Rnas gene expression regulation bacterial. Medical search. Frequent questions

The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. (wikipedia.org)
If the RNA world existed, it was probably followed by an age characterized by the evolution of ribonucleoproteins (RNP world), which in turn ushered in the era of DNA and longer proteins. (wikipedia.org)
Regulation of gene expression by proteins and small RNAs. (otago.ac.nz)
Once thought to be just a messenger that allows genetic information encoded in DNA to direct the formation of proteins, RNA (ribonucleic acid) is now known to be a highly versatile molecule that has multiple roles in cells. (cshlpress.com)
understand the theoretical basis for laboratory work (cloning, recombinant expression of proteins, protein purification, etc. (tum.de)
These thermosensors are part of a regulatory network, such as the production of heat shock proteins mediated by sigma factor 32 (RpoH) in Escherichia coli or the transcriptional repressor of heat-shock genes HrcA in Bacillus subtilis (Hecker et al. (springer.com)
The locus of enterocyte effacement (LEE) in EHEC encodes a type three secretion system and effector proteins, all of which are essential for bacterial adherence to host cells. (nih.gov)
Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. (biomedcentral.com)
In this review, we summarize the current knowledge on the regulation and function of P. aeruginosa sRNAs that titrate regulatory proteins, base-pair with target mRNAs, and which are derived from CRISPR elements. (nih.gov)
Degradations of proteins to amino acids and regulation. (unizg.hr)
Three of the six up-regulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, ZnuC1) suggesting involvement of s479 in regulation of zinc transport. (uni-stuttgart.de)
Interestingly, s479 is not only encoded next to CRISPR-cas genes but the mature s479 contains a crRNA-like 5´ handle and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. (uni-stuttgart.de)
Numerous fundamental cellular processes, including virtually every aspect of gene expression and regulation, depend on the cooperation of RNAs and proteins. (fu-berlin.de)
Specific RNAs and proteins associate to build up some of the most complex macromolecular machineries of living cells, such as ribosomes and spliceosomes, which mediate particular steps of gene expression. (fu-berlin.de)
RNAs and proteins can also engage in more transient interactions, for example during co-transcriptional regulation of RNA polymerases or during post-transcriptional regulation of (pre-)mRNA life cycles. (fu-berlin.de)
We investigate the molecular mechanisms, by which RNAs and proteins cooperate to bring about the biological functions of selected RNPs involved in transcription and pre-mRNA splicing. (fu-berlin.de)
I enjoyed working with yeast RNA mechanisms and the involved proteins, but I was also very happy to collaborate with groups working on other organisms and mechanisms, such as bacterial mechanisms of virulence. (cosminribo.eu)
In eukaryotic cells, chromatin comprises a complex consisting of DNA, RNA, and proteins where covalent modifications correlate with regulation of gene expression [ 1 ]. (biomedcentral.com)
He also showed that double-stranded (ds)RNA- and ZDNA binding proteins had a role in poxvirus pathogenesis. (cdc.gov)
Below is a non-exhaustive list of in-house infrastructures that are categorized into three overarching themes: bio-imaging, proteins, genes & cells and other resources. (lu.se)

We address this idea by measuring the fitness effect of a collection of rifampicin resistance mutations in the β subunit of RNA polymerase (rpoB) across eight strains that span the diversity of the genus Pseudomonas We find that almost 50% of rpoB mutations have background-dependent fitness costs, demonstrating that epistatic interactions between rpoB and the rest of the genome are common. (ox.ac.uk)
Indeed, bacterial genomes carry, on average, from 78% (for genomes containing the polymerase PolC) to 58% (for the other genomes) of their genes on the leading strand [ 3 ]. (biomedcentral.com)
The most generally accepted hypothesis is that co-directional collisions on the leading strand have a weaker effect on RNA polymerase processivity than the head-on collisions occurring on the lagging strand. (biomedcentral.com)
RNA-based processive anti-termination is exemplified by the polymerase utilization ( put ) signal of phage HK022. (fu-berlin.de)
region on a DNA molecule involved in RNA polymerase binding to initiate transcription. (insdc.org)
The RpoS/σS sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. (hal.science)

Ribosomes are the large macromolecular complexes responsible for translating genetic information contained within a messenger RNA (mRNA) into protein in all living organisms. (u-bordeaux.fr)
Our analysis showed that mRNA abundances, gene organization (operon) and gene essentiality are correlated in Buchnera (i.e., the most expressed genes are essential genes organized in operons) whereas no link between mRNA abundances and gene strand bias was found. (biomedcentral.com)
Microbiological, quantitative gene expression, mRNA half-life and genome data for 11 strains of S. aureus combined with bioinformatic analyses were used to identify correlates of increased MDR EP gene expression. (manchester.ac.uk)
On the other hand, mRNA is expressed in similar levels of the carbon supply useful for bacterial development regardless. (bassresearch.com)
For example, in mRNA by base pairing with the transcript through partial complementarity and the aid of the RNA chaperone Hfq (50). (bassresearch.com)
2022. Synergistic regulation of transcription and translation in Escherichia coli revealed by co-directional increases in mRNA concentration and translation efficiency. (toulouse-biotechnology-institute.fr)
Etienne T., Cocaign-Bousquet M. , Ropers D. (2020) Competitive effects in bacterial mRNA decay. (toulouse-biotechnology-institute.fr)
An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)
In a cell, antisense DNA serves as the template for producing messenger RNA (mRNA), which directs the synthesis of a protein. (genome.gov)

MICR 335 will provide a fundamental knowledge of the mechanisms that bacteria use to sense their environment and adapt their gene expression to optimise their growth and survival. (otago.ac.nz)
Consequently, bacteria have developed different systems to sense changes in environmental conditions such as temperature and induce an adaptation of metabolism and gene expression. (springer.com)
Many different principles of thermoregulation have been identified in bacteria, which can be assigned to the class of protein-, DNA- or RNA-thermosensors. (springer.com)
In 1964, Yanofsky and colleagues established that gene sequences and protein sequences are colinear in bacteria. (pharmaceuticalintelligence.com)
Genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. (biomedcentral.com)
Moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. (biomedcentral.com)
This is a perfect illustration of the mutual influence between gene expression levels and chromosomal organization in bacteria. (biomedcentral.com)
Bacteria transcribe their genomes with the help of multi-subunit RNA polymerases (RNAPs), which comprise two large β and β' subunits that form the active site, two regulatory α subunits and an ω subunit that supports RNAP assembly. (fu-berlin.de)
We study the functional interplay of pausing, termination and continued transcription, which constitutes a pervasive gene regulatory principle in bacteria. (fu-berlin.de)
The meeting will cover a broad range of topics related to the mechanism and regulation of transcription in bacteria. (plos.org)
Transcription in all cells is performed by members of a family of multi-subunit RNA polymerases (RNAP) that are highly conserved from bacteria to humans. (plos.org)
Together these studies have revealed the fundamental principles that underlie transcription and its regulation among bacteria, archaea, and eukaryotes. (plos.org)
Small regulatory RNAs (sRNAs) are often employed in bacterial mechanisms of stress adaptation, and there are precedents in and related bacteria for regulation by sRNAs of the expression of genes involved in carbon metabolism (11, 26, 29, 43, 50). (bassresearch.com)
Marraffini, L. A. & Sontheimer, E. J. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. (nature.com)
I am interested in the study of Bacterial Physiology and Metabolism to better understand mechanisms of adaptation of bacteria to their environment and to engineer bacteria for applications in biotechnology. (toulouse-biotechnology-institute.fr)
My major area of study is RNA dynamics in bacteria to better understand genome-wide post-transcriptional regulations, their role in the regulation of gene expression and their potential for engineering bacteria. (toulouse-biotechnology-institute.fr)
More recently, I have also initiated studies on bacterial diversity and heterogeneity, working on various bacteria strains alone, in consortia or in interaction with non-equivalent monoclonal subpopulations. (toulouse-biotechnology-institute.fr)
My research concerns predominantly two model bacteria, Lactococcus lactis and Escherichia coli , using a systems biology approach to elucidate the different levels of metabolic regulation and notably genome wide omic regulations. (toulouse-biotechnology-institute.fr)
The RNeasy Protect Mini Kit and Bacteria Mini Kit include RNeasy spin columns for purifying up to 100 µg of high-quality RNA using silica-membrane technology. (qiagen.com)
It induces both local effects in the gut, as well as alterations in distant organs through stimuli generated by bacteria, structural bacterial components, and microbial metabolites [ 7 ]. (biomedcentral.com)
Here, we used RNA-seq on the sea anemone Exaiptasia pallida (Ep) strain CC7 as a model to depict the innate immune response during the onset of infection with the marine pathogenic bacteria Vibrio parahaemolyticus (Vp) clinical strain O3:K6, and lipopolysaccharides (LPS) exposure. (c3m-nice.fr)

One of the challenges in studying abiogenesis is that the system of reproduction and metabolism utilized by all extant life involves three distinct types of interdependent macromolecules (DNA, RNA, and protein). (wikipedia.org)
Some bacterial pathogens have been shown to substantially modify their surface components in response to the host immune system and modify their energy metabolism and transport pathways to allow efficient growth within the host. (cdc.gov)
Proteome comparison of wild type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. (uni-stuttgart.de)
Extensive regulation by σS of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σS effects on gene transcription that might confer fitness advantages to bacterial cells and/or populations under starving conditions. (hal.science)
While budding yeast has been my "workhorse" until now, other fungal species, such as Cryptococcus neoformans , a major fungal pathogen , are particularly interesting for RNA metabolism. (cosminribo.eu)

With maximum values of 0.23 g/(g h) at 37 °C, this constitutes a more than 60% increase compared to the production rate of 0.14 g/(g h) at the growth optimum of 30 °C. Interestingly however, control experiments unveiled that besides the regulatory effect of the RNA-thermometer, multiple metabolic effects may contribute equally to the observed increase in production rate. (springer.com)
We report here that a small regulatory RNA (sRNA), Esr41, mediates LEE repression and flagellar gene activation. (nih.gov)
There are two major, distinct forms of regulatory small RNAs involved in eukaryotic gene silencing: small interfering (si) RNAs and micro (mi) RNAs. (biomedcentral.com)
The additional information generated by whole genome studies goes far beyond that derived by characterizing in isolation more genes and gene products, because analysis of the whole genome allows complete regulatory networks to be identified and characterized. (cdc.gov)
Adaptive responses to various environmental stresses and stimuli are often regulated by small regulatory RNAs (sRNA). (nih.gov)
His subsequent experiments on the regulation of gene expression led to the discovery of transcriptional attenuation, a process that enables the gene regulatory machinery to fine-tune its response to subtle environmental cues. (pharmaceuticalintelligence.com)
That work also revealed how alterations in RNA structure allow RNA to serve as a regulatory molecule in both bacterial and animal cells. (pharmaceuticalintelligence.com)
While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. (uni-stuttgart.de)
article{marchfelder2021small, abstract = {The function and mode of action of small regulatory RNAs is currently still understudied in archaea. (uni-stuttgart.de)
Regulatory mechanisms for chromosomal genes encoding multidrug resistance (MDR) efflux pumps (EPs) in Staphylococcus aureus are poorly defined. (manchester.ac.uk)
Pausing and termination can be further modulated by elongation factors, such as N-utilization substances A and G. Some regulatory factors or RNAs can stably insulate RNAP from the destabilizing effects of terminators over long distances (processive anti-termination). (fu-berlin.de)
In these processes, transcript-borne regulatory RNAs alone or in conjunction with protein factors assemble on the surface of RNAP and accompany the enzyme during further transcription by an RNA looping mechanism, rendering the elongation complex resistant to pause and/or termination signals downstream of the original modification site. (fu-berlin.de)
In recent years, research on microbial transcription has expanded rapidly due to new atomic-level structures of prokaryotic, archaeal, and eukaryotic RNA polymerases and their respective transcription factors in combination with systems-wide profiling of gene regulatory events. (plos.org)
a transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. (insdc.org)
a regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. (insdc.org)
Associated regulatory elements may include differentially methylated regions and non-coding RNAs. (insdc.org)
Importantly, the σS-controlled downstream network includes small RNAs that might endow σS with post-transcriptional regulatory functions. (hal.science)

The asymmetry of the distribution of the genes between the two strands of DNA is explained as being a means of minimizing interruptions in gene transcription due to collisions between the DNA and RNA polymerases. (biomedcentral.com)
Eukaryotic transcription three types of RNA polymerases. (unizg.hr)

Lecture: developing chemical fundaments of genetics (DNA, RNA), bacterial genetics, gene expression and regulation, pecularities of eukaryotic organisms. (tum.de)
Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. (biomedcentral.com)
Eukaryotic regulation transcriptional activation and repression. (unizg.hr)
Many eukaryotic precursor messenger RNAs (pre-mRNAs) bear coding regions (exons) interspersed with non-coding intervening sequences (introns). (fu-berlin.de)
The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression. (biomedcentral.com)

It can function as an enzyme, scaffold various subcellular structures, and regulate gene expression through a variety of mechanisms, as well as act as a key component of the protein synthesis and splicing machinery. (cshlpress.com)
Further detailed analyses of these responses will increase understanding of the molecular mechanisms of pathogenesis, identify new bacterial virulence factors, and aid in the design of new vaccines. (cdc.gov)
Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? (nature.com)
Meister, G. & Tuschl, T. Mechanisms of gene silencing by double-stranded RNA. (nature.com)
This study also provides a firm basis for future studies to address molecular mechanisms of indirect regulation of gene expression by σS. (hal.science)
I am a scientist working at the Pasteur Institute and interested in the molecular mechanisms that shape gene expression. (cosminribo.eu)
Schematics of the interactions that place Upf1, an RNA helicase, at the center of NMD mechanisms and interactions. (cosminribo.eu)
None of my achievements could have been done without the work of collaborators, especially Laurence Decourty, an amazing colleague with which we worked together on RNA mechanisms in the last 15 years. (cosminribo.eu)
Streptococcal pathogens continue to evade concerted efforts to decipher clear-cut virulence mechanisms, although numerous genes have been implicated in pathogenesis. (cdc.gov)

Translational gene-reporter fusion experiments revealed that Esr41 regulates ler expression at a post-transcriptional level, and pch transcription, probably via an unknown target of Esr41. (nih.gov)
To address this, we utilized RNA-Seq to reveal the transcriptional landscape of S. suis in response to H2O2 stress. (bvsalud.org)
Using the bioinformatics tool MAGICTRICKS and reversible pharmacological inhibition, we found that primed genes required the transcriptional activities of NF-κB. (frontiersin.org)
Microbiological and gene expression data correlated in four instances, existing knowledge of the substrate specificity of NorC resulted in correlation in two others, and a transcriptional/translational disconnect is possible for the remaining two. (manchester.ac.uk)
We also study selected RNP-remodeling enzymes as drivers of molecular RNP machineries and as mediators of co- and post-transcriptional gene regulation. (fu-berlin.de)
Furthermore, the study of bacterial RNAP continues to illuminate key paradigms relevant to transcriptional control in all organisms. (plos.org)
Transcriptional regulation of aquaporins in accessions of Arabidopsis in response to drought stress. (lu.se)

Like DNA, RNA can store and replicate genetic information. (wikipedia.org)
Further concept of RNA as a primordial molecule can be found in papers by Francis Crick and Leslie Orgel, as well as in Carl Woese's 1967 book The Genetic Code. (wikipedia.org)
and his early discovery of colinearity, the linear relationship between the structures of genes and their protein products, considered an essential element in revealing the details of the genetic code. (pharmaceuticalintelligence.com)
18.DNA, RNA and the flow of genetic information. (unizg.hr)
A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)
Exploding the gene myth : how genetic information is produced and manipulated by scientists, physicians, employers, insurance companies, educators, and law enforcers / Ruth Hubbard and Elijah Wald. (who.int)

In addition, Esr41 activated the expression of flagellar Class 3 genes by indirectly inducing the transcription of fliA, which encodes the sigma factor for flagellar synthesis. (nih.gov)
Gene organization in the bacterial chromosome has very well known effects on transcription and a standard example is the organization of genes into operons, which allows for a sophisticated regulation of gene expression [ 9 ]. (biomedcentral.com)
20.Transcription and RNA processing. (unizg.hr)
Bacterial transcription, postranscriptional modifications. (unizg.hr)
The α 2 ββ'ω core enzyme cooperates with transcription factors and responds to signals on DNA templates and nascent RNAs to achieve full functionality in vivo . (fu-berlin.de)
RNA synthesis is terminated intrinsically, when the elongation complex transcribes a stable RNA hairpin followed by a uridine-rich stretch, or with the aid of transcription termination factor ρ. (fu-berlin.de)
Huang YH, Said N, Loll B, Wahl MC (2019) Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis. (fu-berlin.de)
Therefore, bacterial RNAP is the model system of choice for detailed structural and mechanistic studies of transcription. (plos.org)
dsRNA is produced either by RNA viruses during replication or by DNA viruses upon convergent transcription. (cnrs.fr)
2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription. (insdc.org)

RNA codons and protein synthesis. (crossref.org)
Interestingly, the 2-MIB synthesis gene was consistently expressed, regardless of the water temperature. (mdpi.com)
There, he chose to tackle what was, at the time, a little-known form of translational control: the regulation of ribosomal protein synthesis by the nascent polypeptide. (u-bordeaux.fr)
Breakdown and synthesis, regulation. (unizg.hr)
RNP-based processive anti-termination underlies the switching from immediate-early to delayed-early gene expression in other lambdoid phages as well as ribosomal RNA synthesis in Escherichia coli . (fu-berlin.de)
Both folic acid and vitamin B-12 participate in the synthesis of DNA and RNA. (medscape.com)

One version of the hypothesis is that a different type of nucleic acid, termed pre-RNA, was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. (wikipedia.org)
Subsequent chapters examine riboswitches and ribozymes, establishing what the RNA molecule is capable of alone. (cshlpress.com)

The book is thus essential reading for all molecular biologists and biochemists, as well as chemists interested in RNA technology, information storage, or enzyme catalysis. (cshlpress.com)
Enzyme kinetics including its regulation and inhibition, Vitamins and Coenzymes. (entrance-exam.net)
In the early 2010s, scientists realized that CRISPR/Cas9, a bacterial immune defense system against viruses that involves the CRISPR-associated protein #9 (Cas9) endonuclease enzyme, single-guide RNAs (sgRNAs), and PAM recognition, could be used to intentionally manipulate genes, essentially changing gene expression and regulation in such a way that would allow for a customized genome. (authorea.com)

Central to this investigation is an understanding of what gene products are required and expressed during a natural infection and how this expression changes over time (from initial colonization to causation of disease and spread of the pathogen to new hosts) and space (in different cells or tissues within the host). (cdc.gov)
We thus endeavor to understand how the pathogen adapts to the host microenvironment, what selective pressures are acting on the pathogen in each microenvironment, what bacterial factors are responsible for the host damage, and how the immune system is evaded. (cdc.gov)
The correlations proposed provide a guide for further experimentation leading to a better understanding of MDR EP gene expression in this important pathogen. (manchester.ac.uk)
Here, differential RNA sequencing of the human pathogen Streptococcus pyogenes uncovered tracrRNA, a trans -encoded small RNA with 24-nucleotide complementarity to the repeat regions of crRNA precursor transcripts. (nature.com)

Two of these methods, signature-tagged mutagenesis and in vivo expression technology, do not directly measure gene expression and do not allow true genomic-scale analysis, but they have been devised to identify genes necessary for pathogens during real infections. (cdc.gov)
Using an oligonucleotide-based microarray, we normalized the transcriptomic data by genomic DNA signals in order to have access to inter-gene comparison data. (biomedcentral.com)
Past genomic studies have comprehensively described the organization of the bacterial chromosome, for example in terms of gene localization, order and orientation. (biomedcentral.com)
A) Genomic firm of genes encoding the mannitol-specific PTS elements as well as the MtlS sRNA (shaded arrow). (bassresearch.com)
I initiated collaborations with mathematicians to rationalise the use of large-scale genomic data-sets to investigate bacterial physiology. (toulouse-biotechnology-institute.fr)

In this review, I will look at how the CRISPR/Cas9 gene-editing system can be applied in humans to prevent, cure, or treat these diseases, as well as what needs to be done before the CRISPR/Cas9 system can be made publicly available as a medical treatment for diseases. (authorea.com)

This bias is even more important when the essentiality of genes is taken into account, and essential genes distribution bias reaches 76% and 94% in Escherichia coli and Bacillus subtilis respectively [ 4 ]. (biomedcentral.com)

The developing complementary technologies of DNA microarrays and proteomics are allowing the response of bacterial pathogens to different environments to be probed at the whole genome level. (cdc.gov)
Although analyses that give information on the expression of a few genes provide insight and have been responsible for a large proportion of the bacterial pathogenesis literature currently available, our ultimate goal is to understand expression changes across the whole genome. (cdc.gov)
A second group of methods, which includes DNA microarrays and proteomics, have advantages that overcome the limitations implicit in signature-tagged mutagenesis and in vivo expression technology, namely, the ability to directly measure expression (gene or protein) levels on a true genome-wide scale, but their application to analysis of bacterial pathogens during real infections is still in its infancy. (cdc.gov)
The virus has a circular genome of 3,912 nucleotides, three major putative open reading frames, and encodes a Rep gene of 310 amino acids. (bvsalud.org)
The effect of Buchnera genome evolution on gene expression levels has also been analysed in order to assess the constraints imposed by the obligate symbiosis with aphids, underlining the importance of some gene sets for the survival of the two partners. (biomedcentral.com)
Genome size and gene content. (unizg.hr)
In this study, we employed a genome-wide CRISPR-Cas9 loss-of-function screen based on cell survival in order to identify genes implicated in the host response to dsRNA. (cnrs.fr)
Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing, and apoptosis induction in human cells. (cnrs.fr)
Malone, C. D. & Hannon, G. J. Small RNAs as guardians of the genome. (nature.com)
In participating UK research institutions, investigators can publish open access in Genome Research, Genes & Development, RNA, and Learning & Memory without article publication charges and all staff can read the entire renowned Cold Spring Harbor journal collection. (cshlpress.com)
Adenovirus DNA : the viral genome and its expression / edited by Walter Doerfler. (who.int)

Operons regulation by repressor. (unizg.hr)

Here, we show that the putative RNA-binding protein NasT is a positive regulator essential for expression of the nas gene cluster (i.e. nasABGHC). (ox.ac.uk)
We used massively parallel cDNA sequencing (RNA-Seq) to quantitatively identify the transcriptome of V. cholerae grown in the presence and absence of sub-lethal concentrations of the antimicrobial peptide polymyxin B. We evaluated the transcriptome of both wild type V. cholerae and a mutant carrying a deletion of vc1639, a putative sensor kinase of an uncharacterized two-component system, under these conditions. (broadinstitute.org)
Seven putative mycobacterial MTase genes ( Rv0645c , Rv2966c , Rv1988 , Rv1694 , Rv3919c , Rv2756c , and Rv3263 ) and Rv1392 as SAM synthase were selected for analysis. (ac.ir)

Also covered are viral RNAs, telomerase RNA, and tools for scientists who work on RNA. (cshlpress.com)
Double-stranded RNA (dsRNA) is the hallmark of many viral infections. (cnrs.fr)
Aliyari, R. & Ding, S. W. RNA-based viral immunity initiated by the Dicer family of host immune receptors. (nature.com)

One of the most critical components of cells, the ribosome, is composed primarily of RNA. (wikipedia.org)

Simulation of Folding Kinetics for Aligned RNAs. (uni-stuttgart.de)
Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection. (c3m-nice.fr)
Pairwise and time series analyses identified the genes responsive to infection as well as the kinetics of innate immune genes over time. (c3m-nice.fr)

The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)
Autosomal" means that the gene in question is located on one of the numbered, or non-sex, chromosomes. (genome.gov)

The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. (biomedcentral.com)
Antibiotic resistance often evolves by mutations at conserved sites in essential genes, resulting in parallel molecular evolution between divergent bacterial strains and species. (ox.ac.uk)
The presence of qacA/B and/or increased expression of one to two MDR EP genes were identified in eight strains. (manchester.ac.uk)
PCR-sequencing and qRT-PCR were performed to compare mutations and expression levels of MTases in different strains. (ac.ir)
We found a correlation between mycobacterial MTases expression and resistance to antibiotics in M.tb strains. (ac.ir)

When LEE expression is activated, flagellar gene expression is down-regulated because bacterial flagella induce the immune responses of host cells at the infection stage. (nih.gov)
Therefore, this inverse regulation is also important for EHEC infection. (nih.gov)
Although oxidative stress is common occurrence during bacterial growth and infection, the regulation networks of S. suis under oxidative stress remain poorly understood. (bvsalud.org)

We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to analyze primed microglial inflammatory gene expression and modifications to histone H3 lysine 4 trimethylation (H3K4me3) at the promoters of primed genes. (frontiersin.org)
Here, we profile the gut microbiome and chromatin characteristics in colon epithelium from mice fed either an obesogenic or control diet, followed by an analysis of the resultant changes in gene expression. (biomedcentral.com)

siRNAs are produced from double-stranded RNAs of viruses and transposable elements, which are processed by the dicer nuclease, one of the essential components of the RNA-Induced Silencing Complexes (RISCs) [ 7 - 9 ]. (biomedcentral.com)

Bacterial pathogens must be able to gain access to, persist in, and replicate in normally privileged sites within a host. (cdc.gov)
Because the environment encountered within a living host will be quite different from the external environment, pathogens must be able to regulate the necessary genes in coordination as they move from the environment to the host and from one host niche to another. (cdc.gov)
The primary aim of investigating bacterial pathogenesis is to understand the way that pathogens interact with the host to cause disease. (cdc.gov)
Thus, principles that emerge from studies of RNAP and its regulation in microbial systems permit development of strategies to control microbial pathogens. (plos.org)
however, little is known about immunity gene regulation in the host's early response against marine bacterial pathogens over time. (c3m-nice.fr)

Our study reveals a novel pathway of small guide RNA maturation and the first example of a host factor (RNase III) required for bacterial RNA-mediated immunity against invaders. (nature.com)
Both tracrRNA and pre-crRNA confer immunity against acquisition of a protospacer gene derived from a lysogenic phage. (nature.com)

All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)

Bacterial RNA maturation. (otago.ac.nz)
tracrRNA-mediated crRNA maturation is conserved among different bacterial species. (nature.com)

The discovery of the elaborate and versatile systems of RNA silencing in eukaryotes is one of the pivotal advances in biology of the last decade [ 1 - 6 ]. (biomedcentral.com)
Thus, arrest peptides are used for metabolite-dependent gene regulation in both prokaryotes and eukaryotes. (u-bordeaux.fr)

For example, elongating RNAP frequently enters an elemental paused state, and pausing can be stabilized by an RNA hairpin invading the RNA exit tunnel or by RNAP backtracking. (fu-berlin.de)
The bacterial RNAP is the smallest and best characterized member of the multi-subunit RNAP family. (plos.org)
In all cells the control of RNAP activity is a central node in the regulation of gene expression. (plos.org)
In addition, bacterial RNAP is a proven target for antimicrobial therapy. (plos.org)

article{Schafer:2021, abstract = {RNA-RNA inter- and intramolecular interactions are fundamental for numerous biological processes. (uni-stuttgart.de)

Strategies of immune regulation / edited by Eli Sercarz, Alastair J. Cunningham. (who.int)
These products have several anti-inflammatory properties of any/multiple islet autoantibodies (242 and 151 events, respec- such as regulation of immune-related gene expression and cy- tively) and T1D (71 events) by soluble fiber intake were calculated tokine release (8). (lu.se)

Esr41-mediated ler and pch repression was not observed in cells lacking hfq, which encodes an RNA-binding protein essential for most sRNA functions, indicating that Esr41 acts in an Hfq-dependent manner. (nih.gov)
The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. (uni-stuttgart.de)
Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. (uni-stuttgart.de)

Jinek, M. & Doudna, J. A. A three-dimensional view of the molecular machinery of RNA interference. (nature.com)

Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA-RNA interactions. (uni-stuttgart.de)
Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA-RNA interactions that are useful for filtering and statistical assessment. (uni-stuttgart.de)
Here we present RNAnue, a general pipeline for the inference of RNA-RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. (uni-stuttgart.de)

The book goes on to discuss the evolution of ribosomes and the functions of RNPs, before reviewing the recent work that has revolutionized our understanding of gene regulation by non-coding RNAs, including miRNAs and siRNAs. (cshlpress.com)
It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. (biomedcentral.com)

Even so, the evidence for an RNA world is strong enough that the hypothesis has gained wide acceptance. (wikipedia.org)
The concurrent formation of all four RNA building blocks further strengthened the hypothesis. (wikipedia.org)
The phrase "RNA World" was first used by Nobel laureate Walter Gilbert in 1986, in a commentary on how recent observations of the catalytic properties of various forms of RNA fit with this hypothesis. (wikipedia.org)
The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its general acceptance as an explanation for the origin of life requires further evidence. (wikipedia.org)
However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis. (biomedcentral.com)
The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. (biomedcentral.com)
We, therefore, tested the hypothesis that hypoxia would enhance or "prime" microglial pro-inflammatory gene expression in response to a later inflammatory challenge without programmatically increasing basal levels of pro-inflammatory cytokine expression. (frontiersin.org)

Given the important roles of the gut microbiome in regulating host physiology and gene expression, a better understanding of the relationship between the host and the symbiont microbiota should provide new insights into human health and disease risk. (biomedcentral.com)

We have successfully deleted the DiGeorge syndrome critical region gene 8 (dgcr8) in zebrafish germ line and demonstrated that the maternal-zygotic dgcr8 (MZdgcr8) embryos exhibit MZdicer-like phenotypes with morphological defects which could be rescued by miR-430, indicating that canonical microRNAs play critical role in early development. (zfin.org)
Our findings establish that Cre/loxP-mediated tissue-specific gene knockout could be achieved using this BACK strategy and that canonical microRNAs play important roles in early embryonic development in zebrafish. (zfin.org)

Among those molecular cues, double-stranded RNA (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. (cnrs.fr)

Diet-induced obesity led to altered acetylation of lysine 27 on histone H3 (H3K27ac) and to altered monomethylation of lysine 4 on histone H3 (H3K4me1) at numerous loci, with concomitant changes in the expression of genes that were functionally relevant to intestinal cancers. (biomedcentral.com)

Only two mutations were found in isoniazid resistance (INH R ) strain for Rv3919c (T to G in codon 341) and Rv1392 (G to A in codon 97) genes. (ac.ir)

2018-2023-ANR-18-CE43-0010, RIBECO, RNA life cycle engineering for an economic approach to microbial energetics: application to the bioconversion of biomass-derived carbon sources. (toulouse-biotechnology-institute.fr)

Since then, CRISPR technology has revolutionized medical research and the biotechnology industry, and its newfound capabilities have scientists asking if CRISPR can be used to modify genes in such a way that would cure or treat certain harmful or life-threatening diseases. (authorea.com)
A small RNA is linking CRISPR-Cas and zinc transport. (uni-stuttgart.de)

These results suggest that Esr41 plays important roles in the inverse regulation of LEE and flagellar gene expression. (nih.gov)

small RNA. (nih.gov)
We selected a small RNA (s479) from H. volcanii for detailed characterization. (uni-stuttgart.de)
Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella. (hal.science)
He identified periodic acid-Schiff (PAS)-staining granules, most likely representing degenerating bacterial forms, within macrophages isolated from the small bowel as well as other tissue and fluid specimens (eg, pericardium, endocardium, lymph nodes, synovia, lung, brain, meninges) obtained from patients in whom Whipple disease was suspected. (medscape.com)

We identified novel genes responsible for S. suis resistance to oxidative stress, including those involved in DNA repair or protection, and essential for the biosynthesis of amino acids and nucleic acids. (bvsalud.org)

Anatomy19

Organisms17

Diseases4

Chemicals and Drugs78

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes104

Disciplines and Occupations3

Information Science8

Health Care2

Proteins20

Polymerase6

MRNA9

Bacteria21

Metabolism5

Regulatory17

Polymerases2

Eukaryotic5

Mechanisms9

Transcriptional7

Genetic6

Transcription10

Synthesis6

Molecule2

Enzyme3

Pathogen4

Genomic5

Humans1

Escherichia1

Genome11

Operons1

Putative3

Viral3

Ribosome1

Kinetics3

Chromosomes2

Strains5

Infection3

Chromatin2

Transposable Elements1

Pathogens5

Immunity2

Genomes1

Maturation2

Eukaryotes2

RNAP4

Abstract1

Immune2

SRNA3

Interference1

Interactions3

SiRNAs2

Hypothesis7

Physiology1

MicroRNAs2

Double-stranded1

Loci1

Codon1

Microbial1

CRISPR2

Roles1

Small4

Oxidative stress1