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15. Author Correction: Building a global alliance of biofoundries.

Author

Hillson, Nathan, Caddick, Mark, Cai, Yizhi, Carrasco, Jose A, Chang, Matthew Wook, Curach, Natalie C, Bell, David J, Feuvre, Rosalind Le, Friedman, Douglas C, Fu, Xiongfei, Gold, Nicholas D, Herrgård, Markus J, Holowko, Maciej B, Johnson, James R, Johnson, Richard A, Keasling, Jay D, Kitney, Richard I, Kondo, Akihiko, Liu, Chenli, Martin, Vincent JJ, Menolascina, Filippo, Ogino, Chiaki, Patron, Nicola J, Pavan, Marilene, Poh, Chueh Loo, Pretorius, Isak S, Rosser, Susan J, Scrutton, Nigel S, Storch, Marko, Tekotte, Hille, Travnik, Evelyn, Vickers, Claudia E, Yew, Wen Shan, Yuan, Yingjin, Zhao, Huimin, and Freemont, Paul S

Subjects
MD Multidisciplinary
Abstract

The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Advanced Biomanufacturing, University of Queensland.'. The correct version replaces this with '(15) Australian Foundry for Advanced Biomanufacturing (AusFAB), University of Queensland and (16) Australian Genome Foundry, Macquarie University'. This has been corrected in both the PDF and HTML versions of the Comment.

Published
2019

16. Building a global alliance of biofoundries.

Author

Hillson, Nathan, Caddick, Mark, Cai, Yizhi, Carrasco, Jose A, Chang, Matthew Wook, Curach, Natalie C, Bell, David J, Le Feuvre, Rosalind, Friedman, Douglas C, Fu, Xiongfei, Gold, Nicholas D, Herrgård, Markus J, Holowko, Maciej B, Johnson, James R, Johnson, Richard A, Keasling, Jay D, Kitney, Richard I, Kondo, Akihiko, Liu, Chenli, Martin, Vincent JJ, Menolascina, Filippo, Ogino, Chiaki, Patron, Nicola J, Pavan, Marilene, Poh, Chueh Loo, Pretorius, Isak S, Rosser, Susan J, Scrutton, Nigel S, Storch, Marko, Tekotte, Hille, Travnik, Evelyn, Vickers, Claudia E, Yew, Wen Shan, Yuan, Yingjin, Zhao, Huimin, and Freemont, Paul S

Subjects
Organisms, Genetically Modified, Genetic Engineering, Biotechnology, Biomedical Research, International Cooperation, Organisms, Genetically Modified, MD Multidisciplinary
Abstract

Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has recently been established to coordinate activities worldwide.

Published
2019

27. Editing Streptomyces genome using target AID system fused with UGI‐degradation tag.

Author

Apriliana, Pamella, Kahar, Prihardi, Kashiwagi, Norimasa, Kondo, Akihiko, and Ogino, Chiaki

Subjects
CRISPRS, CYTIDINE deaminase, STREPTOMYCES coelicolor, GENE expression, SEA lamprey, IMMUNOGLOBULIN class switching
Abstract

The utilization of Streptomyces as a microbial chassis for developing innovative drugs and medicinal compounds showcases its capability to produce bioactive natural substances. Recent focus on the clustered regularly interspaced short palindromic repeat (CRISPR) technology highlights its potential in genome editing. However, applying CRISPR technology in certain microbial strains, particularly Streptomyces, encounters specific challenges. These challenges include achieving efficient gene expression and maintaining genetic stability, which are critical for successful genome editing. To overcome these obstacles, an innovative approach has been developed that combines several key elements: activation‐induced cytidine deaminase (AID), nuclease‐deficient cas9 variants (dCas9), and Petromyzon marinus cytidine deaminase 1 (PmCDA1). In this study, this novel strategy was employed to engineer a Streptomyces coelicolor strain. The target gene was actVA‐ORF4 (SCO5079), which is involved in actinorhodin production. The engineering process involved introducing a specific construct [pGM1190‐dcas9‐pmCDA‐UGI‐AAV‐actVA‐ORF4 (SCO5079)] to create a CrA10 mutant strain. The resulting CrA10 mutant strain did not produce actinorhodin. This outcome highlights the potential of this combined approach in the genetic manipulation of Streptomyces. The failure of the CrA10 mutant to produce actinorhodin conclusively demonstrates the success of gene editing at the targeted site, affirming the effectiveness of this method for precise genetic modifications in Streptomyces. [ABSTRACT FROM AUTHOR]

Published
2024
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41. Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation.

Author

Pangestu, Radityo, Kahar, Prihardi, Ogino, Chiaki, and Kondo, Akihiko

Abstract

While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose‐derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement. Take‐away: Increasing cell density enhances glycolysis and energy metabolism.Lactic acid generation in flocculent yeast is less dependent on cell density.Flocculation provides protection against acid and other chemical stresses. [ABSTRACT FROM AUTHOR]

Published
2024
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43. Saccharification of pretreated empty bunch by concentrated xylanase and assisted by cellulase.

Author

Wijaya, Hans, Kahar, Prihardi, Sasaki, Kengo, Rahmani, Nanik, Hermiati, Euis, Yopi, Ogino, Chiaki, Prasetya, Bambang, Simarmata, Rumella, Christita, Margaretta, and Kondo, Akihiko

Subjects
CELLULASE, XYLANASES, MEMBRANE separation, ETHANOL, LIGNOCELLULOSE, FILTER paper, SACCHAROMYCES cerevisiae, NANOFILTRATION
Abstract

The effect of the membrane separation process to concentrate the xylanase was tested to restrict cellulase dosage on the lignocellulosic waste. Xylanase produced from Streptomyces lividans expressing an endo-xylanase gene from Kitasatospora sp. was concentrated by nanofiltration membrane NTR-7410. This resulted in a seven-fold increase in xylanase activity without changing its specific activity. The saccharification of dilute acid-pretreated empty fruit bunch (EFB) was performed by applying membrane-concentrated xylanase compared with its un-concentrated to commercial cellulase loaded at one filter paper unit/g-biomass. Both glucose and xylose yields obtained by using concentrated xylanase (19.49% and 41.51%, respectively) were higher compared to un-concentrated xylanase (11.71% and 28.71%, respectively). Xylose-assimilating Saccharomyces cerevisiae yeast at initial of 0.5 g/L was then inoculated into the sugar solutions. The yeast had increased ethanol titer and productivity from sugars obtained by using membrane-concentrated xylanase (7.13±0.60 g/L and 0.59±0.06 g/L/h, respectively), compared by using un-concentrated xylanase (4.56±0.43 g/L and 0.38±0.02 g/L/h, respectively). [ABSTRACT FROM AUTHOR]

Published
2023
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