Molecular genetics of bacteria

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Molecular genetics of bacteria

• Gene regulation and regulation of metabolism
• Genetic exchange among bacteria

• Bacteria are successful because
• They carefully regulate their use of energy in
  metabolic processes by shutting down unneeded
  pathways at the biochemical and genetic levels.
• They share genetic information with other
  bacteria, increasing their ability to adapt to
  their environment.

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Bacteria tightly regulate their activities
Bacteria must respond quickly to changes in the
environment. Bacteria are small compared to
their environment, have no real capacity for
energy storage. Simultaneous transcription and
translation allows them to synthesize the
proteins they need quickly. Wasteful activities
are avoided. If there are sufficient amounts
of some metabolite, bacteria will avoid making
more AND avoid making the enzymes that make the
metabolite. Biosynthesis costs! Biochemical
regulation and genetic regulation.
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Biochemical regulation allosteric enzymes

• Allo other steric space. Many enzymes not
  only have an active site, but an allosteric site.
• Binding of a molecule there causes a shape change
  in the enzyme. This affects its function.

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Feedback inhibition of pathways
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Genetic regulation

• Genotype is not phenotype bacteria possess many
  genes that they are not using at any particular
  time.
• Transcription and translation are expensive why
  spend ATP to make an enzyme you dont need?
• Examples
• Induction of lactose operon
• diauxic growth with sugars.

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More on Regulation

• In biochemical regulation, processes like
  feedback inhibition prevent wasteful synthesis.
• To save more energy, bacteria prevent the
  synthesis of unneeded enzymes by preventing
  transcription.
• In operons, several genes that are physically
  adjacent are regulated together.
• Two important patterns of regulation Induction
  and repression.
• In induction, the genes are off until they are
  needed.
• In repression, the genes normally in use are shut
  off when no longer needed.

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Operons and Regulons

• Nearly 50 years ago, Jacob and Monod proposed the
  operon model.
• Many genes in prokaryotes are grouped together in
  the DNA and are regulated as a unit. Genes are
  usually for enzymes that function together in the
  same pathway.
• At the upstream end are sections of DNA that do
  not code, but rather are binding sites for
  proteins involved in regulation (turning genes on
  and off).
• The Promoter is the site on DNA recognized by RNA
  polymerase as place to begin transcription.
• Operator is location where regulatory proteins
  bind.
• Promoter and Operator are defined by function.

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Our example the lac operon

• Lactose is milk sugar, used by a few bacteria
  like E. coli
• To use lactose, a couple of proteins are
  important the permease which transports the
  sugar into the cell, and the enzyme
  beta-galactosidase which breaks the disaccharide
  lactose into glucose and galactose.
• To prevent the expense of synthesizing these
  enzymes if there is no lactose to use, E. coli
  keeps these genes inactive. But if lactose
  becomes available, these genes must be turned on
  quickly so lactose can be taken in and broken
  down.
• Imagine E. coli in your GI tract at breakfast.

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Structure of the Lac operon
KEY P O are the promoter and operator
regions. lac Z is the gene for
beta-galactosidase. lac Y is the gene for the
permease. lac A is the gene for a
transacetylase. lac I, on a different part of
the DNA, codes for the lac repressor, the
protein which can bind to the operator.
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Products of the lac operon

• Each gene codes for a protein that is involved in
  the use of lactose. Depicted is the mRNA and the
  proteins that result. Note that P and O are
  functional regions of DNA but arent genes for
  proteins no mRNA is made from them.

http//www.med.sc.edu85/mayer/genreg1.jpg
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Binding of small molecules to proteins causes
them to change shape
Characteristic of many DNA-binding
proteins Regulation of operons Inducible
operons Repressor protein comes off
DNARepressible operons Repressor protein
attaches to DNA
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How the lac operon works
When lactose is NOT present, the cell does not
need the enzymes. The lac repressor, a protein
coded for by the lac I gene, binds to the DNA
at the operator, preventing transcription. When
lactose is present, and the enzymes for using it
are needed, lactose binds to the repressor
protein, causing it to change shape and come
off the operator, allowing RNA polymerase to
find the promoter and transcribe.
http//www.med.sc.edu85/mayer/genreg1.jpg
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Lactose is not actually the inducer
Low basal levels of beta-galactosidase exist in
the cell. This converts some lactose to the
related allolactose which binds to the lac
repressor protein. Synthetic inducers such as
IPTG with a similar structure can take the place
of lactose/allolactose for research purposes.
http//www.search.com/reference/Lac_operon
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Glucose is the preferred carbon source
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Positive regulation

• Presence of lactose is not enough
• In diauxic growth graph, lactose is present from
  the start. Why isnt operon induced?
• Presence of glucose prevents positive regulation
• NOT the same as inhibiting
• Active Cyclic AMP receptor protein (CRP) needed
  to bind to DNA to turn ON lactose operon (and
  others)
• Presence of glucose (preferred carbon source)
  prevents activation of CRP.

www.answers.com/.../catabolite-activator-protein
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Plasmids

• Plasmids small, circular, independently
  replicating pieces of DNA with useful, not
  essential info
• Types of plasmids
• Fertility,
• resistance,
• catabolic,
• bacteriocin,
• virulence,
• tumor-inducing, and
• cryptic

http//www.estrellamountain.edu/faculty/farabee/bi
obk/14_1.jpg
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About plasmids-1
Fertility plasmid genes to make a sex pilus
replicates, and a copy is passed to another
cell. Resistance plasmid genes that make the
cell resistant to antibiotics, heavy
metals. Catabolic plasmid example, tol plasmid
with genes for breaking down and using toluene,
an organic solvent.
www.science.siu.edu/.../ micr302/transfer.html
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About plasmids-2

• Bacteriocin plasmid codes for bacteriocins,
  proteins that kill related bacteria.
• Virulence plasmid has genes needed for the
  bacterium to infect the host.
• Tumor-inducing plasmid The Ti plasmid found in
  Agrobacterium tumefaciens. Codes for plant
  growth hormones. When the bacterium infects the
  plant cell, the plasmid is passed to the plant
  cell and the genes are expressed, causing local
  overgrowth of plant tissue gall. Very useful
  plasmid for cloning genes into plants.
• Cryptic who knows?

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Gene transfer

• Ways that bacteria can acquire new genetic info
• Transformation
• Taking up of naked DNA from solution
• Transduction
• Transfer of DNA one to cell to another by a virus
• Conjugation
• Mating transfer of DNA from one bacterium to
  another by direct contact.

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Gene transfer between bacteria

• Transformation uptake of naked DNA from
  medium.
• When Griffith did his experiment combining heat
  killed, virulent cells with live, harmless
  mutants, the living cells took up the DNA from
  solution, changed into capsule-producing,
  disease-causing bacteria.
• Next slide

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Transformation details
DNA must be homologous, so transformation only
occurs between a few, close relatives.
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Gene transfer between bacteria-2

• Transduction transfer of DNA via a virus.

More common, but still requires close relative.
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Conjugation bacterial sex

• If sex is the exchange of genetic material, this
  is as close as bacteria get. Conjugation is
  widespread and does NOT require bacteria to be
  closely related.
• Bacteria attach by means of a sex pilus, hold
  each other close, and DNA is transferred.
• Plasmids other than F plasmids, such as
  resistance plasmids, can also be exchanged,
  leading to antibiotic-resistant bacteria.