References
-
Boehm, S. et al. State of Climate Action 2023. World Resour. Inst https://www.wri.org/research/state-climate-action-2023 (2023).
-
Sollai, S., Porcu, A., Tola, V., Ferrara, F. & Pettinau, A. Renewable methanol production from green hydrogen and captured CO2: a techno-economic assessment. J. CO2 Util. 68, 102345 (2023).
-
Meunier, N., Chauvy, R., Mouhoubi, S., Thomas, D. & De Weireld, G. Alternative production of methanol from industrial CO2. Renew. Energ. 146, 1192–1203 (2020).
-
Kelso, P. A., Chow, L. K. M., Carpenter, A. C., Paulsen, I. T. & Williams, T. C. Toward methanol-based biomanufacturing: emerging strategies for engineering synthetic methylotrophy in Saccharomyces cerevisiae. ACS Synth. Biol. 11, 2548–2563 (2022).
-
Bertau, M., Offermanns, H., Plass, L., Schmidt, F. & Wernicke, H.-J. Methanol: The Basic Chemical and Energy Feedstock of the Future Vol. 1 (Springer, 2014).
-
Patel, S. K. S. et al. Hierarchical macroporous particles for efficient whole-cell immobilization: Application in bioconversion of greenhouse gases to methanol. ACS Appl. Mater. Interfaces 11, 18968–18977 (2019).
-
Bennett, R. K., Steinberg, L. M., Chen, W. & Papoutsakis, E. T. Engineering the bioconversion of methane and methanol to fuels and chemicals in native and synthetic methylotrophs. Curr. Opin. Biotechnol. 50, 81–93 (2018).
-
Ochsner, A. M., Sonntag, F., Buchhaupt, M., Schrader, J. & Vorholt, J. A. Methylobacterium extorquens: methylotrophy and biotechnological applications. Appl. Microbiol. Biotechnol. 99, 517–534 (2015).
-
Mo, X.-H. et al. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl. Microbiol. Biotechnol. 104, 4515–4532 (2020).
-
Schultenkämper, K., Brito, L. F., López, M. G., Brautaset, T. & Wendisch, V. F. Establishment and application of CRISPR interference to affect sporulation, hydrogen peroxide detoxification, and mannitol catabolism in the methylotrophic thermophile Bacillus methanolicus. Appl. Microbiol. Biotechnol. 103, 5879–5889 (2019).
-
Yang, X., Zheng, Z. & Wang, Y. Bacillus methanolicus: an emerging chassis for low-carbon biomanufacturing. Trends Biotechnol. 43, 274–277 (2025).
-
Gao, J., Gao, N., Zhai, X. & Zhou, Y. J. Recombination machinery engineering for precise genome editing in methylotrophic yeast Ogataea polymorpha. iScience 24, 102168 (2021).
-
Wang, L. et al. Efficient CRISPR–Cas9 mediated multiplex genome editing in yeasts. Biotechnol. Biofuels 11, 277 (2018).
-
Liu, Q. et al. CRISPR–Cas9-mediated genomic multiloci integration in Pichia pastoris. Microb. Cell Fact. 18, 144 (2019).
-
Guo, F., Qiao, Y., Xin, F., Zhang, W. & Jiang, M. Bioconversion of C1 feedstocks for chemical production using Pichia pastoris. Trends Biotechnol. 41, 1066–1079 (2023).
-
Cai, P., Gao, J. & Zhou, Y. CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications. Microb. Cell Fact. 18, 63 (2019).
-
Chen, F. Y. H., Jung, H.-W., Tsuei, C.-Y. & Liao, J. C. Converting Escherichia coli to a synthetic methylotroph growing solely on methanol. Cell 182, 933–946.e914 (2020).
-
Nieh, L.-Y. et al. Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol. Nat. Commun. 15, 8840 (2024).
-
Reiter, M. A. et al. A synthetic methylotrophic Escherichia coli as a chassis for bioproduction from methanol. Nat. Catal. 7, 560–573 (2024).
-
Zhan, C. et al. Reprogramming methanol utilization pathways to convert Saccharomyces cerevisiae to a synthetic methylotroph. Nat. Catal. 6, 435–450 (2023).
-
Guo, Y. et al. Engineering yeasts to co-utilize methanol or formate coupled with CO2 fixation. Metab. Eng. 84, 1–12 (2024).
-
Espinosa, M. I. et al. Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae. Nat. Commun. 11, 5564 (2020).
-
Guo, F. et al. Evolutionary engineering of Saccharomyces cerevisiae: Crafting a synthetic methylotroph via self-reprogramming. Sci. Adv. 10, eadq3484 (2024).
-
Attfield, P. V. Stress tolerance: The key to effective strains of industrial baker’s yeast. Nat. Biotechnol. 15, 1351–1357 (1997).
-
Nielsen, J. Yeast systems biology: model organism and cell factory. Biotechnol. J. 14, 1800421 (2019).
-
Lourens-Hattingh, A. & Viljoen, B. C. Growth and survival of a probiotic yeast in dairy products. Food Res. Int. 34, 791–796 (2001).
-
Espinosa, M. I., Williams, T. C., Pretorius, I. S. & Paulsen, I. T. Benchmarking two Saccharomyces cerevisiae laboratory strains for growth and transcriptional response to methanol. Syn. Syst. Biotechnol. 4, 180–188 (2019).
-
Dai, Z. et al. Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae. Bioresour. Technol. 245, 1407–1412 (2017).
-
Lunt, S. Y. & Vander Heiden, M. G. Aerobic glycolysis: Meeting the metabolic requirements of cell proliferation. Annu. Rev. Cell Dev. Bi. 27, 441–464 (2011).
-
Lieven, C., Herrgård, M. J. & Sonnenschein, N. Microbial methylotrophic metabolism: Recent metabolic modeling efforts and their applications in industrial biotechnology. Biotechnol. J. 13, 1800011 (2018).
-
Liu, Z., Wang, K., Chen, Y., Tan, T. & Nielsen, J. Third-generation biorefineries as the means to produce fuels and chemicals from CO2. Nat. Catal. 3, 274–288 (2020).
-
Gregory, G. J., Bennett, R. K. & Papoutsakis, E. T. Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs. Metab. Eng. 71, 99–116 (2022).
-
Kim, S. et al. Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat. Chem. Biol. 16, 538–545 (2020).
-
Yu, H. & Liao, J. C. A modified serine cycle in Escherichia coli coverts methanol and CO2 to two-carbon compounds. Nat. Commun. 9, 3992 (2018).
-
He, H., Höper, R., Dodenhöft, M., Marlière, P. & Bar-Even, A. An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli. Metab. Eng. 60, 1–13 (2020).
-
Wenk, S. et al. Evolution-assisted engineering of E. coli enables growth on formic acid at ambient CO2 via the serine threonine cycle. Metab. Eng. 88, 14–24 (2025).
-
Klein, V. J., Irla, M., Gil López, M., Brautaset, T. & Fernandes Brito, L. Unravelling formaldehyde metabolism in bacteria: Road towards synthetic methylotrophy. Microorganisms 10, 220 (2022).
-
Moioli, E., Mutschler, R. & Züttel, A. Renewable energy storage via CO2 and H2 conversion to methane and methanol: Assessment for small scale applications. Renew. Sust. Enegr. Rev. 107, 497–506 (2019).
-
Zhu, Z., Kin Tam, T., Sun, F., You, C. & Percival Zhang, Y. H. A high-energy-density sugar biobattery based on a synthetic enzymatic pathway. Nat. Commun. 5, 3026 (2014).
-
Ullah, A., Hashim, N. A., Rabuni, M. F. & Mohd Junaidi, M. U. A review on methanol as a clean energy carrier: Roles of zeolite in improving production efficiency. Energies 16, 1482 (2023).
-
Ozimek, P., Kötter, P., Veenhuis, M. & van der Klei, I. J. Hansenula polymorpha and Saccharomyces cerevisiae Pex5p’s recognize different, independent peroxisomal targeting signals in alcohol oxidase. FEBS Lett. 580, 46–50 (2006).
-
Zhong, W., Li, H. & Wang, Y. Design and construction of artificial biological systems for one-carbon utilization. BioDes. Res. 5, 0021 (2023).
-
Sundström, M., Lindqvist, Y., Schneider, G., Hellman, U. & Ronne, H. Yeast TKL1 gene encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids. J. Biol. Chem. 268, 24346–24352 (1993).
-
Navarro-Aviño, J. P., Prasad, R., Miralles, V. J., Benito, R. M. & Serrano, R. A proposal for nomenclature of aldehyde dehydrogenases in Saccharomyces cerevisiae and characterization of the stress-inducible ALD2 and ALD3 genes. Yeast 15, 829–842 (1999).
-
Ruiz-Amil, M., de Torrontegui, G., Palacián, E., Catalina, L. & Losada, M. Properties and function of yeast pyruvate carboxylase. J. Biol. Chem. 240, 3485–3492 (1965).
-
Qin, N. et al. Increased CO2 fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast. Nat. Commun. 15, 1591 (2024).
-
Chandel, N. S. Glycolysis. Cold Spring Harb. Perspect. Biol. 13, a040535 (2021).
-
Kresnowati, M. T. A. P. et al. When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Mol. Syst. Biol. 2, 49 (2006).
-
Byrne, K. P. & Wolfe, K. H. The yeast gene order browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456–1461 (2005).
-
Xia, P. F. et al. Recycling carbon dioxide during xylose fermentation by engineered Saccharomyces cerevisiae. ACS Synth. Biol. 6, 276–283 (2017).
-
Papapetridis, I. et al. Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield. Biotechnol. Biofuels 11, 17–17 (2018).
-
Yasokawa, D. et al. Toxicity of methanol and formaldehyde towards Saccharomyces cerevisiae as assessed by DNA microarray analysis. Appl. Biochem. Biotech. 160, 1685–1698 (2010).
-
Stingele, J. & Jentsch, S. DNA–protein crosslink repair. Nat. Rev. Mol. Cell Bio. 16, 455–460 (2015).
-
Falcone, C. & Mazzoni, C. External and internal triggers of cell death in yeast. Cell. Mol. Life Sci. 73, 2237–2250 (2016).
-
Carmona-Gutierrez, D. et al. Apoptosis in yeast: triggers, pathways, subroutines. Cell Death Differ. 17, 763–773 (2010).
-
Spégel, C. F. et al. Amperometric response from the glycolytic versus the pentose phosphate pathway in Saccharomyces cerevisiae cells. Anal. Chem. 79, 8919–8926 (2007).
-
Lu, X. et al. Constructing a synthetic pathway for acetyl-coenzyme a from one-carbon through enzyme design. Nat. Commun. 10, 1378 (2019).
-
Mao, Y. F. et al. Non-natural aldol reactions enable the design and construction of novel one-carbon assimilation pathways in vitro. Front. Microbiol. 12, 677596 (2021).
-
Nattermann, M. et al. Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo. Nat. Commun. 14, 2682 (2023).
-
Henras, A. K., Plisson-Chastang, C., O’Donohue, M.-F., Chakraborty, A. & Gleizes, P.-E. An overview of pre-ribosomal RNA processing in eukaryotes. WIREs RNA 6, 225–242 (2015).
-
Nomura, M. Ribosomal RNA genes, RNA polymerases, nucleolar structures, and synthesis of rRNA in the yeast Saccharomyces cerevisiae. Cold Spring Harb. Symp. Quant. Biol. 66, 555–565 (2001).
-
Berger, K. H. & Yaffe, M. P. Mitochondrial DNA inheritance in Saccharomyces cerevisiae. Trends Microbiol 8, 508–513 (2000).
-
de Zamaroczy, M. & Bernardi, G. The primary structure of the mitochondrial genome of Saccharomyces cerevisiae – a review. Gene 47, 155–177 (1986).
-
Zhang, Y. et al. A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae. Nat. Commun. 10, 1053 (2019).
-
Naito, Y., Hino, K., Bono, H. & Ui-Tei, K. CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31, 1120–1123 (2015).
-
Evers, M. E., Harder, W. & Veenhuis, M. In vitro dissociation and re-assembly of peroxisomal alcohol oxidases of Hansenula polymorpha and Pichia pastoris. FEBS Lett. 368, 293–296 (1995).
-
Couderc, R. & Baratti, J. Oxidation of methanol by the yeast, Pichia pastoris. purification and properties of the alcohol oxidase. Agric. Biol. Chem. 44, 2279–2289 (1980).
-
SchÜTte, H., Flossdorf, J., Sahm, H. & Kula, M.-R. Purification and properties of formaldehyde dehydrogenase and formate dehydrogenase from Candida boidinii. Eur. J. Biochem. 62, 151–160 (1976).
-
Degrassi, G., Uotila, L., Klima, R. & Venturi, V. Purification and properties of an esterase from the yeast Saccharomyces cerevisiae and identification of the encoding gene. Appl. Environ. Microbiol. 65, 3470–3472 (1999).
-
Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254 (1976).
-
Overkamp, K. M. et al. Functional analysis of structural genes for NAD+-dependent formate dehydrogenase in Saccharomyces cerevisiae. Yeast 19, 509–520 (2002).
-
Seah, T. C. M. & Kaplan, J. G. Purification and properties of the catalase of bakers’ yeast. J. Biol. Chem. 248, 2889–2893 (1973).
-
Ruuska, S. A., Badger, M. R., Andrews, T. J. & von Caemmerer, S. Photosynthetic electron sinks in transgenic tobacco with reduced amounts of Rubisco: little evidence for significant Mehler reaction. J. Exp. Bot. 51, 357–368 (2000).
-
Yamori, W. & von Caemmerer, S. Effect of Rubisco activase deficiency on the temperature response of CO2 assimilation rate and Rubisco activation state: Insights from transgenic tobacco with reduced amounts of Rubisco activase. Plant Physiol. 151, 2073–2082 (2009).
-
Sulpice, R. et al. Description and applications of a rapid and sensitive non-radioactive microplate-based assay for maximum and initial activity of D-ribulose-1,5-bisphosphate carboxylase/oxygenase. Plant Cell Environ. 30, 1163–1175 (2007).
-
MacElroy Robert, D., Mack Henry, M. & Johnson Emmett, J. Properties of phosphoribulokinase from Thiobacillus neapolitanus. J. Bacteriol. 112, 532–538 (1972).
-
Lee, J.-Y., Cheong, D.-E. & Kim, G.-J. A novel assay system for the measurement of transketolase activity using xylulokinase from Saccharomyces cerevisiae. Biotechnol. Lett. 30, 899–904 (2008).
-
Wang, X., Mann Craig, J., Bai, Y., Ni, L. & Weiner, H. Molecular cloning, characterization, and potential roles of cytosolic and mitochondrial aldehyde dehydrogenases in ethanol metabolism in Saccharomyces cerevisiae. J. Bacteriol. 180, 822–830 (1998).
-
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2ΔCT method. Methods 25, 402–408 (2001).
-
Burda, P. et al. Stepwise assembly of the lipid-linked oligosaccharide in the endoplasmic reticulum of Saccharomyces cerevisiae: Identification of the ALG9 gene encoding a putative mannosyl transferase. Proc. Natl. Acad. Sci. USA 93, 7160–7165 (1996).
-
Wang, Y., Parsons, L. R. & Su, X. AccuCor2: isotope natural abundance correction for dual-isotope tracer experiments. Lab. Invest. 101, 1403–1410 (2021).
-
Cota-Sánchez, J. H., Remarchuk, K. & Ubayasena, K. Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue. Plant Mol. Biol. Rep. 24, 161–167 (2006).
-
Sedlazeck, F. J. et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods 15, 461–468 (2018).
-
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).
-
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
-
Shen, S. et al. rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-seq data. Proc. Natl. Acad. Sci. USA 111, E5593–E5601 (2014).
-
Castell, C. H. & Smith, B. Measurement of formaldehyde in fish muscle using TCA extraction and the Nash reagent. J. Fish. Res. Board Can. 30, 91–98 (1973).
-
Kamiloglu, S., Sari, G., Ozdal, T. & Capanoglu, E. Guidelines for cell viability assays. Food Front. 1, 332–349 (2020).
-
Sun, P., Zhang, H., Sun, Y. & Liu, J. The recent development of fluorescent probes for the detection of NADH and NADPH in living cells and in vivo. Spectrochim. Acta A. 245, 118919 (2021).
-
Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat. Methods 14, 513–520 (2017).
-
Yu, F. et al. Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol. Cell. Proteom. 19, 1575–1585 (2020).
-
Flamholz, A., Noor, E., Bar-Even, A. & Milo, R. eQuilibrator-the biochemical thermodynamics calculator. Nucleic Acids Res. 40, D770–D775 (2012).
-
Beber, M. E. et al. eQuilibrator 3.0: a database solution for thermodynamic constant estimation. Nucleic Acids Res. 50, D603–D609 (2022).
