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Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

Ronny Feuer, Katrin Gottlieb, Gero Viertel, Johannes Klotz, Steffen Schober, Martin Bossert, Oliver Sawodny, Georg Sprenger, Michael Ederer
2012 EURASIP Journal on Bioinformatics and Systems Biology  
Selective conditions were controlled in a continuous culture with limited lactate feed and an excess of glycerol feed. After 200-300 generations pyruvate-prototrophic mutants were isolated.  ...  A block of endogenous pyruvate synthesis from glycerol was realized by a knockout of pyruvate kinase and phosphoenolpyruvate carboxylase in E. coli.  ...  We thank Karin Lemuth for her support with the microarray analysis, Natalie Trachtmann for the construction of strain F41malE::pyc and Silvia Lorenz for the labor-intensive analysis of the evolved strains  ... 
doi:10.1186/1687-4153-2012-14 pmid:23033959 pmcid:PMC3534542 fatcat:iq672d2af5b7bjx7gmiduxwgcy

Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model

S. S. Fong, J. Y. Marciniak, B. O. Palsson
2003 Journal of Bacteriology  
We hypothesized that the end point of adaptive evolution of E. coli could be accurately described a priori by our in silico model since adaptive evolution should lead to an optimal phenotype.  ...  Adaptive evolution of E. coli during prolonged exponential growth was performed with M9 minimal medium supplemented with 2 g of ␣-ketoglutarate per liter, 2 g of lactate per liter, or 2 g of pyruvate per  ...  More recently, a constraint-based in silico model of a genome-scale metabolic reconstruction of Escherichia coli has been used to describe the metabolic phenotypes for growth on several substrates and  ... 
doi:10.1128/jb.185.21.6400-6408.2003 pmid:14563875 pmcid:PMC219384 fatcat:xxsamp4s7rb6fpsy65z7z7emve

Activating silent glycolysis bypasses in Escherichia coli [article]

Camillo Iacometti, Katharina Marx, Maria Hoenick, Viktoria Biletskaia, Helena Schulz-Mirbach, Ari Satanowski, Beau Dronsella, Madeleine Bouzon, Volker Doering, Ivan Dubois, Anne Berger, Valerie A. Delmas (+3 others)
2021 bioRxiv   pre-print
To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution.  ...  Finally, to explore which of these alternatives would emerge by natural selection we performed an adaptive laboratory evolution study using an enolase deletion strain.  ...  Acknowledgments We thank Enrico Orsi for critical reading of the manuscript. This study was funded by the Max Planck Society and the CEA Genoscope.  ... 
doi:10.1101/2021.11.18.468982 fatcat:6edjvbriqfdrbh4tykfy6sxjka

Metabolic Characterization of Escherichia coli Strains Adapted to Growth on Lactate

Q. Hua, A. R. Joyce, B. O. Palsson, S. S. Fong
2007 Applied and Environmental Microbiology  
Metabolic mechanisms involved in laboratory evolution of Escherichia coli on gluconeogenic carbon sources, such as lactate, were studied based on intracellular flux states determined from 13 C tracer experiments  ...  In comparison with intensive studies of genetic mechanisms related to biological evolutionary systems, much less analysis has been conducted on metabolic network responses to adaptive evolution that are  ...  The principal investigator and UCSD have a financial interest in Genomatica, Inc.; although this grant has been identified for conflictof-interest management based on the overall scope of the project and  ... 
doi:10.1128/aem.00527-07 pmid:17513588 pmcid:PMC1932837 fatcat:f5qujb63k5ae3lru6oc4ypupau

Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli

R F Rosenzweig, R R Sharp, D S Treves, J Adams
1994 Genetics  
Populations of Escherichia coli initiated with a single clone and maintained for long periods in glucose-limited continuous culture, become polymorphic.  ...  Analysis of these three clones revealed that their stable coexistence could be explained by differential patterns of the secretion and uptake of two alternative metabolites acetate and glycerol.  ...  Here we present evidence that similar interactions underlie genetic diversification within a population, initiated with a single clone of Escherichia coli grown in long term glucose-limited continuous  ... 
pmid:7982572 pmcid:PMC1206068 fatcat:oxz5fgh3qjfylo7w2txgqoknt4

Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

S. S. Fong
2005 Genome Research  
The material in the paper may be related to US patent application US-2002-0142321-A1. The authors thus disclose potential competing interests.  ...  Results In this study, the process of adaptive evolution was investigated using the wild-type K-12 MG1655 strain of Escherichia coli.  ...  on a small subset of genes because of statistical limitations involved in microarray data analysis (Hess et al. 2001; Nadon and Shoemaker 2002) .  ... 
doi:10.1101/gr.3832305 pmid:16204189 pmcid:PMC1240078 fatcat:z65ldjllzrai3ad63liqsmjcxe

CO2 production, O2 consumption and isocitrate dehydrogenase in the marine bacterium Vibrio natriegens

E Berdalet, T Packard, B Lagacé, S Roy, L St-Amand, JP Gagné
1995 Aquatic Microbial Ecology  
The respiratory metabolism of the marine bacterium Vibrio natriegens growing in batch cultures with acetate and pyruvate as carbon sources was studied In particular, the relationship of the activity of  ...  Growth based on acetate was characterized by a higher O2 consumption, lower CO, production, lower respiratory quotient and lower IDH activity than on pyruvate.  ...  The experiments would not have been possible without the help of Dr Ken Lee who klndly provlded us with the Oxymax We thank Dr Dolors Vaque for valuable comments E B recelved a grant from the Spanlsh Minlstry  ... 
doi:10.3354/ame009211 fatcat:hi6oeupesjczxmhd6vzncn6cwm

In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products

Albert Enrique Tafur Rangel, Wendy Ríos, Daisy Mejía, Carmen Ojeda, Ross Carlson, Jorge Mario Gómez Ramírez, Andrés Fernando González Barrios
2021 Frontiers in Genetics  
Three E. coli models were used: a core model, a second model based on the integration of transcriptomics data obtained from growth in an optimized culture media, and a third one obtained after integration  ...  In this study, a systems-based metabolic engineering target prediction was used to increase glycerol bioconversion to succinic acid based on Escherichia coli.  ...  RESULTS Glycerol Consumption of E. coli After Adaptive Laboratory Evolution Luria-Bertani is one of the most common cultures used industrially for the growth of E. coli.  ... 
doi:10.3389/fgene.2021.633073 pmid:33868371 pmcid:PMC8044919 fatcat:ffthrnhh65d7vpm6ql2t4ez74e

Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community

Margie Kinnersley, Jared Wenger, Evgueny Kroll, Julian Adams, Gavin Sherlock, Frank Rosenzweig, Jianzhi Zhang
2014 PLoS Genetics  
We previously showed that a clonal population of E. coli experimentally evolved under continuous glucose limitation gives rise to a genetically diverse community consisting of one clone, CV103, that best  ...  Laboratory experimental evolution offers the benefit of controlling variables that shape fitness landscapes, helping to achieve both goals.  ...  for assisting with fluctuation tests.  ... 
doi:10.1371/journal.pgen.1004430 pmid:24968217 pmcid:PMC4072538 fatcat:v6vf3it6rfgqvp5hvwkqep4une

A synthetic glycerol assimilation pathway demonstrates biochemical constraints of cellular metabolism

Steffen N. Lindner, Selçuk Aslan, Alexandra Müller, Eugenia Hoffart, Patrick Behrens, Christian Edlich‐Muth, Bastian Blombach, Arren Bar‐Even
2019 The FEBS Journal  
In this study, we designed and engineered a novel glycerol assimilation pathway in Escherichia coli.  ...  Long-term evolution failed to improve growth via the pathway, indicating that this limitation was not regulatory but rather relates to fundamental aspects of cellular metabolism.  ...  SNL, EH and BB performed growth experiments. EH and BB measured the accumulation of byproducts in the medium. PB performed long-term cultivation under selective conditions.  ... 
doi:10.1111/febs.15048 pmid:31436884 fatcat:grj7xjpdv5fdde4hzq6sj6fgli

Using genome-scale model to predict the metabolic engineering impact on Escherichia coli metabolism during succinic acid production optimization

ZSOLT BODOR, Sapientia Hungarian University of Transylvania, Department of Bioengineering, Libertatii square, No. 1, 530104, Miercurea Ciuc, Romania, ANDREA (IUHÁSZ) FAZAKAS, KATALIN BODOR, ERIKA KOVÁCS, ILDIKÓ MIKLÓSSY, BEÁTA ALBERT
2020 Romanian Biotechnological Letters  
The in silico simulation of metabolic processes in Escherichia coli has been concluded the possibility of increasing the yield of succinic acid from 0.008 to 0.9 (mol mol -1 glucose) and from 0.0003 to  ...  Using genome-scale model to predict the metabolic engineering impact on Escherichia coli metabolism during succinic acid production optimization.  ...  Identification of metabolites was performed in a GC-MS experiment, data analysis was carried out with MassLab via comparison with mass spectra obtained from different libraries.  ... 
doi:10.25083/rbl/25.3/1666.1676 fatcat:x4dxmt5kzfelblzejyhvtohpqm

Adaptive laboratory evolution – principles and applications for biotechnology

Martin Dragosits, Diethard Mattanovich
2013 Microbial Cell Factories  
Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations  ...  Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations.  ...  Furthermore, we appreciate the valuable input of the anonymous reviewers, which helped us to improve the quality of the manuscript.  ... 
doi:10.1186/1475-2859-12-64 pmid:23815749 pmcid:PMC3716822 fatcat:2smkv7kkbrelnfqqc27cbawnn4

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli

Margie A. Kinnersley, William E. Holben, Frank Rosenzweig, David S. Guttman
2009 PLoS Genetics  
We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones.  ...  In the founder, a cis-regulatory mutation in acs (acetyl CoA synthetase) and a structural mutation in glpR (glycerol-3-phosphate repressor) likely favored evolution of specialists that thrive on overflow  ...  We gratefully acknowledge the work of Mike Fero and Elena Seraia of the Stanford Functional Genomics Core who supervised the printing of our microarrays.  ... 
doi:10.1371/journal.pgen.1000713 pmid:19893610 pmcid:PMC2763269 fatcat:fg7vvi527ffrjltzblgn2uk56u

Hydrogen production by recombinant Escherichia coli strains

Toshinari Maeda, Viviana Sanchez-Torres, Thomas K. Wood
2011 Microbial Biotechnology  
Given its ease of manipulation, the best-studied bacterium Escherichia coli has become a workhorse for enhanced hydrogen production through metabolic engineering, heterologous gene expression, adaptive  ...  The production of hydrogen via microbial biotechnology is an active field of research.  ...  Acknowledgements This research was supported by the National Science Foundation (CBET-0753702) and the Japan Society for the Promotion of Science (22780070 and 21-7007).  ... 
doi:10.1111/j.1751-7915.2011.00282.x pmid:21895995 pmcid:PMC3815781 fatcat:mo3yepif6ngxdlamwm3k32hfiu

Model Driven Analysis of the Biosynthesis of 1,4-butanediol from Renewable Feedstocks in Escherichia coli

Zsolt Bodor, Szabolcs Lanyi, Beata Albert, Katalin Bodor, Aurelia Cristina Nechifor, Ildiko Miklossy
2019 Revista de chimie (Bucuresti)  
Herein, we present a systematic model-driven evaluation of the production potential for Escherichia coli to produce BDO from renewable carbohydrates (glucose, glycerol).  ...  Considering the preliminary outcomes the strain and pathway is stable under fermentative conditions and a limited quantity of BDO ~1 mg L-1 was obtained, therefore long-term adaptive evolution is mandatory  ...  A systematic in silico approach was used to metabolic engineering and for a detailed analysis of the BDO metabolism: an accurate genome-scale metabolic model of E. coli [49] , implementation of the new  ... 
doi:10.37358/rc.19.11.7651 fatcat:vbzgzpk3m5gwngzdwzmivbpusy
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