Skip to main content

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.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

Page 1 of 4

  2. The widespread usage of protein expression systems in Escherichia coli (E. coli) is a workhorse of molecular biology research that has practical applications in biotechnology industry, including the production of...

    Authors: Daria Krefft, Maciej Prusinowski, Paulina Maciszka, Aleksandra Skokowska, Joanna Zebrowska and Piotr M. Skowron
    Citation: Microbial Cell Factories 2022 21:13
    Content type: Research Published on:

  3. L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and special nutri...

    Authors: Hui Gao, Philibert Tuyishime, Xian Zhang, Taowei Yang, Meijuan Xu and Zhiming Rao
    Citation: Microbial Cell Factories 2021 20:172
    Content type: Review Published on:

  4. Poly-γ-glutamic acid (γ-PGA) and nattokinase (NK) are the main substances produced by Bacillus subtilis natto in solid-state fermentation and have wide application prospects. We found that our strains had higher ...

    Authors: Min Li, Zilong Zhang, Shenwei Li, Zhengan Tian and Xia Ma
    Citation: Microbial Cell Factories 2021 20:83
    Content type: Research Published on:

  5. Myriocin is a natural product with antifungal activity and is derived from Bacillus amyloliquefaciens LZN01. Our previous work demonstrated that myriocin can inhibit the growth of Fusarium oxysporum f. sp. niveum

    Authors: Hengxu Wang, Zhigang Wang, Weihui Xu and Kexin Wang
    Citation: Microbial Cell Factories 2021 20:69
    Content type: Research Published on:

  6. Valuable polysaccharides are usually produced using wild-type or metabolically-engineered host microbial strains through fermentation. These hosts act as cell factories that convert carbohydrates, such as mono...

    Authors: Zi-Xu Liu, Si-Ling Huang, Jin Hou, Xue-Ping Guo, Feng-Shan Wang and Ju-Zheng Sheng
    Citation: Microbial Cell Factories 2021 20:62
    Content type: Review Published on:

  7. Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lac...

    Authors: Arief Izzairy Zamani, Susann Barig, Sarah Ibrahim, Hirzun Mohd. Yusof, Julia Ibrahim, Jaime Yoke Sum Low, Shwu Fun Kua, Syarul Nataqain Baharum, Klaus-Peter Stahmann and Chyan Leong Ng
    Citation: Microbial Cell Factories 2020 19:179
    Content type: Research Published on:

  8. Poly-γ-glutamic acid (γ-PGA) is a promising biopolymer and has been applied in many fields. Bacillus siamensis SB1001 was a newly isolated poly-γ-glutamic acid producer with sucrose as its optimal carbon source. ...

    Authors: Dexin Wang, Hyangmi Kim, Sungbeom Lee, Dae-Hyuk Kim and Min-Ho Joe
    Citation: Microbial Cell Factories 2020 19:101
    Content type: Research Published on:

  9. Aspergillus niger is a filamentous fungus used for the majority of global citric acid production. Recent developments in genome editing now enable biotechnologists to engineer and optimize A. niger. Currently, ho...

    Authors: Lihui Zhang, Xiaomei Zheng, Timothy C. Cairns, Zhidan Zhang, Depei Wang, Ping Zheng and Jibin Sun
    Citation: Microbial Cell Factories 2020 19:76
    Content type: Research Published on:

  10. Microbial de novo production of l-serine, which is widely used in a range of cosmetic and pharmaceutical products, has attracted increasing attention due to its environmentally friendly characteristics. Previous ...

    Authors: Chenyang Wang, Junjun Wu, Binchao Shi, Jiping Shi and Zhijun Zhao
    Citation: Microbial Cell Factories 2020 19:66
    Content type: Research Published on:

  11. New semi-synthetic aminoglycoside antibiotics generally use chemical modifications to avoid inactivity from pathogens. One of the most used modifications is 3′,4′-di-deoxygenation, which imitates the structure...

    Authors: Xiaotang Chen, Hui Zhang, Shaotong Zhou, Mingjun Bi, Shizhou Qi, Huiyuan Gao, Xianpu Ni and Huanzhang Xia
    Citation: Microbial Cell Factories 2020 19:62
    Content type: Research Published on:

  12. Amphotericin B (AmB) is widely used against fungal infection and produced mainly by Streptomyces nodosus. Various intracellular metabolites of S. nodosus were identified during AmB fermentation, and the key compo...

    Authors: Bo Zhang, Yi-Teng Zhou, Sheng-Xian Jiang, Yu-Han Zhang, Kai Huang, Zhi-Qiang Liu and Yu-Guo Zheng
    Citation: Microbial Cell Factories 2020 19:18
    Content type: Research Published on:

  13. Chicken feather, a byproduct of poultry-processing industries, are considered a potential high-quality protein supplement owing to their crude protein content of more than 85%. Nonetheless, chicken feathers ha...

    Authors: Zheng Peng, Xinzhe Mao, Juan Zhang, Guocheng Du and Jian Chen
    Citation: Microbial Cell Factories 2019 18:84
    Content type: Research Published on:

  14. l-2-aminobutyric acid (l-ABA) is an unnatural amino acid that is a key intermediate for the synthesis of several important pharmaceuticals. To make the biosynthesis of l-ABA environmental friendly and more suitab...

    Authors: Jian-Miao Xu, Jian-Qiang Li, Bo Zhang, Zhi-Qiang Liu and Yu-Guo Zheng
    Citation: Microbial Cell Factories 2019 18:43
    Content type: RESEARCH Published on:

  15. Citric acid is the world’s largest consumed organic acid and is widely used in beverage, food and pharmaceutical industries. Aspergillus niger is the main industrial workhorse for citric acid production. Since th...

    Authors: Zhenyu Tong, Xiaomei Zheng, Yi Tong, Yong-Cheng Shi and Jibin Sun
    Citation: Microbial Cell Factories 2019 18:28
    Content type: Review Published on:

  16. 2-Keto-l-gulonic acid (2-KGA), the precursor of vitamin C, is currently produced by two-step fermentation. In the second step, l-sorbose is transformed into 2-KGA by the symbiosis system composed of Ketogulonicig...

    Authors: Cai-Yun Wang, Ye Li, Zi-Wei Gao, Li-Cheng Liu, Meng-Yue Zhang, Tian-Yuan Zhang, Chun-Fu Wu and Yi-Xuan Zhang
    Citation: Microbial Cell Factories 2018 17:81
    Content type: RESEARCH Published on:

  18. Thermostable lipases from microbial sources have been substantially overexpressed in E. coli, however, these enzymes are often produced with low-level enzymatic activity and mainly in the form of inclusion bodies...

    Authors: Weiqing Zhang, Jing Lu, Shuwen Zhang, Lu Liu, Xiaoyang Pang and Jiaping Lv
    Citation: Microbial Cell Factories 2018 17:50
    Content type: RESEARCH Published on:

  19. Phenolic compounds generated in hydrolysis of lignocellulosic materials are major limiting factors for biological production of solvents by Clostridia, but it lacks the attention on the study of adaptation or res...

    Authors: Jun Liu, Qinlu Lin, Xueying Chai, Yunchuan Luo and Ting Guo
    Citation: Microbial Cell Factories 2018 17:35
    Content type: RESEARCH Published on:

  20. 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
    Content type: Research Published on:

  21. Griseoviridin (GV) and viridogrisein (VG, also referred as etamycin), both biosynthesized by a distinct 105 kb biosynthetic gene cluster (BGC) in Streptomyces griseoviridis NRRL 2427, are a pair of synergistic st...

    Authors: Yunchang Xie, Junying Ma, Xiangjing Qin, Qinglian Li and Jianhua Ju
    Citation: Microbial Cell Factories 2017 16:177
    Content type: Research Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

  30. (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
    Content type: Research Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. 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
    Content type: Research Published on:

  38. 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
    Content type: Research Published on:

  39. 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
    Content type: Research Published on:

  40. 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
    Content type: Research Published on:

  41. 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
    Content type: Research Published on:

  42. 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
    Content type: Research Published on:

  44. 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
    Content type: Commentary Published on:

  45. 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
    Content type: Research Published on:

  46. 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
    Content type: Research Published on:

  47. 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
    Content type: Research Published on:

  48. 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
    Content type: Research Published on:

  49. 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
    Content type: Research Published on:

  50. 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
    Content type: Research Published on: