scholarly journals Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects onEscherichia coligene expression

2016 ◽  
Author(s):  
Andrea González-González ◽  
Shaun M. Hug ◽  
Alejandra Rodríguez-Verdugo ◽  
Jagdish Suresh Patel ◽  
Brandon S. Gaut
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Large Scale ◽  
Relative Fitness ◽  
Detectable Effect ◽  
Gene Encoding ◽  
Transcriptional Terminator ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Transcriptional Termination

ABSTRACTModifications to transcriptional regulators play a major role in adaptation. Here we compared the effects of multiple beneficial mutations within and betweenEscherichia coli rpoB, the gene encoding the RNA polymerase β subunit, andrho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerousE. colievolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized two alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2°C. Among the eight mutations, tworhomutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of ∼20%. TherpoBmutations altered the expression of ∼1700 genes;rhomutations altered the expression of fewer genes, most of which were a subset of the genes altered byrpoB. Across our eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0°C state. Therhomutations do not enhance transcriptional termination in knownrho-terminated regions, but the genome-wide effects of mutations in both genes was to enhance termination. Although beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, they acted predominantly through parallel phenotypic effects on gene expression and transcriptional termination.

scholarly journals Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression

2017 ◽  
Vol 34 (11) ◽  
pp. 2839-2855 ◽  
Author(s):  
Andrea González-González ◽  
Shaun M. Hug ◽  
Alejandra Rodríguez-Verdugo ◽  
Jagdish Suresh Patel ◽  
Brandon S. Gaut
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Rna Polymerase ◽  
Transcriptional Terminator ◽  
Adaptive Mutations

Real-time monitoring of cotranscriptional riboswitch folding and switching

2019 ◽  
Author(s):  
Boyang Hua ◽  
Christopher P. Jones ◽  
Jaba Mitra ◽  
Peter J. Murray ◽  
Rebecca Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Real Time ◽  
Single Molecule ◽  
Rna Folding ◽  
Its Sequence ◽  
Transcriptional Terminator ◽  
Fate Control ◽  
New Methods ◽  
Nascent Chain

SummaryRiboswitches function through cotranscriptional conformation switching governed by cognate ligand concentration, RNA folding and transcription elongation kinetics. To investigate how these parameters influence riboswitch folding, we developed a novel vectorial folding assay (VF) in which the superhelicase Rep-X sequentially liberates the RNA strand from a heteroduplex in a 5’-to-3’ direction, mimicking the nascent chain emergence during transcription. The RNA polymerase (RNAP)-free VF recapitulates the kinetically controlled cotranscriptional folding of a ZTP riboswitch, whose activation is favored by slower transcription, strategic pausing, or a weakened transcriptional terminator. New methods to observe positions and local rates of individual helicases show an average Rep-X unwinding rate similar to bacterial RNAP elongation (~60 nt/s). Real-time single-molecule monitoring captured folding riboswitches in multiple states, including an intermediate responsible for delayed terminator formation. These methods allow observation of individual folding RNAs as they occupy distinct folding channels within the landscape that controls gene expression and showed that riboswitch fate control is encoded in its sequence and is readily interpreted by a directionally moving protein even in the absence of an RNA polymerase.

scholarly journals Empirical determinants of adaptive mutations in yeast experimental evolution

2015 ◽  
Author(s):  
Celia Payen ◽  
Anna B Sunshine ◽  
Giang T Ong ◽  
Jamie L Pogachar ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
High Throughput Sequencing ◽  
Fitness Landscape ◽  
Genome Structure ◽  
Mutation Spectrum ◽  
Relative Fitness ◽  
Yeast Genome ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
A Genome

High-throughput sequencing technologies have enabled expansion of the scope of genetic screens to identify mutations that underlie quantitative phenotypes, such as fitness improvements that occur during the course of experimental evolution. This new capability has allowed us to describe the relationship between fitness and genotype at a level never possible before, and ask deeper questions, such as how genome structure, available mutation spectrum, and other factors drive evolution. Here we combined functional genomics and experimental evolution to first map on a genome scale the distribution of potential beneficial mutations available as a first step to an evolving population and then compare these to the mutations actually observed in order to define the constraints acting upon evolution. We first constructed a single-step fitness landscape for the yeast genome by using barcoded gene deletion and overexpression collections, competitive growth in continuous culture, and barcode sequencing. By quantifying the relative fitness effects of thousands of single-gene amplifications or deletions simultaneously we revealed the presence of hundreds of accessible evolutionary paths. To determine the actual mutation spectrum used in evolution, we built a catalog of >1000 mutations selected during experimental evolution. By combining both datasets, we were able to ask how and why evolution is constrained. We identified adaptive mutations in laboratory evolved populations, derived mutational signatures in a variety of conditions and ploidy states, and determined that half of the mutations accumulated positively affect cellular fitness. We also uncovered hundreds of potential beneficial mutations never observed in the mutational spectrum derived from the experimental evolution catalog and found that those adaptive mutations become accessible in the absence of the dominant adaptive solution. This comprehensive functional screen explored the set of potential adaptive mutations on one genetic background, and allows us for the first time at this scale to compare the mutational path with the actual, spontaneously derived spectrum of mutations.

scholarly journals G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story

2021 ◽  
Vol 22 (14) ◽  
pp. 7381
Author(s):  
Adriana Volná ◽  
Martin Bartas ◽  
Václav Karlický ◽  
Jakub Nezval ◽  
Kristýna Kundrátová ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gene Expression Regulation ◽  
Uv Light ◽  
Large Subunit ◽  
Expression Regulation ◽  
Gene Encoding ◽  
Additional Layer ◽  
G Quadruplex

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.

scholarly journals Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli

2020 ◽  
Vol 12 (11) ◽  
pp. 2029-2044
Author(s):  
Tiffany N Batarseh ◽  
Shaun M Hug ◽  
Sarah N Batarseh ◽  
Brandon S Gaut
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Expression Patterns ◽  
Temperature Adaptation ◽  
Relative Fitness ◽  
Lethal Temperature ◽  
Adaptive Mutations ◽  
E Coli ◽  
Unstressed State ◽  
Evolutionary Rescue

Abstract Evolutionary rescue occurs when adaptation restores population growth against a lethal stressor. Here, we studied evolutionary rescue by conducting experiments with Escherichia coli at the lethal temperature of 43.0 °C, to determine the adaptive mutations that drive rescue and to investigate their effects on fitness and gene expression. From hundreds of populations, we observed that ∼9% were rescued by genetic adaptations. We sequenced 26 populations and identified 29 distinct mutations. Of these populations, 21 had a mutation in the hslVU or rpoBC operon, suggesting that mutations in either operon could drive rescue. We isolated seven strains of E. coli carrying a putative rescue mutation in either the hslVU or rpoBC operon to investigate the mutations’ effects. The single rescue mutations increased E. coli’s relative fitness by an average of 24% at 42.2 °C, but they decreased fitness by 3% at 37.0 °C, illustrating that antagonistic pleiotropy likely affected the establishment of rescue in our system. Gene expression analysis revealed only 40 genes were upregulated across all seven mutations, and these were enriched for functions in translational and flagellar production. As with previous experiments with high temperature adaptation, the rescue mutations tended to restore gene expression toward the unstressed state, but they also caused a higher proportion of novel gene expression patterns. Overall, we find that rescue is infrequent, that it is facilitated by a limited number of mutational targets, and that rescue mutations may have qualitatively different effects than mutations that arise from evolution to nonlethal stressors.

scholarly journals The bacterial enhancer-dependent RNA polymerase

2016 ◽  
Vol 473 (21) ◽  
pp. 3741-3753 ◽  
Author(s):  
Nan Zhang ◽  
Vidya C. Darbari ◽  
Robert Glyde ◽  
Xiaodong Zhang ◽  
Martin Buck
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Self Assembly ◽  
Transcription Initiation ◽  
Large Scale ◽  
Bacterial Cells ◽  
Transcription Control ◽  
Amino Terminal ◽  
Promoter Dna ◽  
Regulated Gene Expression

Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes. The remodelling of sigma54 occurs through an ATP-binding and hydrolysis reaction carried out by the bEBPs. The regulation of bEBP self-assembly into typically homomeric hexamers allows regulated gene expression since the self-assembly is required for bEBP ATPase activity and its direct engagement with the sigma54 factor during the remodelling reaction. Crystallographic studies have now established that in the closed promoter complex, the sigma54 factor occupies the bacterial RNA polymerase in ways that will physically impede promoter DNA opening and the loading of melted out promoter DNA into the DNA-binding clefts of the RNA polymerase. Large-scale structural re-organizations of sigma54 require contact of the bEBP with an amino-terminal glutamine and leucine-rich sequence of sigma54, and lead to domain movements within the core RNA polymerase necessary for making open promoter complexes and synthesizing the nascent RNA transcript.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

Molecular Epidemiology and Biomarkers in Etiologic Cancer Research: The New in Light of the Old

2020 ◽  
Author(s):  
Lungwani Muungo
Keyword(s):  
Gene Expression ◽  
Cancer Research ◽  
Molecular Epidemiology ◽  
Exposure Assessment ◽  
Large Scale ◽  
First Generation ◽  
Cancer Epidemiology ◽  
Policy Changes ◽  
The Past ◽  
New Generation

The purpose of this review is to evaluate progress inmolecular epidemiology over the past 24 years in canceretiology and prevention to draw lessons for futureresearch incorporating the new generation of biomarkers.Molecular epidemiology was introduced inthe study of cancer in the early 1980s, with theexpectation that it would help overcome some majorlimitations of epidemiology and facilitate cancerprevention. The expectation was that biomarkerswould improve exposure assessment, document earlychanges preceding disease, and identify subgroupsin the population with greater susceptibility to cancer,thereby increasing the ability of epidemiologic studiesto identify causes and elucidate mechanisms incarcinogenesis. The first generation of biomarkers hasindeed contributed to our understanding of riskandsusceptibility related largely to genotoxic carcinogens.Consequently, interventions and policy changes havebeen mounted to reduce riskfrom several importantenvironmental carcinogens. Several new and promisingbiomarkers are now becoming available for epidemiologicstudies, thanks to the development of highthroughputtechnologies and theoretical advances inbiology. These include toxicogenomics, alterations ingene methylation and gene expression, proteomics, andmetabonomics, which allow large-scale studies, includingdiscovery-oriented as well as hypothesis-testinginvestigations. However, most of these newer biomarkershave not been adequately validated, and theirrole in the causal paradigm is not clear. There is a needfor their systematic validation using principles andcriteria established over the past several decades inmolecular cancer epidemiology.

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