Fixing nature’s carbon inefficiencies

Conversion of C2 to C3 compounds is used by nature in abundant processes such as photorespiration but comes at the cost CO2 release. Erb and co-workers recently published an article Nature Catalysis describing a synthetic pathway able convert through carbon fixation step. As climate crisis becomes more urgent, we must tackle major contributors change using collection creative solutions. The concentration greenhouse gases atmosphere, especially CO2, has increased dramatically last century because human activities. In addition significantly reducing emissions, also develop new and/or improved methods capturing fixing inorganic from our environment. developed several ways fix channel it into various metabolic pathways.1Liang B. Zhao Y. Yang J. Recent advances developing artificial autotrophic microorganism for reinforcing fixation.Front. Microbiol. 2020; 11: 592631Crossref PubMed Scopus (10) Google Scholar most well-known these natural pathways Calvin-Benson-Bassham (CBB) cycle, with over 90% occurring this pathway.2Schwander T. Schada von Borzyskowski L. Burgener S. Cortina N.S. T.J. A dioxide vitro.Science. 2016; 354: 900-904Crossref (273) CBB cycle autotrophs ribulose 1,5-bisphosphate (RuBP) glyceraldehyde 3-phosphate (G3P), which can be synthesize sugars starches. two other are aerobic autotrophs—the 3-hydroxypropionate (3HP) bicycle 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle. 3HP primarily found photosynthetic green non-sulfur bacteria forms both acetyl-CoA pyruvate steps. 3HP/4HB carboxylation propionyl-CoA occur eventually produce molecule acetyl-CoA. Three have been discovered anaerobic well. reductive or reverse citric acid (rTCA) archaea and, name suggests, reverses oxidative TCA Through rTCA includes steps, produced. dicarboxylate/4-hydroxybutyrate (DC/HB) similar cycle; however, some enzymes within strictly anaerobic. Lastly, Wood-Ljungdahl pathway, known acetogenesis, converts one formic another CO. Formic reduced fully methyl substituent, combination CO, acetylate CoA. Beyond pathways, there much interest creating novel strategies.3Weigmann K. Fixing carbon: To alleviate change, scientists exploring harness nature’s ability capture atmosphere.EMBO Rep. 2019; 20: e47580Crossref (5) Using combinations engineered proteins design attractive chemical due mild conditions sustainability. Synthetic that, like fatty assimilation, generate species (e.g., glycolate glycoxylate) that further converted compounds.2Schwander Scholar,4Bar-Even A. Noor E. Lewis N.E. Milo R. Design analysis pathways.Proc. Natl. Acad. Sci. USA. 2010; 107: 8889-8894Crossref (297) There no directly without loss CO2. Photorespiration provides example this, whereby equivalents glycoxylate, generated RuBisCO-catalyzed side reaction between molecular oxygen RuBP, R-glycerate (Figure 1). abundance coupled RuBisCO’s poor specificity O2 means any improvement could large consequences global Moreover, problems associated exacerbated hot climates, decreases temperature increases. It estimated agricultural crop yield hotter climates up 50% result photorespiration.5Walker B.J. VanLoocke Bernacchi C.J. Ort D.R. costs food production now future.Annu. Rev. Plant Biol. 67: 107-129Crossref (172) Attempts made increase O2; success limited.2Schwander Alternatively, capable bypassing proposed realized.4Bar-Even Scholar,6Trudeau D.L. Edlich-Muth C. Zarzycki Scheffen M. Goldsmith Khersonsky O. Avizemer Z. Fleishman S.J. Cotton C.A.R. et al.Design vitro realization carbon-conserving photorespiration.Proc. 2018; 115: E11455-E11464Crossref (56) Although realized demonstrated, until-now theoretical tartronyl-CoA (TaCo) would outcompete others energetic efficiency standpoints.6Trudeau recent paper,7Scheffen Marchal D. Beneyton Schuller Klose Diehl Lehmann Pfister P. Carrillo He H. al.A new-to-nature module improve fixation.Nat. Catal. 2021; 4: 105-115Crossref (21) turned theory reality. They structures obtained cryo-electron microscopy (cryo-EM) inform protein engineering efforts designed screening methodology ultimately obtain carboxylase catalyze difficult step TaCo pathway. needed reconstitute were interface photorespiration, ethylene glycol conversion, construct authors find catalyzing three steps direct conversion 2). screened CoA transferases synthetases (ACSs) glycolyl-CoA. From these, they chose ACS Erythrobacter sp. NAP1, had catalytic 20 M−1s−1 glycolate. By optimizing expression strain opening active site rational design, created glycolyl-CoA synthetase (GCS) 42-fold higher efficiency. efforts, identify bifunctional malonyl-CoA reductase Chloroflexus aurantiacus final reduction R-glycerate. Unsurprisingly, proved tartronyl-CoA. identified biotin-dependent (PCC) Methylorubrum extorquens (MePCC) displayed trace measurable activity This exhibited high futile ATP hydrolysis (∼100 ATPs per carboxylation). overcome limitations, determined structure MePCC cryo-EM, structure-guided design. mutations near than 50-fold 15-fold (variant M3). next random mutagenesis carboxyltransferase subunit (GCC) variants hydrolysis. high-throughput microfluidics screen was variants. After rounds screening, variant GCC M5, contained additional mutations, 25-fold decrease uncoupled orders magnitude MePCC. impressive allows M5 acyl-CoA carboxylases. compete systems, sought understand how five accumulated led dramatic activity. 1.96 Å resolution cryo-EM. Biotin-dependent carboxylases contain biotin (BC) domain (CT) domain. BC domain, carboxylated bicarbonate. swinging arm model, swings CT where carboxyl group transferred substrate, case, cryo-EM atomic-resolution density domain; missing, suggesting region highly flexible. hypothesize difference domains indicate participates conformational changes necessary move high-resolution maps allowed probe throughout their directed evolution campaign. Notably, mutation W502R, error-prone PCR, located distal highlights importance combing approaches targeting optimize chances discovering structural described coworkers feats themselves; nonetheless, went even demonstrate reconstructed interfaced important energy demonstrated bypass 2-phosphoglycolate (2-PG) step, 75% 150%, fewer required, 21% less used, 29% needed. Even under mimic 100% oxygenation RuBP RuBisCO, still drive fixation. Additionally, successfully crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) address hurdle carboxylase, thus enabling optimized wild-type enzyme non-native substrate evolution. bioinformatics technology advancing cheaper faster sequencing, tools analyze sequencing data), will continue discover starting points campaigns making use promiscuity.8Chen Arnold F. Engineering activities enzymes.Nat. 3: 203-213Crossref (221) cases when exploiting native promiscuity not option, walking de novo create enzymes.9Zeymer Hilvert Directed Evolution Protein Catalysts.Annu. Biochem. 87: 131-157Crossref (201) Structural biology continues play pivotal role whether informing approaches, confirming development, understanding mutational effects lineage. obvious work, revolution powerful tool atomic-level enzymes.10Tan Y.Z. Carragher Seeing Atoms: Single-Particle Cryo-EM Breaks Atomic Barrier.Mol. Cell. 80: 938-939Abstract Full Text PDF (3) Overall, work filled void taking theoretical, energy-efficient, CO2-dependent assimilation effort showcases potential challenges productivity, combined vivo biotechnology efforts.