Annotation of Signal Transduction Genes in Laccaria bicolor

1. Annotation of Signal Transduction Genes in Laccaria bicolor Preti Jain1, S. Duplessis2, G. K. Podila1, R. Aygun1, P. Wadhwa1, Francis Martin2 1 University of Alabama in Huntsville, USA 2 INRA Interactions Arbres/Microorganisms, institute National de la Recherche Agronomique, INRA France www.bioimages.org.uk.

2. Main Roles of Signal Transduction in Fungi e.g. N. crassa • Conidiation • Hyphal formation • Nutrient sensing • Role in morphogenesis • Pathogenesis • Mating • Photo-morphogenesis e.g. N. crassa e.g. A. nidulans e.g. C. albicans e.g U. maydis and C. neoformans

3. Gβ Gγ Gα Major Signal Transduction Pathways PLC PIP2 RECEPTOR TYROSINE KINASE GPCR DAG IP3 CAP AC GEF PKC Ca ++ cAMP PI-3 K RAS PI(3,4,5)P3 CAM PKA MAPKKK MAPKK MAPK PDK1 CAM Kinase PKB Regulation of Light Response, virulence, hyphae formation and conidiation Cell integrity, pheromone/mating, and osmoregulation Cell survival under oxidative stress, high temperature Glucose de-repression, gene expression and invertase secretion

4. Current Themes in Function Prediction Identity based approaches: Peptide based Advantages: Can be done with short regions. Highly Specific Homology based approaches: BLAST, FASTA Advantage: Covers large evolution distances Disadvantage: Needs a characterized homologue in the database Non-homology approaches: Gene context, Distance from replication origin, Compositional properties Ref: http://caseylab.duke.edu/research.html SVM New Advantage: Does not always require a well characterized homologue Disadvantage: Coverage of evolutionary distance not known

5. Approach 1 Homology Based Method Set of known sequences Approach 2 BLASTP against the whole genome of Laccaria bicolor Proteins extracted from jgi website and whole genome blast New Homologs BLASTP Homologs Curation E value <10-50

6. SignalinggenesinLaccaria

7. SignalinggenesinLaccaria Contd.

8. Flow Chart of SVM Method Database of known G-Proteins Measure and Quantify Compositional Attributes Analyze to select the significant contributors Database of known non-G-Proteins Significant Contributors Training Query Proteins Query Support Vector Machines Prediction results - G-Proteins Detection of known G-Proteins and non - G-Proteins

9. Organism G protein alpha subunit G protein beta subunit G protein gamma subunit No of known proteins No. of proteins Predicted by G-PROT software No of known proteins No. of proteins Predicted by G-PROT software No of known proteins No. of proteins Predicted by G-PROT software H. sapiens 26 28 9 10 14 15 M. musculus 26 27 9 13 23 23 A. thaliana 5 6 4 9 3 3 D. melanogaster 26 27 13 11 8 10 C. Elegans 25 23 3 5 2 3 Genome Analysis

10. Rho1 Rho subfamily Expansion in Laccaria Rho2 cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction Expansion Expansion Rho1 regulatory protein of the beta-1,3-glucan synthase

11. Scaffold distribution of Rho genes • 11 différent scaffolds • 8 genes on scaffold 61 • 4 genes on scaffold 7 • 2 on scaffold 52 Duplication of genes

12. Gβ Gγ Gα Major Signal Transduction Pathways PLC PIP2 RECEPTOR TYROSINE KINASE GPCR 3 1 2 40 DAG IP3 12 CAP AC GEF 1 1 PKC 1 Ca ++ 8 cAMP PI-3 K 5 RAS PI(3,4,5)P3 CAM PKA MAPKKK MAPKK MAPK 7 4 7 (10) 1 PDK1 CAM Kinase 3 ? PKB Regulation of Light Response, virulence, hyphae formation and conidiation Cell integrity, pheromone/mating, and osmoregulation Cell survival under oxidative stress, high temperature Glucose de-repression, gene expression and invertase secretion

13. Future Directions • In silico and Experimental Analysis of Symbiotic Signal transduction pathways. • Complete annotation of Ser Thr Kinases • Development of SVM based Software for other signaling genes such as Kinases.

14. Acknowledgements Dr. G. K. Podila, UAH Dr R. Aygun, UAH Dr. F. Martin, INRA France Dr. S. Duplessis, INRA France UAH NSF

15. Thank You