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Molecular Biology of Gene-for-Gene Interaction. Many R and AVR genes have been cloned. How were R genes and Avr genes cloned. Cloning of First Avr Genes. P. syringae race 5. Avr. P. syringae race 5. P. syringae race 5. P. syringae race 5. P. syringae race 5. P. syringae race 5.

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molecular biology of gene for gene interaction
Molecular Biology of Gene-for-Gene Interaction
  • Many R and AVR genes have been cloned

P. Balint-Kurti Lecture 2

how were r genes and avr genes cloned
How were R genes and Avr genes cloned

P. Balint-Kurti Lecture 2

cloning of first avr genes
Cloning of First Avr Genes

P. Balint-Kurti Lecture 2

slide5

P. syringae race 5

Avr

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 5

P. syringae race 6

Infect Harosay Soybean and look for HR

Genomic Library

P. Balint-Kurti Lecture 2

slide6
Cloned AvrA
  • No known function (I think)

P. Balint-Kurti Lecture 2

cloning an r gene
Cloning an R-gene

P. Balint-Kurti Lecture 2

cf 9 avr9 system
Cf-9/Avr9 system
  • Avr9 was cloned by purifying and sequencing the protein and using this info to get to the gene.

P. Balint-Kurti Lecture 2

what are avr genes
What are AVR genes?
  • And why does the pathogen have them??
  • No common sequence features
    • Caveat- they may share export signals:
      • Guttman et al. Science295 “A Functional Screen for the Type III (Hrp) Secretome of the Plant Pathogen Pseudomonas syringae,”

P. Balint-Kurti Lecture 2

hrp genes
HRP genes
  • Hypersenesitive reaction and pathogenicity.
  • Deletion of hrp genes leads to abolition of both functions.

P. Balint-Kurti Lecture 2

what s going on
What’s going on?
  • Existence of Hrp genes implies that the same processes that control avirulence also condition pathogenicity
  • Any thoughts?

P. Balint-Kurti Lecture 2

hrp genes are clustered in the bacterial genome
Hrp genes are clustered in the bacterial genome.
  • Many are components of the Type III secrection system, which can inject proteins into host cells.
  • Many secreted proteins share some sequence features that allow their recogniton by the TIIISS.

P. Balint-Kurti Lecture 2

slide15

What are AVR genes?

  • Often act as virulence or effector proteins in the absence of corresponding R-gene

P. Balint-Kurti Lecture 2

what kinds of things are these effector proteins doing
What kinds of things are these effector proteins doing
  • Suppression of (PAMP* or AVR-activated) basal defenses

*We’ll come to PAMPS later

P. Balint-Kurti Lecture 2

how do we know
How do we know?

P. Balint-Kurti Lecture 2

some effector avr gene products act to effect plant gene expression
Some Effector/Avr gene products act to effect plant gene expression
  • AvrBs3 (a Xanthamonas campestris Avr gene) induces the expression of upa20 which is itself a transcription factor. Upa20 regulates cell size in tobacco.
  • We’ll come back to AvrBs3!

P. Balint-Kurti Lecture 2

slide20
Some effectors act to suppress components of the deployed defense response
    • E,g, Avr4 is a chitinase inhibitor.

P. Balint-Kurti Lecture 2

fungal and oomycete avr genes
Fungal and Oomycete Avr genes
  • In Phytophthora infestans and other oomycetes, Avr genes have a conserved amino-acid motif- RXLR.
    • Likely a host cell targeting signal
    • Plasmodium species (malaria parasites) use a very similar sequence to target proteins into red blood cells
  • Some evidence that RXLR proteins are pathogenesis effectors
    • Functions of most RXLR gene unknown.
  • Less is known about fungal Avr genes/effectors

P. Balint-Kurti Lecture 2

what do r genes look like
What do R-genes look like?
  • Unlike Avr genes , most (not all) R-genes share some structural features

P. Balint-Kurti Lecture 2

classes of r proteins
Classes of R proteins
  • Class 1 Pto- Serine/Threonine Kinase
  • Class 2 LRR-NBS-LZ/CC
  • Class 3 LRR-NBS-TIR
  • Class 4 Extracellular LRR (Cf genes)
  • Class 5 Extracellular LRR- Serine thronine kinase
  • As defined in Martin et al. Ann Rev Plant Biol 2003 54:23-61

P. Balint-Kurti Lecture 2

slide24

Class 4

Class 2

Class 3

Class 5

Class 1

Plant pathogens and integrated defence responses to infection

Jeffery L. Dangl and Jonathan D. G. Jones

Nature 411, 826-833(14 June 2001)

P. Balint-Kurti Lecture 2

conserved features of resistance genes r genes
Conserved Features of Resistance genes (R-genes)
  • LRR (Leucine –rich- repeat)
    • Present in many proteins of diverse function
    • Important in protein-protein interactions
    • Believed to play a major role in recognition specificity
    • But other regions may play a role too

P. Balint-Kurti Lecture 2

slide26

Annual Reviews

P. Balint-Kurti Lecture 2

how do we know this
How do we know this?
  • Domain swapping experiments:

P. Balint-Kurti Lecture 2

slide28
LRR region plays a major role in recognitional specificity but it’s often more complicated than that

P. Balint-Kurti Lecture 2

conserved features of resistance genes r genes29
Conserved Features of Resistance genes (R-genes)
  • Nucleotide binding site (NBS)
    • Crucial for function (mutational analyses)
    • May be involved in triggering cell death (evidence from homology)
    • Binds and hydrolyzes ATP

P. Balint-Kurti Lecture 2

other common features of r genes
Other common features of R genes
  • Coiled coil (CC)
    • No defined function (yet)
  • Toll/Interleukin 1 recptor (TIR) domain
    • Toll receptors function in animal inate immuntiy
    • TIR-NB-LRR genes not found in monocots
      • They were specifically lost from this lineage
    • CC-NB-LRR and TIR-NB-LRR genes may interact with different sets of downstream components

P. Balint-Kurti Lecture 2

slide31

vs

From Martin et al Ann rev plant Biol. 2003 54:23-61

P. Balint-Kurti Lecture 2

how many r genes are there in the genome
How many R-genes are there in the genome?
  • In some ways this is unanswerable
  • Conserved domains give us a way to look at this in sequenced genomes.
  • In rice there are ~500 R-gene analogues (RGAs)
  • In Arabidopsis about 200
  • Some are clustered, others aren’t

P. Balint-Kurti Lecture 2

other types of resistance genes
Other types of resistance genes
  • What is an R-gene and what is not is something of a semantic issue.
    • Also see quantitative resistance

P. Balint-Kurti Lecture 2

bs3 a new type of r gene
Bs3; A new type of R-gene
  • AvrBs3 acts as a transcription factor in plants
  • It binds to a conserved sequence in the promoter of some plant genes

P. Balint-Kurti Lecture 2

slide37
The Bs3 resistance gene mediates recognition of AvrBs3
  • The Bs3E gene mediates recognition of AvrBs3Δrep16

P. Balint-Kurti Lecture 2

slide39
Recognitional specificity resides in the promoter region of the Bs3 gene.
  • Bs3 is a flavin monooxygenase- a novel type of R-gene

P. Balint-Kurti Lecture 2