric pressure source allows for particles to be directly introduced in the liquid matrix, minimizing sample loss and analysis time. Described in this work are two sample preparation procedures for liquid APMALDI analysis: a C18 functionalized silica nanoparticle for hydrophobic extractions, and an aptamer functionalized magnetite core nanoparticle for rapid, affinity extractions. The C18 particles provide a non-selective support for rapid profiling applications, while the aptamer particles are directed towards reducing the complexity in biological samples. The aptamer functionalized particles provide a more selective analyte-nanoparticle interaction whereby the tertiary structure of the analyte becomes more critical to the extraction. In both cases, the liquid APMALDI matrix provides a support for ionization, and acts as the releasing agent for the analyte-particle interaction. Additionally, analyte enrichment was possible due to the large surface-to-volume ratio of the particles. The experiments conducted with functionalized nanoparticles, in an atmospheric pressure liquid matrix, present a basis for further methodologies and utilities of silica nanoparticles to be developed.
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Affiliation(s)
- Kevin Turney
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611-7200, USA
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