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Liu J, Yang J, Yuan L, Wu C, Jiang Y, Zhuang W, Ying H, Yang S. Modulated Arabinose Uptake and cAMP Signaling Synergistically Improve Glucose and Arabinose Consumption in Recombinant Yeast. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12797-12806. [PMID: 37592391 DOI: 10.1021/acs.jafc.3c04386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
During the production of ethanol from lignocellulose-derived sugars, recombinant yeasts tend to utilize xylose and arabinose after glucose exhaustion. So far, many glucose-insensitive pentose transporters have been reported to counteract this phenomenon, but few studies have described intracellular factors. In this study, the combination of adaptive evolution, comparative genomics, and genetic complementation revealed that the hexokinase-deficient (Hxk0) arabinose-fermenting Saccharomyces cerevisiae requires the arabinose transporter variant Gal2-N376T and the mutations of guanine nucleotide exchange factor Cdc25 to overcome glucose restriction during arabinose assimilation. The results showed that the Hxk0 recombinant yeasts could lower the metabolic/physiological threshold of cell proliferation by downregulating the intracellular cAMP levels, resulting in smaller cells and increased arabinose assimilation under glucose restriction. In the medium containing 80 g/L glucose and 20 g/L arabinose, the evolved strain restoring the hexokinase activity completed fermentation at 22 h, compared to 24 h for the parental strain. Overall, the experimental results provide new insights into glucose repression of biorefinery yeasts.
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Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Junjie Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lihua Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunhua Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
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Bowman EK, Nguyen Hoang PT, Gordillo Sierra AR, Vieira Nogueira KM, Alper HS. Temporal sorting of microdroplets can identify productivity differences of itaconic acid from libraries of Yarrowia lipolytica. LAB ON A CHIP 2023; 23:2249-2256. [PMID: 37013836 DOI: 10.1039/d3lc00020f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microdroplet screening of microorganisms can improve the rate of strain selection and characterization within the canonical design-build-test paradigm. However, a full analysis of the microdroplet environment and how well these conditions translate to culturing conditions and techniques is lacking in the field. Quantification of three different biosensor/analyte combinations at 12 hour timepoints reveals the potential for extended dose-response ranges as compared to traditional in vitro conditions. Using these dynamics, we present an application and analysis of microfluidic droplet screening utilizing whole-cell biosensors, ultimately identifying an altered productivity profile of itaconic acid in a Yarrowia lipolytica-based piggyBac transposon library. Specifically, we demonstrate that the timepoint for microdroplet selection can influence the outcome of the selection and thus shift the identified strain productivity and final titer. In this case, strains selected at earlier timepoints showed increased early productivity in flask scale, with the converse true as well. Differences in response indicate microdroplet assays require tailored development to more accurately sort for phenotypes that are scalable to larger incubation volumes. Likewise, these results further highlight that screening conditions are critical parameters for success in high-throughput applications.
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Affiliation(s)
- Emily K Bowman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA.
| | | | - Angela R Gordillo Sierra
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Karoline M Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Hal S Alper
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA.
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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Dijamentiuk A, Mangavel C, Elfassy A, Michaux F, Burgain J, Rondags E, Delaunay S, Ferrigno S, Revol-Junelles AM, Borges F. Invert emulsions alleviate biotic interactions in bacterial mixed culture. Microb Cell Fact 2023; 22:16. [PMID: 36670385 PMCID: PMC9854087 DOI: 10.1186/s12934-022-02014-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
The large application potential of microbiomes has led to a great need for mixed culture methods. However, microbial interactions can compromise the maintenance of biodiversity during cultivation in a reactor. In particular, competition among species can lead to a strong disequilibrium in favor of the fittest microorganism. In this study, an invert emulsion system was designed by dispersing culture medium in a mixture of sunflower oil and the surfactant PGPR. Confocal laser scanning microscopy revealed that this system allowed to segregate microorganisms in independent droplets. Granulomorphometric analysis showed that the invert emulsion remains stable during at least 24 h, and that the introduction of bacteria did not have a significant impact on the structure of the invert emulsion. A two-strain antagonistic model demonstrated that this invert emulsion system allows the propagation of two strains without the exclusion of the less-fit bacterium. The monitoring of single-strain cultures of bacteria representative of a cheese microbiota revealed that all but Brevibacterium linens were able to grow. A consortium consisting of Lactococcus lactis subsp. lactis biovar diacetylactis, Streptococcus thermophilus, Leuconostoc mesenteroides, Staphylococcus xylosus, Lactiplantibacillus plantarum and Carnobacterium maltaromaticum was successfully cultivated without detectable biotic interactions. Metabarcoding analysis revealed that the system allowed a better maintenance of alpha diversity and produced a propagated bacterial consortium characterized by a structure closer to the initial state compared to non-emulsified medium. This culture system could be an important tool in the field of microbial community engineering.
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Affiliation(s)
- Alexis Dijamentiuk
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Florentin Michaux
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Jennifer Burgain
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Emmanuel Rondags
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Stéphane Delaunay
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Sandie Ferrigno
- grid.29172.3f0000 0001 2194 6418IECL, Equipe BIGS, INRIA Nancy, Université de Lorraine, Nancy, France
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Seo S, Prabhakar RG, Disney-McKeethen S, Song X, Shamoo Y. Microfluidic platform for spatially segregated experimental evolution studies with E. coli. STAR Protoc 2022; 3:101332. [PMID: 35496805 PMCID: PMC9048157 DOI: 10.1016/j.xpro.2022.101332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Microdroplet emulsions allow investigators to build controllable microenvironments for applications in experimental evolution and synthetic ecology. We designed a microfluidic platform that uses highly homogenous microdroplets to enable these experiments. We also present a step-by-step protocol for the rapid production of highly homogeneous microdroplets suitable for experimental evolution. We also describe protocols for the propagation and serial passage of microbial populations across a range of selection schemes and potential spatial structures. For complete details on the use and execution of this protocol, please refer to Seo et al. (2021). Microfluidics for the study of microbial evolution and biomarker discovery Highly homogenous microdroplets as spatially segregated microenvironments Platform to identify evolutionary trajectories leading to antimicrobial resistance
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Elsemman IE, Rodriguez Prado A, Grigaitis P, Garcia Albornoz M, Harman V, Holman SW, van Heerden J, Bruggeman FJ, Bisschops MMM, Sonnenschein N, Hubbard S, Beynon R, Daran-Lapujade P, Nielsen J, Teusink B. Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nat Commun 2022; 13:801. [PMID: 35145105 PMCID: PMC8831649 DOI: 10.1038/s41467-022-28467-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/27/2022] [Indexed: 01/20/2023] Open
Abstract
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation—known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells. Metabolically active organelles compete for cytosolic space and resources during metabolism rewiring. Here, the authors develop a computational model of yeast metabolism and resource allocation to predict condition- and compartment-specific proteome constraints that govern metabolic strategies.
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Affiliation(s)
- Ibrahim E Elsemman
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark.,Department of Information Systems, Faculty of Computers and Information, Assiut University, Assiut, Egypt
| | - Angelica Rodriguez Prado
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Pranas Grigaitis
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Victoria Harman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Stephen W Holman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Johan van Heerden
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark M M Bisschops
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Nikolaus Sonnenschein
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark
| | - Simon Hubbard
- Division of Evolution & Genomic Sciences, University of Manchester, Manchester, UK
| | - Rob Beynon
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Pascale Daran-Lapujade
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark. .,Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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Seo S, Disney-McKeethen S, Prabhakar RG, Song X, Mehta HH, Shamoo Y. Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics. ACS Infect Dis 2022; 8:242-254. [PMID: 34962128 PMCID: PMC10022597 DOI: 10.1021/acsinfecdis.1c00564] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In vitro experimental evolution of pathogens to antibiotics is commonly used for the identification of clinical biomarkers associated with antibiotic resistance. Microdroplet emulsions allow exquisite control of spatial structure, species complexity, and selection microenvironments for such studies. We investigated the use of monodisperse microdroplets in experimental evolution. Using Escherichia coli adaptation to doxycycline, we examined how changes in environmental conditions such as droplet size, starting lambda value, selection strength, and incubation method affected evolutionary outcomes. We also examined the extent to which emulsions could reveal potentially new evolutionary trajectories and dynamics associated with antimicrobial resistance. Interestingly, we identified both expected and unexpected evolutionary trajectories including large-scale chromosomal rearrangements and amplification that were not observed in suspension culture methods. As microdroplet emulsions are well-suited for automation and provide exceptional control of conditions, they can provide a high-throughput approach for biomarker identification as well as preclinical evaluation of lead compounds.
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Affiliation(s)
- Seokju Seo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | | | | | - Xinhao Song
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Heer H Mehta
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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