Argonaute Proteins
Eukaryotic Initiation Factors
RNA-Induced Silencing Complex
RNA Interference
Ribonuclease III
MicroRNAs
RNA, Small Interfering
Alpha-Amanitin
Eukaryotic Initiation Factor-2
Gene Silencing
RNA-Binding Proteins
RNA, Guide
Drosophila Proteins
RNA Stability
Caenorhabditis elegans Proteins
Peptide Initiation Factors
RNA, Double-Stranded
Protein Structure, Tertiary
Caenorhabditis elegans
Drosophila melanogaster
RNA Processing, Post-Transcriptional
RNA, Messenger
Immunoprecipitation
Molecular Sequence Data
Drosophila
Protein Binding
Mutation
Base Sequence
RNA
Gene Expression Regulation
Amino Acid Sequence
RNA, Plant
RNA Cleavage
Binding Sites
RNA, Helminth
Stem cells: A tale of two kingdoms. (1/823)
Homologous genes have recently been shown to regulate stem cell maintenance in animals and plants. This discovery should facilitate elucidation of the poorly understood factors that control stem cell maintenance and differentiation. (+info)piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. (2/823)
piwi represents the first class of genes known to be required for stem cell self-renewal in diverse organisms. In the Drosophila ovary, piwi is required in somatic signaling cells to maintain germline stem cells. Here we show that piwi encodes a novel nucleoplasmic protein present in both somatic and germline cells, with the highly conserved C-terminal region essential for its function. Removing PIWI protein from single germline stem cells significantly decreases the rate of their division. This suggests that PIWI has a second role as a cell-autonomous promoter of germline stem cell division. Consistent with its dual function, over-expression of piwi in somatic cells causes an increase both in the number of germline stem cells and the rate of their division. Thus, PIWI is a key regulator of stem cell division - its somatic expression modulates the number of germline stem cells and the rate of their division, while its germline expression also contributes to promoting stem cell division in a cell-autonomous manner. (+info)AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. (3/823)
Introduction of transgene DNA may lead to specific degradation of RNAs that are homologous to the transgene transcribed sequence through phenomena named post-transcriptional gene silencing (PTGS) in plants, quelling in fungi, and RNA interference (RNAi) in animals. It was shown previously that PTGS, quelling, and RNAi require a set of related proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the isolation of Arabidopsis mutants impaired in PTGS which are affected at the Argonaute1 (AGO1) locus. AGO1 is similar to QDE-2 required for quelling and RDE-1 required for RNAi. Sequencing of ago1 mutants revealed one amino acid essential for PTGS that is also present in QDE-2 and RDE-1 in a highly conserved motif. Taken together, these results confirm the hypothesis that these processes derive from a common ancestral mechanism that controls expression of invading nucleic acid molecules at the post-transcriptional level. As opposed to rde-1 and qde-2 mutants, which are viable, ago1 mutants display several developmental abnormalities, including sterility. These results raise the possibility that PTGS, or at least some of its elements, could participate in the regulation of gene expression during development in plants. (+info)A global profile of germline gene expression in C. elegans. (4/823)
We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new components of embryonic signaling pathways. The germline-intrinsic group, defined as genes expressed similarly in germlines making only sperm or only oocytes, contains a family of piwi-related genes that may be important for stem cell proliferation. Finally, examination of the chromosomal location of germline transcripts revealed that sperm-enriched and germline-intrinsic genes are nearly absent from the X chromosome, but oocyte-enriched genes are not. (+info)Human CD34(+) stem cells express the hiwi gene, a human homologue of the Drosophila gene piwi. (5/823)
Hematopoietic stem cells (HSCs) are characterized by their dual abilities to undergo differentiation into multiple hematopoietic cell lineages or to undergo self-renewal. The molecular basis of these properties remains poorly understood. Recently the piwi gene was found in the embryonic germline stem cells (GSCs) of Drosophila melanogaster and has been shown to be important in GSC self-renewal. This study demonstrated that hiwi, a novel human homologue of piwi, is also present in human CD34(+) hematopoietic progenitor cells but not in more differentiated cell populations. Placing CD34(+) cells into culture conditions that supported differentiation and rapid exit from the stem cell compartment resulted in a loss of hiwi expression by day 5 of a 14-day culture period. Expression of the hiwi gene was detected in many developing fetal and adult tissues. By means of 5' RACE cloning methodology, a novel putative full-length hiwi complementary DNA was cloned from human CD34(+) marrow cells. At the amino acid level, the human HIWI protein was 52% homologous to the Drosophila protein. The transient expression of hiwi in the human leukemia cell line KG1 resulted in a dramatic reduction in cellular proliferation. Overexpression of hiwi led to programmed cell death of KG1 cells as demonstrated by the Annexin V assay system. These studies suggest that hiwi maybe an important negative developmental regulator, which, in part, underlies the unique biologic properties associated with hematopoietic stem and progenitor cells. (+info)Stem cells: so what's in a niche? (6/823)
Much effort is being invested in defining the intrinsic and extrinsic factors that control stem cell maintenance and proliferation. Recent studies have identified a signaling hierarchy involved in coordinating the proliferation of germ line and somatic stem cells in the Drosophila ovary. (+info)Yb modulates the divisions of both germline and somatic stem cells through piwi- and hh-mediated mechanisms in the Drosophila ovary. (7/823)
The coordinated division of distinctive types of stem cells within an organ is crucial for organogenesis and homeostasis. Here we show genetic interactions among fs(1)Yb (Yb), piwi, and hedgehog (hh) that regulate the division of both germline stem cells (GSCs) and somatic stem cells (SSCs), the two constituent stem cell populations of the Drosophila ovary. Yb is required for both GSC and SSC divisions; loss of Yb function eliminates GSCs and reduces SSC division, while Yb overexpression increases GSC number and causes SSC overproliferation. We also show that Yb acts via the piwi- and hh-mediated signaling pathways that emanate from the same signaling cells to control GSC and SSC division, respectively. hh signaling also has a minor effect in GSC division. (+info)Argonaute2, a link between genetic and biochemical analyses of RNAi. (8/823)
Double-stranded RNA induces potent and specific gene silencing through a process referred to as RNA interference (RNAi) or posttranscriptional gene silencing (PTGS). RNAi is mediated by RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys messenger RNAs homologous to the silencing trigger. RISC is known to contain short RNAs ( approximately 22 nucleotides) derived from the double-stranded RNA trigger, but the protein components of this activity are unknown. Here, we report the biochemical purification of the RNAi effector nuclease from cultured Drosophila cells. The active fraction contains a ribonucleoprotein complex of approximately 500 kilodaltons. Protein microsequencing reveals that one constituent of this complex is a member of the Argonaute family of proteins, which are essential for gene silencing in Caenorhabditis elegans, Neurospora, and Arabidopsis. This observation begins the process of forging links between genetic analysis of RNAi from diverse organisms and the biochemical model of RNAi that is emerging from Drosophila in vitro systems. (+info)Argonaute proteins are a family of conserved proteins that play a crucial role in the RNA interference (RNAi) pathway, which is a cellular process that regulates gene expression by post-transcriptional silencing of specific mRNAs. In this pathway, Argonaute proteins function as key components of the RNA-induced silencing complex (RISC), where they bind to small non-coding RNAs such as microRNAs (miRNAs) or small interfering RNAs (siRNAs).
The argonaute protein then uses this small RNA guide to recognize and cleave complementary mRNA targets, leading to their degradation or translational repression. Argonaute proteins contain several domains, including the PIWI domain, which possesses endonuclease activity responsible for the cleavage of target mRNAs.
In addition to their role in RNAi, argonaute proteins have also been implicated in other cellular processes, such as DNA damage repair and transposable element silencing. There are eight argonaute proteins in humans (AGO1-4 and AGO6-8), each with distinct functions and expression patterns. Dysregulation of argonaute proteins has been associated with various diseases, including cancer and neurological disorders.
Eukaryotic initiation factors (eIFs) are a group of proteins that play a crucial role in the process of protein synthesis, also known as translation, in eukaryotic cells. During the initiation phase of translation, these factors help to assemble the necessary components for the formation of the initiation complex on the small ribosomal subunit and facilitate the recruitment of messenger RNA (mRNA) and the transfer RNA carrying the initiator methionine (tRNAi^Met).
There are several eukaryotic initiation factors, each with a specific function in the initiation process. Some of the key eIFs include:
1. eIF1: helps to maintain the correct conformation of the 40S ribosomal subunit and prevents premature binding of tRNAi^Met.
2. eIF1A: stabilizes the interaction between eIF1 and the 40S ribosomal subunit, and also promotes the recruitment of tRNAi^Met.
3. eIF2: forms a ternary complex with GTP and tRNAi^Met, which binds to the 40S ribosomal subunit in an AUG-specific manner.
4. eIF3: interacts with the 40S ribosomal subunit and helps to recruit other initiation factors, including eIF1, eIF1A, and eIF2.
5. eIF4F: a heterotrimeric complex that includes eIF4E (cap-binding protein), eIF4A (DEAD-box RNA helicase), and eIF4G (scaffolding protein). This complex recognizes the 5' cap structure of mRNAs and facilitates their recruitment to the ribosome.
6. eIF5: promotes the hydrolysis of GTP in the eIF2-GTP-tRNAi^Met ternary complex, leading to the dissociation of eIF2-GDP and the formation of a stable 43S preinitiation complex.
7. eIF5B: catalyzes the joining of the 60S ribosomal subunit to form an 80S initiation complex and facilitates the release of eIF1A, eIF2-GDP, and eIF5 from the complex.
These initiation factors play crucial roles in ensuring accurate translation initiation, maintaining translational fidelity, and regulating gene expression at the level of translation. Dysregulation of these processes can lead to various human diseases, including cancer, neurodegenerative disorders, and viral infections.
The RNA-induced silencing complex (RISC) is a multiprotein complex that plays a central role in the RNA interference (RNAi) pathway, which is a post-transcriptional gene regulatory mechanism. The RISC complex mediates sequence-specific mRNA degradation or translational repression through the interaction with small non-coding RNAs called small interfering RNAs (siRNAs) or microRNAs (miRNAs).
The siRNAs are double-stranded RNAs that are generated from long, perfectly complementary dsRNA precursors by the enzyme Dicer. Once incorporated into the RISC complex, one strand of the siRNA duplex is removed, and the remaining single-stranded RNA guides the RISC to target mRNAs with complementary sequences. The binding of the RISC-siRNA complex to the target mRNA results in its cleavage or translational repression, leading to gene silencing.
The miRNAs, on the other hand, are single-stranded RNAs that are generated from hairpin precursors by Dicer. Unlike siRNAs, miRNAs typically have imperfect complementarity to their target mRNAs. The RISC-miRNA complex binds to the 3' untranslated region (UTR) of the target mRNA and represses its translation or induces its degradation, depending on the degree of complementarity between the miRNA and the target mRNA.
Overall, the RISC complex is a critical component of the RNAi pathway that plays a crucial role in regulating gene expression at the post-transcriptional level.
RNA interference (RNAi) is a biological process in which RNA molecules inhibit the expression of specific genes. This process is mediated by small RNA molecules, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), that bind to complementary sequences on messenger RNA (mRNA) molecules, leading to their degradation or translation inhibition.
RNAi plays a crucial role in regulating gene expression and defending against foreign genetic elements, such as viruses and transposons. It has also emerged as an important tool for studying gene function and developing therapeutic strategies for various diseases, including cancer and viral infections.
Ribonuclease III, also known as RNase III or double-stranded RNA specific endonuclease, is an enzyme that belongs to the endoribonuclease family. This enzyme is responsible for cleaving double-stranded RNA (dsRNA) molecules into smaller fragments of approximately 20-25 base pairs in length. The resulting fragments are called small interfering RNAs (siRNAs), which play a crucial role in the regulation of gene expression through a process known as RNA interference (RNAi).
Ribonuclease III functions by recognizing and binding to specific stem-loop structures within dsRNA molecules, followed by cleaving both strands at precise locations. This enzyme is highly conserved across various species, including bacteria, yeast, plants, and animals, indicating its fundamental role in cellular processes. In addition to its involvement in RNAi, ribonuclease III has been implicated in the maturation of other non-coding RNAs, such as microRNAs (miRNAs) and transfer RNAs (tRNAs).
MicroRNAs (miRNAs) are a class of small non-coding RNAs, typically consisting of around 20-24 nucleotides, that play crucial roles in post-transcriptional regulation of gene expression. They primarily bind to the 3' untranslated region (3' UTR) of target messenger RNAs (mRNAs), leading to mRNA degradation or translational repression. MicroRNAs are involved in various biological processes, including development, differentiation, proliferation, and apoptosis, and have been implicated in numerous diseases, such as cancers and neurological disorders. They can be found in various organisms, from plants to animals, and are often conserved across species. MicroRNAs are usually transcribed from DNA sequences located in introns or exons of protein-coding genes or in intergenic regions. After transcription, they undergo a series of processing steps, including cleavage by ribonucleases Drosha and Dicer, to generate mature miRNA molecules capable of binding to their target mRNAs.
Small interfering RNA (siRNA) is a type of short, double-stranded RNA molecule that plays a role in the RNA interference (RNAi) pathway. The RNAi pathway is a natural cellular process that regulates gene expression by targeting and destroying specific messenger RNA (mRNA) molecules, thereby preventing the translation of those mRNAs into proteins.
SiRNAs are typically 20-25 base pairs in length and are generated from longer double-stranded RNA precursors called hairpin RNAs or dsRNAs by an enzyme called Dicer. Once generated, siRNAs associate with a protein complex called the RNA-induced silencing complex (RISC), which uses one strand of the siRNA (the guide strand) to recognize and bind to complementary sequences in the target mRNA. The RISC then cleaves the target mRNA, leading to its degradation and the inhibition of protein synthesis.
SiRNAs have emerged as a powerful tool for studying gene function and have shown promise as therapeutic agents for a variety of diseases, including viral infections, cancer, and genetic disorders. However, their use as therapeutics is still in the early stages of development, and there are challenges associated with delivering siRNAs to specific cells and tissues in the body.
Alpha-Amanitin is a bicyclic octapeptide and the main toxic component found in several species of mushrooms, including the deadly "death cap" (Amanita phalloides) and "destroying angel" (Amanita virosa). It is a potent inhibitor of RNA polymerase II, which is an enzyme responsible for transcribing DNA into messenger RNA (mRNA) in eukaryotic cells. This specific mode of action disrupts protein synthesis and leads to severe cellular damage, primarily affecting the liver, kidneys, and central nervous system.
Clinical symptoms of alpha-amanitin poisoning include gastrointestinal distress (nausea, vomiting, diarrhea) within a few hours after ingestion, followed by a symptom-free period of up to 24 hours. After this latent phase, symptoms reappear and can progress to liver and kidney failure, coma, and even death in severe cases. There is no specific antidote for alpha-amanitin poisoning, and treatment primarily focuses on supportive care, such as fluid replacement, electrolyte management, and organ function support.
Eukaryotic Initiation Factor-2 (eIF-2) is a crucial protein complex in the process of protein synthesis, also known as translation, in eukaryotic cells. It plays a role in the initiation phase of translation, where it helps to recruit and position the initiator tRNA (tRNAiMet) at the start codon on the mRNA molecule.
The eIF-2 complex is made up of three subunits: α, β, and γ. Phosphorylation of the α subunit (eIF-2α) plays a regulatory role in protein synthesis. When eIF-2α is phosphorylated by one of several eIF-2 kinases in response to various stress signals, it leads to a decrease in global protein synthesis, allowing the cell to conserve resources and survive during times of stress. This process is known as the integrated stress response (ISR).
In summary, Eukaryotic Initiation Factor-2 (eIF-2) is a protein complex that plays a critical role in the initiation phase of protein synthesis in eukaryotic cells, and its activity can be regulated by phosphorylation of the α subunit.
Cytoplasmic structures refer to the various organelles and inclusions present within the cytoplasm of a eukaryotic cell, excluding the nucleus. These structures are involved in different cellular functions, such as energy production, protein synthesis, waste management, and intracellular transport.
Some examples of cytoplasmic structures include:
1. Mitochondria - organelles that generate energy for the cell through cellular respiration.
2. Ribosomes - complexes composed of ribosomal RNA (rRNA) and proteins that facilitate protein synthesis.
3. Endoplasmic reticulum (ER) - a network of membranous tubules involved in lipid and protein synthesis, folding, and transport.
4. Golgi apparatus - a series of stacked membrane sacs responsible for modifying, sorting, and packaging proteins and lipids for transport to their destinations.
5. Lysosomes - membrane-bound organelles that contain enzymes for breaking down waste materials, cellular debris, and foreign substances.
6. Peroxisomes - single-membrane bound organelles involved in various metabolic processes, including the breakdown of fatty acids and hydrogen peroxide detoxification.
7. Vacuoles - membrane-bound compartments that store water, nutrients, waste products, or enzymes. In plant cells, vacuoles also help maintain turgor pressure.
8. Cytoskeleton - a network of protein filaments (actin microfilaments, intermediate filaments, and microtubules) responsible for maintaining cell shape, providing structural support, and enabling intracellular transport and movement.
9. Inclusions - various membrane-less structures composed of aggregated proteins or other molecules, such as lipid droplets, glycogen granules, and pigment granules (e.g., melanosomes in melanocytes).
These cytoplasmic structures contribute to the overall functioning and maintenance of a eukaryotic cell.
Gene silencing is a process by which the expression of a gene is blocked or inhibited, preventing the production of its corresponding protein. This can occur naturally through various mechanisms such as RNA interference (RNAi), where small RNAs bind to and degrade specific mRNAs, or DNA methylation, where methyl groups are added to the DNA molecule, preventing transcription. Gene silencing can also be induced artificially using techniques such as RNAi-based therapies, antisense oligonucleotides, or CRISPR-Cas9 systems, which allow for targeted suppression of gene expression in research and therapeutic applications.
RNA-binding proteins (RBPs) are a class of proteins that selectively interact with RNA molecules to form ribonucleoprotein complexes. These proteins play crucial roles in the post-transcriptional regulation of gene expression, including pre-mRNA processing, mRNA stability, transport, localization, and translation. RBPs recognize specific RNA sequences or structures through their modular RNA-binding domains, which can be highly degenerate and allow for the recognition of a wide range of RNA targets. The interaction between RBPs and RNA is often dynamic and can be regulated by various post-translational modifications of the proteins or by environmental stimuli, allowing for fine-tuning of gene expression in response to changing cellular needs. Dysregulation of RBP function has been implicated in various human diseases, including neurological disorders and cancer.
A guide RNA (gRNA) is not a type of RNA itself, but rather a term used to describe various types of RNAs that guide other molecules to specific target sites in the genome or transcriptome. The most well-known example of a guide RNA is the CRISPR RNA (crRNA) used in the CRISPR-Cas system for targeted gene editing.
The crRNA contains a sequence complementary to the target DNA or RNA, and it guides the Cas endonuclease to the correct location in the genome where cleavage and modification can occur. Other types of guide RNAs include small interfering RNAs (siRNAs) and microRNAs (miRNAs), which guide the RNA-induced silencing complex (RISC) to specific mRNA targets for degradation or translational repression.
Overall, guide RNAs play crucial roles in various cellular processes, including gene regulation, genome editing, and defense against foreign genetic elements.
'Drosophila proteins' refer to the proteins that are expressed in the fruit fly, Drosophila melanogaster. This organism is a widely used model system in genetics, developmental biology, and molecular biology research. The study of Drosophila proteins has contributed significantly to our understanding of various biological processes, including gene regulation, cell signaling, development, and aging.
Some examples of well-studied Drosophila proteins include:
1. HSP70 (Heat Shock Protein 70): A chaperone protein involved in protein folding and protection from stress conditions.
2. TUBULIN: A structural protein that forms microtubules, important for cell division and intracellular transport.
3. ACTIN: A cytoskeletal protein involved in muscle contraction, cell motility, and maintenance of cell shape.
4. BETA-GALACTOSIDASE (LACZ): A reporter protein often used to monitor gene expression patterns in transgenic flies.
5. ENDOGLIN: A protein involved in the development of blood vessels during embryogenesis.
6. P53: A tumor suppressor protein that plays a crucial role in preventing cancer by regulating cell growth and division.
7. JUN-KINASE (JNK): A signaling protein involved in stress response, apoptosis, and developmental processes.
8. DECAPENTAPLEGIC (DPP): A member of the TGF-β (Transforming Growth Factor Beta) superfamily, playing essential roles in embryonic development and tissue homeostasis.
These proteins are often studied using various techniques such as biochemistry, genetics, molecular biology, and structural biology to understand their functions, interactions, and regulation within the cell.
RNA stability refers to the duration that a ribonucleic acid (RNA) molecule remains intact and functional within a cell before it is degraded or broken down into its component nucleotides. Various factors can influence RNA stability, including:
1. Primary sequence: Certain sequences in the RNA molecule may be more susceptible to degradation by ribonucleases (RNases), enzymes that break down RNA.
2. Secondary structure: The formation of stable secondary structures, such as hairpins or stem-loop structures, can protect RNA from degradation.
3. Presence of RNA-binding proteins: Proteins that bind to RNA can either stabilize or destabilize the RNA molecule, depending on the type and location of the protein-RNA interaction.
4. Chemical modifications: Modifications to the RNA nucleotides, such as methylation, can increase RNA stability by preventing degradation.
5. Subcellular localization: The subcellular location of an RNA molecule can affect its stability, with some locations providing more protection from ribonucleases than others.
6. Cellular conditions: Changes in cellular conditions, such as pH or temperature, can also impact RNA stability.
Understanding RNA stability is important for understanding gene regulation and the function of non-coding RNAs, as well as for developing RNA-based therapeutic strategies.
'Caenorhabditis elegans' (C. elegans) is a type of free-living, transparent nematode (roundworm) that is often used as a model organism in scientific research. C. elegans proteins refer to the various types of protein molecules that are produced by the organism's genes and play crucial roles in maintaining its biological functions.
Proteins are complex molecules made up of long chains of amino acids, and they are involved in virtually every cellular process, including metabolism, DNA replication, signal transduction, and transportation of molecules within the cell. In C. elegans, proteins are encoded by genes, which are transcribed into messenger RNA (mRNA) molecules that are then translated into protein sequences by ribosomes.
Studying C. elegans proteins is important for understanding the basic biology of this organism and can provide insights into more complex biological systems, including humans. Because C. elegans has a relatively simple nervous system and a short lifespan, it is often used to study neurobiology, aging, and development. Additionally, because many of the genes and proteins in C. elegans have counterparts in other organisms, including humans, studying them can provide insights into human disease processes and potential therapeutic targets.
Peptide initiation factors are a group of proteins involved in the process of protein synthesis in cells, specifically during the initial stage of elongation called initiation. In this phase, they assist in the assembly of the ribosome, an organelle composed of ribosomal RNA and proteins, at the start codon of a messenger RNA (mRNA) molecule. This marks the beginning of the translation process where the genetic information encoded in the mRNA is translated into a specific protein sequence.
There are three main peptide initiation factors in eukaryotic cells:
1. eIF-2 (eukaryotic Initiation Factor 2): This factor plays a crucial role in binding methionyl-tRNAi, the initiator tRNA, to the small ribosomal subunit. It does so by forming a complex with GTP and the methionyl-tRNAi, which then binds to the 40S ribosomal subunit. Once bound, eIF-2-GTP-Met-tRNAi recognizes the start codon (AUG) on the mRNA.
2. eIF-3: This is a large multiprotein complex that interacts with both the small and large ribosomal subunits and helps stabilize their interaction during initiation. It also plays a role in recruiting other initiation factors to the preinitiation complex.
3. eIF-4F: This factor is a heterotrimeric protein complex consisting of eIF-4A (an ATP-dependent RNA helicase), eIF-4E (which binds the m7G cap structure at the 5' end of most eukaryotic mRNAs), and eIF-4G (a scaffolding protein that bridges interactions between eIF-4A, eIF-4E, and other initiation factors). eIF-4F helps unwind secondary structures in the 5' untranslated region (5' UTR) of mRNAs, promoting efficient recruitment of the 43S preinitiation complex to the mRNA.
Together, these peptide initiation factors facilitate the recognition of the correct start codon and ensure efficient translation initiation in eukaryotic cells.
I'm happy to help! However, it seems there might be a slight misunderstanding in your question. RNA, or ribonucleic acid, is typically single-stranded. Unlike DNA, which is double-stranded and forms a double helix, RNA usually exists as a single strand of nucleotides.
There are exceptions to this rule, such as certain types of RNA molecules that can form double-stranded structures in specific contexts. For example:
1. Double-Stranded RNA (dsRNA) viruses: These viruses have genomes made entirely of RNA, which is double-stranded throughout or partially double-stranded. The dsRNA viruses include important pathogens such as rotaviruses and reoviruses.
2. Hairpin loops in RNA structures: Some single-stranded RNA molecules can fold back on themselves to form short double-stranded regions, called hairpin loops, within their overall structure. These are often found in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA) molecules.
So, while 'double-stranded RNA' is not a standard medical definition for RNA itself, there are specific instances where RNA can form double-stranded structures as described above.
Tertiary protein structure refers to the three-dimensional arrangement of all the elements (polypeptide chains) of a single protein molecule. It is the highest level of structural organization and results from interactions between various side chains (R groups) of the amino acids that make up the protein. These interactions, which include hydrogen bonds, ionic bonds, van der Waals forces, and disulfide bridges, give the protein its unique shape and stability, which in turn determines its function. The tertiary structure of a protein can be stabilized by various factors such as temperature, pH, and the presence of certain ions. Any changes in these factors can lead to denaturation, where the protein loses its tertiary structure and thus its function.
'Caenorhabditis elegans' is a species of free-living, transparent nematode (roundworm) that is widely used as a model organism in scientific research, particularly in the fields of biology and genetics. It has a simple anatomy, short lifespan, and fully sequenced genome, making it an ideal subject for studying various biological processes and diseases.
Some notable features of C. elegans include:
* Small size: Adult hermaphrodites are about 1 mm in length.
* Short lifespan: The average lifespan of C. elegans is around 2-3 weeks, although some strains can live up to 4 weeks under laboratory conditions.
* Development: C. elegans has a well-characterized developmental process, with adults developing from eggs in just 3 days at 20°C.
* Transparency: The transparent body of C. elegans allows researchers to observe its internal structures and processes easily.
* Genetics: C. elegans has a fully sequenced genome, which contains approximately 20,000 genes. Many of these genes have human homologs, making it an excellent model for studying human diseases.
* Neurobiology: C. elegans has a simple nervous system, with only 302 neurons in the hermaphrodite and 383 in the male. This simplicity makes it an ideal organism for studying neural development, function, and behavior.
Research using C. elegans has contributed significantly to our understanding of various biological processes, including cell division, apoptosis, aging, learning, and memory. Additionally, studies on C. elegans have led to the discovery of many genes associated with human diseases such as cancer, neurodegenerative disorders, and metabolic conditions.
'Drosophila melanogaster' is the scientific name for a species of fruit fly that is commonly used as a model organism in various fields of biological research, including genetics, developmental biology, and evolutionary biology. Its small size, short generation time, large number of offspring, and ease of cultivation make it an ideal subject for laboratory studies. The fruit fly's genome has been fully sequenced, and many of its genes have counterparts in the human genome, which facilitates the understanding of genetic mechanisms and their role in human health and disease.
Here is a brief medical definition:
Drosophila melanogaster (droh-suh-fih-luh meh-lon-guh-ster): A species of fruit fly used extensively as a model organism in genetic, developmental, and evolutionary research. Its genome has been sequenced, revealing many genes with human counterparts, making it valuable for understanding genetic mechanisms and their role in human health and disease.
Post-transcriptional RNA processing refers to the modifications and regulations that occur on RNA molecules after the transcription of DNA into RNA. This process includes several steps:
1. 5' capping: The addition of a cap structure, usually a methylated guanosine triphosphate (GTP), to the 5' end of the RNA molecule. This helps protect the RNA from degradation and plays a role in its transport, stability, and translation.
2. 3' polyadenylation: The addition of a string of adenosine residues (poly(A) tail) to the 3' end of the RNA molecule. This process is important for mRNA stability, export from the nucleus, and translation initiation.
3. Intron removal and exon ligation: Eukaryotic pre-messenger RNAs (pre-mRNAs) contain intronic sequences that do not code for proteins. These introns are removed by a process called splicing, where the flanking exons are joined together to form a continuous mRNA sequence. Alternative splicing can lead to different mature mRNAs from a single pre-mRNA, increasing transcriptomic and proteomic diversity.
4. RNA editing: Specific nucleotide changes in RNA molecules that alter the coding potential or regulatory functions of RNA. This process is catalyzed by enzymes like ADAR (Adenosine Deaminases Acting on RNA) and APOBEC (Apolipoprotein B mRNA Editing Catalytic Polypeptide-like).
5. Chemical modifications: Various chemical modifications can occur on RNA nucleotides, such as methylation, pseudouridination, and isomerization. These modifications can influence RNA stability, localization, and interaction with proteins or other RNAs.
6. Transport and localization: Mature mRNAs are transported from the nucleus to the cytoplasm for translation. In some cases, specific mRNAs are localized to particular cellular compartments to ensure local protein synthesis.
7. Degradation: RNA molecules have finite lifetimes and undergo degradation by various ribonucleases (RNases). The rate of degradation can be influenced by factors such as RNA structure, modifications, or interactions with proteins.
Messenger RNA (mRNA) is a type of RNA (ribonucleic acid) that carries genetic information copied from DNA in the form of a series of three-base code "words," each of which specifies a particular amino acid. This information is used by the cell's machinery to construct proteins, a process known as translation. After being transcribed from DNA, mRNA travels out of the nucleus to the ribosomes in the cytoplasm where protein synthesis occurs. Once the protein has been synthesized, the mRNA may be degraded and recycled. Post-transcriptional modifications can also occur to mRNA, such as alternative splicing and addition of a 5' cap and a poly(A) tail, which can affect its stability, localization, and translation efficiency.
Germ cells are the reproductive cells, also known as sex cells, that combine to form offspring in sexual reproduction. In females, germ cells are called ova or egg cells, and in males, they are called spermatozoa or sperm cells. These cells are unique because they carry half the genetic material necessary for creating new life. They are produced through a process called meiosis, which reduces their chromosome number by half, ensuring that when two germ cells combine during fertilization, the normal diploid number of chromosomes is restored.
Immunoprecipitation (IP) is a research technique used in molecular biology and immunology to isolate specific antigens or antibodies from a mixture. It involves the use of an antibody that recognizes and binds to a specific antigen, which is then precipitated out of solution using various methods, such as centrifugation or chemical cross-linking.
In this technique, an antibody is first incubated with a sample containing the antigen of interest. The antibody specifically binds to the antigen, forming an immune complex. This complex can then be captured by adding protein A or G agarose beads, which bind to the constant region of the antibody. The beads are then washed to remove any unbound proteins, leaving behind the precipitated antigen-antibody complex.
Immunoprecipitation is a powerful tool for studying protein-protein interactions, post-translational modifications, and signal transduction pathways. It can also be used to detect and quantify specific proteins in biological samples, such as cells or tissues, and to identify potential biomarkers of disease.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
"Drosophila" is a genus of small flies, also known as fruit flies. The most common species used in scientific research is "Drosophila melanogaster," which has been a valuable model organism for many areas of biological and medical research, including genetics, developmental biology, neurobiology, and aging.
The use of Drosophila as a model organism has led to numerous important discoveries in genetics and molecular biology, such as the identification of genes that are associated with human diseases like cancer, Parkinson's disease, and obesity. The short reproductive cycle, large number of offspring, and ease of genetic manipulation make Drosophila a powerful tool for studying complex biological processes.
Protein binding, in the context of medical and biological sciences, refers to the interaction between a protein and another molecule (known as the ligand) that results in a stable complex. This process is often reversible and can be influenced by various factors such as pH, temperature, and concentration of the involved molecules.
In clinical chemistry, protein binding is particularly important when it comes to drugs, as many of them bind to proteins (especially albumin) in the bloodstream. The degree of protein binding can affect a drug's distribution, metabolism, and excretion, which in turn influence its therapeutic effectiveness and potential side effects.
Protein-bound drugs may be less available for interaction with their target tissues, as only the unbound or "free" fraction of the drug is active. Therefore, understanding protein binding can help optimize dosing regimens and minimize adverse reactions.
A mutation is a permanent change in the DNA sequence of an organism's genome. Mutations can occur spontaneously or be caused by environmental factors such as exposure to radiation, chemicals, or viruses. They may have various effects on the organism, ranging from benign to harmful, depending on where they occur and whether they alter the function of essential proteins. In some cases, mutations can increase an individual's susceptibility to certain diseases or disorders, while in others, they may confer a survival advantage. Mutations are the driving force behind evolution, as they introduce new genetic variability into populations, which can then be acted upon by natural selection.
A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.
RNA (Ribonucleic Acid) is a single-stranded, linear polymer of ribonucleotides. It is a nucleic acid present in the cells of all living organisms and some viruses. RNAs play crucial roles in various biological processes such as protein synthesis, gene regulation, and cellular signaling. There are several types of RNA including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), microRNA (miRNA), and long non-coding RNA (lncRNA). These RNAs differ in their structure, function, and location within the cell.
A cell line is a culture of cells that are grown in a laboratory for use in research. These cells are usually taken from a single cell or group of cells, and they are able to divide and grow continuously in the lab. Cell lines can come from many different sources, including animals, plants, and humans. They are often used in scientific research to study cellular processes, disease mechanisms, and to test new drugs or treatments. Some common types of human cell lines include HeLa cells (which come from a cancer patient named Henrietta Lacks), HEK293 cells (which come from embryonic kidney cells), and HUVEC cells (which come from umbilical vein endothelial cells). It is important to note that cell lines are not the same as primary cells, which are cells that are taken directly from a living organism and have not been grown in the lab.
'Gene expression regulation' refers to the processes that control whether, when, and where a particular gene is expressed, meaning the production of a specific protein or functional RNA encoded by that gene. This complex mechanism can be influenced by various factors such as transcription factors, chromatin remodeling, DNA methylation, non-coding RNAs, and post-transcriptional modifications, among others. Proper regulation of gene expression is crucial for normal cellular function, development, and maintaining homeostasis in living organisms. Dysregulation of gene expression can lead to various diseases, including cancer and genetic disorders.
An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.
Ribonucleic acid (RNA) in plants refers to the long, single-stranded molecules that are essential for the translation of genetic information from deoxyribonucleic acid (DNA) into proteins. RNA is a nucleic acid, like DNA, and it is composed of a ribose sugar backbone with attached nitrogenous bases (adenine, uracil, guanine, and cytosine).
In plants, there are several types of RNA that play specific roles in the gene expression process:
1. Messenger RNA (mRNA): This type of RNA carries genetic information copied from DNA in the form of a sequence of three-base code units called codons. These codons specify the order of amino acids in a protein.
2. Transfer RNA (tRNA): tRNAs are small RNA molecules that serve as adaptors between the mRNA and the amino acids during protein synthesis. Each tRNA has a specific anticodon sequence that base-pairs with a complementary codon on the mRNA, and it carries a specific amino acid that corresponds to that codon.
3. Ribosomal RNA (rRNA): rRNAs are structural components of ribosomes, which are large macromolecular complexes where protein synthesis occurs. In plants, there are several types of rRNAs, including the 18S, 5.8S, and 25S/28S rRNAs, that form the core of the ribosome and help catalyze peptide bond formation during protein synthesis.
4. Small nuclear RNA (snRNA): These are small RNA molecules that play a role in RNA processing, such as splicing, where introns (non-coding sequences) are removed from pre-mRNA and exons (coding sequences) are joined together to form mature mRNAs.
5. MicroRNA (miRNA): These are small non-coding RNAs that regulate gene expression by binding to complementary sequences in target mRNAs, leading to their degradation or translation inhibition.
Overall, these different types of RNAs play crucial roles in various aspects of RNA metabolism, gene regulation, and protein synthesis in plants.
RNA cleavage is a biological process in which RNA molecules are cut or split into smaller fragments by enzymes known as ribonucleases (RNases). This process can occur co-transcriptionally, during splicing, or as a means of regulation of RNA stability and function. Cleavage sites are often defined by specific sequences or structures within the RNA molecule. The cleavage products may have various fates, including degradation, further processing, or serving as functional RNA molecules.
In the context of medical and biological sciences, a "binding site" refers to a specific location on a protein, molecule, or cell where another molecule can attach or bind. This binding interaction can lead to various functional changes in the original protein or molecule. The other molecule that binds to the binding site is often referred to as a ligand, which can be a small molecule, ion, or even another protein.
The binding between a ligand and its target binding site can be specific and selective, meaning that only certain ligands can bind to particular binding sites with high affinity. This specificity plays a crucial role in various biological processes, such as signal transduction, enzyme catalysis, or drug action.
In the case of drug development, understanding the location and properties of binding sites on target proteins is essential for designing drugs that can selectively bind to these sites and modulate protein function. This knowledge can help create more effective and safer therapeutic options for various diseases.
RNA (Ribonucleic acid) is a single-stranded molecule that plays a crucial role in the process of gene expression. It acts as a messenger carrying genetic information copied from DNA to the ribosomes, where proteins are synthesized. RNA is also involved in catalyzing chemical reactions and regulating gene expression.
Helminths, on the other hand, refer to parasitic worms that infect humans and animals. They belong to various phyla, including Nematoda (roundworms), Platyhelminthes (flatworms), and Acanthocephala (spiny-headed worms). Helminth infections can cause a range of diseases and conditions, such as intestinal inflammation, anemia, stunted growth, and cognitive impairment.
There is no medical definition for "RNA, Helminth" since RNA is a type of molecule found in all living organisms, including helminths. However, researchers have studied the genetic material of various helminth species to better understand their biology, evolution, and pathogenesis. This includes sequencing and analyzing the RNA transcriptome of these parasites, which can provide insights into their gene expression patterns and help identify potential drug targets for developing new treatments.
Arabidopsis proteins refer to the proteins that are encoded by the genes in the Arabidopsis thaliana plant, which is a model organism commonly used in plant biology research. This small flowering plant has a compact genome and a short life cycle, making it an ideal subject for studying various biological processes in plants.
Arabidopsis proteins play crucial roles in many cellular functions, such as metabolism, signaling, regulation of gene expression, response to environmental stresses, and developmental processes. Research on Arabidopsis proteins has contributed significantly to our understanding of plant biology and has provided valuable insights into the molecular mechanisms underlying various agronomic traits.
Some examples of Arabidopsis proteins include transcription factors, kinases, phosphatases, receptors, enzymes, and structural proteins. These proteins can be studied using a variety of techniques, such as biochemical assays, protein-protein interaction studies, and genetic approaches, to understand their functions and regulatory mechanisms in plants.
Argonaute
MicroRNA
TNRC6B
RNA-induced silencing complex
MOV10
RNA-directed DNA methylation
Piwi like rna-mediated gene silencing 4
Circular RNA
Piwi
RNA interference
Piwi-interacting RNA
Procollagen-proline dioxygenase
Transfer RNA
Wojciech Karlowski
RevCen
IPO8
EIF2C2
Argonaut (animal)
Mir-390 microRNA precursor family
EIF2C1
Trans-acting siRNA
Mir-92 microRNA precursor family
Hydroxyproline
HITS-CLIP
RNA-binding protein database
Transcriptome
RDE-1
TNRC6A
P-bodies
Adaptive immune system
NEB TV Ep.31 - What are Argonaute Proteins? | NEB
New Research Shows Silencing Role for Non-slicer Argonaute Proteins | GenomeWeb
Argonaute Utilization for miRNA Silencing Is Determined by Phosphorylation-Dependent Recruitment of LIM-Domain-Containing...
Protein argonaute-2 (chicken) | Protein Target - PubChem
Argonaute - Wikipedia
Cell Research
DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute
Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs<...
A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway
β-defensin-1 regulates influenza virus infection in human bronchial epithelial cells through the STAT3 signaling pathway
Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA...
Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs<...
Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner - Université Pierre...
Gene regulation by translational inhibition is determined by Dicer partnering proteins | Nature Plants
Frontiers | Small-Molecule Inhibitors Overcome Epigenetic Reprogramming for Cancer Therapy
AGO2 Polyclonal Antibody (PA5-78738)
Kate Jeffrey | Harvard Catalyst Profiles | Harvard Catalyst
Using RNA Interference To Tune Gene Activity In Stem Cells -- New Method For The Study And Treatment Of Disease | ScienceDaily
Fungal pathogen sheds gene silencing machinery and becomes more dangerous | ScienceDaily
Publications
SCOPe 2.03: Domain d1u04a2: 1u04 A:324-770
Role of Alix in miRNA packaging during extracellular vesicle biogenesis
Cellular transporter involved in gene silencing - Importin guides switch molecules to their targets | Max Planck Institute of...
Team Finds Key to Gene-Silencing Activity
Scripps Research Institute Finds Protein that Can Silence Genes- Crop Biotech Update (May 11, 2012) | Crop Biotech Update -...
Where CRISPR Fumbles, Argonaut Can Find a Handle
Viruses | Free Full-Text | Antiviral RNA Interference Activity in Cells of the Predatory Mosquito, Toxorhynchites amboinensis
Discovery lead to better methods for reducing mosquito-to-human transmission of deadly viruses
RNAs14
- Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). (wikipedia.org)
- Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity (base pairing), which then leads to mRNA cleavage, translation inhibition, and/or the initiation of mRNA decay. (wikipedia.org)
- Small RNAs that interact with Argonaute (AGO) proteins play central roles in RNA-mediated silencing. (edu.sa)
- Co-immunoprecipitation of Argonaute proteins with associated RNAs. (cdc.gov)
- For example, ~23 nucleotide (nt)-long small interfering RNAs (siRNAs) are loaded into Argonaute proteins. (anl.gov)
- Ribonucleic acids (RNAs) carry as messenger-RNAs (mRNAs) genetic information from DNA to cellular protein factories, where they are translated into proteins. (mpg.de)
- But they also have important regulatory functions: Small noncoding RNAs (miRNAs) influence mRNA stability and are able to switch off genes by stalling their translation into proteins. (mpg.de)
- Some viruses, for example, produce decoy target RNAs that virtually nullify the activity of the corresponding miRNAs, seemingly by destabilizing the miRNA-Argonaute pairing. (scripps.edu)
- De confirmed that decoy RNAs designed to match miRNAs this way can greatly hasten the miRNAs' "unloading" from Argonautes, thus effectively dialing down these miRNAs' normal gene-silencing activities. (scripps.edu)
- they are taken up by Argonaute proteins as guide RNAs and lead to the silencing of targeted gene transcripts. (scripps.edu)
- In the new study, Dimopoulos and Dong examined the role of Argonaute 2 (Ago2), a protein that in mosquitoes serves as part of an important antiviral mechanism known as the small interfering RNA (siRNA) pathway, which works by recognizing and destroying viral RNAs. (news-medical.net)
- This study demonstrates the pivotal role of EZH2 as well as the involvement of Argonaute proteins and non-coding RNAs in ET pathogenesis and discloses new therapeutic modalities for the use of epigenetic drugs or miRNA therapeutics. (tum.de)
- Diese Arbeit stellt die zentrale Rolle von EZH2 als auch die Beteiligung von Argonaute Proteinen und nicht-kodierenden RNAs in der ET Pathogenese dar und eröffnet damit neue Behandlungsmodalitäten durch die Anwendung epigenetischer Medikamente oder von microRNA Therapeutika. (tum.de)
- We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. (bvsalud.org)
MiRNA22
- Also the degree of complementarity between the two strands of the intermediate RNA duplex defines how the miRNA are sorted into different types of Argonaute proteins. (wikipedia.org)
- In animals, Argonaute associated with miRNA binds to the 3′-untranslated region of mRNA and prevents the production of proteins in various ways. (wikipedia.org)
- The Argonaute-miRNA complex can also affect the formation of functional ribosomes at the 5′-end of the mRNA. (wikipedia.org)
- Also, the Argonaute-miRNA complex can adjust protein production by recruiting cellular factors such as peptides or post translational modifying enzymes, which degrade the growing of polypeptides. (wikipedia.org)
- Here we show that the form of regulatory action directed by a plant miRNA is determined by DRB2, a DICER-LIKE1 (DCL1) partnering protein. (nature.com)
- Furthermore, our results reveal that the core silencing proteins ARGONAUTE1 (AGO1) and SERRATE (SE) are highly regulated by miRNA-guided translational inhibition. (nature.com)
- DRB2 has been remarkably conserved throughout plant evolution, raising the possibility that translational repression is the ancient form of miRNA-directed gene regulation in plants, and that Dicer partnering proteins, such as human TRBP, might play a similar role in other eukaryotic systems. (nature.com)
- Figure 2: Accumulation of miRNA target mRNAs and proteins in the shoot apex of drb1 and drb2 . (nature.com)
- However, only the Ago2 protein displays endonucleolytic or "Slicer" activity and can therefore execute miRNA-directed cleavage of target mRNA, provided that the base-pairing between the Ago2-associated miRNA and the mRNA sequence is perfect. (thermofisher.com)
- Gibbings et al ( 16 ) suggested that the constituents of the miRNA effector complex, such as GW182 and Argonaute 2 (Ago2), are involved in the packaging of miRNAs within multivesicular bodies during exosome biogenesis. (spandidos-publications.com)
- As far as humans are concerned, the argonaute protein Ago-2 is the key cellular binding partner of miRNAs: The Ago-miRNA complex binds to mRNA and impedes their translation into proteins - either by blocking the translation process or by initiating RNA decomposition. (mpg.de)
- Now his group has identified the first protein factor which is required for gene-silencing by Ago-miRNA-complexes: Importin 8. (mpg.de)
- For example, before it starts a search-and-destroy mission against a specific type of target RNA, an Argonaute 2 protein takes on board a target-recognition device: a short length of "guide RNA," also known as a microRNA (miRNA). (scripps.edu)
- But how do an Argonaute protein and its miRNA guide, having formed their partnership, manage to part company? (scripps.edu)
- In an initial set of experiments, the team demonstrated that when an miRNA hooks up with an Argonaute 2, the pair do remain locked together and functioning for an exceptionally long time: days to weeks, whereas solo miRNA normally is degraded within minutes. (scripps.edu)
- Why do these matches and mismatches have such effects on the miRNA-Argonaute pairing? (scripps.edu)
- In a study reported last year, MacRae's laboratory used X-ray crystallography to determine the first high-resolution atomic structure of an Argonaute 2-miRNA complex. (scripps.edu)
- The findings here suggest a new and, in principle, more powerful class of miRNA inhibitors/enhancers, aimed at destabilizing or stabilizing the miRNA-Argonaute complex. (scripps.edu)
- The mature miRNA is then loaded onto an Argonaute protein (Ago2 in humans) where it then interacts with and regulates the mRNA target. (biomedcentral.com)
- Another type of molecule, called micro RNA (miRNA) can bind to mRNA and stop the translation of mRNA into protein. (ukri.org)
- We have found that a protein (called PICK1), which is known to be involved in synaptic plasticity over the timescale of hours, interacts with another protein (called Argonaute2), which is an important component of the cell machinery that promotes the association of miRNA with mRNA to block protein synthesis. (ukri.org)
- Based on our identified miRNA-regulated molecular machinery, an inhibitor of PDK1/Akt BX-912, an anthracycline antibiotic daunorubicin, and a multi-targeted protein kinase inhibitor midostaurin were discovered as potential repositioning drugs for treating lung cancer. (cdc.gov)
PIWI11
- Prokaryotic Argonaute proteins are typically comprised four domains: the MID domain, the PAZ domain, the PIWI domain, and the N domain. (neb.com)
- Once the Argonaute is associated with the small RNA, the enzymatic activity conferred by the PIWI domain cleaves only the passenger strand of the small interfering RNA. (wikipedia.org)
- In plants, once de novo double-stranded (ds) RNA duplexes are generated with the target mRNA, an unknown RNase-III-like enzyme produces new siRNAs, which are then loaded onto the Argonaute proteins containing PIWI domains, lacking the catalytic amino acid residues, which might induce another level of specific gene silencing. (wikipedia.org)
- The Argonaute (AGO) gene family encodes for six characteristic domains: N- terminal (N), Linker-1 (L1), PAZ, Linker-2 (L2), Mid, and a C-terminal PIWI domain. (wikipedia.org)
- The name for the PAZ domain is an acronym made from the gene names of Drosophila piwi, Arabidopsis argonaute-1, and Arabidopsis zwille (also known as pinhead, and later renamed argonaute-10), where the domain was first recognized to be conserved. (wikipedia.org)
- The Drosophila PIWI protein gave its name to this characteristic motif. (wikipedia.org)
- Two interrelated branches of the piRNA system exist: somatic cells that support oogenesis only employ Piwi, whereas germ cells utilize a more elaborate pathway centered on the three gonad-specific Argonaute proteins (Piwi, Aubergine, and Argonaute 3). (nih.gov)
- 1W9H: The Structure of a Piwi protein from Archaeoglobus fulgidus. (rcsb.org)
- The fundamental engines of RNA silencing are RISC and RITS complexes, whose common components are 21-25 nt RNA and an Argonaute protein containing a PIWI domain of unknown function. (rcsb.org)
- The crystal structure of an archaeal Piwi protein (AfPiwi) is organised into two domains, one resembling the sugar-binding portion of the lac repressor and another with similarity to RNase H. Invariant residues and a coordinated metal ion lie in a pocket that surrounds the conserved C-terminus of the protein, defining a key functional region in the PIWI domain. (rcsb.org)
- They associate with the PIWI SUBFAMILY OF ARGONAUTE PROTEINS to form effector complexes known as piRNA-induced silencing complexes, which repress transposons via transcriptional or posttranscriptional mechanisms and maintain germline genome integrity. (bvsalud.org)
Ago27
- When it comes to RNAi in mammals, one Ago protein in particular - Ago2 - has been shown to be a critical component of the RNA-induced silencing complex as it is the only member of this family that is capable of target mRNA cleavage. (genomeweb.com)
- For instance, while some studies have shown residual target knockdown in the absence of Ago2, others have reported not seeing any response to siRNA treatment in cells lacking the protein. (genomeweb.com)
- To better understand the roles of individual mammalian Ago proteins in the RNAi process, the research group, which included scientists from Alnylam Pharmaceuticals, conducted a systematic analysis of the effect of Ago2 absence on the knockdown of endogenous genes by siRNAs targeting either CDS or 3' UTR in vitro . (genomeweb.com)
- The team further observed a persistence of knockdown by siRNAs targeting 3' UTRs of the same three genes, and discovered that both Ago1 and Ago3 proteins present in physiological amounts contribute to residual knockdown observed in the absence of Ago2 in liver, according to the PLOS One report. (genomeweb.com)
- In case of partial complementarity, the Ago2 protein fails to cleave, but instead interferes with translation of the target mRNA via its translational repression activity. (thermofisher.com)
- Furthermore, gene disruption in the mouse demonstrated that the Ago2 protein is essential for embryonic development and a key regulator of B-lymphoid and erythroid development. (thermofisher.com)
- EVs released from HLSCs were enriched with miRNAs and expressed Alix and several RNA-binding proteins, including Argonaute 2 (Ago2), a member of the Argonaute family known to be involved in the transport and the processing of miRNAs. (spandidos-publications.com)
Nucleic acid guides2
- When provided with synthetic nucleic acid guides, prokaryotic Argonautes can be used as programmable nucleases. (neb.com)
- Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides. (umassmed.edu)
MRNA8
- They have also all have been shown to bind microRNAs and siRNA indiscriminately of sequence to interact with a common set of helicases and mRNA-binding proteins, and to localize to P-bodies in mammalian cells with a capability of targeting mRNAs to the general eukaryotic machinery for translation control and mRNA degradation. (genomeweb.com)
- As core components of the microRNA-induced silencing complex (miRISC), Argonaute (AGO) proteins interact with TNRC6 proteins, recruiting other effectors of translational repression/mRNA destabilization. (york.ac.uk)
- The method of inhibition is via the destruction of specific mRNA molecules or by simply suppressing the protein translation. (wikipedia.org)
- Argonaute proteins are the active part of RNA-induced silencing complex, cleaving the target mRNA strand complementary to their bound siRNA. (wikipedia.org)
- The recruitment of Argonaute proteins to targeted mRNA can induce mRNA degradation. (wikipedia.org)
- The mRNA, thus, carries the Argonaute to its target. (isaaa.org)
- An intermediate between DNA and protein is called messenger RNA (mRNA), and neurons can transport mRNA to the parts of the neuron close to synapses and locally control the synthesis of a particular protein that is important for those synapses at a particular time. (ukri.org)
- Pansensitive and panresistant genes to 21 NCCN-recommended drugs with concordant mRNA and protein expression were identified. (cdc.gov)
Prokaryotic Argonaute6
- So the prokaryotic Argonaute is a nucleic acid guided endonuclease, which means unlike normal endonucleases where you'll have a cutting at a lot of random locations, prokaryotic Argonaute uses a short nucleic acid guide to bring its activity to a very specific sequence in a substrate that's complimentary to that guide. (neb.com)
- With a prokaryotic Argonaute, that single guide is only cutting opposite of its complimentary sequence. (neb.com)
- The MID domain of prokaryotic Argonaute binds a short single stranded oligonucleotide guide, which is typically 16 to 18 nucleotides in length. (neb.com)
- Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. (nih.gov)
- In this work, the research team focused on a protein called SPARTA, a short prokaryotic Argonaute (also referred to as Ago), specifically building upon other studies that showed this protein enables Maribacter polysiphoniae bacteria to program their death when they detect a plasmid invasion-when external DNA segments are trying to insert themselves to change bacterial properties. (phys.org)
- All of this points to the fact that oligomerization-the methodical conversion of simple molecules into molecular complexes-is an essential part of activating short prokaryotic Argonaute proteins. (phys.org)
Single stranded2
- However, our mesophilic protein also contains a putative single-stranded DNA binding or repA domain. (genengnews.com)
- Our pAgo candidate nicks and cuts plasmid DNA nonspecifically in the absence of guide in in vitro assays, presumably due to the presence of single-stranded DNA that co-purifies with the protein," the abstract continued. (genengnews.com)
Drosophila1
- The ET-specific fusion protein EWS/FLI1 induces the expression of the histone methyltransferase EZH2 (enhancer of zeste, Drosophila, homolog 2). (tum.de)
RISC4
- The Argonaute protein family, first discovered for its evolutionarily conserved stem cell function, plays a central role in RNA silencing processes as essential components of the RNA-induced silencing complex (RISC). (wikipedia.org)
- RNAi is mediated by the effector complex called RNA-induced silencing complex (RISC), which contains a small RNA and an Argonaute protein at its core. (u-tokyo.ac.jp)
- Now a research group at the University of Tokyo (Research Associates Shintaro Iwasaki, Hiroshi M Sasaki, Hisashi Tadakuma, Professor Yukihide Tomari and their colleagues) has identified all seven proteins necessary for RISC assembly and succeeded in reconstituting RISC in a test tube. (u-tokyo.ac.jp)
- MiRNAs silence target mRNAs via the RNA-induced silencing complex (RISC), of which Argonaute proteins (Ago) are the major subunit. (ukri.org)
Regulate2
- Argonaute 2 and other Argonaute proteins regulate the influence of about a third of the genes found in humans and other mammals-and thus are among the most important modulators of our cells' day-to-day activities. (scripps.edu)
- Using these cells we will be able to understand more about the mechanisms that regulate the local control of protein synthesis in neurons in response to synaptic activity, and hence further our knowledge of the mechanisms that underlie long-term memory. (ukri.org)
Ago11
- The name of this protein family is derived from a mutant phenotype resulting from mutation of AGO1 in Arabidopsis thaliana, which was likened by Bohmert et al. (wikipedia.org)
Induces2
- The most well-studied outcome of the RNAi is post-transcriptional gene silencing, which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by Argonaute, that lies in the core of RNA-induced silencing complex. (wikipedia.org)
- In order to switch off a gene, they interact with so called Argonaute proteins - the subsequent complex induces the shutdown or even degradation of the genetic information. (mpg.de)
Catalytic3
- Here, our structural and functional studies of a bilobed yeast Argonaute protein and its isolated catalytic C-terminal lobe (C-lobe) revealed that the C-lobe alone retains almost all properties of bilobed Argonaute: siRNA-duplex loading, passenger cleavage/ejection, and siRNA-dependent RNA cleavage. (anl.gov)
- A 2.1 Å-resolution crystal structure revealed that the catalytic C-lobe mirrors the bilobed Argonaute in terms of guide-RNA recognition and that all requirements for transitioning to the catalytically active conformation reside in the C-lobe. (anl.gov)
- Furthermore, two Asp residues, conserved in the majority of Argonaute sequences, align spatially with the catalytic Asp residues of RNase H-like catalytic sites, suggesting that in eukaryotic Argonaute proteins the RNase H-like domain may possess nuclease activity. (rcsb.org)
Mechanisms4
- Yet prior studies by other laboratories have hinted at the existence of mechanisms that can hasten the separation of miRNAs from Argonautes. (scripps.edu)
- protein, Argonaute 2, has a key role-;via several biological mechanisms-;in keeping mosquitoes healthy and active despite these infections. (news-medical.net)
- This is the first study to detail structures and mechanisms of a short Argonaute, potentially sketching the beginnings of a blueprint for application to future therapeutic purposes. (phys.org)
- We show that human and chimpanzee cells differentiate in a similar man¬ner and that the difference in interspecies protein abundance is higher than transcript-level differences, suggesting that post-transcriptional mechanisms play a role in the difference between human and chim¬panzee brain development. (lu.se)
RNAi2
- As such, RNAi-based therapeutics might benefit from targeting 3' UTRs in order to engage Ago proteins that lack any slicing activity into the target knockdown process, the scientists wrote in their study. (genomeweb.com)
- Based on their findings, the researchers suggested those using RNAi for either therapeutic or research applications may benefit from targeting 3'UTRs in order to turn non-slicer Argonautes from siRNA deposit/sequestration platforms into active participants of knockdown. (genomeweb.com)
Superfamily1
- The protein belongs to the "superfamily" of Argonaute proteins, which previous research has suggested to be involved in gene silencing, a fundamental process known as RNA interference. (phys.org)
Cleavage2
- Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage. (anl.gov)
- To date, base complementarity is recognized as the major determinant of specific target cleavage (or slicing), but little is known about how Argonaute inspects base pairing before cleavage. (anl.gov)
20231
- Shen, Z. et al, Oligomerization-mediated activation of a short prokaryotic 1 Argonaute, Nature (2023). (phys.org)
NgAgo2
- A new technology based on the protein Argonaute from Natronobacterium gregoryi (NgAgo) could change how gene editing is approached. (genengnews.com)
- In an announcement published on Wednesday, the research team led by Han Chunyu, an associate professor with Hebei University of Science and Technology, said they retracted the paper because of the continued inability of the research community to reproduce the key results in their paper on Argonaute protein (NgAgo), which they claimed to be a powerful genome-editing tool. (chinadaily.com.cn)
Mammalian2
- Little is known, however, about the functionality of siRNA binding to the other three mammalian Ago proteins, and what data are available are conflicting. (genomeweb.com)
- Further, all four Ago proteins encoded in the mammalian genome are expressed in most tissues and cultured mammalian cell lines, the MIT group wrote in their study, which appeared in PLOS One . (genomeweb.com)
Dicer2
- Cleaved lincRNAs are processed via DICER-LIKE4 (DCL4) protein, resulting in production of phasiRNAs. (edu.sa)
- Important proteins involved in these processes are ARGONAUTE and DICER. (bvsalud.org)
Distinct2
- Here, we show that LIMD1 coordinates the assembly of an AGO-TNRC6 containing miRISC complex by binding both proteins simultaneously at distinct interfaces. (york.ac.uk)
- Adding chemical groups to the DNA backbone and modifying histone proteins impart distinct characteristics on chromatin architecture. (frontiersin.org)
Biogenesis1
- Evidence indicates that Alix, an accessory protein of the endosomal sorting complex required for transport (ESCRT), is involved in the biogenesis of extracellular vesicles (EVs). (spandidos-publications.com)
Argonaute27
- The update on RNA-silencing focused on Argonaute2, which is a protein that can switch-off a gene by intercepting and slicing the gene's RNA transcripts before they are translated as proteins. (isaaa.org)
- Though Argonaute2 is not the only type of Argonaute protein, it appears to be the only Argonaute protein capable of terminating target RNA directly. (isaaa.org)
- Preliminary experiments suggest that by interacting with Argonaute2, PICK1 can relieve this block of protein synthesis and increase the production of specific proteins. (ukri.org)
- Our main hypothesis is that PICK1 plays an important role in regulating protein synthesis close to active synapses via its interaction with Argonaute2. (ukri.org)
- We will use established methods for analysing protein synthesis while manipulating the PICK1-Argonaute2 interaction under different conditions of synaptic activity. (ukri.org)
- We will investigate whether PICK1 is involved in local protein synthesis in dendrites and consequent regulation of dendritic spine size via its interaction with Argonaute2. (ukri.org)
- Die graphische Aufarbeitung der Dynamik von humanen Argonaute2-Proteinen (oben gezeigt die Echtzeitänderung des Abstands zwischen den Argonaute-Flügeln gemessen an einem einzelnen Molekül, unten die Kristallstruktur des humanen Argonaute2-Proteins). (idw-online.de)
Gene Silencing3
- It is known as the guide strand, incorporated into the Argonaute protein and leads gene silencing. (wikipedia.org)
- Argonautes' gene-silencing functions also help cells cope with rogue genetic activity from invading viruses or cancer-promoting DNA mutations. (scripps.edu)
- Read more about the gene-silencing protein at http://www.scripps.edu/news/press/2012/20120426mcrae.html . (isaaa.org)
SiRNAs1
- To extend these observations in vivo , the researchers examined the knockdown effect of siRNAs targeting the CDS and 3' UTR of three genes - coagulation factor VII, fatty acid desaturase 1, and Ras-related protein Rab-5C - in mice. (genomeweb.com)
Molecules2
- Furthermore, the scientists discovered a second mode of action of Importin 8: Importins are molecules that are responsible for the transport of proteins into the nucleus. (mpg.de)
- Ago proteins in eukaryotes are known to remain as simple molecules throughout activation, with the ability to bind only to other simple molecules. (phys.org)
Genes4
- However, miRNAs can't shut off genes on their own: They need to form complexes with other proteins. (mpg.de)
- The gene-silencer in question is Argonaute 2, a molecular machine in cells that can grab and destroy the RNA transcripts of specific genes, preventing them from being translated into proteins. (scripps.edu)
- Proteins are made by translating genetic information encoded in DNA sequences (genes). (ukri.org)
- Además de su papel en el silenciamiento de transposones, los ARNpi en diversos organismos intervienen en la regulación de genes celulares. (bvsalud.org)
Molecule1
- Scientists of the Max Planck Institute of Biochemistry have now identified the protein Importin 8 as a central factor, that facilitates the switch molecule to find its target ( Cell , 6th February, 2009). (mpg.de)
Endonucleases2
- In this video, learn more about argonautes, including how these nucleic acid-guided endonucleases differ from Cas enzymes and potential applications. (neb.com)
- Prokaryotic Argonautes are nucleic acid guided endonucleases involved in prokaryotic cellular defense against foreign genetic elements. (neb.com)
Translational2
- Figure 4: Translational and post-translational regulation of DRB1 and DCL1, and evolutionary conservation of DRB1 and DRB2 proteins. (nature.com)
- Proteins of the RsmA-CsrA family are translational regulators in many bacterial species. (biologicmodels.com)
Roles1
- Many have been assigned roles in modulating the local translation of proteins that are essential to dendritic spine morphogenesis, synaptic function and memory formation. (ukri.org)
Eukaryotes2
Putative1
- Additionally, EZH2 occupies promoter regions of putative tumor suppressor as well as oncogenic miRNAs and influences Argonaute Protein 2 expression. (tum.de)
Expression2
Complex1
- Yet Argonautes' workings are complex and not yet entirely understood. (scripps.edu)
Ribosome1
- Blocking ribosome binding explains how the RsmA/CsrA proteins prevent RNA translation. (biologicmodels.com)
Regulation1
- The activity-dependent regulation of Argonaute 2 function in neurons by PICK1. (ukri.org)
Constitute1
- The short version of these prokaryotic proteins constitute 58% of all Argonautes, and are now emerging as a hot spot in the field," said senior author Tianmin Fu, assistant professor of biological chemistry and pharmacology in The Ohio State University College of Medicine. (phys.org)
Nucleus1
- In prokaryotes that have no nucleus, there are two types of Argonaute proteins, long Argonautes and short Argonautes. (phys.org)
Atomic structure1
- Three-dimensional atomic structure of a human protein which is mainly involved in regulating the activities of cells has been identified by the Scripps Research Institute. (isaaa.org)
Functional1
- While oligomerization of proteins is not rare, understanding its role in a protein's activation is key to understanding how a protein interacts with other proteins and to determining its functional purpose. (phys.org)
MicroRNA2
- Here, we summarize the different types of epigenetic enzymes which target corresponding protein domains, emphasize DNA methylation , histone modifications, and microRNA-mediated cooperation with epigenetic modification, and highlight recent achievements in developing targets for epigenetic inhibitor therapy. (frontiersin.org)
- RNA-silencing requires an Argonaute protein and guide RNA called microRNA. (isaaa.org)
Coding sequence1
- NEW YORK (GenomeWeb) - A Massachusetts Institute of Technology-led research team this month reported new data suggesting that an siRNA targeting a messenger RNA's 3' untranslated region (UTR), rather than its coding sequence (CDS), can harness the activity of multiple Argonaute proteins to better suppress its target. (genomeweb.com)
Structural1
- SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
Species2
- So depending on the species that the Argonaute is from, they can target DNA or RNA substrates and they can use DNA or RNA guides. (neb.com)
- Argonautes from different prokaryotic species may utilize either DNA or RNA guides to target DNA or RNA substrates, leading to many potential combinations of guide and substrate preferences. (neb.com)
Separation1
- RNA strand separation and incorporation into the Argonaute protein are guided by the strength of the hydrogen bond interaction at the 5′-ends of the RNA duplex, known as the asymmetry rule. (wikipedia.org)
Target2
Organisms2
- When we talk about one protein that is expressed everywhere, in all organisms, we know this protein is inherently important, even if we don't yet know all of its specific functions," said first author Zhangfei Shen, a postdoctoral scholar in Fu's lab. (phys.org)
- Argonaute protein (Ago) exists in almost all organisms. (bionotatki.com)
Study2
- That problem led us to look for a way to get Argonautes to unload these miRNAs," said Nabanita De, a postdoctoral fellow in MacRae's laboratory who was first author of the new study. (scripps.edu)
- However, the failure of an increasing number of scientists from abroad and home to reproduce the results of the study raised doubts that the protein works as a gene editor. (chinadaily.com.cn)