Monday, November 6, 2017

BacterioFiles 316 - Studying Sizeable Special Synthetases

By Yu et al. 2017, Nat Commun
CC-BY 4.0
This episode: Scientists study how fungi make interesting peptides using large proteins instead of ribosomes.

Download Episode (8.7 MB, 9.5 minutes)

Show notes:
Microbe of the episode: Nerine virus X

News item

Journal Paper:
Yu D, Xu F, Zhang S, Zhan J. 2017. Decoding and reprogramming fungal iterative nonribosomal peptide synthetases. Nat Commun 8:ncomms15349.

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    Episode outline:
    • Background: Fungi often pretty weird (see ep 279)
      • Challenge many things we think are universal about life
    • One thing like that is Central Dogma
      • DNA transcribed to RNA, then that translated to protein by ribosomes
        • Genetic code and codons that code for amino acids that ribosomes assemble into chain
      • Though some viruses start from RNA, and some reverse process, etc
    • But some fungi defy dogma in another way: non-ribosomal peptides or NRPs
      • Put together amino acids into small chains/rings with non-ribosomal peptide synthetases
        • NRPSs
      • Variety of effects from resulting molecules; one is penicillin
      • Some other antibacterial or function as anti-cancer or insecticidal
      • Bacteria have NRPs too
    • So lots of interesting biochemistry and potential usefulness
      • Interest in producing compounds more easily/cheaply
    • What’s new: Now, scientists publishing in Nature Communications have studied these enzymes to understand how they work, and possibly how to modify them to produce different useful products!
    • In fungus: Beauveria bassiana
      • Produces beauvericin and bassianolide
      • Rather pretty chemical structures, lacey rings, at least drawn flat
    • NRPSs are big enzymes with multiple domains, like assembly line
      • Product gets modified in one then passed to next, etc
    • But overall function not well understood
    • Methods: First took synthetase genes and expressed in Saccharomyces cerevisiae
      • Not too easy, they’re gigantic; hard to PCR, hard to synthesize
      • Purified and tested
      • Given right substrates, produced correct product
    • Mutated single aminos of proteins to see how product changed
      • Figure out which model of process was correct
        • moving from one domain to other or building on one
      • Some domains apparently redundant; protein can still produce if one or other is removed
        • Tho removing one reduces production a lot more than other
      • Conclusion is that the moving between domains model is more likely
      • One mystery maybe solved
    • Another is what another kind of domain does
      • Produced it in isolated form and observed what it did to substrate
        • Created certain kind of bond
      • Or removed from rest of protein and observed what resulted
        • Some resulted in no protein at all; required for production
    • Also tried creating chimera enzymes of 2 synthetases
      • Created new products different from either enzyme
      • Similar in monomer structure to one but similar in length to other
      • Thus discovered which section determines length
    • Summary: Broke down functions of different sections of fungal enzymes producing useful compounds
    • Applications and implications: Easier/cheaper to produce various useful compounds
      • Medications, etc
        • Some already produced are interesting; others could be designed
      • Pretty difficult to produce synthetically
    • What do I think: Interesting to have peptides not put together by ribosome
      • But makes sense, no reason why not
      • Wonder how synthetases evolved
    • Good to understand how enzymes work in general; more potential for design

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