Metabolic engineering

  • Article
    | Open Access

    Tripterygium wilfordii is a medical plant that can produce antitumor activity compound triptolide. Here, the authors assemble its genome and identify a cytochrome P450 that can catalyze oxidation of a methyl to the acid moiety of dehydroabietic acid in triptolide biosynthesis by integrating multi-omics data.

    • Lichan Tu
    • , Ping Su
    • , Zhongren Zhang
    • , Linhui Gao
    • , Jiadian Wang
    • , Tianyuan Hu
    • , Jiawei Zhou
    • , Yifeng Zhang
    • , Yujun Zhao
    • , Yuan Liu
    • , Yadi Song
    • , Yuru Tong
    • , Yun Lu
    • , Jian Yang
    • , Cao Xu
    • , Meirong Jia
    • , Reuben J. Peters
    • , Luqi Huang
    •  & Wei Gao
  • Article
    | Open Access

    SCRaMbLE can lead to great genetic diversity for product biosynthesis but is limited by screening methods. Here the authors develop a rapid workflow using automation, ultra-fast LC/MS and barcoded nanopore sequencing to identify best performing strains.

    • G.-O. F. Gowers
    • , S. M. Chee
    • , D. Bell
    • , L. Suckling
    • , M. Kern
    • , D. Tew
    • , D. W. McClymont
    •  & T. Ellis
  • Article
    | Open Access

    In lignocellulose biomass, microbes prefer consuming glucose over xylose, which affects target compound production. Here, the authors achieve simultaneous utilization of glucose and xylose for target chemical production and cell growth, respectively, and realize high-level production of shikimate pathway derivatives.

    • Ryosuke Fujiwara
    • , Shuhei Noda
    • , Tsutomu Tanaka
    •  & Akihiko Kondo
  • Article
    | Open Access

    Accounting for the effects of genetic expression in genome-scale metabolic models is challenging. Here, the authors introduce a model formulation that efficiently simulates thermodynamic-compliant fluxes, enzyme and mRNA concentration levels, allowing omics integration and broad analysis of in silico cellular physiology.

    • Pierre Salvy
    •  & Vassily Hatzimanikatis
  • Article
    | Open Access

    A robust platform to study modular polyketide synthases (PKSs) in vitro is still unavailable. Here, the authors report the reconstitution of the venemycin PKS, engineer hybrid venemycin/pikromycin PKSs, and obtain much improved yields through employing the updated module boundaries.

    • Takeshi Miyazawa
    • , Melissa Hirsch
    • , Zhicheng Zhang
    •  & Adrian T. Keatinge-Clay
  • Article
    | Open Access

    The secretory pathway is used in the production of most biopharmaceuticals, but the associated biosynthetic costs are little understood. Here, the authors integrate the core secretory pathway into genome-scale metabolic models of human, mouse, and CHO cells, enabling in silico analysis.

    • Jahir M. Gutierrez
    • , Amir Feizi
    • , Shangzhong Li
    • , Thomas B. Kallehauge
    • , Hooman Hefzi
    • , Lise M. Grav
    • , Daniel Ley
    • , Deniz Baycin Hizal
    • , Michael J. Betenbaugh
    • , Bjorn Voldborg
    • , Helene Faustrup Kildegaard
    • , Gyun Min Lee
    • , Bernhard O. Palsson
    • , Jens Nielsen
    •  & Nathan E. Lewis
  • Article
    | Open Access

    Genome-scale engineering is generally limited to single methods of alteration such as overexpression, repression or deletion. Here the authors present a tri-functional CRISPR system that can engineer complex synergistic interactions in a genome-wide manner.

    • Jiazhang Lian
    • , Carl Schultz
    • , Mingfeng Cao
    • , Mohammad HamediRad
    •  & Huimin Zhao
  • Article
    | Open Access

    Tightly controlling cell output is challenging, which has limited development and applications of bacterial sensors. Here the authors develop tunable, fast-responding sensors to control production of metabolic pigments and use them to assess zinc deficiency in a low-cost, minimal equipment fashion.

    • Monica P. McNerney
    • , Cirstyn L. Michel
    • , Krishi Kishore
    • , Janet Standeven
    •  & Mark P. Styczynski
  • Article
    | Open Access

    Established bacterial glycoengineering platforms limit access to protein and glycan substrates. Here the authors design a cytoplasmic protein glycosylation system, Glycoli, to generate a variety of multivalent glycostructures.

    • Hanne L. P. Tytgat
    • , Chia-wei Lin
    • , Mikail D. Levasseur
    • , Markus B. Tomek
    • , Christoph Rutschmann
    • , Jacqueline Mock
    • , Nora Liebscher
    • , Naohiro Terasaka
    • , Yusuke Azuma
    • , Michael Wetter
    • , Martin F. Bachmann
    • , Donald Hilvert
    • , Markus Aebi
    •  & Timothy G. Keys
  • Article
    | Open Access

    Existing efforts have been focused on one of the elements in the automation of the design, build, test, and learn (DBTL) cycle for biosystems design. Here, the authors integrate a robotic system with machine learning algorithms to fully automate the DBTL cycle and apply it in optimizing the lycopene biosynthetic pathway.

    • Mohammad HamediRad
    • , Ran Chao
    • , Scott Weisberg
    • , Jiazhang Lian
    • , Saurabh Sinha
    •  & Huimin Zhao
  • Article
    | Open Access

    Existing heavy metal bioremediation systems are mainly based on plants, which require long growing time in specific conditions. Here, the authors mimic the characteristics of plant hyperaccumulators to engineer more tractable baker’s yeast and achieve 10–100-fold higher accumulation of chromium, arsenic, or cadmium.

    • George L. Sun
    • , Erin. E. Reynolds
    •  & Angela M. Belcher
  • Article
    | Open Access

    Flexizymes have been used to expand the scope of chemical substrates for ribosome-directed polymerization in vitro. Here the authors deduce design rules of Flexizyme-mediated tRNA acylation that more effectively predict the incorporation of new monomers into peptides.

    • Joongoo Lee
    • , Kenneth E. Schwieter
    • , Andrew M. Watkins
    • , Do Soon Kim
    • , Hao Yu
    • , Kevin J. Schwarz
    • , Jongdoo Lim
    • , Jaime Coronado
    • , Michelle Byrom
    • , Eric V. Anslyn
    • , Andrew D. Ellington
    • , Jeffrey S. Moore
    •  & Michael C. Jewett
  • Article
    | Open Access

    Microbial production of aromatic amino acid (AAA)-derived chemicals remains an outstanding metabolic engineering challenge. Here, the authors engineer baker’s yeast for high levels p-coumaric acid production by rewiring the central carbon metabolism and channeling more flux to the AAA biosynthetic pathway.

    • Quanli Liu
    • , Tao Yu
    • , Xiaowei Li
    • , Yu Chen
    • , Kate Campbell
    • , Jens Nielsen
    •  & Yun Chen
  • Article
    | Open Access

    Engineering cell lines often requires multiple plasmids with different selection markers. Here the authors present SiMPl, a method based on rationally engineered split enzymes which get reconstituted via intein-mediated protein splicing to maintain two plasmids using a single antibiotic.

    • Navaneethan Palanisamy
    • , Anna Degen
    • , Anna Morath
    • , Jara Ballestin Ballestin
    • , Claudia Juraske
    • , Mehmet Ali Öztürk
    • , Georg A. Sprenger
    • , Jung-Won Youn
    • , Wolfgang W. Schamel
    •  & Barbara Di Ventura
  • Article
    | Open Access

    Engineering Taxol pathway in microbes needs to overcome the difficulty of expressing plant P450 enzymes. Here, the authors use a compartmentalized metabolic engineering strategy to construct the taxanes production pathway in chloroplasts of Nicotiana benthamiana and realize the production of taxadience-5α-ol.

    • Jianhua Li
    • , Ishmael Mutanda
    • , Kaibo Wang
    • , Lei Yang
    • , Jiawei Wang
    •  & Yong Wang
  • Article
    | Open Access

    Power densities of existing microbial biophotovoltaics (BPV) are low and unendurable. Here, the authors develop a BPV based on d-lactate mediated microbial consortium, which can generate an average power density of 135 mW·m−2 for over 40 days in a spatial-temporal separation setup with medium replenishment.

    • Huawei Zhu
    • , Hengkai Meng
    • , Wei Zhang
    • , Haichun Gao
    • , Jie Zhou
    • , Yanping Zhang
    •  & Yin Li
  • Article
    | Open Access

    Metabolic enzymes often form supramolecular complexes to improve product yield. Here the authors use short peptide tags to create scaffold-free assemblies and synthetic metabolic nodes.

    • Wei Kang
    • , Tian Ma
    • , Min Liu
    • , Jiale Qu
    • , Zhenjun Liu
    • , Huawei Zhang
    • , Bin Shi
    • , Shuai Fu
    • , Juncai Ma
    • , Louis Tung Faat Lai
    • , Sicong He
    • , Jianan Qu
    • , Shannon Wing-Ngor Au
    • , Byung Ho Kang
    • , Wilson Chun Yu Lau
    • , Zixin Deng
    • , Jiang Xia
    •  & Tiangang Liu
  • Article
    | Open Access

    Sustainable sources are needed to meet the demand for long-chain polyunsaturated fatty acids. Here the authors construct an artificial biosynthetic gene cluster in Y. lipolytica capable of producing a high concentration of PUFAs.

    • Katja Gemperlein
    • , Demian Dietrich
    • , Michael Kohlstedt
    • , Gregor Zipf
    • , Hubert S. Bernauer
    • , Christoph Wittmann
    • , Silke C. Wenzel
    •  & Rolf Müller
  • Article
    | Open Access

    The wealth of complex polyketides is an essential source for drug discovery. Here, the authors report an evolution-guided rational morphing of modular polyketide synthases (PKSs) for aurothin and neoaurothin biosynthesis, and reveal engineering site suitable for diversifying PKS systems.

    • Huiyun Peng
    • , Keishi Ishida
    • , Yuki Sugimoto
    • , Holger Jenke-Kodama
    •  & Christian Hertweck
  • Article
    | Open Access

    So far, synthetic genetic circuits have relied on digital logic for information processing. Here the authors present metabolic perceptrons that use analog weighted adders to vary the contributions of multiple inputs, resulting in different classification functions.

    • Amir Pandi
    • , Mathilde Koch
    • , Peter L. Voyvodic
    • , Paul Soudier
    • , Jerome Bonnet
    • , Manish Kushwaha
    •  & Jean-Loup Faulon
  • Article
    | Open Access

    Titers of monoterpenoids production in yeast are low due to the fact that the geranyl diphosphate (GPP)-based pathway can redirect metabolic fluxes to growth. Here, the authors build an orthogonal pathway by selecting the cis isomer of GPP as an alternative precursor and achieve high titer monoterpene production.

    • Codruta Ignea
    • , Morten H. Raadam
    • , Mohammed S. Motawia
    • , Antonios M. Makris
    • , Claudia E. Vickers
    •  & Sotirios C. Kampranis
  • Article
    | Open Access

    Current flux rewiring technologies in metabolic engineering are mainly transcriptional regulation. Here, the authors build two sets of controllable protein units using engineered viral proteases and proteolytic signals, and utilize for increasing titers of shikimate and D-xylonate in E. coli.

    • Cong Gao
    • , Jianshen Hou
    • , Peng Xu
    • , Liang Guo
    • , Xiulai Chen
    • , Guipeng Hu
    • , Chao Ye
    • , Harley Edwards
    • , Jian Chen
    • , Wei Chen
    •  & Liming Liu
  • Article
    | Open Access

    Anaerobic bacteria represent a rich source of biological and chemical diversity but are difficult to cultivate and there is a lack of heterologous expression systems. Here the authors develop an expression system based on S. mutans UA159 for biosynthetic gene clusters from anaerobic bacteria.

    • Tingting Hao
    • , Zhoujie Xie
    • , Min Wang
    • , Liwei Liu
    • , Yuwei Zhang
    • , Weicang Wang
    • , Zhao Zhang
    • , Xuejin Zhao
    • , Pengwei Li
    • , Zhengyan Guo
    • , Shushan Gao
    • , Chunbo Lou
    • , Guodong Zhang
    • , Justin Merritt
    • , Geoff P. Horsman
    •  & Yihua Chen
  • Article
    | Open Access

    Tropane alkaloids (TAs) are a group of phytochemicals that are used to treat neurological disorders. Here, the authors engineer baker’s yeast to produce tropine, a key intermediate in the biosynthetic pathway of TAs, and cinnamoyltropine, a non-canonical TA, from simple carbon and nitrogen sources.

    • Prashanth Srinivasan
    •  & Christina D. Smolke
  • Article
    | Open Access

    Formicapyridines are similar to pentacyclic fasamycin and formicamycin aromatic polyketides but with a pyridine moiety. Here the authors rationally mutate the biosynthetic gene cluster to increase production and identify a non-catalytic role for the ABM superfamily of proteins.

    • Zhiwei Qin
    • , Rebecca Devine
    • , Matthew I. Hutchings
    •  & Barrie Wilkinson
  • Article
    | Open Access

    Metabolizing lignocellulosic feedstocks to industrial chemicals by microorganisms requires surmounting  the recalcitrance caused by lignin. Here, the authors pair transgenic lignin modified poplar lines with engineered Caldicellusiruptor bescii to achieve biomass solubilization and ethanol conversion without pretreatment.

    • Christopher T. Straub
    • , Piyum A. Khatibi
    • , Jack P. Wang
    • , Jonathan M. Conway
    • , Amanda M. Williams-Rhaesa
    • , Ilona M. Peszlen
    • , Vincent L. Chiang
    • , Michael W. W. Adams
    •  & Robert M. Kelly
  • Article
    | Open Access

    The efficiency of producing glutarate, a valuable platform C5 compound, by engineered E. coli is low. Here, the authors achieve high titer and yield of glutarate production by pushing and pulling carbon flux in the native pathway and increasing intermediate influx using newly identified transporters.

    • Wenna Li
    • , Lin Ma
    • , Xiaolin Shen
    • , Jia Wang
    • , Qi Feng
    • , Lexuan Liu
    • , Guojun Zheng
    • , Yajun Yan
    • , Xinxiao Sun
    •  & Qipeng Yuan
  • Article
    | Open Access

    Construction of plasmids from multiple fragments often uses customised parts and leaves scars where fragments are joined. Here the authors develop a method for barcoding fragments and constructing plasmids in a scarless manner from a collection of standard parts.

    • Xiaoqiang Ma
    • , Hong Liang
    • , Xiaoyi Cui
    • , Yurou Liu
    • , Hongyuan Lu
    • , Wenbo Ning
    • , Nga Yu Poon
    • , Benjamin Ho
    •  & Kang Zhou
  • Article
    | Open Access

    Brown macroalgae is a good candidate feedstock for biorefinery, but the major carbohydrate alginate cannot be digested by current industrial microbes. Here, the authors isolate Vibrio sp. dhg and engineer it to produce value-added biochemicals from alginate using newly developed genetic tools.

    • Hyun Gyu Lim
    • , Dong Hun Kwak
    • , Sungwoo Park
    • , Sunghwa Woo
    • , Jae-Seong Yang
    • , Chae Won Kang
    • , Beomhee Kim
    • , Myung Hyun Noh
    • , Sang Woo Seo
    •  & Gyoo Yeol Jung
  • Review Article
    | Open Access

    Engineering microbial cell factories for the production of useful plant natural products (PNPs) is a resource-conserving and environmentally-friendly synthesis route. Here, the authors review recent developments that enable engineering of hosts, pathways, and enzymes to make PNPs and PNP derivatives.

    • Aaron Cravens
    • , James Payne
    •  & Christina D. Smolke
  • Article
    | Open Access

    Bioproduction of tetrahydropapaveroline (THP) is limited by the specificity of monoamine oxidase (MAO). Here, the authors identify an insect 3,4-dihydroxyphenylacetaldehyde synthase (DHPAAS) that can bypass MAO for direct aldehyde production and demonstrate bifunctional switching of DHPAAS for efficient THP production.

    • Christopher J. Vavricka
    • , Takanobu Yoshida
    • , Yuki Kuriya
    • , Shunsuke Takahashi
    • , Teppei Ogawa
    • , Fumie Ono
    • , Kazuko Agari
    • , Hiromasa Kiyota
    • , Jianyong Li
    • , Jun Ishii
    • , Kenji Tsuge
    • , Hiromichi Minami
    • , Michihiro Araki
    • , Tomohisa Hasunuma
    •  & Akihiko Kondo
  • Article
    | Open Access

    The microbial synthesis of carbon-containing compounds from single carbon precursors is desirable, yet designed pathways to achieve this goal overlap with host metabolism. Here the authors design a de novo metabolic pathway to assimilate formaldehyde into acetyl-CoA that does not overlap with known metabolic networks.

    • Xiaoyun Lu
    • , Yuwan Liu
    • , Yiqun Yang
    • , Shanshan Wang
    • , Qian Wang
    • , Xiya Wang
    • , Zhihui Yan
    • , Jian Cheng
    • , Cui Liu
    • , Xue Yang
    • , Hao Luo
    • , Sheng Yang
    • , Junran Gou
    • , Luzhen Ye
    • , Lina Lu
    • , Zhidan Zhang
    • , Yu Guo
    • , Yan Nie
    • , Jianping Lin
    • , Sheng Li
    • , Chaoguang Tian
    • , Tao Cai
    • , Bingzhao Zhuo
    • , Hongwu Ma
    • , Wen Wang
    • , Yanhe Ma
    • , Yongjun Liu
    • , Yin Li
    •  & Huifeng Jiang
  • Article
    | Open Access

    A desired product cannot be obtained at higher concentration than its equilibrium concentration when isomerases are used for biotransformation. Here, the authors engineer in vivo oxidoreductive reactions in yeast to overcome the equilibrium limitation of in vitro isomerases-based tagatose production.

    • Jing-Jing Liu
    • , Guo-Chang Zhang
    • , Suryang Kwak
    • , Eun Joong Oh
    • , Eun Ju Yun
    • , Kulika Chomvong
    • , Jamie H. D. Cate
    •  & Yong-Su Jin
  • Article
    | Open Access

    Heterologous production of the glycocins, posttranslationally modified peptide bacteriocins containing a sugar moiety, has not been achieved. Here, the authors express a thermophilic bacterium glycocin biosynthetic gene cluster and S-glycosyltransferase for the production of antibacterial glycocins in E. coli.

    • Arnoldas Kaunietis
    • , Andrius Buivydas
    • , Donaldas J. Čitavičius
    •  & Oscar P. Kuipers
  • Article
    | Open Access

    Metabolic engineering usually focuses on manipulating enzyme(s) within a single pathway. Here, the authors show that a promiscuous enzymatic activity-based multiple-pathway design can minimize cell metabolic burden and allow carbon flow rearrangement, leading to efficient hydroxytyrosol biosynthesis.

    • Wei Chen
    • , Jun Yao
    • , Jie Meng
    • , Wenjing Han
    • , Yong Tao
    • , Yihua Chen
    • , Yixin Guo
    • , Guizhi Shi
    • , Yang He
    • , Jian-Ming Jin
    •  & Shuang-Yan Tang
  • Article
    | Open Access

    Cytosolic lipid droplets are ER-derived organelles that accumulate in seeds to fuel germination. Here, Sadre et al. show that by boosting lipid production and anchoring key terpenoid biosynthetic enzymes to the droplet surface, an efficient terpenoid production platform can be established in leaves.

    • Radin Sadre
    • , Peiyen Kuo
    • , Jiaxing Chen
    • , Yang Yang
    • , Aparajita Banerjee
    • , Christoph Benning
    •  & Bjoern Hamberger
  • Article
    | Open Access

    How cellular noise impacts metabolic trade-offs remains unknown. Here, the authors use a quantitative single-cell mass imaging strategy to reveal that cellular noise impacts cellular biomass and triacylglycerol accumulation, as well as protein and fatty-acid recycling under starvation, differently.

    • A. E. Vasdekis
    • , H. Alanazi
    • , A. M. Silverman
    • , C. J. Williams
    • , A. J. Canul
    • , J. B. Cliff
    • , A. C. Dohnalkova
    •  & G. Stephanopoulos
  • Article
    | Open Access

    End-product toxicity, culture contamination, and energy efficient product recovery are long-standing issues in bioprocessing. Here, the authors address these problems using a fermentation strategy that combines microbial production of branched alcohols with supercritical carbon dioxide extraction.

    • Jason T. Boock
    • , Adam J. E. Freedman
    • , Geoffrey A. Tompsett
    • , Sarah K. Muse
    • , Audrey J. Allen
    • , Luke A. Jackson
    • , Bernardo Castro-Dominguez
    • , Michael T. Timko
    • , Kristala L. J. Prather
    •  & Janelle R. Thompson
  • Article
    | Open Access

    Producing individual cannabinoids by metabolically engineered microbes has proven challenging. Here, the authors develop a cell-free enzymatic prenylating system to generate isoprenyl pyrophosphate substrates directly from glucose and produce both common and rare cannabinoids at >1 g/L.

    • Meaghan A. Valliere
    • , Tyler P. Korman
    • , Nicholas B. Woodall
    • , Gregory A. Khitrov
    • , Robert E. Taylor
    • , David Baker
    •  & James U. Bowie
  • Article
    | Open Access

    Interventions in metabolic networks can improve microbes for chemical production. Here, the authors develop a tool to identify metabolic valves that can decouple growth and production to systematically improve the rate and yield of biochemical production processes.

    • Naveen Venayak
    • , Axel von Kamp
    • , Steffen Klamt
    •  & Radhakrishnan Mahadevan
  • Article
    | Open Access

    Pectin-rich agricultural byproducts are ideal feedstocks for biobased chemicals production. Here, the authors engineer the yeast, S. cerevisiae, in several steps to co-utilize d-galacturonic acid and d-glucose and demonstrate the potential of producing meso-galactaric acid from industrial orange peel.

    • Ryan J. Protzko
    • , Luke N. Latimer
    • , Ze Martinho
    • , Elise de Reus
    • , Tanja Seibert
    • , J. Philipp Benz
    •  & John E. Dueber
  • Article
    | Open Access

    Efficient biosynthesis of lactams is still undesirable due to lacking of suitable enzyme. Here, the authors develop a sensitive transcription factor-based biosensor for high-throughput screening of marine metagenome and find a cyclase that can cyclize ω-amino fatty acids to lactam.

    • Soo-Jin Yeom
    • , Moonjeong Kim
    • , Kil Koang Kwon
    • , Yaoyao Fu
    • , Eugene Rha
    • , Sung-Hyun Park
    • , Hyewon Lee
    • , Haseong Kim
    • , Dae-Hee Lee
    • , Dong-Myung Kim
    •  & Seung-Goo Lee
  • Article
    | Open Access

    Vitamin B12 is an essential nutrient with limited natural sources. Here the authors transfer 28 pathway synthesis genes from several bacteria including R. capsulatus to E. coli and, using metabolic engineering and optimised fermentation conditions, achieve high yields.

    • Huan Fang
    • , Dong Li
    • , Jie Kang
    • , Pingtao Jiang
    • , Jibin Sun
    •  & Dawei Zhang
  • Article
    | Open Access

    Mutating natural enzymes is effective in broadening the substrate or product range, but generally leads to reduced titers. Here the authors engineer hybrid polyketide synthases for efficient production of short-chain ketones from plant biomass hydrolysates in Streptomyces, which can increase the octane of gasoline.

    • Satoshi Yuzawa
    • , Mona Mirsiaghi
    • , Renee Jocic
    • , Tatsuya Fujii
    • , Fabrice Masson
    • , Veronica T. Benites
    • , Edward E. K. Baidoo
    • , Eric Sundstrom
    • , Deepti Tanjore
    • , Todd R. Pray
    • , Anthe George
    • , Ryan W. Davis
    • , John M. Gladden
    • , Blake A. Simmons
    • , Leonard Katz
    •  & Jay D. Keasling
  • Article
    | Open Access

    Diketopiperazine derivatives are bioactive molecules with scaffold formed by the condensation of two amino acids. Here, Yao et al. mine the genomes of Streptomyces strains and identify new biosynthetic machinery for drimentines biosynthesis, which includes cyclodipeptide synthase, prenyltransferase, and terpene cyclase.

    • Tingting Yao
    • , Jing Liu
    • , Zengzhi Liu
    • , Tong Li
    • , Huayue Li
    • , Qian Che
    • , Tianjiao Zhu
    • , Dehai Li
    • , Qianqun Gu
    •  & Wenli Li
  • Article
    | Open Access

    Assimilating the abundant one-carbon compounds by an industrially-relevant microorganism can broaden the substrate range and achieve reactions that are difficult for chemical process. Here the authors show a modified serine cycle can convert methanol and CO2 to two-carbon compounds in an engineered E. coli strain.

    • Hong Yu
    •  & James C. Liao