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Systems biotechnology and metabolic engineering

Edited by Prof Sang Yup Lee

Microbial Cell Factories invites submissions to this ongoing thematic series on the topic of Systems biotechnology and metabolic engineering. It is now time to exploit systems approaches to microbial biotechnology, starting with up-stream (strain, cell and organism development) by metabolic engineering, which will ultimately lead to successful biotechnology development when combined with systems engineering of mid- to down-stream processes. Please see here for further details, including how to submit your new work to the series.

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  1. Research

    Metabolic engineering of Corynebacterium glutamicum for enhanced production of 5-aminovaleric acid

    5-Aminovaleric acid (5AVA) is an important five-carbon platform chemical that can be used for the synthesis of polymers and other chemicals of industrial interest. Enzymatic conversion of l-lysine to 5AVA has bee...

    Jae Ho Shin, Seok Hyun Park, Young Hoon Oh, Jae Woong Choi, Moon Hee Lee, Jae Sung Cho, Ki Jun Jeong, Jeong Chan Joo, James Yu, Si Jae Park and Sang Yup Lee

    Microbial Cell Factories 2016 15:174

    Published on: 7 October 2016

  2. Research

    Heterologous production of raspberry ketone in the wine yeast Saccharomyces cerevisiae via pathway engineering and synthetic enzyme fusion

    Raspberry ketone is the primary aroma compound found in raspberries and naturally derived raspberry ketone is a valuable flavoring agent. The economic incentives for the production of raspberry ketone, combine...

    Danna Lee, Natoiya D. R. Lloyd, Isak S. Pretorius and Anthony R. Borneman

    Microbial Cell Factories 2016 15:49

    Published on: 4 March 2016

  3. Research

    ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae

    With increasing concern about the environmental impact of a petroleum based economy, focus has shifted towards greener production strategies including metabolic engineering of microbes for the conversion of pl...

    Sarah Rodriguez, Charles M. Denby, T. Van Vu, Edward E. K. Baidoo, George Wang and Jay D. Keasling

    Microbial Cell Factories 2016 15:48

    Published on: 3 March 2016

  4. Research

    Using synthetic biology to increase nitrogenase activity

    Nitrogen fixation has been established in protokaryotic model Escherichia coli by transferring a minimal nif gene cluster composed of 9 genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV) from Paenib...

    Xin-Xin Li, Qi Liu, Xiao-Meng Liu, Hao-Wen Shi and San-Feng Chen

    Microbial Cell Factories 2016 15:43

    Published on: 20 February 2016

  5. Research

    Increased availability of NADH in metabolically engineered baker’s yeast improves transaminase-oxidoreductase coupled asymmetric whole-cell bioconversion

    Saccharomyces cerevisiae can be engineered to perform a multitude of different chemical reactions that are not programmed in its original genetic code. It has a large potential to func...

    Jan Dines Knudsen, Cecilia Hägglöf, Nora Weber and Magnus Carlquist

    Microbial Cell Factories 2016 15:37

    Published on: 15 February 2016

  6. Research

    Transcriptome-enabled discovery and functional characterization of enzymes related to (2S)-pinocembrin biosynthesis from Ornithogalum caudatum and their application for metabolic engineering

    (2S)-Pinocembrin is a chiral flavanone with versatile pharmacological and biological activities. Its health-promoting effects have spurred on research effects on the microbial production of (2S)-pinocembrin. Howe...

    Lei Guo, Xi Chen, Li-Na Li, Wei Tang, Yi-Ting Pan and Jian-Qiang Kong

    Microbial Cell Factories 2016 15:27

    Published on: 4 February 2016

  7. Research

    High yield 1,3-propanediol production by rational engineering of the 3-hydroxypropionaldehyde bottleneck in Citrobacter werkmanii

    Imbalance in cofactors causing the accumulation of intermediates in biosynthesis pathways is a frequently occurring problem in metabolic engineering when optimizing a production pathway in a microorganism. In ...

    Veerle E. T. Maervoet, Sofie L. De Maeseneire, Fatma G. Avci, Joeri Beauprez, Wim K. Soetaert and Marjan De Mey

    Microbial Cell Factories 2016 15:23

    Published on: 28 January 2016

  8. Research

    Adaptive evolution and metabolic engineering of a cellobiose- and xylose- negative Corynebacterium glutamicum that co-utilizes cellobiose and xylose

    An efficient microbial cell factory requires a microorganism that can utilize a broad range of substrates to economically produce value-added chemicals and fuels. The industrially important bacterium Corynebacter...

    Jungseok Lee, Jack N. Saddler, Youngsoon Um and Han Min Woo

    Microbial Cell Factories 2016 15:20

    Published on: 22 January 2016

  9. Research

    Metabolic engineering of Escherichia coli for the production of cinnamaldehyde

    Plant parasitic nematodes are harmful to agricultural crops and plants, and may cause severe yield losses. Cinnamaldehyde, a volatile, yellow liquid commonly used as a flavoring or food additive, is increasing...

    Hyun Bae Bang, Yoon Hyeok Lee, Sun Chang Kim, Chang Keun Sung and Ki Jun Jeong

    Microbial Cell Factories 2016 15:16

    Published on: 19 January 2016

  10. Research

    Designing intracellular metabolism for production of target compounds by introducing a heterologous metabolic reaction based on a Synechosystis sp. 6803 genome-scale model

    Designing optimal intracellular metabolism is essential for using microorganisms to produce useful compounds. Computerized calculations for flux balance analysis utilizing a genome-scale model have been perfor...

    Tomokazu Shirai, Takashi Osanai and Akihiko Kondo

    Microbial Cell Factories 2016 15:13

    Published on: 18 January 2016

  11. Research

    Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose

    Sustainable alternatives for the production of fuels and chemicals are needed to reduce our dependency on fossil resources and to avoid the negative impact of their excessive use on the global climate. Lignoce...

    Stefan Marcus Gaida, Andrea Liedtke, Andreas Heinz Wilhelm Jentges, Benedikt Engels and Stefan Jennewein

    Microbial Cell Factories 2016 15:6

    Published on: 13 January 2016

  12. Research

    Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis

    With the increasing global crude oil crisis and resulting environmental concerns, the production of biofuels from renewable resources has become increasingly important. One of the major challenges faced during...

    Furong Tan, Bo Wu, Lichun Dai, Han Qin, Zongxia Shui, Jingli Wang, Qili Zhu, Guoquan Hu and Mingxiong He

    Microbial Cell Factories 2016 15:4

    Published on: 13 January 2016

  13. Research

    Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds

    As a metabolic engineering tool, an adaptive laboratory evolution (ALE) experiment was performed to increase the specific growth rate (µ) in an Escherichia coli strain lacking PTS, originally engineered to increa...

    César Aguilar, Noemí Flores, Fernando Riveros-McKay, Diana Sahonero-Canavesi, Susy Beatriz Carmona, Otto Geiger, Adelfo Escalante and Francisco Bolívar

    Microbial Cell Factories 2015 14:194

    Published on: 1 December 2015

  14. Research

    Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    High-throughput screening methods assume that the output measured is representative of changes in metabolic flux toward the desired product and is not affected by secondary phenotypes. However, metabolic engin...

    Mareike Bongers, Panagiotis K. Chrysanthopoulos, James B. Y. H. Behrendorff, Mark P. Hodson, Claudia E. Vickers and Lars K. Nielsen

    Microbial Cell Factories 2015 14:193

    Published on: 26 November 2015

  15. Research

    Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)

    Methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. However, the application of natural methanotrophic strains to large-scale production of...

    Andrea de la Torre, Aisha Metivier, Frances Chu, Lieve M. L. Laurens, David A. C. Beck, Philip T. Pienkos, Mary E. Lidstrom and Marina G. Kalyuzhnaya

    Microbial Cell Factories 2015 14:188

    Published on: 25 November 2015

  16. Research

    Metabolic pathway engineering using the central signal processor PII

    PII signal processor proteins are wide spread in prokaryotes and plants where they control a multitude of anabolic reactions. Efficient overproduction of metabolites requires relaxing the tight cellular control c...

    Björn Watzer, Alicia Engelbrecht, Waldemar Hauf, Mark Stahl, Iris Maldener and Karl Forchhammer

    Microbial Cell Factories 2015 14:192

    Published on: 25 November 2015

  17. Research

    BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B12 by Propionibacterium freudenreichii

    Propionibacterium freudenreichii is a food grade bacterium that has gained attention as a producer of appreciable amounts of cobalamin, a cobamide with activity of vitamin B12. Product...

    Paulina Deptula, Petri Kylli, Bhawani Chamlagain, Liisa Holm, Risto Kostiainen, Vieno Piironen, Kirsi Savijoki and Pekka Varmanen

    Microbial Cell Factories 2015 14:186

    Published on: 23 November 2015

  18. Research

    Compositional regulation of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) by replacement of granule-associated protein in Ralstonia eutropha

    Phasin (PhaP), a kind of polyhydroxyalkanoate (PHA) granule-associated proteins, has a role in controlling the properties of PHA granules surface, and is thought to have influence on PHA biosynthesis in PHA-pr...

    Yui Kawashima, Izumi Orita, Satoshi Nakamura and Toshiaki Fukui

    Microbial Cell Factories 2015 14:187

    Published on: 23 November 2015

  19. Research

    Engineering Corynebacterium glutamicum for the production of 2,3-butanediol

    2,3-Butanediol is an important bulk chemical with a wide range of applications. In bacteria, this metabolite is synthesised from pyruvate via a three-step pathway involving α-acetolactate synthase, α-acetolact...

    Dušica Radoš, Ana Lúcia Carvalho, Stefan Wieschalka, Ana Rute Neves, Bastian Blombach, Bernhard J. Eikmanns and Helena Santos

    Microbial Cell Factories 2015 14:171

    Published on: 29 October 2015

  20. Research

    Designed biosynthesis of 25-methyl and 25-ethyl ivermectin with enhanced insecticidal activity by domain swap of avermectin polyketide synthase

    Avermectin and milbemycin are important 16-membered macrolides that have been widely used as pesticides in agriculture. However, the wide use of these pesticides inevitably causes serious drug resistance, it i...

    Ji Zhang, Yi-Jun Yan, Jing An, Sheng-Xiong Huang, Xiang-Jing Wang and Wen-Sheng Xiang

    Microbial Cell Factories 2015 14:152

    Published on: 24 September 2015

  21. Research

    Catabolism of coniferyl aldehyde, ferulic acid and p-coumaric acid by Saccharomyces cerevisiae yields less toxic products

    Lignocellulosic substrates and pulping process streams are of increasing relevance to biorefineries for second generation biofuels and biochemical production. They are known to be rich in sugars and inhibitors...

    Peter Temitope Adeboye, Maurizio Bettiga, Fredrik Aldaeus, Per Tomas Larsson and Lisbeth Olsson

    Microbial Cell Factories 2015 14:149

    Published on: 21 September 2015

  22. Research

    Metabolic engineering of Escherichia coli into a versatile glycosylation platform: production of bio-active quercetin glycosides

    Flavonoids are bio-active specialized plant metabolites which mainly occur as different glycosides. Due to the increasing market demand, various biotechnological approaches have been developed which use Escherich...

    Frederik De Bruyn, Maarten Van Brempt, Jo Maertens, Wouter Van Bellegem, Dries Duchi and Marjan De Mey

    Microbial Cell Factories 2015 14:138

    Published on: 16 September 2015

  23. Research

    Optimization of ethylene glycol production from (d)-xylose via a synthetic pathway implemented in Escherichia coli

    Ethylene glycol (EG) is a bulk chemical that is mainly used as an anti-freezing agent and a raw material in the synthesis of plastics. Production of commercial EG currently exclusively relies on chemical synth...

    Ceren Alkim, Yvan Cam, Debora Trichez, Clément Auriol, Lucie Spina, Amélie Vax, François Bartolo, Philippe Besse, Jean Marie François and Thomas Walther

    Microbial Cell Factories 2015 14:127

    Published on: 4 September 2015

  24. Research

    Enhanced 2,3-butanediol production from biodiesel-derived glycerol by engineering of cofactor regeneration and manipulating carbon flux in Bacillus amyloliquefaciens

    Bacillus amyloliquefaciens B10-127 exhibited an excellent ability for industrial-scale microbial fermentation of 2,3-butanediol (2,3-BD) from biodiesel-derived glycerol. However, the a...

    Taowei Yang, Zhiming Rao, Xian Zhang, Meijuan Xu, Zhenghong Xu and Shang-Tian Yang

    Microbial Cell Factories 2015 14:122

    Published on: 22 August 2015

  25. Research

    Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain

    A Saccharomyces cerevisiae strain carrying deletions in all three pyruvate decarboxylase (PDC) genes (also called Pdc negative yeast) represents a non-ethanol producing platform strain for the production of pyruv...

    Yiming Zhang, Guodong Liu, Martin K M Engqvist, Anastasia Krivoruchko, Björn M Hallström, Yun Chen, Verena Siewers and Jens Nielsen

    Microbial Cell Factories 2015 14:116

    Published on: 8 August 2015

  26. Research

    CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae

    One of the bottlenecks in production of biochemicals and pharmaceuticals in Saccharomyces cerevisiae is stable and homogeneous expression of pathway genes. Integration of genes into the genome of the production o...

    Carlotta Ronda, Jérôme Maury, Tadas Jakočiu̅nas, Simo Abdessamad Baallal Jacobsen, Susanne Manuela Germann, Scott James Harrison, Irina Borodina, Jay D Keasling, Michael Krogh Jensen and Alex Toftgaard Nielsen

    Microbial Cell Factories 2015 14:97

    Published on: 7 July 2015

  27. Research

    Identification of enhanced hydrogen and ethanol Escherichia coli producer strains in a glycerol-based medium by screening in single-knock out mutant collections

    Earth’s climate is warming as a result of anthropogenic emissions of greenhouse gases from fossil fuel combustion. Bioenergy, which includes biodiesel, biohydrogen and bioethanol, has emerged as a sustainable ...

    Antonio Valle, Gema Cabrera, Domingo Cantero and Jorge Bolivar

    Microbial Cell Factories 2015 14:93

    Published on: 28 June 2015

  28. Research

    Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis

    The overexpression of key enzymes in a metabolic pathway is a frequently used genetic engineering strategy for strain improvement. Metabolic control analysis has been proposed to quantitatively determine key e...

    Yanfei Zhang, Qinglong Meng, Hongwu Ma, Yongfei Liu, Guoqiang Cao, Xiaoran Zhang, Ping Zheng, Jibin Sun, Dawei Zhang, Wenxia Jiang and Yanhe Ma

    Microbial Cell Factories 2015 14:86

    Published on: 13 June 2015

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