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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. Content type: Research

    Trichoderma reesei is one of the most important fungi utilized for cellulase production. However, its cellulase system has been proven to be present in suboptimal ratio for deconstruct...

    Authors: Yuanchao Qian, Lixia Zhong, Jia Gao, Ningning Sun, Yifan Wang, Guoyong Sun, Yinbo Qu and Yaohua Zhong

    Citation: Microbial Cell Factories 2017 16:207

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  2. Content type: Research

    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...

    Authors: 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

    Citation: Microbial Cell Factories 2016 15:174

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  3. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:49

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  4. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:48

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  5. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:43

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  6. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:37

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  7. Content type: Research

    (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...

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

    Citation: Microbial Cell Factories 2016 15:27

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  8. Content type: Research

    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 ...

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

    Citation: Microbial Cell Factories 2016 15:23

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  9. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:20

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  10. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:16

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  11. Content type: Research

    Protoilludene is a valuable sesquiterpene and serves as a precursor for several medicinal compounds and antimicrobial chemicals. It can be synthesized by heterologous expression of protoilludene synthase in Esche...

    Authors: Liyang Yang, Chonglong Wang, Jia Zhou and Seon-Won Kim

    Citation: Microbial Cell Factories 2016 15:14

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  12. Content type: Research

    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...

    Authors: Tomokazu Shirai, Takashi Osanai and Akihiko Kondo

    Citation: Microbial Cell Factories 2016 15:13

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  13. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:4

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  14. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2016 15:6

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  15. Content type: Research

    Isepamicin is a weakly toxic but highly active aminoglycoside antibiotic derivative of gentamicin B. Gentamicin B is a naturally occurring minor component isolated from Micromonospora echinospora. 2ʹ-NH2-containi...

    Authors: Xianpu Ni, Zhenpeng Sun, Yawen Gu, Hao Cui and Huanzhang Xia

    Citation: Microbial Cell Factories 2016 15:1

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  16. Content type: Research

    Although some microorganisms can convert glycerol into valuable products such as polyunsaturated fatty acids, the yields are relative low due primarily to an inefficient assimilation of glycerol. Mortierella alpi...

    Authors: Guangfei Hao, Haiqin Chen, Zhennan Gu, Hao Zhang, Wei Chen and Yong Q. Chen

    Citation: Microbial Cell Factories 2015 14:205

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  17. Content type: Research

    Methylxanthines are natural and synthetic compounds found in many foods, drinks, pharmaceuticals, and cosmetics. Aside from caffeine, production of many methylxanthines is currently performed by chemical synth...

    Authors: Khalid H. R. Algharrawi, Ryan M. Summers, Sridhar Gopishetty and Mani Subramanian

    Citation: Microbial Cell Factories 2015 14:203

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  18. Content type: Commentary

    Promoters are indispensable elements of a standardized parts collection for synthetic biology. Regulated promoters of a wide variety of well-defined induction ratios and expression strengths are highly interes...

    Authors: Brigitte Gasser, Matthias G. Steiger and Diethard Mattanovich

    Citation: Microbial Cell Factories 2015 14:196

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  19. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:194

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  20. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:193

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  21. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:192

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  22. Content type: Research

    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...

    Authors: 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

    Citation: Microbial Cell Factories 2015 14:188

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  23. Content type: Research

    Quorum sensing (QS) networks are more commonly known as acyl homoserine lactone (HSL) networks. Recently, p-coumaroyl-HSL has been found in a photosynthetic bacterium. p-coumaroyl-HSL is derived from a lignin mon...

    Authors: Sun-Young Kang, Jae Kyoung Lee, Jae-Hyuk Jang, Bang Yeon Hwang and Young-Soo Hong

    Citation: Microbial Cell Factories 2015 14:191

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  24. Content type: Research

    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...

    Authors: Yui Kawashima, Izumi Orita, Satoshi Nakamura and Toshiaki Fukui

    Citation: Microbial Cell Factories 2015 14:187

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  25. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:186

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  26. Content type: Research

    Poly(3-hydroxybutyrate) (PHB), have been considered to be good candidates for completely biodegradable polymers due to their similar mechanical properties to petroleum-d...

    Authors: Zhenquan Lin, Yan Zhang, Qianqian Yuan, Qiaojie Liu, Yifan Li, Zhiwen Wang, Hongwu Ma, Tao Chen and Xueming Zhao

    Citation: Microbial Cell Factories 2015 14:185

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  27. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:171

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  28. Content type: Research

    The industrial production of riboflavin mostly relies on the microbial fermentation of flavinogenic microorganisms and Ashbya gossypii is the main industrial producer of the vitamin. Accordingly, bioengineering s...

    Authors: Rodrigo Ledesma-Amaro, Cristina Serrano-Amatriain, Alberto Jiménez and José Luis Revuelta

    Citation: Microbial Cell Factories 2015 14:163

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  29. Content type: Research

    The microbial conversion of plant biomass into value added products is an attractive option to address the impacts of petroleum dependency. The Gram-negative bacterium Escherichia coli is commonly used as host fo...

    Authors: Dongfang Gao, Yaqi Luan, Qian Wang, Quanfeng Liang and Qingsheng Qi

    Citation: Microbial Cell Factories 2015 14:159

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  30. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:152

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  31. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:149

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  32. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:138

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  33. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:127

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  34. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:122

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  35. Content type: Research

    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...

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

    Citation: Microbial Cell Factories 2015 14:116

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  36. Content type: Research

    Sugar alcohols have been widely applied in the fields of food and medicine owing to their unique properties. Compared to chemical production, microbial production of sugar alcohols has become attractive becaus...

    Authors: Guoqiang Zhang, Yuping Lin, Xianni Qi, Lixian Wang, Peng He, Qinhong Wang and Yanhe Ma

    Citation: Microbial Cell Factories 2015 14:112

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  37. Content type: Research

    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...

    Authors: 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

    Citation: Microbial Cell Factories 2015 14:97

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