References
Andersen, M. R., Lehmann, L., & Nielsen, J. (2009). Systemic analysis
of the response of Aspergillus niger to ambient pH. Genome
Biology , 10 (5), R47.
Bekers, K. M., Heijnen, J. J., & Van Gulik, W. M. (2015). Determination
of the in vivo NAD: NADH ratio in Saccharomyces cerevisiae under
anaerobic conditions, using alcohol dehydrogenase as sensor reaction.Yeast , 32 (8), 541–557.
Benjaphokee, S., Hasegawa, D., Yokota, D., Asvarak, T., Auesukaree, C.,
Sugiyama, M., … Harashima, S. (2012). Highly efficient bioethanol
production by a Saccharomyces cerevisiae strain with multiple stress
tolerance to high temperature, acid and ethanol. New
Biotechnology , 29 (3), 379–386.
https://doi.org/10.1016/j.nbt.2011.07.002
Blank, L. M., & Sauer, U. (2004). TCA cycle activity in Saccharomyces
cerevisiae is a function of the environmentally determined specific
growth and glucose uptake rates. Microbiology , 150 (4),
1085–1093. https://doi.org/10.1099/mic.0.26845-0
Çalik, P., & Ileri, N. (2007). pH influences intracellular reaction
network of β-lactamase producing Bacillus licheniformis. Chemical
Engineering Science , 62 (18–20), 5206–5211.
https://doi.org/10.1016/j.ces.2007.01.081
Chidi, B. S., Rossouw, D., & Bauer, F. F. (2016). Identifying and
assessing the impact of wine acid-related genes in yeast. Current
Genetics , 62 (1), 149–164.
https://doi.org/10.1007/s00294-015-0498-6
Contador, C. A., Shene, C., Olivera, A., Yoshikuni, Y., Buschmann, A.,
Andrews, B. A., & Asenjo, J. A. (2015). Analyzing redox balance in a
synthetic yeast platform to improve utilization of brown macroalgae as
feedstock. Metabolic Engineering Communications , 2 ,
76–84. https://doi.org/10.1016/j.meteno.2015.06.004
Daran-Lapujade, P., Jansen, M. L. A., Daran, J. M., Van Gulik, W., De
Winde, J. H., & Pronk, J. T. (2004). Role of Transcriptional Regulation
in Controlling Fluxes in Central Carbon Metabolism of Saccharomyces
cerevisiae: A chemostat culture study. Journal of Biological
Chemistry , 279 (10), 9125–9138.
https://doi.org/10.1074/jbc.M309578200
Dong, Y., Hu, J., Fan, L., & Chen, Q. (2017). RNA-Seq-based
transcriptomic and metabolomic analysis reveal stress responses and
programmed cell death induced by acetic acid in Saccharomyces
cerevisiae. Scientific Reports , 7 , 42659.
Edwards, J. S., Covert, M., & Palsson, B. (2002). Metabolic modelling
of microbes: The flux-balance approach. Environmental
Microbiology , 4 (3), 133–140.
https://doi.org/10.1046/j.1462-2920.2002.00282.x
Gerosa, L., Haverkorn Van Rijsewijk, B. R. B., Christodoulou, D.,
Kochanowski, K., Schmidt, T. S. B., Noor, E., & Sauer, U. (2015).
Pseudo-transition Analysis Identifies the Key Regulators of Dynamic
Metabolic Adaptations from Steady-State Data. Cell Systems ,1 (4), 270–282. https://doi.org/10.1016/j.cels.2015.09.008
Jo, J. H., Lee, D. S., & Park, J. M. (2008). The effects of pH on
carbon material and energy balances in hydrogen-producing Clostridium
tyrobutyricum JM1. Bioresource Technology , 99 (17),
8485–8491. https://doi.org/10.1016/j.biortech.2008.03.060
Jones, C. W., & Doelle, H. W. (1991). Kinetic control of ethanol
production by Zymomonas mobilis. Applied Microbiology and
Biotechnology , 35 (1), 4–9. https://doi.org/10.1007/BF00180626
Joshi, B., Joshi, J., Bhattarai, T., & Sreerama, L. (2019).Currently Used Microbes and Advantages of Using Genetically
Modified Microbes for Ethanol . Bioethanol Production from Food
Crops . Elsevier Inc. https://doi.org/10.1016/B978-0-12-813766-6/00015-1
Kalnenieks, U. Z., Pankova, L. M., & Shvinka, Y. (1987). Proton motive
force in the bacterium Zymomonas mobilis. Biogeochemistry ,52 (5), 617–620.
Krulwich, T. A., Sachs, G., & Padan, E. (2011). Molecular aspects of
bacterial pH sensing and homeostasis. Nature Reviews
Microbiology , 9 (5), 330–343.
https://doi.org/10.1038/nrmicro2549
Kuroda, K., Hammer, S. K., Watanabe, Y., Montaño López, J., Fink, G. R.,
Stephanopoulos, G., … Avalos, J. L. (2019). Critical Roles of the
Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in
Yeast. Cell Systems , 9 (6), 534–547.e5.
https://doi.org/10.1016/j.cels.2019.10.006
Martinez, K. A., Kitko, R. D., Mershon, J. P., Adcox, H. E., Malek, K.
A., Berkmen, M. B., & Slonczewski, J. L. (2012). Cytoplasmic pH
response to acid stress in individual cells of Escherichia coli and
Bacillus subtilis observed by fluorescence ratio imaging microscopy.Applied and Environmental Microbiology , 78 (10),
3706–3714. https://doi.org/10.1128/AEM.00354-12
Mo, M. L., Palsson, B. Ø., & Herrgård, M. J. (2009). Connecting
extracellular metabolomic measurements to intracellular flux states in
yeast. BMC Systems Biology , 3 (1), 37.
Monk, J. M., Koza, A., Campodonico, M. A., Machado, D., Seoane, J. M.,
Palsson, B. O., … Feist, A. M. (2016). Multi-omics Quantification
of Species Variation of Escherichia coli Links Molecular Features with
Strain Phenotypes. Cell Systems , 3 (3), 238–251.e12.
https://doi.org/10.1016/j.cels.2016.08.013
Motamedian, E., Saeidi, M., & Shojaosadati, S. A. (2016).
Reconstruction of a charge balanced genome-scale metabolic model to
study the energy-uncoupled growth of Zymomonas mobilis ZM1.Molecular BioSystems , 12 (4), 1241–1249.
Motamedian, E., Sarmadi, M., & Derakhshan, E. (2019). Development of a
regulatory defined medium using a system-oriented strategy to reduce the
intracellular constraints. Process Biochemistry .
Naghshbandi, M. P., Tabatabaei, M., Aghbashlo, M., Gupta, V. K.,
Sulaiman, A., Karimi, K., … Maleki, M. (2019). Progress toward
improving ethanol production through decreased glycerol generation in
Saccharomyces cerevisiae by metabolic and genetic engineering
approaches. Renewable and Sustainable Energy Reviews ,115 (August), 109353. https://doi.org/10.1016/j.rser.2019.109353
Narendranath, N. V, & Power, R. (2005). Relationship between pH and
medium dissolved solids in terms of growth and metabolism of
lactobacilli and Saccharomyces cerevisiae during ethanol production.Appl. Environ. Microbiol. , 71 (5), 2239–2243.
Orij, R., Brul, S., & Smits, G. J. (2011). Intracellular pH is a
tightly controlled signal in yeast. Biochimica et Biophysica Acta
- General Subjects , 1810 (10), 933–944.
https://doi.org/10.1016/j.bbagen.2011.03.011
Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A.
M., & Palsson, B. Ø. (2011). A comprehensive genome‐scale
reconstruction of Escherichia coli metabolism—2011. Molecular
Systems Biology , 7 (1).
Pagliardini, J., Hubmann, G., Alfenore, S., Nevoigt, E., Bideaux, C., &
Guillouet, S. E. (2013). The metabolic costs of improving ethanol yield
by reducing glycerol formation capacity under anaerobic conditions in
Saccharomyces cerevisiae. Microbial Cell Factories , 12 (1),
1–14. https://doi.org/10.1186/1475-2859-12-29
Papapetridis, I., Van Dijk, M., Dobbe, A. P. A., Metz, B., Pronk, J. T.,
& Maris, A. J. A. (2016). Improving ethanol yield in acetate-reducing
Saccharomyces cerevisiae by cofactor engineering of 6-phosphogluconate
dehydrogenase and deletion of ALD6. Microbial Cell Factories ,15 (1), 1–16. https://doi.org/10.1186/s12934-016-0465-z
Park, J. M., Kim, T. Y., & Lee, S. Y. (2011). Genome-scale
reconstruction and in silico analysis of the Ralstonia eutropha H16 for
polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl
citric acid production. BMC Systems Biology , 5 (1), 101.
Reed, J. L., Vo, T. D., Schilling, C. H., & Palsson, B. O. (2003). An
expanded genome-scale model of Escherichia coli K-12 (i JR904 GSM/GPR).Genome Biology , 4 (9), R54.
Scalcinati, G., Otero, J. M., Van Vleet, J. R. H., Jeffries, T. W.,
Olsson, L., & Nielsen, J. (2012). Evolutionary engineering of
Saccharomyces cerevisiae for efficient aerobic xylose consumption.FEMS Yeast Research , 12 (5), 582–597.
https://doi.org/10.1111/j.1567-1364.2012.00808.x
Shioi, J. I., Matsuura, S., & Imae, Y. (1980). Quantitative
measurements of proton motive force and motility in Bacillus subtilis.Journal of Bacteriology , 144 (3), 891–897.
https://doi.org/10.1128/jb.144.3.891-897.1980
Slonczewski, J. L., Fujisawa, M., Dopson, M., & Krulwich, T. A. (2009).Cytoplasmic pH Measurement and Homeostasis in Bacteria and
Archaea . Advances in Microbial Physiology (Vol. 55). Elsevier.
https://doi.org/10.1016/S0065-2911(09)05501-5
Slonczewski, J. L., Rosen, B. P., Alger, J. R., & Macnab, R. M. (1981).
pH homeostasis in Escherichia coli: measurement by 31P nuclear magnetic
resonance of methylphosphonate and phosphate. Proceedings of the
National Academy of Sciences of the United States of America ,78 (10 I), 6271–6275. https://doi.org/10.1073/pnas.78.10.6271
Swayambhu, G., Moscatello, N., Atilla-Gokcumen, G. E., & Pfeifer, B. A.
(2020). Flux Balance Analysis for Media Optimization and Genetic Targets
to Improve Heterologous Siderophore Production. IScience ,23 (4), 101016. https://doi.org/10.1016/j.isci.2020.101016
Valgepea, K., Adamberg, K., Seiman, A., & Vilu, R. (2013). Escherichia
coli achieves faster growth by increasing catalytic and translation
rates of proteins. Molecular BioSystems , 9 (9), 2344–2358.
https://doi.org/10.1039/c3mb70119k
Valgepea, K., de Souza Pinto Lemgruber, R., Meaghan, K., Palfreyman, R.
W., Abdalla, T., Heijstra, B. D., … Marcellin, E. (2017).
Maintenance of ATP Homeostasis Triggers Metabolic Shifts in
Gas-Fermenting Acetogens. Cell Systems , 4 (5), 505–515.e5.
https://doi.org/10.1016/j.cels.2017.04.008
Valli, M., Sauer, M., Branduardi, P., Borth, N., Porro, D., &
Mattanovich, D. (2005). Intracellular pH distribution in Saccharomyces
cerevisiae cell populations, analyzed by flow cytometry. Appl.
Environ. Microbiol. , 71 (3), 1515–1521.
Vojinović, V., & Von Stockar, U. (2009). Influence of uncertainties in
pH, pMg, activity coefficients, metabolite concentrations, and other
factors on the analysis of the thermodynamic feasibility of metabolic
pathways. Biotechnology and Bioengineering , 103 (4),
780–795. https://doi.org/10.1002/bit.22309
Williams-Rhaesa, A. M., Rubinstein, G. M., Scott, I. M., Lipscomb, G.
L., Poole, F. L., Kelly, R. M., & Adams, M. W. W. (2018). Engineering
redox-balanced ethanol production in the cellulolytic and extremely
thermophilic bacterium, Caldicellulosiruptor bescii. Metabolic
Engineering Communications , 7 .
https://doi.org/10.1016/j.mec.2018.e00073
Yang, S., Land, M. L., Klingeman, D. M., Pelletier, D. A., Lu, T. Y. S.,
Martin, S. L., … Brown, S. D. (2010). Paradigm for industrial
strain improvement identifies sodium acetate tolerance loci in Zymomonas
mobilis and Saccharomyces cerevisiae. Proceedings of the National
Academy of Sciences of the United States of America , 107 (23),
10395–10400. https://doi.org/10.1073/pnas.0914506107