A computational study of the gene expression in the tryptophan operon with two types of cooperativity

2019 ◽  
Vol 45 (4) ◽  
pp. 1843-1851
Author(s):  
José Roberto Cantú-González ◽  
O. Díaz-Hernández ◽  
Elizeth Ramírez-Álvarez ◽  
C. I. Enríquez Flores ◽  
A. Flores Rosas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Computational Study ◽  
Tryptophan Operon

Complexation of short ds RNA/DNA oligonucleotides with Gemini micelles: a time resolved SAXS and computational study

2017 ◽  
Vol 19 (4) ◽  
pp. 3046-3055 ◽  
Author(s):  
Sara Falsini ◽  
Emanuela Di Cola ◽  
Martin In ◽  
Maria Giordani ◽  
Stefano Borocci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Therapy ◽  
Nucleic Acid ◽  
Computational Study ◽  
Nucleic Acid Delivery ◽  
Time Resolved ◽  
Dna Oligonucleotides ◽  
P Gene

Gene therapy is based on nucleic acid delivery to pathogenic cells in order to modulate their gene expression.

scholarly journals Different RNA splicing mechanisms contribute to diverse infective outcome of classical swine fever viruses of differing virulence: insights from the deep sequencing data in swine umbilical vein endothelial cells

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2113 ◽  
Author(s):  
Pengbo Ning ◽  
Yulu Zhou ◽  
Wulong Liang ◽  
Yanming Zhang
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Rna Splicing ◽  
Molecular Mechanisms ◽  
Computational Study ◽  
Umbilical Vein ◽  
Classical Swine Fever ◽  
Pathway Enrichment Analysis ◽  
Splicing Regulation ◽  
Umbilical Vein Endothelial Cells

Molecular mechanisms underlying RNA splicing regulation in response to viral infection are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen and C strains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen and C strains disturbed ‘RNA splicing’ of SUVEC, resulting in differential ‘gene expression’ in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance.

Computational study of switching mechanism in add A-riboswitch

2020 ◽  
Vol 19 (03) ◽  
pp. 2040001 ◽  
Author(s):  
Ting Zhou ◽  
Huiwen Wang ◽  
Linlu Song ◽  
Yunjie Zhao
Keyword(s):  
Gene Expression ◽  
Small Molecules ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Potential Solution ◽  
Conformational Switching ◽  
Regulate Gene Expression ◽  
Switching Mechanism ◽  
Molecule Recognition ◽  
Regulate Gene

Riboswitch can bind small molecules to regulate gene expression. Unlike other RNAs, riboswitch relies on its conformational switching for regulation. However, the understanding of the switching mechanism is still limited. Here, we focussed on the add A-riboswitch to illustrate the dynamical switching mechanism as an example. We performed molecular dynamics simulation, conservation and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding, whereas the switching base pairings are co-evolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design.

scholarly journals Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Hungyo Kharerin ◽  
Paike J. Bhat ◽  
John F. Marko ◽  
Ranjith Padinhateeri
Keyword(s):  
Gene Expression ◽  
Computational Study ◽  
Promoter Regions ◽  
Long Tail ◽  
Nucleosome Dynamics ◽  
Sequence Effects ◽  
Nucleosome Disassembly ◽  
Open Question ◽  
Kinetics Of

Abstract Studying nucleosome dynamics in promoter regions is crucial for understanding gene regulation. Nucleosomes regulate gene expression by sterically occluding transcription factors (TFs) and other non–histone proteins accessing genomic DNA. How the binding competition between nucleosomes and TFs leads to transcriptionally compatible promoter states is an open question. Here, we present a computational study of the nucleosome dynamics and organization in the promoter region of PHO5 gene in Saccharomyces cerevisiae. Introducing a model for nucleosome kinetics that takes into account ATP-dependent remodeling activity, DNA sequence effects and kinetics of TFs (Pho4p), we compute the probability of obtaining different “promoter states” having different nucleosome configurations. Comparing our results with experimental data, we argue that the presence of local remodeling activity (LRA) as opposed to basal remodeling activity (BRA) is crucial in determining transcriptionally active promoter states. By modulating the LRA and Pho4p binding rate, we obtain different mRNA distributions—Poisson, bimodal and long-tail. Through this work we explain many features of the PHO5 promoter such as sequence-dependent TF accessibility and the role of correlated dynamics between nucleosomes and TFs in opening/coverage of the TATA box. We also obtain possible ranges for TF binding rates and the magnitude of LRA.

scholarly journals Computational study of parameter sensitivity in DevR regulated gene expression

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0228967
Author(s):  
Jagannath Das ◽  
Tarunendu Mapder ◽  
Sudip Chattopadhyay ◽  
Suman K. Banik
Keyword(s):  
Gene Expression ◽  
Computational Study ◽  
Parameter Sensitivity ◽  
Regulated Gene Expression

Genes

2019 ◽  
pp. 186-204
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Regulatory System ◽  
The Body ◽  
Internal Cell ◽  
Wide Range ◽  
Tryptophan Operon ◽  
Bacterial Genes

Gene expression patterns are dependent on their internal cell environment of their DNA, their immediate internal cell environment, and the integrity of their DNA. It also depends on the cell's external environment comprised of signals from other parts of the body including chemicals, nutrients, and/or mechanical stress. Gene regulation is achieved by a wide range of mechanisms that cells use to control whether genes are transcribed, when they are transcribed, and to regulate the quantity of certain proteins based on the cellular and/or environmental feedback. Proper regulation of gene expression is required by organisms to respond to continually changing environmental conditions. Some bacterial genes are transcribed as a unit under a regulatory system called an operon which contains functionally related genes. Three well studied operons include the lactose operon, histidine operon, and tryptophan operon. Gene regulation in higher organisms can occur at various stages from DNA level to protein assembly. This chapter explores this aspect of genes.

scholarly journals TRANSLATIONAL COUPLING DURING EXPRESSION OF THE TRYPTOPHAN OPERON OF ESCHERICHIA COLI

Genetics ◽  
1980 ◽  
Vol 95 (4) ◽  
pp. 785-795 ◽  
Author(s):  
Daniel S Oppenheim ◽  
Charles Yanofsky
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Gene Products ◽  
Translational Coupling ◽  
E Coli ◽  
Functional Complex ◽  
Tryptophan Operon

ABSTRACT E. coli trpE polar mutations are 10 times more polar on trpD gene expression than on downstream (trpC, B, or A) gene expression. This effect was shown to be the result of "translational coupling," in which efficient translation of trpD mRNA reqiures efficient translation of the end of trpE mRNA. The trpE-trpD intercistronic punctuation region consists of overlapping stop and start codons, and the trpE and trpD gene products form a functional complex in the cell. In light of these observations and characteristics, several models for the mechanism of translational coupling are considered.

Sign in / Sign up

Export Citation Format

Share Document