Evolutionary Analysis of Domain ArrangeMents (EVADAM); Evolutionäre Analyse von Domänenarrangements

• Applicant: Professor Dr. Erich Bornberg-Bauer
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2008 to 2013
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 69260766

• Final Report Year: 2015

Final Report Abstract

Protein evolution can, to a large extent, be described as the rearrangement of modules, typically structural domains. Many modules are versatile as they occur in many different combinations, or linear arrangements. Their sequence signatures, e.g. HMM profiles, are stored in databases such as PRODOM or Pfam. Proteins can thus not only be represented as strings of amino acids but also as strings of domain IDs (IDentifiers) taken from these data bases. Only recently it emerged that this representation is efficient and useful, for example for finding bio-medically important links or constructing phylogenies. This project is embedded in a larger effort as we also develop methods to investigate arrangements and their evolution by reconstructing their phylogenies, multiple alignments and visualisation tools. In a series of papers we have shown that: • Domains are frequently lost in a stochastic manner, i.e. at a fairly constant rate reminiscent of the molecular clock principle. • Novel domains arise rarely but if they arrive they are only fixed if they confer strong adaptive benefits and, consequently, are replicated within the lineage. • Therefore, novel domains and their radiation establish a third way to detect adaptation by comparative genome analysis and complements KaKs and family expansion/reduction. • Fusions and terminal losses dominate the creation of novel arrangements. • Rates on overall are very similar across several and very diverse clades. • The rates can – and will – be used to develop future methods for deep phylogeny reconstruction • These insights so far have been used and will continued to be used for genome analysis.

Publications

• Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 5963:327-342 (2010)
  JH Werren, A Telschow, A Schuler, AD Moore, E Bornberg-Bauer, et al.
  
• Molecular and phylogenetic characterisation of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants; BMC Plant Biology, 10:219 (2010)
  B Rüping, AM Ernst, SB Jekat, S Nordzieke, AR Reineke, B Müller, E Bornberg-Bauer, D Prüfer and GA Noll
  
• Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution; Genome Biology and Evolution; 4:316 – 29; 2012
  A Kersting, E Bornberg-Bauer, AD Moore and S Grath
  
• The dynamics and evolutionary potential of domain gain and loss; Molecular Biology and Evolution; 29:787 – 796; 2012
  AD Moore and Erich Bornberg-Bauer
  
• Quantification and Functional Analysis of Modular Protein Evolution in a Dense Phylogenetic Tree; Biochimica et Biophysica Acta - Proteins and Proteomics 1834(5):898-907; 2013
  AD Moore, S Grath, A Schueler, AK Huylmans and E Bornberg-Bauer
  
• DoMosaicS: Software for domain arrangement visualisation and domain-centric analysis of proteins Bioinformatics 30:282 – 283; 2014
  AD Moore, A Held, J3rd Weiner, N Terrapon and E Bornberg-Bauer
  
• Rapid similarity search of proteins using alignments of domain arrangements; Bioinformatics 30:274 – 281; 2014
  N Terrapon, J3rd Weiner, S Grath, AD Moore and E Bornberg-Bauer
  
• The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol. 24:76 (2015)
  BM Sadd, Barribeau SM, Bornberg-Bauer E, Klasberg S, Gibbs RA, Schmid-Hempel P, Worley KC, et al.
  
• The rise and fall of TRP-N, an ancient family of mechanogated ion channels, in metazoa; Genome Biol Evol; 7:1713–1727; 2015
  A Schüler, G Schmitz, A Reft, S Ozbek, U Thurm and E Bornberg-Bauer