evolutionary history and stress responsiveness of plant receptor-like kinases
DESCRIPTION
Evolutionary History and Stress Responsiveness of Plant Receptor-Like Kinases. Melissa Lehti-Shiu Shiu lab. The evolution of duplicate genes. Phylogenetic tree of the Arabidopsis RLK/Pelle gene family. When and how did gene duplication occur? How do gene duplicates diverge in function? - PowerPoint PPT PresentationTRANSCRIPT
Evolutionary History and Stress Responsiveness of Plant Receptor-
Like Kinases
Melissa Lehti-Shiu
Shiu lab
The evolution of duplicate genes
• When and how did gene duplication occur?
• How do gene duplicates diverge in function?
• Why are some duplicates more likely to be retained than others?
Shiu, S.-H., et al. Plant Physiol. 2003;132:530-543
Phylogenetic tree of the Arabidopsis RLK/Pelle gene family
• Background– Duplication mechanisms– Models for duplicate retention– What evolutionary histories can tell us– The RLK/Pelle gene family
• The Evolutionary history of the Receptor-Like Kinase (RLK)/Pelle gene family
• RLKs and stress response
• Whole genome duplication (polyploidization)
• Tandem duplication
• Segmental duplication
• Replicative transposition
Duplication mechanisms
+
Why is knowing duplication mechanism important?
• Gene duplicates are formed at different rates depending on mechanism– Tandem >> whole genome duplication
• How genes are duplicated affects duplicate retention– e.g. tandem repeats are enriched with genes that
are involved in stress response (Rizzon et al., 2006; Hanada and Shiu, unpublished results)
Why are genes retained after duplication?
A. Subfunctionalization:– Ancestral functions are divided
between both genes
B. Neofunctionalization:– One or both copies gain a new
function
C. Dosage:– Additional copies of the gene
may be advantageous
D. Neutral processes:– Both genes kept just because
they are not selected against
A.
B.
C., D.
What can we learn from studying the evolutionary histories of gene families?
Grape 1
Grape 2
Grape 3
Grape 4
Poplar 1
Rice 1
Rice 2
AncestralGene
Arabidopsis 1
http://www.sheppardsoftware.com/Europeweb/factfile/Unique-facts-Europe33.htm
Protein kinase gene families unique
*: Clusters of Markov clustering using all-against-all BLAST E values as distance measures
Protein kinase:~1000
Hanada & Shiu, in prep.
The RLK/Pelle family has experienced dramatic differential expansion
Shiu et al., 2004
Arabidopsis
Rice
RLK/Pelle members have diverse kinase configurations
RLKs function in signal transduction pathways
Flagellin
FLS2(LRR-XII)
Flagellin defense relatedgene expression
CLV1(LRR-XI)
LRR
LRR
LRR
CLV2
CLV3
Meristem proliferation
PAMP recognition Development
Kin
ase
Kin
ase
Identify kinases from sequenced plant genomes
http://genome.jgi-psf.org/Ostta4/Ostta4.home.html
http://genome.jgi-psf.org/Chlre3/Chlre3.home.html
http://www.jgi.doe.gov/sequencing/why/CSP2005/physcomitrella.html
http://www.genomics.zju.edu.cn/ricetdna.html
Chlamydomonasreinhardtii
Ostreococcustauri
Physcomitrellapatens
Oryza sativa
Arabidopsisthaliana
Populustrichocarpa
http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html
http://www.pg.ipw.biol.ethz.ch/Title.html
Kinase classification
• Align kinase domains from all species and construct a phylogenetic tree
• Assign kinases to families based on grouping with known Arabidosis kinases
• Assign RLK/Pelle kinases to subfamilies based on the classification from Shiu et al., 2004
Shiu, S.-H., et al. Plant Cell 2004;16:1220-1234
Chlamydomonasreinhardtii
Ostreococcustauri
Physcomitrellapatens (M)
Oryza sativa (O)
Arabidopsisthaliana (A)
Populustrichocarpa (P)
356
73
256
388148
462
376
159
911
453
187
1003
When was the receptor kinase configuration established?
424
2
93
RLKRLCKOther Kinases
ECD Kinase
Kinase
How many receptor kinase configurations are present in moss?
What innovation in receptor configuration has occurred?
LysM
GDPD
CHASE
LRR
LRR
LRR
Thaumatin
ThaumatinThaumatin
GH18
GH18
DUF26
DUF26DUF26
Calculating lineage-specific gene gains
AB common ancestor
A1 A2-1 A2-2 B2
Species divergence
Duplication inspecies A
Gains Losses Net Gain
Species A
Species B
1 0 1
0 1 -1
B1
Gene lossin species B
(2 genes)
Which RLK subfamilies have undergone lineage-specific expansion?
-15-10-505
101520253035404550556065707580859095
100
C-LECCR4L
CrRLK1L-1Extensin
L-LECLRR_XVI
LRR-ILRR-IILRR-IIILRR-IVLRR-VLRR-VI-1LRR-VI-2
LRR-VIILRR-VIII-1LRR-VIII-2
LRR-IXLRR-XaLRR-XbLRR-XILRR-XIILRR-XIIIaLRR-XIIIbLRR-XIVLRR-XV
LysM-ILysM-IIPERKRKF3SD-2bURK-1
WAK_LRK
Gains since the APOM common ancestor
ArabidopsisPoplarRiceMoss
Subfamilies not found in moss: DUF26, LRK10L-2, SD1, WAK
Which RLK subfamilies have undergone lineage-specific expansion?
-0.4
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4
0.5
0.6
0 10 20 30 40 50 60 70 80 90 100
% of subfamily members in tandem repeats
Expansion rate (number of gains since
APO ancestor normalized by
subfamily size)
Rice
Arabidopsis
Poplar
Linear (Poplar)
Linear (Rice)
Linear (Arabidopsis)
Is there a correlation between expansion rate and location in tandem repeats?
r2 =0.66p<0.001
r2 =0.62p<0.001
r2 =0.37p=0.01
Evolutionary History of the RLK/Pelle family• The receptor kinase configuration was established early in
the evolution of land plants
• Differential of expansion of the RLK/Pelle family has occurred
• New kinase configurations were formed through domain shuffling in all lineages
• Dramatic increase in RLK/Pelle genes in rice and poplar can be explained by expansion of a relatively few subfamilies
• See a significant correlation between recent expansion and tandem duplication
AtGenExpress: stress array data
Raw intensity
Normalizedintensity
16 conditionsw/ time series
GCRMA
Genes withDiff. expr.
LIMMA
http://www.weigelworld.org/resources/microarray/AtGenExpress/
BioticavrRpm1DC3000
Flg22HrcC-HrpZLPSPsph
P. infestans
AbioticColdHeat
DroughtSalt
OsmoticGenotoxicWounding
UV-B
Genes differentially up (1) or down (-1) regulated under each condition
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 1 0 0 0 0 0 0 0 0 0 -1 0 -1 -1
-1 0 1 1 0 0 -11/-1
0 0 0 0 0 0 1 0
1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0
At1g1
At1g2
At1g3
At1g4
At1g5
At1g6
avrR
pm
1
DC
3000
Flg
22
Hrc
C-
Hrp
Z
LP
S
P.
infe
stan
s
Psp
h
Co
ld
Dro
ug
ht
Gen
oto
xic
Hea
t
Osm
oti
c
Sal
t
UV
-B
Wo
un
din
g
Is the number of RLKs up or down regulated by stress different from the genome average?
Is the number of tandem RLKs regulated by stress different from non-tandem RLKs?
Is subfamily responsiveness to stress correlated with the proportion found in tandem repeats?
C-LEC
CR4L
CrRLK1L-1
Cold Drought Heat … flg22 Responsiveness
0 0 0 … 0 0.0
0 0 0 … 0.125 0.93
0.2 0 0.14 … 1.0 2.875
Fraction of subfamily membersup (or down) regulated by coldTreatment (e.g. 5 out of 10=0.5)
Sum of fractions for all16 conditions
Stress responsiveness and tandem RLKs
(subfamilies with ≥ 10 genes)
X1
0
Relationship between RLKs, stress and tandem duplication
• Stress responsiveness– RLK > genome average– Tandem genes > non-tandem genes.– Biotic > abiotic
• Duplication rate (event per unit time):– Whole genome duplication: 1 event / ~50 million years– Tandem duplication: multiple events / generation
• Rate of recombination– Recombination rate: Pathogen attack > control
• Lucht et al., 2002. Nature.
– Recombination rate: Tandem > non-tandem• Zhang & Gaut, 2003. Genome Res.
The “RLK swarm” model
Acknowledgements
• Shiu lab – Shinhan Shiu– Kousuke Hanada– Cheng Zou– Jessica Oswald– Amanda Tabbert– Gaurav Moghe
• Funding:
–
–