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Book club


          Andreas Wagner,
The Origins of Evolutionary Innovations


              Chapter 4

Book club presented by G. M. Dall'Olio,
      Pompeu Fabra, IBE-CEXS
Reminder:
               Genotype network
   A genotype network is a set of genotypes that have the same 
      phenotype, and are connected by single pairwise differences
         AAAAA     AAAAC     AAAAG     AAAAT     AAATT
         AAACA     AAACC     AAACG     AAACT     AAATC
         AACCA     AACCC     AACCG     AACCT     …..
         ACCCA     ACCCC     ACCCG     ACCCT     …..
         CCCCA     CCCCC     CCCCG     CCCCT     …..
         …..       …..       …..       …..       …..



   Yellow = same phenotype = a genotype network
   Note: genotype network == neutral network
Genotype Networks
      better representation!
   The Genotype Space can be represented as a Hamming Graph




               https://bitbucket.org/dalloliogm/genotype_space
Chapter 4:
            Novel Molecules
   This chapter describes the relationship between 
     protein/RNA sequence and tertiary structure
   Most RNA/Proteins have the same fold but 
     different sequences
Novel Molecules,
              definitions (1)
   Genotype: 
          def 1: the aminoacid sequence of a protein 
             (or the list of hydrophobic)
          def 2: the nucleotidic sequence of a RNA 
A genotype space of
    sequences
A genotype space of
      sequences (simplified)
   O = any Hydrophobic aminoacid
   Y = any Hydrophilic aminoacid
Novel Molecules
               definitions (2)
   Phenotype: 
          The fold of a protein sequence
          The secondary structure of a RNA molecule
Protein Structures
   It is also possible to 
       predict the fold of a 
       protein
   But it is difficult, so 
     here we focus on 
     “lattice models”
   In a lattice model, we 
      only use hydrophobic 
      or hydrophilic 
      aminoacids
A Genotype network
   In this example, all orange sequences have the same fold:
More sequences than folds
   Li et al, 1996: study on lattice protein models:
          There are many more protein sequences than folds
          Some phenotypes are formed by more sequences 
             than others
          Sequences that produce the same fold can be very 
             different
   Rost, 1997: study on 272 proteins with similar 
     folds. They shared 8.5% of aa seq
There are many more
     protein sequences than
          protein folds
   Globins are a very common protein domain
   Most globins have different sequence, but the same 
     fold
   Among some hemoglobins, only 12.4% of aa 
     residues are identical
Do globins have a common
         origin?




                   Bailly, X., Chabasse, C.,
                   Hourdez, S., Dewilde, S., Martial,
                   S., Moens, L. and Zal, F. (2007),
                   Globin gene family evolution and
                   functional diversification in
                   annelids. FEBS Journal, 274:
                   2641–2652. doi: 10.1111/j.1742-
                   4658.2007.05799.x
                   Goodman M, Pedwaydon J,
                   Czelusniak J, Suzuki T, Gotoh T,
                   Moens L, Shishikura F, Walz D,
                   Vinogradov S. An evolutionary
                   tree for invertebrate globin
                   sequences. J Mol Evol.
                   1988;27(3):236-49. PubMed
                   PMID: 3138426.
Some folds are more
                    common than others
      Some folds can be obtained by an higher number of 
         sequences than others
      Number of proteins Sequences by structure (Ferrada, 
        Wagner 2010): 




    Ferrada, E. & Wagner, A., 2010. Evolutionary innovations and the organization of protein functions in genotype space. PloS one, 5(11), p.e14172. Available at:
    http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2994758&tool=pmcentrez&rendertype=abstract
The 10 most structurally
     promiscuous functions
   Promiscuity of a function: when the function can be 
      obtained by different structures/sequences




                                             Ferrada, E. & Wagner, A., 2010.
                                             Evolutionary innovations and the
                                             organization of protein functions in
                                             genotype space. PloS one, 5(11),
                                             p.e14172. Available at:
                                             http://www.pubmedcentral.nih.gov/article
Genotype networks of
        protein sequences
   Sequences that have 
      the same fold tend to 
      be connected in a 
      genotype network 
      (from Li et al, 1996)
   More the case of figure 
     1 (above) than figure 
     2 (below)
RNA structures
   RNA secondary structures can be predicted in silico




                        http://rna.ucsc.edu/rnacenter/ribosome_images.html
RNA structure videogame
   There is even a 
     videogame on 
     predicting RNA 
     structure:
          http://eterna.cmu.edu/
   So, predicting RNA 
     structures is 
     (relatively) easy
Innovations in RNA folds
   All the observations made for protein sequences are 
     also valid for RNA, in a bigger scale:
          On average, 400 million RNA seqs per fold
          Very long RNA sequences tend to similar folds
There are many more RNA
    sequences than RNA folds
   Size rank of genotype set by frequency




    Wagner, A., 2008. Robustness and evolvability: a paradox resolved. Proceedings. Biological sciences / The Royal Society, 275(1630), pp.91-100. Available at:
    http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2562401&tool=pmcentrez&rendertype=abstract
Frequent RNA structures
   def. frequent RNA structure: a RNA structure that 
      can be obtained by > 5000 sequences
   Only 10% of RNA structures are frequent
   93% of RNA sequences belong to frequent RNA 
      structures
RNA sequences can
withstand a lot of changes,
without modifying the fold
   Maximal genotype distance in a RNA gen. network:




                            A. Wagner, The Origins of Evolutionary Innovations. Figure 4.6
RNA sequences can
withstand a lot of changes,
without modifying the fold
   Different sequence, same fold:




                                     http://eterna.cmu.edu/
Neighbors of points in the
        genotype network
   Most neighbors of sequences in the space have the 
     same fold




                             A. Wagner, The Origins of Evolutionary Innovations. Figure 4.7
Neighbors of points in the
        genotype network
   Most neighbors of sequences in the space have the same 
     fold
   This means that the genotype network of a RNA fold is 
      usually dense
   RNA genotype network is more likely to fig 1 than fig 2:




Fig 1                                                   Fig 2
Neighbors of genotypes in a
    genotype network
   Two sequences on a 
     genotype network 
     have, by definition, 
     the same fold.
   But what about their 
     neighbors?




                             A. Wagner, The Origins of Evolutionary Innovations. Figure 2.6
Phenotype of neighbors of
       genotype network
   Neighbor of genotypes 
     can have very 
     different phenotypes
Novel RNA phenotypes
   Schultes and Bartel: 
      designed a new 
      rybozime from two 
      existing ones
   Existing enzymes had 
     <25% sequence 
     similarity and no 
     common structure
   Few mutations needed 
      to obtain the hybrid   Schultes, E. a & Bartel, D.P., 2000. One sequence, two ribozymes: implications
                             for the emergence of new ribozyme folds. Science (New York, N.Y.), 289(5478),
                             pp.448-52. Available at: http://www.ncbi.nlm.nih.gov/pubmed/10903205
Take Home messages
   There are many more sequences than protein/RNA 
     folds
   Some folds correspond to more sequences than 
     others
   Sequences that produce the same fold can be very 
      different
   New folds can be reached by changing few bases
A Genotype network
   All blue sequences have the same fold

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Wagner chapter 4

  • 1. Book club Andreas Wagner, The Origins of Evolutionary Innovations Chapter 4 Book club presented by G. M. Dall'Olio, Pompeu Fabra, IBE-CEXS
  • 2. Reminder: Genotype network  A genotype network is a set of genotypes that have the same  phenotype, and are connected by single pairwise differences AAAAA AAAAC AAAAG AAAAT AAATT AAACA AAACC AAACG AAACT AAATC AACCA AACCC AACCG AACCT ….. ACCCA ACCCC ACCCG ACCCT ….. CCCCA CCCCC CCCCG CCCCT ….. ….. ….. ….. ….. …..  Yellow = same phenotype = a genotype network  Note: genotype network == neutral network
  • 3. Genotype Networks better representation!  The Genotype Space can be represented as a Hamming Graph https://bitbucket.org/dalloliogm/genotype_space
  • 4. Chapter 4: Novel Molecules  This chapter describes the relationship between  protein/RNA sequence and tertiary structure  Most RNA/Proteins have the same fold but  different sequences
  • 5. Novel Molecules, definitions (1)  Genotype:   def 1: the aminoacid sequence of a protein  (or the list of hydrophobic)  def 2: the nucleotidic sequence of a RNA 
  • 6. A genotype space of sequences
  • 7. A genotype space of sequences (simplified)  O = any Hydrophobic aminoacid  Y = any Hydrophilic aminoacid
  • 8. Novel Molecules definitions (2)  Phenotype:   The fold of a protein sequence  The secondary structure of a RNA molecule
  • 9. Protein Structures  It is also possible to  predict the fold of a  protein  But it is difficult, so  here we focus on  “lattice models”  In a lattice model, we  only use hydrophobic  or hydrophilic  aminoacids
  • 10. A Genotype network  In this example, all orange sequences have the same fold:
  • 11. More sequences than folds  Li et al, 1996: study on lattice protein models:  There are many more protein sequences than folds  Some phenotypes are formed by more sequences  than others  Sequences that produce the same fold can be very  different  Rost, 1997: study on 272 proteins with similar  folds. They shared 8.5% of aa seq
  • 12. There are many more protein sequences than protein folds  Globins are a very common protein domain  Most globins have different sequence, but the same  fold  Among some hemoglobins, only 12.4% of aa  residues are identical
  • 13. Do globins have a common origin? Bailly, X., Chabasse, C., Hourdez, S., Dewilde, S., Martial, S., Moens, L. and Zal, F. (2007), Globin gene family evolution and functional diversification in annelids. FEBS Journal, 274: 2641–2652. doi: 10.1111/j.1742- 4658.2007.05799.x Goodman M, Pedwaydon J, Czelusniak J, Suzuki T, Gotoh T, Moens L, Shishikura F, Walz D, Vinogradov S. An evolutionary tree for invertebrate globin sequences. J Mol Evol. 1988;27(3):236-49. PubMed PMID: 3138426.
  • 14. Some folds are more common than others  Some folds can be obtained by an higher number of  sequences than others  Number of proteins Sequences by structure (Ferrada,  Wagner 2010):  Ferrada, E. & Wagner, A., 2010. Evolutionary innovations and the organization of protein functions in genotype space. PloS one, 5(11), p.e14172. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2994758&tool=pmcentrez&rendertype=abstract
  • 15. The 10 most structurally promiscuous functions  Promiscuity of a function: when the function can be  obtained by different structures/sequences Ferrada, E. & Wagner, A., 2010. Evolutionary innovations and the organization of protein functions in genotype space. PloS one, 5(11), p.e14172. Available at: http://www.pubmedcentral.nih.gov/article
  • 16. Genotype networks of protein sequences  Sequences that have  the same fold tend to  be connected in a  genotype network  (from Li et al, 1996)  More the case of figure  1 (above) than figure  2 (below)
  • 17. RNA structures  RNA secondary structures can be predicted in silico http://rna.ucsc.edu/rnacenter/ribosome_images.html
  • 18. RNA structure videogame  There is even a  videogame on  predicting RNA  structure:  http://eterna.cmu.edu/  So, predicting RNA  structures is  (relatively) easy
  • 19. Innovations in RNA folds  All the observations made for protein sequences are  also valid for RNA, in a bigger scale:  On average, 400 million RNA seqs per fold  Very long RNA sequences tend to similar folds
  • 20. There are many more RNA sequences than RNA folds  Size rank of genotype set by frequency Wagner, A., 2008. Robustness and evolvability: a paradox resolved. Proceedings. Biological sciences / The Royal Society, 275(1630), pp.91-100. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2562401&tool=pmcentrez&rendertype=abstract
  • 21. Frequent RNA structures  def. frequent RNA structure: a RNA structure that  can be obtained by > 5000 sequences  Only 10% of RNA structures are frequent  93% of RNA sequences belong to frequent RNA  structures
  • 22. RNA sequences can withstand a lot of changes, without modifying the fold  Maximal genotype distance in a RNA gen. network: A. Wagner, The Origins of Evolutionary Innovations. Figure 4.6
  • 23. RNA sequences can withstand a lot of changes, without modifying the fold  Different sequence, same fold: http://eterna.cmu.edu/
  • 24. Neighbors of points in the genotype network  Most neighbors of sequences in the space have the  same fold A. Wagner, The Origins of Evolutionary Innovations. Figure 4.7
  • 25. Neighbors of points in the genotype network  Most neighbors of sequences in the space have the same  fold  This means that the genotype network of a RNA fold is  usually dense  RNA genotype network is more likely to fig 1 than fig 2: Fig 1 Fig 2
  • 26. Neighbors of genotypes in a genotype network  Two sequences on a  genotype network  have, by definition,  the same fold.  But what about their  neighbors? A. Wagner, The Origins of Evolutionary Innovations. Figure 2.6
  • 27. Phenotype of neighbors of genotype network  Neighbor of genotypes  can have very  different phenotypes
  • 28. Novel RNA phenotypes  Schultes and Bartel:  designed a new  rybozime from two  existing ones  Existing enzymes had  <25% sequence  similarity and no  common structure  Few mutations needed  to obtain the hybrid Schultes, E. a & Bartel, D.P., 2000. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science (New York, N.Y.), 289(5478), pp.448-52. Available at: http://www.ncbi.nlm.nih.gov/pubmed/10903205
  • 29. Take Home messages  There are many more sequences than protein/RNA  folds  Some folds correspond to more sequences than  others  Sequences that produce the same fold can be very  different  New folds can be reached by changing few bases
  • 30. A Genotype network  All blue sequences have the same fold