1
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Verzino SJ, Priyev SA, Estrada VAS, Crowley GX, Rutkowski A, Lam AC, Nazginov ES, Kotemelo P, Bacelo A, Sukhram DT, Vázquez FX, Juárez JF. Expanding salivary biomarker detection by creating a synthetic neuraminic acid sensor via chimeragenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598939. [PMID: 38915506 PMCID: PMC11195194 DOI: 10.1101/2024.06.13.598939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Accurate and timely diagnosis of oral squamous cell carcinoma (OSCC) is crucial in preventing its progression to advanced stages with a poor prognosis. As such, the construction of sensors capable of detecting previously established disease biomarkers for the early and non-invasive diagnosis of this and many other conditions has enormous therapeutic potential. In this work, we apply synthetic biology techniques for the development of a whole-cell biosensor (WCB) that leverages the physiology of engineered bacteria in vivo to promote the expression of an observable effector upon detection of a soluble molecule. To this end, we have constructed a bacterial strain expressing a novel chimeric transcription factor (Sphnx) for the detection of N-acetylneuraminic acid (Neu5Ac), a salivary biomolecule correlated with the onset of OSCC. This WCB serves as the proof-of-concept of a platform that can eventually be applied to clinical screening panels for a multitude of oral and systemic medical conditions whose biomarkers are present in saliva.
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2
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Wu S, Guo JT. Improved prediction of DNA and RNA binding proteins with deep learning models. Brief Bioinform 2024; 25:bbae285. [PMID: 38856168 PMCID: PMC11163377 DOI: 10.1093/bib/bbae285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024] Open
Abstract
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in essential biological processes. To facilitate functional annotation and accurate prediction of different types of NABPs, many machine learning-based computational approaches have been developed. However, the datasets used for training and testing as well as the prediction scopes in these studies have limited their applications. In this paper, we developed new strategies to overcome these limitations by generating more accurate and robust datasets and developing deep learning-based methods including both hierarchical and multi-class approaches to predict the types of NABPs for any given protein. The deep learning models employ two layers of convolutional neural network and one layer of long short-term memory. Our approaches outperform existing DBP and RBP predictors with a balanced prediction between DBPs and RBPs, and are more practically useful in identifying novel NABPs. The multi-class approach greatly improves the prediction accuracy of DBPs and RBPs, especially for the DBPs with ~12% improvement. Moreover, we explored the prediction accuracy of single-stranded DNA binding proteins and their effect on the overall prediction accuracy of NABP predictions.
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Affiliation(s)
- Siwen Wu
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, United States
| | - Jun-tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, United States
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3
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Eigenfeld M, Lupp KFM, Schwaminger SP. Role of Natural Binding Proteins in Therapy and Diagnostics. Life (Basel) 2024; 14:630. [PMID: 38792650 PMCID: PMC11122601 DOI: 10.3390/life14050630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.
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Affiliation(s)
- Marco Eigenfeld
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kilian F. M. Lupp
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Sebastian P. Schwaminger
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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4
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Wickline SA, Hou KK, Pan H. Peptide-Based Nanoparticles for Systemic Extrahepatic Delivery of Therapeutic Nucleotides. Int J Mol Sci 2023; 24:ijms24119455. [PMID: 37298407 DOI: 10.3390/ijms24119455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Peptide-based nanoparticles (PBN) for nucleotide complexation and targeting of extrahepatic diseases are gaining recognition as potent pharmaceutical vehicles for fine-tuned control of protein production (up- and/or down-regulation) and for gene delivery. Herein, we review the principles and mechanisms underpinning self-assembled formation of PBN, cellular uptake, endosomal release, and delivery to extrahepatic disease sites after systemic administration. Selected examples of PBN that have demonstrated recent proof of concept in disease models in vivo are summarized to offer the reader a comparative view of the field and the possibilities for clinical application.
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Affiliation(s)
- Samuel A Wickline
- Division of Cardiology, Department of Medical Engineering, University of South Florida, Tampa, FL 33602, USA
| | - Kirk K Hou
- Department of Ophthalmology, Stein and Doheny Eye Institutes, University of California, Los Angeles, CA 90095, USA
| | - Hua Pan
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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5
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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6
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Li X, Han M, Zhang H, Liu F, Pan Y, Zhu J, Liao Z, Chen X, Zhang B. Structures and biological functions of zinc finger proteins and their roles in hepatocellular carcinoma. Biomark Res 2022; 10:2. [PMID: 35000617 PMCID: PMC8744215 DOI: 10.1186/s40364-021-00345-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022] Open
Abstract
Zinc finger proteins are transcription factors with the finger domain, which plays a significant role in gene regulation. As the largest family of transcription factors in the human genome, zinc finger (ZNF) proteins are characterized by their different DNA binding motifs, such as C2H2 and Gag knuckle. Different kinds of zinc finger motifs exhibit a wide variety of biological functions. Zinc finger proteins have been reported in various diseases, especially in several cancers. Hepatocellular carcinoma (HCC) is the third leading cause of cancer-associated death worldwide, especially in China. Most of HCC patients have suffered from hepatitis B virus (HBV) and hepatitis C virus (HCV) injection for a long time. Although the surgical operation of HCC has been extremely developed, the prognosis of HCC is still very poor, and the underlying mechanisms in HCC tumorigenesis are still not completely understood. Here, we summarize multiple functions and recent research of zinc finger proteins in HCC tumorigenesis and progression. We also discuss the significance of zinc finger proteins in HCC diagnosis and prognostic evaluation.
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Affiliation(s)
- Xinxin Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Mengzhen Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Hongwei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Furong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Jinghan Zhu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China.
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China.
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China.
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7
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Nishida H, Nosaki S, Suzuki T, Ito M, Miyakawa T, Nomoto M, Tada Y, Miura K, Tanokura M, Kawaguchi M, Suzaki T. Different DNA-binding specificities of NLP and NIN transcription factors underlie nitrate-induced control of root nodulation. THE PLANT CELL 2021; 33:2340-2359. [PMID: 33826745 PMCID: PMC8364233 DOI: 10.1093/plcell/koab103] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/03/2021] [Indexed: 05/20/2023]
Abstract
Leguminous plants produce nodules for nitrogen fixation; however, nodule production incurs an energy cost. Therefore, as an adaptive strategy, leguminous plants halt root nodule development when sufficient amounts of nitrogen nutrients, such as nitrate, are present in the environment. Although legume NODULE INCEPTION (NIN)-LIKE PROTEIN (NLP) transcription factors have recently been identified, understanding how nodulation is controlled by nitrate, a fundamental question for nitrate-mediated transcriptional regulation of symbiotic genes, remains elusive. Here, we show that two Lotus japonicus NLPs, NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1)/LjNLP4 and NRSYM2/LjNLP1, have overlapping functions in the nitrate-induced control of nodulation and act as master regulators for nitrate-dependent gene expression. We further identify candidate target genes of LjNLP4 by combining transcriptome analysis with a DNA affinity purification-seq approach. We then demonstrate that LjNLP4 and LjNIN, a key nodulation-specific regulator and paralog of LjNLP4, have different DNA-binding specificities. Moreover, LjNLP4-LjNIN dimerization underlies LjNLP4-mediated bifunctional transcriptional regulation. These data provide a basic principle for how nitrate controls nodulation through positive and negative regulation of symbiotic genes.
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Affiliation(s)
- Hanna Nishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shohei Nosaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Momoyo Ito
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takuya Miyakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Kenji Miura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masaru Tanokura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Author for correspondence:
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8
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Emamjomeh A, Choobineh D, Hajieghrari B, MahdiNezhad N, Khodavirdipour A. DNA-protein interaction: identification, prediction and data analysis. Mol Biol Rep 2019; 46:3571-3596. [PMID: 30915687 DOI: 10.1007/s11033-019-04763-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022]
Abstract
Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA-protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA-protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.
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Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran.
| | - Darush Choobineh
- Agricultural Biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, 74135-111, Iran.
| | - Nafiseh MahdiNezhad
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran
| | - Amir Khodavirdipour
- Division of Human Genetics, Department of Anatomy, St. John's hospital, Bangalore, India
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9
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Chrysouli M, Banti C, Kourkoumelis N, Panayiotou N, Markopoulos G, Tasiopoulos A, Hadjikakou S. Chloro(triphenylphosphine)gold(I) a forefront reagent in gold chemistry as apoptotic agent for cancer cells. J Inorg Biochem 2018; 179:107-120. [DOI: 10.1016/j.jinorgbio.2017.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/30/2017] [Accepted: 11/04/2017] [Indexed: 12/19/2022]
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10
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Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study. JOURNAL OF BIOPHYSICS 2017; 2017:1059216. [PMID: 28321253 PMCID: PMC5340175 DOI: 10.1155/2017/1059216] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/15/2017] [Indexed: 11/20/2022]
Abstract
The use of gene therapeutics, including short interfering RNA (siRNA), is limited by the lack of efficient delivery systems. An appealing approach to deliver gene therapeutics involves noncovalent complexation with cell penetrating peptides (CPPs) which are able to penetrate the cell membranes of mammals. Although a number of CPPs have been discovered, our understanding of their complexation and translocation of siRNA is as yet insufficient. Here, we report on computational studies comparing the binding affinities of CPPs with siRNA, considering a variety of CPPs. Specifically, seventeen CPPs from three different categories, cationic, amphipathic, and hydrophobic CPPs, were studied. Molecular mechanics were used to minimize structures, while molecular docking calculations were used to predict the orientation and favorability of sequentially binding multiple peptides to siRNA. Binding scores from docking calculations were highest for amphipathic peptides over cationic and hydrophobic peptides. Results indicate that initial complexation of peptides will likely occur along the major groove of the siRNA, driven by electrostatic interactions. Subsequent binding of CPPs is likely to occur in the minor groove and later on bind randomly, to siRNA or previously bound CPPs, through hydrophobic interactions. However, hydrophobic CPPs do not show this binding pattern. Ultimately binding yields a positively charged nanoparticle capable of noninvasive cellular import of therapeutic molecules.
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11
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Rawtani D, Kuntmal B, Agrawal Y. Charge transfer in DNA and its diverse modelling approaches. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1207570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Deepak Rawtani
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
| | - Binal Kuntmal
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
| | - Y. Agrawal
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
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12
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Dinda AK, Chattaraj S, Ghosh S, Tripathy DR, Dasgupta S. DNA melting properties of the dityrosine cross-linked dimer of Ribonuclease A. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:535-543. [PMID: 27475778 DOI: 10.1016/j.jphotobiol.2016.06.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/19/2022]
Abstract
Several DNA binding proteins exist in dimeric form when bound with DNA to be able to exhibit various biological processes such as DNA repair, DNA replication and gene expression. Various dimeric forms of Ribonuclease A (RNase A) and other members of the ribonuclease A superfamily are endowed with a multitude of biological activities such as antitumor and antiviral activity. In the present study, we have compared the DNA binding properties between the RNase A monomer and the dityrosine (DT) cross-linked RNase A dimer, and checked the inhibitory effect of DNA on the ribonucleolytic activity of the dimeric protein. An agarose gel based assay shows that like the monomer, the dimer also binds with DNA. The number of nucleotides bound per monomer unit of the dimer is higher than the number of nucleotides that bind with the each monomer. From fluorescence measurements, the association constant (Ka) values for complexation of the monomer and the dimer with ct-DNA are (4.95±0.45)×10(4)M(-1) and (1.29±0.05)×10(6)M(-1) respectively. Binding constant (Kb) values for the binding of the monomer and the dimer with ct-DNA were determined using UV-vis spectroscopy and were found to be (4.96±1.67)×10(4)M(-1) and (4.32±0.31)×10(5)M(-1) respectively. Circular dichroism studies shows that the dimer possesses significant effect on DNA conformation. The melting profile for the ct-DNA-dimer indicated that the melting temperature (Tm) for the ct-DNA-dimer complex is lower compared to the ct-DNA-monomer complex. The ribonucleolytic activity of the dimer, like the monomer, diminishes upon binding with DNA.
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Affiliation(s)
- Amit Kumar Dinda
- Department of Chemistry, Indian Institute of Technology Kharagpur, 721302, India
| | - Saparya Chattaraj
- Department of Chemistry, Indian Institute of Technology Kharagpur, 721302, India
| | - Sudeshna Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, 721302, India
| | - Debi Ranjan Tripathy
- Department of Chemistry, Indian Institute of Technology Kharagpur, 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, 721302, India.
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13
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Wang P, Wu J, Su P, Shan C, Zhou P, Ge Y, Liu D, Liu W, Tang Y. A novel fluorescent chemosensor based on tetra-peptides for detecting zinc ions in aqueous solutions and live cells. J Mater Chem B 2016; 4:4526-4533. [DOI: 10.1039/c6tb00794e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A novel fluorescent chemosensor (HL) based on tetra-peptides conjugated with dansyl groups has been designed and synthesized, which is a promising analytical tool for detecting Zn2+ in aqueous solutions and live cells.
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Affiliation(s)
- Peng Wang
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Jiang Wu
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Pingru Su
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Changfu Shan
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Panpan Zhou
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Yushu Ge
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Life Sciences
- University of Sciences and Technology of China
- Hefei
- P. R. China
| | - Dan Liu
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Life Sciences
- University of Sciences and Technology of China
- Hefei
- P. R. China
| | - Weisheng Liu
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Yu Tang
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
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14
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Wang P, Wu J, Liu L, Zhou P, Ge Y, Liu D, Liu W, Tang Y. A peptide-based fluorescent chemosensor for measuring cadmium ions in aqueous solutions and live cells. Dalton Trans 2015; 44:18057-64. [PMID: 26411376 DOI: 10.1039/c5dt03156g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel peptide fluorescent chemosensor (H2L) with a lysine backbone and both -NH2 sites conjugated with cysteine and dansyl groups has been designed and synthesized by solid phase peptide synthesis with Fmoc chemistry. This chemosensor is a promising analytical tool for detecting Cd(2+) based on the photo-induced electron transfer (PET) effect by turn-on response in 100% aqueous solutions. As designed, H2L exhibits excellent cell permeation and low biotoxicity as well as displaying relatively high selectivity and sensitivity. The chemosensor penetrated live HeLa cells and detected intracellular Cd(2+) by turn-on response. The binding stoichiometry and affinity, interference test, pH sensitivity, fluorescence quantum yield, quantum mechanical calculations, lifetimes, and cytotoxicity of the chemosensor H2L to Cd(2+) were also investigated. Moreover, H2L exhibits low biotoxicity with a limit of detection (LOD) for Cd(2+) of about 52 nM, implying that H2L can be used as a highly selective and sensitive peptide fluorescent chemosensor in biological systems.
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Affiliation(s)
- Peng Wang
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, P. R. China.
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15
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Vujanac M, Iyer VS, Sengupta M, Ajdic D. Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR. Mol Oral Microbiol 2015; 30:280-94. [PMID: 25580872 DOI: 10.1111/omi.12093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
Streptococcus mutans is implicated in human dental caries, and the carbohydrate metabolism of this organism plays an important role in the formation of this disease. Carbohydrate transport and metabolism are essential for the survival of S. mutans in the oral cavity. It is known that a unique phosphoenolpyruvate-sugar phosphotransferase system PTS(B) (io) of S. mutans UA159 is expressed in sucrose-grown biofilms (Mol Oral Microbiol 28: 2013; 114). In this study we analyzed the transcriptional regulation of the operon (O(B) (io) ) encoding the PTS(B) (io) and showed that it was repressed by NigR, a LacI-like transcriptional regulator. Using electro-mobility shift assay, we described two operators to which NigR bound with different affinities. We also identified the transcriptional start site and showed that one of the operators overlaps with the promoter and presumably represses initiation of transcription. Mutational analyses revealed the key nucleotides in the operators required for high-affinity binding of NigR. PTS(B) (io) is expressed in S. mutans biofilms so understanding its regulation may provide improved strategies for caries treatment and prevention.
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Affiliation(s)
- M Vujanac
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V S Iyer
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - M Sengupta
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D Ajdic
- Miller School of Medicine, University of Miami, Miami, FL, USA
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Correia IL, Franco IS, de Sá-Nogueira I. Towards novel amino acid-base contacts in gene regulatory proteins: AraR--a case study. PLoS One 2014; 9:e111802. [PMID: 25364981 PMCID: PMC4218819 DOI: 10.1371/journal.pone.0111802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/07/2014] [Indexed: 01/08/2023] Open
Abstract
AraR is a transcription factor involved in the regulation of carbon catabolism in Bacillus subtilis. This regulator belongs to the vast GntR family of helix-turn-helix (HTH) bacterial metabolite-responsive transcription factors. In this study, AraR-DNA specific interactions were analysed by an in vitro missing-contact probing and validated using an in vivo model. We show that amino acid E30 of AraR, a highly conserved residue in GntR regulators, is indirectly responsible for the specificity of amino acid-base contacts, and that by mutating this residue it will be possible to achieve new specificities towards DNA contacts. The results highlight the importance in DNA recognition and binding of highly conserved residues across certain families of transcription factors that are located in the DNA-binding domain but not predicted to specifically contact bases on the DNA. These new findings not only contribute to a more detailed comprehension of AraR-operator interactions, but may also be useful for the establishment of a framework of rules governing protein-DNA recognition.
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Affiliation(s)
- Isabel Lopes Correia
- Departamento de Ciências da Vida (DCV), Centro de Recursos Microbiológicos (CREM), Faculdade de Ciências e Tecnologia (FCT-UNL), Caparica, Portugal
- Instituto Tecnologia Química e Biológica (ITQB-UNL), Oeiras, Portugal
| | | | - Isabel de Sá-Nogueira
- Departamento de Ciências da Vida (DCV), Centro de Recursos Microbiológicos (CREM), Faculdade de Ciências e Tecnologia (FCT-UNL), Caparica, Portugal
- * E-mail:
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17
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DNA binders in clinical trials and chemotherapy. Bioorg Med Chem 2014; 22:4506-21. [DOI: 10.1016/j.bmc.2014.05.030] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/09/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023]
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18
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Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer. PLoS Genet 2014; 10:e1004171. [PMID: 24586200 PMCID: PMC3937220 DOI: 10.1371/journal.pgen.1004171] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 12/26/2013] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major force driving bacterial evolution. Because of their ability to cross inter-species barriers, bacterial plasmids are essential agents for HGT. This ability, however, poses specific requisites on plasmid physiology, in particular the need to overcome a multilevel selection process with opposing demands. We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria. Transcriptional analysis by fluorescence expression profiling and quantitative PCR revealed a regulatory network controlled by six transcriptional repressors. The regulatory network relied on strong promoters, which were tightly repressed in negative feedback loops. Computational simulations and theoretical analysis indicated that this architecture would show a transcriptional burst after plasmid conjugation, linking the magnitude of the feedback gain with the intensity of the transcriptional burst. Experimental analysis showed that transcriptional overshooting occurred when the plasmid invaded a new population of susceptible cells. We propose that transcriptional overshooting allows genome rebooting after horizontal gene transfer, and might have an adaptive role in overcoming the opposing demands of multilevel selection. In the environment, bacteria often evolve by the acquisition of new genes from different species. Plasmids are small DNA molecules that mediate horizontal gene transfer in bacteria, thus they are fundamental agents for the spread of antibiotic resistances. Plasmids replicate inside the bacterial cytoplasm, and propagate infectiously by contact. Plasmids control these two ways of multiplication, but like many other symbionts they suffer from a tradeoff. If plasmids become very infective, they can spread fast and successfully, but this damages the bacterial hosts they depend upon. If, on the contrary, plasmids become very mild, the host is able to grow better but the ability of plasmids to infect new hosts is hampered. We have studied the regulatory mechanisms plasmids use to overcome this paradox. We discovered that negative feedback, a regulatory motif ubiquitous in the plasmid network, allows transient activation of plasmid functions immediately after plasmids invade a new host. This might be an adaptive strategy for plasmids to be highly infective without damaging their hosts, and it illustrates a natural mechanism for DNA transplantation that could be implemented in synthetic genomic transplants.
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19
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Goni MO. A new approach to implement absorbing boundary condition in biomolecular electrostatics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:799-804. [PMID: 24091411 DOI: 10.1109/tcbb.2013.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.
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Affiliation(s)
- Md Osman Goni
- Khulna University of Engineering and Technology, khulna
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20
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Kellenbach ER, van den Elst H, Boelens R, van der Marel GA, van Boom JH, Kaptein R. A convenient synthesis of DNA fragments nitrogen-15 labeled at the exocyclic cytosine amino group. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19911100907] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Lindemose S, Nielsen PE, Møllegaard NE. Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system. Nucleic Acids Res 2008; 36:4797-807. [PMID: 18653536 PMCID: PMC2504297 DOI: 10.1093/nar/gkn452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The DNA interaction of the Escherichia coli cyclic AMP receptor protein (CRP) represents a typical example of a dual recognition mechanism exhibiting both direct and indirect readout. We have dissected the direct and indirect components of DNA recognition by CRP employing in vitro selection of a random library of DNA-binding sites containing inosine (I) and 2,6-diaminopurine (D) instead of guanine and adenine, respectively. Accordingly, the DNA helix minor groove is structurally altered due to the ‘transfer’ of the 2-amino group of guanine (now I) to adenine (now D), whereas the major groove is functionally intact. The majority of the selected sites contain the natural consensus sequence TGTGAN6TCACA (i.e. TITIDN6TCDCD). Thus, direct readout of the consensus sequence is independent of minor groove conformation. Consequently, the indirect readout known to occur in the TG/CA base pair step (primary kink site) in the consensus sequence is not affected by I–D substitutions. In contrast, the flanking regions are selected as I/C rich sequences (mostly I-tracts) instead of A/T rich sequences which are known to strongly increase CRP binding, thereby demonstrating almost exclusive indirect readout of helix structure/flexibility in this region through (anisotropic) flexibility of I-tracts.
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Affiliation(s)
- Søren Lindemose
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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22
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Crameri R, Jaussi R, Menz G, Blaser K. Display of Expression Products of cDNA Libraries on Phage Surfaces. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1432-1033.1994.00t53.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Husbands A, Bell EM, Shuai B, Smith HM, Springer PS. LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins. Nucleic Acids Res 2007; 35:6663-71. [PMID: 17913740 PMCID: PMC2095788 DOI: 10.1093/nar/gkm775] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD proteins have previously been predicted to be transcription factors, however supporting evidence has only been circumstantial. To address the biochemical function of LBD proteins, we identified a 6-bp consensus motif recognized by a wide cross-section of LBD proteins, and showed that LATERAL ORGAN BOUNDARIES (LOB), the founding member of the family, is a transcriptional activator in yeast. Thus, the LBD genes encode a novel class of DNA-binding transcription factors. Post-translational regulation of transcription factors is often crucial for control of gene expression. In our study, we demonstrate that members of the basic helix–loop–helix (bHLH) family of transcription factors are capable of interacting with LOB. The expression patterns of bHLH048 and LOB overlap at lateral organ boundaries. Interestingly, the interaction of bHLH048 with LOB results in reduced affinity of LOB for the consensus DNA motif. Thus, our studies suggest that bHLH048 post-translationally regulates the function of LOB at lateral organ boundaries.
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24
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Puig O, Bragado-Nilsson E, Koski T, Séraphin B. The U1 snRNP-associated factor Luc7p affects 5' splice site selection in yeast and human. Nucleic Acids Res 2007; 35:5874-85. [PMID: 17726058 PMCID: PMC2034479 DOI: 10.1093/nar/gkm505] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
yLuc7p is an essential subunit of the yeast U1 snRNP and contains two putative zinc fingers. Using RNA-protein cross-linking and directed site-specific proteolysis (DSSP), we have established that the N-terminal zinc finger of yLuc7p contacts the pre-mRNA in the 5' exon in a region close to the cap. Modifying the pre-mRNA sequence in the region contacted by yLuc7p affects splicing in a yLuc7p-dependent manner indicating that yLuc7p stabilizes U1 snRNP-pre-mRNA interaction, thus reminding of the mode of action of another U1 snRNP component, Nam8p. Database searches identified three putative human yLuc7p homologs (hLuc7A, hLuc7B1 and hLuc7B2). These proteins have an extended C-terminal tail rich in RS and RE residues, a feature characteristic of splicing factors. Consistent with a role in pre-mRNA splicing, hLuc7A localizes in the nucleus and antibodies raised against hLuc7A specifically co-precipitate U1 snRNA from human cell extracts. Interestingly, hLuc7A overexpression affects splicing of a reporter in vivo. Taken together, our data suggest that the formation of a wide network of protein-RNA interactions around the 5' splice site by U1 snRNP-associated factors contributes to alternative splicing regulation.
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Affiliation(s)
- Oscar Puig
- European Molecular Biology Laboratory, Meyerhofstrasse, 1, 69117 Heidelberg, Germany, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland and CGM, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
- *To whom correspondence should be addressed. +358 9191 59423+358 9191 59366 Correspondence may also be addressed to Bertrand Séraphin. +33 1 69 82 38 84+33 1 69 82 38 77
| | - Elisabeth Bragado-Nilsson
- European Molecular Biology Laboratory, Meyerhofstrasse, 1, 69117 Heidelberg, Germany, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland and CGM, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Terhi Koski
- European Molecular Biology Laboratory, Meyerhofstrasse, 1, 69117 Heidelberg, Germany, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland and CGM, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | - Bertrand Séraphin
- European Molecular Biology Laboratory, Meyerhofstrasse, 1, 69117 Heidelberg, Germany, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland and CGM, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
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25
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White CM, Satz AL, Gawron LS, Bruice TC, Beerman TA. Inhibiting transcription factor/DNA complexes using fluorescent microgonotropens (FMGTs). BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1574:100-8. [PMID: 11955618 DOI: 10.1016/s0167-4781(01)00351-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fluorescent microgonotropens (FMGTs) are A/T selective, minor groove-binding bisbenzimidazole ligands. Basic side chains extending from these agents electrostatically contact the major groove side of the phosphodiester backbone of DNA, endowing them with high binding affinity. Here, we evaluate the potential of these agents as inhibitors of transcription factor (TF) binding to DNA and explore whether their ability to contact both grooves enhances their inhibitory activity. A series of FMGTs (L2-L5), with polyamine tails of varying lengths and degrees of branching, were compared to an analog lacking these basic side chains (L1), and the classical bisbenzimidazole Hoechst 33342 for effects on TF complex formation on the c-fos serum response element (SRE). Although L1 could not inhibit TF/SRE interactions, L2-L5 did so at submicromolar concentrations. Moreover, the FMGTs were up to 50 times more potent than Hoechst 33342 in inhibiting TF complex formation in electrophoretic mobility shift assays. The FMGTs also inhibited c-fos promoter-driven cell-free transcription and topoisomerase II activity in nuclei. These studies establish the potential of FMGTs as TF/DNA complex inhibitors in cell-free systems, provide insight into the relationship between their structure and biological activities, and demonstrate the benefits of functionalizing minor groove binding-agents with major groove-contacting groups.
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Affiliation(s)
- Christine M White
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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26
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White CM, Satz AL, Bruice TC, Beerman TA. Inhibition of transcription factor-DNA complexes and gene expression by a microgonotropen. Proc Natl Acad Sci U S A 2001; 98:10590-5. [PMID: 11535831 PMCID: PMC58510 DOI: 10.1073/pnas.191374698] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Developing minor groove-binding drugs to selectively inhibit transcription factor (TF)/DNA interactions and accompanying gene expression is a current goal in drug development studies. Equipping minor groove-binding agents with positively charged, major groove-contacting side chains yields microgonotropens (MGTs). Previously, we demonstrated that MGTs were superior inhibitors of TF/DNA complexes in cell-free assays compared with "classical" groove binders, but MGTs showed limited ability to inhibit gene expression. To determine what chemical characteristics contribute to or improve activity, we evaluate five MGTs for their effectiveness in inhibiting TF complex formation and resultant transcription by using the c-fos serum response element (SRE) as a target. MGT L1 binds DNA via a bisbenzimidazole equipped with a tripyrrole moiety. It is compared with analog L2, which has been functionalized with propylamines on each of the three pyrroles. L2, which binds DNA at subpicomolar concentrations, was at least three orders of magnitude more potent than L1 at inhibiting TF binding to the c-fos SRE in cell-free assays. Unlike L1 and previous MGTs, L2 also inhibited endogenous c-fos expression in NIH 3T3 cells at micromolar levels. Structure/activity relationships suggest that, although the tripyrrole/polyamine functional group of L2 may be largely responsible for its inhibition of TF complexes in cell-free assays, its bisbenzimidazole moiety appears to impart improved cellular uptake and activity. These findings make L2 a promising lead candidate for future, rational MGT design.
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Affiliation(s)
- C M White
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
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27
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Brunetti A, Manfioletti G, Chiefari E, Goldfine ID, Foti D. Transcriptional regulation of human insulin receptor gene by the high-mobility group protein HMGI(Y). FASEB J 2001; 15:492-500. [PMID: 11156965 DOI: 10.1096/fj.00-0190com] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have previously identified two closely related nuclear binding proteins that specifically interact with two unique functional AT-rich sequences of the 5' regulatory region of the human insulin receptor gene. Expression of these nuclear binding proteins increases during myocyte and adipocyte differentiation, and in other tissues appears to correlate with insulin receptor content. We have hypothesized, therefore, that insulin receptor expression in the insulin target tissues is regulated at least in part by these nuclear proteins. Here we show data on purification and biochemical characterization of these DNA binding proteins. Using a conventional chromatographic purification procedure combined with electrophoresis mobility shift assay and immunoblot analyses, a unique approximately 15 kDa protein, either identical to or highly related to the architectural transcription factor HMGI(Y), has now been identified, suggesting an essential role for HMGI(Y) in regulating insulin receptor gene transcription. Direct evidence of HMGI(Y) insulin receptor promoter interactions is provided by functional analysis with the CAT reporter gene and by hormone binding studies in cells expressing HMGI(Y) antisense RNA. In these experiments, antisense HMGI(Y) specifically inhibits insulin receptor promoter function and insulin receptor protein expression, indicating that HMGI(Y) is required for proper transcription of insulin receptor gene. Moreover, our data consistently support the hypothesis that a putative defect in this nuclear binding protein may cause insulin receptor dysfunction with subsequent impairment of insulin signaling and action.
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Affiliation(s)
- A Brunetti
- Dipartimento di Medicina Sperimentale e Clinica G. Salvatore, Cattedra di Endocrinologia, Università degli Studi di Catanzaro Magna Graecia, Catanzaro, Italy
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28
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Seong GH, Niimi T, Yanagida Y, Kobatake E, Aizawa M. Single-molecular AFM probing of specific DNA sequencing using RecA-promoted homologous pairing and strand exchange. Anal Chem 2000; 72:1288-93. [PMID: 10740872 DOI: 10.1021/ac990893h] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The specific sequence in a linearlized double-stranded DNA target has been identified at a single-molecular level by atomic force microscopy (AFM). This was accomplished using RecA-coated, single-stranded DNA probes which were paired with a specific complementary DNA sequence in a linear double-stranded DNA target by strand-exchange reaction at a homologous sequence site with target DNA. The sites of interaction between the nucleoprotein filaments and the double-stranded DNA targets were directly visualized by AFM in solution containing 4 mM magnesium acetate. Measurements of the position of RecA-coated probes paired to individual target DNA showed that DNA probes specifically paired at their corresponding homologous target sequences. Strand exchange promoted by RecA and the visualization by AFM provided a rapid and efficient way to identify homologous sequence on a single-molecule target DNA.
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Affiliation(s)
- G H Seong
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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29
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Mohana-Borges R, Pacheco AB, Sousa FJ, Foguel D, Almeida DF, Silva JL. LexA repressor forms stable dimers in solution. The role of specific dna in tightening protein-protein interactions. J Biol Chem 2000; 275:4708-12. [PMID: 10671501 DOI: 10.1074/jbc.275.7.4708] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cooperativity in the interactions among proteins subunits and DNA is crucial for DNA recognition. LexA repressor was originally thought to bind DNA as a monomer, with cooperativity leading to tighter binding of the second monomer. The main support for this model was a high value of the dissociation constant for the LexA dimer (micromolar range). Here we show that the protein is a dimer at nanomolar concentrations under different conditions. The reversible dissociation of LexA dimer was investigated by the effects of hydrostatic pressure or urea, using fluorescence emission and polarization to monitor the dissociation process. The dissociation constant lies in the picomolar range (lower than 20 pM). LexA monomers associate with an unusual large volume change (340 ml/mol), indicating the burial of a large surface area upon dimerization. Whereas nonspecific DNA has no stabilizing effect, specific DNA induces tightening of the dimer and a 750-fold decrease in the K(d). In contrast to the previous model, a tight dimer rather than a monomer is the functional repressor. Accordingly, the LexA dimer only loses its ability to recognize a specific DNA sequence by RecA-induced autoproteolysis. Our work provides insights into the linkage between protein-protein interactions, DNA recognition, and DNA repair.
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Affiliation(s)
- R Mohana-Borges
- Departamento de Bioquímica Médica-ICB, Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas and Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-590 Rio de Janeiro, RJ, Brazil
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30
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Myokai F, Takashiba S, Lebo R, Amar S. A novel lipopolysaccharide-induced transcription factor regulating tumor necrosis factor alpha gene expression: molecular cloning, sequencing, characterization, and chromosomal assignment. Proc Natl Acad Sci U S A 1999; 96:4518-23. [PMID: 10200294 PMCID: PMC16364 DOI: 10.1073/pnas.96.8.4518] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/1998] [Accepted: 02/18/1999] [Indexed: 01/18/2023] Open
Abstract
Lipopolysaccharide (LPS) is a potent stimulator of monocytes and macrophages, causing secretion of tumor necrosis factor alpha (TNF-alpha) and other inflammatory mediators. Given the deleterious effects to the host of TNF-alpha, it has been postulated that TNF-alpha gene expression must be tightly regulated. The nature of the nuclear factor(s) that control TNF-alpha gene transcription in humans remains obscure, although NF-kappaB has been suggested. Our previous studies pertaining to macrophage response to LPS identified a novel DNA-binding domain located from -550 to -487 in the human TNF-alpha promoter that contains transcriptional activity, but lacks any known NF-kappaB-binding sites. We have used this DNA fragment to isolate and purify a 60-kDa protein binding to this fragment and obtained its amino-terminal sequence, which was used to design degenerate probes to screen a cDNA library from THP-1 cells. A novel cDNA clone (1.8 kb) was isolated and fully sequenced. Characterization of this cDNA clone revealed that its induction was dependent on LPS activation of THP-1 cells; hence, the name LPS-induced TNF-alpha factor (LITAF). Inhibition of LITAF mRNA expression in THP-1 cells resulted in a reduction of TNF-alpha transcripts. In addition, high level of expression of LITAF mRNA was observed predominantly in the placenta, peripheral blood leukocytes, lymph nodes, and the spleen. Finally, chromosomal localization using fluorescence in situ hybridization revealed that LITAF mapped to chromosome 16p12-16p13.3. Together, these findings suggest that LITAF plays an important role in the activation of the human TNF-alpha gene and proposes a new mechanism to control TNF-alpha gene expression.
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Affiliation(s)
- F Myokai
- Boston University, Department of Periodontology and Oral Biology, School of Dental Medicine, Boston, MA 02118, USA
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Holmlin RE, Dandliker PJ, Barton JK. Ladungsübertragung durch den DNA-Basenstapel. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971092404] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Duan X, Gimble FS, Quiocho FA. Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell 1997; 89:555-64. [PMID: 9160747 DOI: 10.1016/s0092-8674(00)80237-8] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PI-Scel is a bifunctional yeast protein that propagates its mobile gene by catalyzing protein splicing and site-specific DNA double-strand cleavage. Here, we report the 2.4 A crystal structure of the PI-Scel protein. The structure is composed of two separate domains (I and II) with novel folds and different functions. Domain I, which is elongated and formed largely from seven beta sheets, harbors the N and C termini residues and two His residues that are implicated in protein splicing. Domain II, which is compact and is primarily composed of two similar alpha/beta motifs related by local two-fold symmetry, contains the putative nuclease active site with a cluster of two acidic residues and one basic residue commonly found in restriction endonucleases. This report presents prototypic structures of domains with single endonuclease and protein splicing active sites.
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Affiliation(s)
- X Duan
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, USA
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Osborne MJ, Wallis R, Leung KY, Williams G, Lian LY, James R, Kleanthous C, Moore GR. Identification of critical residues in the colicin E9 DNase binding region of the Im9 protein. Biochem J 1997; 323 ( Pt 3):823-31. [PMID: 9169618 PMCID: PMC1218388 DOI: 10.1042/bj3230823] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
1H-15N NMR studies, in conjunction with mutagenesis experiments, have been used to delineate the DNase-binding surface of the colicin E9 inhibitor protein Im9 (where Im stands for immunity protein). Complexes were formed between the 15 kDa unlabelled E9 DNase domain and the 9.5 kDa Im9 protein uniformly labelled with 15N. Approx. 90% of the amide resonances of the bound Im9 were assigned and spectral parameters obtained from 1H-15N heteronuclear single quantum coherence (HSQC) spectra were compared with those for the free Im9 assigned previously. Many of the amide resonances were shifted on complex formation, some by more than 2 p.p.m. in the 15N dimension and more than 0.5 p.p.m. in the 1H dimension. Most of the strongly shifted amides are located on the surfaces of two of the four helices, helix II and helix III. Whereas helix II had already been identified through genetic and biochemical investigations as an important determinant of biological specificity, helix III had not previously been implicated in binding to the DNase. To test the robustness of the NMR-delineated DNase-binding site, a selection of Im9 alanine mutants were constructed and their dissociation rate constants from E9 DNase-immunity protein complexes quantified by radioactive subunit exchange kinetics. Their off-rates correlated well with the NMR perturbation analysis; for example, residues that were highly perturbed in HSQC experiments, such as residues 34 (helix II) and 54 (helix III), had a marked effect on the DNase-immunity protein dissociation rate when replaced by alanine. The NMR and mutagenesis data are consistent with a DNase-binding region on Im9 composed of invariant residues in helix III and variable residues in helix II. The relationship of this binding site model to the wide range of affinities (Kd values in the range 10(-4) to 10(-16)M) that have been measured for cognate and non-cognate colicin DNase-immunity protein interactions is discussed.
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Affiliation(s)
- M J Osborne
- School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
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Bloch DB, de la Monte SM, Guigaouri P, Filippov A, Bloch KD. Identification and characterization of a leukocyte-specific component of the nuclear body. J Biol Chem 1996; 271:29198-204. [PMID: 8910577 DOI: 10.1074/jbc.271.46.29198] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The nuclear body (NB) is a cellular organelle that is involved in the pathogenesis of acute promyelocytic leukemia and viral infection. The NB is also a target of antibodies in the serum of patients with the autoimmune disease primary biliary cirrhosis. In this study, serum from a patient with primary biliary cirrhosis was used to identify a cDNA encoding a novel component of the NB, a 140-kDa protein designated Sp140. The predicted amino acid sequence of the amino-terminal portion of Sp140 was similar to Sp100, a previously identified NB protein. The carboxyl portion of Sp140 contained a zinc-finger domain and a bromodomain, motifs that are present in proteins regulating gene transcription. High levels of Sp140 mRNA were detected in human spleen and peripheral blood leukocytes, but not other human tissues. The level of SP140 mRNA in myeloid precursor cell lines HL60 and NB4 markedly increased in response to chemically induced cellular differentiation. Immunohistochemical techniques were used to demonstrate that SP140 localized to the NB in differentiated HL60 and NB4 cells. The location of Sp140 in the NB, and expression of this gene in cells involved in host defense, suggest that Sp140 may be involved in the pathogenesis of acute promyelocytic leukemia and viral infection.
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Affiliation(s)
- D B Bloch
- Department of Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.
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Brooks DJ, Woodward S, Thompson FH, Dos Santos B, Russell M, Yang JM, Guan XY, Trent J, Alberts DS, Taetle R. Expression of the zinc finger gene EVI-1 in ovarian and other cancers. Br J Cancer 1996; 74:1518-25. [PMID: 8932329 PMCID: PMC2074868 DOI: 10.1038/bjc.1996.583] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The EVI-1 gene was originally detected as an ectopic viral insertion site and encodes a nuclear zinc finger DNA-binding protein. Previous studies showed restricted EVI-1 RNA or protein expression during ontogeny; in a kidney and an endometrial carcinoma cell line; and in normal murine oocytes and kidney cells. EVI-1 expression was also detected in a subset of acute myeloid leukaemias (AMLs) and myelodysplasia. Because EVI-1 is expressed in the urogenital tract during development, we examined ovarian cancers and normal ovaries for EVI-1 RNA expression using reverse transcription polymerase chain reaction (RT-PCR) and RNAase protection. Chromosome abnormalities were examined using karyotypes and whole chromosome 3 and 3q26 fluorescence in situ hybridisation (FISH). RNA from six primary ovarian tumours, five normal ovaries and 47 tumour cell lines (25 ovarian, seven melanoma, three prostate, seven breast and one each of bladder, endometrial, lung, epidermoid and histiocytic lymphoma) was studied. Five of six primary ovarian tumours, three of five normal ovaries and 22 of 25 ovarian cell lines expressed EVI-1 RNA. A variety of other non-haematological cancers also expressed EVI-1 RNA. Immunostaining of ovarian cancer cell lines revealed nuclear EVI-1 protein. In contrast, normal ovary stained primarily within oocytes and faintly in stroma. Primary ovarian tumours showed nuclear and intense, diffuse cytoplasmic staining. Quantitation of EVI-1 RNA, performed using RNAase protection, showed ovarian carcinoma cells expressed 0 to 40 times the EVI-1 RNA in normal ovary, and 0-6 times the levels in leukaemia cell lines. Southern analyses of ovarian carcinoma cell lines showed no amplification or rearrangements involving EVI-1. In some acute leukaemias, activation of EVI-1 transcription is associated with translocations involving 3q26, the site of the EVI-1 gene. Ovarian carcinoma karyotypes showed one line with quadruplication 3(q24q27), but no other clonal structural rearrangements involving 3q26. However, whole chromsome 3 and 3q26 FISH performed on lines with high EVI-1 expression showed translocations involving chromosome 3q26. EVI-1 is overexpressed in ovarian cancer compared with normal ovaries, suggesting a role for EVI-1 in solid tumour carcinogenesis or progression. Mechanisms underlying EVI-1 overexpression remain unclear, but may include rearrangements involving chromosome 3q26.
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Affiliation(s)
- D J Brooks
- Department of Medicine, University of Arizona and Arizona Cancer Center, Tucson 85724, USA
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Brunetti A, Brunetti L, Foti D, Accili D, Goldfine ID. Human diabetes associated with defects in nuclear regulatory proteins for the insulin receptor gene. J Clin Invest 1996; 97:258-62. [PMID: 8550844 PMCID: PMC507088 DOI: 10.1172/jci118400] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The control of gene transcription is mediated by sequence-specific DNA-binding proteins (trans-acting factors) that bind to upstream regulatory elements (cis elements). We have previously identified two DNA-binding proteins that specifically interact with two unique AT-rich sequences of the 5' regulatory region of the insulin receptor gene which have in vivo promoter activity. Herein we have investigated the expression of these DNA-binding proteins in cells from two unrelated patients with insulin resistance and non-insulin-dependent diabetes mellitus. In these patients, the insulin receptor gene was normal. In EBV-transformed lymphoblasts from both patients, insulin receptor mRNA levels and insulin receptor expression were decreased. The expression of nuclear-binding proteins for the 5' regulatory region of the insulin receptor gene was markedly reduced, and this defect paralleled the decrease in insulin receptor protein expression. These studies indicate that DNA-binding proteins to the regulatory region of the insulin receptor gene are important for expression of the insulin receptor. Further, they suggest that in affected individuals, defects in the expression of these proteins may cause decreased insulin receptor expression and insulin resistance.
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Affiliation(s)
- A Brunetti
- Cattedra di Endocrinologia, Università degil Studi di Reggio Calabria, Facoltà di Medicina e Chirurgia, Catanzaro, Italy
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Reardon BJ, Gordon D, Ballard MJ, Winter E. DNA binding properties of the Saccharomyces cerevisiae DAT1 gene product. Nucleic Acids Res 1995; 23:4900-6. [PMID: 8532535 PMCID: PMC307481 DOI: 10.1093/nar/23.23.4900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The DAT1 gene of Saccharomyces cerevisiae encodes a DNA binding protein (Dat1p) that specifically recognizes the minor groove of non-alternating oligo(A).oligo(T) tracts. Sequence-specific recognition requires arginine residues found within three perfectly repeated pentads (G-R-K-P-G) of the Dat1p DNA binding domain [Reardon, B. J., Winters, R. S., Gordon, D., and Winter, E. (1993) Proc. Natl. Acad. Sci. USA 90, 11327-1131]. This report describes a rapid and simple method for purifying the Dat1p DNA binding domain and the biochemical characterization of its interaction with oligo(A).oligo(T) tracts. Oligonucleotide binding experiments and the characterization of yeast genomic Dat1p binding sites show that Dat1p specifically binds to any 11 base sequence in which 10 bases conform to an oligo(A).oligo(T) tract. Binding studies of different sized Dat1p derivatives show that the Dat1p DNA binding domain can function as a monomer. Competition DNA binding assays using poly(I).poly(C), demonstrate that the minor groove oligo(A).oligo(T) constituents are not sufficient for high specificity DNA binding. These data constrain the possible models for Dat1p/oligo(A).oligo(T) complexes, suggest that the DNA binding domain is in an extended structure when complexed to its cognate DNA, and show that Dat1p binding sites are more prevalent than previously thought.
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Affiliation(s)
- B J Reardon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Harris LF, Sullivan MR, Popken-Harris PD, Hickok DF. A one nanosecond molecular dynamics simulation of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence in a 10 Angstrom water layer. J Biomol Struct Dyn 1995; 13:423-40. [PMID: 8825722 DOI: 10.1080/07391102.1995.10508852] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We investigated protein/DNA interactions, using molecular dynamics simulations computed for one nanosecond, between a 10 Angstom water layer model of the glucocorticoid receptor (GR) DNA binding domain (DBD) amino acids and DNA of a glucocorticoid receptor response element (GRE) consisting of 29 nucleotide base pairs. Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic interaction energies were calculated. Amino acids of the GR DBD DNA recognition helix formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the GRE DNA right major groove halfsite. Likewise amino acids in a beta strand structure adjacent to the DNA recognition helix formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within both the GRE right and left major groove halfsites. In addition, amino acids within a predicted alpha helix located on the carboxyl terminus of the GR DBD interacted at codon-anticodon nucleotide sites on the DNA backbone of the GRE right major groove flanking nucleotides. These interactions together induced breakage of Watson-Crick nucleotide base pairing hydrogen bonds, resulting in significant structural changes and bending of the DNA into the protein.
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Affiliation(s)
- L F Harris
- Abbott Northwestern Hospital Cancer Research Laboratory, Minneapolis, MN 55407, USA
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40
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Voyer N, Lamothe J. The use of peptidic frameworks for the construction of molecular receptors and devices. Tetrahedron 1995. [DOI: 10.1016/0040-4020(95)00569-t] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Affiliation(s)
- A Brunetti
- Cattedra di Endocrinologia, Università di Reggio Calabria, Catanzaro, Italy
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42
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Takashiba S, Van Dyke TE, Shapira L, Amar S. Lipopolysaccharide-inducible and salicylate-sensitive nuclear factor(s) on human tumor necrosis factor alpha promoter. Infect Immun 1995; 63:1529-34. [PMID: 7890420 PMCID: PMC173185 DOI: 10.1128/iai.63.4.1529-1534.1995] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Lipopolysaccharide (LPS) is one of the most potent trigger substances for monocytes and macrophages causing secretion of tumor necrosis factor alpha (TNF-alpha) and other inflammatory mediators. The nature of the nuclear factors involved in human TNF-alpha gene regulation is still unknown. Nuclear factor kappa B (NF-kappa B) proteins have been suggested to play an important role in gene transcription of inflammatory mediators when monocytes are stimulated with LPS. However, it remains unclear whether these nuclear factors are the only ones involved in human TNF-alpha gene regulation. In this report, to further the identification of nuclear factor(s) involved in TNF-alpha gene regulation, human monocytic THP-1 cells were transfected with a series of truncated versions of human TNF-alpha promoter. A 98-bp region located from nucleotides -584 to -487 demonstrated strong promoter activity. Electrophoretic mobility shift assays demonstrated that a 64-bp fragment located within the 98-bp region and lacking any potential NF-kappa B-binding sites avidly bound LPS-challenged THP-1 nuclear protein. Although this binding was inhibited in salicylate-treated cells, as was binding of NF-kappa B, the pattern of binding was found to differ from that noted for NF-kappa B. Analysis of this 64-bp fragment disclosed the absence of an NF-kappa B consensus sequence, suggesting a novel nuclear DNA-binding protein necessary for the initiation of human TNF-alpha transcription other than, or in addition to, NF-kappa B.
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Affiliation(s)
- S Takashiba
- Department of Periodontology, Eastman Dental Center, Rochester, New York 14620
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43
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44
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Barawkar DA, Ganesh KN. Fluorescent d(CGCGAATTCGCG): characterization of major groove polarity and study of minor groove interactions through a major groove semantophore conjugate. Nucleic Acids Res 1995; 23:159-64. [PMID: 7870581 PMCID: PMC306644 DOI: 10.1093/nar/23.1.159] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The major and minor groove in duplex DNA are sites of specific molecular recognition by DNA-binding agents such as proteins, drugs and metal complexes and have functional significance. In view of this, understanding of the inherent differences in their environment and the allosteric information transfer between them induced by DNA-binding agents assumes importance. Site-specific incorporation of 5-aminodansyl-dU, (U*) in oligonucleotides d(CGCGAAU*TCGCG) and d(CGCGAATU*CGCG) leads to fluorogenic nucleic acids, in which the reporter group resides in the major groove. The fluorescent observables from such a probe are used to estimate the dielectric constant of the major groove to be approximately 55D, in comparison to the reported non polar environment of the minor groove (approximately 20D) in poly d[AT]-poly d[AT]. An exclusive minor groove event such as DNA-netropsin association can be quantitatively monitored by fluorescence of the dansyl moiety located in the major groove. This suggests existence of an information network among the two grooves. The fluorescent DNA probes as reported here may have potential applications in the study of structural polymorphisms in DNA, DNA-ligand interactions and triple helix structure.
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Affiliation(s)
- D A Barawkar
- Division of Organic Chemistry, National Chemical Laboratory, Pune, India
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45
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Mechulam Y, Meinnel T, Blanquet S. A family of RNA-binding enzymes. the aminoacyl-tRNA synthetases. Subcell Biochem 1995; 24:323-376. [PMID: 7900181 DOI: 10.1007/978-1-4899-1727-0_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- Y Mechulam
- Laboratoire de Biochimie, CNRS n. 240, Ecole Polytechnique, Palaiseau, France
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46
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Pandit HM. An energy imbalance (cellular energy lesion) as an etiological factor in the development of cancer: a new insight. Acta Biotheor 1994; 42:315-23. [PMID: 7801730 DOI: 10.1007/bf00707396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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47
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Crameri R, Jaussi R, Menz G, Blaser K. Display of expression products of cDNA libraries on phage surfaces. A versatile screening system for selective isolation of genes by specific gene-product/ligand interaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 226:53-8. [PMID: 7957259 DOI: 10.1111/j.1432-1033.1994.tb20025.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Techniques for cloning cDNAs from bacteriophage libraries immobilised on solid supports are well established. However, these techniques do not allow selective enrichment of clones expressing proteins of interest. Screening of cDNA libraries would be simplified if the proteins encoded by cDNAs could be expressed on the surface of phage. Phage carrying genes encoding proteins for which a ligand is available can be selected directly by affinity interaction [Crameri, R. & Suter, M. (1993) Gene (Amst.) 137, 69-75]. The expression products from a cDNA library from Aspergillus fumigatus have been displayed on the surface of the filamentous phage M13 and screened for gene products binding to human serum IgE. The physical linkage of cDNA-encoded proteins to the genetic information required for their production, achieved by exploiting the high-affinity interaction of the Jun and Fos leucine zippers, allows screening of up to 1 x 10(10) independent clones in 50-microliters aliquots applied to a well of a microtiter plate coated with the ligand. Phage displaying IgE-binding proteins were selectively enriched 10(5)-10(6)-fold over non-specific phage after six rounds of growth and selection. The apparent molecular mass of the proteins selected from the cDNA library was in the range 20-40 kDa. Restriction enzyme analysis and preliminary sequence determination of 12 selected inserts revealed different sequences. The ability of the proteins to bind to human serum IgE was corroborated by enzyme-linked immunosorbent assay and by Western-blot analysis. The developed cloning strategy allows isolation of cDNAs encoding proteins for which a ligand is available and circumvents immobilisation of the libraries on solid-phase supports which hamper selective enrichment of clones expressing the desired protein.
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Affiliation(s)
- R Crameri
- Swiss Institute of Allergy and Asthma Research, Davos
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48
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Schütz B, Niessing J. Cloning and structure of a chicken zinc finger cDNA: restricted expression in developing neural crest cells. Gene 1994; 148:227-36. [PMID: 7958949 DOI: 10.1016/0378-1119(94)90693-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The cloning, DNA sequence analysis and expression pattern of a chicken cDNA, cKr2, is described. cKr2 is a 4492-bp cDNA that encodes a 1173-amino-acid (aa) protein with two domains: the N-terminal portion contains 16 zinc fingers (Zf) of the 2Cys + 2His class, while the C-terminal domain contains a stretch of 181 aa which consists of seven consecutive sequence repeats each being 24 aa in length. The aa sequence repeats harbor a putative DNA-binding helix-turn-helix motif. Northern and Western blotting experiments indicate cKr2 expression from days 2 to 12 of development. In situ hybridization and immunohistochemical analyses using an anti-cKr2 antibody and the HNK-1 antibody, a marker of neural crest cells, revealed cKr2 activity in cephalic and trunk neural crest-derived cells. cKr2 is expressed predominantly in differentiating Schwann cells lining the nerves which innervate the branchial arches and limb buds, in cells of the sympathetic ganglia and aortic plexus, and in putative neuroblasts of dorsal root ganglia. The nuclear localization of the cKr2-encoded protein is consistent with its presumed role as a transcription factor.
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Affiliation(s)
- B Schütz
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Germany
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49
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Kessler B, Timmis KN, de Lorenzo V. The organization of the Pm promoter of the TOL plasmid reflects the structure of its cognate activator protein XylS. MOLECULAR & GENERAL GENETICS : MGG 1994; 244:596-605. [PMID: 7969028 DOI: 10.1007/bf00282749] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The toluate catabolic operon carried by the TOL plasmid pWW0 of Pseudomonas putida is positively regulated by the benzoate-responsive XylS protein which, when activated, stimulates transcription from the operon promoter Pm. In this study, the mode in which XylS effects the activity of the Pm promoter was examined in vivo by genetic analysis of both protein and promoter variants. Substitution of His31Asp/Ser32Pro,Leu113Pro,Phe214Leu/Glu215A sp/Arg216Pro or Thr312Pro, all predicted to disrupt the secondary structure, renders XylS inactive and unable to compete with the native protein for activation of Pm. In contrast, Pro substitutions at Ser64 or Gly160 had no or only minor effects on XylS activity, and a protein with residual capacity to activate Pm resulted when Glu11 was altered to Pro. None of a collection of truncated variants, of XylS protein deleted for more than 10 terminal amino acids retained activity or were able to negatively interact the wild-type XylS protein. These data indicate that amino- and carboxy-terminal portions of the protein sequence depend on each other for the maintenance of their functional structure, rather than being arranged as independent domains. Pm promoter derivatives, in which the two half-sites of the direct repeat sequence that confers responsiveness to XylS were separated and/or inverted by one-half or one complete DNA helix turn, lost responsiveness in vivo. These results favour a model for XylS-mediated activation of Pm in which a tandem dimer is the protein form that binds the Pm promoter.
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Affiliation(s)
- B Kessler
- Gesellschaft für Biotechnologische Forschung, Bereich Mikrobiologie, Braunschweig, Germany
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50
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Abstract
Consideration is given to alternative approaches to the development of DNA sequence selective binding agents because of their potential applications in diagnosis and treatment of cancer as well as in molecular biology. The concept of lexitropsins, or information-reading molecules, is introduced within the antigene strategy as an alternative to, and complementary with, the antisense approach for cellular intervention and gene control. The chemical, physical and pharmacological factors involved in the design of effective lexitropsins are discussed and illustrated with experimental results. Among the factors contributing to the molecular recognition processes are: the presence and disposition of hydrogen bond accepting and donating groups, ligand shape, chirality, stereochemistry, flexibility and charge. For longer ligands, such as are required to target unique sequences in biological systems (14-16 base pairs), the critical feature is the phasing or spatial correspondence between repeat units in the ligand and the receptor. The recently discovered 2:1 lexitropsin-DNA binding motif provides a further refinement in molecular recognition in permitting discrimination between GC and CG base pairs. The application of these factors in the design and synthesis of novel agents which exhibit anticancer, antiviral and antiretroviral properties, and inhibition of critical cellular enzymes including topoisomerases is discussed. The emerging evidence of a relationship between sequence selectivity of the new agents and the biological responses they invoked is also described.
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Affiliation(s)
- J W Lown
- Department of Chemistry, University of Alberta, Edmonton, Canada
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