Where are regulatory sequences located?
Why are regulator hub genes important?
How does transcription repression work?
What is the regulation of the lac operon in E. coli?
How can we reconstruct regulatory networks?
How do regulatory networks differ from metabolic networks?
Which kinase domain is responsible for binding to specific phosphotyrosine residues?
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Where do DNA binding regulatory proteins bind on DNA?
All TFs bind at the promoters just upstream of eukaryotic genes, similar to bacterial regulatory proteins. However, they also bind at regions called enhancers, which can be oriented forward or backwards and located upstream or downstream or even in the introns of a gene, and still activate gene expression.
What do regulatory genes bind to?
Regulatory genes through their influence on several downstream genes are known to increase the production of secondary metabolites. Transcription factors are one such regulatory gene known to bind to the promoter region and upregulate genes in a metabolic pathway.
What binds to regulatory sequences?
Key to this control is the recruitment of transcription factors (TFs) that bind to regulatory sequences, such as promoters, enhancers, repressors and insulators. These target sequences are spread across DNA.
How does a regulatory protein identify its binding site?
One commonly used approach to identify transcription factor-binding sites is to delineate a group of coregulated genes [e.g., by clustering genes on the basis of their expression profiles (2, 3), or functional annotation] and search for common sequence patterns in their upstream regulatory regions.
How do regulatory proteins work?
Regulatory proteins, such as transcription factors (TFs), protect their binding DNA sequences from nuclease cleavage, resulting in the markedly increased accessibility surrounding their binding sites and over neighboring chromatin (Hesselberth et al., 2009).
Where are the regulatory genes located?
They are present upstream near the transcription start sites of genes in between the operator and structural gene. Regulatory gene regulates the expression of structural genes by its protein products that are mostly transcription factors.
Where do most transcription regulators bind?
How or where do most transcription regulators bind? Most transcriptional regulator proteins bind DNA as dimers. Dimerization roughly doubles the area of contact with the DNA, making the interaction tighter and more specific.
Are regulatory sequences bound by proteins?
In DNA, regulation of gene expression normally happens at the level of RNA biosynthesis (transcription). It is accomplished through the sequence-specific binding of proteins (transcription factors) that activate or inhibit transcription.
What is a regulatory protein for a gene?
regulatory protein (gene-regulatory protein) Any protein that influences the regions of a DNA molecule that are transcribed by RNA polymerase during the process of transcription. These proteins, which include transcription factors, therefore help control the synthesis of proteins in cells. A Dictionary of Biology.
Where is the binding site found?
A binding site is a position on a protein that binds to an incoming molecule that is smaller in size comparatively, called ligand. In proteins, binding sites are small pockets on the tertiary structure where ligands bind to it using weak forces (non-covalent bonding).
What are the three binding sites on a ribosome?
tRNA molecules bind to the ribosome in a solvent-accessible channel at the subunit interface. Three binding sites for tRNA, called the aminoacyl site (A site), peptidyl site (P site), and exit site (E site), have been identified on both the large and small subunit (Fig.
Is the promoter the binding site?
Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase.
What does a regulatory gene do in an operon?
In the Operon Model, the regulatory genes are those that code for the production of regulatory proteins. For instance, the regulatory gene in lac operon is the lac I gene that codes for the lac repressor. The repressor protein binds to operator gene, which consequently prevents the production of a specific enzyme.
Are regulatory genes part of the operon?
Not always included within the operon, but important in its function is a regulatory gene, a constantly expressed gene which codes for repressor proteins. The regulatory gene does not need to be in, adjacent to, or even near the operon to control it.
What does the repressor bind to?
A repressor, as related to genomics, is a protein that inhibits the expression of one or more genes. The repressor protein works by binding to the promoter region of the gene(s), which prevents the production of messenger RNA (mRNA).
What does the regulatory gene do in lac operon?
However, the lacI gene (regulatory gene for lac operon) produces a protein that blocks RNAP from binding to the operator of the operon. This protein can only be removed when allolactose binds to it, and inactivates it. The protein that is formed by the lacI gene is known as the lac repressor.
What are regulatory proteins?
Regulatory proteins, such as transcription factors (TFs), protect their binding DNA sequences from nuclease cleavage, resulting in the markedly increased accessibility surrounding their binding sites and over neighboring chromatin ( Hesselberth et al., 2009 ). Therefore, TF binding sites can be inferred within open-chromatin sites by the regions with a steep drop in accessibility. Both high-depth DNase-seq and paired-end ATAC-seq data can be used to systematically reveal the genome-wide cis-regulatory elements, that is, digital genomic footprinting (DGF) ( Hesselberth et al., 2009 ). BinDNase is a supervised method to detect TF footprinting by automatically extracting features from the DNase-seq (or ATAC-seq) data for each TF that maximally discriminate bound and unbound genomic locations ( Kahara and Lahdesmaki, 2015 ). Bivariate genomic footprinting (BaGFoot) is another approach that effectively detects TF activity by capturing two TF-dependent effects on chromatin accessibility, footprinting and motif-flanking accessibility ( Baek et al., 2017 ). BaGFoot is robust to different accessibility assays (DNase-seq and ATAC-seq), all examined peak-calling programs, and to a variety of cut bias correction approaches.
Which receptors associate with proteins that have tyrosine kinase activity?
Tyrosine kinase-associated receptors associate with proteins which have tyrosine kinase activity.
What is the CFTR protein?
The CFTR protein is composed of a linear stretch of 1480 amino acids that form an integral membrane glycoprotein. A comparison of the nucleotide sequence across available databases places this protein as a member of the ABC transporter superfamily. The topology of the protein contains the common features of twofold symmetry with six transmembrane domains and an intracellular nucleotide-binding fold. The CFTR is unique in the presence of a central intracellular R domain enriched in phosphorylation sites used by the protein kinases A and C. Although most members of the superfamily are transporters (e.g., the multidrug resistance transporter (MDR) transports chemotherapy agents), the CFTR is a cAMP-regulated chloride and bicarbonate channel that must function for the outwardly rectifying chloride channel (ORCC) to transport chloride. Functional CFTR also downregulates the epithelial sodium channel (ENaC) in those cells in which both reside. More controversial functions have been reported, including transport of nucleotides and fatty acids.
What are the regulatory proteins of calcineurin?
A family of 22–24-kDa proteins, regulators of calcineurin (RCANs), identified in both yeast and mammalian cells acts as feedback inhibitors of calcineurin. The mammalian proteins are identical to proteins encoded in the Down's syndrome critical region 1 (DSCR1) gene (ZAK1-4, DSCRIL1, and DSCRIL). The expression of these proteins is upregulated by a calcineurin/NFAT-dependent mechanism. RCANs inhibit both calcineurin expression and activity. These proteins can interact with calcineurin through multiple interaction sites. Two sites are located in exon 7 of RCAN, a PxIxxIT motif similar to the PxIxIT motif found in NFAT and an ELHA motif. Another highly conserved serine–proline motif (FLSPP) is similar to sequences found in calcineurin substrates. The interaction of RCANs with calcineuin does not require, but is facilitated by, the presence of Ca 2+ and CaM. Phosphorylation of RCANs by GSK3 prevents their inhibitory activity suggesting that in vivo, depending on their phosphorylation state, RCANs could act as activators as well as inhibitors of calcineurin.
What is the receptor that secretes cyclic GMP?
Receptor guanylate (sometimes called guanylyl) cyclases catalyse the production of cyclic GMP. An example of this group is the atrial natriuretic peptide (ANP) receptor. ANP is secreted by the atrium of the heart when blood pressure rises and stimulates the kidney to secrete Na + and water, and also induces the smooth muscle of vessel walls to relax. The binding of ANP activates the intracellular catalytic domain (guanylate cyclase) to produce cyclic GMP, which in turn binds to and activates a G-kinase; this phosphorylates serine and threonine residues on specific proteins. There are few members in this family.
What is the lac operon?
The lac operon is the classic system used to investigate gene regulation in bacterial genetics. The lac repressor protein (LacI) forms a tetramer when binding DNA. The size and charge of the LacI tetramer are important in bending the DNA around this protein. Several slightly different structural models have been proposed for wrapping DNA around the LacI tetramer. Many DNA-binding regulatory proteins bind two separate sequences located a few base pairs apart. This is true for LacI whose tetramer is arranged as a dimer of dimers and forms a V-shape. It makes contact twice with the DNA, at each of the tips of the V.
What is an enzyme-linked receptor?
Unlike G-protein-linked receptors, enzyme-linked receptors are single-pass transmembrane proteins with (like G-proteins) the ligand-binding site outside the cell and the catalytic unit inside the cell. Instead of the cytosolic domain interacting with a G-protein, the cytosolic domain has its own enzyme activity or associates directly with an enzyme. There are five known classes of enzyme-linked linked receptor:
How are gene regulatory proteins purified?
They were eventually purified by fractionating cell extracts. Once isolated, the proteins were shown to bind to specific DNAsequences close to the genes that they regulate.
How does gene regulation work in biology?
A gene regulatory proteinrecognizes a specific DNAsequence because the surface of the protein is extensively complementaryto the special surface features of the double helixin that region. In most cases the protein makes a large number of contacts with the DNA, involving hydrogen bonds, ionic bonds, and hydrophobic interactions. Although each individual contact is weak, the 20 or so contacts that are typically formed at the protein-DNA interface add together to ensure that the interaction is both highly specific and very strong (Figure 7-12). In fact, DNA-protein interactions include some of the tightest and most specific molecular interactions known in biology.
What is the bending of DNA induced by the binding of the catabolite activator protein (CAP)?
The bending of DNA induced by the binding of the catabolite activator protein (CAP). CAP is a gene regulatory protein from E. coli. In the absence of the bound protein, this DNA helix is straight.
How did gene regulation begin?
The first step toward understanding generegulation was the isolation of mutantstrains of bacteria and bacteriophage lambda that were unable to shut off specific sets of genes. It was proposed at the time, and later proven, that most of these mutants were deficient in proteins acting as specific repressors for these sets of genes. Because these proteins, like most gene regulatory proteins, are present in small quantities, it was difficult and time-consuming to isolate them. They were eventually purified by fractionating cell extracts. Once isolated, the proteins were shown to bind to specific DNAsequences close to the genes that they regulate. The precise DNA sequences that they recognized were then determinedby a combination of classical genetics, DNA sequencing, and DNA-footprinting experiments (discussed in Chapter 8).
How does a cell determine which genes to transcribe?
How does a cell determine which of its thousands of genes to transcribe? As mentioned briefly in Chapters 4 and 6, the transcription of each gene is controlled by a regulatory region of DNA relatively near the site where transcription begins. Some regulatory regions are simple and act as switches that are thrown by a single signal. Many others are complex and act as tiny microprocessors, responding to a variety of signals that they interpret and integrate to switch the neighboring gene on or off. Whether complex or simple, these switching devices contain two types of fundamental components: (1) short stretches of DNA of defined sequence and (2) gene regulatory proteins that recognize and bind to them.
How many contacts are there between DNA and protein?
The binding of a gene regulatory protein to the major groove of DNA. Only a single contact is shown. Typically, the protein-DNA interface would consist of 10 to 20 such contacts, involving different amino acids, each contributing to the strength of the (more...)
Where does DNA come from?
The DNA fragments are derived from the small, circular mitochondrial DNA molecules of a trypanosome. Although the fragments are only about 200 nucleotide pairs long, many of (more...) A related and equally important variable feature of DNAstructure is the extent to which the double helixis deformable.
How long do proteins last in a cell?
It is possible for a cell to make proteins that last for months ; hemoglobin in red blood cells is a good example. However, many proteins are not this long-lasting; they may be degraded in days, hours, or even minutes. What is the advantage of short-lived proteins?
Which operon controls the metabolism of athelose?
Metabolism of athelose is controlled by the ath operon. The genes of the ath operon code for the enzymes necessary to use athelose as an energy source. You have found the following: The genes of the ath operon are expressed only when the concentration of athelose in the bacterium is high.
What are the letters in the lac operon?
The figure shows a structure of the lac operon. Letters from A to E mark the definite structures of the operon. Letter A marks the gen before structural genes. Letter B marks the part of the operon, which consists of lacZ, lacY, and LacA genes. Letter C indicates the enzyme, which moves along the operon. Letter D marks the part, named lacl. This part is located before others in the sequence. Letter E indicates the molecule, which can bind to the structure A.
Is an operon transcribed?
operon is transcribed, but not sped up through positive control:
What is binding of a repressornear the transcription start site?
For example, the binding of a repressornear the transcription start site can block the interaction of RNA polymeraseor general transcription factorswith the promoter, which is similar to the action of repressors in bacteria. Other repressors compete with activators for binding to specific regulatory sequences.
How are genes controlled in eukaryotes?
The expression of eukaryotic genes is controlled primarily at the level of initiation of transcription, although in some cases transcription may be attenuated and regulated at subsequent steps. As in bacteria, transcription in eukaryotic cells is controlled by proteins that bind to specific regulatory sequences and modulate the activity of RNA polymerase. The intricate task of regulating gene expression in the many differentiated cell types of multicellular organisms is accomplished primarily by the combined actions of multiple different transcriptional regulatory proteins. In addition, the packaging of DNA into chromatin and its modification by methylation impart further levels of complexity to the control of eukaryotic gene expression.
Why do transcription factors loop?
DNA looping. Transcription factors bound at distant enhancers are able to interact with general transcription factors at the promoter because the intervening DNA can form loops. There is therefore no fundamental difference between the action of transcription (more...)
Where are enhancers located in a cell?
In contrast to the relatively simple organization of CCAAT and GC boxes in the herpes thymidine kinase promoter, many genes in mammalian cells are controlled by regulatory sequences located farther away (sometimes more than 10 kilobases) from the tran scriptionstart site . These sequences, called enhancers, were first identified by Walter Schaffner in 1981 during studies of the promoter of another virus, SV40 (Figure 6.20). In addition to a TATA boxand a set of six GC boxes, two 72-base-pair repeats located farther upstream are required for efficient transcription from this promoter. These sequences were found to stimulate transcription from other promoters as well as from that of SV40, and, surprisingly, their activity depended on neither their distance nor their orientation with respect to the transcription initiation site (Figure 6.21). They could stimulate transcription when placed either upstream or downstream of the promoter, in either a forward or backward orientation.
What are cis-acting regulatory sequences?
cis-Acting Regulatory Sequences: Promoters and Enhancers. As already discussed, transcriptionin bacteria is regulated by the binding of proteinsto cis-acting sequences (e.g., the lacoperator) that control the transcription of adjacent genes. Similar cis-acting sequences regulate the expression of eukaryotic genes.
Which sequences are binding sites for transcription factors?
Other cis-acting sequences serve as binding sites for a wide variety of regulatory factors that control the expression of individual genes.
Does methylation inhibit transcription?
Methylation inhibits transcription of these genes via the action of a protein, MeCP2, that specifically binds to methylated DNA and represses transcription. Interestingly, MeCP2 functions as a complex with histone deacetylase, linking DNA methylation to alterations in histone acetylation and nucleosomestructure.
What is negative regulation?
Negative Regulation. The binding of a specific protein ( repressor) inhibits transcription from occurring. DNA bound repressors often act to prevent RNA polymerase from binding to the promoter, or by blocking the movement of RNA polymerase. In order to be effective, activators and repressors must be able to exist in 2 states.
What is the role of activators in transcription?
Positive Regulation. The binding of specific protein ( activator) is required for transcription to begin. DNA bound activators can regulate transcription by helping with ignition. To do this they sometimes tether RNA polymerase to the promoter. Negative Regulation. The binding of a specific protein ( repressor) inhibits transcription from occurring.
Where are regulatory sequences located?
In addition to the promoter, the control region of a gene typically contains a number of additional regulatory sequences (also called cis - elements ). These can be located before ( upstream) or, less frequently, after ( downstream) the actual coding region. Regulatory sequences need not be close to the gene, but can in fact be located several thousand bases away.
Why are regulator hub genes important?
Regulator hub genes are more likely to have interactions with miRNAs, because they regulate large number of targets. miRNAs together with master TFs prefer to coregulate their targets. Regulator hub genes are very important constituents in the GRNs, since perturbations on them can disturb functions of numerous target genes. As miRNAs buffer stochastic perturbations, their preference to regulator hub genes could provide robustness of the regulatory network [19].
How does transcription repression work?
Transcriptional repression is a key mechanism to control the activity of prokaryotic promoters. Enzymes used in a specific metabolic pathway are often organized into an operon that is transcribed into a single polycistronic mRNA. Specific repressor proteins then control the transcriptional activity of the operon by regulating RNA polymerase binding to the promoter. Repressor proteins are DNA-binding proteins that typically block RNA polymerase access to the −10 and/or −35 regions in the promoter or transcription elongation by associating with an operator sequence that is positioned downstream of the start site of transcription. Usually these regulatory proteins undergo allosteric changes in response to binding of a specific ligand. The paradigm of a prokaryotic operon regulated by a specific repressor protein is the lac operon in E. coli. In this system synthesis of proteins necessary for usage of lactose as a carbon source is repressed by the lac repressor protein if cells have the possibility to use glucose for growth. Thus, in the presence of glucose the lac repressor binds to its operator sequence, which overlaps the transcription start site in the lac operon ( Fig. 6 ), and blocks RNA polymerase binding to the lac promoter. If cells are grown on lactose as the carbon source, lactose functions as an inducer of lac operon transcription by binding to the lac repressor and converting it to an inactive form that does not bind DNA ( Fig. 6) and therefore is unable to inhibit transcription of the lac operon. The polycistronic lac mRNA encodes for the specific proteins necessary for metabolism of lactose. The lac operon represents an example of an inducible system where an inducer activates transcription. However, inducers can also have the opposite effect and repress transcription of an operon, like the trp operon in E. coli.
What is the regulation of the lac operon in E. coli?
coli. The lac I gene encodes for a transcriptional repressor protein that binds to an operator sequence in the lac operon, thereby preventing synthesis of the structural genes required for metabolism of lactose. If E. coli is grown on lactose as the sole carbon source, lactose binds to the lac I repressor protein and inactivates it as a repressor of lac operon transcription. As a consequence, the β-galactosidase ( lac Z ), the permease ( lac Y ), and the β-galactosidase transacetylase ( lac A) enzymes are synthesized.
How can we reconstruct regulatory networks?
Notwithstanding these challenges to those wishing to study regulation, two high-throughput technologies have made it possible to reconstruct regulatory networks at the large scale. First, microarray analysis enables the determination of the expression profile of an entire genome in one experiment ( Gardner et al. 2003 ). Second, it is now possible to determine with some accuracy where all of the transcription factors are binding in the genome under a given set of experimental conditions ( Lee et al. 2002 ). These two approaches, especially when used in combination with each other or with the existing literature, are a powerful way of characterizing a regulatory network ( Hartemink et al. 2002; Herrgard et al. 2003 ).
How do regulatory networks differ from metabolic networks?
Regulatory networks differ from metabolic networks in ways that impact the network reconstruction as well as modeling approaches ( Herrgard et al. 2004). First, the components are different. Whereas metabolic networks involve metabolites, enzymes, and transport proteins, regulatory networks involve regulatory proteins and the promoter regions of target genes. Second, most of the metabolic proteins are well conserved across species. Regulatory proteins may also be conserved. However, the cis regulatory regions are generally not conserved across species, and transcription factor binding sites are extremely difficult to find in promoter regions due to their short length, although progress is being made ( Beer et al. 2004 ). In addition, the interactions of transcription factors at one promoter region can be extremely complex ( Davidson et al. 2002 ), and even a single nucleotide difference in a transcription factor binding site can change the specificity of cofactor binding ( Leung et al. 2004 ).
Which kinase domain is responsible for binding to specific phosphotyrosine residues?
This tight regulatory mechanism was first identified in cytoplasmic tyrosine protein kinases of the src-family ( Harrison 2003 ), which in addition to the protein kinase domain possess an src-homology (SH)2 domain facilitating binding to specific phosphotyrosine residues localized within certain binding motifs and an SH3 domain mediating binding to proline-rich motifs. In addition to cytoplasmic tyrosine kinases, several cell surface receptors possess a tyrosine kinase domain in their cytoplasmic part. Receptor tyrosine kinases —such as the epidermal growth factor receptor (EGF-R) ( Schlessinger 2002) and the platelet-derived growth factor receptor (PDGF-R) ( Heldin 1992 )—are characterized by specific domains within the extracellular portion that interacts with the ligand, by a single transmembrane domain, and by a tyrosine kinase domain in part exposed to the cell interior.
