BacterioFiles 316 - Studying Sizeable Special Synthetases

Beauvericin
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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Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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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