101
|
Effect of ammonium in medium on ansamitocin P-3 production by Actinosynnema pretiosum. BIOTECHNOL BIOPROC E 2010. [DOI: 10.1007/s12257-009-3054-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
102
|
Gallo G, Renzone G, Alduina R, Stegmann E, Weber T, Lantz AE, Thykaer J, Sangiorgi F, Scaloni A, Puglia AM. Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina. Proteomics 2010; 10:1336-58. [DOI: 10.1002/pmic.200900175] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
103
|
Computational analysis of phenotypic space in heterologous polyketide biosynthesis—Applications to Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. J Theor Biol 2010; 262:197-207. [DOI: 10.1016/j.jtbi.2009.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 10/05/2009] [Accepted: 10/06/2009] [Indexed: 11/21/2022]
|
104
|
Maiti SK, Singh KP, Lantz AE, Bhushan M, Wangikar PP. Substrate uptake, phosphorus repression, and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation. Biotechnol Bioeng 2010; 105:109-20. [DOI: 10.1002/bit.22505] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
105
|
Yang YH, Song E, Park SH, Kim JN, Lee K, Kim E, Kim YG, Kim BG. Loss of phosphomannomutase activity enhances actinorhodin production in Streptomyces coelicolor. Appl Microbiol Biotechnol 2009; 86:1485-92. [PMID: 20024545 DOI: 10.1007/s00253-009-2368-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 11/11/2009] [Accepted: 11/13/2009] [Indexed: 11/30/2022]
Abstract
Phosphomannomutase (ManB), whose main function is the conversion of mannose-6-phosphate to mannose-1-phosphate, is involved in biosynthesis of GDP-mannose for numerous processes such as synthesis of structural carbohydrates, production of alginates and ascorbic acid, and post-translational modification of proteins in prokaryotes and eukaryotes. ManB isolated from Streptomyces coelicolor was shown to have both phosphomannomutase and phosphoglucomutase activities. Deletion of manB in S. coelicolor caused a dramatic increase in actinorhodin (ACT) production in the low-glucose Difco nutrient (DN) medium, whereas the wild-type strain did not produce ACT on this medium. Experiments involving complementation of the manB deletion showed that increased ACT production in DN media was due to blockage of phosphomannomutase activity rather than phosphoglucomutase activity. This result therefore provides useful information for the design of strategies that enhance antibiotic production through the control of carbon flux.
Collapse
Affiliation(s)
- Yung-Hun Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | | | | | | | | | | | | | | |
Collapse
|
106
|
Sumarah MW, Miller JD. Anti-Insect Secondary Metabolites from Fungal Endophytes of Conifer Trees. Nat Prod Commun 2009. [DOI: 10.1177/1934578x0900401112] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Choristoneura fumiferana is the most economically-important insect pest in eastern North America. Historically, strategies to control epidemics have relied on chemical pesticides that are no longer approved for use. The presence of fungal endophytes in cool area grass species and their role in reducing the impact of herbivorous insects is well understood. Recent work has demonstrated that foliar endophytes of conifers also produce anti-insect toxins. Field and nursery studies testing trees infected with the rugulosin producing endophyte Phialocephala scopiformis reduced the growth and development of C. fumiferana. The study of foliar endophytes from a variety of conifers including: Picea mariana, P. rubens and P. glauca as well as Abies balsamea and Larix laricina for the discovery of other anti-insect toxins are discussed. These endophytes are horizontally transmitted thus they are not present in nursery seedlings. Inoculating seedlings with toxigenic endophyte strains has been demonstrated to be effective in providing the tree with tolerance to herbivorous insects.
Collapse
Affiliation(s)
- Mark W. Sumarah
- Ottawa-Carleton Institute of Chemistry, Carleton University, Ottawa, Ontario, K1S 5B6, Canada
| | - J. David Miller
- Ottawa-Carleton Institute of Chemistry, Carleton University, Ottawa, Ontario, K1S 5B6, Canada
| |
Collapse
|
107
|
Chorin A, Bijeire L, Monje M, Baziard G, Lebrihi A, Mathieu F. Expression of pyrrothineN-acyltransferase activities inSaccharothrix algeriensisNRRL B-24137: new insights into dithiolopyrrolone antibiotic biosynthetic pathway. J Appl Microbiol 2009; 107:1751-62. [DOI: 10.1111/j.1365-2672.2009.04496.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
108
|
Woolley JF, Al-Rubeai M. The isolation and identification of a secreted biomarker associated with cell stress in serum-free CHO cell culture. Biotechnol Bioeng 2009; 104:590-600. [PMID: 19544303 DOI: 10.1002/bit.22408] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
One approach to improving mammalian culture productivity has been to reduce cell stress and cell death in the bioreactor, thus enhancing productivity through a longer phase of viability. Here we describe the isolation and identification of a biomarker for stress and viability loss in CHO culture. Using SELDI-TOF mass spectrometry to profile the protein component of supernatant culture media we have identified a peak at 7.7 kDa that was associated with loss of viability toward the end of the culture and simulated stress from both toxic metabolite accumulation and nutrient depletion. The relative intensity (signal/noise ratio) of the peak increased rapidly at the onset of dropping viability toward the end of the growth phase. Also, the peak height was seen to increase significantly when cells were grown under conditions emulating ammonia accumulation and glutamine deprivation. The species has been identified as a fragment of Galectin-1 (Gal-1) via MS/MS fingerprinting. We propose that this peak could be utilized as a marker for early onset of stress in cell culture. This work demonstrates the efficacy of SELDI technology to identify biomarkers in mammalian cell culture and highlights its value as a tool for the monitoring and improvement of culture processes.
Collapse
Affiliation(s)
- John F Woolley
- School of Chemical and Bioprocess Engineering, and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | | |
Collapse
|
109
|
Santos VC, Pereira JFB, Haga RB, Rangel-Yagui CO, Teixeira JAC, Converti A, Pessoa A. Stability of clavulanic acid under variable pH, ionic strength and temperature conditions. A new kinetic approach. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.02.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
110
|
Zerikly M, Challis GL. Strategies for the discovery of new natural products by genome mining. Chembiochem 2009; 10:625-33. [PMID: 19165837 DOI: 10.1002/cbic.200800389] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Natural products have a very broad spectrum of applications. Many natural products are used clinically as antibacterial, antifungal, antiparasitic, anticancer and immunosuppressive agents and are therefore of utmost importance for our society. When in the 1940s the golden age of antibiotics was ushered in, a "gold rush fever" of natural product discovery in the pharmaceutical industry ensued for many decades. However, the traditional process of discovering new bioactive natural products is generally long and laborious, and known natural products are frequently rediscovered. A mass-withdrawal of pharmaceutical companies from new natural product discovery and natural products research has thus occurred in recent years. In this article, the concept of genome mining for novel natural product discovery, which promises to provide a myriad of new bioactive natural compounds, is summarized and discussed. Genome mining for new natural product discovery exploits the huge and constantly increasing quantity of DNA sequence data from a wide variety of organisms that is accumulating in publicly accessible databases. Genes encoding enzymes likely to be involved in natural product biosynthesis can be readily located in sequenced genomes by use of computational sequence comparison tools. This information can be exploited in a variety of ways in the search for new bioactive natural products.
Collapse
Affiliation(s)
- Malek Zerikly
- Department of Chemistry, University of Warwick, Coventry, UK
| | | |
Collapse
|
111
|
Hu C, Zou Y, Zhao W. Effect of soybean oil on the production of mycelial biomass and pleuromutilin in the shake-flask culture of Pleurotus mutilis. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0064-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
112
|
Danchin A. Bacteria as computers making computers. FEMS Microbiol Rev 2009; 33:3-26. [PMID: 19016882 PMCID: PMC2704931 DOI: 10.1111/j.1574-6976.2008.00137.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 09/20/2008] [Accepted: 09/21/2008] [Indexed: 12/13/2022] Open
Abstract
Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.
Collapse
Affiliation(s)
- Antoine Danchin
- Génétique des Génomes Bactériens, Institut Pasteur, Paris, France.
| |
Collapse
|
113
|
Skálová T, Dohnálek J, Østergaard LH, Østergaard PR, Kolenko P, Dušková J, Štěpánková A, Hašek J. The Structure of the Small Laccase from Streptomyces coelicolor Reveals a Link between Laccases and Nitrite Reductases. J Mol Biol 2009; 385:1165-78. [DOI: 10.1016/j.jmb.2008.11.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 11/13/2008] [Accepted: 11/15/2008] [Indexed: 01/17/2023]
|
114
|
Heide L. Aminocoumarins mutasynthesis, chemoenzymatic synthesis, and metabolic engineering. Methods Enzymol 2009; 459:437-55. [PMID: 19362650 DOI: 10.1016/s0076-6879(09)04618-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The aminocoumarin antibiotics novobiocin, clorobiocin and coumermycin A(1) are formed by different Streptomyces strains and are potent inhibitors of bacterial gyrase. Their biosynthetic gene clusters have been analyzed in detail by genetic and biochemical investigations. Heterologous expression of these gene clusters by site-specific integration into the genome of the fully sequenced host Streptomyces coelicolor A3(2) readily results in an accumulation of the antibiotics in yields similar to the wildtype strains. In recent years, the aminocoumarins have developed into a model system for the generation of new antibiotics by genetic methods. Prior to heterologous expression in S. coelicolor, cosmids containing the complete biosynthetic clusters can be manipulated in Escherichia coli by lambda RED-mediated recombination, creating single or multiple gene replacements or gene deletions. Thereby, mutant strains are generated which are blocked in the synthesis of certain intermediates or in specific tailoring reactions. For instance, mutasynthetic experiments can subsequently be carried out to generate aminocoumarin antibiotics that contain modified acyl moieties attached to the aminocoumarin core, and chemoenzymatic synthesis can be employed for the acylation of the deoxysugar moiety of structural analogues of the aminocoumarin antibiotics. Metabolic engineering-the combination of gene deletions and foreign gene expression via replicative expression vectors-can be used to generate further structural variants of these antibiotics. These methods can be combined, allowing the generation of a wide variety of new compounds. This chapter may provide general pointers for the use of genetic methods in the generation of new antibiotics.
Collapse
Affiliation(s)
- Lutz Heide
- Pharmazeutische Biologie, Pharmazeutisches Institut, Universität Tübingen, Tübingen, Germany
| |
Collapse
|
115
|
|
116
|
De novo biosynthetic pathways: rational design of microbial chemical factories. Curr Opin Biotechnol 2008; 19:468-74. [PMID: 18725289 DOI: 10.1016/j.copbio.2008.07.009] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 07/25/2008] [Accepted: 07/29/2008] [Indexed: 12/18/2022]
Abstract
Increasing interest in the production of organic compounds from non-petroleum-derived feedstocks, especially biomass, is a significant driver for the construction of new recombinant microorganisms for this purpose. As a discipline, Metabolic Engineering has provided a framework for the development of such systems. Efforts have traditionally been focused, first, on the optimization of natural producers, later progressing towards re-construction of natural pathways in heterologous hosts. To maximize the potential of microbes for biosynthetic purposes, new tools and methodologies within Metabolic Engineering are needed for the proposition and construction of de novo designed pathways. This review will focus on recent advances towards the design and assembly of biosynthetic pathways, and provide a Synthetic Biology perspective for the construction of microbial chemical factories.
Collapse
|
117
|
Chen GQ, Lu FP, Du LX. Natamycin production by Streptomyces gilvosporeus based on statistical optimization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:5057-5061. [PMID: 18537260 DOI: 10.1021/jf800479u] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Natamycin has been widely used as a natural preservative to prevent mold contamination in food. In this study, statistically based experimental designs were employed for the optimization of medium components for natamycin production by Streptomyces gilvosporeus. After glucose, yeast extract, and soy peptone were screened as suitable carbon and nitrogen sources, a full factorial design was used to evaluate the effects of various factors on natamycin production. Glucose and pH were identified as having significant effects (with confidence level >90%). Glucose concentration and initial pH were subsequently optimized by use of a central composite design. The result indicated that glucose and pH had a significant interactive effect on natamycin production. The optimal glucose concentration and initial pH value were 38.2 g/L and 7.8, respectively. This optimization strategy led to a natamycin yield of 2.45 g/L, which was nearly 90% higher than that in the original medium.
Collapse
Affiliation(s)
- Guan-Qun Chen
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, 29 Thirteenth Avenue, TEDA, Tianjin 300457, China.
| | | | | |
Collapse
|