Prokaryotes and eukaryotes alter gene expression in response to their changing environment .
Bacteria often respond to environmental change by regulating transcription
Natural selection has favored bacteria that produce only the products needed by that cell.
A cell can regulate the production of enzymes by feedback inhibition or by gene regulation.
Gene expression in bacteria is controlled by the operon model.
Fig. 18-2 Regulation of gene expression trpE gene trpD gene trpC gene trpB gene trpA gene (b) Regulation of enzyme production (a) Regulation of enzyme activity Enzyme 1 Enzyme 2 Enzyme 3 Tryptophan Precursor Feedback inhibition
An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control
regulator promoter operator genes
regulator promoter operator genes
Makes a repressor which binds to operator and stops/starts transcription RNA polymerase binds here
System initially off
The presence of an inducer (usually a substrate that needs to be broken down) turns it on.
The inducer binds to the repressor and makes it inactive so transcription can occur.
The inducer acts as an allosteric effector and changes the shape of the repressor.
Ex- Lac (lactose) operon
Fig. 18-4a (a) Lactose absent, repressor active, operon off DNA Protein Active repressor RNA polymerase Regulatory gene Promoter Operator mRNA 5 3 No RNA made lac I lacZ
Lactose present, repressor inactive, operon ON Fig. 18-4b (b) Lactose present, repressor inactive, operon on mRNA Protein DNA mRNA 5 Inactive repressor Allolactose (inducer) 5 3 RNA polymerase Permease Transacetylase lac operon -Galactosidase lacY lacZ lacA lac I
System initially ON, transcription ongoing and making a product
Operator can be turned off by a repressor which is made active by being activated by a corepressor molecule (usually the end product)
Ex – tryptophan operon – trytophan acts as a corepressor inhibitng further synthesis of enzymes involved in the process
Tryptophan absent, repressor inactive, operon ON Fig. 18-3a Polypeptide subunits that make up enzymes for tryptophan synthesis (a) Tryptophan absent, repressor inactive, operon on DNA mRNA 5 Protein Inactive repressor RNA polymerase Regulatory gene Promoter Promoter trp operon Genes of operon Operator Stop codon Start codon mRNA trpA 5 3 trpR trpE trpD trpC trpB A B C D E
Tryptophan present, repressor active, operon OFF Fig. 18-3b-1 (b) Tryptophan present, repressor active, operon off Tryptophan (corepressor) No RNA made Active repressor mRNA Protein DNA
INDUCIBLE REPRESSABLE OFF ON turned on by turned off by inducer corepressor used in catabolic used in anabolic pathways pathways Both use allosteric effectors and are NEGATIVE CONTROL.
Positive Gene Regulation
Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription
When glucose (a preferred food source of E. coli ) is scarce, CAP is activated by binding with cyclic AMP
Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription
Fig. 18-5 (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized cAMP DNA Inactive lac repressor Allolactose Inactive CAP lac I CAP-binding site Promoter Active CAP Operator lacZ RNA polymerase binds and transcribes Inactive lac repressor lacZ Operator Promoter DNA CAP-binding site lac I RNA polymerase less likely to bind Inactive CAP (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized
When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate
CAP helps regulate other operons that encode enzymes used in catabolic pathways
Control of Gene Expression in Eukaryotes
In response to environmental signals
Essential for development and cell specialization in multicellular organisms
RNA is important in gene expression.
All cells contain the same DNA so controlling gene expression is essential.
Human cells only 20% genes expressed; only 1.5% code for proteins
Commonly occurs at level of transcription; hence, gene expression = transcription of DNA
Eukaryotic gene expression can be regulated at any stage < A>
Fig. 18-6 DNA Signal Gene NUCLEUS Chromatin modification Chromatin Gene available for transcription Exon Intron Tail RNA Cap RNA processing Primary transcript mRNA in nucleus Transport to cytoplasm mRNA in cytoplasm Translation CYTOPLASM Degradation of mRNA Protein processing Polypeptide Active protein Cellular function Transport to cellular destination Degradation of protein Transcription
Fig. 18-6a DNA Signal Gene NUCLEUS Chromatin modification Chromatin Gene available for transcription Exon Intron Tail RNA Cap RNA processing Primary transcript mRNA in nucleus Transport to cytoplasm CYTOPLASM Transcription
Fig. 18-6b mRNA in cytoplasm Translation CYTOPLASM Degradation of mRNA Protein processing Polypeptide Active protein Cellular function Transport to cellular destination Degradation of protein
1) State of chromatin (nucleosomes)
Heterochromatin – genes not expressed due to tightly wound DNA
- Histone acetylation – promotes transcription by inhibiting binding between nucleosomes so keeps DNA spread out; also may recruit transcription factors
- Methylation of DNA – inhibits transcription (indicated in inactive X)
Epigenetic inheritance – not involved DNA sequence but inherited defects in chromatin modification enzymes
There may be more to inheritance than genes alone. New clues reveal that a second epigenetic chemical code sits on top of our regular DNA and controls how our genes are expresse.
2) Transcription Level
Remember, transcription factors bind to DNA promoters, then RNA polymerase binds to promoter region to form the Transcription Initiation Complex
Transcription Factors: General
Bind to RNA polymerase and each other to initiate transcription of all protein-coding genes
Low rate of transcription
Specific Transcription Factors
( a) enhancers : proximal (close to promoters) and distal; specific for a gene
(b) some are repressors and can block anywhere in the scheme and can also recruit proteins to affect chromatin structure
(c) enhancers contain control elements (up to 10 different ones); the combination is specific for transcription factors. Also explains how genes in a related pathway are correlated (like flags on mailboxes to know which mail to pick up). The combination signals which genes are expressed.
Fig. 18-9-1 Enhancer TATA box Promoter Activators DNA Gene Distal control element
Fig. 18-9-2 Enhancer TATA box Promoter Activators DNA Gene Distal control element Group of mediator proteins DNA-bending protein General transcription factors
Fig. 18-9-3 Enhancer TATA box Promoter Activators DNA Gene Distal control element Group of mediator proteins DNA-bending protein General transcription factors RNA polymerase II RNA polymerase II Transcription initiation complex RNA synthesis
Fig. 18-10 Control elements Enhancer Available activators Albumin gene (b) Lens cell Crystallin gene expressed Available activators LENS CELL NUCLEUS LIVER CELL NUCLEUS Crystallin gene Promoter (a) Liver cell Crystallin gene not expressed Albumin gene expressed Albumin gene not expressed
3. Post-transcriptional Control
Alternative RNA splicing (mRNA can last a long time and be subject to various intron splicing)
The mRNA life span is determined in part by sequences in the leader and trailer regions
Fig. 18-11 or RNA splicing mRNA Primary RNA transcript Troponin T gene Exons DNA
Alteration of polypeptide - can be cut, groups added, or transported to target locations
Selective degradation of proteins – the protein ubiquitin are added to proteins for degradation. Proteasomes recognize them and destroy them.
Fig. 18-12 Proteasome and ubiquitin to be recycled Proteasome Protein fragments (peptides) Protein entering a proteasome Ubiquitinated protein Protein to be degraded Ubiquitin
Noncoding RNAs play multiple roles in controlling gene expression
Only a small fraction of DNA codes for proteins, rRNA, and tRNA
A significant amount of the genome may be transcribed into noncoding RNAs
Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration
Effects on mRNAs by MicroRNA’s
MicroRNAs (miRNAs ) are small single-stranded RNA molecules that can bind to mRNA
These can degrade mRNA or block its translation
Long RNA precursors fold on themselves and look like hairpins. The hairpins are cut off and an enzyme called Dicer trims the ends. One strand becomes a microRNA (miRNA).
These bind with proteins and block translation or degrades the mRNA.
Fig. 18-13 miRNA- protein complex (a) Primary miRNA transcript Translation blocked Hydrogen bond (b) Generation and function of miRNAs Hairpin miRNA miRNA Dicer 3 mRNA degraded 5
An estimated 1/3 of human genes are regulated by miRNAs
Small Interfering RNA’s
The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi)
Cells cut up the RNA into small interfering RNAs (siRNAs) that can inhibit expression like miRNA’s
siRNAs and miRNAs are similar but form from different RNA precursors
CANCER AND GENE EXPRESSION Cancer results from genetic changes that affect cell cycle control
Cancer can be caused by mutations to genes that regulate cell growth and division
- mutagens are chemicals, X-rays, tumor viruses in animals
Fig. 18-21c (c) Effects of mutations EFFECTS OF MUTATIONS Cell cycle not inhibited Protein absent Increased cell division Protein overexpressed Cell cycle overstimulated
Oncogenes and Proto-Oncogenes
Oncogenes are cancer-causing genes
Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division
Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle
Amplification of normal growth-stimulating gene
Translocation of growth gene under control of a more active promoter
Point mutation in control element or gene itself to make a hyperactive or degradation resistent growth protein.
Fig. 18-20 Normal growth- stimulating protein in excess New promoter DNA Proto-oncogene Gene amplification: Translocation or transposition: Normal growth-stimulating protein in excess Normal growth- stimulating protein in excess Hyperactive or degradation- resistant protein Point mutation: Oncogene Oncogene within a control element within the gene
help prevent uncontrolled cell growth
Repair damaged DNA
Control cell adhesion
Inhibit the cell cycle
How do cancer genes work?
30% cancers – ras proto-oncogene gene is mutated
Ras gene codes for a protein that stimlates the production of a cell cycle stimulating protein; mutations cause a hyperactive protein
50% cancers – p 53 gene mutated; codes for a transcription factor for growth-inhibiting proteins. These proteins bind to a p21 gene whose product binds to CDK’s and halt cell cycle. It can also activate DNA repair genes or “suicide genes” if DNA can’t be repaired.
p53 gene and DNA repair Fig. 18-21b MUTATION Protein kinases DNA DNA damage in genome Defective or missing transcription factor, such as p53, cannot activate transcription Protein that inhibits the cell cycle Active form of p53 UV light (b) Cell cycle–inhibiting pathway 2 3 1
P53 and suicide genes
Multistep Model of Cancer Development
More than one somatic mutation is needed
Both alleles must be defective
In some, genes for telomerase becomes activated and cells divided continually
Breat cancer gene
Inherited Predisposition and Other Factors Contributing to Cancer
Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes
Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer
Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers
Even if you have cancer genes, it does not mean you will have cancer.
Genes can be modified by siRNA’s, epigenesis, and the environment