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Evolutionary History and Stress Responsiveness of the Plant Receptor-Like Kinase Family

Evolutionary History and Stress Responsiveness of the Plant Receptor-Like Kinase Family. Shin-Han Shiu and Melissa D. Lehti-Shiu Department of Plant Biology Michigan State University. Protein kinase: ~1000. Intro 1: Duplicate genes in the genome.

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Evolutionary History and Stress Responsiveness of the Plant Receptor-Like Kinase Family

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  1. Evolutionary History and Stress Responsiveness of the Plant Receptor-Like Kinase Family Shin-Han Shiu and Melissa D. Lehti-Shiu Department of Plant Biology Michigan State University

  2. Protein kinase: ~1000 Intro 1: Duplicate genes in the genome *: Clusters of Markov clustering using all-against-all BLAST E values as distance measures Hanada & Shiu, in prep.

  3. Intro 2: Plant vs. animal Gain rate relative to within genome average Higher Lower Shiu et al., 2006

  4. Intro 3: The RLK/Pelle family • Gene count differences among families indicate differential expansion • Animal homolog: • Drsophila: Pelle • Mammalian: IRAKs Shiu et al., 2004

  5. Intro 4: Diversity of RLK/Pelles Shiu & Bleecker 2001

  6. Intro 5: RLK function and expansion Shiu et al., 2004

  7. Major questions • Diversity • When were the receptor configuration established? • Expansion history • What are the patterns of expansion of RLK subfamilies over land plant evolution? • Stress responsiveness • What are the properties of stress responsive RLKs? AtGenExpress microarray dataset 22 stress conditions

  8. ~400 The kinase superfamily in land plants • RLK/Pelle members vs. other kinases

  9. Establishment of receptor kinase subfamily

  10. LysM GDPD Thaumatin CHASE DUF26 LRR GH18 LRR LRR DUF26 GH18 DUF26 Thaumatin Thaumatin Innovation

  11. 3 4 2 5 1 6 7 Family size over land plant evolution • Substantial differences in # of gene gains among lineages • N1-N7: 0.14 genes / 106 yr • N1-N2: 0.52 • N2-N4: 0.91 • N2-N5: 6.71 • N2-N6: 5.5

  12. Differences in subfamily turnover patterns

  13. 4 distinct patterns of turnover

  14. Differences in recent expansion among lineages

  15. Stress responsiveness of RLKs Low expansion rates High expansion rates Non-tandem Tandem Shiu et al., 2004

  16. Likelihood ratio test • Hypothesis: • Gene in class A is significantly more responsive to a stress condition than random expectation. Cumulative chi square distribution function

  17. Stress responsiveness of RLKs • Hypothesis 1: RLKs are more responsive to stress than genome average

  18. Stress responsiveness of RLKs • Hypothesis 2: Tandem RLKs are more responsive to stress than non-tandem RLKs

  19. Comparison against AP2 transcription factors • Large number of AP2 family members are stress responsive

  20. Properties of RLK subfamilies

  21. Stress responsiveness and tandem RLKs • Responsiveness (R) of an RLK subfamily • For subfamilies with ≥ 10 genes • i: subfamily • j: condition • UP: # of up-regulated genes • DN: # of down-regulated

  22. Why tandem RLKs • Stress responsiveness • Tandem genes > non-tandem genes. • RLK > genome average • 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.

  23. The “RLK swarm” model

  24. Summary • Innovation in the RLK/Pelle family • Most RK configuration established > 700 million ago. • Plenty evidence of domain shuffling, but the rate is not high. • Shuffled domains suggest involvement in biotic stress perception. • History of expansion • 4 major turnover patterns • Substantially more recent gains in poplar and rice • Mostly involved subfamilies with lots of tandem repeats • Stress responsiveness • RLK > genome average • Tandem > non-tandem • Biotic > abiotic • The RLK swarm model

  25. Acknowledgement • Lab members • Past member • Funding: Melissa Lehti-Shiu Cheng Zou Kousuke Hanada

  26. The kinase superfamily in land plants

  27. AtGenExpress: stress array data • Do certain RLKs induced under specific subset of stress conditions? • Are tandemly duplicated RLKs tend to be induced under stress conditions? 22 conditions w/ time series Raw intensity GCRMA Normalized intensity LIMMA Genes with Diff. expr.

  28. + Duplication mechanisms • Whole genome duplication • Tandem duplication • Segmental duplication • Replicative transposition

  29. Breadth of stress responsiveness • # of up-regulaton conditions per gene per subfamily

  30. Sizes of different types of RLKs

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