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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.

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.

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  1. Clostridium acetobutylicum fermentations are promising for production of commodity chemicals from heterogeneous biomass due to the wide range of substrates the organism can metabolize. Much work has been done to...

    Authors: Matthew D Servinsky, Sanchao Liu, Elliot S Gerlach, Katherine L Germane and Christian J Sund
    Citation: Microbial Cell Factories 2014 13:139
    Content type: Research Published on:

  2. Isopentenols, such as prenol and isoprenol, are promising advanced biofuels because of their higher energy densities and better combustion efficiencies compared with ethanol. Microbial production of isopenteno...

    Authors: Huaiwei Liu, Yang Wang, Qiang Tang, Wentao Kong, Wook-Jin Chung and Ting Lu
    Citation: Microbial Cell Factories 2014 13:135
    Content type: Research Published on:

  3. The gene encoding the putative reductase component (KshB) of 3-ketosteroid 9α-hydroxylase was cloned from Rhodococcus equi USA-18, a cholesterol oxidase-producing strain formerly named Arthrobacter simplex USA-18...

    Authors: Chin-Hsing Yeh, Yung-Shun Kuo, Che-Ming Chang, Wen-Hsiung Liu, Meei-Ling Sheu and Menghsiao Meng
    Citation: Microbial Cell Factories 2014 13:130
    Content type: Research Published on:

  4. The production of aromatic amino acids using fermentation processes with recombinant microorganisms can be an advantageous approach to reach their global demands. In addition, a large array of compounds with a...

    Authors: Alberto Rodriguez, Juan A Martnez, Noem Flores, Adelfo Escalante, Guillermo Gosset and Francisco Bolivar
    Citation: Microbial Cell Factories 2014 13:126
    Content type: Review Published on:

  5. Styrene is an important building-block petrochemical and monomer used to produce numerous plastics. Whereas styrene bioproduction by Escherichia coli was previously reported, the long-term potential of ...

    Authors: Rebekah McKenna, Brian Thompson, Shawn Pugh and David R Nielsen
    Citation: Microbial Cell Factories 2014 13:123
    Content type: Research Published on:

  6. The methylotrophic yeast, Hansenula polymorpha is an industrially important microorganism, and belongs to the best studied yeast species with well-developed tools for ...

    Authors: Olena O Kurylenko, Justyna Ruchala, Orest B Hryniv, Charles A Abbas, Kostyantyn V Dmytruk and Andriy A Sibirny
    Citation: Microbial Cell Factories 2014 13:122
    Content type: Research Published on:

  7. Itaconic acid is on the DOE (Department of Energy) top 12 list of biotechnologically produced building block chemicals and is produced commercially by Aspergillus terreus. However, the production cost of itaconic...

    Authors: Xuenian Huang, Mei Chen, Xuefeng Lu, Yueming Li, Xia Li and Jian-Jun Li
    Citation: Microbial Cell Factories 2014 13:108
    Content type: Research Published on:

  8. Itaconic acid, which has been declared to be one of the most promising and flexible building blocks, is currently used as monomer or co-monomer in the polymer industry, and produced commercially by Aspergillus te...

    Authors: Xuenian Huang, Xuefeng Lu, Yueming Li, Xia Li and Jian-Jun Li
    Citation: Microbial Cell Factories 2014 13:119
    Content type: Research Published on:

  9. Bioplastics, like polylactic acid (PLA), are renewable alternatives for petroleum-based plastics. Lactic acid, the monomer of PLA, has traditionally been produced biotechnologically with bacteria. Wi...

    Authors: Kari T Koivuranta, Marja Ilmén, Marilyn G Wiebe, Laura Ruohonen, Pirkko Suominen and Merja Penttilä
    Citation: Microbial Cell Factories 2014 13:107
    Content type: Research Published on:

  11. Purine nucleotides are essential metabolites for living organisms because they are involved in many important processes, such as nucleic acid synthesis, energy supply, and biosynthesis of several amino acids a...

    Authors: Ting Shi, Yongcheng Wang, Zhiwen Wang, Guanglu Wang, Dingyu Liu, Jing Fu, Tao Chen and Xueming Zhao
    Citation: Microbial Cell Factories 2014 13:101
    Content type: Research Published on:

  12. For the production of L-phenylalanine (L-Phe), two molecules of phosphoenolpyruvate (PEP) and one molecule erythrose-4-phosphate (E4P) are necessary. PEP stems from glycolysis whereas E4P is formed in the pent...

    Authors: Katrin Gottlieb, Christoph Albermann and Georg A Sprenger
    Citation: Microbial Cell Factories 2014 13:96
    Content type: Research Published on:

  13. Pseudomnas putida is a natural producer of medium chain length polyhydroxyalkanoates (mcl-PHA), a polymeric precursor of bioplastics. A two-fold increase of mcl-PHA production via inactivation of the glucose deh...

    Authors: José Manuel Borrero-de Acuña, Agata Bielecka, Susanne Häussler, Max Schobert, Martina Jahn, Christoph Wittmann, Dieter Jahn and Ignacio Poblete-Castro
    Citation: Microbial Cell Factories 2014 13:88
    Content type: Research Published on:

  14. L-Lactic acid, one of the most important chiral molecules and organic acids, is produced via pyruvate from carbohydrates in diverse microorganisms catalyzed by an NAD+-dependent L-lactate dehydrogenase. Naturally...

    Authors: Dandan Niu, Kangming Tian, Bernard A Prior, Min Wang, Zhengxiang Wang, Fuping Lu and Suren Singh
    Citation: Microbial Cell Factories 2014 13:78
    Content type: Research Published on:

  15. Lactobacillus reuteri converts glycerol to 3-hydroxypropionic acid (3HP) and 1,3-propanediol (1,3PDO) via 3-hydroxypropionaldehyde (3HPA) as an intermediate using enzymes encoded in its propanediol-utilization (

    Authors: Tarek Dishisha, Luciana P Pereyra, Sang-Hyun Pyo, Robert A Britton and Rajni Hatti-Kaul
    Citation: Microbial Cell Factories 2014 13:76
    Content type: Research Published on:

  16. To attain a sustainable bioeconomy, fuel, or valuable product, production must use biomass as substrate. Starch is one of the most abundant biomass resources and is present as waste or as a food and agroindust...

    Authors: Luis Manuel Rosales-Colunga and Agustino Martínez-Antonio
    Citation: Microbial Cell Factories 2014 13:74
    Content type: Research Published on:

  17. 1,3-propanediol (PDO) is a substantially industrial metabolite used in the polymer industry. Although several natural PDO production hosts exist, e.g. Klebsiella sp., Citrobacter sp. and Clostridium sp., the PDO ...

    Authors: Veerle ET Maervoet, Sofie L De Maeseneire, Fatma G Avci, Joeri Beauprez, Wim K Soetaert and Marjan De Mey
    Citation: Microbial Cell Factories 2014 13:70
    Content type: Research Published on:

  18. 3-hydroxypropionic acid (3HP) is an important chemical precursor for the production of bioplastics. Microbial production of 3HP from glycerol has previously been developed through the optimization of culture c...

    Authors: Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa and Hiroshi Shimizu
    Citation: Microbial Cell Factories 2014 13:64
    Content type: Research Published on:

  20. Thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. However, the thermoto...

    Authors: Na-Rae Lee, Meiyappan Lakshmanan, Shilpi Aggarwal, Ji-Won Song, Iftekhar A Karimi, Dong-Yup Lee and Jin-Byung Park
    Citation: Microbial Cell Factories 2014 13:61
    Content type: Research Published on:

  21. Saccharopolyspora spinosa is an important producer of antibiotic spinosad with clarified biosynthesis pathway but its complex regulation networks associated with primary metabolism and secondary metabolites prod...

    Authors: Qi Yang, Xuezhi Ding, Xuemei Liu, Shuang Liu, Yunjun Sun, Ziquan Yu, Shengbiao Hu, Jie Rang, Hao He, Lian He and Liqiu Xia
    Citation: Microbial Cell Factories 2014 13:27
    Content type: Research Published on:

  22. Shikimic acid (SA) produced from the seeds of Chinese star anise (Illicium verum) is a key intermediate for the synthesis of neuraminidase inhibitors such as oseltamivir (Tamiflu®), an anti-influenza drug. Howeve...

    Authors: Yan-Yan Cui, Chen Ling, Yuan-Yuan Zhang, Jian Huang and Jian-Zhong Liu
    Citation: Microbial Cell Factories 2014 13:21
    Content type: Research Published on:

  23. Sabinene, one kind of monoterpene, accumulated limitedly in natural organisms, is being explored as a potential component for the next generation of aircraft fuels. And demand for advanced fuels impels us to d...

    Authors: Haibo Zhang, Qiang Liu, Yujin Cao, Xinjun Feng, Yanning Zheng, Huibin Zou, Hui Liu, Jianming Yang and Mo Xian
    Citation: Microbial Cell Factories 2014 13:20
    Content type: Research Published on:

  24. Nowadays, carotenoids are valuable molecules in different industries such as chemical, pharmaceutical, poultry, food and cosmetics. These pigments not only can act as vitamin A precursors, but also they have c...

    Authors: Luis Carlos Mata-Gómez, Julio César Montañez, Alejandro Méndez-Zavala and Cristóbal Noé Aguilar
    Citation: Microbial Cell Factories 2014 13:12
    Content type: Review Published on:

  25. Aspergillus terreus is a natural producer of itaconic acid and is currently used to produce itaconic acid on an industrial scale. The metabolic process for itaconic acid biosynthesis is very similar to the produ...

    Authors: Laura van der Straat, Marloes Vernooij, Marieke Lammers, Willy van den Berg, Tom Schonewille, Jan Cordewener, Ingrid van der Meer, Andries Koops and Leo H de Graaff
    Citation: Microbial Cell Factories 2014 13:11
    Content type: Research Published on:

  26. Over the recent years the production of Ehrlich pathway derived chemicals was shown in a variety of hosts such as Escherichia coli, Corynebacterium glutamicum, and yeast. Exemplarily the production of isobutyric ...

    Authors: Karsten Lang, Jessica Zierow, Katja Buehler and Andreas Schmid
    Citation: Microbial Cell Factories 2014 13:2
    Content type: Research Published on:

  27. Moths (Lepidoptera) are highly dependent on chemical communication to find a mate. Compared to conventional unselective insecticides, synthetic pheromones have successfully served to lure male moths as a speci...

    Authors: Åsa K Hagström, Hong-Lei Wang, Marjorie A Liénard, Jean-Marc Lassance, Tomas Johansson and Christer Löfstedt
    Citation: Microbial Cell Factories 2013 12:125
    Content type: Research Published on:

  28. Poly(4-hydroxybutyrate) (P4HB), belonging to the family of bacterial polyhydroxyalkanoates (PHAs), is a strong, flexible and absorbable material which has a large variety of medical applications like tissue en...

    Authors: Sylvaine Le Meur, Manfred Zinn, Thomas Egli, Linda Thöny-Meyer and Qun Ren
    Citation: Microbial Cell Factories 2013 12:123
    Content type: Research Published on:

  29. Polyoxin, a peptidyl nucleoside antibiotic, consists of three building blocks including a nucleoside skeleton, polyoximic acid (POIA), and carbamoylpolyoxamic acid (CPOAA), however, little is known about the “...

    Authors: Wenqing Chen, Daofeng Dai, Changchun Wang, Tingting Huang, Lipeng Zhai and Zixin Deng
    Citation: Microbial Cell Factories 2013 12:121
    Content type: Research Published on:

  30. Isobutanol is an important target for biorefinery research as a next-generation biofuel and a building block for commodity chemical production. Metabolically engineered microbial strains to produce isobutanol ...

    Authors: Fumio Matsuda, Jun Ishii, Takashi Kondo, Kengo Ida, Hironori Tezuka and Akihiko Kondo
    Citation: Microbial Cell Factories 2013 12:119
    Content type: Research Published on:

  31. The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production h...

    Authors: Harish Nagarajan, Merve Sahin, Juan Nogales, Haythem Latif, Derek R Lovley, Ali Ebrahim and Karsten Zengler
    Citation: Microbial Cell Factories 2013 12:118
    Content type: Research Published on:

  34. The stabilizing and function-preserving effects of ectoines have attracted considerable biotechnological interest up to industrial scale processes for their production. These rely on the release of ectoines fr...

    Authors: Judith Becker, Rudolf Schäfer, Michael Kohlstedt, Björn J Harder, Nicole S Borchert, Nadine Stöveken, Erhard Bremer and Christoph Wittmann
    Citation: Microbial Cell Factories 2013 12:110
    Content type: Research Published on:

  35. Natural aromatic polymers, mainly melanins, have potential and current applications in the cosmetic, pharmaceutical and chemical industries. The biotechnological production of this class of compounds is based ...

    Authors: María I Chávez-Béjar, Victor E Balderas-Hernandez, Aída Gutiérrez-Alejandre, Alfredo Martinez, Francisco Bolívar and Guillermo Gosset
    Citation: Microbial Cell Factories 2013 12:108
    Content type: Research Published on:

  36. The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhy...

    Authors: Changhao Bi, Peter Su, Jana Müller, Yi-Chun Yeh, Swapnil R Chhabra, Harry R Beller, Steven W Singer and Nathan J Hillson
    Citation: Microbial Cell Factories 2013 12:107
    Content type: Research Published on:

  38. Rewiring and optimization of metabolic networks to enable the production of commercially valuable chemicals is a central goal of metabolic engineering. This prospect is challenged by the complexity of metaboli...

    Authors: Andrew Garst, Michael Lynch, Ron Evans and Ryan T Gill
    Citation: Microbial Cell Factories 2013 12:99
    Content type: Review Published on:

  39. Production of bioethanol from lignocellulosic biomass requires the development of robust microorganisms that can tolerate the stressful conditions prevailing in lignocellulosic hydrolysates. Several inhibitors...

    Authors: Magnus Ask, Valeria Mapelli, Heidi Höck, Lisbeth Olsson and Maurizio Bettiga
    Citation: Microbial Cell Factories 2013 12:87
    Content type: Research Published on:

  40. During the last two decades many efforts have been directed towards obtaining efficient microbial processes for the production of shikimic acid (SA); however, feeding high amounts of substrate to increase the ...

    Authors: Alberto Rodriguez, Juan A Martínez, José L Báez-Viveros, Noemí Flores, Georgina Hernández-Chávez, Octavio T Ramírez, Guillermo Gosset and Francisco Bolivar
    Citation: Microbial Cell Factories 2013 12:86
    Content type: Research Published on:

  41. Heterologous microbial production of rare plant terpenoids of medicinal or industrial interest is attracting more and more attention but terpenoid yields are still low. Escherichia coli and Saccharomyces cerevisi...

    Authors: Evamaria Gruchattka, Oliver Hädicke, Steffen Klamt, Verena Schütz and Oliver Kayser
    Citation: Microbial Cell Factories 2013 12:84
    Content type: Research Published on:

  42. Glycolic acid is a C2 hydroxy acid that is a widely used chemical compound. It can be polymerised to produce biodegradable polymers with excellent gas barrier properties. Currently, glycolic acid is produced i...

    Authors: Outi M Koivistoinen, Joosu Kuivanen, Dorothee Barth, Heidi Turkia, Juha-Pekka Pitkänen, Merja Penttilä and Peter Richard
    Citation: Microbial Cell Factories 2013 12:82
    Content type: Research Published on:

  43. Succinic acid (SA) has become a prominent biobased platform chemical with global production quantities increasing annually. Numerous genetically modified E. coli strains have been developed with the main aim of i...

    Authors: Carel D van Heerden and Willie Nicol
    Citation: Microbial Cell Factories 2013 12:80
    Content type: Research Published on:

  44. Polyketides are one of the most important classes of secondary metabolites and usually make good drugs. Currently, heterologous production of fungal polyketides for developing a high potential industrial appli...

    Authors: Limei Gao, Menghao Cai, Wei Shen, Siwei Xiao, Xiangshan Zhou and Yuanxing Zhang
    Citation: Microbial Cell Factories 2013 12:77
    Content type: Research Published on:

  45. The genome of the important industrial host Bacillus subtilis does not encode the glyoxylate shunt, which is necessary to utilize overflow metabolites, like acetate or acetoin, as carbon source. In this study, th...

    Authors: Johannes Kabisch, Isabel Pratzka, Hanna Meyer, Dirk Albrecht, Michael Lalk, Armin Ehrenreich and Thomas Schweder
    Citation: Microbial Cell Factories 2013 12:72
    Content type: Research Published on:

  46. Conjugated linoleic acid (CLA) has been extensively studied for decades because of its health benefits including cancer prevention, anti-atherogenic and anti-obesity effects, and modulation of the immune syste...

    Authors: Baixi Zhang, Haiqin Chen, Min Li, Zhennan Gu, Yuanda Song, Colin Ratledge, Yong Q Chen, Hao Zhang and Wei Chen
    Citation: Microbial Cell Factories 2013 12:70
    Content type: Research Published on:

  47. Numerous studies have examined the direct fermentation of cellulosic materials by cellulase-expressing yeast; however, ethanol productivity in these systems has not yet reached an industrial level. Certain mic...

    Authors: Yuki Nakatani, Ryosuke Yamada, Chiaki Ogino and Akihiko Kondo
    Citation: Microbial Cell Factories 2013 12:66
    Content type: Research Published on:

  49. The optimization of metabolic pathways is critical for efficient and economical production of biofuels and specialty chemicals. One such significant pathway is the cellobiose utilization pathway, identified as...

    Authors: Dawn T Eriksen, Pei Chiun Helen Hsieh, Patrick Lynn and Huimin Zhao
    Citation: Microbial Cell Factories 2013 12:61
    Content type: Research Published on:

  50. L-ascorbic acid (L-AA) is naturally synthesized in plants from D-glucose by 10 steps pathway. The pathway branch to synthesize L-galactose, the key intermediate for L-ascorbic acid biosynthesis, has been recen...

    Authors: Júlio César Câmara Rosa, Lívia Tavares Colombo, Mariana Caroline Tocantins Alvim, Nelson Avonce, Patrick Van Dijck and Flávia Maria Lopes Passos
    Citation: Microbial Cell Factories 2013 12:59
    Content type: Research Published on: