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Shweta Deshpande, Fares Z. Najar and Bruce A. Roe Department of Chemistry and Biochemistry

Expression Profile and Genomic Organization Of Regions Containing Clusters Of NBS-LRR Genes In Medicago truncatula. Shweta Deshpande, Fares Z. Najar and Bruce A. Roe Department of Chemistry and Biochemistry Stephenson Research and Technology Center University of Oklahoma

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Shweta Deshpande, Fares Z. Najar and Bruce A. Roe Department of Chemistry and Biochemistry

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  1. Expression Profile and Genomic Organization Of Regions Containing Clusters Of NBS-LRR Genes In Medicago truncatula Shweta Deshpande, Fares Z. Najar and Bruce A. Roe Department of Chemistry and Biochemistry Stephenson Research and Technology Center University of Oklahoma 101 David L. Boren Blvd, Norman, Oklahoma, 73019

  2. Abstract As a member of the international consortium sequencing the model legume, Medicago truncatula, our laboratory is sequencing chromosomes 1, 4, 6 and 8.With over 1566 BACs sequenced representing over half of the euchromatic region, we now have begun a genomic analysis focusing initially on the disease resistance genes with sequence homology to known NBS-LRR genes. For example; the NBS-LRR superfamily of plant resistance genes; is the largest and most common of the disease resistance gene group. Many hypothetical mechanisms have been proposed for these NBS-LRR genes. Mapping of the NBS-LRR containing BAC contigs and ESTs representing resistance genes now reveals that chromosomes 4 and 6 of Medicago truncatula contains most of the TIR type NBS-LRR disease resistance genes while a large portion of the non-TIR type map to chromosome 3, 5 and 8. A preliminary blastN analysis of these NBS-LRR regions against the Medicago truncatula EST libraries reveals that these genes are expressed in the mixed tissue, leaves, seedling roots, immature pod walls and roots nodules. Furthermore when the genomic regions with clustered NBS-LRR genes were examined, we observed that each separate cluster encodes genes with its own unique resistance specificity, often with high levels of conservation in their encoded motifs but with significant divergence in their flanking sequences. Therefore a picture now is emerging that is consistent with the notion that duplication of disease resistant genes is a critical factor in broadening a meaningful plant response to various external stress related factors.

  3. NBS-LRR • NBS-LRRs are grouped into two classes depending on the domains present at their N-terminal : • TIR (toll / Interleukin receptor) • Non-TIR : This class encodes 2 domains: • Coiled coil (CC) • Leucine Zipper (LZ) • Structure of NBS-LRR : TIR domain ~ 200 amino acids. NBS domain ~ 300 amino acids. LRR domain ~ 10 – 40 leucines.

  4. Genetic mapping of TIR and non-TIR NBS sequences in Medicago truncatula

  5. Overview of the Chromosomal Location of NBS-LRR Genes To date there are 49 contigs that contain clusters of NBS-LRR genes, spread over the genome. Among these contigs there are 70 BACs that contain clusters, totaling 335 clustered NBS-LRR genes. NBS-LRR

  6. Mechanisms of NBS-LRR • “Receptor-Ligand Model” • Avr-dependant ligand binds to LRR of resistance protein once attacked by a pathogen. • Formation of intracellular signaling molecules and induction of phosphorylation and dephosphorylation cascade. • Activation of resistance gene expression. • Cell death. • “Guard Hypothesis” • The NBS-LRR resistance protein act as a "surveillance system" for another protein. • When avirulence products interact with a protein NBS-LRR detects it and as a result this complex undergoes a conformational change. • Resistance protein is induced in-turn and produces defense responses.

  7. BlastN results against EST libraries Blast all Medicago truncatula BAC sequences against known NBS-LRR genes in the NCBI Blast these NBS-LRR genes against the EST libraries Categorized them according to their expression. Of the 852 NBS-LRR genes on chromosomes 1,4,6, and 8, blastN was performed and 132 genes were studied in detail. Blast parameters??

  8. BlastN results against EST libraries Collected all NBS-LRR genes from literature. BlastP to Medicago predicted ORFs With a score of 100 and above BlastN NBS-LRR homologous ORFs against medicago EST database with a score of 500 and above Genes categorized based on expression patterns

  9. Nematode resistance genes on BAC mth2-23l11 • Nematodes affect the growth and development of plants by physically injuring the roots while feeding, penetrating and moving through them. • BAC mth2-23l11, which maps to chromosome 4 on contig 65, has a cluster of 3 putative Nematode resistance genes. • The genes have highly conserved TIR and NBS domains, especially at the kinase motif. • The genes diverge in the LRR domain. NBS-LRR genes On chromosome 4

  10. ClustalW alignment of the mth2-23l11 predicted NBS-LRR proteins TIR Domain LRR domain Kinase 1a NBS Domain Kinase 2a Kinase 3a GLPL motif

  11. Comparison of nematode-resistance genes between Mt and Gm

  12. NBS-LRR genes

  13. Conclusions • Proper understanding of the plant disease resistance mechanism will improve crop yields. • NBS-LRR genes are expressed in various plant tissues but majority of them are expressed in roots • The NBS-LRR gene clusters show homology to the same disease resistance gene, resulting from sequence local duplications within the genome.

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