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Publisher: Ke Ai   (Total: 15 journals)   [Sort by number of followers]

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Advances in Climate Change Research     Open Access   (Followers: 13, SJR: 0.485, CiteScore: 1)
Animal Nutrition     Open Access   (Followers: 18, SJR: 0.442, CiteScore: 1)
Bioactive Materials     Open Access   (Followers: 1)
Chronic Diseases and Translational Medicine     Open Access  
Emerging Contaminants     Open Access   (SJR: 1.233, CiteScore: 3)
Geodesy and Geodynamics     Open Access   (SJR: 0.469, CiteScore: 1)
Green Energy & Environment     Open Access   (Followers: 2)
Infectious Disease Modelling     Open Access   (Followers: 2)
J. of Finance and Data Science     Open Access   (Followers: 3)
J. of Natural Gas Geoscience     Open Access   (SJR: 0.783, CiteScore: 1)
Non-coding RNA Research     Open Access  
Petroleum     Open Access  
Plant Diversity     Open Access  
Synthetic and Systems Biotechnology     Open Access   (SJR: 0.841, CiteScore: 0)
World J. of Otorhinolaryngology - Head and Neck Surgery     Open Access  
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Synthetic and Systems Biotechnology
Journal Prestige (SJR): 0.841
Number of Followers: 0  

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ISSN (Print) 2405-805X
Published by Ke Ai Homepage  [15 journals]
  • RiPPing apart the rules for peptide natural products

    • Abstract: Publication date: Available online 5 April 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Aman S. Imani, Michael F. Freeman

      PubDate: 2018-04-13T15:13:24Z
  • Prospective study of probiotic supplementation results in immune
           stimulation and improvement of upper respiratory infection rate

    • Abstract: Publication date: Available online 12 March 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Hong Zhang, Chiajung Yeh, Zonglian Jin, Liwei Ding, Bryan Y. Liu, Li Zhang, H. Kathleen Dannelly
      The human gut microbiota is an important environmental factor for human health with evolutionarily conserved roles in immunity, metabolism, development, and behavior of the host. Probiotic organisms are claimed to offer several functional properties including stimulation of immune system. The purpose of this study is to investigate the effects of a probiotic supplementation on adult volunteers who have contracted the common cold four or more times in the past year. This study is a single center, double-blind, randomized, controlled, prospective trial. Subjects received a probiotic drink containing Lactobacillus paracasei (at least 3 × 107 colony forming units (CFU) ml−1), Lactobacillus casei 431® (at least 3 × 107 CFU ml−1) and Lactobacillus fermentium PCC® (at least 3 × 106 CFU ml−1) or an identical placebo without probiotics for a 12-week study period. The consumption of probiotics significantly reduced the incidence of upper respiratory infection (p < 0.023) and flu-like symptoms with an oral temperature higher than 38 °C (p < 0.034) as compared to the placebo group. Subjects that consumed probiotics demonstrated a significantly higher level of IFN-γ in the serum (p < 0.001) and sIgA in the gut (p < 0.010) as compared to the placebo group and a significant higher level of serum IFN-γ (p < 0.001) and gut sIgA (p < 0.001) as compared to their baseline test results. In contrast, there were no significant differences in the serum IL-4, IL-10, IgA, IgG or IgM between the probiotics and the placebo groups. Results of this study demonstrated that probiotics were safe and effective for fighting the common cold and influenza-like respiratory infections by boosting the immune system.

      PubDate: 2018-03-13T16:33:22Z
  • Synergistic and non-specific nucleic acid production by T7 RNA polymerase
           and Bsu DNA polymerase catalyzed by single-stranded polynucleotides

    • Abstract: Publication date: Available online 3 March 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Nicholas J. Emery, Sagardip Majumder, Allen P. Liu
      Point-of-care molecular diagnostic tests show great promise for providing accurate, timely results in low-infrastructure healthcare settings and at home. The design space for these tests is limited by a variety of possible background reactions, which often originate from relatively weak promiscuous activities of the enzymes used for nucleic acid amplification. When this background signal is amplified alongside the signal of the intended biomarker, the dynamic range of the test can be severely compromised. Therefore, a detailed knowledge of potential side reactions arising from enzyme promiscuity can improve rational design of point-of-care molecular diagnostic tests. Towards this end, we report a previously unknown synergistic reaction between T7 RNA polymerase and Bsu DNA polymerase that produces nucleic acid in the presence of single-stranded DNA or RNA. This reaction occurs in the absence of any previously reported substrates for either polymerases and compromises a theoretical microRNA amplification scheme utilizing these polymerases.

      PubDate: 2018-03-13T16:33:22Z
  • Cell-free protein synthesis enabled rapid prototyping for metabolic
           engineering and synthetic biology

    • Abstract: Publication date: Available online 22 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Lihong Jiang, Jiarun Zhao, Jiazhang Lian, Zhinan Xu
      Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS) has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors) to speed up design-build-test (DBT) cycles of metabolic engineering and synthetic biology.

      PubDate: 2018-03-01T19:20:22Z
  • Cell-free synthesis of stable isotope-labeled internal standards for
           targeted quantitative proteomics

    • Abstract: Publication date: Available online 21 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Ryohei Narumi, Keiko Masuda, Takeshi Tomonaga, Jun Adachi, Hiroki R. Ueda, Yoshihiro Shimizu
      High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis. Cell-free protein synthesis (CFPS) or in vitro translation (IVT) systems in particular provide high-throughput and low-cost preparation methods, and various cell types and reconstituted forms are now commercially available. Herein, we review the use of such systems for precise and reliable protein quantification.

      PubDate: 2018-03-01T19:20:22Z
  • Cell-free synthetic biology for in vitro biosynthesis of
           pharmaceutical natural products

    • Abstract: Publication date: Available online 17 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Jian Li, Lingkai Zhang, Wanqiu Liu
      Natural products with significant biological activities continuously act as rich sources for drug discovery and development. To harness the potential of these valuable compounds, robust methods need to be developed for their rapid and sustainable production. Cell-free biosynthesis of pharmaceutical natural products by in vitro reconstruction of the entire biosynthetic pathways represents one such solution. In this review, we focus on in vitro biosynthesis of two important classes of natural products, polyketides (PKs) and nonribosomal peptides (NRPs). First, we summarize purified enzyme-based systems for the biosynthesis of PKs, NRPs, and PK/NRP hybrids. Then, we introduce the cell-free protein synthesis (CFPS)-based technology for natural product production. With that, we discuss challenges and opportunities of cell-free synthetic biology for in vitro biosynthesis of natural products.

      PubDate: 2018-02-21T15:20:45Z
  • Metabolic pathway engineering

    • Abstract: Publication date: Available online 13 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Hal S. Alper, José L. Avalos

      PubDate: 2018-02-21T15:20:45Z
  • Puromycin A, B and C, cryptic nucleosides identified from Streptomyces
           alboniger NRRL B-1832 by PPtase-based activation

    • Abstract: Publication date: Available online 12 February 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Xiaoli Yan, Benyin Zhang, Wenya Tian, Qi Dai, Xiaoqin Zheng, Ke Hu, Xinxin Liu, Zixin Deng, Xudong Qu
      Natural product discovery is pivot for drug development, however, this endeavor is often challenged by the wide inactivation or silence of natural products biosynthetic pathways. We recently developed a highly efficient approach to activate cryptic/silenced biosynthetic pathways through augmentation of the phosphopantetheinylation of carrier proteins. By applying this approach in the Streptomyces alboniger NRRL B-1832, we herein identified three cryptic nucleosides products, including one known puromycin A and two new derivatives (puromycin B and C). The biosynthesis of these products doesn't require the involvement of carrier protein, indicating the phosphopantetheinyl transferase (PPtase) indeed plays a fundamental regulatory role in metabolites biosynthesis. These results demonstrate that the PPtase-based approach have a much broader effective scope than the previously assumed carrier protein-involving pathways, which will benefit future natural products discovery and biosynthetic studies.

      PubDate: 2018-02-21T15:20:45Z
  • Investigating the consequences of asymmetric endoplasmic reticulum
           inheritance in Saccharomyces cerevisiae under stress using a combination
           of single cell measurements and mathematical modelling

    • Abstract: Publication date: Available online 17 January 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Felix R.H. Jonas, Kate E. Royle, Rochelle Aw, Guy-Bart V. Stan, Karen M. Polizzi
      Adaptation allows organisms to maintain a constant internal environment, which is optimised for growth. The unfolded protein response (UPR) is an example of a feedback loop that maintains endoplasmic reticulum (ER) homeostasis, and is characteristic of how adaptation is often mediated by transcriptional networks. The more recent discovery of asymmetric division in maintaining ER homeostasis, however, is an example of how alternative non-transcriptional pathways can exist, but are overlooked by gold standard transcriptomic or proteomic population-based assays. In this study, we have used a combination of fluorescent reporters, flow cytometry and mathematical modelling to explore the relative roles of asymmetric cell division and the UPR in maintaining ER homeostasis. Under low ER stress, asymmetric division leaves daughter cells with an ER deficiency, necessitating activation of the UPR and prolonged cell cycle during which they can recover ER functionality before growth. Mathematical analysis of and simulation results from our mathematical model reinforce the experimental observations that low ER stress primarily impacts the growth rate of the daughter cells. These results demonstrate the interplay between homeostatic pathways and the importance of exploring sub-population dynamics to understand population adaptation to quantitatively different stresses.
      Graphical abstract image

      PubDate: 2018-01-18T22:24:48Z
  • Engineering metabolic pathways in Amycolatopsis japonicum for the
           optimization of the precursor supply for heterologous brasilicardin
           congeners production

    • Abstract: Publication date: Available online 12 January 2018
      Source:Synthetic and Systems Biotechnology
      Author(s): Paul N. Schwarz, Luisa Roller, Andreas Kulik, Wolfgang Wohlleben, Evi Stegmann
      The isoprenoid brasilicardin A is a promising immunosuppressant compound with a unique mode of action, high potency and reduced toxicity compared to today's standard drugs. However, production of brasilicardin has been hampered since the producer strain Nocardia terpenica IFM0406 synthesizes brasilicardin in only low amounts and is a biosafety level 2 organism. Previously, we were able to heterologously express the brasilicardin gene cluster in the nocardioform actinomycete Amycolatopsis japonicum. Four brasilicardin congeners, intermediates of the BraA biosynthesis, were produced. Since chemical synthesis of the brasilicardin core structure has remained elusive we intended to produce high amounts of the brasilicardin backbone for semi synthesis and derivatization. Therefore, we used a metabolic engineering approach to increase heterologous production of brasilicardin in A. japonicum. Simultaneous heterologous expression of genes encoding the MVA pathway and expression of diterpenoid specific prenyltransferases were used to increase the provision of the isoprenoid precursor isopentenyl diphosphate (IPP) and to channel the precursor into the direction of diterpenoid biosynthesis. Both approaches contributed to an elevated heterologous production of the brasilicardin backbone, which can now be used as a starting point for semi synthesis of new brasilicardin congeners with better properties.

      PubDate: 2018-01-18T22:24:48Z
  • Introduction to the Special Issue: “Arnold Demain – Industrial
           microbiologist extraodinaire”

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Mattheos Koffas, Qiang Gao, Lixin Zhang

      PubDate: 2018-01-08T16:02:21Z
  • Conditional knockout tools: Application of site-specific incorporation of
           unnatural amino acid via genetic code expansion in viral and parasite
           vaccine development

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Pinghua Liu, Lubin Jiang

      PubDate: 2018-01-08T16:02:21Z
  • Development of fungal cell factories for the production of secondary
           metabolites: Linking genomics and metabolism

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Jens Christian Nielsen, Jens Nielsen
      The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being identified. New computational tools are driven by genomics and metabolomics analysis, and enables rapid identification of novel secondary metabolites. To translate this increased discovery rate into industrial exploitation, it is necessary to integrate secondary metabolite pathways in the metabolic engineering process. In this review, we will describe the novel advances in discovery of secondary metabolites produced by filamentous fungi, highlight the utilization of genome-scale metabolic models (GEMs) in the design of fungal cell factories for the production of secondary metabolites and review strategies for optimizing secondary metabolite production through the construction of high yielding platform cell factories.

      PubDate: 2018-01-08T16:02:21Z
  • Reactive oxygen species and antioxidant properties from mushrooms

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Carmen Sánchez
      Preventive medicine and food industry have shown an increased interest in the development of natural antioxidants, since those most commonly used synthetic antioxidants may have restricted use in food. This could explain why there is currently much research on the antioxidant properties from natural products such as mushrooms. Many mushrooms have been reported to possess antioxidant properties, which enable them to neutralize free radicals. The oxygen molecule is a free radical, which lead to the generation of the reactive oxygen species and can damage the cells. Cell damage caused by free radicals appears to be a major contributor to aging and degenerative diseases. Mushrooms antioxidant components are found in fruit bodies, mycelium and culture both, which include polysaccharides, tocopherols, phenolics, carotenoids, ergosterol and ascorbic acid among others. Fruit bodies or mycelium can be manipulated to produce active compounds in a relatively short period of time, which represent a significant advantage in antioxidant compounds extraction from mushrooms. Antioxidant compounds may be extracted to be used as functional additives or mushrooms can be incorporated into our food regime, representing an alternative source of food to prevent damage caused by oxidation in the human body.

      PubDate: 2018-01-08T16:02:21Z
  • Cell-free synthetic biology: Engineering in an open world

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Yuan Lu
      Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.

      PubDate: 2018-01-08T16:02:21Z
  • Evaluation of fermentation conditions triggering increased antibacterial
           activity from a near-shore marine intertidal environment-associated
           Streptomyces species

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): A.L. English, A. Boufridi, R.J. Quinn, D.I. Kurtböke
      A near-shore marine intertidal environment-associated Streptomyces isolate (USC-633) from the Sunshine Coast Region of Queensland, Australia, cultivated under a range of chemically defined and complex media to determine optimal parameters resulting in the secretion of diverse array of secondary metabolites with antimicrobial properties against various antibiotic resistant bacteria. Following extraction, fractioning and re-testing of active metabolites resulted in persistent antibacterial activity against Escherichia coli (Migula) (ATCC 13706) and subsequent Nuclear Magnetic Resonance (NMR) analysis of the active fractions confirmed the induction of metabolites different than the ones in fractions which did not display activity against the same bacterial species. Overall findings again confirmed the value of One Strain–Many Compounds (OSMAC) approach that tests a wide range of growth parameters to trigger bioactive compound secretion increasing the likelihood of finding novel therapeutic agents. The isolate was found to be adaptable to both marine and terrestrial conditions corresponding to its original near-shore marine intertidal environment. Wide variations in its morphology, sporulation and diffusible pigment production were observed when different growth media were used.

      PubDate: 2018-01-08T16:02:21Z
  • Proteome-wide alterations in an industrial clavulanic acid producing
           strain of Streptomyces clavuligerus

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Eser Ünsaldı, Aslıhan Kurt-Kızıldoğan, Birgit Voigt, Dörte Becher, Gülay Özcengiz
      The usefulness of genetic/metabolic engineering for further improvement of industrial strains is subject of discussion because of the general lack of knowledge on genetic alterations introduced by iterative cycles of random mutagenesis in such strains. An industrial clavulanic acid (CA)-overproducer Streptomyces clavuligerus DEPA was assessed to understand proteome-wide changes that have occurred in a local industrial CA overproducer developed through succesive mutagenesis programs. The proteins that could be identified corresponded to 33 distinct ORFs for underrepresented ones and 60 ORFs for overrepresented ones. Three CA biosynthetic enzymes were overrepresented in S. clavuligerus DEPA; carboxyethylarginine synthase (Ceas2), clavaldehyde dehydrogenase (Car) and carboxyethyl-arginine beta-lactam-synthase (Bls2) whereas the enzymes of two other secondary metabolites were underrepresented along with two important global regulators [two-component system (TCS) response regulator (SCLAV_2102) and TetR-family transcriptional regulator (SCLAV_3146)] that might be related with CA production and/or differentiation. γ-butyrolactone biosynthetic protein AvaA2 was 2.6 fold underrepresented in S. clavuligerus DEPA. The levels of two glycolytic enzymes, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase and phosophoglycerate kinase were found decreased while those of dihydrolipoyl dehydrogenase (E3) and isocitrate dehydrogenase, with two isoforms were found as significantly increased. A decrease of amino acid metabolism, methionine biosynthesis in particular, as well as S-adenosylmethionine synthetase appeared as one of the prominent mechanisms of success of S. clavuligerus DEPA strain as a prolific producer of CA. The levels of two enzymes of shikimate pathway that leads to the production of aromatic amino acids and aromatic secondary metabolites were also underrepresented. Some of the overrepresented stress proteins in S. clavuligerus DEPA included polynucleotide phosphorylase/polyadenylase (PNPase), ATP-dependent DNA helicase, two isoforms of an anti-sigma factor and thioredoxin reductase. Downregulation of important proteins of cell wall synthesis and division was recorded and a protein with β-lactamase domain (SCLAV_p1007) appeared in 12 isoforms, 5 of which were drastically overrepresented in DEPA strain. These results described herein provide useful information for rational engineering to improve CA production in Streptomyces clavuligerus.

      PubDate: 2018-01-08T16:02:21Z
  • Novel polysaccharide-protein conjugates provide an immunogenic 13-valent
           pneumococcal conjugate vaccine for S. pneumoniae

    • Abstract: Publication date: March 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 1
      Author(s): Allison E.B. Turner, Jonas E. Gerson, Helen Y. So, Daniel J. Krasznai, Adrienne J. St. Hilaire, Donald F. Gerson
      Pneumonia remains the single leading cause of childhood death worldwide. Despite the commercial availability of multiple pneumococcal conjugate vaccines (PCVs), high dosage cost and supply shortages prevent PCV delivery to much of the developing world. The current work presents high-yield pneumococcal conjugates that are immunogenic in animals and suitable for use in human vaccine development. The 13-valent pneumococcal conjugate vaccine (PCV-13) investigated in this research incorporated serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F. Pneumococcal polysaccharides (PnPSs) and CRM197 carrier protein were produced and purified in-house, and used to prepare PnPS-CRM conjugates using unique, cyanide-free, in vacuo glycation conjugation methods. In vitro characterization confirmed the generation of higher molecular weight PnPS-CRM conjugates low in free protein. In vivo animal studies were performed to compare PnuVax's PCV-13 to the commercially available PCV-13, Prevnar®13 (Pfizer, USA). A boost dose was provided to all groups post-dose 1 at t = 14 days. Post-dose 2 results at t = 28 days showed that all 13 serotypes in PnuVax's PCV-13 were boostable. Per serotype IgG GMCs demonstrated that PnuVax's PCV-13 is immunogenic for all 13 serotypes, with 10 of the 13 serotypes statistically the same or higher than Prevnar®13 post-dose 2. As a result, the novel polysaccharide-protein conjugates developed in this work are highly promising for use in human PCV development. The in vacuo conjugation technique applied in this work could also be readily adapted to develop many other conjugate vaccines.

      PubDate: 2018-01-08T16:02:21Z
  • Comprehensive relative quantitative metabolomics analysis of lycopodium
           alkaloids in different tissues of Huperzia serrata

    • Abstract: Publication date: Available online 26 December 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Shiwen Wu, Zhen Fan, Youli Xiao
      Qian ceng Ta, the whole plant of Huperzia serrata, is an important landscape and medicinal herbs and contains abundant bioactive lycopodium alkaloids. Although the structures of more than 100 lycopodium alkaloids in Huperzia serrata have been isolated and identified, the content and distribution of these alkaloids in different tissues are still unclear. In current study, an ultra-performance liquid chromatography-mass spectrometry based comprehensive metabolomics strategy was developed, including the extraction, separation, identification, and statistical analysis. The results showed that different types lycopodium alkaloids could be separated at different time-windows, which was helpful for further metabolite identification. Peak4388 and peak3954 were metabolite biomarkers for the different tissues according to the principle component analysis and partial least squares-discriminant analysis model. A computational tool based in-house database was also built up and used for putative identification. Of the 2354 true peaks after four-step filtration, 118 peaks were putatively identified as lycopodium alkaloids by using in-house database, and four of which was identified by authentic standards. Alternatively, another computational software was used to predict the fragmentation pattern, to dereplicate the structure of identified peaks, and identified the peak3585 to N-methylhuperzine A. The integration of both computational tools could be used for more metabolites identification.

      PubDate: 2017-12-30T06:13:32Z
  • Thank you note

    • Abstract: Publication date: December 2017
      Source:Synthetic and Systems Biotechnology, Volume 2, Issue 4

      PubDate: 2017-12-30T06:13:32Z
  • Expanding beyond canonical metabolism: Interfacing alternative elements,
           synthetic biology, and metabolic engineering

    • Abstract: Publication date: Available online 19 December 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Kevin B. Reed, Hal S. Alper
      Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially) be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.

      PubDate: 2017-12-20T10:09:48Z
  • Methods and approaches to disease mechanisms using systems kinomics

    • Abstract: Publication date: Available online 18 December 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Alicia Berard, Andrea Kroeker, Peter McQueen, Kevin M. Coombs
      All cellular functions, ranging from regular cell maintenance and homeostasis, specialized functions specific to cellular types, or generating responses due to external stimulus, are mediated by proteins within the cell. Regulation of these proteins allows the cell to alter its behavior under different circumstances. A major mechanism of protein regulation is utilizing protein kinases and phosphatases; enzymes that catalyze the transfer of phosphates between substrates [1]. Proteins involved in phosphate signaling are well studied and include kinases and phosphatases that catalyze opposing reactions regulating both structure and function of the cell. Kinomics is the study of kinases, phosphatases and their targets, and has been used to study the functional changes in numerous diseases and infectious diseases with aims to delineate the cellular functions affected. Identifying the phosphate signaling pathways changed by certain diseases or infections can lead to novel therapeutic targets. However, a daunting 518 putative protein kinase genes have been identified [2], indicating that this protein family is very large and complex. Identifying which enzymes are specific to a particular disease can be a laborious task. In this review, we will provide information on large-scale systems biology methodologies that allow global screening of the kinome to more efficiently identify which kinase pathways are pertinent for further study.

      PubDate: 2017-12-20T10:09:48Z
  • Simple glycolipids of microbes: Chemistry, biological activity and
           metabolic engineering

    • Abstract: Publication date: Available online 15 December 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Ahmad Mohammad Abdel-Mawgoud, Gregory Stephanopoulos
      Glycosylated lipids (GLs) are added-value lipid derivatives of great potential. Besides their interesting surface activities that qualify many of them to act as excellent ecological detergents, they have diverse biological activities with promising biomedical and cosmeceutical applications. Glycolipids, especially those of microbial origin, have interesting antimicrobial, anticancer, antiparasitic as well as immunomodulatory activities. Nonetheless, GLs are hardly accessing the market because of their high cost of production. We believe that experience of metabolic engineering (ME) of microbial lipids for biofuel production can now be harnessed towards a successful synthesis of microbial GLs for biomedical and other applications. This review presents chemical groups of bacterial and fungal GLs, their biological activities, their general biosynthetic pathways and an insight on ME strategies for their production.

      PubDate: 2017-12-20T10:09:48Z
  • Does the eclipse limit bacterial nucleoid complexity and cell width'

    • Abstract: Publication date: Available online 29 November 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Arieh Zaritsky, Avinoam Rabinovitch, Chenli Liu, Conrad L. Woldringh
      Cell size of bacteria M is related to 3 temporal parameters: chromosome replication time C, period from replication-termination to subsequent division D, and doubling time τ. Steady-state, bacillary cells grow exponentially by extending length L only, but their constant width W is larger at shorter τ‘s or longer C's, in proportion to the number of chromosome replication positions n (= C/τ), at least in Escherichia coli and Salmonella typhimurium. Extending C by thymine limitation of fast-growing thyA mutants result in continuous increase of M, associated with rising W, up to a limit before branching. A set of such puzzling observations is qualitatively consistent with the view that the actual cell mass (or volume) at the time of replication-initiation Mi (or Vi), usually relatively constant in growth at varying τ′s, rises with time under thymine limitation of fast-growing, thymine-requiring E. coli strains. The hypothesis will be tested that presumes existence of a minimal distance l min between successive moving replisomes, translated into the time needed for a replisome to reach l min before a new replication-initiation at oriC is allowed, termed Eclipse E. Preliminary analysis of currently available data is inconsistent with a constant E under all conditions, hence other explanations and ways to test them are proposed in an attempt to elucidate these and other results. The complex hypothesis takes into account much of what is currently known about Bacterial Physiology: the relationships between cell dimensions, growth and cycle parameters, particularly nucleoid structure, replication and position, and the mode of peptidoglycan biosynthesis. Further experiments are mentioned that are necessary to test the discussed ideas and hypotheses.

      PubDate: 2017-12-08T15:13:49Z
  • Improving acarbose production and eliminating the by-product component C
           with an efficient genetic manipulation system of Actinoplanes sp. SE50/110

    • Abstract: Publication date: Available online 27 November 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Qinqin Zhao, Huixin Xie, Yao Peng, Xinran Wang, Linquan Bai
      The α-glucosidase inhibitor acarbose is commercially produced by Actinoplanes sp. and used as a potent drug in the treatment of type-2 diabetes. In order to improve the yield of acarbose, an efficient genetic manipulation system for Actinoplanes sp. was established. The conjugation system between E. coli carrying ØC31-derived integrative plasmids and the mycelia of Actinoplanes sp. SE50/110 was optimized by adjusting the parameters of incubation time of mixed culture (mycelia and E. coli), quantity of recipient cells, donor-to-recipient ratio and the concentration of MgCl2, which resulted in a high conjugation efficiency of 29.4%. Using this integrative system, a cloned acarbose biosynthetic gene cluster was introduced into SE50/110, resulting in a 35% increase of acarbose titer from 2.35 to 3.18 g/L. Alternatively, a pIJ101-derived replicating plasmid combined with the counter-selection system CodA(sm) was constructed for gene inactivation, which has a conjugation frequency as high as 0.52%. Meanwhile, almost all 5-flucytosine-resistant colonies were sensitive to apramycin, among which 75% harbored the successful deletion of targeted genes. Using this replicating vector, the maltooligosyltrehalose synthase gene treY responsible for the accumulation of component C was inactivated, and component C was eliminated as detected by LC-MS. Based on an efficient genetic manipulation system, improved acarbose production and the elimination of component C in our work paved a way for future rational engineering of the acarbose-producing strains.

      PubDate: 2017-11-28T10:29:17Z
  • A review of computational tools for design and reconstruction of metabolic

    • Abstract: Publication date: Available online 15 November 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Lin Wang, Satyakam Dash, Chiam Yu Ng, Costas D. Maranas
      Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.

      PubDate: 2017-11-17T13:38:55Z
  • Rapid generation of recombinant Pseudomonas putida secondary metabolite
           producers using yTREX

    • Abstract: Publication date: Available online 15 November 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Andreas Domröse, Robin Weihmann, Stephan Thies, Karl-Erich Jaeger, Thomas Drepper, Anita Loeschcke
      Microbial secondary metabolites represent a rich source of valuable compounds with a variety of applications in medicine or agriculture. Effective exploitation of this wealth of chemicals requires the functional expression of the respective biosynthetic genes in amenable heterologous hosts. We have previously established the TREX system which facilitates the transfer, integration and expression of biosynthetic gene clusters in various bacterial hosts. Here, we describe the yTREX system, a new tool adapted for one-step yeast recombinational cloning of gene clusters. We show that with yTREX, Pseudomonas putida secondary metabolite production strains can rapidly be constructed by random targeting of chromosomal promoters by Tn5 transposition. Feasibility of this approach was corroborated by prodigiosin production after yTREX cloning, transfer and expression of the respective biosynthesis genes from Serratia marcescens. Furthermore, the applicability of the system for effective pathway rerouting by gene cluster adaptation was demonstrated using the violacein biosynthesis gene cluster from Chromobacterium violaceum, producing pathway metabolites violacein, deoxyviolacein, prodeoxyviolacein, and deoxychromoviridans. Clones producing both prodigiosin and violaceins could be readily identified among clones obtained after random chromosomal integration by their strong color-phenotype. Finally, the addition of a promoter-less reporter gene enabled facile detection also of phenazine-producing clones after transfer of the respective phenazine-1-carboxylic acid biosynthesis genes from Pseudomonas aeruginosa. All compounds accumulated to substantial titers in the mg range. We thus corroborate here the suitability of P. putida for the biosynthesis of diverse natural products, and demonstrate that the yTREX system effectively enables the rapid generation of secondary metabolite producing bacteria by activation of heterologous gene clusters, applicable for natural compound discovery and combinatorial biosynthesis.

      PubDate: 2017-11-17T13:38:55Z
  • Experimental evolution and proximate mechanisms in biology

    • Abstract: Publication date: Available online 6 November 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Xiao Yi
      Biological functions – studied by molecular, systems and behavioral biology – are referred to as proximate mechanisms. Why and how they have emerged from the course of evolution are referred to as ultimate mechanisms. Despite the conceptual and technical schism between the disciplines that focus on each, studies from one side can benefit the other. Experimental evolution is an emerging field at the crossroads of functional and evolutionary biology. Herein microorganisms and mammalian cell lines evolve in well-controlled laboratory environments over multiple generations. Phenotypic changes arising from the process are then characterized in genetics and function to understand the evolutionary process. While providing empirical tests to evolutionary questions, such studies also offer opportunities of new insights into proximate mechanisms. Experimental evolution optimizes biological systems by means of adaptation; the adapted systems with their mutations present unique perturbed states of the systems that generate new and often unexpected output/performance. Hence, learning about these states not only adds to but also might deepen knowledge on the proximate processes. To demonstrate this point, five examples in experimental evolution are introduced, and their relevance to functional biology explicated. In some examples, from evolution experiments, updates were made to known proximate processes – gene regulation and cell polarization. In some examples, new contexts were found for known proximate processes – cell division and drug resistance of cancer. In one example, a new cellular mechanism was discovered. These cases identify ways the approach of experimental evolution can be used to ask questions in functional biology.

      PubDate: 2017-11-10T04:15:58Z
  • Production of anthocyanins in metabolically engineered microorganisms:
           Current status and perspectives

    • Abstract: Publication date: Available online 31 October 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Jian Zha, Mattheos A.G. Koffas
      Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes. Here, we review the recent progress on anthocyanin biosynthesis in engineered bacteria, with a special focus on the systematic engineering modifications such as selection and engineering of biosynthetic enzymes, engineering of transportation, regulation of UDP-glucose supply, as well as process optimization. These promising engineering strategies will facilitate successful microbial production of anthocyanins in industry in the near future.

      PubDate: 2017-11-03T18:30:15Z
  • A systems approach using OSMAC, Log P and NMR fingerprinting: An approach
           to novelty

    • Abstract: Publication date: Available online 21 October 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Miaomiao Liu, Tanja Grkovic, Xueting Liu, Jianying Han, Lixin Zhang, Ronald J. Quinn
      The growing number of sequenced microbial genomes has revealed a remarkably large number of secondary metabolite biosynthetic clusters for which the compounds are still unknown. The aim of the present work was to apply a strategy to detect newly induced natural products by cultivating microorganisms in different fermentation conditions. The metabolomic analysis of 4160 fractions generated from 13 actinomycetes under 32 different culture conditions was carried out by 1H NMR spectroscopy and multivariate analysis. The principal component analysis (PCA) of the 1H NMR spectra showed a clear discrimination between those samples within PC1 and PC2. The fractions with induced metabolites that are only produced under specific growth conditions was identified by PCA analysis. This method allows an efficient differentiation within a large dataset with only one fractionation step. This work demonstrates the potential of NMR spectroscopy in combination with metabolomic data analysis for the screening of large sets of fractions.
      Graphical abstract image

      PubDate: 2017-10-27T12:28:08Z
  • Engineering of Yarrowia lipolytica for production of astaxanthin

    • Abstract: Publication date: Available online 20 October 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Kanchana Rueksomtawin Kildegaard, Belén Adiego-Pérez, David Doménech Belda, Jaspreet Kaur Khangura, Carina Holkenbrink, Irina Borodina
      Astaxanthin is a red-colored carotenoid, used as food and feed additive. Astaxanthin is mainly produced by chemical synthesis, however, the process is expensive and synthetic astaxanthin is not approved for human consumption. In this study, we engineered the oleaginous yeast Yarrowia lipolytica for de novo production of astaxanthin by fermentation. First, we screened 12 different Y. lipolytica isolates for β-carotene production by introducing two genes for β-carotene biosynthesis: bi-functional phytoene synthase/lycopene cyclase (crtYB) and phytoene desaturase (crtI) from the red yeast Xanthophyllomyces dendrorhous. The best strain produced 31.1 ± 0.5 mg/L β-carotene. Next, we optimized the activities of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG1) and geranylgeranyl diphosphate synthase (GGS1/crtE) in the best producing strain and obtained 453.9 ± 20.2 mg/L β-carotene. Additional downregulation of the competing squalene synthase SQS1 increased the β-carotene titer to 797.1 ± 57.2 mg/L. Then we introduced β-carotene ketolase (crtW) from Paracoccus sp. N81106 and hydroxylase (crtZ) from Pantoea ananatis to convert β-carotene into astaxanthin. The constructed strain accumulated 10.4 ± 0.5 mg/L of astaxanthin but also accumulated astaxanthin biosynthesis intermediates, 5.7 ± 0.5 mg/L canthaxanthin, and 35.3 ± 1.8 mg/L echinenone. Finally, we optimized the copy numbers of crtZ and crtW to obtain 3.5 mg/g DCW (54.6 mg/L) of astaxanthin in a microtiter plate cultivation. Our study for the first time reports engineering of Y. lipolytica for the production of astaxanthin. The high astaxanthin content and titer obtained even in a small-scale cultivation demonstrates a strong potential for Y. lipolytica-based fermentation process for astaxanthin production.

      PubDate: 2017-10-27T12:28:08Z
  • Rapid evolution of regulatory element libraries for tunable
           transcriptional and translational control of gene expression

    • Abstract: Publication date: Available online 19 October 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Erqing Jin, Lynn Wong, Yun Jiao, Jake Engel, Benjamin Holdridge, Peng Xu
      Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5′UTR, terminator and trans-activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5′UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans-activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.

      PubDate: 2017-10-20T09:54:57Z
  • Protein engineering of oxidoreductases utilizing nicotinamide-based
           coenzymes, with applications in synthetic biology

    • Abstract: Publication date: Available online 6 October 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Chun You, Rui Huang, Xinlei Wei, Zhiguang Zhu, Yi-Heng Percival Zhang
      Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects. This review focuses on the methodology of nicotinamide-based coenzyme engineering, with its application in improving product yields and decreasing production costs. Biomimetic nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural coenzymes. Recent advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this review. Engineering coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering, especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.

      PubDate: 2017-10-13T16:25:26Z
  • Transcription control engineering and applications in synthetic biology

    • Abstract: Publication date: Available online 4 October 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Michael D. Engstrom, Brian F. Pfleger
      In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein), a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity) levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators (cis-factors) were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators (trans-factors), giving examples of how cis- and trans-acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli, we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

      PubDate: 2017-10-05T09:20:21Z
  • Engineering bacteria for enhanced polyhydroxyalkanoates (PHA) biosynthesis

    • Abstract: Publication date: Available online 22 September 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Guo-Qiang Chen, Xiao-Ran Jiang
      Polyhydroxyalkanoates (PHA) have been produced by some bacteria as bioplastics for many years. Yet their commercialization is still on the way. A few issues are related to the difficulty of PHA commercialization: namely, high cost and instabilities on molecular weights (Mw) and structures, thus instability on thermo-mechanical properties. The high cost is the result of complicated bioprocessing associated with sterilization, low conversion of carbon substrates to PHA products, and slow growth of microorganisms as well as difficulty of downstream separation. Future engineering on PHA producing microorganisms should be focused on contamination resistant bacteria especially extremophiles, developments of engineering approaches for the extremophiles, increase on carbon substrates to PHA conversion and controlling Mw of PHA. The concept proof studies could still be conducted on E. coli or Pseudomonas spp. that are easily used for molecular manipulations. In this review, we will use E. coli and halophiles as examples to show how to engineer bacteria for enhanced PHA biosynthesis and for increasing PHA competitiveness.

      PubDate: 2017-09-28T15:37:09Z
  • Fundamental CRISPR-Cas9 tools and current applications in microbial

    • Abstract: Publication date: Available online 8 September 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Pingfang Tian, Jia Wang, Xiaolin Shen, Justin Forrest Rey, Qipeng Yuan, Yajun Yan
      Derived from the bacterial adaptive immune system, CRISPR technology has revolutionized conventional genetic engineering methods and unprecedentedly facilitated strain engineering. In this review, we outline the fundamental CRISPR tools that have been employed for strain optimization. These tools include CRISPR editing, CRISPR interference, CRISPR activation and protein imaging. To further characterize the CRISPR technology, we present current applications of these tools in microbial systems, including model- and non-model industrial microorganisms. Specially, we point out the major challenges of the CRISPR tools when utilized for multiplex genome editing and sophisticated expression regulation. To address these challenges, we came up with strategies that place emphasis on the amelioration of DNA repair efficiency through CRISPR-Cas9-assisted recombineering. Lastly, multiple promising research directions were proposed, mainly focusing on CRISPR-based construction of microbial ecosystems toward high production of desired chemicals.

      PubDate: 2017-09-10T19:46:25Z
  • Engineered polyketides: Synergy between protein and host level engineering

    • Abstract: Publication date: Available online 7 September 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Jesus F. Barajas, Jacquelyn M. Blake-Hedges, Constance B. Bailey, Samuel Curran, Jay. D. Keasling
      Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds. In this review, we discuss PKS engineering efforts applied at both the protein and cellular level for the generation of a diverse range of chemical structures, and we examine future applications of PKSs in the production of medicines, fuels and other industrially relevant chemicals.

      PubDate: 2017-09-10T19:46:25Z
  • On monospecific genera in prokaryotic taxonomy

    • Abstract: Publication date: Available online 2 September 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Guanghong Zuo, Bailin Hao
      A monospecific genus contains a single species ever since it was proposed. Though formally more than half of the known prokaryotic genera are monospecific, we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides. Taking monophyly as a guiding principle, our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes, as provided by the LVTree Viewer and CVTree Web Server, respectively. The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis. Therefore, we refrain from making formal emendations for the time being.

      PubDate: 2017-09-05T16:26:02Z
  • Genome and metabolic engineering in non-conventional yeasts: Current
           advances and applications

    • Abstract: Publication date: Available online 31 August 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Ann-Kathrin Löbs, Cory Schwartz, Ian Wheeldon
      Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisiae is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

      PubDate: 2017-09-05T16:26:02Z
  • Metabolic engineering for the microbial production of isoprenoids:
           Carotenoids and isoprenoid-based biofuels

    • Abstract: Publication date: Available online 30 August 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Fu-Xing Niu, Qian Lu, Yi-Fan Bu, Jian-Zhong Liu
      Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels.

      PubDate: 2017-09-05T16:26:02Z
  • Heterologous biosynthesis of natural product naringenin by co-culture

    • Abstract: Publication date: Available online 26 August 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Vijaydev Ganesan, Zhenghong Li, Xiaonan Wang, Haoran Zhang
      Co-culture engineering is an emerging approach for microbial biosynthesis of a variety of biochemicals. In this study, E. coli-E. coli co-cultures were developed for heterologous biosynthesis of the natural product naringenin. The co-cultures were composed of two independent E. coli strains dedicated to functional expression of different portions of the biosynthetic pathway, respectively. The co-culture biosynthesis was optimized by investigating the effect of carbon source, E. coli strain selection, timing of IPTG induction and the inoculation ratio between the co-culture strains. Compared with the mono-culture strategy, the utilization of the designed co-cultures significantly improved the naringenin production, largely due to the reduction of metabolic stress, employment of proper hosts for improving pathway enzyme activities, and flexible adjustment of the relative biosynthetic strength between the co-culture strains. The findings of this study extend the applicability of co-culture engineering in complex natural product biosynthesis.

      PubDate: 2017-09-05T16:26:02Z
  • Bacterial cell-free expression technology to in vitro systems
           engineering and optimization

    • Abstract: Publication date: Available online 7 August 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Filippo Caschera
      Cell-free expression system is a technology for the synthesis of proteins in vitro. The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.

      PubDate: 2017-08-15T08:32:46Z
  • Systems metabolic engineering strategies for the production of amino acids

    • Abstract: Publication date: Available online 2 August 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Qian Ma, Quanwei Zhang, Qingyang Xu, Chenglin Zhang, Yanjun Li, Xiaoguang Fan, Xixian Xie, Ning Chen
      Systems metabolic engineering is a multidisciplinary area that integrates systems biology, synthetic biology and evolutionary engineering. It is an efficient approach for strain improvement and process optimization, and has been successfully applied in the microbial production of various chemicals including amino acids. In this review, systems metabolic engineering strategies including pathway-focused approaches, systems biology-based approaches, evolutionary approaches and their applications in two major amino acid producing microorganisms: Corynebacterium glutamicum and Escherichia coli, are summarized.

      PubDate: 2017-08-04T21:51:40Z
  • Targeted mutagenesis: A sniper-like diversity generator in microbial

    • Abstract: Publication date: Available online 14 July 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Xiang Zheng, Xin-Hui Xing, Chong Zhang
      Mutations, serving as the raw materials of evolution, have been extensively utilized to increase the chances of engineering molecules or microbes with tailor-made functions. Global and targeted mutagenesis are two main methods of obtaining various mutations, distinguished by the range of action they can cover. While the former one stresses the mining of novel genetic loci within the whole genomic background, targeted mutagenesis performs in a more straightforward manner, bringing evolutionary escape and error catastrophe under control. In this review, we classify the existing techniques of targeted mutagenesis into two categories in terms of whether the diversity is generated in vitro or in vivo, and briefly introduce the mechanisms and applications of them separately. The inherent connections and development trends of the two classes are also discussed to provide an insight into the next generation evolution research.

      PubDate: 2017-07-20T06:51:33Z
  • Characterization of the metallo-dependent amidohydrolases responsible for
           “auxiliary” leucinyl removal in the biosynthesis of 2,2′-bipyridine

    • Abstract: Publication date: Available online 13 July 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Ming Chen, Bo Pang, Ya-nan Du, Yi-peng Zhang, Wen Liu
      2,2′-Bipyridine (2,2′-BiPy) is an attractive core structure present in a number of biologically active natural products, including the structurally related antibiotics caerulomycins (CAEs) and collismycins (COLs). Their biosynthetic pathways share a similar key 2,2′-BiPy-l-leucine intermediate, which is desulfurated or sulfurated at C5, arises from a polyketide synthase/nonribosomal peptide synthetase hybrid assembly line. Focusing on the common off-line modification steps, we here report that the removal of the “auxiliary” l-leucine residue relies on the metallo-dependent amidohydrolase activity of CaeD or ColD. This activity leads to the production of similar 2,2′-BiPy carboxylate products that then receive an oxime functionality that is characteristic for both CAEs and COLs. Unlike many metallo-dependent amidohydrolase superfamily proteins that have been previously reported, these proteins (particularly CaeD) exhibited a strong zinc ion-binding capacity that was proven by site-specific mutagenesis studies to be essential to proteolytic activity. The kinetics of the conversions that respectively involve CaeD and ColD were analyzed, showing the differences in the efficiency and substrate specificity of these two proteins. These findings would generate interest in the metallo-dependent amidohydrolase superfamily proteins that are involved in the biosynthesis of bioactive natural products.

      PubDate: 2017-07-20T06:51:33Z
  • Improvement of pristinamycin I (PI) production in Streptomyces
           pristinaespiralis by metabolic engineering approaches

    • Abstract: Publication date: Available online 8 June 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Jiali Meng, Rongrong Feng, Guosong Zheng, Mei Ge, Yvonne Mast, Wolfgang Wohlleben, Jufang Gao, Weihong Jiang, Yinhua Lu
      Pristinamycin, produced by Streptomyces pristinaespiralis, which is a streptogramin-like antibiotic consisting of two chemically unrelated components: pristinamycin I (PI) and pristinamycin II (PII), shows potent activity against many antibiotic-resistant pathogens. However, so far pristinamycin production titers are still quite low, particularly those of PI. In this study, we constructed a PI single component producing strain by deleting the PII biosynthetic genes (snaE1 and snaE2). Then, two metabolic engineering approaches, including deletion of the repressor gene papR3 and chromosomal integration of an extra copy of the PI biosynthetic gene cluster (BGC), were employed to improve PI production. The final engineered strain ΔPIIΔpapR3/PI produced a maximum PI level of 132 mg/L, with an approximately 2.4-fold higher than that of the parental strain S. pristinaespiralis HCCB10218. Considering that the PI biosynthetic genes are clustered in two main regions in the 210 kb “supercluster” containing the PI and PII biosynthetic genes as well as a cryptic polyketide BGC, these two regions were cloned separately and then were successfully assembled into the PI BGC by the transformation-associated recombination (TAR) system. Collectively, the metabolic engineering approaches employed is very efficient for strain improvement in order to enhance PI titer.

      PubDate: 2017-06-10T22:03:46Z
  • Modules for in vitro metabolic engineering: Pathway assembly for
           bio-based production of value-added chemicals

    • Abstract: Publication date: Available online 7 June 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Hironori Taniguchi, Kenji Okano, Kohsuke Honda
      Bio-based chemical production has drawn attention regarding the realization of a sustainable society. In vitro metabolic engineering is one of the methods used for the bio-based production of value-added chemicals. This method involves the reconstitution of natural or artificial metabolic pathways by assembling purified/semi-purified enzymes in vitro. Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel, enabling easier pathway design with high modularity. Multiple modules have been designed, built, tested, and improved by different groups for different purpose. In this review, we focus on these in vitro metabolic engineering modules, especially focusing on the carbon metabolism, and present an overview of input modules, output modules, and other modules related to cofactor management.

      PubDate: 2017-06-10T22:03:46Z
  • Streptophage-mediated control of off-flavour taint producing
           streptomycetes isolated from barramundi ponds

    • Abstract: Publication date: Available online 2 May 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Jodi Anne Jonns, Peter Richard Brooks, Paul Exley, Sue Poole, D. İpek Kurtböke
      Off-flavour taint of aquaculture products is a global issue reducing consumer confidence in the farmed produce as they are taken up via the gills of fish, and deposited in the lipids of the animal. If the fish are not purged, resulting undesirable muddy earthy flavour taint can be tasted by consumers. These undesirable flavour and odour is caused by the terpenoid compounds namely geosmin and 2-methylisoborneol, produced as secondary metabolites by certain bacteria including the cyanobacteria and actinomycetes. Current strategies to remediate the problem rely on treating the symptoms not the cause and involve the use of time consuming purging methods and costly chemicals. Biological control using bacteriophages, specific to the problem causing bacteria, offers a natural alternative to chemical control, which might reduce further complications of copper based algaecides and its subsequent implications on water quality. In an adaptation of such biological control approach streptomycetes isolated from barramundi ponds were tested for their susceptibility to streptophages to understand whether host destruction via phage lysis would subsequently eliminate off-flavour taint productions by these isolates. Following the determination of the streptophage susceptibility of the isolates one of the most odourous streptomycete species (USC-14510) was selected to be tested further using different pond simulations resembling real-life applications. Geosmin was tested as the indicator of off-flavour taint production and as it has been previously reported that the cyanobacteria-actinomycete interactions occurring in ponds result in even greater levels of geosmin and 2-methylisoborneol, the geosmin levels for the isolate in the presence of cyanobacteria and streptophages were also tested. Findings indicated that the highly odourous Streptomyces species (USC-14510) once infected with streptophages, can lose its capacity to produce off-flavour taints. Pond simulation studies also revealed geosmin production was significantly reduced when streptophages were introduced into the pond water where streptomycete species were grown. The bacteriophage control method developed in the presented study might again confirm significant potential for the bacteriophage-mediated remediation strategy to be adapted by the aquaculture industry.

      PubDate: 2017-05-05T12:03:30Z
  • Rational synthetic combination genetic devices boosting high temperature
           ethanol fermentation

    • Abstract: Publication date: Available online 29 April 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Huan Sun, Haiyang Jia, Jun Li, Xudong Feng, Yueqin Liu, Xiaohong Zhou, Chun Li
      The growth and production of yeast in the industrial fermentation are seriously restrained by heat stress and exacerbated by heat induced oxidative stress. In this study, a novel synthetic biology approach was developed to globally boost the viability and production ability of S. cerevisiae at high temperature through rationally designing and combing heat shock protein (HSP) and superoxide dismutase (SOD) genetic devices to ultimately synergistically alleviate both heat stress and oxidative stress. HSP and SOD from extremophiles were constructed to be different genetic devices and they were preliminary screened by heat resistant experiments and anti-oxidative experiments, respectively. Then in order to customize and further improve thermotolerance of S. cerevisiae, the HSP genetic device and SOD genetic device were rationally combined. The results show the simply assemble of the same function genetic devices to solve heat stress or oxidative stress could not enhance the thermotolerance considerably. Only S. cerevisiae with the combination genetic device (FBA1p-sod-MB4-FBA1p-shsp-HB8) solving both stress showed 250% better thermotolerance than the control and displayed further 55% enhanced cell density compared with the strains with single FBA1p-sod-MB4 or FBA1p-shsp-HB8 at 42 °C. Then the most excellent combination genetic device was introduced into lab S. cerevisiae and industrial S. cerevisiae for ethanol fermentation. The ethanol yields of the two strains were increased by 20.6% and 26.3% compared with the control under high temperature, respectively. These results indicate synergistically defensing both heat stress and oxidative stress is absolutely necessary to enhance the thermotolerance and production of S. cerevisiae.

      PubDate: 2017-05-05T12:03:30Z
  • Systematic assessment of Pichia pastoris system for optimized β
           -galactosidase production

    • Abstract: Publication date: Available online 25 April 2017
      Source:Synthetic and Systems Biotechnology
      Author(s): Hongbing Sun, Olufemi Emmanuel Bankefa, Ijeoma Onyinyechi Ijeoma, Liangtian Miao, Taicheng Zhu, Yin Li

      PubDate: 2017-04-29T19:09:46Z
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