Industrial microbiology articles within Nature Communications

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  • Article
    | Open Access

    Engineering synthetic methylotrophy remains challenging. Here, the authors engineer a methanol-essential E. coli by an in silico-guided multiple knockout approach and show a laboratory evolved strain can incorporate up to 24% methanol into core metabolites during growth.

    • Fabian Meyer
    • , Philipp Keller
    •  & Julia A. Vorholt

  • Article
    | Open Access

    Production of aromatic monoterpene molecules in hop flowers is affected by genetic, environmental, and processing factors. Here, the authors engineer brewer’s yeast for the production of linalool and geraniol, and show pilot-scale beer produced by engineered strains reconstitutes some qualities of hop flavor.

    • Charles M. Denby
    • , Rachel A. Li
    •  & Jay D. Keasling

  • Article
    | Open Access

    Fermentative production of aromatic polyesters from glucose has been unsuccessful. Here, the authors achieve the objective by one-step fermentation of metabolically engineered E. coli expressing a isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase and an evolved polyhydroxyalkanoate synthase.

    • Jung Eun Yang
    • , Si Jae Park
    •  & Sang Yup Lee

  • Article
    | Open Access

    Metalloproteinase inhibitors are leads for drug development, but their biosynthetic pathways are often unknown. Here the authors show that the acyl branched warhead of actinonin and matlystatins derives from an ethylmalonyl-CoA-like pathway and the structural diversity of matlystatins is due to the activity of a decarboxylase-dehydrogenase enzyme.

    • Franziska Leipoldt
    • , Javier Santos-Aberturas
    •  & Leonard Kaysser

  • Article
    | Open Access

    Terephthalic acid (TPA) is an important commodity chemical typically produced from the oxidation of fossil fuel-derivedp-xylene (pX) at high temperature and pressure. Here the authors report an engineered Escherichia coli strain that can transform pX into TPA with a high conversion yield.

    • Zi Wei Luo
    •  & Sang Yup Lee

  • Article
    | Open Access

    The use of anammox microbiomes to treat wastewater is an escalating biotechnology, yet the functional role heterotrophic bacteria play in these systems remains poorly understood. Here, Lawsonet al. use metagenomics and metatranscriptomics to reveal that heterotrophs degrade free peptides, while recycling nitrate to nitrite.

    • Christopher E. Lawson
    • , Sha Wu
    •  & Daniel R. Noguera

  • Article
    | Open Access

    Corynebacterium glutamicum is an important industrial microbe, however it has proven difficult to genetically engineer using Cas9 from Streptococcus pyogenes. Here the authors report effective genome engineering of the bacterium using Cpf1 from Francisella novicida.

    • Yu Jiang
    • , Fenghui Qian
    •  & Sheng Yang

  • Article
    | Open Access

    Microbial fermentation yield is limited by CO2 loss in glycolysis. Here, the authors engineered Clostridium ljungdahlii for the anaerobic, non-photosynthetic mixotrophy production of acetone, increasing carbon product yield while reducing CO2emissions from a biogenic feedstock fermentation.

    • Shawn W. Jones
    • , Alan G. Fast
    •  & Bryan P. Tracy

  • Article
    | Open Access

    Optogenetics has emerged as a promising means to achieve gene expression control in bioprocess engineering, but current systems cannot respond to fluctuations in growth conditions. Here the authors overcome this limitation and develop an automated optogenetic feedback control system for precise and robust control of protein production in E. coli.

    • Andreas Milias-Argeitis
    • , Marc Rullan
    •  & Mustafa Khammash

  • Article
    | Open Access

    There is a need for small-scale reactors that convert methane emissions to more valuable products to reduce climate impacts. Here, the authors show that printing 3D structures of the pMMO enzyme enables continuous methane conversion under ambient conditions and reduces mass transfer limitations.

    • Craig D. Blanchette
    • , Jennifer M. Knipe
    •  & Sarah E. Baker

  • Article
    | Open Access

    Bacteria of the genus Streptomyces produce a great variety of natural products, the biosynthesis of which is subject to complex regulatory networks. Here the authors present a high-resolution, genome-wide analysis of the transcriptome and translatome of Streptomyces coelicolorunder various growth conditions.

    • Yujin Jeong
    • , Ji-Nu Kim
    •  & Byung-Kwan Cho

  • Article
    | Open Access

    While yeast is an attractive alternative to bacteria for the production of biofuels it currently has low production yields. Here, the authors systematically engineer Saccharomyces cerevisiae for high-level production of fatty acids, alkanes and fatty alcohols, which are important fuel precursors.

    • Yongjin J. Zhou
    • , Nicolaas A. Buijs
    •  & Jens Nielsen

  • Article
    | Open Access

    ANaerobic AMMonium OXidation (ANAMMOX) combined with partial nitritation has been adopted for removal of ammonium from wastewater. Here, Speth et al. describe the bacterial metagenome of a partial-nitritation/anammox (PNA) reactor, and provide 23 draft genomes, 19 of which were previously uncharacterized/sequenced/cultivated.

    • Daan R. Speth
    • , Michiel H. in ’t Zandt
    •  & Mike S. M. Jetten

  • Article
    | Open Access

    Achieving high carbon yields is crucial for biotechnological production of metabolites in engineered microorganisms. Here, Tashiroet al. generate E. colistrains that produce acetyl-CoA and a derived metabolite (isobutyl acetate) in the absence of pyruvate decarboxylation, leading to increased carbon yields.

    • Yohei Tashiro
    • , Shuchi H. Desai
    •  & Shota Atsumi

  • Article
    | Open Access

    Ionic liquids (ILs) are important solvents in the microbial production of biofuels, but can inhibit microbial growth. Here, the authors transfer newly discovered IL-resistance genes from rain forest soil bacteria to E. coliand report growth and biofuel production at IL levels that are otherwise toxic to native strains.

    • Thomas L. Ruegg
    • , Eun-Mi Kim
    •  & Michael P. Thelen

  • Article
    | Open Access

    Horizontal gene transfers are known to play an important role in prokaryote evolution but their impact and prevalence in eukaryotes is less clear. Here, the authors sequence the genomes of cheese making fungi P. roqueforti and P. camemberti, and provide evidence for recent horizontal transfers of a large genomic region.

    • Kevin Cheeseman
    • , Jeanne Ropars
    •  & Yves Brygoo

  • Article |

    4-hydroxycoumarin (4HC), a precursor for anticoagulant drugs such as warfarin, has a major role in the treatment of thromboembolic diseases. Here, the authors present an artificial biosynthetic pathway for 4HC production in E. coliand demonstrate its potential for large-scale microbial production.

    • Yuheng Lin
    • , Xiaolin Shen
    •  & Yajun Yan

  • Article |

    Genome-wide variation in the directed evolution of metabolite-overproducing microbes requires high-throughput screening platforms. Yang et al.show that synthetic RNA devices can sense target metabolites, enrich pathway optimisation, and expedite the evolution of metabolite-producing microbes.

    • Jina Yang
    • , Sang Woo Seo
    •  & Gyoo Yeol Jung

  • Article |

    Microbial fatty acid-derived fuels represent promising alternatives to the traditionally used fossil fuels. Koffas and colleagues report that E. colicentral metabolism can be modified to produce large quantities of fatty acids through a modular pathway engineering strategy.

    • Peng Xu
    • , Qin Gu
    •  & Mattheos A.G. Koffas

  • Article
    | Open Access

    The ability of oleaginous fungi to produce lipids for biofuels remains untapped, in part due to a lack of genetic information required to engineer industrial strains. Zhuet al. present the genome of R. toruloides, and identify transcriptomic and proteomic changes associated with lipid production.

    • Zhiwei Zhu
    • , Sufang Zhang
    •  & Zongbao K. Zhao

  • Article |

    Genome-scale metabolic models for bacterial species allow a systematic study of inter-species interactions. Here, competitive and cooperative potential is predicted between 6,903 pairs of species, to explore the role of these interactions in shaping coexistence patterns in natural communities.

    • Shiri Freilich
    • , Raphy Zarecki
    •  & Eytan Ruppin

  • Article
    | Open Access

    Secondary metabolites are widely used in human health and nutrition, but extraction yields from plants are often low. Nakagawaet al. have engineered the metabolism of Escherichia colito develop a fermentation system that produces plant alkaloids from simple carbon sources.

    • Akira Nakagawa
    • , Hiromichi Minami
    •  & Hidehiko Kumagai

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