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Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. Nat Commun 2024; 15:6636. [PMID: 39107287 PMCID: PMC11303717 DOI: 10.1038/s41467-024-50348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology. The biochemical and biophysical properties of these motifs determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
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Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
- Department of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA.
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Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.563609. [PMID: 38014227 PMCID: PMC10680705 DOI: 10.1101/2023.11.15.563609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
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Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
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3
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Eisner D, Neher E, Taschenberger H, Smith G. Physiology of intracellular calcium buffering. Physiol Rev 2023; 103:2767-2845. [PMID: 37326298 DOI: 10.1152/physrev.00042.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/08/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
Calcium signaling underlies much of physiology. Almost all the Ca2+ in the cytoplasm is bound to buffers, with typically only ∼1% being freely ionized at resting levels in most cells. Physiological Ca2+ buffers include small molecules and proteins, and experimentally Ca2+ indicators will also buffer calcium. The chemistry of interactions between Ca2+ and buffers determines the extent and speed of Ca2+ binding. The physiological effects of Ca2+ buffers are determined by the kinetics with which they bind Ca2+ and their mobility within the cell. The degree of buffering depends on factors such as the affinity for Ca2+, the Ca2+ concentration, and whether Ca2+ ions bind cooperatively. Buffering affects both the amplitude and time course of cytoplasmic Ca2+ signals as well as changes of Ca2+ concentration in organelles. It can also facilitate Ca2+ diffusion inside the cell. Ca2+ buffering affects synaptic transmission, muscle contraction, Ca2+ transport across epithelia, and the killing of bacteria. Saturation of buffers leads to synaptic facilitation and tetanic contraction in skeletal muscle and may play a role in inotropy in the heart. This review focuses on the link between buffer chemistry and function and how Ca2+ buffering affects normal physiology and the consequences of changes in disease. As well as summarizing what is known, we point out the many areas where further work is required.
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Affiliation(s)
- David Eisner
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Erwin Neher
- Membrane Biophysics Laboratory, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Godfrey Smith
- School of Cardiovascular and Metabolic Health, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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4
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Sadihov-Hanoch H, Bandela AK, Chotera-Ouda A, Ben David O, Cohen-Luria R, Lynn DG, Ashkenasy G. Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras. SOFT MATTER 2023; 19:3940-3945. [PMID: 37211859 DOI: 10.1039/d2sm01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.
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Affiliation(s)
- Hava Sadihov-Hanoch
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Anil Kumar Bandela
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Agata Chotera-Ouda
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Oshrat Ben David
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, USA
| | - Gonen Ashkenasy
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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5
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Guillaume O, Butnarasu C, Visentin S, Reimhult E. Interplay between biofilm microenvironment and pathogenicity of Pseudomonas aeruginosa in cystic fibrosis lung chronic infection. Biofilm 2022; 4:100089. [PMID: 36324525 PMCID: PMC9618985 DOI: 10.1016/j.bioflm.2022.100089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
Pseudomonas aeruginosa (PA) is a highly, if not the most, versatile microorganism capable of colonizing diverse environments. One of the niches in which PA is able to thrive is the lung of cystic fibrosis (CF) patients. Due to a genetic aberration, the lungs of CF-affected patients exhibit impaired functions, rendering them highly susceptible to bacterial colonization. Once PA attaches to the epithelial surface and transitions to a mucoid phenotype, the infection becomes chronic, and antibiotic treatments become inefficient. Due to the high number of affected people and the severity of this infection, CF-chronic infection is a well-documented disease. Still, numerous aspects of PA CF infection remain unclear. The scientific reports published over the last decades have stressed how PA can adapt to CF microenvironmental conditions and how its surrounding matrix of extracellular polymeric substances (EPS) plays a key role in its pathogenicity. In this context, it is of paramount interest to present the nature of the EPS together with the local CF-biofilm microenvironment. We review how the PA biofilm microenvironment interacts with drugs to contribute to the pathogenicity of CF-lung infection. Understanding why so many drugs are inefficient in treating CF chronic infection while effectively treating planktonic PA is essential to devising better therapeutic targets and drug formulations.
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Affiliation(s)
- Olivier Guillaume
- 3D Printing and Biofabrication Group, Institute of Materials Science and Technology, TU Wien (Technische Universität Wien), Getreidemarkt 9/308, 1060, Vienna, Austria,Austrian Cluster for Tissue Regeneration, Austria,Corresponding author. 3D Printing and Biofabrication Group, Institute of Materials Science and Technology, TU Wien (Technische Universität Wien), Getreidemarkt 9/308, 1060, Vienna, Austria.
| | - Cosmin Butnarasu
- Department of Molecular Biotechnology and Health Science, University of Turin, Turin, 10135, Italy
| | - Sonja Visentin
- Department of Molecular Biotechnology and Health Science, University of Turin, Turin, 10135, Italy
| | - Erik Reimhult
- Institute of Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190, Vienna, Austria
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Stiekema M, Houben F, Verheyen F, Borgers M, Menzel J, Meschkat M, van Zandvoort MAMJ, Ramaekers FCS, Broers JLV. The Role of Lamins in the Nucleoplasmic Reticulum, a Pleiomorphic Organelle That Enhances Nucleo-Cytoplasmic Interplay. Front Cell Dev Biol 2022; 10:914286. [PMID: 35784476 PMCID: PMC9243388 DOI: 10.3389/fcell.2022.914286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/24/2022] [Indexed: 12/15/2022] Open
Abstract
Invaginations of the nuclear membrane occur in different shapes, sizes, and compositions. Part of these pleiomorphic invaginations make up the nucleoplasmic reticulum (NR), while others are merely nuclear folds. We define the NR as tubular invaginations consisting of either both the inner and outer nuclear membrane, or only the inner nuclear membrane. Specifically, invaginations of both the inner and outer nuclear membrane are also called type II NR, while those of only the inner nuclear membrane are defined as type I NR. The formation and structure of the NR is determined by proteins associated to the nuclear membrane, which induce a high membrane curvature leading to tubular invaginations. Here we review and discuss the current knowledge of nuclear invaginations and the NR in particular. An increase in tubular invaginations of the nuclear envelope is associated with several pathologies, such as laminopathies, cancer, (reversible) heart failure, and Alzheimer’s disease. Furthermore, viruses can induce both type I and II NR. In laminopathies, the amount of A-type lamins throughout the nucleus is generally decreased or the organization of lamins or lamin-associated proteins is disturbed. Also, lamin overexpression or modulation of lamin farnesylation status impacts NR formation, confirming the importance of lamin processing in NR formation. Virus infections reorganize the nuclear lamina via (de)phosphorylation of lamins, leading to an uneven thickness of the nuclear lamina and in turn lobulation of the nuclear membrane and the formation of invaginations of the inner nuclear membrane. Since most studies on the NR have been performed with cell cultures, we present additional proof for the existence of these structures in vivo, focusing on a variety of differentiated cardiovascular and hematopoietic cells. Furthermore, we substantiate the knowledge of the lamin composition of the NR by super-resolution images of the lamin A/C and B1 organization. Finally, we further highlight the essential role of lamins in NR formation by demonstrating that (over)expression of lamins can induce aberrant NR structures.
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Affiliation(s)
- Merel Stiekema
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
- GROW-School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Frederik Houben
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
- Department of Healthcare, PXL University College, Hasselt, Belgium
| | - Fons Verheyen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Marcel Borgers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | | | | | - Marc A. M. J. van Zandvoort
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
- GROW-School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, Netherlands
- CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, Maastricht, Netherlands
- Institute for Molecular Cardiovascular Research IMCAR, RWTH Aachen University, Aachen, Germany
| | - Frans C. S. Ramaekers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
- GROW-School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Jos L. V. Broers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
- GROW-School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, Netherlands
- CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, Maastricht, Netherlands
- *Correspondence: Jos L. V. Broers,
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7
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Fan H, Yu Y, Nan H, Hoyt M, Reger MK, Prizment A, Anderson KE, Zhang J. Associations between intake of calcium, magnesium and phosphorus and risk of pancreatic cancer: a population-based, case-control study in Minnesota. Br J Nutr 2021; 126:1549-1557. [PMID: 33494844 DOI: 10.1017/s0007114521000283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Experimental studies suggest that abnormal levels of Ca, Mg and phosphorus are implicated in pancreatic carcinogenesis. We investigated the associations between intakes of these minerals and the risk of pancreatic cancer in a case-control study conducted in 1994-1998. Cases of pancreatic cancer (n 150) were recruited from all hospitals in the metropolitan area of the Twin Cities and Mayo Clinic, Minnesota. Controls (n 459) were randomly selected from the general population and frequency matched to cases by age, sex and race. All dietary variables were adjusted for energy intake using the residual method prior to data analysis. Logistic regression was performed to evaluate the associations between intake of three nutrients examined and the risk of pancreatic cancer. Total intake of Ca (936 v. 1026 mg/d) and dietary intake of Mg (315 v. 331 mg/d) and phosphorus (1350 v. 1402 mg/d) were significantly lower in cases than in controls. After adjustment for confounders, there were not significant associations of total and dietary intakes of Ca, Mg and phosphorus with the risk of pancreatic cancer. In addition, no significant interactions exist between intakes of these minerals and total fat on pancreatic cancer risk. In conclusion, the present study does not suggest that intakes of Ca, Mg and phosphorus were significantly associated with the risk of pancreatic cancer.
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Affiliation(s)
- Hao Fan
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN, USA
| | - Yunpeng Yu
- Department of Biostatistics, Indiana University Richard M. Fairbanks School of Public Health and School of Medicine, Indianapolis, IN, USA
| | - Haocheng Nan
- Department of Surgery, Shaanxi Provincial People's Hospital, Xi'an, People's Republic of China
| | - Margaret Hoyt
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN, USA
| | - Michael K Reger
- College of Health Professions, Ferris State University, Big Rapids, MI, USA
| | - Anna Prizment
- Division of Hematology, Oncology and Transplantation, Medical School and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Kristin E Anderson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jianjun Zhang
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA
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8
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Donia T, Jyoti B, Suizu F, Hirata N, Tanaka T, Ishigaki S, F PTJ, Nio-Kobayashi J, Iwanaga T, Chiorini JA, Noguchi M. Identification of RNA aptamer which specifically interacts with PtdIns(3)P. Biochem Biophys Res Commun 2019; 517:146-154. [PMID: 31351587 DOI: 10.1016/j.bbrc.2019.07.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022]
Abstract
The phosphinositide PtdIns(3)P plays an important role in autophagy; however, the detailed mechanism of its activity remains unclear. Here, we used a Systematic Evolution of Ligands by EXponential enrichment (SELEX) screening approach to identify an RNA aptamer of 40 nucleotides that specifically recognizes and binds to intracellular lysosomal PtdIns(3)P. Binding occurs in a magnesium concentration- and pH-dependent manner, and consequently inhibits autophagy as determined by LC3II/I conversion, p62 degradation, formation of LC3 puncta, and lysosomal accumulation of Phafin2. These effects in turn inhibited lysosomal acidification, and the subsequent hydrolytic activity of cathepsin D following induction of autophagy. Given the essential role of PtdIns(3)P as a key targeting molecule for autophagy induction, identification of this novel PtdIns(3)P RNA aptamer provides new opportunities for investigating the biological functions and mechanisms of phosphoinositides.
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Affiliation(s)
- Thoria Donia
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan; Chemistry Department, Faculty of Science, Tanta University, Egypt
| | - Bala Jyoti
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan; Molsys Scientific, 01 Kogilu, Mittiganahalli cross Yelahanka, Bangalore, 560064, India
| | - Futoshi Suizu
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Noriyuki Hirata
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tsutomu Tanaka
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan; National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Satoko Ishigaki
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Pranzatelli Thomas J F
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Junko Nio-Kobayashi
- Laboratory of Histology and Cytology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshihiko Iwanaga
- Laboratory of Histology and Cytology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - John A Chiorini
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Masayuki Noguchi
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
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9
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Tessier SN, Zhang Y, Wijenayake S, Storey KB. MAP kinase signaling and Elk1 transcriptional activity in hibernating thirteen-lined ground squirrels. Biochim Biophys Acta Gen Subj 2017; 1861:2811-2821. [DOI: 10.1016/j.bbagen.2017.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/07/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022]
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10
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Guimarães E, Machado R, Fonseca MDC, França A, Carvalho C, Araújo e Silva AC, Almeida B, Cassini P, Hissa B, Drumond L, Gonçalves C, Fernandes G, De Brot M, Moraes M, Barcelos L, Ortega JM, Oliveira A, Leite MF. Inositol 1, 4, 5-trisphosphate-dependent nuclear calcium signals regulate angiogenesis and cell motility in triple negative breast cancer. PLoS One 2017; 12:e0175041. [PMID: 28376104 PMCID: PMC5380351 DOI: 10.1371/journal.pone.0175041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/20/2017] [Indexed: 01/19/2023] Open
Abstract
Increases in nuclear calcium concentration generate specific biological outcomes that differ from those resulting from increased cytoplasmic calcium. Nuclear calcium effects on tumor cell proliferation are widely appreciated; nevertheless, its involvement in other steps of tumor progression is not well understood. Therefore, we evaluated whether nuclear calcium is essential in other additional stages of tumor progression, including key steps associated with the formation of the primary tumor or with the metastatic cascade. We found that nuclear calcium buffering impaired 4T1 triple negative breast cancer growth not just by decreasing tumor cell proliferation, but also by enhancing tumor necrosis. Moreover, nuclear calcium regulates tumor angiogenesis through a mechanism that involves the upregulation of the anti-angiogenic C-X-C motif chemokine 10 (CXCL10-IP10). In addition, nuclear calcium buffering regulates breast tumor cell motility, culminating in less cell invasion, likely due to enhanced vinculin expression, a focal adhesion structural protein. Together, our results show that nuclear calcium is essential for triple breast cancer angiogenesis and cell migration and can be considered as a promising strategic target for triple negative breast cancer therapy.
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Affiliation(s)
- Erika Guimarães
- Department of Molecular Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Machado
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Matheus de Castro Fonseca
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, Brazil
| | - Andressa França
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Clarissa Carvalho
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Brígida Almeida
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Puebla Cassini
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bárbara Hissa
- Department of Physics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luciana Drumond
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Carlos Gonçalves
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Fernandes
- Genomics Sciences and Biotechnology of Universidade Católica de Brasília, Brasília, Brazil
| | - Marina De Brot
- Department of Pathological Anatomy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Márcio Moraes
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Lucíola Barcelos
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - José Miguel Ortega
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - André Oliveira
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - M. Fátima Leite
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Brazil
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11
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Zhang Y, Storey KB. Regulation of gene expression by NFAT transcription factors in hibernating ground squirrels is dependent on the cellular environment. Cell Stress Chaperones 2016; 21:883-94. [PMID: 27344571 PMCID: PMC5003805 DOI: 10.1007/s12192-016-0713-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/30/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022] Open
Abstract
Calcineurin is a calmodulin-stimulated phosphatase that regulates the nuclear translocation of nuclear factor of activated T cell (NFAT) c1-4 through dephosphorylation. We believe that this mechanism plays various roles in the remodeling and maintenance of Ictidomys tridecemlineatus skeletal muscle. During hibernation, bouts of torpor and arousal take place, and squirrels do not lose muscle mass despite being inactive. Protein expression of Ca(2+) signaling proteins were studied using immunoblotting. A DNA-protein interaction ELISA technique was created to test the binding of NFATs in the nucleus to DNA probes containing the NFAT response element under environmental conditions reflective of those during hibernation. Calcineurin protein levels increased by 3.08-fold during torpor (compared to euthermic control), whereas calpain1 levels also rose by 3.66-fold during torpor. Calmodulin levels were elevated upon entering torpor. NFATc4 binding to DNA showed a 1.4-fold increase during torpor, and we found that this binding was further enhanced when 600 nM of Ca(2+) was supplemented. We also found that decreasing the temperature of ELISAs resulted in progressive decreases in the binding of NFATs c1, c3, and c4 to DNA. In summary, calmodulin and calpain1 appear to activate calcineurin and NFATc4 during torpor. NFAT binding to target promoters is affected by intranuclear [Ca(2+)] and environmental temperatures. Therefore, Ca(2+) signaling and temperature changes play key roles in regulation of the NFAT-calcineurin pathway in skeletal muscle of hibernating 13-lined ground squirrels over the torpor-arousal cycle, and they may contribute to the avoidance of disuse-induced muscle atrophy that occurs naturally in these animals.
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Affiliation(s)
- Yichi Zhang
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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12
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Quantitative imaging of magnesium distribution at single-cell resolution in brain tumors and infiltrating tumor cells with secondary ion mass spectrometry (SIMS). J Neurooncol 2015; 127:33-41. [PMID: 26703785 DOI: 10.1007/s11060-015-2022-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023]
Abstract
Glioblastoma multiforme (GBM) is one of the deadliest forms of human brain tumors. The infiltrative pattern of growth of these tumors includes the spread of individual and/or clusters of tumor cells at some distance from the main tumor mass in parts of the brain protected by an intact blood-brain-barrier. Pathophysiological studies of GBM could be greatly enhanced by analytical techniques capable of in situ single-cell resolution measurements of infiltrating tumor cells. Magnesium homeostasis is an area of active investigation in high grade gliomas. In the present study, we have used the F98 rat glioma as a model of human GBM and an elemental/isotopic imaging technique of secondary ion mass spectrometry, a CAMECA IMS-3f ion microscope, for studying Mg distribution with single-cell resolution in freeze-dried brain tissue cryosections. Quantitative observations were made on tumor cells in the main tumor mass, contiguous brain tissue, and infiltrating tumor cells in adjacent normal brain. The brain tissue contained a significantly lower total Mg concentration of 4.70 ± 0.93 mmol/kg wet weight (mean ± SD) in comparison to 11.64 ± 1.96 mmol/kg wet weight in tumor cells of the main tumor mass and 10.72 ± 1.76 mmol/kg wet weight in infiltrating tumor cells (p < 0.05). The nucleus of individual tumor cells contained elevated levels of bound Mg. These observations have established that there was enhanced influx and increased binding of Mg in tumor cells. They provide strong support for further investigation of altered Mg homeostasis and activation of Mg-transporting channels in GBMs as possible therapeutic targets.
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Anderson BN, Assad ON, Gilboa T, Squires AH, Bar D, Meller A. Probing solid-state nanopores with light for the detection of unlabeled analytes. ACS NANO 2014; 8:11836-45. [PMID: 25363680 PMCID: PMC4334260 DOI: 10.1021/nn505545h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanopore sensing has enabled label-free single-molecule measurements on a wide variety of analytes, including DNA, RNA, and protein complexes. Much progress has been made toward biotechnological applications; however, electrically probing the ion current introduces nonideal noise components. Here we further develop a method to couple an ionic current to a photon-by-photon counting of fluorescent signal from Ca(2+)-sensitive dyes and demonstrate label-free optical detection of biopolymer translocation through solid-state nanopores using TIRF and confocal microscopy. We show that by fine adjustment of the CaCl2 gradient, EGTA concentration, and voltage, the optical signals can be localized to the immediate vicinity of the pore. Consequently, the noise spectral density distribution in the optical signal exhibits a nearly flat distribution throughout the entire frequency range. With the use of high-speed photon counting devices in confocal microscopy and higher photon count rates using stronger light sources, we can improve the signal-to-noise ratio of signal acquisition, while the use of wide-field imaging in TIRF can allow for simultaneous quantitative imaging of large arrays of nanopores.
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Affiliation(s)
- Brett N. Anderson
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Ossama N. Assad
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Tal Gilboa
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Allison H. Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Daniel Bar
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Amit Meller
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
- Address correspondence to
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Wehbe M, Labib M, Muharemagic D, Zamay AS, Berezovski MV. Switchable aptamers for biosensing and bioseparation of viruses (SwAps-V). Biosens Bioelectron 2014; 67:280-6. [PMID: 25190090 DOI: 10.1016/j.bios.2014.08.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/08/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022]
Abstract
There is a widespread interest in the development of aptamer-based affinity chromatographic methods for purification of biomolecules. Regardless of the many advantages exhibited by aptamers when compared to other recognition elements, the lack of an efficient regeneration technique that can be generalized to all targets has encumbered further integration of aptamers into affinity-based purification methods. Here we offer switchable aptamers (SwAps) that have been developed to solve this problem and move aptamer-based chromatography forward. SwAps are controlled-affinity aptamers, which have been employed here to purify vesicular stomatitis virus (VSV) as a model case, however this technique can be extended to all biologically significant molecules. VSV is one oncolytic virus out of an arsenal of potential candidates shown to provide selective destruction of cancer cells both in vitro and in vivo. These SwAps were developed in the presence of Ca(2+) and Mg(2+) ions where they cannot bind to their target VSV in absence of these cations. Upon addition of EDTA and EGTA, the divalent cations were sequestered from the stabilized aptameric structure causing a conformational change and subsequently release of the virus. Both flow cytometry and electrochemical impedance spectroscopy were employed to estimate the binding affinities between the selected SwAps and VSV and to determine the coefficient of switching (CoS) upon elution. Among fifteen sequenced SwAps, four have exhibited high affinity to VSV and ability to switch upon elution and thus were further integrated into streptavidin-coated magnetic beads for purification of VSV.
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Affiliation(s)
- Mohamed Wehbe
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | - Mahmoud Labib
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Anna S Zamay
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada; Institute of Chemistry and Chemical Technology SB RAS, 50 Akademgorodok, Krasnoyarsk 660036, Russia
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Agoston DV. Great insight created by tiny holes; celebrating 40 years of brain micropunch technique. Front Neuroanat 2014; 8:61. [PMID: 25071466 PMCID: PMC4092355 DOI: 10.3389/fnana.2014.00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/13/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Denes V Agoston
- Anatomy, Physiology and Genetics, Uniformed Services University Bethesda, MD, USA ; Experimental Traumatology, Department of Neuroscience, Karolinska Institute Stockholm, Sweden
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16
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Schenke D, Cai D. The interplay of transcription factors in suppression of UV-B induced flavonol accumulation by flg22. PLANT SIGNALING & BEHAVIOR 2014; 9:e28745. [PMID: 24721804 PMCID: PMC4091570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 02/28/2024]
Abstract
Biotic stress can be mimicked by application of elicitors, which comprise of microbe-associated molecular patterns (MAMPs). Treatment of plant cell cultures with MAMPs such as flg22 suppressed the expression of UV-B-induced flavonol pathway genes (FPGs) in parsley, carrot and Arabidopsis. This is thought to allow the plant focusing its secondary metabolism on the pathogen defense during MAMP-triggered immunity (MTI). Recently we reported that this suppression also depends on prevention of histone 3 acetylation at lysine 9 (H3K9ac), a hallmark for gene activation. Here we describe a possible regulation between UV-B and flg22 signaling cascades, and the interplay of MYB and WRKY transcription factors in regulating the expression of the FPGs.
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Affiliation(s)
- Dirk Schenke
- Department Molecular Phytopathology; Christian-Albrechts University of Kiel; Kiel, Germany
| | - Daguang Cai
- Department Molecular Phytopathology; Christian-Albrechts University of Kiel; Kiel, Germany
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Schenke D, Cai D. The interplay of transcription factors in suppression of UV-B induced flavonol accumulation by flg22. PLANT SIGNALING & BEHAVIOR 2014; 9:28745. [PMID: 24721804 PMCID: PMC4091570 DOI: 10.4161/psb.28745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 05/31/2023]
Abstract
Biotic stress can be mimicked by application of elicitors, which comprise of microbe-associated molecular patterns (MAMPs). Treatment of plant cell cultures with MAMPs such as flg22 suppressed the expression of UV-B-induced flavonol pathway genes (FPGs) in parsley, carrot and Arabidopsis. This is thought to allow the plant focusing its secondary metabolism on the pathogen defense during MAMP-triggered immunity (MTI). Recently we reported that this suppression also depends on prevention of histone 3 acetylation at lysine 9 (H3K9ac), a hallmark for gene activation. Here we describe a possible regulation between UV-B and flg22 signaling cascades, and the interplay of MYB and WRKY transcription factors in regulating the expression of the FPGs.
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18
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Affiliation(s)
- Ferenc Horkay
- Section on Tissue Biophysics and Biomimetics; NICHD, National Institutes of Health; 13 South Drive; Bethesda; MD; 20892; USA
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19
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Resende RR, Andrade LM, Oliveira AG, Guimarães ES, Guatimosim S, Leite MF. Nucleoplasmic calcium signaling and cell proliferation: calcium signaling in the nucleus. Cell Commun Signal 2013; 11:14. [PMID: 23433362 PMCID: PMC3599436 DOI: 10.1186/1478-811x-11-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 02/12/2013] [Indexed: 01/19/2023] Open
Abstract
Calcium (Ca2+) is an essential signal transduction element involved in the regulation of several cellular activities and it is required at various key stages of the cell cycle. Intracellular Ca2+ is crucial for the orderly cell cycle progression and plays a vital role in the regulation of cell proliferation. Recently, it was demonstrated by in vitro and in vivo studies that nucleoplasmic Ca2+ regulates cell growth. Even though the mechanism by which nuclear Ca2+ regulates cell proliferation is not completely understood, there are reports demonstrating that activation of tyrosine kinase receptors (RTKs) leads to translocation of RTKs to the nucleus to generate localized nuclear Ca2+ signaling which are believed to modulate cell proliferation. Moreover, nuclear Ca2+ regulates the expression of genes involved in cell growth. This review will describe the nuclear Ca2+ signaling machinery and its role in cell proliferation. Additionally, the potential role of nuclear Ca2+ as a target in cancer therapy will be discussed.
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Affiliation(s)
- Rodrigo R Resende
- Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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20
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Holland JG, Geiger FM. Importance of length and sequence order on magnesium binding to surface-bound oligonucleotides studied by second harmonic generation and atomic force microscopy. J Phys Chem B 2012; 116:6302-10. [PMID: 22571519 DOI: 10.1021/jp301573g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be -32.1(4) and -35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5'-A(10)G(10)-3', 5'-(AG)(10)-3', and 5'-G(10)A(10)-3' (here the -3' end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be -33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3' end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg(II) ions are bound to the strand.
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Affiliation(s)
- Joseph G Holland
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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21
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Kiddle G, Hardinge P, Buttigieg N, Gandelman O, Pereira C, McElgunn CJ, Rizzoli M, Jackson R, Appleton N, Moore C, Tisi LC, Murray JAH. GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use. BMC Biotechnol 2012; 12:15. [PMID: 22546148 PMCID: PMC3388468 DOI: 10.1186/1472-6750-12-15] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 04/30/2012] [Indexed: 11/12/2022] Open
Abstract
Background There is an increasing need for quantitative technologies suitable for molecular detection in a variety of settings for applications including food traceability and monitoring of genetically modified (GM) crops and their products through the food processing chain. Conventional molecular diagnostics utilising real-time polymerase chain reaction (RT-PCR) and fluorescence-based determination of amplification require temperature cycling and relatively complex optics. In contrast, isothermal amplification coupled to a bioluminescent output produced in real-time (BART) occurs at a constant temperature and only requires a simple light detection and integration device. Results Loop mediated isothermal amplification (LAMP) shows robustness to sample-derived inhibitors. Here we show the applicability of coupled LAMP and BART reactions (LAMP-BART) for determination of genetically modified (GM) maize target DNA at low levels of contamination (0.1-5.0% GM) using certified reference material, and compare this to RT-PCR. Results show that conventional DNA extraction methods developed for PCR may not be optimal for LAMP-BART quantification. Additionally, we demonstrate that LAMP is more tolerant to plant sample-derived inhibitors, and show this can be exploited to develop rapid extraction techniques suitable for simple field-based qualitative tests for GM status determination. We also assess the effect of total DNA assay load on LAMP-BART quantitation. Conclusions LAMP-BART is an effective and sensitive technique for GM detection with significant potential for quantification even at low levels of contamination and in samples derived from crops such as maize with a large genome size. The resilience of LAMP-BART to acidic polysaccharides makes it well suited to rapid sample preparation techniques and hence to both high throughput laboratory settings and to portable GM detection applications. The impact of the plant sample matrix and genome loading within a reaction must be controlled to ensure quantification at low target concentrations.
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Affiliation(s)
- Guy Kiddle
- Lumora Ltd, Bartholomew Walk, Cambridgeshire Business Park, Ely, Cambridgeshire CB7 4EA, UK.
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22
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Algar WR, Krull UJ. Characterization of the adsorption of oligonucleotides on mercaptopropionic acid-coated CdSe/ZnS quantum dots using fluorescence resonance energy transfer. J Colloid Interface Sci 2011; 359:148-54. [PMID: 21486671 DOI: 10.1016/j.jcis.2011.03.058] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 03/13/2011] [Accepted: 03/17/2011] [Indexed: 01/10/2023]
Abstract
Semiconductor quantum dots (QDs) coated with thioalkyl acid ligands are often used as probes and reporters for nucleic acid sensing, or protein sensing using aptamers, and are also potential vectors for gene delivery. In such applications, the interactions that potentially lead to the adsorption of oligonucleotides onto the surface of colloidal QDs are an important consideration. To explore such interactions, fluorescence resonance energy transfer (FRET) between QDs and oligonucleotides labeled with a fluorescent dye was used to identify and characterize a set of conditions that favor strong adsorption on 3-mercaptopropionic acid (MPA)-coated CdSe/ZnS QDs. Adsorption curves and competitive binding experiments were used to determine that the order of affinity for nucleobase adsorption was dC>dA≥dG≫dT. The length of the oligonucleotide sequence was also important, with an 80-mer sequence adsorbing more strongly than its 20-mer analog. Adsorption decreased with increasing pH and corresponded to the ionization of the carboxylic acid groups of the MPA ligands. Increased ionic strength partially offsets ligand ionization and increased the extent of adsorption. The interaction between QDs and oligonucleotides was labile, with increases in adsorption at lower concentrations of oligonucleotide and with an increasing number of oligonucleotides per QD. The results were consistent with a hydrogen-bonding model for adsorption, where neutral thioalkyl acid ligands interact favorably with nucleobases and ionized ligands resist adsorption.
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Affiliation(s)
- W Russ Algar
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. North, Mississauga, Ontario, Canada L5L 1C6
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Abstract
There is ample evidence to suggest that a dramatic decrease in mitochondrial Ca(2+) retention may contribute to the cell death associated with stroke, excitotoxicity, ischemia and reperfusion, and neurodegenerative diseases. Mitochondria from all studied tissues can accumulate and store Ca(2+) , but the maximum Ca(2+) storage capacity varies widely and exhibits striking tissue specificity. There is currently no explanation for this fact. Precipitation of Ca(2+) and phosphate in the mitochondrial matrix has been suggested to be the major form of storage of accumulated Ca(2+) in mitochondria. How this precipitate is formed is not known. The molecular identity of almost all proteins involved in Ca(2+) transport, storage and formation of the permeability transition pore is also unknown. This review summarizes studies aimed at identifying these proteins, and describes the properties of a known mitochondrial protein that may be involved in Ca(2+) transport and the structure of the permeability transition pore.
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Ivanovska I, Swift J, Harada T, Pajerowski JD, Discher DE. Physical plasticity of the nucleus and its manipulation. Methods Cell Biol 2010; 98:207-20. [PMID: 20816236 DOI: 10.1016/s0091-679x(10)98009-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The genome is virtually identical in all cells within an organism, with epigenetic changes contributing largely to the plasticity in gene expression during both development and aging. These changes include covalent modifications of chromatin components and altered chromatin organization as well as changes in other nuclear components, such as nuclear envelope lamins. Given that DNA in each chromosome is centimeters long and dozens of chromosomes are compacted into a microns-diameter nucleus through non-trivial interactions with the bounding envelope, the polymer physics of such a structure under stress can be complex but perhaps systematic. We summarize micromanipulation methods for measuring the physical plasticity of the nucleus, with recent studies documenting the extreme flexibility of human embryonic stem cells and the rigidification in model aging of progerin-type nuclei. Lamin-A/C is a common molecular factor, and methods are presented for its knockdown and measurement.
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Affiliation(s)
- Irena Ivanovska
- Biophysical Engineering Laboratory, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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25
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Rodrigues MA, Gomes DA, Nathanson MH, Leite MF. Nuclear calcium signaling: a cell within a cell. ACTA ACUST UNITED AC 2008; 42:17-20. [PMID: 18982194 DOI: 10.1590/s0100-879x2008005000050] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 09/29/2008] [Indexed: 11/21/2022]
Abstract
Calcium (Ca2+) is a versatile second messenger that regulates a wide range of cellular functions. Although it is not established how a single second messenger coordinates diverse effects within a cell, there is increasing evidence that the spatial patterns of Ca2+ signals may determine their specificity. Ca2+ signaling patterns can vary in different regions of the cell and Ca2+ signals in nuclear and cytoplasmic compartments have been reported to occur independently. No general paradigm has been established yet to explain whether, how, or when Ca2+ signals are initiated within the nucleus or their function. Here we highlight that receptor tyrosine kinases rapidly translocate to the nucleus. Ca2+ signals that are induced by growth factors result from phosphatidylinositol 4,5-bisphosphate hydrolysis and inositol 1,4,5-trisphosphate formation within the nucleus rather than within the cytoplasm. This novel signaling mechanism may be responsible for growth factor effects on cell proliferation.
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Affiliation(s)
- M A Rodrigues
- Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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26
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CHANDRA S. Subcellular imaging of RNA distribution and DNA replication in single mammalian cells with SIMS: the localization of heat shock induced RNA in relation to the distribution of intranuclear bound calcium. J Microsc 2008; 232:27-35. [DOI: 10.1111/j.1365-2818.2008.02081.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Mellström B, Savignac M, Gomez-Villafuertes R, Naranjo JR. Ca2+-Operated Transcriptional Networks: Molecular Mechanisms and In Vivo Models. Physiol Rev 2008; 88:421-49. [DOI: 10.1152/physrev.00041.2005] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Calcium is the most universal signal used by living organisms to convey information to many different cellular processes. In this review we present well-known and recently identified proteins that sense and decode the calcium signal and are key elements in the nucleus to regulate the activity of various transcriptional networks. When possible, the review also presents in vivo models in which the genes encoding these calcium sensors-transducers have been modified, to emphasize the critical role of these Ca2+-operated mechanisms in many physiological functions.
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Fischer DF, Backendorf C. Identification of regulatory elements by gene family footprinting and in vivo analysis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 104:37-64. [PMID: 17290818 DOI: 10.1007/10_027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Gene families of recently duplicated but subsequently diverged genes provide an unique opportunity for comparative analysis of regulatory elements. We have studied the human SPRR gene family of small proline rich proteins involved in barrier function of stratified squamous epithelia. These genes are all expressed in normal human keratinocytes, but respond differently to environmental insults. Comparisons of the functional promoter regions allows the rapid identification of both conserved and of novel regulatory elements that appeared after gene duplication. Competitive electrophoretic mobility shift assays can be used to confirm their presence. Here we show the power of gene family footprinting by the identification of two novel elements in the SPRR3 promoter, not present in SPRR1A and SPRR2A. One of these elements binds a protein similar to GAAP-1, a pro-apoptotic activator of IRF-1 and p53. In vivo analysis shows that this element functions as an inhibitor of SPRR3 transcription. The second novel element functions as an activator of promoter activity and is characterized by its A/T rich sequence. The latter interacting protein indeed binds through contacts in the minor groove, and strikingly, depends on the presence of calcium for DNA interaction.
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Affiliation(s)
- David F Fischer
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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29
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Abstract
The role of the nucleus in protecting and sequestering the genome is intrinsically mechanical, and disease-causing structural mutants in lamins and other components underscore this function. Various methods to measure nuclear mechanics, isolated or in situ, are outlined here in some detail.
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Affiliation(s)
- Jan Lammerding
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital,/Harvard Medical School, Boston, Massachusetts 02115, USA
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30
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Dobi A, Szemes M, Lee C, Palkovits M, Lim F, Gyorgy A, Mahan MA, Agoston DV. AUF1 is expressed in the developing brain, binds to AT-rich double-stranded DNA, and regulates enkephalin gene expression. J Biol Chem 2006; 281:28889-900. [PMID: 16769718 DOI: 10.1074/jbc.m511858200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During our search for transcriptional regulators that control the developmentally regulated expression of the enkephalin (ENK) gene, we identified AUF1. ENK, a peptide neurotransmitter, displays precise cell-specific expression in the adult brain. AUF1 (also known as heterogeneous nuclear ribonucleoprotein D) has been known to regulate gene expression through altering the stability of AU-rich mRNAs. We show here that in the developing brain AUF1 proteins are expressed in a spatiotemporally defined manner, and p37 and p40/42 isoforms bind to an AT-rich double-stranded (ds) DNA element of the rat ENK (rENK) gene. This AT-rich dsDNA sequence acts as a cis-regulatory DNA element and is involved in regulating the cell-specific expression of the ENK gene in primary neuronal cultures. The AT-rich dsDNA elements are present at approximately 2.5 kb 5'upstream of the rat, human, and mouse ENK genes. AUF1 proteins are shown here to provide direct interaction between these upstream AT-rich DNA sequences and the TATA region of the rENK gene. Double immunohistochemistry demonstrated that in the developing brain AUF1 proteins are expressed by proliferating neural progenitors and by differentiating neurons populating brain regions, which will not express the ENK gene in the adult, suggesting a repressor role for AUF1 proteins during enkephalinergic differentiation. Their subnuclear distribution and interactions with AT-rich DNA suggest that in the developing brain they can be involved in complex nuclear regulatory mechanisms controlling the development- and cell-specific expression of the ENK gene.
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Affiliation(s)
- Albert Dobi
- Department of Anatomy, Physiology, and Genetics, School of Medicine, Uniformed Services University, Bethesda, Maryland 20814, USA
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31
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Griffiths KK, Russu IM. Specific Interactions of Divalent Metal Ions with a DNA Duplex Containing the d(CA)n/(GT)nTandem Repeat. J Biomol Struct Dyn 2006; 23:667-76. [PMID: 16615812 DOI: 10.1080/07391102.2006.10507091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Divalent metal ions are essential for maintaining functional states of the DNA molecule. Their participation in DNA structure is modulated by the base sequence and varies depending on the nature of the ion. The present investigation addresses the interaction of Ca2+ ions with a tandem repeat of two CA dinucleotides, (CA)2/(TG)2. The binding of Ca2+ to the repeat is monitored by nuclear magnetic resonance (NMR) spectroscopy using chemical shift mapping. Parallel experiments monitor binding of Mg2+ ions to the repeat as well as binding of each ion to a DNA duplex in which the (CA)2/(TG)2 repeat is eliminated. The results reveal that the direction and the magnitude of chemical shift changes induced by Ca2+ ions in the NMR spectra of the repeat are different from those induced by Mg2+ ions. The differences between the two cations are significantly diminished by the elimination of the (CA)2/(TG)2 repeat. These findings suggest a specific interaction of Ca2+ ions with the (CA)2/(TG)2 motif. The specificity of the interaction resides in the two A-T base pairs of the repeat, and it involves the major groove of the first A-T base pair and both grooves of the second A-T base pair.
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Affiliation(s)
- Keren K Griffiths
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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Harris SE, Chand AL, Winship IM, Gersak K, Nishi Y, Yanase T, Nawata H, Shelling AN. INHA promoter polymorphisms are associated with premature ovarian failure. ACTA ACUST UNITED AC 2006; 11:779-84. [PMID: 16390856 DOI: 10.1093/molehr/gah219] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Inhibin is an important glycoprotein that is involved in folliculogenesis. INHA, the gene encoding the inhibin alpha subunit, was recently proposed as a candidate for premature ovarian failure (POF), a syndrome that leads to the cessation of ovarian function under the age of 40 years. 70 POF patients and 70 controls were screened for the previously identified INHA -16C>T transition mutation. The T allele was found in 31/70 (44.3%) of controls, but only 18/70 (25.7%) of POF patients. This result indicates that the T allele is significantly underrepresented in the POF patient population (Fisher's exact test, two-tail: P = 0.033). Sequence analysis of the INHA promoter in 50 POF patients and 50 controls identified a highly polymorphic imperfect TG repeat at approximately -300 bp, that consisted of four common haplotypes (A, B, C and D). The -16T allele is linked to the shortest repeat haplotype (haplotype C). Despite the association between haplotype C and POF, no significant difference was found between the promoter activity of a luciferase reporter construct containing haplotype C, and most of the other haplotypes tested. Interestingly, haplotype B failed to show any promoter activity. We conclude that the inheritance of specific INHA promoter haplotypes predispose to the development of premature ovarian failure.
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Affiliation(s)
- Sarah E Harris
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
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33
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Dahl KN, Engler AJ, Pajerowski JD, Discher DE. Power-law rheology of isolated nuclei with deformation mapping of nuclear substructures. Biophys J 2005; 89:2855-64. [PMID: 16055543 PMCID: PMC1366783 DOI: 10.1529/biophysj.105.062554] [Citation(s) in RCA: 233] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Accepted: 07/19/2005] [Indexed: 01/21/2023] Open
Abstract
Force-induced changes in genome expression as well as remodeling of nuclear architecture in development and disease motivate a deeper understanding of nuclear mechanics. Chromatin and green fluorescent protein-lamin B dynamics were visualized in a micropipette aspiration of isolated nuclei, and both were shown to contribute to viscoelastic properties of the somatic cell nucleus. Reversible swelling by almost 200% in volume, with changes in salt, demonstrates the resilience and large dilational capacity of the nuclear envelope, nucleoli, and chromatin. Swelling also proves an effective way to separate the mechanical contributions of nuclear elements. In unswollen nuclei, chromatin is a primary force-bearing element, whereas swollen nuclei are an order of magnitude softer, with the lamina sustaining much of the load. In both cases, nuclear deformability increases with time, scaling as a power law-thus lacking any characteristic timescale-when nuclei are either aspirated or indented by atomic force microscopy. The nucleus is stiff and resists distortion at short times, but it softens and deforms more readily at longer times. Such results indicate an essentially infinite spectrum of timescales for structural reorganization, with implications for regulating genome expression kinetics.
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Liu SZ, Jiang MX, Yan LY, Jiang Y, Ouyang YC, Sun QY, Chen DY. Parthenogenetic and nuclear transfer rabbit embryo development and apoptosis after activation treatments. Mol Reprod Dev 2005; 72:48-53. [PMID: 15952217 DOI: 10.1002/mrd.20332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Previous studies mainly evaluated the effect of culture conditions on preimplantation embryo apoptosis. In order to inhibit apoptosis of nuclear transfer (NT) embryos, putative apoptosis inhibitors were used to treat donor cells. However, little is known about the effect of activation treatments on embryo apoptosis. We firstly investigated the effect of various parthenogenetic activation (PA) treatments on embryo development, blastocyst cell number, and apoptosis, and then one of these activation treatments proved to be most efficient was selected for activation rabbit NT embryos. The activation by electrical pulses and 30 min later, electroporation with 25 muM D-myoinositol 1,4,5-trisphosphate (IP3) in Ca(2+)- and Mg(2+)-free PBS, then exposure to 2.0 mM 6-dimethylaminopurine (6-DMAP) for 3 hr effectively activated rabbit oocytes, and resulted in significantly a higher blastocyst development rate (72.7%) and total cell number (175 +/- 14.1), and markedly lower apoptosis level of blastocyst (4.3 +/- 0.5) than all the other groups. When the same activation protocol was applied in NT embryo activation, we found that exposure of the embryos to 6-DMAP for 3 hr could decrease the apoptosis level of blastocyst and increase blastocyst rate and cell number. The results demonstrate that oocyte activation affects not only embryo development and quality but also embryo apoptosis.
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Affiliation(s)
- Shu-Zhen Liu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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35
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Echevarría W, Leite MF, Guerra MT, Zipfel WR, Nathanson MH. Regulation of calcium signals in the nucleus by a nucleoplasmic reticulum. Nat Cell Biol 2003; 5:440-6. [PMID: 12717445 PMCID: PMC3572851 DOI: 10.1038/ncb980] [Citation(s) in RCA: 293] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Revised: 01/09/2003] [Accepted: 03/03/2003] [Indexed: 12/17/2022]
Abstract
Calcium is a second messenger in virtually all cells and tissues. Calcium signals in the nucleus have effects on gene transcription and cell growth that are distinct from those of cytosolic calcium signals; however, it is unknown how nuclear calcium signals are regulated. Here we identify a reticular network of nuclear calcium stores that is continuous with the endoplasmic reticulum and the nuclear envelope. This network expresses inositol 1,4,5-trisphosphate (InsP3) receptors, and the nuclear component of InsP3-mediated calcium signals begins in its locality. Stimulation of these receptors with a little InsP3 results in small calcium signals that are initiated in this region of the nucleus. Localized release of calcium in the nucleus causes nuclear protein kinase C (PKC) to translocate to the region of the nuclear envelope, whereas release of calcium in the cytosol induces translocation of cytosolic PKC to the plasma membrane. Our findings show that the nucleus contains a nucleoplasmic reticulum with the capacity to regulate calcium signals in localized subnuclear regions. The presence of such machinery provides a potential mechanism by which calcium can simultaneously regulate many independent processes in the nucleus.
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MESH Headings
- Active Transport, Cell Nucleus/physiology
- Calcium/metabolism
- Calcium Channels/metabolism
- Calcium Signaling/genetics
- Cell Membrane/metabolism
- Cell Nucleus Structures/metabolism
- Cell Nucleus Structures/ultrastructure
- Cytosol/metabolism
- Endoplasmic Reticulum/metabolism
- Endoplasmic Reticulum/ultrastructure
- Eukaryotic Cells/cytology
- Eukaryotic Cells/metabolism
- Humans
- Inositol 1,4,5-Trisphosphate/metabolism
- Inositol 1,4,5-Trisphosphate/pharmacology
- Inositol 1,4,5-Trisphosphate Receptors
- Microscopy, Confocal
- Nuclear Envelope/metabolism
- Nuclear Envelope/ultrastructure
- Photochemistry
- Protein Kinase C/metabolism
- Protein Transport/physiology
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- Wihelma Echevarría
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520-801, USA
| | - M. Fatima Leite
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Mateus T. Guerra
- Departments of Medicine and Cell Biology, Yale University School of Medicine, New Haven, CT 06520-801, USA
| | - Warren R. Zipfel
- Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Michael H. Nathanson
- Departments of Medicine and Cell Biology, Yale University School of Medicine, New Haven, CT 06520-801, USA
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36
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Le Y, Gagneten S, Larson T, Santha E, Dobi A, v Agoston D, Sauer B. Far-upstream elements are dispensable for tissue-specific proenkephalin expression using a Cre-mediated knock-in strategy. J Neurochem 2003; 84:689-97. [PMID: 12562513 DOI: 10.1046/j.1471-4159.2003.01573.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Several cis-regulatory DNA elements are present in the 5' upstream regulatory region of the enkephalin gene (ENK) promoter. To determine their role in conferring organ-specificity of ENK expression in mice and to circumvent the position effects from random gene insertion that are known to often frustrate such analysis in transgenic mice, we used a Cre-mediated gene knock-in strategy to target reporter constructs to a "safe haven" loxP-tagged locus in the hypoxanthine phosphoribosyltransferase (HPRT) gene. Here we report reliable and reproducible reporter gene expression under the control of the 5' upstream regulatory region of the mouse ENK gene in gene-modified mice using this Cre-mediated knock-in strategy. Comparison of two 5'ENK regulatory regions (one with and the other without known cis-regulatory DNA elements) in the resulting adult mice showed that conserved far-upstream cis-regulatory DNA elements are dispensable for correct organ-specific gene expression. Thus the proximal 1.4 kb of the murine ENK promoter region is sufficient for organ-specificity of ENK gene expression when targeted to a safe-haven genomic locus. These results suggest that conservation of the far-upstream DNA elements serves more subtle roles, such as the developmental or cell-specific expression of the ENK gene.
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Affiliation(s)
- Yunzheng Le
- Laboratory of Biochemistry and Metabolism, National Institute of Diabetes, Digestive and Kidney Diseases/NIH, Bethesda, Maryland, USA
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37
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Abstract
The dinucleotide CA found at the termini of transposable phage Mu also occurs at the termini of a large class of transposable elements, including HIV, all retroviruses and many retrotransposons. In order to understand the importance of this sequence conservation, the activity of all 16 dinucleotide permutations of the termini was first examined using a sensitive plasmid-based in vivo transposition assay. The reactivity of these substrates varied over several orders of magnitude in vivo, with substitutions at the A position being more severely impaired than those at the C position. The same general hierarchy of reactivity was observed in vitro using mutant oligonucleotide substrates. These experiments revealed that CA was not important for the chemistry of strand transfer, and that the block in the activity of the mutant substrates was at the stage of assembly of a stable transpososome. Given that DNA at the Mu-host junctions is melted/distorted concomitantly with transpososome assembly, we consider the hypothesis that the CA dinucleotide has been selected at transposon termini primarily for its significant conformational mobility.
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Affiliation(s)
- I Lee
- Section of Molecular Genetics & Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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38
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Rai P, Cole TD, Wemmer DE, Linn S. Localization of Fe(2+) at an RTGR sequence within a DNA duplex explains preferential cleavage by Fe(2+) and H2O2. J Mol Biol 2001; 312:1089-101. [PMID: 11580252 DOI: 10.1006/jmbi.2001.5010] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nicking of duplex DNA by the iron-mediated Fenton reaction occurs preferentially at a limited number of sequences. Of these, purine-T-G-purine (RTGR) is of particular interest because it is a required element in the upstream regulatory regions of many genes involved in iron and oxidative-stress responses. In order to study the basis of this preferential nicking, NMR studies were undertaken on the RTGR-containing duplex oligonucleotide, d(CGCGATATGACACTAG)/d(CTAGTGTCATATCGCG). One-dimensional and two-dimensional 1H NMR measurements show that Fe(2+) interacts preferentially and reversibly at the ATGA site within the duplex at a rate that is rapid relative to the chemical-shift timescale, while selective paramagnetic NMR line-broadening of the ATGA guanine H8 suggests that Fe(2+) interacts with the guanine N7 moiety. Localization at this site is supported by Fe(2+) titrations of a duplex containing a 7-deazaguanine substitution in place of the guanine in the ATGA sequence. The addition of a 100-fold excess of Mg(2+) over Fe(2+) does not affect the Fe(2+)-dependent broadening. When the ATGA site in the duplex is replaced by ATGT, an RTGR site (GTGA) is created on the opposite strand. Preferential iron localization then takes place at the 3' guanine in GTGA but no longer at the guanine in ATGT, consistent with the lack of preferential cleavage of ATGT sites relative to ATGA sites.
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Affiliation(s)
- P Rai
- Biophysics Graduate Group, University of California, Berkeley, CA 94720-3206, USA
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39
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Rokita SE. Chemical reagents for investigating the major groove of DNA. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2001; Chapter 6:Unit 6.6. [PMID: 18428867 DOI: 10.1002/0471142700.nc0606s05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Chemical modification provides an inexpensive and rapid method for characterizing the structure of DNA and its association with drugs and proteins. Numerous conformation-specific probes are available, but most investigations rely on only the most common and readily available of these. The major groove of DNA is typically characterized by reaction with dimethyl sulfate, diethyl pyrocarbonate, potassium permanganate, osmium tetroxide, and, quite recently, bromide with monoperoxysulfate. This commentary discusses the specificity of these reagents and their applications in protection, interference, and missing contact experiments.
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Affiliation(s)
- S E Rokita
- University of Maryland, College Park, Maryland, USA
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40
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CNS region-specific oxytocin receptor expression: importance in regulation of anxiety and sex behavior. J Neurosci 2001. [PMID: 11264328 DOI: 10.1523/jneurosci.21-07-02546.2001] [Citation(s) in RCA: 296] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The oxytocin receptor (OTR) is differentially expressed in the CNS. Because there are multiple mechanisms by which the OTR can be transcriptionally induced, we hypothesized that differences in OTR expression may be explained by activation of distinct signal transduction pathways and may be critical for the control of anxiety and sex behaviors. To determine the regulation and functional significance of this expression, we infused female rats with modifiers of protein kinases before assaying for behavior and oxytocin receptor binding. In the ventromedial nucleus of the hypothalamus (VMH), estrogen-dependent induction of oxytocin receptors required protein kinase C activation, and oxytocin infused here promoted female sex behavior but had no effect on anxiety. In contrast, dopamine controlled tonic oxytocin receptor expression in the central nucleus of the amygdala (cAmyg) through activation of protein kinase A, and oxytocin infused here was anxiolytic but had no effect on female sex behavior. Therefore, we have identified brain region-specific regulation of the OTR in the VMH and cAmyg. Distinct signal transduction pathways regulating receptor expression and binding in each brain region may mediate in part the ability of oxytocin to exert these differential behavioral effects.
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41
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Bale TL, Davis AM, Auger AP, Dorsa DM, McCarthy MM. CNS region-specific oxytocin receptor expression: importance in regulation of anxiety and sex behavior. J Neurosci 2001; 21:2546-52. [PMID: 11264328 PMCID: PMC6762393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2000] [Revised: 01/02/2001] [Accepted: 01/23/2001] [Indexed: 02/19/2023] Open
Abstract
The oxytocin receptor (OTR) is differentially expressed in the CNS. Because there are multiple mechanisms by which the OTR can be transcriptionally induced, we hypothesized that differences in OTR expression may be explained by activation of distinct signal transduction pathways and may be critical for the control of anxiety and sex behaviors. To determine the regulation and functional significance of this expression, we infused female rats with modifiers of protein kinases before assaying for behavior and oxytocin receptor binding. In the ventromedial nucleus of the hypothalamus (VMH), estrogen-dependent induction of oxytocin receptors required protein kinase C activation, and oxytocin infused here promoted female sex behavior but had no effect on anxiety. In contrast, dopamine controlled tonic oxytocin receptor expression in the central nucleus of the amygdala (cAmyg) through activation of protein kinase A, and oxytocin infused here was anxiolytic but had no effect on female sex behavior. Therefore, we have identified brain region-specific regulation of the OTR in the VMH and cAmyg. Distinct signal transduction pathways regulating receptor expression and binding in each brain region may mediate in part the ability of oxytocin to exert these differential behavioral effects.
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Affiliation(s)
- T L Bale
- Neurobiology and Behavior Program, Departments of Pharmacology and Psychiatry, University of Washington, Seattle, Washington 98195, USA.
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42
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Ozil JP, Huneau D. Activation of rabbit oocytes: the impact of the Ca2+ signal regime on development. Development 2001; 128:917-28. [PMID: 11222146 DOI: 10.1242/dev.128.6.917] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Postfertilization manipulation of mammalian embryos results in various developmental alterations. To determine whether the manipulation of the Ca2+ regime causing oocyte activation is a valuable experimental means in helping understand the biological process by which embryos integrate signals from outside and later regulate gene expression, we linked Ca2+ signal parameters i.e. amplitude, number and frequency, with the efficiency and quality of postimplantation development. Freshly ovulated rabbit oocytes were subjected to repetitive and modulated Ca2+ influx. The results provide three major pieces of information. Firstly, the Ca2+ stimulus is the most efficient signal activating mammalian eggs when it is applied in a repetitive manner, the amplitude being the crucial factor. Secondly, the dynamics of early cleavage does not appear to be determined by either the frequency or the amplitude of modulation of the Ca2+ signal that activates the oocyte. Thirdly, amplitude and temporal modulation of the Ca2+ signal in the early minutes influences the developmental performance and the morphology of the rabbit parthenogenetic conceptus at day 11.5 of pregnancy. The results demonstrate the importance of epigenetic events during postfertilization as well as the possible uses of Ca2+ modulation in studying long term developmental effects.
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Affiliation(s)
- J P Ozil
- Unité de Biologie du Développement et Biotechnologies, INRA, France.
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43
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Altura BM, Zhang A, Cheng TP, Altura BT. Extracellular magnesium regulates nuclear and perinuclear free ionized calcium in cerebral vascular smooth muscle cells: possible relation to alcohol and central nervous system injury. Alcohol 2001; 23:83-90. [PMID: 11331105 DOI: 10.1016/s0741-8329(00)00131-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Quantitative digital imaging microscopy, confocal laser scanning microscopy (CLSM), and multiple molecular fluorescent probes were utilized to test the hypothesis that cerebral vascular muscle cell nuclear ([Ca(2+)](n)), perinuclear ([Ca(2+)](pn)), and cytoplasmic free calcium ([Ca(2+)](i)) levels are regulated by the concentration of extracellular free magnesium ions ([Mg(2+)](o)). Primary cultured canine cerebral vascular smooth muscle cells were loaded with either fura-2/AM, indo-1/AM, or fluo-3/AM, and the subcellular Ca(2+) responses to stepwise reduction in [Mg(2+)](o) (i.e., from 1.36 to 0.17 mM) were analyzed over time. With normal 1.36 mM [Mg(2+)](o)-containing incubation media, basal mean [Ca(2+)](i) was 89.6+/-15 nM. Lowering [Mg(2+)](o) to 1.07, 0.88, 0.48, and 0.17 mM resulted in rapid (<4 min) increments in [Ca(2+)](i) going to 213+/-43, 368+/-67, 471+/-77, and 642+/-98 nM, respectively; the longer the exposure time (up to 30 min) to lowered [Mg(2+)](o), the higher the [Ca(2+)](i). Restoration of [Mg(2+)](o) to normal caused decreases in [Ca(2+)](i) to 215.9+/-42.3 nM, but only complete removal of [Ca(2+)](o) returned [Ca(2+)](i) to basal levels. Results show that basal [Ca(2+)](pn) (282+/-92 nM) exceeds basal cytoplasmic Ca(2+) (61+/-27.8 nM) and [Ca(2+)](n) (20+/-7.6 nM). However, reduction of normal [Mg(2+)](o) to 0.48 mM resulted in dramatic, rapid rises in all subcellular compartments, where [Ca(2+)](pn) (1503+/-102 nM)>cytoplasmic Ca(2+) (688+/-49 nM) approximately equal to [Ca(2+)](n) (674+/-12 nM). Nuclear Ca(2+) rose dramatically (e.g., 35-40 times basal levels). Both verapamil (1 microM) and Ni(2+) (5 mM) prevented, completely, the rises in Ca(2+) in all compartments, suggesting that Mg(2+)-dependent Ca(2+) accumulation may be dependent on nuclear, endoplasmic reticulum-Golgi, and cytoplasmic L-type voltage membrane-regulated Ca(2+) channels. The normally low [Ca(2+)](n) suggests that Ca(2+) does not transport passively across the nuclear membrane in cerebral vascular smooth muscle cells. These results may help to explain much of the impact of hypomagnesemic states on cerebral-central nervous system pathobiology, and, particularly, alcohol-induced strokes.
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MESH Headings
- Alcoholism/metabolism
- Animals
- Calcium/metabolism
- Calcium Channels, L-Type/drug effects
- Calcium Channels, L-Type/metabolism
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Cells, Cultured
- Cerebral Cortex
- Cytoplasm/drug effects
- Cytoplasm/metabolism
- Dogs
- Dose-Response Relationship, Drug
- Golgi Apparatus/drug effects
- Golgi Apparatus/metabolism
- Magnesium/pharmacology
- Magnesium/physiology
- Male
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Stroke/metabolism
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Affiliation(s)
- B M Altura
- Department of Physiology, Health Science Center, State University of New York at Brooklyn, Brooklyn, NY 11203, USA
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44
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Korolev N, Lyubartsev AP, Rupprecht A, Nordenskiöld L. Competitive binding of Mg2+, Ca2+, Na+, and K+ ions to DNA in oriented DNA fibers: experimental and Monte Carlo simulation results. Biophys J 1999; 77:2736-49. [PMID: 10545373 PMCID: PMC1300547 DOI: 10.1016/s0006-3495(99)77107-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Competitive binding of the most common cations of the cytoplasm (K(+), Na(+), Ca(2+), and Mg(2+)) with DNA was studied by equilibrating oriented DNA fibers with ethanol/water solutions (65 and 52% v/v EtOH) containing different combinations and concentrations of the counterions. The affinity of DNA for the cations decreases in the order Ca > Mg >> Na approximately K. The degree of Ca(2+) and/or Mg(2+) binding to DNA displays maximum changes just at physiological concentrations of salts (60-200 mM) and does not depend significantly on the ethanol concentration or on the kind of univalent cation (Na(+) or K(+)). Ca(2+) is more tightly bound to DNA and is replaced by the monovalent cations to a lesser extent than is Mg(2+). Similarly, Ca(2+) is a better competitor for binding to DNA than Mg(2+): the ion exchange equilibrium constant for a 1:1 mixture of Ca(2+) and Mg(2+) ions, K(c)(Ca)(Mg), changes from K(c)(Ca)(Mg) approximately 2 in 65% EtOH (in 3-30 mM NaCl and/or KCl) to K(c)(Ca)(Mg) approximately 1.2-1.4 in 52% EtOH (in 300 mM NaCl and/or KCl). DNA does not exhibit selectivity for Na(+) or K(+) in ethanol/water solutions either in the absence or in the presence of Ca(2+) and/or Mg(2+). The ion exchange experimental data are compared with results of grand canonical Monte Carlo (GCMC) simulations of systems of parallel and hexagonally ordered, uniformly and discretely charged polyions with the density and spatial distribution of the charged groups modeling B DNA. A quantitative agreement with experimental data on divalent-monovalent competition has been obtained for discretely charged models of the DNA polyion (for the uniformly charged cylinder model, coincidence with experiment is qualitative). The GCMC method gives also a qualitative description of experimental results for DNA binding competitions of counterions of the same charge (Ca(2+) with Mg(2+) or K(+) with Na(+)).
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Affiliation(s)
- N Korolev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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45
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v Agoston D, Santha E, Shieh G, Lala R, Dobi A. Isolation and structural and genetic analysis of the mouse enkephalin gene and its d(AC/TG)n repeats. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1999; 9:217-26. [PMID: 10520752 DOI: 10.3109/10425179809105208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enkephalins, the endogenous opioids, mediate a wide variety of intercellular communications through ontogeny and their involvement has been suggested in drug addiction and alcohol abuse as well as in various neuropsychiatric disorders. In order to generate a genetic model, we have isolated the mouse enkephalin (mENK) gene, analyzed its regulatory region and compared its structure to the well characterized rat ENK (rENK) gene. We analyzed 2600 bp and found 3 highly homologous regions: The highest level (98%) of positional and sequence homology between mice and rats was in the TATA/proximal regulatory region. This region contains all the inducible regulatory elements (enkCRE1, NF1, AP-2, NFkappaB, etc.) and also an octamer-like element at -543 bp. This high homology is interrupted in both mice and rats by the typically polymorphic d(AC/TG)n and d(TC/GA)n dinucleotide repeats positioned between nucleotides -670 and -950. The position and orientation of these repetitive elements differ substantially in the two species. Genomic PCR analysis of the d(AC/TG)n repeat in various mouse strains, including aberrant behavioral or neurological phenotypes, showed lack of polymorphism at this repeat. The positional and sequence homologies between the rat and the mouse ENK genes decrease in more upstream regions due to the presence of nonhomologues repetititve DNA sequences.
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Affiliation(s)
- D v Agoston
- Molecular Control of Neurodifferentiation, NICHD, NIH, Bethesda, MD 20892, USA.
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46
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Valverde P, Koren G. Purification and preliminary characterization of a cardiac Kv1.5 repressor element binding factor. Circ Res 1999; 84:937-44. [PMID: 10222341 DOI: 10.1161/01.res.84.8.937] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have previously demonstrated that the cell-specific expression of Kv1.5 promoter is regulated by a silencer (Kv1.5 repressor element; KRE) containing a dinucleotide-repetitive element, (GT)19(GA)1(CA) 15(GA)16. Electromobility gel shift assays (EMSAs) of KRE with GH3 nuclear extracts detected a unique DNA-protein complex, which was not detectable in Chinese hamster ovary or COS-7 cells. We further delineated KRE and determined that a 52-bp fragment that contained a (GT)10(GA)1(CA)10 dinucleotide-repetitive element was sufficient for silencer activity. EMSAs using nuclear extracts isolated from the heart and from GH3 cells demonstrated that the 52-bp element formed specific and identical gel shift effects. These complexes were not detectable in EMSA experiments with liver nuclear extracts. Magnetic DNA affinity purification and UV cross-linking experiments identified a 27-kDa KRE binding factor (KBF) in GH3 cell nuclear extracts. Purified KBF reacted specifically with double-stranded KRE, abolishing the formation of multimeric KRE-DNA complexes. Thus, the interaction between KRE and KBF may play an important role in regulating the GH3- and cardiac-specific expression of Kv1.5.
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Affiliation(s)
- P Valverde
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Mass. 02115, USA
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