scholarly journals Generic estimator of biomass concentration for Escherichia coli and Saccharomyces cerevisiae fed-batch cultures based on cumulative oxygen consumption rate

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Renaldas Urniezius ◽  
Arnas Survyla ◽  
Dziugas Paulauskas ◽  
Vladas Algirdas Bumelis ◽  
Vytautas Galvanauskas
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Exponential Growth ◽  
Biomass Concentration ◽  
Estimation Procedure ◽  
Exponential Growth Phase ◽  
Fed Batch ◽  
Batch Cultures ◽  
E Coli ◽  
Substrate Feeding

Abstract Background The focus of this study is online estimation of biomass concentration in fed-batch cultures. It describes a bioengineering software solution, which is explored for Escherichia coli and Saccharomyces cerevisiae fed-batch cultures. The experimental investigation of both cultures presents experimental validation results since the start of the bioprocess, i.e. since the injection of inoculant solution into bioreactor. In total, four strains were analyzed, and 21 experiments were performed under varying bioprocess conditions, out of which 7 experiments were carried out with dosed substrate feeding. Development of the microorganisms’ culture invariant generic estimator of biomass concentration was the main goal of this research. Results The results show that stoichiometric parameters provide acceptable knowledge on the state of biomass concentrations during the whole cultivation process, including the exponential growth phase of both E. coli and S. cerevisiae cultures. The cell culture stoichiometric parameters are estimated by a procedure based on the Luedeking/Piret-model and maximization of entropy. The main input signal of the approach is cumulative oxygen uptake rate at fed-batch cultivation processes. The developed noninvasive biomass estimation procedure was intentionally made to not depend on the selection of corresponding bioprocess/bioreactor parameters. Conclusions The precision errors, since the bioprocess start, when inoculant was injected to a bioreactor, confirmed that the approach is relevant for online biomass state estimation. This included the lag and exponential growth phases for both E. coli and S. cerevisiae. The suggested estimation procedure is identical for both cultures. This approach improves the precision achieved by other authors without compromising the simplicity of the implementation. Moreover, the suggested approach is a candidate method to be the microorganisms’ culture invariant approach. It does not depend on any numeric initial optimization conditions, it does not require any of bioreactor parameters. No numeric stability issues of convergence occurred during multiple performance tests. All this makes this approach a potential candidate for industrial tasks with adaptive feeding control or automatic inoculations when substrate feeding profile and bioreactor parameters are not provided.

scholarly journals The Putrescine Importer PuuP of Escherichia coli K-12

2009 ◽  
Vol 191 (8) ◽  
pp. 2776-2782 ◽  
Author(s):  
Shin Kurihara ◽  
Yuichi Tsuboi ◽  
Shinpei Oda ◽  
Hyeon Guk Kim ◽  
Hidehiko Kumagai ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Growth Phase ◽  
Exponential Growth ◽  
Minimal Medium ◽  
Exponential Growth Phase ◽  
E Coli ◽  
Genes Encoding ◽  
K 12 ◽  
Utilization Pathway

ABSTRACT The Puu pathway is a putrescine utilization pathway involving gamma-glutamyl intermediates. The genes encoding the enzymes of the Puu pathway form a gene cluster, the puu gene cluster, and puuP is one of the genes in this cluster. In Escherichia coli, three putrescine importers, PotFGHI, PotABCD, and PotE, were discovered in the 1990s and have been studied; however, PuuP had not been discovered previously. This paper shows that PuuP is a novel putrescine importer whose kinetic parameters are equivalent to those of the polyamine importers discovered previously. A puuP + strain absorbed up to 5 mM putrescine from the medium, but a ΔpuuP strain did not. E. coli strain MA261 has been used in previous studies of polyamine transporters, but PuuP had not been identified previously. It was revealed that the puuP gene of MA261 was inactivated by a point mutation. When E. coli was grown on minimal medium supplemented with putrescine as the sole carbon or nitrogen source, only PuuP among the polyamine importers was required. puuP was expressed strongly when putrescine was added to the medium or when the puuR gene, which encodes a putative repressor, was deleted. When E. coli was grown in M9-tryptone medium, PuuP was expressed mainly in the exponential growth phase, and PotFGHI was expressed independently of the growth phase.

scholarly journals Generic Model Control Applied to E. coli BL21(DE3) Fed-Batch Cultures

Processes ◽  
2020 ◽  
Vol 8 (7) ◽  
pp. 772 ◽  
Author(s):  
Merouane Abadli ◽  
Laurent Dewasme ◽  
Sihem Tebbani ◽  
Didier Dumur ◽  
Alain Vande Wouwer
Keyword(s):  
Mechanistic Model ◽  
Biomass Concentration ◽  
Generic Model ◽  
Control Law ◽  
Overflow Metabolism ◽  
Fed Batch ◽  
Batch Cultures ◽  
E Coli ◽  
Model Control ◽  
Generic Model Control

This work proposes a Generic Model Control (GMC) strategy to regulate biomass growth in fed-batch cultures of Escherichia coli BL21(DE3). The control law is established using a previously validated mechanistic model based on the overflow metabolism paradigm. A model reduction is carried out to prevent the controller from relying on kinetics, which may be uncertain. In order to limit the controller to the use of a single measurement, i.e., biomass concentration which is readily available, a Kalman filter is designed to reconstruct the nonmeasurable information from the outlet gas and the remaining stoichiometry. Several numerical simulations are presented to assess the controller robustness with respect to model uncertainty. Experimental validation of the proposed GMC strategy is achieved with a lab-scale bioreactor.

scholarly journals Production of Poly(3-Hydroxybutyrate) by Fed-Batch Culture of Recombinant Escherichia coliwith a Highly Concentrated Whey Solution

2000 ◽  
Vol 66 (8) ◽  
pp. 3624-3627 ◽  
Author(s):  
Woo Suk Ahn ◽  
Si Jae Park ◽  
Sang Yup Lee
Keyword(s):  
Escherichia Coli ◽  
Batch Culture ◽  
Fed Batch ◽  
Batch Cultures ◽  
E Coli ◽  
Alcaligenes Latus ◽  
Stable Plasmid ◽  
Ph Stat ◽  
Fed Batch Culture

ABSTRACT Fermentation strategies for the production of poly(3-hydroxybutyrate) (PHB) from whey by recombinantEscherichia coli strain CGSC 4401 harboring theAlcaligenes latus polyhydroxyalkanoate (PHA) biosynthesis genes were developed. The pH-stat fed-batch cultures of E. coli CGSC 4401 harboring pJC4, a stable plasmid containing theA. latus PHA biosynthesis genes, were carried out with a concentrated whey solution containing 280 g of lactose equivalent per liter. Final cell and PHB concentrations of 119.5 and 96.2 g/liter, respectively, were obtained in 37.5 h, which resulted in PHB productivity of 2.57 g/liter/h.

scholarly journals A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures

2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Stefano Mazzoleni ◽  
Carmine Landi ◽  
Fabrizio Cartenì ◽  
Elisabetta de Alteriis ◽  
Francesco Giannino ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Microbial Growth ◽  
Fed Batch ◽  
Batch Cultures

Fed-batch cultures of recombinant Escherichia coli with inhibitory substance concentration monitoring

1988 ◽  
Vol 66 (2) ◽  
pp. 187-191 ◽  
Author(s):  
Norio Shimizu ◽  
Shinichi Fukuzono ◽  
Kiyoshi Fujimori ◽  
Nabuko Nishimura ◽  
Yoji Odawara
Keyword(s):  
Escherichia Coli ◽  
Recombinant Escherichia Coli ◽  
Fed Batch ◽  
Inhibitory Substance ◽  
Batch Cultures ◽  
Substance Concentration

Quantitative profiling and dynamics of mRNA modifications in Escherichia coli

2021 ◽  
Author(s):  
Dimitar Plamenov Petrov ◽  
Steffen Kaiser ◽  
Stefanie Kaiser ◽  
Kirsten Jung
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Stationary Phase ◽  
Exponential Growth ◽  
Gel Electrophoresis ◽  
E Coli ◽  
Physiological Processes ◽  
Mrna Methylation ◽  
Important Regulator ◽  
Quantitative Profiling

mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. In contrast to the large number of eukaryotic mRNA modifications that have been described, N6-methyladenosine (m6A) is the only modification of bacterial mRNA identified to date. Here, we used a gel electrophoresis-based RNA separation method and quantitatively analyzed the mRNA-specific modification profile of Escherichia coli using mass spectrometry. In addition to m6A, we provide evidence for the presence of 7-methylguanosine (m7G), and we found first hints for 5-methylcytidine (m5C), N6,N6-dimethyladenosine (m6,6A), 1-methylguanosine (m1G), 5-methyluridine (m5U), and pseudouridine (Ψ) in the mRNA of E. coli, which implies that E. coli has a complex mRNA modification pattern. Furthermore, we observed changes in the abundance of some mRNA modifications during the transition of E. coli from the exponential growth to the stationary phase as well as upon exposure to stress. This study reveals a previously underestimated level of regulation between transcription and translation in bacteria.

scholarly journals Biophysical Properties of Escherichia coli Cytoplasm in Stationary Phase by Superresolution Fluorescence Microscopy

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Yanyu Zhu ◽  
Mainak Mustafi ◽  
James C. Weisshaar
Keyword(s):  
Escherichia Coli ◽  
Fluorescence Microscopy ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Exponential Growth ◽  
Mean Square Displacement ◽  
Quiescent State ◽  
Chromosomal Dna ◽  
Content Type ◽  
E Coli

ABSTRACT In nature, bacteria must survive long periods of nutrient deprivation while maintaining the ability to recover and grow when conditions improve. This quiescent state is called stationary phase. The biochemistry of Escherichia coli in stationary phase is reasonably well understood. Much less is known about the biophysical state of the cytoplasm. Earlier studies of harvested nucleoids concluded that the stationary-phase nucleoid is “compacted” or “supercompacted,” and there are suggestions that the cytoplasm is “glass-like.” Nevertheless, stationary-phase bacteria support active transcription and translation. Here, we present results of a quantitative superresolution fluorescence study comparing the spatial distributions and diffusive properties of key components of the transcription-translation machinery in intact E. coli cells that were either maintained in 2-day stationary phase or undergoing moderately fast exponential growth. Stationary-phase cells are shorter and exhibit strong heterogeneity in cell length, nucleoid volume, and biopolymer diffusive properties. As in exponential growth, the nucleoid and ribosomes are strongly segregated. The chromosomal DNA is locally more rigid in stationary phase. The population-weighted average of diffusion coefficients estimated from mean-square displacement plots is 2-fold higher in stationary phase for both RNA polymerase (RNAP) and ribosomal species. The average DNA density is roughly twice as high as that in cells undergoing slow exponential growth. The data indicate that the stationary-phase nucleoid is permeable to RNAP and suggest that it is permeable to ribosomal subunits. There appears to be no need to postulate migration of actively transcribed genes to the nucleoid periphery. IMPORTANCE Bacteria in nature usually lack sufficient nutrients to enable growth and replication. Such starved bacteria adapt into a quiescent state known as the stationary phase. The chromosomal DNA is protected against oxidative damage, and ribosomes are stored in a dimeric structure impervious to digestion. Stationary-phase bacteria can recover and grow quickly when better nutrient conditions arise. The biochemistry of stationary-phase E. coli is reasonably well understood. Here, we present results from a study of the biophysical state of starved E. coli. Superresolution fluorescence microscopy enables high-resolution location and tracking of a DNA locus and of single copies of RNA polymerase (the transcription machine) and ribosomes (the translation machine) in intact E. coli cells maintained in stationary phase. Evidently, the chromosomal DNA remains sufficiently permeable to enable transcription and translation to occur. This description contrasts with the usual picture of a rigid stationary-phase cytoplasm with highly condensed DNA.

scholarly journals Biosynthesis and turnover of outer-membrane proteins in Escherichia coli ML308-225

1979 ◽  
Vol 182 (2) ◽  
pp. 407-412 ◽  
Author(s):  
R J Allen ◽  
G K Scott
Keyword(s):  
Escherichia Coli ◽  
Protein Synthesis ◽  
Outer Membrane ◽  
Bacterial Growth ◽  
Growth Phase ◽  
Exponential Growth ◽  
Outer Membrane Proteins ◽  
Exponential Growth Phase ◽  
Outer Membranes ◽  
Dilution Experiments

Isolated outer membranes and outer-membrane extracts from Escherichia coli ML308-225 in the early-exponential growth phase contain more protein than do corresponding preparations from late-exponential- or stationary-phase bacteria. Isotope-dilution experiments show that this is due to a loss of protein from the membrane during the exponential growth phase. Inhibition of bacterial growth and protein synthesis stabilizes the outer-membrane-protein concentration. Protein synthesis in the absence of bacterial growth results in higher concentrations of protein in the outer membrane.

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