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Khayer N, Jalessi M, Jahanbakhshi A, Tabib Khooei A, Mirzaie M. Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. Sci Rep 2021; 11:20943. [PMID: 34686726 PMCID: PMC8536755 DOI: 10.1038/s41598-021-00431-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults associated with increased mortality and morbidity. Although pituitary adenomas are commonly considered slow-growing benign brain tumors, numerous of them possess an invasive nature. Such tumors destroy sella turcica and invade the adjacent tissues such as the cavernous sinus and sphenoid sinus. In these cases, the most critical obstacle for complete surgical removal is the high risk of damaging adjacent vital structures. Therefore, the development of novel therapeutic strategies for either early diagnosis through biomarkers or medical therapies to reduce the recurrence rate of NFPAs is imperative. Identification of gene interactions has paved the way for decoding complex molecular mechanisms, including disease-related pathways, and identifying the most momentous genes involved in a specific disease. Currently, our knowledge of the invasion of the pituitary adenoma at the molecular level is not sufficient. The current study aimed to identify critical biomarkers and biological pathways associated with invasiveness in the NFPAs using a three-way interaction model for the first time. In the current study, the Liquid association method was applied to capture the statistically significant triplets involved in NFPAs invasiveness. Subsequently, Random Forest analysis was applied to select the most important switch genes. Finally, gene set enrichment (GSE) and gene regulatory network (GRN) analyses were applied to trace the biological relevance of the statistically significant triplets. The results of this study suggest that "mRNA processing" and "spindle organization" biological processes are important in NFAPs invasiveness. Specifically, our results suggest Nkx3-1 and Fech as two switch genes in NFAPs invasiveness that may be potential biomarkers or target genes in this pathology.
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Affiliation(s)
- Nasibeh Khayer
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Jalessi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran.
- ENT and Head & Neck Research Center and Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Amin Jahanbakhshi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabib Khooei
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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Weng C, Xi J, Li H, Cui J, Gu A, Lai S, Leskov K, Ke L, Jin F, Li Y. Single-cell lineage analysis reveals extensive multimodal transcriptional control during directed beta-cell differentiation. Nat Metab 2020; 2:1443-1458. [PMID: 33257854 PMCID: PMC7744443 DOI: 10.1038/s42255-020-00314-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/22/2020] [Indexed: 11/08/2022]
Abstract
The in vitro differentiation of insulin-producing beta-like cells can model aspects of human pancreatic development. Here, we generate 95,308 single-cell transcriptomes and reconstruct a lineage tree of the entire differentiation process from human embryonic stem cells to beta-like cells to study temporally regulated genes during differentiation. We identify so-called 'switch genes' at the branch point of endocrine/non-endocrine cell fate choice, revealing insights into the mechanisms of differentiation-promoting reagents, such as NOTCH and ROCKII inhibitors, and providing improved differentiation protocols. Over 20% of all detectable genes are activated multiple times during differentiation, even though their enhancer activation is usually unimodal, indicating extensive gene reuse driven by different enhancers. We also identify a stage-specific enhancer at the TCF7L2 locus for diabetes, uncovered by genome-wide association studies, that drives a transient wave of gene expression in pancreatic progenitors. Finally, we develop a web app to visualize gene expression on the lineage tree, providing a comprehensive single-cell data resource for researchers studying islet biology and diabetes.
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Affiliation(s)
- Chen Weng
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jiajia Xi
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Haiyan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jian Cui
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Anniya Gu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Medical Scientist Training Program (MSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sisi Lai
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Konstantin Leskov
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Luxin Ke
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Master of Science in Biology Program, Department of Biology, College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Population and Quantitative Health Sciences, Department of Electrical Engineering and Computer Science, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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3
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Paci P, Fiscon G, Conte F, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L. Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. Sci Rep 2020; 10:3361. [PMID: 32099002 PMCID: PMC7042269 DOI: 10.1038/s41598-020-60228-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called "switch genes" - for the disease. Genes contributing to common biological processes or defining given cell types are usually co-regulated and co-expressed, forming expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.
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Affiliation(s)
- Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
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4
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Loh CY, Chai JY, Tang TF, Wong WF, Sethi G, Shanmugam MK, Chong PP, Looi CY. The E-Cadherin and N-Cadherin Switch in Epithelial-to-Mesenchymal Transition: Signaling, Therapeutic Implications, and Challenges. Cells 2019; 8:cells8101118. [PMID: 31547193 PMCID: PMC6830116 DOI: 10.3390/cells8101118] [Citation(s) in RCA: 637] [Impact Index Per Article: 127.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/17/2022] Open
Abstract
Epithelial-to-Mesenchymal Transition (EMT) has been shown to be crucial in tumorigenesis where the EMT program enhances metastasis, chemoresistance and tumor stemness. Due to its emerging role as a pivotal driver of tumorigenesis, targeting EMT is of great therapeutic interest in counteracting metastasis and chemoresistance in cancer patients. The hallmark of EMT is the upregulation of N-cadherin followed by the downregulation of E-cadherin, and this process is regulated by a complex network of signaling pathways and transcription factors. In this review, we summarized the recent understanding of the roles of E- and N-cadherins in cancer invasion and metastasis as well as the crosstalk with other signaling pathways involved in EMT. We also highlighted a few natural compounds with potential anti-EMT property and outlined the future directions in the development of novel intervention in human cancer treatments. We have reviewed 287 published papers related to this topic and identified some of the challenges faced in translating the discovery work from bench to bedside.
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Affiliation(s)
- Chin-Yap Loh
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya 47500, Malaysia.
| | - Jian Yi Chai
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya 47500, Malaysia.
| | - Ting Fang Tang
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Muthu Kumaraswamy Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya 47500, Malaysia.
| | - Chung Yeng Looi
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya 47500, Malaysia.
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5
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Rojas M, Yu Q, Williams-Carrier R, Maliga P, Barkan A. Engineered PPR proteins as inducible switches to activate the expression of chloroplast transgenes. Nat Plants 2019; 5:505-511. [PMID: 31036912 DOI: 10.1038/s41477-019-0412-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/22/2019] [Indexed: 05/08/2023]
Abstract
The engineering of plant genomes presents exciting opportunities to modify agronomic traits and to produce high-value products in plants. Expression of foreign proteins from transgenes in the chloroplast genome offers advantages that include the capacity for prodigious protein output, the lack of transgene silencing and the ability to express multicomponent pathways from polycistronic mRNA. However, there remains a need for robust methods to regulate plastid transgene expression. We designed orthogonal activators that boost the expression of chloroplast transgenes harbouring cognate cis-elements. Our system exploits the programmable RNA sequence specificity of pentatricopeptide repeat proteins and their native functions as activators of chloroplast gene expression. When expressed from nuclear transgenes, the engineered proteins stimulate the expression of plastid transgenes by up to ~40-fold, with maximal protein abundance approaching that of Rubisco. This strategy provides a means to regulate and optimize the expression of foreign genes in chloroplasts and to avoid deleterious effects of their products on plant growth.
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Affiliation(s)
- Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Qiguo Yu
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | | | - Pal Maliga
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
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6
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Perez-Carrasco R, Guerrero P, Briscoe J, Page KM. Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches. PLoS Comput Biol 2016; 12:e1005154. [PMID: 27768683 PMCID: PMC5074595 DOI: 10.1371/journal.pcbi.1005154] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/19/2016] [Indexed: 01/08/2023] Open
Abstract
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules—morphogens—guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms. Here, we explore the dynamics of the toggle switch and use exact numerical simulations of the kinetic reactions, the corresponding Chemical Langevin Equation, and Minimum Action Path theory to establish a framework for studying the effect of gene expression noise on patterning time and boundary position. This provides insight into the time scale, gene expression trajectories and directionality of stochastic switching events between cell states. Taking gene expression noise into account predicts that the final boundary position of a morphogen-induced toggle switch, although robust to changes in the details of the noise, is distinct from that of the deterministic system. Moreover, the dramatic increase in patterning time close to the boundary predicted from the deterministic case is substantially reduced. The resulting stochastic switching introduces differences in patterning time along the morphogen gradient that result in a patterning wave propagating away from the morphogen source with a velocity determined by the intrinsic noise. The wave sharpens and slows as it advances and may never reach steady state in a biologically relevant time. This could explain experimentally observed dynamics of pattern formation. Together the analysis reveals the importance of dynamical transients for understanding morphogen-driven transcriptional networks and indicates that gene expression noise can qualitatively alter developmental patterning. The bistable switch, a common regulatory sub-network, is found in many biological processes. It consists of cross-repressing components that generate a switch-like transition between two possible states. In developing tissues, bistable switches, created by cross-repressing transcriptional determinants, are often controlled by gradients of secreted signalling molecules—morphogens. These provide a mechanism to convert a morphogen gradient into stripes of gene expression that determine the arrangement of distinct cell types. Here we use mathematical models to analyse the temporal response of such a system. We find that the behaviour is highly dependent on the intrinsic fluctuations that result from the stochastic nature of gene expression. This noise has a marked effect on both patterning time and the location of the stripe boundary. One of the techniques we use, Minimum Action Path theory, identifies key features of the switch without computationally expensive calculations. The results reveal a noise driven switching wave that propels the stripe boundary away from the morphogen source to eventually settle, at steady state, further from the morphogen source than in the deterministic description. Together the analysis highlights the importance dynamics in patterning and demonstrates a set of mathematical tools for studying this problem.
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Affiliation(s)
- Ruben Perez-Carrasco
- Department of Mathematics, University College London, Gower Street, London WC1E 6BT, UK
- * E-mail:
| | - Pilar Guerrero
- Department of Mathematics, University College London, Gower Street, London WC1E 6BT, UK
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Karen M. Page
- Department of Mathematics, University College London, Gower Street, London WC1E 6BT, UK
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7
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Anderson MZ, Porman AM, Wang N, Mancera E, Huang D, Cuomo CA, Bennett RJ. A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues. PLoS Genet 2016; 12:e1006353. [PMID: 27711197 PMCID: PMC5053522 DOI: 10.1371/journal.pgen.1006353] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/09/2016] [Indexed: 11/18/2022] Open
Abstract
Heritable epigenetic changes underlie the ability of cells to differentiate into distinct cell types. Here, we demonstrate that the fungal pathogen Candida tropicalis exhibits multipotency, undergoing stochastic and reversible switching between three cellular states. The three cell states exhibit unique cellular morphologies, growth rates, and global gene expression profiles. Genetic analysis identified six transcription factors that play key roles in regulating cell differentiation. In particular, we show that forced expression of Wor1 or Efg1 transcription factors can be used to manipulate transitions between all three cell states. A model for tristability is proposed in which Wor1 and Efg1 are self-activating but mutually antagonistic transcription factors, thereby forming a symmetrical self-activating toggle switch. We explicitly test this model and show that ectopic expression of WOR1 can induce white-to-hybrid-to-opaque switching, whereas ectopic expression of EFG1 drives switching in the opposite direction, from opaque-to-hybrid-to-white cell states. We also address the stability of induced cell states and demonstrate that stable differentiation events require ectopic gene expression in combination with chromatin-based cues. These studies therefore experimentally test a model of multistate stability and demonstrate that transcriptional circuits act synergistically with chromatin-based changes to drive cell state transitions. We also establish close mechanistic parallels between phenotypic switching in unicellular fungi and cell fate decisions during stem cell reprogramming.
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Affiliation(s)
- Matthew Z. Anderson
- Department of Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
| | - Allison M. Porman
- Department of Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
| | - Na Wang
- Department of Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
| | - Eugenio Mancera
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Denis Huang
- Department of Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Richard J. Bennett
- Department of Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
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8
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Horbal L, Luzhetskyy A. Dual control system - A novel scaffolding architecture of an inducible regulatory device for the precise regulation of gene expression. Metab Eng 2016; 37:11-23. [PMID: 27040671 PMCID: PMC4915818 DOI: 10.1016/j.ymben.2016.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 12/17/2022]
Abstract
Here, we present a novel scaffolding architecture of an inducible regulatory device. This dual control system is completely silent in the off stage and is coupled to the regulation of gene expression at both the transcriptional and translational levels. This system also functions as an AND gate. We demonstrated the effectiveness of the cumate-riboswitch dual control system for the control of pamamycin production in Streptomyces albus. Placing the cre recombinase gene under the control of this system permitted the construction of synthetic devices with non-volatile memory that sense the signal and respond by altering DNA at the chromosomal level, thereby producing changes that are heritable. In addition, we present a library of synthetic inducible promoters based on the previously described cumate switch. With only one inducer and different promoters, we demonstrate that simultaneous modulation of the expression of several genes to different levels in various operons is possible. Because all modules of the AND gates are functional in bacteria other than Streptomyces, we anticipate that these regulatory devices can be used to control gene expression in other Actinobacteria. The features described in this study make these systems promising tools for metabolic engineering and biotechnology in Actinobacteria.
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Affiliation(s)
- L Horbal
- Helmholtz Institute for Pharmaceutical Research, 66123 Saarbrücken, Germany; University of Saarland, Pharmaceutical Biotechnology, 66123 Saarbrucken, Germany
| | - A Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, 66123 Saarbrücken, Germany; University of Saarland, Pharmaceutical Biotechnology, 66123 Saarbrucken, Germany.
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9
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Sikosek T, Krobath H, Chan HS. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches. PLoS Comput Biol 2016; 12:e1004960. [PMID: 27253392 PMCID: PMC4890782 DOI: 10.1371/journal.pcbi.1004960] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022] Open
Abstract
Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein’s folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the GA all-α and GB α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between GA and GB. In agreement with experiment, we observe conformational switching from GA to GB upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp GA/GB switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches. The biological functions of globular proteins are intimately related to their folded structures and their associated conformational fluctuations. Evolution of new structures is an important avenue to new functions. Although many mutations do not change the folded state, experiments indicate that a single amino acid substitution can lead to a drastic change in the folded structure. The physics of this switch-like behavior remains to be elucidated. Here we develop a computational model for the relevant physical forces, showing that mutations can lead to new folds by passing through intermediate sequences where the old and new folds occur with varying probabilities. Our approach helps provide a general physical account of conformational switching in evolution and mutational effects on conformational dynamics.
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Affiliation(s)
- Tobias Sikosek
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Heinrich Krobath
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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10
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Fabiilli ML, Phanse RA, Moncion A, Fowlkes JB, Franceschi RT. Use of Hydroxyapatite Doping to Enhance Responsiveness of Heat-Inducible Gene Switches to Focused Ultrasound. Ultrasound Med Biol 2016; 42:824-30. [PMID: 26712417 PMCID: PMC4744111 DOI: 10.1016/j.ultrasmedbio.2015.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/03/2015] [Accepted: 11/08/2015] [Indexed: 05/04/2023]
Abstract
Recently, we demonstrated that ultrasound-based hyperthermia can activate cells containing a heat-activated and ligand-inducible gene switch in a spatio-temporally controlled manner. These engineered cells can be incorporated into hydrogel scaffolds (e.g., fibrin) for in vivo implantation, where ultrasound can be used to non-invasively pattern transgene expression. Due to their high water content, the acoustic attenuation of fibrin scaffolds is low. Thus, long ultrasound exposures and high acoustic intensities are needed to generate sufficient hyperthermia for gene activation. Here, we demonstrate that the attenuation of fibrin scaffolds and the resulting hyperthermia achievable with ultrasound can be increased significantly by doping the fibrin with hydroxyapatite (HA) nanopowder. The attenuation of a 1% (w/v) fibrin scaffold with 5% (w/v) HA was similar to soft tissue. Transgene activation of cells harboring the gene switch occurred at lower acoustic intensities and shorter exposures when the cells were encapsulated in HA-doped fibrin scaffolds versus undoped scaffolds. Inclusion of HA in the fibrin scaffold did not affect the viability of the encapsulated cells.
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Affiliation(s)
- Mario L Fabiilli
- Department of Radiology, University of Michigan Health System, Ann Arbor, MI, USA; Applied Physics Program, University of Michigan, Ann Arbor, MI, USA.
| | - Rahul A Phanse
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Moncion
- Department of Radiology, University of Michigan Health System, Ann Arbor, MI, USA; Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
| | - J Brian Fowlkes
- Department of Radiology, University of Michigan Health System, Ann Arbor, MI, USA; Applied Physics Program, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Renny T Franceschi
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; School of Dentistry, University of Michigan, Ann Arbor, MI, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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11
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Abstract
Synaptic receptors in the human brain consist of multiple protein subunits, many of which have multiple variants, coded by different genes, and are differentially expressed across brain regions and developmental stages. The brain can tune the electrophysiological properties of synapses to regulate plasticity and information processing by switching from one protein variant to another. Such condition-dependent variant switch during development has been demonstrated in several neurotransmitter systems including NMDA and GABA. Here we systematically detect pairs of receptor-subunit variants that switch during the lifetime of the human brain by analyzing postmortem expression data collected in a population of donors at various ages and brain regions measured using microarray and RNA-seq. To further detect variant pairs that co-vary across subjects, we present a method to quantify age-corrected expression correlation in face of strong temporal trends. This is achieved by computing the correlations in the residual expression beyond a cubic-spline model of the population temporal trend, and can be seen as a nonlinear version of partial correlations. Using these methods, we detect multiple new pairs of context dependent variants. For instance, we find a switch from GLRA2 to GLRA3 that differs from the known switch in the rat. We also detect an early switch from HTR1A to HTR5A whose trends are negatively correlated and find that their age-corrected expression is strongly positively correlated. Finally, we observe that GRIN2B switch to GRIN2A occurs mostly during embryonic development, presumably earlier than observed in rodents. These results provide a systematic map of developmental switching in the neurotransmitter systems of the human brain. Synapses change their properties during development affecting information processing and learning. Most synaptic receptors consist of several proteins, each having several variants coded by closely related genes. These protein variants are similar in structure, yet often differ slightly in their biophysical attributes. Switching a synapse from using one variant to another provides the brain with a way to fine-tune electrophysiological properties of synapses and has been described in NMDA and GABA receptors. Here we describe a systematic approach to detect pairs of context-dependent variants at a genome-wide scale based on a set of post-mortem expression measurements taken from brains at multiple ages. We take into account both the profile of expression as it changes along life and also the detrended age-corrected correlation among genes. This method characterizes the landscape of developmental switches in brain transcriptome, putting forward new candidates pairs for deeper analysis. The abundance of switching between context-dependent variants through life suggests that it is a major mechanism by which the brain tunes its plasticity and information processing.
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Affiliation(s)
- Ossnat Bar-Shira
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
| | - Ronnie Maor
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
| | - Gal Chechik
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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12
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Abstract
The potential of genetic clock lies in its role to triggering logic reaction for sequential biological circuits. In general, biochemical reaction of the biological system is extremely slow. However, a square wave generator used as a genetic clock the transient response should be fast enough to catch the reaction change between two logic levels. Therefore, the requirement for instantaneous changes in logic status is not likely to exist in biological systems. This paper presents a method of synthesizing a genetic clock generator based on the combination of a toggle switch with two biological logic gates. A dual repressor is used to connect the two fundamental biologic circuits. Analysis of the characteristic responses of this genetic clock with its relation to the key parameters is provided.
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13
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Jaruszewicz J, Kimmel M, Lipniacki T. Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:022710. [PMID: 25353512 DOI: 10.1103/physreve.89.022710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Indexed: 06/04/2023]
Abstract
Bistable regulatory elements are important for nongenetic inheritance, increase of cell-to-cell heterogeneity allowing adaptation, and robust responses at the population level. Here, we study computationally the bistable genetic toggle switch-a small regulatory network consisting of a pair of mutual repressors-in growing and dividing bacteria. We show that as cells with an inhibited growth exhibit high stability of toggle states, cell growth and divisions lead to a dramatic increase of toggling rates. The toggling rates were found to increase with rate of cell growth, and can be up to six orders of magnitude larger for fast growing cells than for cells with the inhibited growth. The effect is caused mainly by the increase of protein and mRNA burst sizes associated with the faster growth. The observation that fast growth dramatically destabilizes toggle states implies that rapidly growing cells may vigorously explore the epigenetic landscape enabling nongenetic evolution, while cells with inhibited growth adhere to the local optima. This can be a clever population strategy that allows the slow growing (but stress resistant) cells to survive long periods of unfavorable conditions. Simultaneously, at favorable conditions, this stress resistant (but slowly growing-or not growing) subpopulation may be replenished due to a high switching rate from the fast growing population.
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Affiliation(s)
- Joanna Jaruszewicz
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Marek Kimmel
- Departments of Statistics and Bioengineering, Rice University, Houston, Texas 77005, USA and Systems Engineering Group, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland and Department of Statistics, Rice University, Houston, Texas 77005, USA
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14
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Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P. RNA nanotechnology for computer design and in vivo computation. Philos Trans A Math Phys Eng Sci 2013; 371:20120310. [PMID: 24000362 PMCID: PMC3758167 DOI: 10.1098/rsta.2012.0310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.
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Affiliation(s)
- Meikang Qiu
- Department of Computer Engineering, San Jose State University, San Jose, CA 95192, USA
| | - Emil Khisamutdinov
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Zhengyi Zhao
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Cheryl Pan
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742, Korea
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Peixuan Guo
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
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15
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Nené NR, Zaikin A. Decision making in noisy bistable systems with time-dependent asymmetry. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 87:012715. [PMID: 23410367 DOI: 10.1103/physreve.87.012715] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 12/03/2012] [Indexed: 06/01/2023]
Abstract
Our work draws special attention to the importance of the effects of time-dependent parameters on decision making in bistable systems. Here, we extend previous studies of the mechanism known as speed-dependent cellular decision making in genetic circuits by performing an analytical treatment of the canonical supercritical pitchfork bifurcation problem with an additional time-dependent asymmetry and control parameter. This model has an analogous behavior to the genetic switch. In the presence of transient asymmetries and fluctuations, slow passage through the critical region in both systems increases substantially the probability of specific decision outcomes. We also study the relevance for attractor selection of reaching maximum values for the external asymmetry before and after the critical region. Overall, maximum asymmetries should be reached at an instant where the position of the critical point allows for compensation of the detrimental effects of noise in retaining memory of the transient asymmetries.
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Affiliation(s)
- Nuno R Nené
- Department of Mathematics, Imperial College London, South Kensington Campus, SW7 2AZ London, United Kingdom
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16
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Zagorski M, Krzywicki A, Martin OC. Edge usage, motifs, and regulatory logic for cell cycling genetic networks. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 87:012727. [PMID: 23410379 DOI: 10.1103/physreve.87.012727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/09/2012] [Indexed: 06/01/2023]
Abstract
The cell cycle is a tightly controlled process, yet it shows marked differences across species. Which of its structural features follow solely from the ability to control gene expression? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressions. We focus on three cell cycle profiles coming from baker's yeast, fission yeast, and mammals. First, we show that the networks in each of the ensembles use just a few interactions that are repeatedly reused as building blocks. Second, we find an enrichment in network motifs that is similar in the two yeast cell cycle systems investigated. These motifs do not have autonomous functions, yet they reveal a regulatory logic for cell cycling based on a feed-forward cascade of activating interactions.
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Affiliation(s)
- M Zagorski
- Marian Smoluchowski Institute of Physics and Mark Kac Complex Systems Research Centre, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
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17
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Abstract
The major goal of evolutionary oncology is to explain how malignant traits evolve to become cancer ``hallmarks." One such hallmark---the angiogenic switch---is difficult to explain for the same reason altruism is difficult to explain. An angiogenic clone is vulnerable to ``cheater" lineages that shunt energy from angiogenesis to proliferation, allowing the cheater to outcompete cooperative phenotypes in the environment built by the cooperators. Here we show that cell- or clone-level selection is sufficient to explain the angiogenic switch, but not because of direct selection on angiogenesis factor secretion---angiogenic potential evolves only as a pleiotropic afterthought. We study a multiscale mathematical model that includes an energy management system in an evolving angiogenic tumor. The energy management model makes the counterintuitive prediction that ATP concentration in resting cells increases with increasing ATP hydrolysis, as seen in other theoretical and empirical studies. As a result, increasing ATP hydrolysis for angiogenesis can increase proliferative potential, which is the trait directly under selection. Intriguingly, this energy dynamic allows an evolutionary stable angiogenesis strategy, but this strategy is an evolutionary repeller, leading to runaway selection for extreme vascular hypo- or hyperplasia. The former case yields a tumor-on-a-tumor, or hypertumor, as predicted in other studies, and the latter case may explain vascular hyperplasia evident in certain tumor types.
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Affiliation(s)
- John D Nagy
- Department of Life Sciences, Scottsdale Community College, 9000 E. Chaparral Rd., Scottsdale, AZ 85256, United States.
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18
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Zhu XM, Yin L, Hood L, Ao P. ROBUSTNESS, STABILITY AND EFFICIENCY OF PHAGE λ GENETIC SWITCH: DYNAMICAL STRUCTURE ANALYSIS. J Bioinform Comput Biol 2011; 2:785-817. [PMID: 15617166 DOI: 10.1142/s0219720004000946] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2004] [Revised: 09/16/2004] [Accepted: 09/18/2004] [Indexed: 11/18/2022]
Abstract
Based on the dynamical structure theory for complex networks recently developed by one of us and on the physical-chemical models for gene regulation, developed by Shea and Ackers in the 1980's, we formulate a direct and concise mathematical framework for the genetic switch controlling phage λ life cycles, which naturally includes the stochastic effect. The dynamical structure theory states that the dynamics of a complex network is determined by its four elementary components: The dissipation (analogous to degradation), the stochastic force, the driving force determined by a potential, and the transverse force. The potential may be interpreted as a landscape for the phage development in terms of attractive basins, saddle points, peaks and valleys. The dissipation gives rise to the adaptivity of the phage in the landscape defined by the potential: The phage always has the tendency to approach the bottom of the nearby attractive basin. The transverse force tends to keep the network on the equal-potential contour of the landscape. The stochastic fluctuation gives the phage the ability to search around the potential landscape by passing through saddle points.With molecular parameters in our model fixed primarily by the experimental data on wild-type phage and supplemented by data on one mutant, our calculated results on mutants agree quantitatively with the available experimental observations on other mutants for protein number, lysogenization frequency, and a lysis frequency in lysogen culture. The calculation reproduces the observed robustness of the phage λ genetic switch. This is the first mathematical description that successfully represents such a wide variety of major experimental phenomena. Specifically, we find: (1) The explanation for both the stability and the efficiency of phage λ genetic switch is the exponential dependence of saddle point crossing rate on potential barrier height, a result of the stochastic motion in a landscape; and (2) The positive feedback of cI repressor gene transcription, enhanced by the CI dimer cooperative binding, is the key to the robustness of the phage λ genetic switch against mutations and fluctuations in kinetic parameter values.
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Affiliation(s)
- X-M Zhu
- GenMath, Corp. 5525 27th Ave.N.E., Seattle, WA 98105, USA
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19
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Assaf M, Roberts E, Luthey-Schulten Z. Determining the stability of genetic switches: explicitly accounting for mRNA noise. Phys Rev Lett 2011; 106:248102. [PMID: 21770603 DOI: 10.1103/physrevlett.106.248102] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Indexed: 05/31/2023]
Abstract
Cells use genetic switches to shift between alternate gene-expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on-off switch. Unlike protein-only models, we explicitly account for stochastic fluctuations of mRNA, which have a dramatic impact on switch dynamics. Employing the WKB theory to treat the underlying chemical master equations, we obtain accurate results for the quasistationary distributions of mRNA and protein copy numbers and for the mean switching time, starting from either state. Our analytical results agree well with Monte Carlo simulations. Importantly, one can use the approach to study the effect of varying biological parameters on switch stability.
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Affiliation(s)
- Michael Assaf
- Departments of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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20
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Wang H, Song W, Huang G, Zhou Z, Ding Y, Chen J. Candida albicans Zcf37, a zinc finger protein, is required for stabilization of the white state. FEBS Lett 2011; 585:797-802. [PMID: 21315072 DOI: 10.1016/j.febslet.2011.02.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 12/31/2010] [Accepted: 02/04/2011] [Indexed: 11/19/2022]
Abstract
Candida albicans, the most prevalent human fungal pathogen, can switch stochastically between white and opaque phases. In this study, we identified Zcf37, a zinc finger protein, as a new regulator of white-opaque switching. Deletion of ZCF37 increased white-to-opaque switching frequency and stabilized the opaque state. Overexpression of ZCF37 promoted conversion of opaque cells to white phase, but needed existence of Efg1, a key regulator required for maintenance of the white state. Deletion of EFG1 abolished the effect of ectopically expressed Zcf37 on opaque-to-white switching, whereas ectopic expression of EFG1 promoted white cell formation without presence of Zcf37. Our results suggest that Zcf37 acts as an activator of white cell formation and a repressor of opaque state and functions upstream of Efg1.
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Affiliation(s)
- Huafeng Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, SIBS, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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21
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Hnisz D, Tscherner M, Kuchler K. Morphological and molecular genetic analysis of epigenetic switching of the human fungal pathogen Candida albicans. Methods Mol Biol 2011; 734:303-315. [PMID: 21468996 DOI: 10.1007/978-1-61779-086-7_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Candida albicans is a pleiomorphic fungal pathogen whose morphogenetic plasticity has long been considered as a major virulence factor. In addition to the yeast-filament transition, C. albicans cells also have the unique ability to switch between two epigenetic phases referred to as white and opaque. White and opaque cells harbor identical genomes yet they differ in cellular morphologies, gene expression profiles, mating abilities, and virulence properties. The switching process is regulated by a small network of transcription factors and is suggested to be driven by stochastic fluctuations of the regulatory components, which correlates with altered switching frequencies. Traditionally, phase variants have been identified based on cellular morphologies and expression levels of a few marker transcripts, yet it has recently become clear that several other criteria are also essential and relevant, because phase markers are regulated at multiple branching sites of transcriptional circuitry regulating switching. Here, we describe basic methods to discriminate between white and opaque switching variants, based on cellular and macroscopic morphologies, expression levels of phase-specific transcripts, Wor1 protein levels, as well as quantitative mating assays.
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Affiliation(s)
- Denes Hnisz
- Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories, Campus Vienna Biocenter, Vienna, Austria
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22
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Marucci L, Barton DAW, Cantone I, Ricci MA, Cosma MP, Santini S, di Bernardo D, di Bernardo M. How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch. PLoS One 2009; 4:e8083. [PMID: 19997611 PMCID: PMC2784219 DOI: 10.1371/journal.pone.0008083] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 11/02/2009] [Indexed: 11/23/2022] Open
Abstract
Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA). Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.
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Affiliation(s)
- Lucia Marucci
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Computer and Systems Engineering, Federico II University, Naples, Italy
| | - David A. W. Barton
- Bristol Centre for Applied Nonlinear Mathematics, University of Bristol, Bristol, United Kingdom
| | - Irene Cantone
- MRC Clinical Sciences Centre Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Maria Pia Cosma
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Stefania Santini
- Department of Computer and Systems Engineering, Federico II University, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Computer and Systems Engineering, Federico II University, Naples, Italy
- * E-mail: (DDB); (MDB)
| | - Mario di Bernardo
- Department of Computer and Systems Engineering, Federico II University, Naples, Italy
- Bristol Centre for Applied Nonlinear Mathematics, University of Bristol, Bristol, United Kingdom
- * E-mail: (DDB); (MDB)
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23
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Zordan RE, Miller MG, Galgoczy DJ, Tuch BB, Johnson AD. Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans. PLoS Biol 2007; 5:e256. [PMID: 17880264 PMCID: PMC1976629 DOI: 10.1371/journal.pbio.0050256] [Citation(s) in RCA: 224] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 07/27/2007] [Indexed: 11/23/2022] Open
Abstract
The human pathogen Candida albicans can assume either of two distinct cell types, designated “white” and “opaque.” Each cell type is maintained for many generations; switching between them is rare and stochastic, and occurs without any known changes in the nucleotide sequence of the genome. The two cell types differ dramatically in cell shape, colony appearance, mating competence, and virulence properties. In this work, we investigate the transcriptional circuitry that specifies the two cell types and controls the switching between them. First, we identify two new transcriptional regulators of white-opaque switching, Czf1 and white-opaque regulator 2 (Wor2). Analysis of a large set of double mutants and ectopic expression strains revealed genetic relationships between CZF1, WOR2, and two previously identified regulators of white-opaque switching, WOR1 and EFG1. Using chromatin immunoprecipitation, we show that Wor1 binds the intergenic regions upstream of the genes encoding three additional transcriptional regulators of white-opaque switching (CZF1, EFG1, and WOR2), and also occupies the promoters of numerous white- and opaque-enriched genes. Based on these interactions, we have placed these four genes in a circuit controlling white-opaque switching whose topology is a network of positive feedback loops, with the master regulator gene WOR1 occupying a central position. Our observations indicate that a key role of the interlocking feedback loop network is to stably maintain each epigenetic state through many cell divisions. The opportunistic fungal pathogen Candida albicans can switch between two heritable states—the “white” and “opaque” states. These two cell types differ in many characteristics, including cell structure, mating competence, and virulence. Recent studies of the molecular mechanism of regulating the white-opaque switch identified a master transcriptional regulator, Wor1. In this study, we identified two transcriptional regulators, Czf1 and Wor2, as new regulators of white-opaque switching. By constructing a series of single and double mutants and by examining where the master regulator Wor1 binds throughout the genome, we generated a molecular model of the bistable switch that regulates white-opaque switching. The regulatory model consists of interlocking positive feedback loops, which mutually reinforce one another and stabilize the opaque state. These results show how an organism can exist in two distinctive, heritable states without changes in the nucleotide sequence of its genome. Analysis of mutations inCandida albicans indicates that the four genes in a circuit controlling white-opaque switching form a network of positive feedback loops, with the master regulatorWOR1 occupying a central position.
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Affiliation(s)
- Rebecca E Zordan
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Mathew G Miller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - David J Galgoczy
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Brian B Tuch
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Alexander D Johnson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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24
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Affiliation(s)
- Jörg S Hartig
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
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25
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Kazanov MD, Vitreschak AG, Gelfand MS. Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics 2007; 8:347. [PMID: 17908319 PMCID: PMC2211319 DOI: 10.1186/1471-2164-8-347] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 10/01/2007] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes. RESULTS Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198). CONCLUSION This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes.
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Affiliation(s)
- Marat D Kazanov
- Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetnyi per. 19, Moscow, 127994, Russia
| | - Alexey G Vitreschak
- Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetnyi per. 19, Moscow, 127994, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetnyi per. 19, Moscow, 127994, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia
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26
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Abstract
Genetic engineering of plants using transgenic technology is targeted to enhance agronomic performance or improved quality traits in a wide variety of plant species, and has become a fundamental tool for basic research in plant biotechnology. Constitutive promoters are presently the primary means used to express transgenes in plants. However, inducible gene regulation systems based on specific chemicals have many potential applications in agriculture and for enhancing the basic understanding of gene function. As a result, several gene switches have been developed. The ecdysone receptor gene switch is one of the best inducible gene regulation systems available, because the chemical, methoxyfenozide, required for its regulation is registered for field use. An EcR gene switch with a potential for use in large-scale field applications has been developed by adopting a two-hybrid format. In a two-hybrid switch format, the GAL4 DNA binding domain (GAL4 DBD) was fused to the ligand binding domain (LBD) of the Choristoneura fumiferana ecdysone receptor (CfEcR); and, the VP16 activation domain (VP16 AD) was fused to the LBD of Locust migratoria retinoid X receptor (LmRXR). The sensitivity of the CfEcR gene switch was improved from micromolar to nanomolar concentrations of ligand by using the CfEcR:LmRXR two-hybrid switch. In this report, we demonstrate the utility of CfEcR:LmRXR two-hybrid gene switch in functional genomics applications for regulating the expression of a Superman-like single zinc finger protein 11 (ZFP11) gene in both Arabidopsis and tobacco transgenic plants.
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Affiliation(s)
- Venkata S Tavva
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA
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27
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Abstract
We propose what we believe is a new model to quantitatively describe the lambda-phage SWITCH system. The model incorporates facilitated transfer mechanism of transcription factor, which can be simplified into a two-step reaction. We first sequentially obtain two indispensable parameters by fitting our model to experimental data of two simple systems, and then apply them to study the natural lambda-SWITCH system. By incorporating the facilitated transfer mechanism, we find that in RecA(-) host Escherichia coli, the wild-type lambda-lysogenic state is in a monostable regime rather than in a bistable regime. Furthermore, the model explains the weak role of Cro protein and probably sheds light on the evolution of lambda-Cro protein, which is known to be structurally distinct from the other Cros in lambdoid family members.
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Affiliation(s)
- Chunbo Lou
- Center for Theoretical Biology and School of Physics, Peking University, Beijing, 100871, China
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28
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Dumitru R, Navarathna DHMLP, Semighini CP, Elowsky CG, Dumitru RV, Dignard D, Whiteway M, Atkin AL, Nickerson KW. In vivo and in vitro anaerobic mating in Candida albicans. Eukaryot Cell 2007; 6:465-72. [PMID: 17259544 PMCID: PMC1828919 DOI: 10.1128/ec.00316-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Candida albicans cells of opposite mating types are thought to conjugate during infection in mammalian hosts, but paradoxically, the mating-competent opaque state is not stable at mammalian body temperatures. We found that anaerobic conditions stabilize the opaque state at 37 degrees C, block production of farnesol, and permit in vitro mating at 37 degrees C at efficiencies of up to 84%. Aerobically, farnesol prevents mating because it kills the opaque cells necessary for mating, and as a corollary, farnesol production is turned off in opaque cells. These in vitro observations suggest that naturally anaerobic sites, such as the efficiently colonized gastrointestinal (GI) tract, could serve as niches for C. albicans mating. In a direct test of mating in the mouse GI tract, prototrophic cells were obtained from auxotrophic parent cells, confirming that mating will occur in this organ. These cells were true mating products because they were tetraploid, mononuclear, and prototrophic, and they contained the heterologous hisG marker from one of the parental strains.
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MESH Headings
- Anaerobiosis/physiology
- Animals
- Candida albicans/cytology
- Candida albicans/genetics
- Candida albicans/metabolism
- Conjugation, Genetic/physiology
- Farnesol/metabolism
- Farnesol/pharmacology
- Female
- Gastrointestinal Tract/microbiology
- Gastrointestinal Tract/physiology
- Gene Expression Regulation, Fungal/drug effects
- Gene Expression Regulation, Fungal/genetics
- Genes, Mating Type, Fungal/drug effects
- Genes, Mating Type, Fungal/genetics
- Genes, Switch/genetics
- Mice
- Mice, Inbred Strains
- Microscopy, Fluorescence
- Microscopy, Phase-Contrast
- Phenotype
- Signal Transduction
- Species Specificity
- Temperature
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Affiliation(s)
- Raluca Dumitru
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0666, USA
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29
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Abstract
Controlling gene activity in space and time represents a cornerstone technology in gene and cell therapeutic applications, bioengineering, drug discovery as well as fundamental and applied research. This chapter provides a comprehensive overview of the different approaches for regulating gene activity and product protein formation at different biosynthetic levels, from genomic rearrangements over transcription and translation control to strategies for engineering inducible secretion and protein activity with a focus on the development during the past 2 years. Recent advances in designing second-generation gene switches, based on novel inducer administration routes (gas phase) as well as on the combination of heterologous switches with endogenous signals, will be complemented by an overview of the emerging field of mammalian synthetic biology, which enables the design of complex synthetic and semisynthetic gene networks. This article will conclude with an overview of how the different gene switches have been applied in gene therapy studies, bioengineering and drug discovery.
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Affiliation(s)
- W Weber
- Institute for Chemical and Bioengineering, ETH Zurich, ETH Hoenggerberg HCI F 115, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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30
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Abstract
Riboswitches are noncoding RNA elements found in the 5'-untranslated region of messenger RNA (mRNA) that mediate gene expression in a cis fashion in the absence of protein. This common regulatory strategy in bacteria is achieved through the interplay of two distinct domains: an aptamer domain responsible for sensing intracellular concentrations of a specific metabolite and a domain containing a secondary structural switch directly controlling expression. In a recent study, riboswitches have been discovered that are capable of regulating transcription by using an RNA architecture mimicking a Boolean NOR logic gate. Tandem arrangement of elements that recognize S-adenosylmethionine and coenzyme B12 yields an mRNA that is only expressed when both metabolites are in low concentration in the cell.
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Affiliation(s)
- Colby D Stoddard
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Campus Box 215, Boulder, Colorado 80309-0215, USA
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31
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Abstract
Regulated expression of transgene is essential in basic research as well as for many therapeutic applications. The main purpose of the present study is to understand the functioning of the ecdysone receptor (EcR)-based gene switch in mammalian cells and to develop improved versions of EcR gene switches. We utilized EcR mutants to develop new EcR gene switches that showed higher ligand sensitivity and higher magnitude of induction of reporter gene expression in the presence of ligand. We also developed monopartite versions of EcR gene switches with reduced size of the components that are accommodated into viral vectors. Ligand binding assays revealed that EcR alone could not bind to the nonsteroidal ligand, RH-2485. The EcR's heterodimeric partner, ultraspiracle, is required for efficient binding of EcR to the ligand. The essential role of retinoid X receptor (RXR) or its insect homolog, ultraspiracle, in EcR function is shown by RXR knockdown experiments using RNAi. Chromatin immunoprecipitation assays demonstrated that VP16 (activation domain, AD):GAL4(DNA binding domain, DBD):EcR(ligand binding domain, LBD) or GAL4(DBD):EcR(LBD) fusion proteins can bind to GAL4 response elements in the absence of ligand. The VP16(AD) fusion protein of a chimera between human and locust RXR could heterodimerize with GAL4(DBD):EcR(LBD) in the absence of ligand but the VP16(AD) fusion protein of Homo sapiens RXR requires ligand for its heterodimerization with GAL4(DBD):EcR(LBD).
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Affiliation(s)
- Siva K Panguluri
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
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32
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Mullick A, Xu Y, Warren R, Koutroumanis M, Guilbault C, Broussau S, Malenfant F, Bourget L, Lamoureux L, Lo R, Caron AW, Pilotte A, Massie B. The cumate gene-switch: a system for regulated expression in mammalian cells. BMC Biotechnol 2006; 6:43. [PMID: 17083727 PMCID: PMC1654148 DOI: 10.1186/1472-6750-6-43] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Accepted: 11/03/2006] [Indexed: 11/24/2022] Open
Abstract
Background A number of expression systems have been developed where transgene expression can be regulated. They all have specific characteristics making them more suitable for certain applications than for others. Since some applications require the regulation of several genes, there is a need for a variety of independent yet compatible systems. Results We have used the regulatory mechanisms of bacterial operons (cmt and cym) to regulate gene expression in mammalian cells using three different strategies. In the repressor configuration, regulation is mediated by the binding of the repressor (CymR) to the operator site (CuO), placed downstream of a strong constitutive promoter. Addition of cumate, a small molecule, relieves the repression. In the transactivator configuration, a chimaeric transactivator (cTA) protein, formed by the fusion of CymR with the activation domain of VP16, is able to activate transcription when bound to multiple copies of CuO, placed upstream of the CMV minimal promoter. Cumate addition abrogates DNA binding and therefore transactivation by cTA. Finally, an adenoviral library of cTA mutants was screened to identify a reverse cumate activator (rcTA), which activates transcription in the presence rather than the absence of cumate. Conclusion We report the generation of a new versatile inducible expression system.
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Affiliation(s)
- Alaka Mullick
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- Départment de microbiologie et immunologie de l'Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Yan Xu
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - René Warren
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
| | - Maria Koutroumanis
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- Invitrogen, 688 East Main Street, Branford, CT, 06405, USA
| | - Claire Guilbault
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Sophie Broussau
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- Départment de microbiologie et immunologie de l'Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Félix Malenfant
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Lucie Bourget
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Linda Lamoureux
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- AstraZeneca, 7171, Frédérick-Banting, Ville St.-Laurent, Montréal, Québec, H4S 1Z9, Canada
| | - Rita Lo
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Antoine W Caron
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Amelie Pilotte
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- Départment de microbiologie et immunologie de l'Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Bernard Massie
- Institut de Recherche en Biotechnologie, Conseil National de Recherches du Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
- INRS-IAF, Université du Québec, Laval, Québec, H7N 4Z3, Canada
- Départment de microbiologie et immunologie de l'Université de Montréal, Montréal, Québec, H3C 3J7, Canada
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33
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Srikantha T, Borneman AR, Daniels KJ, Pujol C, Wu W, Seringhaus MR, Gerstein M, Yi S, Snyder M, Soll DR. TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell 2006; 5:1674-87. [PMID: 16950924 PMCID: PMC1595353 DOI: 10.1128/ec.00252-06] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Candida albicans, the a1-alpha2 complex represses white-opaque switching, as well as mating. Based upon the assumption that the a1-alpha2 corepressor complex binds to the gene that regulates white-opaque switching, a chromatinimmunoprecipitation-microarray analysis strategy was used to identify 52 genes that bound to the complex. One of these genes, TOS9, exhibited an expression pattern consistent with a "master switch gene." TOS9 was only expressed in opaque cells, and its gene product, Tos9p, localized to the nucleus. Deletion of the gene blocked cells in the white phase, misexpression in the white phase caused stable mass conversion of cells to the opaque state, and misexpression blocked temperature-induced mass conversion from the opaque state to the white state. A model was developed for the regulation of spontaneous switching between the opaque state and the white state that includes stochastic changes of Tos9p levels above and below a threshold that induce changes in the chromatin state of an as-yet-unidentified switching locus. TOS9 has also been referred to as EAP2 and WOR1.
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Affiliation(s)
- Thyagarajan Srikantha
- Department of Biological Sciences, 302 BBE, The University of Iowa, Iowa City, IA 52242, USA
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34
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Hull CM. Single gene control of a complex phenotype hangs in the balance. Proc Natl Acad Sci U S A 2006; 103:12659-60. [PMID: 16908836 PMCID: PMC1568903 DOI: 10.1073/pnas.0605675103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Christina M Hull
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, 1300 University Avenue, 587 Medical Science Center, Madison, WI 53706, USA.
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35
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Huang G, Wang H, Chou S, Nie X, Chen J, Liu H. Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans. Proc Natl Acad Sci U S A 2006; 103:12813-8. [PMID: 16905649 PMCID: PMC1540355 DOI: 10.1073/pnas.0605270103] [Citation(s) in RCA: 229] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Candida albicans, a commensal organism and a pathogen of humans, can switch stochastically between a white phase and an opaque phase without an intermediate phase. The white and opaque phases have distinct cell shapes and gene expression programs. Once switched, each phase is stable for many cell divisions. White-opaque switching is under a1-alpha2 repression and therefore only happens in a or alpha cells. Mechanisms that control the switching are unknown. Here, we identify Wor1 (white-opaque regulator 1) as a master regulator of white-opaque switching. The deletion of WOR1 blocks opaque cell formation. The ectopic expression of WOR1 converts all cells to stable opaque cells in a or alpha cells. In addition, the ectopic expression of WOR1 in a/alpha cells is sufficient to induce opaque cell formation. Importantly, WOR1 expression displays an all-or-none pattern. It is undetectable in white cells, and it is highly expressed in opaque cells. The ectopic expression of Wor1 induces the transcription of WOR1 from the WOR1 locus, which correlates with the switch to opaque phase. We present genetic evidence for feedback regulation of WOR1 transcription. The feedback regulation explains the bistable and stochastic nature of white-opaque switching.
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Affiliation(s)
- Guanghua Huang
- *State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China; and
| | - Huafeng Wang
- *State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China; and
| | - Song Chou
- Department of Biological Chemistry, College of Medicine, University of California, Irvine, CA 92697-1700
| | - Xinyi Nie
- *State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China; and
| | - Jiangye Chen
- *State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China; and
- To whom correspondence may be addressed. E-mail:
or
| | - Haoping Liu
- Department of Biological Chemistry, College of Medicine, University of California, Irvine, CA 92697-1700
- To whom correspondence may be addressed. E-mail:
or
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36
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Zordan RE, Galgoczy DJ, Johnson AD. Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc Natl Acad Sci U S A 2006; 103:12807-12. [PMID: 16899543 PMCID: PMC1535343 DOI: 10.1073/pnas.0605138103] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
White-opaque switching in the human fungal pathogen Candida albicans is an alternation between two distinct types of cells, white and opaque. White and opaque cells differ in their appearance under the microscope, the genes they express, their mating behaviors, and the host tissues for which they are best suited. Each state is heritable for many generations, and switching between states occurs stochastically, at low frequency. In this article, we identify a master regulator of white-opaque switching (Wor1), and we show that this protein is a transcriptional regulator that is needed to both establish and maintain the opaque state. We show that in opaque cells, Wor1 forms a positive feedback loop: It binds its own DNA regulatory region and activates its own transcription leading to the accumulation of high levels of Wor1. We further show that this feedback loop is self-sustaining: Once activated, it persists for many generations. We propose that this Wor1 feedback loop accounts, at least in part, for the heritability of the opaque state. In contrast, white cells (and their descendents) lack appreciable levels of Wor1, and the feedback loop remains inactive. Thus, this simple model can account for both the heritability of the white and opaque states and the stochastic nature of the switching between them.
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Affiliation(s)
| | | | - Alexander D. Johnson
- Departments of *Biochemistry and Biophysics and
- Microbiology and Immunology, 600 16th Street, University of California, San Francisco, CA 94158
- To whom correspondence should be addressed. E-mail:
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37
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Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 2005; 6:R70. [PMID: 16086852 PMCID: PMC1273637 DOI: 10.1186/gb-2005-6-8-r70] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 06/15/2005] [Accepted: 07/01/2005] [Indexed: 12/30/2022] Open
Abstract
Comparative sequence analysis and structural probing identified five RNA elements in the intergenic region of Agrobacterium tumefaciens and other α-proteobacteria. One of these RNA elements is probably a SAM-II, the only riboswitch class identified so far that is not found in Gram-positive bacteria. Background Riboswitches are RNA elements in the 5' untranslated leaders of bacterial mRNAs that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. Riboswitches are most common in the genomes of low GC Gram-positive bacteria (for example, Bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group. Results We used comparative sequence analysis and structural probing to identify five RNA elements (serC, speF, suhB, ybhL, and metA) that reside in the intergenic regions of Agrobacterium tumefaciens and many other α-proteobacteria. One of these, the metA motif, is found upstream of methionine biosynthesis genes and binds S-adenosylmethionine (SAM). This natural aptamer most likely functions as a SAM riboswitch (SAM-II) with a consensus sequence and structure that is distinct from the class of SAM riboswitches (SAM-I) predominantly found in Gram-positive bacteria. The minimal functional SAM-II aptamer consists of fewer than 70 nucleotides, which form a single stem and a pseudoknot. Despite its simple architecture and lower affinity for SAM, the SAM-II aptamer strongly discriminates against related compounds. Conclusion SAM-II is the only metabolite-binding riboswitch class identified so far that is not found in Gram-positive bacteria, and its existence demonstrates that biological systems can use multiple RNA structures to sense a single chemical compound. The two SAM riboswitches might be 'RNA World' relics that were selectively retained in certain bacterial lineages or new motifs that have emerged since the divergence of the major bacterial groups.
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Affiliation(s)
- Keith A Corbino
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Jeffrey E Barrick
- Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Jinsoo Lim
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Rüdiger Welz
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
- Department of Chemistry, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Brian J Tucker
- Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Izabela Puskarz
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Maumita Mandal
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
- Department of Physics, University of California, Berkeley, CA 94720-7200, USA
| | - Noam D Rudnick
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
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38
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Guntas G, Mansell TJ, Kim JR, Ostermeier M. Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc Natl Acad Sci U S A 2005; 102:11224-9. [PMID: 16061816 PMCID: PMC1183557 DOI: 10.1073/pnas.0502673102] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe an iterative approach for creating protein switches involving the in vitro recombination of two nonhomologous genes. We demonstrate this approach by recombining the genes coding for TEM1 beta-lactamase (BLA) and the Escherichia coli maltose binding protein (MBP) to create a family of MBP-BLA hybrids in which maltose is a positive or negative effector of beta-lactam hydrolysis. Some of these MBP-BLA switches were effectively "on-off" in nature, with maltose altering catalytic activity by as much as 600-fold. The ability of these switches to confer an effector-dependent growth/no growth phenotype to E. coli cells was exploited to rapidly identify, from a library of 4 x 10(6) variants, MBP-BLA switch variants that respond to sucrose as the effector. The transplantation of these mutations into wild-type MBP converted MBP into a "sucrose-binding protein," illustrating the switches potential as a tool to rapidly identify ligand-binding proteins.
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Affiliation(s)
- Gurkan Guntas
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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39
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40
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Abstract
With the use of polymerases having 3' to 5' exonuclease activity and 3' phosphorothioate-modified allele-specific primers, we recently devised a SNP-operated on/off switch controlling DNA polymerization. One advantage of this novel on/off switch is its adaptability to arrayed primer extension. To further expand its application in genetic analysis, this new on/off switch was evaluated in discrimination of the match/mismatch status of single nucleotides upstream from the primer 3' terminal. A set of seven amplicons was developed with the templates differing from each other by a single nucleotide. Using this set of amplicons, the new on/off switch was shown to be able to efficiently discriminate single nucleotide polymorphisms from the primer 3' terminus to the -6 position from the primer 3' terminus. These data, illustrating the broad single nucleotide discrimination ability of this novel on/off switch, explain why the SNP-operated on/off switch is powerful in SNP analysis, and also indicate useful applications to genetic analysis additional to SNP assay. First, these data broaden the application of the novel on/off switch in the analysis of mutations other than SNPs. Second, it raises a nucleotide-walking algorithm suitable for de novo array-based sequencing analysis.
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Affiliation(s)
- Kai Li
- SNP Institute, Hengyang, Hunan, China.
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41
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Li Q, Han H, Ye X, Stafford M, Barkess G, Stamatoyannopoulos G. Transcriptional potentials of the beta-like globin genes at different developmental stages in transgenic mice and hemoglobin switching. Blood Cells Mol Dis 2005; 33:318-25. [PMID: 15528151 DOI: 10.1016/j.bcmd.2004.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Indexed: 11/17/2022]
Abstract
Developmental-stage-specific regulation and physiological levels of expression of the globin genes can be recaptured in transgenic mice carrying a YAC/BAC- or cosmid-based construct. By contrast, proper developmental regulation and high-level expression cannot be achieved coordinately in transgenic mice carrying a more manipulated construct, such as a plasmid-based globin gene construct. These differences provide us an opportunity to define the requirements for a developmentally regulated, high-level expression of the globin genes in vivo. To achieve this, as a first step, we studied maximum transcriptional potentials of the beta-globin genes at various stages of development. microLCR-enhanced expression of the epsilon-, gamma-, and beta-globin genes driven by their minimal promoters was estimated and compared with that in betaYAC transgenic mice. Quantitative measurements of steady state mRNA levels of the epsilon-, gamma-, and beta-globin genes showed that the microLCR was able to enhance expression of each beta-like globin gene to levels similar to those in the betaYAC mice. Moreover, transcriptional potentials of each globin gene were unchanged during the entire course of development. These observations indicate that the highest level of expression of the globin genes can be achieved in both embryonic and definitive erythropoiesis regardless of developmental specificity of the genes. This finding implies that transcription suppression is the major mechanism of the developmental specificity of the expression of the beta-like globin genes.
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Affiliation(s)
- Qiliang Li
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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42
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Kaykov A, Arcangioli B. A programmed strand-specific and modified nick in S. pombe constitutes a novel type of chromosomal imprint. Curr Biol 2005; 14:1924-8. [PMID: 15530393 DOI: 10.1016/j.cub.2004.10.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 09/09/2004] [Indexed: 01/30/2023]
Abstract
The sexual locus mat1, in the fission yeast Schizosaccharomyces pombe, efficiently switches between the two mating types, P and M, by a process similar to gene conversion, using the silent mat2-P and mat3-M loci, respectively, as donors of the P and M genetic information . It has been proposed that an asymmetrically inherited, site- and strand-specific imprint at mat1 initiates the mating-type switching process . The molecular nature of the imprint is controversial; it was initially described as a double-strand break and then as a single-strand lesion or a strand-specific, alkali-labile modification . Here, we use E. coli DNA ligase in vitro to demonstrate that the imprint is a nick with no resection of nucleotides. By using ligation-mediated PCR, we show that the nick contains 3'OH and 5'OH unphosphorylated termini resistant to RNase treatments. This nonmutational mark on one of the DNA strands provides the first example of a novel type of imprint.
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Affiliation(s)
- Atanas Kaykov
- Unité de dynamique du Génome, Unités de Recherche Associées, 1644 du Centre National de la Recherche Scientifique, Département de la Structure et Dynamique des Génomes, Institut Pasteur, 75724 Paris 15, France
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Sonoki T, Willis TG, Oscier DG, Karran EL, Siebert R, Dyer MJS. Rapid amplification of immunoglobulin heavy chain switch (IGHS) translocation breakpoints using long-distance inverse PCR. Leukemia 2004; 18:2026-31. [PMID: 15496980 DOI: 10.1038/sj.leu.2403500] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Molecular cloning of immunoglobulin heavy chain (IGH) translocation breakpoints identifies genes of biological importance in the development of normal and malignant B cells. Long-distance inverse PCR (LDI-PCR) was first applied to amplification of IGH gene translocations targeted to the joining (IGHJ) regions. We report here successful amplification of the breakpoint of IGH translocations targeted to switch (IGHS) regions by LDI-PCR. To detect IGHS translocations, Southern blot assays using 5' and 3' switch probes were performed. Illegitimate Smu rearrangements were amplified from the 5' end (5'Smu LDI-PCR) from the alternative derivative chromosome, and those of Sgamma or Salpha were amplified from the 3' end (3'Sgamma or 3'alpha LDI-PCR) from the derivative chromosome 14. Using a combination of these methods, we have succeeded in amplifying IGHS translocation breakpoints involving FGFR3/MMSET on 4p16, BCL6 on 3q27, MYC on 8q24, IRTA1 on 1q21 and PAX5 on 9p13 as well as BCL11A on 2p13 and CCND3 on 6p21. The combination of LDI-PCR for IGHJ and IGHS allows rapid molecular cloning of almost all IGH gene translocation breakpoints.
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MESH Headings
- Base Sequence
- Blotting, Southern
- Carrier Proteins/genetics
- Chromosome Breakage/genetics
- Chromosomes, Human, Pair 14
- Cloning, Molecular
- DNA-Binding Proteins/genetics
- Gene Rearrangement
- Genes, Switch/genetics
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Switch Region/genetics
- Immunoglobulin mu-Chains/genetics
- Lymphoma/genetics
- Molecular Sequence Data
- Nuclear Proteins/genetics
- PAX5 Transcription Factor
- Polymerase Chain Reaction
- Protein-Tyrosine Kinases/genetics
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins c-bcl-6
- Proto-Oncogene Proteins c-myc/genetics
- Receptor, Fibroblast Growth Factor, Type 3
- Receptors, Fibroblast Growth Factor/genetics
- Repressor Proteins
- Transcription Factors/genetics
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- T Sonoki
- Academic Haematology and Cytogenetics, Institute of Cancer Research, UK
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Abstract
Schizosaccharomyces pombe has the remarkable potential to switch mating type as often as every generation, through selective interaction of an expressor locus with either of two transcriptionally silent donor loci. Recent results demonstrate that selection of the appropriate donor locus likely occurs through mating-type and heterochromatin-dependent spreading of a protein complex that marks the correct donor locus.
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Affiliation(s)
- James R Broach
- Department of Molecular Biology, Princeton University, Princeton, NJ 08558, USA.
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Roberts RW. Engineering switches, genetically. Chem Biol 2004; 11:1475-6. [PMID: 15555994 DOI: 10.1016/j.chembiol.2004.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Ostermeier, Guntas, and Mitchel describe a new approach to design enzymes that are allosterically regulated by an unrelated ligand . The resulting protein, constructed by nonhomologous recombination and genetic screens, displays switch-like behavior.
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Affiliation(s)
- Richard W Roberts
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Krings G, Bastia D. swi1- and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 2004; 101:14085-90. [PMID: 15371597 PMCID: PMC521093 DOI: 10.1073/pnas.0406037101] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Replication forks are arrested at specific sequences to facilitate a variety of DNA transactions. Forks also stall at sites of DNA damage, and the regression of stalled forks without rescue can cause genetic instability. Therefore, unraveling the mechanisms of fork arrest and of rescue of stalled forks is of considerable general interest. In Schizosaccharomyces pombe, products of two mating-type switching genes, swi1 and swi3, participate in fork arrest at the mating-type switch locus. Here, we show that these proteins also act at three termini (Ter) also called replication fork barriers in the spacer regions of rDNA but not at a fourth site, RFP4, which is nonfunctional when present in a plasmid. Two of the Swi1p- and Swi3p-dependent sites were also dependent on the transcription terminator Reb1p. Furthermore, hydroxyurea-induced replication stress mimicked the effect of swi1 or swi3 mutations at these sites. A swi1 mutant that failed to arrest forks at the mating-type fork barrier RTS1 was functional at the rDNA Ter sites, suggesting some specificity of action. Both WT and mutant forms of Swi1p were physically localized at the Ter sites in vivo. The results support the notion that Swi1p and Swi3p act at several different protein-DNA complexes in the rDNA spacer regions to arrest replication but that not all fork barriers required their activity to arrest forks.
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Affiliation(s)
- Gregor Krings
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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47
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Warren PB, ten Wolde PR. Enhancement of the stability of genetic switches by overlapping upstream regulatory domains. Phys Rev Lett 2004; 92:128101. [PMID: 15089712 DOI: 10.1103/physrevlett.92.128101] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Indexed: 05/24/2023]
Abstract
We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterized by a well-defined lifetime, which grows very rapidly, albeit subexponentially, with the number of copies of the most-expressed transcription factor. The switch stability can be drastically enhanced by overlapping the upstream regulatory domains such that competing regulatory molecules mutually exclude each other. Our results suggest that robustness against biochemical noise can provide a selection pressure that drives operons together in the course of evolution.
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Affiliation(s)
- Patrick B Warren
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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48
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Abstract
Targeted gene expression has become a standard technique for the study of biological questions in Drosophila. Until recently, transgene expression could be targeted in the dimension of either time or space, but not both. Several new systems have recently been developed to direct transgene expression simultaneously in both time and space. We describe here two such systems that we developed in our laboratory. The first system provides a general method for temporal and regional gene expression targeting (TARGET) with the conventional GAL4-upstream activator sequence (UAS) system and a temperature-sensitive GAL80 molecule, which represses GAL4 transcriptional activity at permissive temperatures. The second system, termed Gene-Switch, is based on a GAL4-progesterone receptor chimera that is hormone-inducible. We have used both systems for simultaneous spatial and temporal rescue of memory dysfunction in the rutabaga (rut) memory mutant of Drosophila. In this protocol, we provide guidelines for the use of these two novel systems, which should have general utility in studying Drosophila biology and in using the fly as a model for human disease.
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Affiliation(s)
- Sean E McGuire
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
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Affiliation(s)
- David R Soll
- Department of Biological Sciences, The University of Iowa, Iowa City, Iowa 52242, USA.
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50
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Borday C, Abadie V, Chatonnet F, Thoby-Brisson M, Champagnat J, Fortin G. Developmental molecular switches regulating breathing patterns in CNS. Respir Physiol Neurobiol 2003; 135:121-32. [PMID: 12809613 DOI: 10.1016/s1569-9048(03)00031-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The present paper presents some of the molecular switches that may operate at early embryonic stages to make development of the brainstem respiratory rhythm generator a robust and irreversible process. We concentrate on the role of transient Hox-related gene expression patterns in register with the regionalisation of the rhombencephalic neural tube along the antero-posterior axis. Using different recording and isolation procedures in chick embryos, we show that the hindbrain is subdivided at E1 into developmental units (rhombomeres) intrinsically able to produce rhythm generating neuronal circuits active at E5. At E6, intrinsic cues also allow a progressive maturation of episodic rhythm generators that persists after isolation of the hindbrain in vitro and requires odd/even rhombomeric interactions at E1. From these results and from respiratory pathologies observed in transgenic mice, we are beginning to understand that, despite diversity of breathing patterns and adaptations, there are links between developmental control genes and adult respiration.
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Affiliation(s)
- Caroline Borday
- UPR 2216 Neurobiologie Génétique et Intégrative, Institut de Neurobiologie Alfred Fessard, C.N.R.S., 1, av. de la Terrasse, 91198, Gif-sur-Yvette, France.
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