Combinatorial synthetic pathway fine-tuning and comparative transcriptomics for metabolic engineering of Raoultella ornithinolytica BF60 to efficiently synthesize 2,5-furandicarboxylic acid.


:The compound 5-hydroxymethylfurfural (HMF) has attracted much attention due to its versatility as an important bio-based platform chemical. Here, we engineered Raoultella ornithinolytica BF60 as a whole-cell biocatalyst for a highly efficient synthesis of 2,5-furandicarboxylic acid (FDCA) from HMF. Specifically, various expression cassettes of key genes, such as hmfH (gene encoding HMF/furfural oxidoreductase [HmfH]) and hmfo (gene encoding HMF oxidase), were designed and constructed for fine-tuning FDCA synthesis from HMF. The FDCA titer reached 108.9 mM with a yield of 73% when 150 mM HMF was used as the substrate. This yield was 16% higher than that without balancing key gene expression in FDCA synthetic pathways. Additionally, to strengthen HmfH expression at the translational level, ribosomal binding site (RBS) sequences, which were computationally designed using the RBS calculator, were assembled into HmfH expression cassettes. The HmfH expression in the presence of these sequences enhanced FDCA titer to 139.6 mM with a yield of 93%. Next, previously unknown candidate genes, such as aldR, dkgA, akR, AdhP1, and AdhP2, which encode enzymes that catalyze the reactions leading to the formation of the undesired product 2,5-bis(hydroxymethyl)furan (HMF alcohol) from HMF, were identified by RNA-sequencing-based transcriptomics. Combinatorial deletion of these five candidate genes led to an 88% reduction in HMF alcohol formation and 12% enhancement in FDCA production (175.6 mM). Finally, FDCA synthesis was further improved by the substrate pulse-feeding strategy, and 221.5 mM FDCA with an 88.6% yield was obtained. The combinatorial synthetic pathway fine-tuning and comparative transcriptomics approach may be useful for improving the biocatalysis efficiency of other industrially useful compounds.


Biotechnol Bioeng


Yuan H,Liu Y,Li J,Shin HD,Du G,Shi Z,Chen J,Liu L




Has Abstract


2018-09-01 00:00:00












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    authors: Harinarayan C,Mueller J,Ljunglöf A,Fahrner R,Van Alstine J,van Reis R

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  • Action of shear on enzymes: studies with alcohol dehydrogenase.

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    authors: Thomas CR,Nienow AW,Dunnill P

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    journal_title:Biotechnology and bioengineering

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    authors: Kawakami M,Koya H,Gondo S

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    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Regestein L,Maskow T,Tack A,Knabben I,Wunderlich M,Lerchner J,Büchs J

    更新日期:2013-05-01 00:00:00

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    abstract::The tumor necrosis factor-alpha (TNFalpha) plays an important role in a number of chronic inflammatory disorders. Monoclonal camelidae variable heavy chain domain-only antibodies (V(H)H) have been developed to antagonize the action of human TNFalpha (anti-TNF-V(H)H). Here we describe a strategy to obtain functional di...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Giersberg M,Floss DM,Kipriyanov S,Conrad U,Scheller J

    更新日期:2010-05-01 00:00:00

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    abstract::A 3D printed ultrafiltration/diafiltration (UF/DF) module is presented allowing the continuous, simultaneous concentration of retained (bio-)molecules and reduction or exchange of the salt buffer. Differing from the single-pass UF concepts known from the literature, DF operation does not require the application of sev...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Tan R,Franzreb M

    更新日期:2020-03-01 00:00:00

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    authors: Wu MS,Pan KL,Chou CP

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    authors: De Swaaf ME,Sijtsma L,Pronk JT

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    authors: Aldarf M,Fourcade F,Amrane A,Prigent Y

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    authors: Chamas A,Pham HTM,Jähne M,Hettwer K,Uhlig S,Simon K,Einspanier A,Baronian K,Kunze G

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    authors: Nath S,Schütte H,Hustedt H,Deckwer WD

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    authors: Bachinski N,Martins AS,Paschoalin VM,Panek AD,Paiva CL

    更新日期:1997-04-05 00:00:00

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    authors: Andrews BA,Asenjo JA

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    authors: Yu B,Chang TM

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    authors: Chen Y,Zhou S,Cadman J,Li Q

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  • 3D tumor spheroids as in vitro models to mimic in vivo human solid tumors resistance to therapeutic drugs.

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    authors: Nunes AS,Barros AS,Costa EC,Moreira AF,Correia IJ

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    authors: Comfort AR,Albert E,Langer R

    更新日期:1989-12-20 00:00:00

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    authors: McTaggart TL,Bever D,Bassett S,Da Silva NA

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    authors: Gemeiner P,Docolomansky P,Nahálka J,Stefuca V,Danielsson B

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    authors: Meyer F,Gehmlich I,Guthke R,Górak A,Knorre WA

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