1 Gene Regulation Organisms have lots of genetic information, but they don’t necessarily want to use all of it (or use it fully) at one particular time. Eukaryotes: Development, differentiation, and homeostasis –In going from zygote to fetus, e.g., many genes are used that are then turned off. –Liver cells, brain cells, use only certain genes –Cells respond to internal, external signals

2 Gene regulation continued Prokaryotes: respond rapidly to environment –Transcription and translation are expensive Each nucleotide = 2 ATP in transcription Several GTP/ATP per amino acid in translation If protein is not needed, don’t waste energy! –Changes in food availability, environmental conditions lead to differential gene expression Degradation genes turned on to use C source Bacteria respond to surfaces, new flagella etc. Quorum sensing: sufficient # of individuals turns on genes.

3 On/off, up/down, together Sometimes genes are off completely and never transcribed again; some are just turned up or down –Eukaryotic genes typically turned up and down a little compared to huge increases for prokaryotes. Genes that are “on” all the time = Constitutive Many genes can be regulated “coordinately” –Eukaryotes: genes may be scattered about, turned up or down by competing signals. –Prokaryotes: genes often grouped in operons, several genes transcribed together in 1 mRNA.

4 How is gene expression controlled? 1.Transcription: most common step in control. 2.RNA processing: only in eukaryotes. Alternate splicing changes type/amount of protein. 3.Translation: prokaryotes, stops transl. early. 4.Stability of mRNA: longer lived, more product. 5.Post-translational: change protein after it’s made. Process precursor or add PO 4 group. 6.DNA rearrangements. Genes change position relative to promoters, or exons shuffled.

5 Gene regulation in Prokaryotes Bacteria were models for working out the basic mechanisms, but eukaryotes are different. Some genes are constitutive, others go from extremely low expression (“off”) to high expression when “turned on”. Many genes are coordinately regulated. –Operon: consecutive genes regulated, transcribed together; polycistronic mRNA. –Regulon: genes scattered, but regulated together.

6 Rationale for Operon Many metabolic pathways require several enzymes working together. In bacteria, transcription of a group of genes is turned on simultaneously, a single mRNA is made, so all the enzymes needed can be produced at once.

7 Proteins change shape When a small molecule binds to the protein, it changes shape. If this is a DNA-binding protein, the new shape may cause it to attach better to the DNA, or “fall off” the DNA.

8 Definitions concerning operon regulation Control can be Positive or Negative –Positive control means a protein binds to the DNA which increases transcription. –Negative control means a protein binds to the DNA which decreases transcription. Induction –Process in which genes normally off get turned on. –Usually associated with catabolic genes. Repression –Genes normally on get turned off. – Usually associated with anabolic genes.

9 Structure of an Operon 1.Regulatory protein gene: need not be in the same area as the operon. Protein binds to DNA. 2.Promoter region: site for RNA polymerase to bind, begin transcription. 3.Operator region: site where regulatory protein binds. 4.Structural genes: actual genes being regulated.

10 Animations Animation showing the effects of the lactose repressor on the lac operon. Cut and paste addresses into your browser; will give you some idea of how repressor proteins interact with operator regions to control transcription.

11 The Lactose Operon The model system for prokaryotic gene regulation, worked out by Jacob and Monod, France, The setting: E. coli has the genes for using lactose (milk sugar), but seldom sees it. Genes are OFF. –Repressor protein (product of lac I gene) is bound to the operator, preventing transcription by RNA polymerase. Green: repressor protein Purple: RNA polymerase

12 Lactose operon-2 When lactose does appear, E. coli wants to use it. Lactose binds to repressor, causing shape change; repressor falls off DNA, allows unhindered transcription by RNA polymerase. Translation of mRNA results in enzymes needed to use lactose.

13 Lactose operon definitions Control is Negative –When repressor protein is bound to the DNA, transcription is shut off. This operon is inducible –Lactose is normally not available as a carbon source; genes are “shut off” –In bacteria, many similar operons exist for using other organic molecules. –Genes for transporting the sugar, breaking it down are produced.

14 Repressible operons Operon codes for enzymes that make a needed amino acid (for example); genes are “on”. –Repressor protein is NOT attached to DNA –Transcription of genes for enzymes needed to make amino acid is occurring. The change: amino acid is now available in the culture medium. Enzymes normally needed for making it are no longer needed. –Amino acid, now abundant in cell, binds to repressor protein which changes shape, causing it to BIND to operator region of DNA. Transcription is stopped. This is also Negative regulation (protein + DNA = off).

15 Repression picture Transcription by RNA polymerase prevented.

16 Regulation can be fine tuned The more of the amino acid present in the cell, the more repressor-amino acid complex is formed; the more likely that transcription will be prevented.

17 Positive regulation Binding of a regulatory protein to the DNA increases (turns on) transcription. –More common in eukaryotes. Prokaryotic example: the CAP-cAMP system –Catabolite-activating Protein –cAMP: ATP derivative, acts as signal molecule –When CAP binds to cAMP, creates a complex that binds to DNA, turning ON transcription. –Whether there is enough cAMP in the cell to combine with CAP depends on glucose conc.

18 Positive regulation-2 Glucose is preferred nutrient source –Other sugars (lactose, etc.) are not. Glucose inhibits activity of adenylate cyclase, the enzyme that makes cAMP from ATP. When glucose is high, cAMP is low, less cAMP is available to bind to CAP. –CAP is “free”, doesn’t bind to DNA, genes not on. When glucose is low, cAMP is high –Lots of cAMP, so CAP-cAMP forms, genes on. Works in conjunction with induction.

19 Cartoon of Positive Regulation

20 Attenuation: fine tuning repression Attenuation occurs in prokaryotic repressible operons. Happens when transcription is on. Regulation at the level of translation Several things important: –Depends on base-pairing between complementary sequences of mRNA –Requires simultaneous transcription/translation –Involves delays in progression of ribosomes on mRNA

21 Mechanism of attenuation- tryp operon

22 Mech. of attenuation -2

23 Attenuation-3