Genome Evolution Course 2011

www.yanaiweb.com/genome

Itai Yanai, Technion – Israel Institute of Technology

Michal Levin, Teaching assistant

Problem Set #4 assigned May 9^th, 2011

To be submitted by email as a PDF or WORD document in English or Hebrew by midnight May 23^rd, 2011 to Michal Levin mlevin@tx.technion.ac.il.

Evolution by Domains. Solve the following five problems.

Problem 1: Evolution of structures. Offer two competing hypotheses that explain why two superfamilies may share the same fold.

Problem 2: Domain architecture network. Identify the network for the proteins domains S_TKc, SH3, PDZ, PH, and GED. Each domain is a node and each edge represents an instance(s) where the two domains are found in the same protein (without regard to the organism in which it is present). Use the SMART database (http://smart.embl-heidelberg.de/). Go to “Genomic mode”. Enter your queries on the right side of the site, labeled ‘Architecture Analysis’ (for example enter query: ‘SH3 AND S_TKc’ and then click “Architecture query”. To display the domain architecture graphically then click ‘ALL (52)’). The network should be submitted as a network figure as shown in the lecture. For each edge note one example protein and the organism from which it comes (for example “AGAP001683-PA - Anopheles gambiae”).

Problem 3: Protein similarity networks. In the network below the nodes correspond to protein sequences and edges correspond to sequence similarity between a pair of sequences. Assume that if a pair of proteins have a domain in common it can be detected by sequence similarity. Given that there are 5 domains altogether among the sequences (domain = recurrent sequence), what is the distribution of domains among the proteins? To answer this question, for each domain (domain A, domain B, domain C, domain D, and domain E) state in which proteins (1-8) it occurs.

Problem 4: Domain Age. Get to know the Interpro database. Using the phylogenetic distribution associated with each Interpro domain (in the Taxonomy section), find an example of each of the following distributions:

• A universal domain (present in all 3 kingdoms, not necessarily viral)
• A prokaryotic specific domain
• A eukaryotic specific
• A virus specific
• A metazoan specific

For example, RanBP1 is a Eukaryotic specific domain.

Problem 5: Domain Rearrangements. I have prepared a list of human-fly-worm orthologs with links to the InterPro database. Each line represents a set of human, fly and worm orthologous genes. Describe two instances where domain architecture has evolved in any of the three lineages for a given orthologous group. For example: Human gene Q9Y3E5 and Drosophila gene O97067 have a “Peptidyl-tRNA hydrolase II” domain, while the C. elegans O76387 gene has also a “Ubiquitin-associated/translation elongation factor EF1B, N-terminal” domain.