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      Engineered E. coli W enables efficient 2,3-butanediol production from glucose and sugar beet molasses using defined minimal medium as economic basis

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          Abstract

          Background

          Efficient microbial production of chemicals is often hindered by the cytotoxicity of the products or by the pathogenicity of the host strains. Hence 2,3-butanediol, an important drop-in chemical, is an interesting alternative target molecule for microbial synthesis since it is non-cytotoxic. Metabolic engineering of non-pathogenic and industrially relevant microorganisms, such as Escherichia coli, have already yielded in promising 2,3-butanediol titers showing the potential of microbial synthesis of 2,3-butanediol. However, current microbial 2,3-butanediol production processes often rely on yeast extract as expensive additive, rendering these processes infeasible for industrial production.

          Results

          The aim of this study was to develop an efficient 2,3-butanediol production process with E. coli operating on the premise of using cost-effective medium without complex supplements, considering second generation feedstocks. Different gene donors and promoter fine-tuning allowed for construction of a potent E. coli strain for the production of 2,3-butanediol as important drop-in chemical. Pulsed fed-batch cultivations of E. coli W using microaerobic conditions showed high diol productivity of 4.5 g l −1 h −1. Optimizing oxygen supply and elimination of acetoin and by-product formation improved the 2,3-butanediol titer to 68 g l −1, 76% of the theoretical maximum yield, however, at the expense of productivity. Sugar beet molasses was tested as a potential substrate for industrial production of chemicals. Pulsed fed-batch cultivations produced 56 g l −1 2,3-butanediol, underlining the great potential of E. coli W as production organism for high value-added chemicals.

          Conclusion

          A potent 2,3-butanediol producing E. coli strain was generated by considering promoter fine-tuning to balance cell fitness and production capacity. For the first time, 2,3-butanediol production was achieved with promising titer, rate and yield and no acetoin formation from glucose in pulsed fed-batch cultivations using chemically defined medium without complex hydrolysates. Furthermore, versatility of E. coli W as production host was demonstrated by efficiently converting sucrose from sugar beet molasses into 2,3-butanediol.

          Electronic supplementary material

          The online version of this article (10.1186/s12934-018-1038-0) contains supplementary material, which is available to authorized users.

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          Most cited references45

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          Biotechnological production of 2,3-butanediol--current state and prospects.

          Biotechnological production of 2,3-butanediol (hereafter referred to as 2,3-BD) from wastes and excessive biomass is a promising and attractive alternative for traditional chemical synthesis. In the face of scarcity of fossil fuel supplies the bio-based process is receiving a significant interest, since 2,3-BD may have multiple practical applications (e.g. production of synthetic rubber, plasticizers, fumigants, as an antifreeze agent, fuel additive, octane booster, and many others). Although the 2,3-BD pathway is well known, microorganisms able to ferment biomass to 2,3-BD have been isolated and described, and attempts of pilot scale production of this compound were made, still much has to be done in order to achieve desired profitability. This review summarizes hitherto gained knowledge and experience in biotechnological production of 2,3-BD, sources of biomass used, employed microorganisms both wild type and genetically improved strains, as well as operating conditions applied.
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            The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli

            Genome engineering methods in E. coli allow for easy to perform manipulations of the chromosome in vivo with the assistance of the λ-Red recombinase system. These methods generally rely on the insertion of an antibiotic resistance cassette followed by removal of the same cassette, resulting in a two-step procedure for genomic manipulations. Here we describe a method and plasmid system that can edit the genome of E. coli without chromosomal markers. This system, known as Scarless Cas9 Assisted Recombineering (no-SCAR), uses λ-Red to facilitate genomic integration of donor DNA and double stranded DNA cleavage by Cas9 to counterselect against wild-type cells. We show that point mutations, gene deletions, and short sequence insertions were efficiently performed in several genomic loci in a single-step with regards to the chromosome and did not leave behind scar sites. The single-guide RNA encoding plasmid can be easily cured due to its temperature sensitive origin of replication, allowing for iterative chromosomal manipulations of the same strain, as is often required in metabolic engineering. In addition, we demonstrate the ability to efficiently cure the second plasmid in the system by targeting with Cas9, leaving the cells plasmid-free.
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              The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

              Background Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses. Results We have sequenced and annotated the genome of E. coli W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also present. W has unique features relative to other sequenced laboratory strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than A. W also grows on a much broader range of carbon sources than does K-12. A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. Conclusions The genome of W is more similar to commensal and pathogenic B1 strains than phylogroup A strains, and therefore has greater utility for comparative analyses with these strains. W should therefore be the strain of choice, or 'type strain' for group B1 comparative analyses. The genome annotation and tools created here are expected to allow further utilization and development of E. coli W as an industrial organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction allow it to more accurately define E. coli metabolism relative to previous models.
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                Author and article information

                Contributors
                anna.erian@boku.ac.at
                martin.gibisch@web.de
                stefan.pfluegl@tuwien.ac.at
                Journal
                Microb Cell Fact
                Microb. Cell Fact
                Microbial Cell Factories
                BioMed Central (London )
                1475-2859
                30 November 2018
                30 November 2018
                2018
                : 17
                : 190
                Affiliations
                ISNI 0000 0001 2348 4034, GRID grid.5329.d, Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, , Technische Universität Wien, ; Gumpendorfer Straße 1a, 1060 Vienna, Austria
                Author information
                http://orcid.org/0000-0001-8472-5073
                Article
                1038
                10.1186/s12934-018-1038-0
                6267845
                30501633
                84432309-497f-436e-b7ac-99d10820677c
                © The Author(s) 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 1 October 2018
                : 23 November 2018
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100004955, Österreichische Forschungsförderungsgesellschaft;
                Award ID: 858702
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2018

                Biotechnology
                e. coli w,pyka knock-out,high rate and yield 2,3-butanediol production,sugar beet molasses,chemically defined medium,metabolic engineering,promoter fine tuning,acetoin,complex protein hydrolysates

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