Oriented Fermentation of Food Waste Towards High-Value Products: a Review
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Fungal Evolutionary Genomics Provides Insight Into The
Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes Pierre Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela Aguileta, Damien de Vienne, Ricardo C. Rodriguez de la Vega, Sara Branco, Tatiana Giraud To cite this version: Pierre Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela Aguileta, et al.. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Molecular Ecology, Wiley, 2014, 23 (4), pp.753-773. 10.1111/mec.12631. hal-01302695 HAL Id: hal-01302695 https://hal.archives-ouvertes.fr/hal-01302695 Submitted on 14 Apr 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Molecular Ecology (2014) 23, 753–773 doi: 10.1111/mec.12631 INVITED REVIEWS AND SYNTHESES Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes PIERRE GLADIEUX,*†‡ JEANNE ROPARS,*† HELENE BADOUIN,*† ANTOINE BRANCA,*† GABRIELA AGUILETA,§¶ DAMIEN M. DE VIENNE,§¶** RICARDO C. RODRIGUEZ DE LA VEGA,*† SARA BRANCO‡ -
A Single Gal4-Like Transcription Factor Activates the Crabtree Effect in Komagataella Phaffii
ARTICLE DOI: 10.1038/s41467-018-07430-4 OPEN A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii Özge Ata1,2, Corinna Rebnegger1,3, Nadine E. Tatto1,4,5, Minoska Valli1,4, Teresa Mairinger4,6,8, Stephan Hann4,6, Matthias G. Steiger 1,4,Pınar Çalık 2,7 & Diethard Mattanovich 1,4 The Crabtree phenotype defines whether a yeast can perform simultaneous respiration and fermentation under aerobic conditions at high growth rates. It provides Crabtree positive 1234567890():,; yeasts an evolutionary advantage of consuming glucose faster and producing ethanol to outcompete other microorganisms in sugar rich environments. While a number of genetic events are associated with the emergence of the Crabtree effect, its evolution remains unresolved. Here we show that overexpression of a single Gal4-like transcription factor is sufficient to convert Crabtree-negative Komagataella phaffii (Pichia pastoris) into a Crabtree positive yeast. Upregulation of the glycolytic genes and a significant increase in glucose uptake rate due to the overexpression of the Gal4-like transcription factor leads to an overflow metabolism, triggering both short-term and long-term Crabtree phenotypes. This indicates that a single genetic perturbation leading to overexpression of one gene may have been sufficient as the first molecular event towards respiro-fermentative metabolism in the course of yeast evolution. 1 Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria. 2 Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, 06800 Ankara, Turkey. 3 CD-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria. -
Production of Succinic Acid by E.Coli from Mixtures of Glucose
2005:230 CIV MASTER’S THESIS Production of Succinic Acid by E. coli from Mixtures of Glucose and Fructose ANDREAS LENNARTSSON MASTER OF SCIENCE PROGRAMME Chemical Engineering Luleå University of Technology Department of Chemical Engineering and Geosciences Division of Biochemical and Chemical Engineering 2005:230 CIV • ISSN: 1402 - 1617 • ISRN: LTU - EX - - 05/230 - - SE Abstract Succinic acid, derived from fermentation of renewable feedstocks, has the possibility of replacing petrochemicals as a building block chemical. Another interesting advantage with biobased succinic acid is that the production does not contribute to the accumulation of CO2 to the environment. The produced succinic acid can therefore be considered as a “green” chemical. The bacterium used in this project is a strain of Escherichia coli called AFP184 that has been metabolically engineered to produce succinic acid in large quantities from glucose during anaerobic conditions. The objective with this thesis work was to evaluate whether AFP184 can utilise fructose, both alone and in mixtures with glucose, as a carbon source for the production of succinic acid. Hydrolysis of sucrose yields a mixture of fructose and glucose in equal ratio. Sucrose is a common sugar and the hydrolysate is therefore an interesting feedstock for the production of succinic acid. Fermentations with an initial sugar concentration of 100 g/L were conducted. The sugar ratios used were 100 % fructose, 100 % glucose and a mixture with 50 % fructose and glucose, respectively. The fermentation media used was a lean, low- cost media based on corn steep liquor and a minimal addition of inorganic salts. Fermentations were performed with a 12 L bioreactor and the acid and sugar concentrations were analysed with an HPLC system. -
Complete Genome Sequence and the Expression Pattern of Plasmids Of
Yang et al. Biotechnol Biofuels (2018) 11:125 https://doi.org/10.1186/s13068-018-1116-x Biotechnology for Biofuels RESEARCH Open Access Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose‑utilizing derivatives 8b and 2032 Shihui Yang1,2*† , Jessica M. Vera3†, Jef Grass3, Giannis Savvakis4, Oleg V. Moskvin3, Yongfu Yang1, Sean J. McIlwain3, Yucai Lyu3,8, Irene Zinonos4, Alexander S. Hebert3, Joshua J. Coon3, Donna M. Bates3, Trey K. Sato3, Steven D. Brown5,6,9, Michael E. Himmel7, Min Zhang2, Robert Landick3, Katherine M. Pappas4* and Yaoping Zhang3*† Abstract Background: Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2–8 native plasmids. However, systematic verifcation of predicted Z. mobilis plasmid genes and their contribution to cell ftness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain. Results: In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identifed in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. -
The Formate Channel Foca Exports the Products of Mixed-Acid Fermentation
The formate channel FocA exports the products of mixed-acid fermentation Wei Lü, Juan Du, Nikola J. Schwarzer, Elke Gerbig-Smentek, Oliver Einsle, and Susana L. A. Andrade1 Institute of Organic Chemistry and Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany Edited by Christopher Miller, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, and approved July 10, 2012 (received for review March 11, 2012) Formate is a major metabolite in the anaerobic fermentation of and is then oxidized to CO2 by a periplasmic formate de- glucose by many enterobacteria. It is translocated across cellular hydrogenase, FDH-N or FDH-O, resulting in the generation of membranes by the pentameric ion channel/transporter FocA that, proton motive force (11–13). In addition, the complex pathway together with the nitrite channel NirC, forms the formate/nitrite of mixed-acid fermentation produces acetate, ethanol, lactate, transporter (FNT) family of membrane transport proteins. Here we and succinate as further end products (Fig. 1A). FocA acts as have carried out an electrophysiological analysis of FocA from Sal- a passive exporter for formate anions generated in the cyto- monella typhimurium to characterize the channel properties and plasm, but a remarkable functional switch of transport mode was assess its specificity toward formate and other possible permeat- found for this protein when the pH of the growth medium ing ions. Single-channel currents for formate, hypophosphite and dropped below 6.8 (14). With ample protons available in the nitrite revealed two mechanistically distinct modes of gating that periplasm, the cell switches to active import of formate and reflect different types of structural rearrangements in the trans- again uses FocA for the task. -
Diversity and Adaptive Evolution of Saccharomyces Wine Yeast: a Review Souhir Marsit, Sylvie Dequin
Diversity and adaptive evolution of Saccharomyces wine yeast: a review Souhir Marsit, Sylvie Dequin To cite this version: Souhir Marsit, Sylvie Dequin. Diversity and adaptive evolution of Saccharomyces wine yeast: a review. FEMS Yeast Research, Oxford University Press (OUP), 2015, 15 (7), 12 p. 10.1093/femsyr/fov067. hal-01837757 HAL Id: hal-01837757 https://hal.archives-ouvertes.fr/hal-01837757 Submitted on 28 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. FEMS Yeast Research, 15, 2015, fov067 doi: 10.1093/femsyr/fov067 Advance Access Publication Date: 23 July 2015 Minireview MINIREVIEW Diversity and adaptive evolution of Saccharomyces wine yeast: a review Souhir Marsit1,2,3 and Sylvie Dequin1,2,3,∗ 1INRA, UMR1083, SPO, F-34060 Montpellier, France, 2Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France and 3Montpellier University, UMR1083, SPO, F-34060 Montpellier, France ∗ Corresponding author: Institut national de la recherche agronomique, Unite´ mixte de recherche Sciences pour l’œnologie, 2 place Viala, Montpellier, 34060, France. Tel: +33-4-99-61-25-28; Fax: +33-4-99-61-28-57; E-mail: [email protected] One sentence summary: This review summarizes current knowledge and recent advances on the diversity and evolutionary history of Saccharomyces cerevisiae wine yeasts, focusing on the domestication fingerprints identified in these strains. -
Aneuploidy and Ethanol Tolerance in Saccharomyces Cerevisiae
fgene-10-00082 February 11, 2019 Time: 16:56 # 1 ORIGINAL RESEARCH published: 12 February 2019 doi: 10.3389/fgene.2019.00082 Aneuploidy and Ethanol Tolerance in Saccharomyces cerevisiae Miguel Morard1,2, Laura G. Macías1,2, Ana C. Adam2, María Lairón-Peris2, Roberto Pérez-Torrado2, Christina Toft1,2† and Eladio Barrio1,2* 1 Departament de Genètica, Universitat de València, Valencia, Spain, 2 Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Valencia, Spain Response to environmental stresses is a key factor for microbial organism growth. One of the major stresses for yeasts in fermentative environments is ethanol. Saccharomyces cerevisiae is the most tolerant species in its genus, but intraspecific ethanol-tolerance variation exists. Although, much effort has been done in the last years to discover evolutionary paths to improve ethanol tolerance, this phenotype is still hardly Edited by: Ed Louis, understood. Here, we selected five strains with different ethanol tolerances, and used University of Leicester, comparative genomics to determine the main factors that can explain these phenotypic United Kingdom differences. Surprisingly, the main genomic feature, shared only by the highest ethanol- Reviewed by: tolerant strains, was a polysomic chromosome III. Transcriptomic data point out that Alfredo Ghezzi, University of Puerto Rico, Río Piedras chromosome III is important for the ethanol stress response, and this aneuploidy can Campus, Puerto Rico be an advantage to respond rapidly to ethanol stress. We found that chromosome III Juan Lucas Argueso, Colorado State University, copy numbers also explain differences in other strains. We show that removing the United States extra chromosome III copy in an ethanol-tolerant strain, returning to euploidy, strongly *Correspondence: compromises its tolerance. -
Accelerated Electro-Fermentation of Acetoin in Escherichia Coli by Identifying Physiological Limitations of the Electron Transfer Kinetics and the Central Metabolism
microorganisms Article Accelerated Electro-Fermentation of Acetoin in Escherichia coli by Identifying Physiological Limitations of the Electron Transfer Kinetics and the Central Metabolism 1, 1 1,2, Sebastian Beblawy y, Laura-Alina Philipp and Johannes Gescher * 1 Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany; [email protected] (S.B.); [email protected] (L.-A.P.) 2 Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany * Correspondence: [email protected] Current affiliation: Environmental Biotechnology, Centre for Applied Geosciences, University of Tübingen, y Schnarrenbergstr. 94-96, 72074 Tübingen, Germany. Received: 25 September 2020; Accepted: 21 November 2020; Published: 23 November 2020 Abstract: Anode-assisted fermentations offer the benefit of an anoxic fermentation routine that can be applied to produce end-products with an oxidation state independent from the substrate. The whole cell biocatalyst transfers the surplus of electrons to an electrode that can be used as a non-depletable electron acceptor. So far, anode-assisted fermentations were shown to provide high carbon efficiencies but low space-time yields. This study aimed at increasing space-time yields of an Escherichia coli-based anode-assisted fermentation of glucose to acetoin. The experiments build on an obligate respiratory strain, that was advanced using selective adaptation and targeted strain development. Several transfers under respiratory conditions led to point mutations in the pfl, aceF and rpoC gene. These mutations increased anoxic growth by three-fold. Furthermore, overexpression of genes encoding a synthetic electron transport chain to methylene blue increased the electron transfer rate by 2.45-fold. -
An Evolutionary Perspective on the Crabtree Effect
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector PERSPECTIVE ARTICLE published: 21 October 2014 MOLECULAR BIOSCIENCES doi: 10.3389/fmolb.2014.00017 An evolutionary perspective on the Crabtree effect Thomas Pfeiffer* and Annabel Morley New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand Edited by: The capability to ferment sugars into ethanol is a key metabolic trait of yeasts. Thomas Nägele, University of Crabtree-positive yeasts use fermentation even in the presence of oxygen, where they Vienna, Austria could, in principle, rely on the respiration pathway. This is surprising because fermentation Reviewed by: has a much lower ATP yield than respiration (2 ATP vs. approximately 18 ATP per Luciana Hannibal, Cleveland Clinic, USA glucose). While genetic events in the evolution of the Crabtree effect have been identified, Bas Teusink, VU University the selective advantages provided by this trait remain controversial. In this review we Amsterdam, Netherlands analyse explanations for the emergence of the Crabtree effect from an evolutionary and *Correspondence: game-theoretical perspective. We argue that an increased rate of ATP production is likely Thomas Pfeiffer, New Zealand the most important factor behind the emergence of the Crabtree effect. Institute for Advanced Study, Massey University, Private Bag Keywords: yeast energy metabolism, Crabtree effect, evolution of metabolism, respiro-fermentation, evolutionary 102904, North Shore Mail Centre, game theory Auckland 0745, New Zealand e-mail: [email protected] INTRODUCTION all organisms (Berg et al., 2002). In the initial reactions of Adenosine triphosphate (ATP) is a key compound in cellular glycolysis, 2 ATP are consumed per glucose, and the result- energy metabolism, where it drives free-energy dependent pro- ing fructose 1,6-bisphosphate is transformed into two 3-carbon cesses such as motion, transport, biosynthesis and growth. -
Elucidating Flux Regulation of the Fermentation Modes of Lactococcus Lactis a Mutlilevel Study
Downloaded from orbit.dtu.dk on: Oct 10, 2021 Elucidating Flux Regulation of the Fermentation Modes of Lactococcus lactis A Mutlilevel Study Chan, Siu Hung Joshua Link to article, DOI: 10.11581/DTU:00000016 Publication date: 2014 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Chan, S. H. J. (2014). Elucidating Flux Regulation of the Fermentation Modes of Lactococcus lactis: A Mutlilevel Study. Technical University of Denmark. https://doi.org/10.11581/DTU:00000016 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Elucidating Flux Regulation of the Fermentation Modes of Lactococcus lactis: A Mutlilevel Study PhD Thesis Siu Hung Joshua Chan November, 2014 Supervisors: Associate Professor Christian Solem Professor Peter Ruhdal Jensen Systems Biotechnology and Biorefining National Food Institute Technical University of Denmark Summary The long history of application to the dairy industry has established Lactococcus lactis (L. -
On-Line Analysis and in Situ Ph Monitoring of Mixed Acid Fermentation by Escherichia Coli Using Combined FTIR and Raman Techniques
This is a repository copy of On-line analysis and in situ pH monitoring of mixed acid fermentation by Escherichia coli using combined FTIR and Raman techniques. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/164855/ Version: Published Version Article: Metcalfe, G.D., Smith, T.W. and Hippler, M. orcid.org/0000-0002-3956-3922 (2020) On-line analysis and in situ pH monitoring of mixed acid fermentation by Escherichia coli using combined FTIR and Raman techniques. Analytical and Bioanalytical Chemistry. ISSN 1618-2642 https://doi.org/10.1007/s00216-020-02865-5 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Analytical and Bioanalytical Chemistry https://doi.org/10.1007/s00216-020-02865-5 RESEARCH PAPER On-line analysis and in situ pH monitoring of mixed acid fermentation by Escherichia coli using combined FTIR and Raman techniques George D. Metcalfe1 & Thomas W. Smith1,2 & Michael Hippler1 Received: 27 May 2020 /Revised: 23 July 2020 /Accepted: 5 August 2020 # The Author(s) 2020 Abstract We introduce an experimental setup allowing continuous monitoring of bacterial fermentation processes by simultaneous optical density (OD) measurements, long-path FTIR headspace monitoring of CO2, acetaldehyde and ethanol, and liquid Raman spectroscopy of acetate, formate, and phosphate anions, without sampling. -
Redalyc.EFFECT of AERATION on the FERMENTATIVE ACTIVITY OF
Revista Mexicana de Ingeniería Química ISSN: 1665-2738 [email protected] Universidad Autónoma Metropolitana Unidad Iztapalapa México Estela-Escalante, W.; Rychtera, M.; Melzoch, K.; Hatta-Sakoda, B. EFFECT OF AERATION ON THE FERMENTATIVE ACTIVITY OF Saccharomyces cerevisiae CULTURED IN APPLE JUICE Revista Mexicana de Ingeniería Química, vol. 11, núm. 2, 2012, pp. 211-226 Universidad Autónoma Metropolitana Unidad Iztapalapa Distrito Federal, México Available in: http://www.redalyc.org/articulo.oa?id=62026895002 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Revista Mexicana deIngenier´ıaQu´ımica Academia Mexicana de Investigaci´ony Docencia en Ingenier´ıaQu´ımica, A.C. Revista Mexicana de Ingeniería Química Volumen 11, N´umero2, Agosto 2012 ISSN 1665-2738 Vol. 11,CONTENIDO No. 2 (2012) 211-226 1 EFFECT OF AERATION ON THE FERMENTATIVE ACTIVITY OF Saccharomyces Volumen 8, número cerevisiae3, 2009 / VolumeCULTURED 8, number IN 3, APPLE 2009 JUICE 1 ´ EFECTO DE LA AIREACION EN LA ACTIVIDAD FERMENTATIVA DE Saccharomyces cerevisiae CULTIVADO EN JUGO DE MANZANA 213 Derivation and application of the Stefan-Maxwell equations W. Estela-Escalante1;3∗, M. Rychtera1, K. Melzoch1 and B. Hatta-Sakoda2 1Department (Desarrollo of Fermentation y aplicación Chemistry de las ecuaciones and Bioengineering, de Stefan-Maxwell) Faculty of Food and Biochemical Engineering. Institute of Stephen ChemicalWhitaker Technology Prague. Technick´a5, 166 28. Praha 6, Dejvice. Czech Republic. 2 Facultad de Ingenier´ıade Industrias Alimentarias, Universidad Nacional Agraria La Molina.