Tackling climate change through ruminal methanogenesis

By Andres Hernandez Maduro

Of the many industrial processes that contribute to anthropogenic greenhouse gas (GHG) emissions, none produces as much methane and nitrous oxide as agriculture. Around half of all methane and three-quarters of all nitrous oxide emissions originate from agricultural activity,1 with livestock farms being the most significant contributors. Since approximately 81% of GHGs from the livestock sector come from ruminants,2 it is of key interest to better understand how these mammals emit GHGs.

Generally, ruminants like cows or goats possess four stomachs to thoroughly digest their feed. After rumination – wherein grass is chewed, swallowed, regurgitated, rechewed and swallowed again – cud enters the first of these stomachs to be processed.3 Microbes play an important role here, breaking down large, fibrous molecules that would otherwise be indigestible by the ruminant’s gastrointestinal system. Unfortunately, some of these microbes possess metabolic pathways associated with higher methane levels. Microbiome studies have found animals harbouring the archaea Methanobrevibacter gottschalkii (a methanogen, which obtains ATP primarily by synthesising methane) to emit greater amounts of methane, for example. Guts ridden with ciliate protozoa and bacteria that produce H2 molecules display a similar effect2 – however, further research is needed to comprehend how the composition of the gut flora induces GHG emissions.

Thankfully, the biochemistry of methanogenesis is generally well-understood. All known methanogens can be categorised into one of three major pathways: hydrogenotrophic, aceticlastic or methylotrophic methanogenesis.4 The first of these uses hydrogen and methanofuran (MFR) to convert carbon dioxide into MFR-CHO, which in turn is repeatedly reduced (while MFR is exchanged for tetrahydromethanopterin, or H4MPT) to create H4MPT-CH3. This can then transfer a methyl group to Coenzyme M (CoM) via the enzyme catalysis of a sodium ion channel, pumping sodium ions outside the cell and ultimately resulting in the central molecule of the puzzle: CoM-CH3.

Compared to the above, aceticlastic methanogenesis produces H4MPT-CH3 directly from acetyl CoA and H4MPT, while the methylotrophic route utilises methanol and methyltransferase enzymes to turn CoM into CoM-CH3.4 After obtaining CoM-CH3, all these pathways become identical. At this point, CoM-CH3 is reacted with Coenzyme B (CoB) to produce both CoM-S-S-CoB and CH4 (i.e., methane), with the cycle ending when CoM-S-S-CoB is split back into its two constituent coenzymes. Note that this process also pumps hydrogen ions out of the cell in non-hydrogenotrophic methanogenesis. Altogether, the sodium and hydrogen ions transported out can then re-enter the cell through ATP synthase – indirectly generating the biological energy needed to grow and survive.5

In order to reduce methane gas emissions, scientists could try to find drugs to inhibit each methanogenic pathway separately. This would take an unnecessarily large amount of time and effort, however, especially since recent research has found a variety of new substrates that regularly kickstart methanogenesis in some microbes.5 Needless to say, targeting a universal mechanism would be preferable – as is the case with the catalysis of methyl-coenzyme M reductase (MCR). Three methanogenic MCR isozymes have been discovered so far – MCRI, MCRII and MCRIII – and all of them catalyse the reaction between CoM-CH3 and CoB.6 As this occurs in practically all methanogens, studying the structure and function of MCRs is a promising lead for methanogenesis inhibition.

As a dimer of heterotrimers, MCR forms two identical rings that are each constructed of three subunits, with a nickel tetrahydrocorphinoid molecule (coenzyme F430) placed in each ring’s active site.6 X-ray structures have further revealed that the nickel atom in coenzyme F430 can take different oxidation states during the reaction coordinate. Here, Ni(I) is redox-active while Ni(II) is inactive, with Ni(III) possibly being involved in the intermediate steps of the enzyme’s reaction mechanism.6,7 Although it has been established that the nickel must be in its +1 oxidation state to initiate catalysis, the subsequent mechanism is still under scrutiny.

Previous experiments using kinetic, spectroscopic and computational approaches7 have provided some evidence that points to the ‘methyl radical mechanism’, a model postulating that a Ni(II)-thiolate and a methyl radical are produced in the process. With enough research, uncovering the full mechanism should only be limited by a matter of time – particularly since imitating intermediates/transition states in the reaction could help us produce drugs targeting it. Furthermore, current investigations into MCR’s posttranslational modifications (PTMs) are steadily proving their significance in methanogenesis. One such PTM is the methylation of a ring subunit’s arginine residue (its exact position differs between species), catalysed by methanogenesis marker protein 10 (Mmp10).8

In the methanogen Methanococcus maripaludis, simply knocking out the gene for Mmp10 has already been shown to decrease methane formation by up to 60%.8 Mmp10 has consequently started to receive much attention in the scientific community, with studies detailing its dependency on cobalamin (vitamin B12) as an intermediate carrier,9 for example. New crystallographic images have now elucidated the atomic resolution structure of Mmp10, and analytical biochemistry techniques have interpreted the images to understand its arginine methylation mechanism.10

This article touches the surface of ruminal methanogenesis – and knowledge on the topic will only expand with time. As such, there should be nothing stopping us from applying it to mitigate climate change soon.

References:

  1. Lynch J, et al. Agriculture’s Contribution to Climate Change and Role in Mitigation Is Distinct From Predominantly Fossil CO2-Emitting Sectors. Frontiers in Sustainable Food Systems 2021. Available from: https://doi.org/10.3389/fsufs.2020.518039 
  2. Tapio I, Snelling TJ, Strozzi F, et al. The ruminal microbiome associated with methane emissions from ruminant livestock. Journal of Animal Science and Biotechnology 2017;8:7. Available from: https://doi.org/10.1186/s40104-017-0141-0 
  3. Beauchemin KA. Invited review: Current perspectives on eating and rumination activity in dairy cows. Journal of Dairy Science 2018;101(6):4762-4784. Available from: https://doi.org/10.3168/jds.2017-13706 
  4. Lyu Z, et al. Methanogenesis. Current Biology 2018;28(13):PR727-R732. Available from: https://doi.org/10.1016/j.cub.2018.05.021 
  5. Kurth JM, Op den Camp HJM & Welte CU. Several ways one goal—methanogenesis from unconventional substrates. Applied Microbiology and Biotechnology 2020;104:6839–6854. Available from: https://doi.org/10.1007/s00253-020-10724-7 
  6. Chen H, Gan Q & Fan C. Methyl-Coenzyme M Reductase and Its Post-translational Modifications. Frontiers in Microbiology 2020. Available from: https://doi.org/10.3389/fmicb.2020.578356 
  7. Wongnate T, et al. The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase. Science 2016;352(6288):953-8. Available from: https://doi.org/10.1126/science.aaf0616 
  8. Lyu Z, et al. Posttranslational methylation of arginine in methyl coenzyme M reductase has a profound impact on both methanogenesis and growth of Methanococcus maripaludis. Journal of Bacteriology 2020;202:e00654–19. Available from: https://doi.org/10.1128/jb.00654-19 
  9. Radle MI, Miller DV, Laremore TN & Booker SJ. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. Journal of Biological Chemistry 2019;294:11712–11725. Available from: https://doi.org/10.1074/jbc.RA119.007609 
  10. Fyfe CD, Bernardo-García N, Fradale L, et al. Crystallographic snapshots of a B12-dependent radical SAM methyltransferase. Nature 2022;602:336–342. Available from: https://doi.org/10.1038/s41586-021-04355-9 

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