The Heavy Metal-Regulatory Transcription Factor MTF-1
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Metallothionein-Protein Interactions
DOI 10.1515/bmc-2012-0049 BioMol Concepts 2013; 4(2): 143–160 Review S í lvia Atrian * and Merc è Capdevila Metallothionein-protein interactions Abstract: Metallothioneins (MTs) are a family of univer- Introduction sal, small proteins, sharing a high cysteine content and an optimal capacity for metal ion coordination. They take Metallothioneins (MTs) are a family of small ( < 10 kDa), part in a plethora of metal ion-related events (from detoxi- extremely heterogeneous proteins, sharing a high cysteine fication to homeostasis, storage, and delivery), in a wide content (15 – 30 % ) that confers them an optimal capacity range of stress responses, and in different pathological for metal ion coordination. After their discovery in horse processes (tumorigenesis, neurodegeneration, and inflam- kidneys by Bert Vallee in 1957 (1) , MTs have been identi- mation). The information on both intracellular and extra- fied and characterized in most prokaryotic and all eukary- cellular interactions of MTs with other proteins is here otic organisms. Besides metal ion detoxification, they comprehensively reviewed. In mammalian kidney, MT1/ have been related to a plethora of physiological events, MT2 interact with megalin and related receptors, and with from the homeostasis, storage, and delivery of physiologi- the transporter transthyretin. Most of the mammalian MT cal metals, to the defense against a wide range of stresses partners identified concern interactions with central nerv- and pathological processes (tumor genesis, neurodegen- ous system (mainly brain) proteins, both through physical eration, inflammation, etc.). It is now a common agree- contact or metal exchange reactions. Physical interactions ment among MT researchers that the ambiguity when mainly involve neuronal secretion multimers. -
Eucaryotic Metallothioneins: Proteins, Gene Regulation and Copper Homeostasis
Cah. Biol. Mar. (2001) 42 : 125-135 Eucaryotic metallothioneins: proteins, gene regulation and copper homeostasis. Alejandra MOENNE Laboratorio de Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 correo 33, Santiago, Chile. Fax number: 56-2-6812108 - E-mail: [email protected] Abstract: Heavy metals such as copper, iron and zinc are essential for eucaryotic cell viability and they are required only in trace amounts. High concentrations of these metals are toxic for the cells and they trigger different molecular response mechanisms. One of the best studied of such responses involves the synthesis of metallothioneins (MTs) which are low molecular weight, cysteine-rich proteins that bind heavy metals by means of their cysteine residues. MTs have been purified from different eucaryotic cells and their structural and heavy metal binding properties have been determined. MT genes have been cloned from animal cells, fungi, plants and algae and their transcriptional activation by heavy metals has been characterized. The overexpression of MTs results in the accumulation of heavy metals in the cells. The best studied model for copper tolerance and homeostasis is the yeast Saccharomyces cerevisiae. In this fungus, high concentrations of copper activate transcription of the gene coding for CUP1 MT. This process involves the binding of ACE1 transcription factor to the promoter of cup-1 gene. ACE1 directly binds copper ions and undergoes a conformational change that allows its binding to the promoter region. On the other hand, copper starvation triggers the transcriptional activation of at least two copper transporter genes and a copper reductase gene. -
[3 TD$DIFF]Interdisciplinary Team Science in Cell Biology
TICB 1268 No. of Pages 3 Scientific Life Cell biology, beginning largely as micro- detailed physical–chemical mechanisms Interdisciplinary[3_TD$IF] scopic observations, followed[1_TD$IF]the molec- [7]. The data required for these models ular biology revolution, which viewed are now in sight. New gene editing meth- Team Science in genes, cells, and the machinery that ods are providing endogenous expression underlies their activities as molecular sys- of tagged and mutant cells [8], and new Cell Biology tems that could be fully characterized and live-cell imaging methods are promising Rick Horwitz1,* understood using methods of genetics biochemistry in living cells, measuring con- and biochemistry. Viewing the cell as a centrations, dynamics, equilibria, and complex, dynamic molecular composite organization [9]. Similarly, super-resolution The cell is complex. With its multi- brought insights from chemistry and phys- microscopy and cryoEM tomography, tude of components, spatial– ics to bear on biological problems. Just as which allow structure determination and [6_TD$IF] temporal character, and gene the molecular genetic era was codified by organization in situ [3,4], imaging mass expression diversity, it is challeng- the publication of Watson's book, Molec- spectrometry [10], and single-cell and ing to comprehend the cell as an ular Biology of the Gene [1], two decades spatially-resolved genomic approaches integrated system and to develop later[8_TD$IF]the Molecular Biology of the Cell by [11–13], among other image-based tech- models that predict its behaviors. I Alberts, et al. [2] served a similar purpose nologies, all point to a new golden era of suggest an approach to address for cell biology. -
Engineering Zinc-Finger Protein and CRISPR/Cas9 Constructs to Model the Epigenetic and Transcriptional Phenomena That Underlie Cocaine-Related Behaviors
Engineering zinc-finger protein and CRISPR/Cas9 constructs to model the epigenetic and transcriptional phenomena that underlie cocaine-related behaviors Hamilton PJ, Heller EA, Ortiz Torres I, Burek DD, Lombroso SI, Pirpinias ST, Neve RL, Nestler EJ Multiple studies have implicated genome-wide epigenetic remodeling events in brain reward regions following drug exposure. However, only recently has it become possible to target a given type of epigenetic remodeling to a single gene of interest, in order to probe the causal relationship between such regulation and neuropsychiatric disease (Heller et al., Nat Neurosci, 2014). Our group has successfully utilized synthetic zinc- finger proteins (ZFPs), fused to either the transcriptional repressor, G9a, that promotes histone methylation or the transcriptional activator, p65, that promotes histone acetylation, to determine the behavioral effects of targeted in vivo epigenetic reprogramming in a locus-specific and cell-type specific manner. Given the success of our ZFP approaches, we have broadened our technical repertoire to include the more novel and flexible CRISPR/Cas9 technology. We designed guide RNAs to target nuclease-dead Cas9 (dCas9) fused to effector domains to the fosB gene locus, a locus heavily implicated in the pathogenesis of drug abuse. We observe that dCas9 fused to the transcriptional activator, VP64, or the transcriptional repressor, KRAB, and targeted to specific sites in the fosB promoter is sufficient to regulate FosB and ΔFosB mRNA levels, in both cultured cells and in the nucleus accumbens (NAc) of mice receiving viral delivery of CRISPR constructs. Next, we designed a fusion construct linking the dCas9 moiety to a pseudo-phosphorylated isoform of the transcription factor CREB (dCas9 CREB(S133D)). -
Summary of Supportive Science Regarding Thimerosal Removal
Summary of Supportive Science Regarding Thimerosal Removal Updated December 2012 www.safeminds.org Science Summary on Mercury in Vaccines (Thimerosal Only) SafeMinds Update – December 2012 Contents ENVIRONMENTAL IMPACT ................................................................................................................................. 4 A PILOT SCALE EVALUATION OF REMOVAL OF MERCURY FROM PHARMACEUTICAL WASTEWATER USING GRANULAR ACTIVATED CARBON (CYR 2002) ................................................................................................................................................................. 4 BIODEGRADATION OF THIOMERSAL CONTAINING EFFLUENTS BY A MERCURY RESISTANT PSEUDOMONAS PUTIDA STRAIN (FORTUNATO 2005) ......................................................................................................................................................................... 4 USE OF ADSORPTION PROCESS TO REMOVE ORGANIC MERCURY THIMEROSAL FROM INDUSTRIAL PROCESS WASTEWATER (VELICU 2007)5 HUMAN & INFANT RESEARCH ............................................................................................................................ 5 IATROGENIC EXPOSURE TO MERCURY AFTER HEPATITIS B VACCINATION IN PRETERM INFANTS (STAJICH 2000) .................................. 5 MERCURY CONCENTRATIONS AND METABOLISM IN INFANTS RECEIVING VACCINES CONTAINING THIMEROSAL: A DESCRIPTIVE STUDY (PICHICHERO 2002) ...................................................................................................................................................... -
Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis Vinifera L.): Insights Into the Roles in the Pollen Development Regulation
G C A T T A C G G C A T genes Article Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation Oscar Arrey-Salas 1,* , José Carlos Caris-Maldonado 2, Bairon Hernández-Rojas 3 and Enrique Gonzalez 1 1 Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; [email protected] 2 Center for Research and Innovation (CRI), Viña Concha y Toro, Ruta k-650 km 10, 3550000 Pencahue, Chile; [email protected] 3 Ph.D Program in Sciences Mention in Modeling of Chemical and Biological Systems, Faculty of Engineering, University of Talca, Calle 1 Poniente, 1141, 3462227 Talca, Chile; [email protected] * Correspondence: [email protected] Abstract: Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine Citation: Arrey-Salas, O.; remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte Caris-Maldonado, J.C.; development, we performed a genome-wide identification and characterization of genes encoding Hernández-Rojas, B.; Gonzalez, E. ZFP (VviZFP family). -
Genomic Divergence and Brain Evolution: How Regulatory DNA Influences Development of the Cerebral Cortex
Prospects & Overviews Review essays Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex Debra L. Silver1)2)3)4) The cerebral cortex controls our most distinguishing higher Introduction cognitive functions. Human-specific gene expression dif- ferences are abundant in the cerebral cortex, yet we have A large six-layered neocortex is a unique feature of only begun to understand how these variations impact brain mammalian brains. This specialized outer covering of the brain controls our higher cognitive functions including function. This review discusses the current evidence linking abstract thought and language, which together help uniquely non-coding regulatory DNA changes, including enhancers, define us as humans. Our distinguishing cognitive capacities with neocortical evolution. Functional interrogation using are specified within discrete cortical areas and are driven by animal models reveals converging roles for our genome in dynamic communication between neurons of the neocortex key aspects of cortical development including progenitor and other brain regions, as well as glial cell populations (including oligodendrocytes, microglia, and astrocytes). cell cycle and neuronal signaling. New technologies, Neurons are initially generated during human embryonic includingiPS cells and organoids, offerpotential alternatives and early fetal development, where they migrate to appropri- to modeling evolutionary modifications in a relevant species ate regions and begin establishing functional connections context. Several diseases rooted in the cerebral cortex during fetal and postnatal stages (Fig. 1). Disruptions to uniquely manifest in humans compared to other primates, cerebral cortex function arising during either development or thus highlighting the importance of understanding human adulthood, can result in neurodevelopmental and neurode- generative disorders. -
A New C2H 2 Zinc Finger Protein and a C2C2 Steroid Receptor-Like Component
Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Proteins that bind to Drosophila chorion cis-regulatory elements: A new C2H 2 zinc finger protein and a C2C2 steroid receptor-like component Martin J. Shea, 1 Dennis L. King, 1 Michael J. Conboy, 2 Brian D. Mariani, 3 and Fotis C. Kafatos 1,3 ~Department of Cellular and Developmental Biology, Harvard University Biological Laboratories, Cambridge, Massachusetts 02138 USA; ZJefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 USA; 3Institute of Molecular Biology and Biotechnology, Research Center of Crete, and Department of Biology, University of Crete, Heraklion 711 10, Crete, Greece Gel mobility-shift assays have been used to identify proteins that bind specifically to the promoter region of the Drosophila s15 chorion gene. These proteins are present in nuclear extracts of ovarian follicles, the tissue where s15 is expressed during development, and bind to specific elements of the promoter that have been shown by transformation analysis to be important for in vivo expression. The DNA binding specificity has been used for molecular cloning of two components from expression cDNA libraries and for their tentative identification with specific DNA-binding proteins of the nuclear extracts. The mRNAs for both of these components, CF1 and CF2, are differentially enriched in the follicles. DNA sequence analysis suggests that both CF1 and CF2 are novel Drosophila transcription factors. CF2 is a member of the C2H2 family of zinc finger proteins, whereas CF1 is a member of the family of steroid hormone receptors. The putative DNA-binding domain of CF1 is highly similar to the corresponding domains of certain vertebrate hormone receptors and recognizes a region of DNA with similar, hyphenated palindromic sequences. -
MOLECULAR CLOCKS Definition Introduction
MOLECULAR CLOCKS 583 Kishino, H., Thorne, J. L., and Bruno, W. J., 2001. Performance of Thorne, J. L., Kishino, H., and Painter, I. S., 1998. Estimating the a divergence time estimation method under a probabilistic model rate of evolution of the rate of molecular evolution. Molecular of rate evolution. Molecular Biology and Evolution, 18,352–361. Biology and Evolution, 15, 1647–1657. Kodandaramaiah, U., 2011. Tectonic calibrations in molecular dat- Warnock, R. C. M., Yang, Z., Donoghue, P. C. J., 2012. Exploring ing. Current Zoology, 57,116–124. uncertainty in the calibration of the molecular clock. Biology Marshall, C. R., 1997. Confidence intervals on stratigraphic ranges Letters, 8, 156–159. with nonrandom distributions of fossil horizons. Paleobiology, Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., 23, 165–173. and Tavaré, S., 2011. Dating primate divergences through an Müller, J., and Reisz, R. R., 2005. Four well-constrained calibration integrated analysis of palaeontological and molecular data. Sys- points from the vertebrate fossil record for molecular clock esti- tematic Biology, 60,16–31. mates. Bioessays, 27, 1069–1075. Yang, Z., and Rannala, B., 2006. Bayesian estimation of species Parham, J. F., Donoghue, P. C. J., Bell, C. J., et al., 2012. Best practices divergence times under a molecular clock using multiple fossil for justifying fossil calibrations. Systematic Biology, 61,346–359. calibrations with soft bounds. Molecular Biology and Evolution, Peters, S. E., 2005. Geologic constraints on the macroevolutionary 23, 212–226. history of marine animals. Proceedings of the National Academy Zuckerkandl, E., and Pauling, L., 1962. Molecular disease, evolution of Sciences, 102, 12326–12331. -
Metallothionein-3 As a Multifunctional Player in the Control of Cellular Processes and Diseases Jae-Young Koh1,2 and Sook-Jeong Lee3*
Koh and Lee Molecular Brain (2020) 13:116 https://doi.org/10.1186/s13041-020-00654-w REVIEW Open Access Metallothionein-3 as a multifunctional player in the control of cellular processes and diseases Jae-Young Koh1,2 and Sook-Jeong Lee3* Abstract Transition metals, such as iron, copper, and zinc, play a very important role in life as the regulators of various physiochemical reactions in cells. Abnormal distribution and concentration of these metals in the body are closely associated with various diseases including ischemic seizure, Alzheimer’s disease, diabetes, and cancer. Iron and copper are known to be mainly involved in in vivo redox reaction. Zinc controls a variety of intracellular metabolism via binding to lots of proteins in cells and altering their structure and function. Metallothionein-3 (MT3) is a representative zinc binding protein predominant in the brain. Although the role of MT3 in other organs still needs to be elucidated, many reports have suggested critical roles for the protein in the control of a variety of cellular homeostasis. Here, we review various biological functions of MT3, focusing on different cellular molecules and diseases involving MT3 in the body. Keywords: Autophagy, Alzheimer’s disease, Lysosome, Metallothionein-3, Neurodegenerative disease, Oxidative stress, Zinc Introduction Metallothioneins (MTs) are proteins that bind or re- Intracellular transition metals exist in various forms- lease cellular transition metals, an interaction that de- free or attached to proteins or organelles. Most metals pends on specific cell situations. MTs were first reported in the cells are involved in diverse cellular function, in- by Vallee and Margoshe as Cd-binding protein from cluding the recycling of organelles and proteins as well horse renal cortex [1]. -
Biology & Biochemistry
Top Peer Reviewed Journals – Biology & Biochemistry Presented to Iowa State University Presented by Thomson Reuters Biology & Biochemistry The subject discipline for Biology & Biochemistry is made of 14 narrow subject categories from the Web of Science. The 14 categories that make up Biology & Biochemistry are: 1. Anatomy & Morphology 8. Cytology & Histology 2. Biochemical Research Methods 9. Endocrinology & Metabolism 3. Biochemistry & Molecular Biology 10. Evolutionary Biology 4. Biology 11. Medicine, Miscellaneous 5. Biology, Miscellaneous 12. Microscopy 6. Biophysics 13. Parasitology 7. Biotechnology & Applied Microbiology 14. Physiology The chart below provides an ordered view of the top peer reviewed journals within the 1st quartile for Biology & Biochemistry based on Impact Factors (IF), three year averages and their quartile ranking. Journal 2009 IF 2010 IF 2011 IF Average IF ANNUAL REVIEW OF BIOCHEMISTRY 29.87 29.74 34.31 31.31 PHYSIOLOGICAL REVIEWS 37.72 28.41 26.86 31.00 NATURE BIOTECHNOLOGY 29.49 31.09 23.26 27.95 CANCER CELL 25.28 26.92 26.56 26.25 ENDOCRINE REVIEWS 19.76 22.46 19.92 20.71 NATURE METHODS 16.87 20.72 19.27 18.95 ANNUAL REVIEW OF BIOPHYSICS AND 18.95 18.95 BIOMOLECULAR STRUCTURE ANNUAL REVIEW OF PHYSIOLOGY 18.17 16.1 20.82 18.36 Annual Review of Biophysics 19.3 17.52 13.57 16.80 Nature Chemical Biology 16.05 15.8 14.69 15.51 NATURE STRUCTURAL & MOLECULAR 12.27 13.68 12.71 12.89 BIOLOGY PLOS BIOLOGY 12.91 12.47 11.45 12.28 TRENDS IN BIOCHEMICAL SCIENCES 11.57 10.36 10.84 10.92 QUARTERLY REVIEWS OF BIOPHYSICS -
Zinc Finger Proteins: Getting a Grip On
Zinc finger proteins: getting a grip on RNA Raymond S Brown C2H2 (Cys-Cys-His-His motif) zinc finger proteins are members others, such as hZFP100 (C2H2) [11] and tristetraprolin of a large superfamily of nucleic-acid-binding proteins in TTP (CCCH) [12], are involved in histone pre-mRNA eukaryotes. On the basis of NMR and X-ray structures, we processing and the degradation of tumor necrosis factor know that DNA sequence recognition involves a short a helix a mRNA, respectively. In addition, there are reports of bound to the major groove. Exactly how some zinc finger dual RNA/DNA-binding proteins, such as the thyroid proteins bind to double-stranded RNA has been a complete hormone receptor (CCCC) [13] and the trypanosome mystery for over two decades. This has been resolved by the poly-zinc finger PZFP1 pre-mRNA processing protein long-awaited crystal structure of part of the TFIIIA–5S RNA (CCHC) [14]. Whether their interactions with RNA are complex. A comparison can be made with identical fingers in a based on the same mechanisms as protein–DNA binding TFIIIA–DNA structure. Additionally, the NMR structure of is an intriguing structural question that has remained TIS11d bound to an AU-rich element reveals the molecular unanswered until now. details of the interaction between CCCH fingers and single-stranded RNA. Together, these results contrast the What follows is an attempt to expose both similarities different ways that zinc finger proteins bind with high and differences between C2H2 zinc finger protein bind- specificity to their RNA targets. ing to RNA and DNA based on recent X-ray structures.