evolutionary history and stress responsiveness of plant receptor-like kinases

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are involved in stress response (Rizzon et al., 2006; Hanada and Shiu, unpublished results)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:

–

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