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      Xylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production

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          Abstract

          Plant-sourced aromatic amino acid (AAA) derivatives are a vast group of compounds with broad applications. Here, we present the development of a yeast consortium for efficient production of ( S)-norcoclaurine, the key precursor for benzylisoquinoline alkaloid biosynthesis. A xylose transporter enables the concurrent mixed-sugar utilization in Scheffersomyces stipitis, which plays a crucial role in enhancing the flux entering the highly regulated shikimate pathway located upstream of AAA biosynthesis. Two quinate permeases isolated from Aspergillus niger facilitates shikimate translocation to the co-cultured Saccharomyces cerevisiae that converts shikimate to ( S)-norcoclaurine, resulting in the maximal titer (11.5 mg/L), nearly 110-fold higher than the titer reported for an S. cerevisiae monoculture. Our findings magnify the potential of microbial consortium platforms for the economical de novo synthesis of complex compounds, where pathway modularization and compartmentalization in distinct specialty strains enable effective fine-tuning of long biosynthetic pathways and diminish intermediate buildup, thereby leading to increases in production.

          Abstract

          It’s challenging to produce natural products using single strains of engineered microbes fed by renewable carbon sources. Here, the authors assemble a microbial consortium consisting of engineered S. stipitis and S. cerevisiae for streamlined production of ( S)-norcoclaurine from glucose and xylose simultaneously.

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          Most cited references74

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          High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method.

          Here we describe a high-efficiency version of the lithium acetate/single-stranded carrier DNA/PEG method of transformation of Saccharomyces cerevisiae. This method currently gives the highest efficiency and yield of transformants, although a faster protocol is available for small number of transformations. The procedure takes up to 1.5 h, depending on the length of heat shock, once the yeast culture has been grown. This method is useful for most transformation requirements.
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            Site-directed mutagenesis by overlap extension using the polymerase chain reaction

            Overlap extension represents a new approach to genetic engineering. Complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends. These fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the 3' extension of the complementary strand. The resulting fusion product is amplified further by PCR. Specific alterations in the nucleotide (nt) sequence can be introduced by incorporating nucleotide changes into the overlapping oligo primers. Using this technique of site-directed mutagenesis, three variants of a mouse major histocompatibility complex class-I gene have been generated, cloned and analyzed. Screening of mutant clones revealed at least a 98% efficiency of mutagenesis. All clones sequenced contained the desired mutations, and a low frequency of random substitution estimated to occur at approx. 1 in 4000 nt was detected. This method represents a significant improvement over standard methods of site-directed mutagenesis because it is much faster, simpler and approaches 100% efficiency in the generation of mutant product.
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              DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

              The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional d-xylose utilization pathway (∼9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (∼11 kb DNA consisting of five genes) and a functional combined d-xylose utilization and zeaxanthin biosynthesis pathway (∼19 kb consisting of eight genes) with high efficiencies (70–100%) either on a plasmid or on a yeast chromosome. As this new method only requires simple DNA preparation and one-step yeast transformation, it represents a powerful tool in the construction of biochemical pathways for synthetic biology, metabolic engineering and functional genomics studies.
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                Author and article information

                Contributors
                zyshao@iastate.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                28 November 2023
                28 November 2023
                2023
                : 14
                : 7797
                Affiliations
                [1 ]Department of Chemical and Biological Engineering, Iowa State University, ( https://ror.org/04rswrd78) Ames, IA USA
                [2 ]NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, ( https://ror.org/04rswrd78) Ames, IA USA
                [3 ]Interdepartmental Microbiology Program, Iowa State University, ( https://ror.org/04rswrd78) Ames, IA USA
                [4 ]Bioeconomy Institute, Iowa State University, ( https://ror.org/04rswrd78) Ames, IA USA
                [5 ]The Ames Laboratory, ( https://ror.org/041m9xr71) Ames, IA USA
                [6 ]DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, ( https://ror.org/047426m28) Urbana, IL USA
                Author information
                http://orcid.org/0000-0003-2399-3175
                http://orcid.org/0000-0001-6817-8006
                Article
                43049
                10.1038/s41467-023-43049-w
                10684500
                38016984
                d40f168c-5f03-4f2b-aa3f-6e22155f9639
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 30 July 2022
                : 30 October 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000001, National Science Foundation (NSF);
                Award ID: 1716837
                Award ID: EEC-0813570
                Award ID: 1749782
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100009227, Iowa State University (Iowa State University of Science and Technology);
                Award ID: PG110304
                Award Recipient :
                Categories
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                Custom metadata
                © Springer Nature Limited 2023

                Uncategorized
                metabolic engineering,applied microbiology,microbiome
                Uncategorized
                metabolic engineering, applied microbiology, microbiome

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