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siswa setyahadi 2014 Regulation of gene expression siswa setyahadi 2014 siswa setyahadi 2014 • Gene: A DNA segment that encodes the all genetic information required to produce functional biological products (Note that: not all transcripts are messenger RNA). • G.enome: A. complete set of genes of a given species. • Gene expression: A process of gene transcription and/or gene translation siswa setyahadi 2014 • Most of prokaryotic genomes contain 4.000 or so genes, although some simple bacteria have only 500-600 genes. • The human genomes contain about 35.000 genes Specificity of gene expression siswa setyahadi 2014 • Temporal specificity (also called stage specificity) • Spatial specificity (also called tissue specificity) Type of gene expression a. Constitutive expression siswa setyahadi 2014 • Some genes are essential and necessary for life, and therefore are continuously expressed, such as those enzymes involved in TCA • These genes are called housekeeping genes. siswa setyahadi 2014 • b. Induction and repression • In addition to constitutively expressed genes, all cells contain genes that are expressed only in special circumstances • Such genes are said to be regulated • Both prokaryotic and eukaryotic cells adapt to changes in their environment by turning the expression genes on and off siswa setyahadi 2014 • Some genes demonstrate higher expression level once being activated, such as enzymes involved in DNA repairing. It is called induced expression . • On the other hand, some genes are repressed and their expression levels are lower, such as the enzymes for Trp synthesis when Trp is abundant. It is called repressed expression Regulatory Elements siswa setyahadi 2014 • Gene expression is a multiple-level process. • Gene expression is also a multiple components process. • In general, every step that is required to make an active gene product can be the focus of a regulatory event. • In fact, the most important stage for the regulation of most genes is when transcription initiation because it would be a waste to make the RNA if neither the RNA nor its encoded protein is needed. Basic Elements • Basic elements that regulate the transcription include: a. Special DNA sequences b. Regulatory proteins c. DNA-protein interaction and protein-protein interaction siswa setyahadi 2014 d. RNA polymerase a. Special DNA sequence • Gene expression of prokaryotic systems is regulated based on the operon model which is composed of structural genes, promoter, operator and other regulatory sites. promoter operator siswa setyahadi 2014 Other regulatory sites Structural gene • Operons that include two to six genes transcribed as a unit are common; some operons contain 20 or more genes. • Is a set of adjacent genes whose mRNA is synthesized in one piece, plus the adjacent regulatory signals that affect transcription of the genes Activator binding site promoter A B C Regulatory sequences Genes transcribed as a unit siswa setyahadi 2014 DNA Repressor Binding site (operator) Types of operons siswa setyahadi 2014 • Inducible: substrate needs to be present before transcription of genes involved in its breakdown occurs. Mostly metabolic pathways-breaking things down for energy, e.g. lac operon • Repressible: anabolic pathways (building things)- no reason to make protein to build a molecule that is already available. E.g. tryptophan operon. An E. coli cell won’t waste a bunch of energy making tryptophan if it is available from the medium. Tryptophan represses its own synthesis siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 RNA synthesis is blocked by repressor siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 • Promoter. The DNA sequence that RNA-pol can bind and initiate the transcription. siswa setyahadi 2014 siswa setyahadi 2014 • As mentioned earlier, RNA polymerases bind to DNA and initiate transcription at promoters. • The nucleotide sequences of promoters vary considerably, affecting the binding affinity of RNA polymerases and thus the frequency of transcription initiation. • By convention, DNA sequences are shown as they exist in the nontemplate strand, with the 5-terminus on left • Most base substitutions in the -10 regions have a negative effect on function. • For example, mutations that result in a shift away from the consensus sequence usually decrease promoter function; conversely, mutations toward consensus usually enhance promoter function. siswa setyahadi 2014 • Most E. coli promoters have a sequence close to a consensus • Operator. The DNA sequence adjacent to the structural genes that the repressor protein can bind to and prevent the transcription of structural genes • The operators are generally near a promoter. siswa setyahadi 2014 Coding sequences b. Regulatory proteins • For prokaryotic systems: • Repressor: • It binds to the operator and prevent the transcription, known as negative regulation. • Activator: siswa setyahadi 2014 • It associates with DNA near the initiation point, resulting in the increase of RNA-pol binding affinity and the enhancement of the transcription efficiency. siswa setyahadi 2014 • Specific factor: It facilitates the binding of RNA-pol to particular DNA sequence once associating with other elements. • Catabolite gene activator protein (CAP) is a typical one. For some genes, RNA pol cannot bind to the promoter without CAP. siswa setyahadi 2014 • Regulation by means of a repressor protein that blocks transcription is referred to as negative regulation. • Activators provide a molecular counterpoint to repressors; they bind to DNA and enhance the activity of RNA polymerase at a promoter; this is positive regulation. siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 • General concepts • Prokaryotes • Eukaryotes • Controls • Chromosome organization • Transcription • Post-transcription • Translation • Post translation siswa setyahadi 2014 oIn prokaryotes, gene expression is controlled by the external environment. Ex. fuel availability oIn eukaryotes, gene expression is controlled by the internal environment. Ex. Hormones, toxic substances, etc. siswa setyahadi 2014 Regulation of Gene Expression in Prokaryotes siswa setyahadi 2014 • In prokaryotes, control of gene expression occurs at 3 levels: • Transcription • Translation • Post translation Figure 17-1 Life span (stability) of mRNA Translation rate Onset of transcription Protein activation or inhibition (by chemical modification) Protein Ribosome mRNA RNA polymerase RNA polymerase DNA Translational control Post-translational control siswa setyahadi 2014 Transcriptional control Common Features • Prokaryotic systems were developed earlier. Their internal and external conditions are relative simple. • Prokaryotic genes are polycistron systems, that is, several relevant genes are organized together in a series format. siswa setyahadi 2014 • The majority of gene regulation is negative. • Inducers are used to remove the repression. siswa setyahadi 2014 Lac Operon Lactose metabolism in E. coli siswa setyahadi 2014 • Galactoside permease: transport lactose into the cell across the cell membrane • β -Galactosidase: hydrolyze lactose to glucose and galactose or convert lactose to allolactose • Thiogalactoside transacetylase: may involved in the detoxification. • For lacl· system, all three enzymes are expressed continuously regardless of the presence of lactose. • For lacl+ system, bacteria do not express these three enzymes when glucose is available. However, bacteria produce those enzymes if lactose is present and glucose is absent siswa setyahadi 2014 Inducible Expression siswa setyahadi 2014 • lac gene demonstrate how bacteria use different types of nutrient as the source of carbon. • Glucose is the most abundant and prevailing nutrient, and use of it is the most efficient way. • Lactose is an alternative choice when glucose is exhausted. Sequence of lac operon • lac operon has a weak promoter (TTTACA/TATGTT), and has a basal expression level. • CAP (Catabolite gene activator protein) binding site is at - 60 region. siswa setyahadi 2014 • CAP is a homodimer with binding ability to DNA and cAMP. siswa setyahadi 2014 • Glucose inhibits the formation of cAMP. siswa setyahadi 2014 • When glucose is present, [cAMP] is lower. • Only after glucose is exhausted, [cAMP] becomes higher. The CAP-cAMP complex is formed, and this complex binds to the CAP binding site on lac operon. siswa setyahadi 2014 Situation 1 • lac/ gene has its own promoter, and its expression can produce Lac/ repressor. • The tetrameric Lac repressor binds to the lac operator site 01ac· • The binding blocks the RNA-pol moving on DNA template, and no lacZ, lacY, and lacA are expressed. siswa setyahadi 2014 • No use of lactose due to the negative regulation. siswa setyahadi 2014 Situation 2 • The galactosidase is weakly expressed (at the basal level}. • When lactose is present, it is converted to allolactose that binds to the repressor. siswa setyahadi 2014 • The repressor can no longer bind to the operator, and lac gene can be expressed. • Allolactose and IPTG are referred to as inducer. siswa setyahadi 2014 Inducers Presence of Lactose • The lacZ, Y and siswa setyahadi 2014 A RNA transcript is very unstable and could be degraded quickly. Therefore, the synthesis of three enzymes will be cease under normal condition. Situation 3 siswa setyahadi 2014 • When glucose is present, the [cAMP] is low, no CAP-cAMP is formed and the expression of the lac operon is still low. Situation 4 siswa setyahadi 2014 • When glucose is absent and lactose is present, the CAP-cAMP complex binds to the CAP site to activate the lac gene. siswa setyahadi 2014 lac Operon Undergoes Positive Regulation Coordinate Regulation • It is the interaction between CAP-cAMP and RNApol that greatly stimulates the activation of lac gene. • The positive regulation and removal of the negative regulation of Lac/ repressor allow bacteria to use lactose as the source of carbon. siswa setyahadi 2014 • The positive regulation of CAP-cAMP and the negative regulation of Lac/ repressor constitute a coordinated regulation unit. siswa setyahadi 2014 Regulation of Gene Expression in Eukaryotes siswa setyahadi 2014 • In eukaryotes, control of gene expression occurs at these same 3 levels + 2 other levels: • Chromosome organization (remodeling) • RNA processing siswa setyahadi 2014 • Transcription in the eukaryotic nucleus is separated from translation in the cytoplasm in both space and time. • Regulation of eukaryotic gene expression occurs at multiple levels, including transcription, processing, mRNA stability, and translation. • However, like prokaryotic gene, the initiation of transcription is also a crucial regulation point for eukaryotic gene expression Structural Features siswa setyahadi 2014 • Large genome : 3 x 109 bps, 35,000 genes. • Monocistron : One gene is transcribed into one mRNA, and one mRNA then is translated into one polypeptide. • Repeated sequences : different lengths and different frequencies. Often inverted repeats: complementary and opposite orientation. • Split genes : separated by introns and exons alternatively. Regulation Features • RNA-pol: 3 forms (I, II, and Ill) for different RNAs • Changes of chromosomal structure: • Hypersensitive site siswa setyahadi 2014 • Base modification : 5°/o of A are methylated. • Isomers-conversion: from negative supercoil in the native form to positive supercoil after activation • Histone changes • Positive regulation : • more accurate regulation and more efficient. • Transcription and translation are separated : at different locations. siswa setyahadi 2014 • Post-transcriptional modification : more complicated than prokaryotes. • Regulation through intercellular and intracellular signals : • hormone. Gene Regulatory Sequences • The expression of eukaryotic protein coding genes is regulated by multiple protein-binding DNA sequences, generically referred to as gene regulatory sequences . siswa setyahadi 2014 • These include promoters, enhancer and silencer. Cis-acting Elements siswa setyahadi 2014 • Note that the gene regulatory sequences are also called cis-acting elements since they are on the same DNA molecule as the gene being controlled (cis is Latin for “on the side”) • Promoter: TATA box, CAAT box, and GC box TATA Box • Sequence: TATAAAA • Location: - 25-- 30 bp siswa setyahadi 2014 • Function: It is the binding site for TFII D, which is required for RNA polymerase binding. Without TATA box, the 5'-end of transcriptional product is random. • Sequence: GCCAAT • Location: - - 80 bp • Function: It is the binding site for CTF1 (CAATbinding transcription factor) and C/EBP. The DNA-binding domain of TF1 is rich in basic Aas, and most likely it is in the alpha-helical conformation. C/EBP binds to DNA in a dimer known as leucine zipper. • Eukaryotes frequently have CAAT boxes, a strong promoter, usually located around -80 relative to the transcription start site siswa setyahadi 2014 CAAT Box GC Box • Sequence: GGGCGG siswa setyahadi 2014 • Location: -30 - -110 bp • Function: It is the binding site for a protein called Sp1. The DNA-binding domain of Sp1 is near the Cterminus and contains three zinc fingers . • One or more copies of GC-rich sequences are also referred to as CpG island. • These genes, which generally are transcribed at low rates, have been found upstream from the transcription start sites of "housekeeping genes." • Transcription from many eukaryotic promoters can be stimulated by control elements located thousands of base pairs away from the start site. • Such long-distance transcription control elements, referred to as enhancers, are common in eukaryotic genomes but fairly rare in bacterial genomes. • An enhancer is typically 100-200 bp long. • Enhance has no functionality without promoter. • Enhances can exert their stimulatory actions over distances of several thousand base pairs in presence of promoter. • They can be upstream, downstream, or even in the midst of a transcribed gene. siswa setyahadi 2014 Enhancer siswa setyahadi 2014 • Their functions are dependent on recognition by specific transcription factors. • A specific transcription factor bound at an enhancer element stimulates transcription by interacting with RNA polymerase II at a near by promoter siswa setyahadi 2014 Silencer siswa setyahadi 2014 • Silencers are control elements that can inhibit transcription. • A specific transcription factor that binds to a silencer control element and blocks transcription is called a repressor. • The protein transcription factors that bind to these specific sequences are known as trans-acting factors in that the genes that encode them can be on different DNA molecules {different chromosomes). • Trans-acting proteins bind indirectly to cis-acting elements and then regulate the transcription initiation. • Due to the complexity of eukaryotic transcription, there are many protein factors in transcription. The transacting factors can be transcription factors (TF). siswa setyahadi 2014 Trans-acting Factors General Structure of TF • DNA-binding domain siswa setyahadi 2014 • Activation domain • Protein-protein interaction domain Promoter and Regulatory Proteins co-activator RNA pol II complex siswa setyahadi 2014 TFIID • CTD of RNA-pol II is an important point of interaction with mediators and other protein complexes. siswa setyahadi 2014 • Cofactors facilitate the TF assembly. siswa setyahadi 2014 Transcription Repressor DNA-protein interactions siswa setyahadi 2014 • Regulatory proteins have discrete DNA-binding domains of particular structure, i,.e., binding motif • They can recognize DNA sequences in a affinity 104-106 times higher than usual • The AA side chains of regulatory proteins interact with bases of DNA through H bonds Motif • When several local peptides of defined secondary structures are close enough in space, they are able to form a particular "supersecondary " structure. siswa setyahadi 2014 • Zinc finger • HLH (helix-loop-helix) HTH (helix-turn-helix) Leucine zipper siswa setyahadi 2014 Leucine Zipper siswa setyahadi 2014 Yeast activator protein in GCN4 (PDB ID 1YSA) siswa setyahadi 2014 Zinc Finger siswa setyahadi 2014 Steroid Hormone Receptor Gene Specific Regulatory Proteins siswa setyahadi 2014 • As mentioned earlier, in order to initiate transcription, RNA polymerase II requires the assistance of general (basal) transcription factors since no eukaryotic RNA polymerase binds specifically to promoters by itself. • This binding process involves at least six basal transcription factors (labeled as TFIIs, transcription factors for RNA polymerase II). siswa setyahadi 2014 • Withonly these transcription (or basal) factors and RNA polymerase II attached (the basal transcription complex), the gene is transcribed at a low or basal rate. • However, the rate of transcription can be further increased by binding of other regulatory DNA binding proteins to additional gene regulatory sequences (such as the enhancer regions). • These regulatory DNA binding proteins are called gene-specific transcription factors (or transactivators} because they are specific to the gene involved. • They also can be called activators, inducers, repressors, or nuclear receptors. siswa setyahadi 2014 • In activation of gene, the DNA between the enhancer and the promoter loops out to allow the transcription factors bound to the enhancer to interact with the general transcription factors, other regulatory proteins or the RNA polymerase itself to increase the rate of transcription. • Gene repressor proteins that inhibit the transcription of specific genes in eukaryotes also exist. For example, when a repressor has attached to the silencer region near the enhancers, activators can be prevented from binding to the enhancers, and transcription is • repressed. • Thus, positive regulations predominate in all systems characterized of eukaryotes. siswa setyahadi 2014 • Note that, as already noted, eukaryotic RNA polymerases have little or no intrinsic affinity for their promoters. • The initiation of transcription is almost always dependent on the action of multiple activator proteins. • One important reason is that the storage of DNA within chromatin effectively renders most promoters inaccessible, so genes are normally silent in the absence of other regulation. siswa setyahadi 2014 Nucleus 1. Chromatin remodeling 2. Transcription Chromatin (DNA-protein complex) “Open” DNA (Some DNA not closely bound to proteins) Primary transcript (pre-mRNA) 3. RNA processing Cap Tail Mature mRNA Cytoplasm 4. mRNA stability Degraded mRNA (mRNA lifespan varies) 5. Translation mRNA Polypeptide modification (folding, transport, activation, degradation of protein) Active protein siswa setyahadi 2014 6. Post-translational Regulating the macromolecular composition of Cells • Which genes? • Amount of primary RNA transcript • RNA processing/transport • RNA degradation • Proteins • translation from mRNA • Covalent/Allosteric modulation • Degradation siswa setyahadi 2014 • Protein modification/transport 1. Principle of gene regulation Molecular circuits ------------------------------House keeping genes; constitutive gene expression Inducible; induction; repressible; repression siswa setyahadi 2014 RNA polymerase binds to DNA at promoters siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 Many prokaryotic genes are clustered and regulated in operons siswa setyahadi 2014 Lactose metabolism in E. coli siswa setyahadi 2014 The lac operon The control of gene expression © 2007 Paul Billiet ODWS siswa setyahadi 2014 • Each cell in the human contains all the genetic material for the growth and development of a human • Some of these genes will be need to be expressed all the time • These are the genes that are involved in of vital biochemical processes such as respiration • Other genes are not expressed all the time • They are switched on an off at need Operons • An operon is a group of genes that are transcribed at the same time. • They usually control an important biochemical process. • They are only found in prokaryotes. Jacob, Monod & Lwoff © 2007 Paul Billiet ODWS siswa setyahadi 2014 © NobelPrize.org The lac Operon © 2007 Paul Billiet ODWS siswa setyahadi 2014 The lac operon consists of three genes each involved in processing the sugar lactose One of them is the gene for the enzyme β-galactosidase This enzyme hydrolyses lactose into glucose and galactose Adapting to the environment © 2007 Paul Billiet ODWS siswa setyahadi 2014 • E. coli can use either glucose, which is a monosaccharide, or lactose, which is a disaccharide • However, lactose needs to be hydrolysed (digested) first • So the bacterium prefers to use glucose when it can 1. When glucose is present and lactose is absent the E. coli does not produce β-galactosidase. 2. When glucose is present and lactose is present the E. coli does not produce β-galactosidase. 3. When glucose is absent and lactose is absent the E. coli does not produce β-galactosidase. 4. When glucose is absent and lactose is present the E. coli does produce β-galactosidase © 2007 Paul Billiet ODWS siswa setyahadi 2014 Four situations are possible © 2007 Paul Billiet ODWS siswa setyahadi 2014 The control of the lac operon 1. When lactose is absent • A repressor protein is continuously synthesised. It sits on a sequence of DNA just in front of the lac operon, the Operator site • The repressor protein blocks the Promoter site where the RNA polymerase settles before it starts transcribing DNA I Regulator gene © 2007 Paul Billiet ODWS Blocked O Operator site z RNA polymerase y lac operon a siswa setyahadi 2014 Repressor protein 2. When lactose is present DNA I © 2007 Paul Billiet ODWS O z y a siswa setyahadi 2014 • A small amount of a sugar allolactose is formed within the bacterial cell. This fits onto the repressor protein at another active site (allosteric site) • This causes the repressor protein to change its shape (a conformational change). It can no longer sit on the operator site. RNA polymerase can now reach its promoter site 2. When lactose is present DNA I © 2007 Paul Billiet ODWS O z y a Promotor site siswa setyahadi 2014 • A small amount of a sugar allolactose is formed within the bacterial cell. This fits onto the repressor protein at another active site (allosteric site) • This causes the repressor protein to change its shape (a conformational change). It can no longer sit on the operator site. RNA polymerase can now reach its promoter site 3. When both glucose and lactose are present © 2007 Paul Billiet ODWS siswa setyahadi 2014 • This explains how the lac operon is transcribed only when lactose is present. • BUT….. this does not explain why the operon is not transcribed when both glucose and lactose are present. • When glucose and lactose are present RNA polymerase can sit on the promoter site but it is unstable and it keeps falling off Repressor protein removed DNA I O z y a Promotor site siswa setyahadi 2014 RNA polymerase 4. When glucose is absent and lactose is present • Another protein is needed, an activator protein. This stabilises RNA polymerase. • The activator protein only works when glucose is absent • In this way E. coli only makes enzymes to metabolise other sugars in the absence of glucose Activator protein steadies the RNA polymerase I © 2007 Paul Billiet ODWS O z y Promotor site a siswa setyahadi 2014 DNA Transcription Summary Carbohydrates Activator protein Repressor protein RNA polymerase lac Operon Not bound to DNA Lifted off operator site Keeps falling off promoter site No transcription + GLUCOSE - LACTOSE Not bound to DNA Bound to operator site Blocked by the repressor No transcription - GLUCOSE - LACTOSE Bound to DNA Bound to operator site Blocked by the repressor No transcription - GLUCOSE + LACTOSE Bound to DNA Lifted off Sits on the operator site promoter site Transcription © 2007 Paul Billiet ODWS siswa setyahadi 2014 + GLUCOSE + LACTOSE Two Main Mechanisms to Regulate Transcription in Bacteria • Use of different factors • These recognize different classes of promoters • Allows coordinated expression of different sets of genes • Binding other proteins (transcription factors) to promoters These recognize promoters of specific genes These may bind small signaling molecules These may undergo post-translational modifications The protein’s affinity toward DNA is altered by ligand binding or post-translational modifications • Allows expression of a specific genes in response to signals in the environment siswa setyahadi 2014 • • • • Regulation by Factors Sigma 70 consensus– Responsible for the Bulk of mRNA siswa setyahadi 2014 Sigma 32 consensus– Responsible for “Heat Shock” mRNA siswa setyahadi 2014 Regulation by Transcription Factors Bacterial Operons • Operons provide for coordinated expression of genes. Include promoter, binding sites for activators and repressors, and functional groupings of genes. siswa setyahadi 2014 • In this example, A, B, and C are transcribed as one polycistronic mRNA that is translated into three proteins •The trp operon • Is similar to the lac operon, but functions somewhat differently Promoter Operator Genes DNA Active repressor Active repressor Tryptophan Inactive repressor Inactive repressor Lactose lac operon trp operon siswa setyahadi 2014 Figure 11.1C Regulation of Gene Expression in Eukaryotes Not all genes in an organism are “turned on” in all cells or at all times in particular cell. All cells of an organism have the same set of genes, but cells from different tissues look very different and function very different from one another. -Development, Stem cells, differentiated cells siswa setyahadi 2014 - In an adult organism, certain genes are active or inactive at different times. siswa setyahadi 2014 Differentiated Cells Lactose Metabolism in E. coli • Lactose is a secondary Carbon source • Glucose preferred. Enzymes for lactose metabolism are inducible. • Lactose transport into the cell siswa setyahadi 2014 • Lactose is hydrolysis into monosaccharides The lac Operon has Three Sites for Binding the Lac Repressor siswa setyahadi 2014 • Lac Repressor binds with high affinity to O1(also O2&3) • Allolactose reduces affinity siswa setyahadi 2014 Model for cooperative binding • LacR tetramer siswa setyahadi 2014 • Sugar binding Domain tetramer “core” • DNA binding dimer headpieces siswa setyahadi 2014 IPTG (lactose analog) causes subtle conformational change – loss of affinity siswa setyahadi 2014 Lac inducer IPTG, structurally similar to lactose Helix-Turn-Helix Motif is Common in DNABinding Proteins siswa setyahadi 2014 • One of the helixes (red) fits into the major groove of DNA • Four DNA-binding helixturn-helix motifs (gray) in the Lac repressor siswa setyahadi 2014 Binding of Proteins to DNA Often Involves Hydrogen Bonding Conformational Change in Repressor Upon Ligand Binding • Binding of allolactose or other lactose analogs, such as IPTG induces a conformational change in repressor • The ligand-bound repressor dissociates from DNA siswa setyahadi 2014 • Genes needed for lactose metabolism are transcribed Activation of Transcription of the lac Operon by CRP • cAMP receptor protein (CRP) is a positive regulator of the lac operon • CRP binds to the lac operon in the absence of glucose siswa setyahadi 2014 • Binding of CRP stimulates expression of the lac operon CRP-RNAP contacts compensate for weak RNAP- DNA siswa setyahadi 2014 • A region of CRP interacts favorably with RNA polymerase, stimulating transcription of genes in the lac operon • When lactose is low, repressor is bound: inhibition • When lactose is high, repressor dissociates permitting transcription • When glucose is high, CRP is not bound and transcription is dampened • When glucose is low, cAMP is high and CRP is bound: activation siswa setyahadi 2014 Combined Effects of Glucose and Lactose on the lac Operon siswa setyahadi 2014 The trp Operon – Dual Control Dimeric Trp Repressor Binds to DNA in the Presence of Tryptophan siswa setyahadi 2014 • Tryptophan required for repression • Notice that helix-turn-helix motifs interact with DNA via the major groove siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 siswa setyahadi 2014 SOS response in E. coli siswa setyahadi 2014 Site-Specific Recombination Regulates flagellin genes in Salmonella siswa setyahadi 2014 Regulation of Transcription in Eukaryotes • General transcription factors • TATA box binding protein (TBP) • Transcription factors for the assembly of the initiation complex • Promoter proximal / distal enhancer binding factors siswa setyahadi 2014 • Homeodomain proteins share similarities with helix-turn-helix bacterial counterparts nut often involve water bridges between DNA and protein • Leucine zippers are made of two amphipathic polypeptides. One side of each peptide is hydrophobic, facilitating dimerization • Zinc fingers form elongated loops held together by a single Zn++ ion Homeodomain Proteins siswa setyahadi 2014 • Also a helix-turnhelix interacts with DNA via the major groove • One domain of multidomain – multiprotein complex Leucine Zipper – Dimerization Domains siswa setyahadi 2014 B (for basic) –Zip proteins Eukaryotic Promoters and Regulatory Proteins siswa setyahadi 2014 Integration of multiple signals, chromatin, local and remote binding sites, assembly, histone modifcation, scaffolding proteins siswa setyahadi 2014 Regulation of transcription of GAL genes in yeast siswa setyahadi 2014 Chromatin Structure/ Activation Domains siswa setyahadi 2014 Gene silencing by RNA interference siswa setyahadi 2014 siswa setyahadi 2014 The Hox gene clusters direct human development in much the same way as flies siswa setyahadi 2014 Homeotic mutations transform one body part into another. siswa setyahadi 2014 Butterfly colors on a Fruit Fly – Sean Carrol – U of Wisconsin