scholarly journals DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12

2021 ◽  
Vol 3 (8) ◽  
Author(s):  
Gustavo Sganzerla Martinez ◽  
Scheila de Ávila e Silva ◽  
Aditya Kumar ◽  
Ernesto Pérez-Rueda
Keyword(s):  
Transcription Factor ◽  
Genetic Information ◽  
Promoter Activity ◽  
Statistical Tests ◽  
Promoter Sequence ◽  
Promoter Sequences ◽  
Promoter Recognition ◽  
Intergenic Regions ◽  
K 12 ◽  
Base Pair Stacking

AbstractThe gene transcription of bacteria starts with a promoter sequence being recognized by a transcription factor found in the RNAP enzyme, this process is assisted through the conservation of nucleotides as well as other factors governing these intergenic regions. Faced with this, the coding of genetic information into physical aspects of the DNA such as enthalpy, stability, and base-pair stacking could suggest promoter activity as well as protrude differentiation of promoter and non-promoter data. In this work, a total of 3131 promoter sequences associated to six different sigma factors in the bacterium E. coli were converted into numeric attributes, a strong set of control sequences referring to a shuffled version of the original sequences as well as coding regions is provided. Then, the parameterized genetic information was normalized, exhaustively analyzed through statistical tests. The results suggest that strong signals in the promoter sequences match the binding site of transcription factor proteins, indicating that promoter activity is well represented by its conversion into physical attributes. Moreover, the features tested in this report conveyed significant variances between promoter and control data, enabling these features to be employed in bacterial promoter classification. The results produced here may aid in bacterial promoter recognition by providing a robust set of biological inferences.

scholarly journals The Retinoblastoma Protein Binds the Promoter of the Survival Gene bcl-2 and Regulates Its Transcription in Epithelial Cells through Transcription Factor AP-2

2002 ◽  
Vol 22 (22) ◽  
pp. 7877-7888 ◽  
Author(s):  
Stephanie Decary ◽  
Julien T. Decesse ◽  
Vasily Ogryzko ◽  
John C. Reed ◽  
Irina Naguibneva ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Epithelial Cells ◽  
Gene Promoter ◽  
Promoter Sequence ◽  
Promoter Sequences ◽  
Survival Gene ◽  
Nih 3T3 ◽  
First Time ◽  
E Cadherin

ABSTRACT The retinoblastoma (RB) gene product has been shown to restrict cell proliferation, promote cell differentiation, and inhibit apoptosis. Loss of RB function can induce both p53-dependent apoptosis and p53-independent apoptosis; little is known about the mechanisms of RB-regulated p53-independent apoptosis. Here we show that RB specifically activates transcription of the survival gene bcl-2 in epithelial cells but not in NIH 3T3 mesenchymal cells. This transcriptional activity is mediated by the transcription factor AP-2. By monitoring protein-DNA interactions in living cells using formaldehyde cross-linking and chromatin immunoprecipitation, we show that endogenous RB and AP-2 both bind to the same bcl-2 promoter sequence. In addition, we demonstrate that RB and AP-2 also bind to the E-cadherin gene promoter in vivo, consistent with regulation of this promoter by both AP-2 and RB in epithelial cells. This study provides evidence that RB activates bcl-2 and E-cadherin by binding directly to the respective promoter sequences and not indirectly by repressing an inhibitor. This recruitment is mediated by a transcription factor, in this case AP-2. For the first time, our results suggest a direct molecular mechanism by which RB might inhibit apoptosis independently of p53. The results are discussed in a context where RB and Bcl-2 contribute under nonpathological conditions to the maintenance of cell viability in association with a differentiated phenotype, contributing to the tumor suppressor function of RB and playing important roles in normal development.

Role of AP2 consensus sites in regulation of rat Npt2 (sodium-phosphate cotransporter) promoter

2000 ◽  
Vol 278 (3) ◽  
pp. F406-F416 ◽  
Author(s):  
C. Shachaf ◽  
K. L. Skorecki ◽  
M. Tzukerman
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Proximal Tubule ◽  
Cell Lines ◽  
Promoter Activity ◽  
Promoter Sequence ◽  
Luciferase Reporter ◽  
Inverted Repeats ◽  
Proximal Tubule Cell ◽  
Flanking Sequence

Expression of the Npt2 gene, encoding the type II sodium-dependent phosphate cotransporter, is restricted to renal proximal tubule epithelium. We have isolated a 4,740-bp fragment of the 5′-flanking sequence of the rat Npt2 gene, identified the transcription initiation site, and demonstrated that this 5′-flanking sequence drives luciferase-reporter gene expression, following transfection in the proximal tubule cell-derived opossum kidney (OK) cell line but not in unrelated cell lines. Analysis of the promoter sequence revealed the presence of 10 consensus binding motifs for the AP2 transcription factor. Transient transfection assays revealed an important effect of the number of tandemly repeated AP2 sites in enhancing promoter activity. The promoter sequence also revealed a pair of inverted repeats enclosing 1,324 bp of intervening sequence and containing 8 of the total 10 AP2 consensus sites in the promoter sequence. Deletion or reversal of orientation of the distal inverted repeat resulted in marked enhancement of promoter activity. Electrophoretic mobility shift analysis revealed a distinct pattern of transcription factor binding to oligonucleotides containing AP2 sites, using nuclear extracts from OK cells, compared with unrelated cell lines. Taken together, these results suggest an important role for AP2 consensus binding sites in regulating Npt2 gene expression and suggest a mechanism of regulation mediated by the interaction of inverted repeats enclosing these sites.

scholarly journals Identification of Drosophila Promoter Using Positional Differential Matrix and Support Vector Machine from Sequence Data

1970 ◽  
Vol 18 (2) ◽  
pp. 123-130
Author(s):  
Azizul Haque ◽  
Firoz Anwar ◽  
Taskeed Jabid ◽  
Syed Murtuza Baker ◽  
Haseena Khan ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Sequence Data ◽  
Focal Point ◽  
Living Organism ◽  
Promoter Sequence ◽  
Computational Method ◽  
Support Vector ◽  
Promoter Sequences ◽  
Promoter Recognition ◽  
Transcription Initiation Complex

Promoter region plays an important role in controlling gene expression of any living organism. It regulates gene transcription by providing space to the RNA polymerase and transcription factors to bind and interact with. Binding of appropriate transcription initiation complex is determined by the specific promoter sequence carrying gene specific motifs. The promoter recognition process is a part of the complex process where genes interact with each other over time and actually regulates the whole working process of a cell. Thus computational method for identifying promoter is a focal point for researchers. This paper presents an algorithm for identifying Drosophila melanogaster promoter using differential positional frequency matrix between promoter and non-promoter sequences which shows maximum 90.36% tenfold cross validation accuracy. The proposed method exhibits greater accuracy for detecting promoters. Also higher sensitivity and specificity results elucidate that the proposed method is less prone to false negatives and false positives compared to some other existing methods.  Key words:  Drosophila, Promoter, Sequence data D.O.I. 10.3329/ptcb.v18i2.3394 Plant Tissue Cult. & Biotech. 18(2): 123-130, 2008 (December)

scholarly journals The Length of Promoter Sequence Affects The De Novo Initiation By T7 RNA Polymerase in Vitro: New Insights Into The Evolution of Promoters For Single Subunit RNA Polymerases

2019 ◽  
Author(s):  
Ramesh Padmanabhan ◽  
Dennis Miller
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
De Novo ◽  
Promoter Sequence ◽  
Rna Polymerases ◽  
T7 Rna Polymerase ◽  
Promoter Sequences ◽  
Promoter Recognition ◽  
Single Subunit

1.1AbstractRNA polymerases (RNAPs) differ from other polymerases in that they can bind promoter sequences and initiate de novo transcription. Promoter recognition requires the presence of specific DNA binding domains in the polymerase. The structure and mechanistic aspects of transcription by the bacteriophage T7 RNA polymerase (T7 RNAP) are well characterized. This single subunit RNAP belongs to the family of RNAPs which also includes the T3, SP6 and mitochondrial RNAPs. High specificity for its promoter, the requirement of no additional transcription factors, and high fidelity of initiation from a specific site in the promoter makes it the polymerase of choice to study the mechanistic aspects of transcription. The structure and function of the catalytic domains of this family of polymerases are highly conserved suggesting a common mechanism underlying transcription. Although the two groups of single subunit RNAPs, mitochondrial and bacteriophage, have remarkable structural conservation, they recognize quite dissimilar promoters. Specifically, the bacteriophage promoters recognize a 23 nucleotide promoter extending from −17 to + 6 nucleotides relative to the site of transcription initiation, while the well characterized promoter recognized by the yeast mitochondrial RNAP is nine nucleotides in length extending from −8 to +1 relative to the site of transcription initiation. Promoters recognized by the bacteriophage RNAPs are also well characterized with distinct functional domains involved in promoter recognition and transcription initiation. Thorough mutational studies have been conducted by altering individual base-pairs within these domains. Here we describe experiments to determine whether the prototype bacteriophage RNAP is able to recognize and initiate at truncated promoters similar to mitochondrial promoters. Using an in vitro oligonucleotide transcriptional system, we have assayed transcription initiation activity by T7 RNAP. When a complete or almost complete (20 to 16 nucleotide) double stranded T7 RNAP promoter sequence is present, small RNA’s are produced through template-independent and promoter-dependent stuttering corresponding to abortive initiation, and this effect was lost with a scrambled promoter sequence. When partial double stranded promoter sequences (10 to 12 nucleotides) are supplied, template dependent de novo initiation of RNA occurs at a site different from the canonical +1-initiation site. The site of transcription initiation is determined by a recessed 3’ end based paired to the template strand of DNA rather than relative to the partial promoter sequence. Understanding the mechanism underlying this observation helps us to understand the role of the elements in the T7 promoter, and provides insights into the promoter evolution of the single-subunit RNAPs.

scholarly journals Synthetic Promoter Design in Escherichia coli based on Generative Adversarial Network

2019 ◽  
Author(s):  
Ye Wang ◽  
Haochen Wang ◽  
Liyang Liu ◽  
Xiaowo Wang
Keyword(s):  
Escherichia Coli ◽  
Sequence Space ◽  
Promoter Activity ◽  
Promoter Sequence ◽  
Similarity Score ◽  
Generative Models ◽  
Fine Tuning ◽  
Generative Adversarial Network ◽  
Promoter Sequences ◽  
Adversarial Network

ABSTRACTSynthetic promoters are commonly applied elements in circuit design for fine-tuning the protein expression levels. Promoter engineering was mostly focused on the random mutation or combination of regulation elements such as transcription factor binding sites. However, the size of promoter sequence space is still overwhelming and better navigation method is required. On the other hand, the generative adversarial network (GAN) is known for its great ability to reduce the searching space by learning to generate new data on the similar manifold of original data. Here, we applied WGAN-GP model into de novo promoter sequence design to generate entirely new promoter sequences. In total, 83 of model-generated promoter sequences were tested in promoter activity screening by regulating the expression of sfGFP gene in Escherichia coli. As a result, 26 out of 83 newly designed promoters were found functional and successfully expressed with varying activities, with similarity score to natural promoters all less than 0.7. Moreover, 3 of them showed higher promoter strength than the wild type promoters and their highly expression mutants. The much higher successful rate and promoter activity with much lower similarity score in our model-designed novel promoters confirmed the effectiveness of promoter sequence learning. Our work provides insights into an area of navigation of novel functional promoter sequence space automatically, as well as speeding up evolution process of naturally existing promoters, indicating the potential ability for deep generative models to be applied into genetic element designing in the future.

scholarly journals The Investigation of Promoter Sequences of Marseilleviruses Highlights a Remarkable Abundance of the AAATATTT Motif in Intergenic Regions

2017 ◽  
Vol 91 (21) ◽  
Author(s):  
Graziele Pereira Oliveira ◽  
Maurício Teixeira Lima ◽  
Thalita Souza Arantes ◽  
Felipe Lopes Assis ◽  
Rodrigo Araújo Lima Rodrigues ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Promoter Sequence ◽  
Content Type ◽  
Promoter Sequences ◽  
Promoter Motif ◽  
Wide Range ◽  
Multiple Copies ◽  
Intergenic Regions ◽  
Foreign Genes

ABSTRACT Viruses display a wide range of genomic profiles and, consequently, a variety of gene expression strategies. Specific sequences associated with transcriptional processes have been described in viruses, and putative promoter motifs have been elucidated for some nucleocytoplasmic large DNA viruses (NCLDV). Among NCLDV, the Marseilleviridae is a well-recognized family because of its genomic mosaicism. The marseilleviruses have an ability to incorporate foreign genes, especially from sympatric organisms inhabiting Acanthamoeba, its main known host. Here, we identified for the first time an eight-nucleotide A/T-rich promoter sequence (AAATATTT) associated with 55% of marseillevirus genes that is conserved in all marseilleviruses lineages, a higher level of conservation than that of any giant virus described to date. We instigated our prediction about the promoter motif by biological assays and by evaluating how single mutations in this octamer can impact gene expression. The investigation of sequences that regulate the expression of genes relative to lateral transfer revealed that the promoter motifs do not appear to be incorporated by marseilleviruses from donor organisms. Indeed, analyses of the intergenic regions that regulate lateral gene transfer-related genes have revealed an independent origin of the marseillevirus intergenic regions that does not match gene-donor organisms. About 50% of AAATATTT motifs spread throughout intergenic regions of the marseilleviruses are present as multiple copies. We believe that such multiple motifs are associated with increased expression of a given gene or are related to incorporation of foreign genes into the mosaic genome of marseilleviruses. IMPORTANCE The marseilleviruses draw attention because of the peculiar features of their genomes; however, little is known about their gene expression patterns or the factors that regulate those expression patterns. The limited published research on the expression patterns of the marseilleviruses and their unique genomes has led us to study the promoter motif sequences in the intergenic regions of the marseilleviruses. This work is the first to analyze promoter sequences in the genomes of the marseilleviruses. We also suggest a strong capacity to acquire foreign genes and to express those genes mediated by multiple copies of the promoter motifs available in intergenic regions. These findings contribute to an understanding of genomic expansion and plasticity observed in these giant viruses.

scholarly journals The Glucocorticoid Receptor (GR) Stimulates Herpes Simplex Virus 1 Productive Infection, in Part Because the Infected Cell Protein 0 (ICP0) Promoter Is Cooperatively Transactivated by the GR and Krüppel-Like Transcription Factor 15

2019 ◽  
Vol 93 (6) ◽  
Author(s):  
Jeffery B. Ostler ◽  
Kelly S. Harrison ◽  
Kayla Schroeder ◽  
Prasanth Thunuguntla ◽  
Clinton Jones
Keyword(s):  
Transcription Factor ◽  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Infected Cell ◽  
Promoter Activity ◽  
Productive Infection ◽  
Cell Protein ◽  
Herpes Simplex Virus 1 ◽  
Infected Cell Protein ◽  
Infected Cell Protein 0

ABSTRACTFollowing acute infection, herpes simplex virus 1 (HSV-1) establishes lifelong latency in neurons. Physical, emotional, and chemical stresses are linked to increasing the incidence of reactivation from latency, but the mechanism of action is not well understood. In general, stress increases corticosteroid levels, leading to activation of the glucocorticoid receptor (GR), a pioneer transcription factor. Consequently, we hypothesized that stress-mediated activation of the GR can stimulate productive infection and viral gene expression. New studies demonstrated that the GR-specific antagonist (CORT-108297) significantly reduced HSV-1 productive infection in mouse neuroblastoma cells (Neuro-2A). Additional studies demonstrated that the activated GR and Krüppel-like transcription factor 15 (KLF15) cooperatively transactivated the infected cell protein 0 (ICP0) promoter, a crucial viral regulatory protein. Interestingly, the synthetic corticosteroid dexamethasone and GR or KLF15 alone had little effect on ICP0 promoter activity in transfected Neuro-2A or Vero cells. Chromatin immunoprecipitation (ChIP) studies revealed that the GR and KLF15 occupied ICP0 promoter sequences important for transactivation at 2 and 4 h after infection; however, binding was not readily detected at 6 h after infection. Similar results were obtained for cells transfected with the full-length ICP0 promoter. ICP0 promoter sequences lack a consensus “whole” GR response element (GRE) but contain putative half-GREs that were important for dexamethasone induced promoter activity. The activated GR stimulates expression of, and interacts with, KLF15; consequently, these data suggest KLF15 and the GR form a feed-forward loop that activates viral gene expression and productive infection following stressful stimuli.IMPORTANCEThe ability of herpes simplex virus 1 (HSV-1) to periodically reactivate from latency results in virus transmission and recurrent disease. The incidence of reactivation from latency is increased by chronic or acute stress. Stress increases the levels of corticosteroids, which bind and activate the glucocorticoid receptor (GR). Since GR activation is an immediate early response to stress, we tested whether the GR influences productive infection and the promoter that drives infected cell protein 0 (ICP0) expression. Pretreatment of cells with a GR-specific antagonist (CORT-108297) significantly reduced virus replication. Although the GR had little effect on ICP0 promoter activity alone, the Krüppel-like transcription factor 15 (KLF15) cooperated with the GR to stimulate promoter activity in transfected cells. In transfected or infected cells, the GR and KLF15 occupied ICP0 sequences important for transactivation. Collectively, these studies provide insight into how stress can directly stimulate productive infection and viral gene expression.

scholarly journals DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 853
Author(s):  
Siti Aisyah Faten Mohamed Sa’dom ◽  
Sweta Raikundalia ◽  
Shaharum Shamsuddin ◽  
Wei Cun See Too ◽  
Ling Ling Few
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Binding Site ◽  
Promoter Activity ◽  
Cytosine Methylation ◽  
Cpg Island ◽  
Cpg Islands ◽  
Site Directed Mutagenesis ◽  
Choline Kinase ◽  
Mcf 7

Choline kinase (CK) is the enzyme catalyzing the first reaction in CDP-choline pathway for the biosynthesis of phosphatidylcholine. Higher expression of the α isozyme of CK has been implicated in carcinogenesis, and inhibition or downregulation of CKα (CHKA) is a promising anticancer approach. This study aimed to investigate the regulation of CKα expression by DNA methylation of the CpG islands found on the promoter of this gene in MCF-7 cells. Four CpG islands have been predicted in the 2000 bp promoter region of ckα (chka) gene. Six CpG island deletion mutants were constructed using PCR site-directed mutagenesis method and cloned into pGL4.10 vectors for promoter activity assays. Deletion of CpG4C region located between –225 and –56 significantly increased the promoter activity by 4-fold, indicating the presence of important repressive transcription factor binding site. The promoter activity of methylated full-length promoter was significantly lower than the methylated CpG4C deletion mutant by 16-fold. The results show that DNA methylation of CpG4C promotes the binding of the transcription factor that suppresses the promoter activity. Electrophoretic mobility shift assay analysis showed that cytosine methylation at MZF1 binding site in CpG4C increased the binding of putative MZF1 in nuclear extract. In conclusion, the results suggest that DNA methylation decreased the promoter activity by promoting the binding of putative MZF1 transcription factor at CpG4C region of the ckα gene promoter.

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