Industrial microbiology articles within Nature Communications

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  • Article
    | Open Access

    3-Hydroxypropionic acid (3HP) is an important platform chemical. Here, the authors engineer Halomonas bluephagenesis by deleting newly identified degradation pathway and balancing redox state to achieve high level production of 3HP and its copolymer under open and unsterile conditions.

    • Xiao-Ran Jiang
    • , Xu Yan
    •  & Guo-Qiang Chen

  • Article
    | Open Access

    Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production.

    • Felipe Senne de Oliveira Lino
    • , Djordje Bajic
    •  & Morten Otto Alexander Sommer

  • Article
    | Open Access

    The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.

    • Joseph H. Collins
    • , Kevin W. Keating
    •  & Eric M. Young

  • Article
    | Open Access

    Chondroitin sulfate (CS) is a type of sulfated glycosaminoglycan that is manufactured by extraction from animal tissues for the treatment of osteoarthritis and in drug delivery applications. Here, the authors report the development of single microbial cell factories capable of compete, one-step biosynthesis of animal-free CS production in E. coli.

    • Abinaya Badri
    • , Asher Williams
    •  & Mattheos A. G. Koffas

  • Article
    | Open Access

    Direct cloning of biosynthetic gene clusters is difficult due to their size and repetitive nature. Here, the authors present CAPTURE, which uses Cas12a and in vivo Cre-lox recombination for efficient cloning of gene clusters up to 113 kb, and demonstrate how this method can be used for large-scale discovery of novel natural products.

    • Behnam Enghiad
    • , Chunshuai Huang
    •  & Huimin Zhao

  • Article
    | Open Access

    Short-chain primary amines (SCPAs) are industrially important compounds that are commonly produced under harsh synthetic conditions. Here, the authors report a combination of retrobiosynthesis and precursor selection step for design of biosynthetic pathways leading to production of SCPAs, using valine decarboxylase-expressing Escherichia coli strains.

    • Dong In Kim
    • , Tong Un Chae
    •  & Sang Yup Lee

  • Article
    | Open Access

    The development of techniques capable of orchestrating the assembly of living cells into multicellular ensembles with synergistic and function is challenge. Here, the authors construct algal or algal/bacterial cells-based core shell-like structure based on aqueous two-phase system for synergic photosynthetic H2 production.

    • Zhijun Xu
    • , Shengliang Wang
    •  & Stephen Mann

  • Article
    | Open Access

    The structural programmability and functionality of peptide materials can be leverage for various next-generation devices such as non-volatile memories. The authors report a proton-coupled mechanism in tyrosine-rich peptides for realizing multimodal memory devices.

    • Min-Kyu Song
    • , Seok Daniel Namgung
    •  & Jang-Yeon Kwon

  • Article
    | Open Access

    Rare earth elements are used in electronics, but increase in demand could lead to low supply. Here the authors conduct experiments on the International Space Station and show microbes can extract rare elements from rocks at low gravity, a finding that could extend mining potential to other planets.

    • Charles S. Cockell
    • , Rosa Santomartino
    •  & René Demets

  • Article
    | Open Access

    An imbalance between cell growth and bioproduction of engineered microbes often reduces production efficiency. Here, the authors report genetic code expansion-based cell growth and biosynthesis balance engineering to achieve high levels production of N-acetylglucosamine in E. coli and N-acetylneuraminic acid in B. subtilis.

    • Rongzhen Tian
    • , Yanfeng Liu
    •  & Jian Chen

  • Article
    | Open Access

    Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.

    • Dennis Della Corte
    • , Hugo L. van Beek
    •  & Jan Marienhagen

  • Article
    | Open Access

    Successful application of microbial community for bioproduction relies on the selection of appropriate heterotroph and phototroph partners. Here, the authors construct community metabolic models to guide strain selection and experimentally validate metabolic exchanges that sustain the heterotrophs in minimal media.

    • Cristal Zuñiga
    • , Tingting Li
    •  & Karsten Zengler

  • Article
    | Open Access

    Bioproduction of hyaluronan needs increases in yield and greater diversity of the molecular weights. Here, the author increases hyaluronan production and diversifies the molecular weights through engineering the hyaluronan biosynthesis pathway and disruption of Corynebacterium glutamicum encapsulation caused by secreted hyaluronan.

    • Yang Wang
    • , Litao Hu
    •  & Zhen Kang

  • Article
    | Open Access

    Manipulation of genes controlling microbial shapes can affect bio-production. Here, the authors employ an optogenetic method to realize dynamic morphological engineering of E. coli replication and division and show the increased production of acetoin and poly(lactate-co-3-hydroxybutyrate).

    • Qiang Ding
    • , Danlei Ma
    •  & Xiulai Chen

  • Article
    | Open Access

    Fermentation parameters of industrial processes are often not the ideal growth conditions for industrial microbes. Here, the authors reveal that young genes are more responsive to environmental stress than ancient genes using a new gene age assignment method and provide targeted genes for metabolic engineering.

    • Tyler W. Doughty
    • , Iván Domenzain
    •  & John P. Morrissey

  • Article
    | Open Access

    Malate dehydrogenase (MDH) is one of the key enzymes for succinic acid (SA) bioproduction. Here, the authors report biochemical and structural analyses of various MDHs to reveal amino acids influencing the specific activity and susceptibility to substrate inhibition, and achieve industrial-level SA production.

    • Jung Ho Ahn
    • , Hogyun Seo
    •  & Sang Yup Lee

  • Article
    | Open Access

    Corn fiber is a difficult feedstock to utilize due to its recalcitrant hemicellulose. Here, the authors characterize the recalcitrant structures, isolate a new bacterium to consume the hemicellulose, identify its enzymes, and show the benefit with increased conversion of corn fiber to ethanol.

    • Dhananjay Beri
    • , William S. York
    •  & Christopher D. Herring

  • Article
    | Open Access

    Combining genome mining and heterologous expression in a genetically tractable host can lead to bioactive natural products discovery and production. Here, the authors employ this strategy for new decalin-containing diterpenoid pyrenes production by expressing native, extended, and shunt pathways in Aspergillus oryzae.

    • Kento Tsukada
    • , Shono Shinki
    •  & Teigo Asai

  • Article
    | Open Access

    Developing cyanobacteria as CO2-neutral cell factories relies on the knowledge of the regulation mechanisms for growth and metabolism. Here, the authors develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803 and screens genes potentially affecting growth and L-lactate tolerance and production.

    • Lun Yao
    • , Kiyan Shabestary
    •  & Elton P. Hudson

  • Article
    | Open Access

    Biosynthetic mechanism for the type 2 diabetes treatment drug acarbose is not fully revealed. Here, the authors show that shunt pathways and inefficient amino-deoxyhexose biosynthesis lead to 1-epi-valienol and valienol accumulation, and minimizing the flux to these shunt products can increase acarbose titer in Actinoplanes species.

    • Qinqin Zhao
    • , Yuchang Luo
    •  & Zixin Deng

  • Article
    | Open Access

    Aspergillus fungi classified within the section Flavi include harmful and beneficial species. Here, Kjærbølling et al. analyse the genomes of 23 Flavi species, showing high genetic diversity and potential for synthesis of over 13,700 CAZymes and 1600 secondary metabolites.

    • Inge Kjærbølling
    • , Tammi Vesth
    •  & Mikael R. Andersen

  • 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
    •  & 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

    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
    •  & Yun Chen

  • 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
    •  & Yin Li

  • 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
    •  & 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

    Copper is well known for its high antimicrobial efficacy; however, cost, appearance and metallic properties limit application. Here the authors describe a stable, water dispersible copper-glass ceramic powder with long-term antimicrobial activity as an additive for antimicrobial surfaces.

    • Timothy M. Gross
    • , Joydeep Lahiri
    •  & Michael J. Snyder

  • 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
    •  & Janelle R. Thompson

  • Article
    | Open Access

    Typically, preparation of the polymer precursors α,ω-dinitriles requires hydrogen cyanide. Here, the authors use aldoxime hydratase to produce adiponitrile and related aliphatic linear dinitriles under ambient conditions starting from readily available substrates without needing hydrogen cyanide.

    • Tobias Betke
    • , Manuel Maier
    •  & Harald Gröger

  • 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
    •  & John E. Dueber

  • Article
    | Open Access

    Aerobic ethanol production, a phenomenon referred as Crabtree effect, allows yeast to outcompete other microorganisms in sugar rich environments. Here, the authors show that overexpression of a Gal4-like transcription factor can transform Komagataella phaffii from Crabtree effect negative to positive.

    • Özge Ata
    • , Corinna Rebnegger
    •  & Diethard Mattanovich

  • 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
    •  & 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
    •  & Jay D. Keasling

  • Article
    | Open Access

    The bacterial diterpene synthase CotB2 catalyses the cyclisation of geranylgeranyl diphosphate to cyclooctat-9-en7-ol. Here the authors present various CotB2 structures including a trapped abrupt reaction product that were used for molecular dynamic simulations and allowed them to model all intermediates along the reaction cascade.

    • Ronja Driller
    • , Sophie Janke
    •  & Bernhard Loll

  • Article
    | Open Access

    Organic solvent n-butanol is produced mainly by petrochemical method. Here, the authors revive the historical Weizmann process by engineering Clostridium acetobutylicum strain and developing low pressure distillation and high cell density cultures for n-butanol continuous production at high-yield titer and productivity.

    • Ngoc-Phuong-Thao Nguyen
    • , Céline Raynaud
    •  & Philippe Soucaille

  • Article
    | Open Access

    Reducing aerobic ethanol production, a phenomenon referred to as the Crabtree effect, may open up new perspectives for using yeast as a cell factory. Here, the authors turn the Crabtree-positive yeast into Crabtree negative by combined engineering of cytosolic acetyl-CoA metabolism and mutating the RNA polymerase II mediator complex.

    • Zongjie Dai
    • , Mingtao Huang
    •  & Jens Nielsen

  • Article
    | Open Access

    The engineering of synthetic microbial communities necessitates the use of synthetic, orthogonal cell-to-cell communication channels. Here the authors present a library of characterised AHL-receiver devices and a software tool for the automatic identification of non-interfering chemical communication channels.

    • Nicolas Kylilis
    • , Zoltan A. Tuza
    •  & Karen M. Polizzi

  • Article
    | Open Access

    Achieving high titer yield and productivity of target chemicals in industrial organism depends on multidimensional pathway optimization. Here, the authors use a refined modular method called multidimensional heuristic process to improve production of astaxanthin, nerolidol and linalool in E. coli.

    • Congqiang Zhang
    • , Vui Yin Seow
    •  & Heng-Phon Too

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