Bioinformatics Analysis of the Drosophila spp. Siz gene C. MacKinnon

1. Bioinformatics Analysis of the Drosophila spp. Siz gene C. MacKinnon University of Incarnate Word San Antonio, TX

2. Learning Objectives: 1. Utilize BLAST searches of the siz gene to determine its function. 2 Use Phobius, Pfam and Interpo databases to infer putative gene function. 3. Correlate gene sequence to protein structure/function.

3. Background: • Students in BIOL 3461, Genetics & Lab, conducted a gene annotation project through the Genomics Education Partnership (GEP). • Fall Semester 2011, students annotated the “siz” gene in Drosophila erecta. • A connection between gene structure and protein function/structure is needed to improve the learning outcomes of an annotation project.

4. What bioinformatics skills do students learn doing gene annotation? Genome Browser FosmidgDNA is analyzed with UCSC Genome Browser: • Genes in fosmidgDNA are predicted based on genome information of Drosophila melanogaster.

5. Bioinformatics skills, con’t: BLASTx searches • BLASTx searches are conducted using fosmidgDNA and predicted exon sequences of predicted genes, and predicted physical position of exons are obtained from BLASTx report

6. Summary of GEP gene annotation: Annotation Process USCS Genome Broswer used to find the physical position [in nucleotides] of the start codon, exon/intron splice sites of each exon, and stop codon.

7. GEP Annotation Data: Exon Phase Scores

8. Ideas to add to ASM/JGI skills to class project:What is the function of the annotated gene? BLASTp search of amino acid sequence [available from FlyBase] identifies putative function and structure domain.

9. NCBI Protein Conserved Domains Data

10. NCBI Conserved Domain Text Report: • Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. • The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity

11. Student projects: Find more information about protein! What is a Sec 7 domain? What type of proteins have this domain? What is a guanine-nucleotide-exchange factors (GEFs)? Do they function in a specific biochemical pathway? What is ADP-ribosylation factor family of small GTPases (ARFs)? Do they function in a specific biochemical pathway Obtain data from: Phobius Pfam Interpro Might also do an alignment activity with Sec 7 sequences from various genera; also might do a phylogenetic tree.

12. “Instructor Prep: Phobius”

13. “Instructor Prep: Pfam”

14. “Instructor Prep: InterPro”

15. Function data and other questions…. • One Interpro result: • Pleckstrin homology (PH) domains are small modular domains that occur in a large variety of proteins: • The domains can bind phosphatidylinositol within biological membranes • Through these interactions, PH domains play a role in recruiting proteins to different membranes, thus targeting them to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways. • Sequence alignments? • The 3D structure of several PH domains has been determined. • Can do Consuf analysis