scholarly journals A two-state photoconversion model predicts the spectral response dynamics of optogenetic systems

2016 ◽  
Author(s):  
Evan J. Olson ◽  
Constantine N. Tzouanas ◽  
Jeffrey J. Tabor
Keyword(s):  
Gene Expression ◽  
Biological Pathways ◽  
Programming Approach ◽  
Response Dynamics ◽  
Gene Expression Response ◽  
Control Of Gene Expression ◽  
Wide Range ◽  
Light Signals

AbstractIn optogenetics, light signals are used to control genetically engineered photoreceptors, and in turn manipulate biological pathways with unmatched precision. Recently, evolved photoreceptors with diverse in vitro-measured wavelength and intensity-dependent photoswitching properties have been repurposed for synthetic control of gene expression, proteolysis, and numerous other cellular processes. However, the relationship between the input light spectrum and in vivo photoreceptor response dynamics is poorly understood, restricting the utility of these optogenetic tools. Here, we advance a classic in vitro two-state photoreceptor model to reflect the in vivo environment, and combine it with simplified mathematical descriptions of signal transduction and output gene expression through our previously engineered green/red and red/far red photoreversible bacterial two-component systems (TCSs). Additionally, we leverage our recent open-source optical instrument to develop a workflow of spectral and dynamical characterization experiments to parameterize the model for both TCSs. To validate our approach, we challenge the model to predict experimental responses to a series of complex light signals very different from those used during parameterization. We find that the model generalizes remarkably well, predicting the results of all categories of experiments with high quantitative accuracy for both systems. Finally, we exploit this predictive power to program two simultaneous and independent dynamical gene expression signals in bacteria expressing both TCSs. This multiplexed gene expression programming approach will enable entirely new studies of how metabolic, signaling, and decision-making pathways integrate multiple gene expression signals. Additionally, our approach should be compatible with a wide range of optogenetic tools and model organisms.Significance statementLight-switchable signaling pathways (optogenetic tools) enable precision studies of how biochemical networks underlie cellular behaviors. We have developed a versatile mathematical model based on a two-state photoconversion mechanism that we have applied to the E. coli CcaSR and Cph8-OmpR optogenetic tools. This model enables accurate prediction of the gene expression response to virtually any light source or mixture of light sources. We express both optogenetic tools in the same cell and apply our model to program two simultaneous and independent gene expression signals in the same cell. This method can be used to study how biological pathways integrate multiple inputs and should be extensible to other optogenetic tools and host organisms.

DEFECTIVE STEROIDAL SYNTHESIS BY ADRENAL TISSUE: THE CONTROL OF GENE EXPRESSION CAUSING LOSS OF ACTIVE STEROIDOGENIC ENZYMES

1974 ◽  
Vol 77 (2) ◽  
pp. 325-336
Author(s):  
K. Williams
Keyword(s):  
Gene Expression ◽  
Adrenal Glands ◽  
Hydroxysteroid Dehydrogenase ◽  
Ascites Cell ◽  
Control Of Gene Expression ◽  
Adrenocortical Hyperplasia ◽  
Normal Human ◽  
Adrenocortical Tumour

ABSTRACT RNA was isolated from normal human adrenal glands and found to cause the formation of Δ5-3β-hydroxysteroid dehydrogenase-isomerase and steroid 21-hydroxylase activities by a Krebs II ascites cell-free protein synthesising system. Although no functional steroid 21-hydroxylase in vivo or in vitro was found in a gland from a patient with virilism due to congenital adrenocortical hyperplasia the RNA would still give steroid 21-hydroxylase-like activity in the protein synthesising system which suggests that the inherited defect was not in the structural gene. Activity could not be induced by RNA from a 'non-functioning' adrenocortical tumour or rat liver.

Gene expression response of the rat small intestine following oralSalmonellainfection

2007 ◽  
Vol 30 (2) ◽  
pp. 123-133 ◽  
Author(s):  
Wendy Rodenburg ◽  
Ingeborg M. J. Bovee-Oudenhoven ◽  
Evelien Kramer ◽  
Roelof van der Meer ◽  
Jaap Keijer
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Inflammatory Marker ◽  
Molecular Response ◽  
Lipocalin 2 ◽  
Ileal Mucosa ◽  
Gene Expression Response ◽  
Expression Response

Data on the molecular response of the intestine to the food-borne pathogen Salmonella are derived from in vitro studies, whereas in vivo data are lacking. We performed an oral S. enteritidis infection study in Wistar rats to obtain insight in the in vivo response in time. Expression profiles of ileal mucosa (IM) and Peyer's patches (PP) were generated using DNA microarrays at days 1, 3, and 6 postinfection. An overview of Salmonella-regulated processes was obtained and confirmed by quantitative real-time PCR on pooled and individual samples. Salmonella-induced gene expression responses in vivo are fewer and smaller than observed in vitro, and the response develops over a longer period of time. Few effects are seen at day 1 and mainly occur in IM, suggesting the mucosa as the primary site of invasion. Later, a bigger response is observed, especially in PP. Decreased expression of anti-microbial peptides genes (in IM at day 1) suggests inhibition of this process by Salmonella. Newly identified target processes are carbohydrate transport (increased expression in IM at day 1) and phase I and phase II detoxification (decreased expression at days 3 and 6). Increase of cytokine and chemokine expression occurs at later time points, both in PP and IM. Pancreatitis-associated protein, lipocalin 2, and calprotectin, potential inflammatory marker proteins, showed induced expression from day 3 onward. We conclude that the in vivo gene expression response of the ileum to Salmonella differs to a large extent from the response seen in vitro.

scholarly journals Regulation and Characterization of Two Nitroreductase Genes, nprA and nprB, of Rhodobacter capsulatus

2005 ◽  
Vol 71 (12) ◽  
pp. 7643-7649 ◽  
Author(s):  
Eva Pérez-Reinado ◽  
Rafael Blasco ◽  
Francisco Castillo ◽  
Conrado Moreno-Vivián ◽  
M. Dolores Roldán
Keyword(s):  
Gene Expression ◽  
Salicylic Acid ◽  
Rhodobacter Capsulatus ◽  
Sequence Data ◽  
Regulatory System ◽  
Wide Range ◽  
Nitrofuran Derivatives ◽  
Response To Stress

ABSTRACT Among photosynthetic bacteria, strains B10 and E1F1 of Rhodobacter capsulatus photoreduce 2,4-dinitrophenol (DNP), which is stoichiometrically converted into 2-amino-4-nitrophenol by a nitroreductase activity. The reduction of DNP is inhibited in vivo by ammonium, which probably acts at the level of the DNP transport system and/or physiological electron transport to the nitroreductase, since this enzyme is not inhibited by ammonium in vitro. Using the complete genome sequence data for strain SB1003 of R. capsulatus, two putative genes coding for possible nitroreductases were isolated from R. capsulatus B10 and disrupted. The phenotypes of these mutant strains revealed that both genes are involved in the reduction of DNP and code for two major nitroreductases, NprA and NprB. Both enzymes use NAD(P)H as the main physiological electron donor. The nitroreductase NprA is under ammonium control, whereas the nitroreductase NprB is not. In addition, the expression of the nprB gene seems to be constitutive, whereas nprA gene expression is inducible by a wide range of nitroaromatic and heterocyclic compounds, including several dinitroaromatics, nitrofuran derivatives, CB1954, 2-aminofluorene, benzo[a]pyrene, salicylic acid, and paraquat. The identification of two putative mar/sox boxes in the possible promoter region of the nprA gene and the induction of nprA gene expression by salicylic acid and 2,4-dinitrophenol suggest a role in the control of the nprA gene for the two-component MarRA regulatory system, which in Escherichia coli controls the response to some antibiotics and environmental contaminants. In addition, upregulation of the nprA gene by paraquat indicates that this gene is probably a member of the SoxRS regulon, which is involved in the response to stress conditions in other bacteria.

scholarly journals The RNA–RNA base pairing potential of human Dicer and Ago2 proteins

2019 ◽  
Vol 77 (16) ◽  
pp. 3231-3244 ◽  
Author(s):  
Maria Pokornowska ◽  
Marek C. Milewski ◽  
Kinga Ciechanowska ◽  
Agnieszka Szczepańska ◽  
Marta Wojnicka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Rna Structure ◽  
Small Interfering Rnas ◽  
Base Pairing ◽  
Complementary Sequence ◽  
Control Of Gene Expression ◽  
Complementary Sequences

Abstract The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.

scholarly journals Characterization of five purine riboswitches in cellular and cell-free expression systems

2021 ◽  
Author(s):  
Milca Rachel da Costa Ribeiro Lins ◽  
Graciely Gomes Correa ◽  
Laura Araujo da Silva Amorim ◽  
Rafael Augusto Lopes Franco ◽  
Nathan Vinicius Ribeiro ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
In Vitro Transcription ◽  
Vitro Assay ◽  
Control Of Gene Expression ◽  
Transcription Terminator ◽  
Variable Expression ◽  
Expression Platform

Bacillus subtilis employs five purine riboswitches for the control of purine de novo synthesis and transport at the transcription level. All of them are formed by a structurally conserved aptamer, and a variable expression platform harboring a rho-independent transcription terminator. In this study, we characterized all five purine riboswitches under the context of active gene expression processes both in vitro and in vivo. We identified transcription pause sites located in the expression platform upstream of the terminator of each riboswitch. Moreover, we defined a correlation between in vitro transcription readthrough and in vivo gene expression. Our in vitro assay demonstrated that the riboswitches operate in the micromolar range of concentration for the cognate metabolite. Our in vivo assay showed the dynamics of control of gene expression by each riboswitch. This study deepens the knowledge of the regulatory mechanism of purine riboswitches.

scholarly journals MTHFD1 is a genetic interactor of BRD4 and links folate metabolism to transcriptional regulation

2018 ◽  
Author(s):  
Sara Sdelci ◽  
André F. Rendeiro ◽  
Philipp Rathert ◽  
Gerald Hofstätter ◽  
Anna Ringler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Direct Interaction ◽  
Direct Role ◽  
Control Of Gene Expression ◽  
Folate Pathway ◽  
Important Regulator ◽  
Pharmacologic Inhibitors ◽  
Brd4 Inhibition

The histone acetyl-reader BRD4 is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for genetic and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1. We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. Inhibition of either BRD4 or MTHFD1 results in similar changes in nuclear metabolite composition and gene expression, and pharmacologic inhibitors of the two pathways synergize to impair cancer cell viability in vitro and in vivo. Our finding that MTHFD1 and other metabolic enzymes are chromatin-associated suggests a direct role for nuclear metabolism in the control of gene expression.

scholarly journals Precise tuning of gene expression output levels in mammalian cells

2018 ◽  
Author(s):  
Yale S. Michaels ◽  
Mike B. Barnkob ◽  
Hector Barbosa ◽  
Toni A. Baeumler ◽  
Mary K. Thompson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
High Throughput Sequencing ◽  
Regulation Of Gene Expression ◽  
Antigen Expression ◽  
Control Of Gene Expression ◽  
Precise Control ◽  
Mouse Melanoma Model

ABSTRACTPrecise, analogue regulation of gene expression is critical for development, homeostasis and regeneration in mammals. In contrast, widely employed experimental and therapeutic approaches such as knock-in/out strategies are more suitable for binary control of gene activity, while RNA interference (RNAi) can lead to pervasive off-target effects and unpredictable levels of repression. Here we report on a method for the precise control of gene expression levels in mammalian cells based on engineered, synthetic microRNA response elements (MREs). To develop this system, we established a high-throughput sequencing approach for measuring the efficacy of thousands of miR-17 MRE variants. This allowed us to create a library of microRNA silencing-mediated fine-tuners (miSFITs) of varying strength that can be employed to control the expression of user specified genes. To demonstrate the value of this technology, we used a panel of miSFITs to tune the expression of a peptide antigen in a mouse melanoma model. This analysis revealed that antigen expression level is a key determinant of the anti-tumour immune response in vitro and in vivo. miSFITs are a powerful tool for modulating gene expression output levels with applications in research and cellular engineering.

scholarly journals 3 X-LINKED GENE EXPRESSION IN BOVINE PRE-IMPLANTATION EMBRYOS OBTAINED IN VIVO AND IN VITRO AS A MEASURE OF IMPACT OF EMBRYO PRODUCTION TECHNOLOGIES

2005 ◽  
Vol 17 (2) ◽  
pp. 152
Author(s):  
M.I. Nino-Soto ◽  
W.A. King
Keyword(s):  
Gene Expression ◽  
Embryo Production ◽  
Good Tool ◽  
Significance Level ◽  
Ideal System ◽  
Wide Range ◽  
Light Cycler ◽  
The Impact

The X chromosome provides an ideal system to study the impact of assisted reproduction technologies on gene expression because it holds a wide range of diversely functional genes and also the epigenetic features of X-inactivation are inherently susceptible to in vitro culture-mediated alterations. Using quantitative real-time RT-PCR we studied the expression of a panel of X-linked genes (ANT3, GAB3, RPS4, MECP2, XIAP, XIST) in pooled pre-attachment bovine embryos produced in vivo and in vitro. We collected pools of ten embryos in vivo (de la Fuente R. et al. 1999 Biol. Reprod. 60, 769–775) at the morula (n = 3 pools) and blastocyst (n = 3 pools) stages. Pools of ten matured oocytes (n = 10 pools), 2–4 cell (n = 10 pools), 8–16 cell (n = 10 pools), morula (n = 7 pools) and blastocyst (n = 7 pools) stage embryos were produced in LSOF (Robert et al. Biol. Reprod. 67, 1465–1472) and TCM-199/bovine oviductal epithelial cells (BOEC) co-culture (de la Fuente et al. 1999 Biol. Reprod. 60, 769–775). Total RNA was extracted with the Absolutely RNA® Microprep kit (Stratagene, La Jolla, CA, USA) and reverse transcribed using Oligo-dT12–18 primers and Superscript II RT (Invitrogen, Burlington, Ontario, Canada). Specific primers were designed for each gene and PCR products were used to build standard curves for absolute quantification in a Light Cycler™ instrument with the Light Cycler FastStart DNA Master Mix SYBRGreenI kit (Roche Diagnostics, Laval, Quebec, Canada). The data were analyzed with SAS (SAS Institute Inc., Cary, NC, USA) using a factorial ANOVA design and a log transformation. Significance level was set at α = 0.05. There were no significant differences in transcript levels between IVF systems in mature oocytes, morulae, or blastocysts. Significant differences were observed for some of the genes tested at the 2–4-cell (XIAP) and at the 8–16-cell stages (ANT3, GAB3, XIAP) but not others. There were significant differences between IVF (both BOEC and LSOF) and in vivo embryos at the morula and blastocyst stages, with IVF embryos showing an average of 8 (ANT3), 10 (XIAP), 127 (MECP2), and 593 (XIST) times more transcripts than their in vivo counterparts. GAB3 was detected in only a few samples prior to the blastocyst stage where it was consistently detected in IVF but not in vivo embryos. It was concluded that there is an effect of the IVF system on gene transcription just before and during the period of activation of the embryonic genome during the 4th cell cycle, as well as marked differences between IVF and in vivo produced embryos that are evident in the differential expression of X-linked genes. This system provides a good tool to monitor the effects of embryo production conditions and help in their improvement. This project was supported with grants from NSERC, FSBC, and OMAF.

scholarly journals Regulation of mRNA translation by a photoriboswitch

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Kelly A Rotstan ◽  
Michael M Abdelsayed ◽  
Luiz FM Passalacqua ◽  
Fabio Chizzolini ◽  
Kasireddy Sudarshan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Expression ◽  
In Vitro Selection ◽  
Mrna Translation ◽  
Spatiotemporal Analysis ◽  
Control Of Gene Expression ◽  
Reading Frame ◽  
Controlled Systems

Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)–a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.

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