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Biocatalytic C-C Bond Formation for One Carbon Resource Utilization

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Biocatalytic C-C Bond Formation for One Carbon Resource Utilization International Journal of Molecular Sciences Review Biocatalytic C-C Bond Formation for One Carbon Resource Utilization Qiaoyu Yang 1,2,3, Xiaoxian Guo 1,2, Yuwan Liu 1,2,* and Huifeng Jiang 1,2,* 1 Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; [email protected] (Q.Y.); [email protected] (X.G.) 2 National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China 3 University of Chinese Academy of Sciences, Beijing 100049, China * Correspondence: [email protected] (Y.L.); [email protected] (H.J.) Abstract: The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C- C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO2, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided. Keywords: C1 resource utilization; carboxylases; C-C ligases; designed pathway Citation: Yang, Q.; Guo, X.; Liu, Y.; Jiang, H. Biocatalytic C-C Bond Formation for One Carbon Resource 1. Introduction Utilization. Int. J. Mol. Sci. 2021, 22, It has been estimated that more than 35% of industrial chemicals will be produced by 1890. https://doi.org/10.3390/ bio-manufacturing until 2030 [1]. C1 resources, including methane, methanol, formalde- ijms22041890 hyde, formic acid, and carbon dioxide, are ideal raw materials for bio-manufacturing, due to their low cost and easy availability. In nature, six CO2 fixation pathways have been Academic Editor: Gianfranco Gilardi identified in photoautotrophic and chemoautotrophic microorganisms [2]. In addition to Calvin–Benson–Bassham (CBB) cycle, there are three major pathways that operate in Received: 22 December 2020 methanotrophs or methylotrophic yeast for assimilation of methane or methanol, which Accepted: 5 February 2021 are first oxidized to formaldehyde, and then is assimilated via the ribulose monophosphate Published: 14 February 2021 (RuMP) cycle, serine cycle, or xylulose monophosphate pathway (XuMP) [3]. Engineer- ing natural C1 assimilation pathways to achieve the production of biofuels or industrial Publisher’s Note: MDPI stays neutral chemicals has always been a research hotspot in synthetic biology [4–16]. However, the with regard to jurisdictional claims in biotransformation of C1 resources is restricted in the industry by low production efficiency, published maps and institutional affil- limited product types, and high production costs. iations. With the development of synthetic biology, more and more C1 utilization pathways have been exploited in recent years. These pathways can be broadly divided into two categories. One refers to C1 transformation in vitro. Carboxylases and C-C ligases from naturally occurring C1 assimilation pathways are highly specialized, and thus, restricted Copyright: © 2021 by the authors. their use for the C1 biotransformation in vitro. It has been shown that (de)carboxylases in- Licensee MDPI, Basel, Switzerland. volved in the secondary metabolism are generally reversible and promiscuous [17], several This article is an open access article C-C ligases, such as aldolases and thiamine diphosphate (ThDP)-dependent enzymes [18], distributed under the terms and can receive formaldehyde as a receptor. These newly mined (de)carboxylases and C-C conditions of the Creative Commons Attribution (CC BY) license (https:// ligases greatly expand the scope of C1 resource utilization in vitro. The other refers to C1 creativecommons.org/licenses/by/ assimilation in vivo. Based on highly active carboxylases or designed C-C ligases, several 4.0/). artificial C1 assimilation pathways have been constructed, such as malyl-CoA-glycerate Int. J. Mol. Sci. 2021, 22, 1890. https://doi.org/10.3390/ijms22041890 https://www.mdpi.com/journal/ijms Int.Int. J.J. Mol.Mol. Sci.Sci. 20212021,, 2222,, xx FORFOR PEERPEER REVIEWREVIEW 22 ofof 2323 Int. J. Mol. Sci. 2021, 22, x FOR PEER REVIEW 2 of 23 Int. J. Mol. Sci. 2021, 22, x FOR PEER REVIEW 2 of 23 involvedinvolved inin thethe secondarysecondary metabolismmetabolism areare generallygenerally reversiblereversible andand promiscuouspromiscuous [17],[17], involved in the secondary metabolism are generally reversible and promiscuous [17], severalseveral C-CC-C ligases,ligases, suchsuch asas aldolasesaldolases anandd thiaminethiamine diphosphatediphosphate (ThDP)-dependent(ThDP)-dependent several C-C ligases, such as aldolases and thiamine diphosphate (ThDP)-dependent enzymesenzymes [18],[18], cancan receivereceive formaldehydeformaldehyde asas aa receptor.receptor. TheseThese newlynewly minedmined enzymes [18], can receive formaldehyde as a receptor. These newly mined (de)carboxylases(de)carboxylasesinvolved in the secondaryandand C-CC-C ligaseligase metabolismss greatlygreatly are expandexpand generally thethe reversiblescopescope ofof C1C1and resourceresource promiscuous utilizationutilization [17], inin (de)carboxylases and C-C ligases greatly expand the scope of C1 resource utilization in vitro.vitro.several TheThe C-C otherother ligases, refersrefers such toto C1C1 as assimilationassimilation aldolases an inind vivo. vivo.thiamine BasedBased diphosphate onon highlyhighly active active(ThDP)-dependent carboxylasescarboxylases oror vitro. The other refers to C1 assimilation in vivo. Based on highly active carboxylases or designeddesignedenzymes C-CC-C[18], ligases,ligases, can severalseveralreceive artificialartificialformaldehyde C1C1 asassimilationsimilation as a receptor. pathwayspathways These havehave beenbeennewly constructed,constructed, mined designed C-C ligases, several artificial C1 assimilation pathways have been constructed, suchsuch(de)carboxylases asas malyl-CoA-glyceratemalyl-CoA-glycerate and C-C ligase s greatlypathwaypathway expand (MCG)(MCG) the scope[19],[19], ofcrotonyl-CoA/ethylmalonyl- crotonyl-CoA/ethylmalonyl-C1 resource utilization in Int. J. Mol. Sci. 2021, 22, 1890 suchvitro. asThe malyl-CoA-glycerateother refers to C1 assimilation pathway in vivo.(MCG) Based [19], on highly crotonyl-CoA/ethylmalonyl- active carboxylases or2 of 22 CoA/hydroxybutyryl-CoACoA/hydroxybutyryl-CoA cyclecycle pathwaypathway (CETCH)(CETCH) [20,21],[20,21], formolaseformolase pathwaypathway (FLS)(FLS) [22],[22], CoA/hydroxybutyryl-CoAdesigned C-C ligases, several cycle artificial pathway C1 (CETCH)assimilation [20,21], pathways formolase have beenpathway constructed, (FLS) [22], andand syntheticsynthetic acetyl-CoAacetyl-CoA pathwapathwayy (SACA)(SACA) [23].[23]. ComparedCompared toto thethe naturalnatural C1C1 assimilationassimilation andsuch synthetic as malyl-CoA-glycerate acetyl-CoA pathwa ypathway (SACA) [23].(MCG) Compared [19], crotonyl-CoA/ethylmalonyl- to the natural C1 assimilation pathways,pathways, thesethese artificialartificial pathwayspathways havehave obviousobvious advantagesadvantages inin catalyticcatalytic efficiency,efficiency, pathways,CoA/hydroxybutyryl-CoA these artificial cyclepathways pathway have (CETCH) obvious [20,21], advantages formolase in pathway catalytic (FLS) efficiency, [22], biomassbiomasspathway yield,yield, (MCG) andand [ driving19driving], crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA force,force, andand areare expectexpecteded toto improveimprove thethe efficiencyefficiency ofof C1C1 cycle resourceresource path- biomassand synthetic yield, andacetyl-CoA driving pathwa force, andy (SACA) are expect [23]. edCompared to improve to the the natural efficiency C1 assimilationof C1 resource utilizationutilizationway (CETCH) inin thethe [ future.20future.,21], formolase pathway (FLS) [22], and synthetic acetyl-CoA pathway utilizationpathways, in these the future. artificial pathways have obvious advantages in catalytic efficiency, (SACA)TheThe overall [overall23]. Compared efficiencyefficiency to ofof the C1C1 natural transformationtransformation C1 assimilation inin vitrovitro pathways, andand C1C1 theseassimilationassimilation artificial inin pathways vivovivo isis biomassThe overallyield, and efficiency driving force,of C1 and transformation are expected to in improve vitro and the C1efficiency assimilation of C1 resource in vivo is generallygenerallyhave obvious determineddetermined advantages byby thethe in biochemical catalyticbiochemical efficiency, proppropertieserties biomass ofof carboxylasescarboxylases yield, and driving andand C-CC-C force, ligases.ligases. and areAA generallyutilization determined in the future. by the biochemical properties of carboxylases and C-C ligases. A betterbetterexpected understandingunderstanding to improve theofof the efficiencythe catalyticcatalytic of C1mechanmechan resourceismsisms utilization ofof thesethese inenzymesenzymes the future. isis necessarynecessary forfor better Theunderstanding overall efficiency of the of catalyticC1 transformation mechanisms in vitro of theseand C1 enzymes assimilation is necessary in
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