Monday, August 6, 2018

BacterioFiles 350 - Microbes Mysteriously Make Methane

Nitrogenase protein structure
By Jjsjjsjjs - Own work
CC BY-SA 3.0
This episode: A version of the microbial enzyme that fixes nitrogen can also convert carbon dioxide to methane!

Download Episode (11.8 MB, 12.9 minutes)

Show notes:
Microbe of the episode: Human mastadenovirus D

Journal Paper:
Zheng Y, Harris DF, Yu Z, Fu Y, Poudel S, Ledbetter RN, Fixen KR, Yang Z-Y, Boyd ES, Lidstrom ME, Seefeldt LC, Harwood CS. 2018. A pathway for biological methane production using bacterial iron-only nitrogenase. Nat Microbiol 3:281–286.

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Episode outline:
  • Background: Microbes do things nothing else does
    • consume methane – bacteria called methanotrophs
    • Create methane – archaea called methanogens living in anaerobic marshes and guts
      • Also some other minor pathways
    • Important cos more potent greenhouse gas than CO2, also fuel
  • Also fixing N2 gas – high-energy process, only microbes can do it
    • Makes ~half of nitrogen fixed in world; other half is industrial fertilizer :O
    • Nitrogenases are cool - ammonia, nitrogen source for protein etc from air
      • Core is cluster of metal atoms, mostly iron
      • But 3 different versions, each with unique central atom – Mo, V, and another Fe
      • Fixing species all have Mo, only some have V or Fe or both
        • No more than 9% of fixing species have Fe
      • All fix nitrogen, but have different protein sequences, structures, and kinetics
      • In lab, cells mostly use Mo whenever it's available, repress others (most efficient)
        • Others just backups?
      • But evidence of V more effective in cold, and both active unexpectedly
      • So consider possibility of other functions, more complex inter-relatedness in wild
  • What’s new: Now, scientists publishing in Nature Microbiology have discovered one interesting possible function of the iron-center nitrogenase: producing methane!
  • All versions actually not very specific to nitrogen
    • Test for any activity uses acetylene – 2 C with triple bond – conversion to ethylene
    • V and slightly Mo can reduce CO to ethylene + more
    • Other stuff too, depending on version
    • Mutated Mo can reduce CO2 to methane
  • Methods: Here, wanted to test if other versions can do same
  • Microbe is Rhodopseudomonas palustris – phototroph bacterium
  • Mutated V protein same as Mo version, 2 amino acids in active site
    • Wild V produced very small amounts of methane; mutant made a lot
  • Tried Fe protein too, same mutations
    • But mutant produced hardly any methane, while wild produced surprising amount
    • Apparently reduces CO2 naturally
  • But actually from CO2? Tested with stable isotope-labeled bicarbonate
    • Cells produced methane that showed up on MS as 1 neutron extra
  • Then purified nitrogenase and tested production
    • Produced a lot of ammonia and ~3x more hydrogen, and relatively little methane
    • But all three at once
  • Tested Fe nitrogenases from 3 other species too
    • Rhodospirillum rubrum, Rhodobacter capsulatus, and Azotobacter vinelandii
    • Each also showed methane production when growing with Fe nitrogenase
  • Finally tested co-culture with methanotroph
    • Methane produced by nitrogenase was enough to support growth
    • Confirmed using 13C-labeled methane
  • Summary: A version of the enzyme that converts nitrogen gas to biologically useful forms also converts CO2 to methane, a component of natural gas
  • Applications and implications: Not very efficient biofuel production by itself
    • But in addition to fertilizer and/or hydrogen production, maybe byproduct
  • What do I think: Raises interesting questions about history of nitrogenase
    • 1st weird that Mo version is oldest and most common
      • Harder to gather Fe + Mo vs. just Fe, seems like
    • But possible that alternates interact more than just N cycle
      • Link between C and N
      • Can produce methane that other organisms can consume
        • Symbiosis
      • Interesting interaction to study to see if it affects nitrogenase regulation
  • Microbes have some very interesting features

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