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31 Gene regulation in bacteria. Lecture Outline 11/18/05. Finish up from last time: Transposable elements (“jumping genes”) Gene Regulation in Bacteria Transcriptional control Cells adjust to their environment by turning genes on and off The operon concept

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lecture outline 11 18 05
Lecture Outline 11/18/05
  • Finish up from last time:
  • Transposable elements (“jumping genes”)
  • Gene Regulation in Bacteria
    • Transcriptional control
    • Cells adjust to their environment by turning genes on and off
  • The operon concept
    • Repressors, Inducers, Operators, Promoters
  • Repressible operons (e.g. trp)
  • Inducible operons (e.g. lac)
transposable elements
Transposable elements
  • Normal and ubiquitous
    • Prokaryotes-
      • Genes transpose to/from cell’s chromosome, plasmid, or a phage chromosome.
    • Eukaryotes-
      • Genes transpose to/from same or a different chromosome.
  • Cause genetic changes
    • Chromosome breaks
    • Duplications
    • Knock-out genes
i ll talk about 2 kinds
I’ll talk about 2 kinds:
  • Insertion sequences
  • Ac/Ds elements in corn
  • A third major class: Retrotransposons
    • Uses RNA intermediate and reverse transcriptase
    • Most Important class in mammalian genomes
insertion sequence is elements
Insertion sequence (IS) elements:
  • Simplest type of transposable element
    • Found in bacterial chromosomes and plasmids.
    • Encode only genes for mobilization and insertion.

Inverted terminal repeats

integration of an insertion element

IS element carries transposase gene

Integration of an Insertion Element

Transposase recognizes terminal repeats

Don’t worry about the details, just the concept

Staggered cut at target site

Insert IS element

Fill in the gaps

transposons
Transposons

Have additional genes, such as those for antibiotic resistance

  • (examples Tn3 (ampicillin), Tn10 (tetracycline)

Transposon

Antibioticresistance gene

Insertion sequence

Insertion sequence

5

3

5

3

Inverted repeats

Transposase gene

Figure 18.19b

barbara mcclintock s discovery of transposons in corn
Barbara McClintock’s discovery of transposons in corn:
  • Kernel color alleles/traits were “unstable”.
  • McClintock concluded transposon called “Ds” inserted into the “C” gene for colored kernels

Nobel prize, 1983

transposon effects on corn kernel color
Transposon effects on corn kernel color.

Ac can make transposase

Ds can move, but lacks enzyme

Two transposable elements in different sites

Normal gene for purple kernels

Ac activates Ds

Ds element inserts into color gene and inactivates it

one method for conservative transposition
One method for Conservative Transposition

“Cut and Paste”

Transposable element is cut out by transposase and inserts in another location.

No increase in the number of transposable elements- just a change in position

From Griffiths, Intro to Genetic Analysis

one method for replicative transposition
One method for replicative transposition

From Griffiths, Intro to Genetic Analysis

gene regulation in bacteria
Gene regulation in bacteria

E.coli bacteria eat whatever we eat!

But ALL organisms must adjust to changes in their environment and all have evolved numerous control mechanisms.

regulation of metabolism occurs at two levels

(a) Regulation of enzyme activity

(b) Regulation of enzyme production

Precursor

Feedback

inhibition

Enzyme 1

Gene 1

Regulation

of gene

expression

Enzyme 2

Gene 2

Gene 3

Enzyme 3

Gene 4

Enzyme 4

Gene 5

Enzyme 5

Tryptophan

Figure 18.20a, b

Regulation of metabolism occurs at two levels:
  • Adjusting the activity of metabolic enzymes already present
  • Regulating the genes encoding the metabolic enzymes
types of regulated genes
Types of Regulated Genes
  • Constitutive genes are always expressed
    • Tend to be vital for basic cell functions (often called “housekeeping genes”)
  • Inducible genes are normally off, but can be turned on when substrate is present
      • Common for catabolic enzymes (i.e. for the utilization of particular resources)
  • Repressible genes are normally on, but can be turned off when the end product is abundant
      • Common for anabolic enzymes
in bacteria genes are often clustered into operons
In bacteria, genes are often clustered into operons

Operons have:

  • Several genes for metabolic enzymes
  • One promoter
  • An operator, or control site

(“on-off” switch)

  • A separate gene that makes a repressor or activatorprotein that binds to the operator

R

P

P

O

1

2

3

the trp operon

Controlled by a single promoter and operator

The trp Operon

5 genes: E, D, C, B, A

Same order as enzymes for trp synthesis

more terminology
More Terminology
  • Repressors and Activators are proteins that bind to DNA and control transcription.
  • Co-repressors and Inducers: small “effector” molecules that bind to repressors or activators
the trp operon regulated synthesis of repressible enzymes

trp operon

Promoter

RNA polymerase

Polypeptides that make up

enzymes for tryptophan synthesis

The trp operon: regulated synthesis of repressible enzymes

Regulatory

gene

Genes of operon

trpR

trpD

trpC

trpB

trpE

trpA

DNA

Operator

mRNA

3

5

mRNA

5

C

E

D

B

A

Protein

Figure 18.21a

Tryptophan absent -> repressor inactive -> operon “on”

slide19

Active repressor can bind to operator and block transcription

DNA

No RNA made

mRNA

Protein

Active

repressor

Tryptophan

(corepressor)

Tryptophan present -> repressor active -> operon “off”.

Figure 18.21b

slide21

Promoter

Regulatorygene

Operator

DNA

lacl

lacZ

NoRNAmade

3

RNApolymerase

mRNA

5

Activerepressor

Protein

(a)

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

Figure 18.22a

  • The lac operon: regulated synthesis of inducible enzymes
slide22

lac operon

DNA

lacl

lacz

lacY

lacA

RNApolymerase

3

mRNA 5

mRNA 5\'

mRNA

5

-Galactosidase

Permease

Transacetylase

Protein

Inactiverepressor

Allolactose(inducer)

(b)

Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.

Figure 18.22b

positive gene regulation
Positive Gene Regulation
  • Both the trp and lac operons involve negative control of genes
    • because the operons are switched off by the active form of the repressor protein
  • Some operons are also subject to positive control
    • Via a stimulatory activator protein, such as catabolite activator protein (CAP)
positive gene regulation cap

Operator

RNA

polymerase

can bindand transcribe

Promoter

DNA

lacl

lacZ

CAP-binding site

ActiveCAP

cAMP

Inactive lac

repressor

InactiveCAP

(a)

Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized.If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for the lactose pathway.

Figure 18.23a

Positive Gene Regulation- CAP
  • In E. coli, when glucose is always the preferred food source
  • When glucose is scarce, the lac operon is activated by the binding of the catabolite activator protein (CAP)
slide26

Promoter

Operator

DNA

lacl

lacZ

CAP-binding site

RNA

polymerase

can’t bind

InactiveCAP

Inactive lac

repressor

Lactose present, glucose present (cAMP level low): little lac mRNA synthesized.When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription.

(b)

Figure 18.23b

  • When glucose is abundant,
    • CAP detaches from the lac operon, which prevents RNA polymerase from binding to the promoter
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