Methanol-specific methyltransferase isozymes have large carbon kinetic isotope effects that impact methane isotopic signatures

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Abstract
The stable carbon and hydrogen isotopic composition of methane is widely used to determine its sources. Methanogenic growth on methanol generates methane with significantly lower 13 C/ 12 C ratios relative to other substrates, which is used as a marker for this metabolism in environmental samples. The biochemical basis for the large carbon isotope effect associated with methanol growth is currently unknown. Here, we measure the change in the carbon and hydrogen stable isotopic compositions of the methane produced by Methanosarcina acetivorans during growth on methanol. We couple these results with an inverse modeling approach to calculate the kinetic isotopic effects (KIEs) of the rate-limiting step, catalyzed by the methanol-specific methyltransferase complex (MTA). Through this process, we estimate the carbon KIE of MTA ( 13 ε MTA ) to be −66‰ and the hydrogen KIE of MTA ( 2 ε MTA ) to be −56‰. Our results indicate that the 13 ε MTA contributes substantially to the large carbon isotope effect observed on methanol. We also show that mutant strains that express only a single copy of the MTA complex (MtaC1B1A1, MtaC2B2A1, or MtaC3B3A1) have 13 ε MTA and 2 ε MTA that are indistinguishable from the wild-type strain. Finally, we propose that methanol activation by MTA will remain rate-limiting, even at low environmental methanol concentrations, and the large 13 ε MTA would be expressed in situ as well. IMPORTANCE: Mapping the biological sources of methane is vital for accurately modeling global emissions of this potent greenhouse gas. Methanogenic growth on methanol produces methane with a uniquely depleted carbon isotope signature, which is commonly used as an environmental indicator of this metabolism. The biochemical mechanisms driving this isotopic signature have remained unclear. In this study, we identify the methanol-specific methyltransferase (MTA) complex as the primary driver of these large carbon isotope effects in the model methanogen, Methanosarcina acetivorans . By utilizing M. acetivorans mutants that express a single MTA complex, we demonstrate that these effects are consistent across MTA isozymes that are expressed during different growth phases. Our results suggest these isotopic signatures are intrinsic to the enzyme complex and persist in natural environments. These findings provide a critical biochemical foundation for using stable isotopes to track methane production from methanol in diverse natural ecosystems.
Funding Information
  • David and Lucile Packard Foundation
  • U.S. Department of Energy (S589706)
  • Alfred P. Sloan Foundation
  • Simons Foundation
  • European Molecular Biology Organization
  • Kinship Foundation
  • US Department of Energy, Office of Basic Energy Sciences (DE- AC02-­ 05CH11231)

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