Visit to BPRC. Data is crucial! Case study: Evolution of AIRE protein 6/7/13

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1 Visit to BPRC Adres: Lange Kleiweg 161, 2288 GJ Rijswijk Utrecht CS à Den Haag CS 9:44 Spoor 9a, arrival 10:22 Den Haag CS à Delft 10:28 Spoor 1, arrival 10:44 10:48 Delft Voorzijde à Bushalte TNO/Lange Kleiweg, Bus 130, arrival 10:56 If you can not join, pls. send me an today! Final list for security check and lunch will be made soon. Comparative Immunology When did the adaptive immune system evolve? Are there several other forms of the adaptive immune system? Do the immune system of the plants and mammals have anything in common? Such questions can be adressed by studying the evolution of individual genes Data is crucial! Case study: Evolution of AIRE protein Two sources: Isolation and sequencing of specific genes by molecular techniques Ø Sequence alignment followed by phylogeny Completely sequenced genomes Ø Look for homologous genes (orthologs) using BLAST, and then sequence alignments, followed by a phylogenetic analysis è è Tissue specific antigens are expressed in the thymus due to AIRE reactivity. Therefore T cells can learn what self is. AIRE deficiency causes polyglandular syndrome type I: a broad autoimmune disease. 1

2 For the comparative approach, next to the new sequences, we need also the existing AIRE sequences: extracted from NCBI Starting from human/mouse sequence, we need to find AIRE sequences in other species. 2

3 Comparing different sequences: After Alignment Composition of the proteins: Domains Proteins often have a modular architecture Consisting of discrete structural and functional regions called domains In many cases Different exons code for the different domains in a protein DNA Gene Exon 1 Intron Exon 2 Intron Exon 3 Transcription RNA processing Translation Domain 3 Campbell, Figure Domain 2 Polypeptide Domain 1 3

4 Domains in AIRE Although Frog AIRE has a different domain composition, function remains the same Phylogeny! 4

5 Phylogeny of PHD2 What did we learn? Teleost fish have also AIRE genes (sequencing, not bioinformatics) The domain structure fish AIRE is more similar to mammalian AIRE than tetrapod AIRE (Bioinformatics). AIRE seems to function similarly in Frog (measured expression in thymus) What did we learn? What did we learn? AIRE sequences among mammalians are well conserved (Bioinformatics) Conservation of different domains are different, PHD1 being most conserved (Bioinformatics). Also most important for the function? In patients having AIRE deficiency 17 point mutations are found, 14 at highly conserved regions. 5

6 Data is crucial! Orthology/paralogy/homology Two sources: Isolation and sequencing of specific genes by molecular techniques Ø Sequence alignment followed by phylogeny Completely sequenced genomes Ø Look for homologous genes (orthologs) using BLAST, and then sequence alignments, followed by a phylogenetic analysis TLR TLR2 TLR2 TLR2 TLR2 Orthologous genes are homologous (corresponding) genes in different species Paralogous genes are homologous genes within the same species (genome) Operational definition of orthology Evolution of TLR3 Bi-directional best hit: Blast gene A in genome 1 against genome 2: gene B is best hit Blast gene B against genome 1: if gene A is best hit à A and B are orthologous A number of other criteria is also in use (part of which is based on phylogeny) Astakhova et al 2009 Immunogenetics 6

7 Evolution of TLR7 and TLR8 Solid lines are TLR7 and dotted lines TLR8 One of the more unexpected findings from our analysis of sea urchin immune genes was the identification of a Rag1/2-like gene cluster (36). The presence of this cluster, along with other recent findings (37), suggested the possibility that these genes had been part of animal genomes for longer than previously considered. 7