scholarly journals Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

2020 ◽  
Vol 16 (11) ◽  
pp. e1008433
Author(s):  
Magdalena San Roman ◽  
Andreas Wagner
Keyword(s):  
Carbon Source ◽  
Experimental Evolution ◽  
Phenotypic Diversity ◽  
Carbon Sources ◽  
Metabolic Modeling ◽  
Metabolic Changes ◽  
E Coli ◽  
Biochemical Pathways ◽  
Genome Scale ◽  
Feeding Interactions

The evolution of cross-feeding among individuals of the same species can help generate genetic and phenotypic diversity even in completely homogeneous environments. Cross-feeding Escherichia coli strains, where one strain feeds on a carbon source excreted by another strain, rapidly emerge during experimental evolution in a chemically minimal environment containing glucose as the sole carbon source. Genome-scale metabolic modeling predicts that cross-feeding of 58 carbon sources can emerge in the same environment, but only cross-feeding of acetate and glycerol has been experimentally observed. Here we use metabolic modeling to ask whether acetate and glycerol cross-feeding are especially likely to evolve, perhaps because they require less metabolic change, and thus perhaps also less genetic change than other cross-feeding interactions. However, this is not the case. The minimally required metabolic changes required for acetate and glycerol cross feeding affect dozens of chemical reactions, multiple biochemical pathways, as well as multiple operons or regulons. The complexity of these changes is consistent with experimental observations, where cross-feeding strains harbor multiple mutations. The required metabolic changes are also no less complex than those observed for multiple other of the 56 cross feeding interactions we study. We discuss possible reasons why only two cross-feeding interactions have been discovered during experimental evolution and argue that multiple new cross-feeding interactions may await discovery.

scholarly journals Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach

2016 ◽  
Vol 55 (2) ◽  
pp. 81-90 ◽  
Author(s):  
M.A. Prieto-Calvo ◽  
M.K. Omer ◽  
O. Alvseike ◽  
M. López ◽  
A. Alvarez-Ordóñez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Carbon Source ◽  
Carbon Sources ◽  
23S Rrna ◽  
Local Alignment ◽  
Taxonomic Structure ◽  
Sequencing Data ◽  
E Coli ◽  
Additional Information ◽  
Ft Ir

AbstractPhenotypic, chemotaxonomic and genotypic data from 12 strains ofEscherichia coli werecollected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems forE. coliand to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing ofE. colito species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification ofE. coli. The results showed that identification ofE. colistrains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.

scholarly journals Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets

2021 ◽  
Vol 17 (11) ◽  
Author(s):  
Kuoyuan Cheng ◽  
Laura Martin‐Sancho ◽  
Lipika R Pal ◽  
Yuan Pu ◽  
Laura Riva ◽  
...  
Keyword(s):  
Metabolic Modeling ◽  
Metabolic Changes ◽  
Antiviral Targets ◽  
Genome Scale

scholarly journals Optimization of Cellulase Production from Bacteria Isolated from Soil

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Sonia Sethi ◽  
Aparna Datta ◽  
B. Lal Gupta ◽  
Saksham Gupta
Keyword(s):  
Bacillus Subtilis ◽  
Carbon Source ◽  
Pseudomonas Fluorescens ◽  
Carbon Sources ◽  
Nitrogen Sources ◽  
Fermentation Medium ◽  
Cellulase Production ◽  
Culture Conditions ◽  
Optimum Conditions ◽  
E Coli

Cellulase-producing bacteria were isolated from soil and identified as Pseudomonas fluorescens, Bacillus subtilIs, E. coli, and Serratia marcescens. Optimization of the fermentation medium for maximum cellulase production was carried out. The culture conditions like pH, temperature, carbon sources, and nitrogen sources were optimized. The optimum conditions found for cellulase production were 40°C at pH 10 with glucose as carbon source and ammonium sulphate as nitrogen source, and coconut cake stimulates the production of cellulase. Among bacteria, Pseudomonas fluorescens is the best cellulase producer among the four followed by Bacillus subtilis, E. coli, and Serratia marscens.

scholarly journals EXPERIMENTAL EVOLUTION OF A NEW ENZYMATIC FUNCTION. II. EVOLUTION OF MULTIPLE FUNCTIONS FOR EBG ENZYME IN E. COLI

Genetics ◽  
1978 ◽  
Vol 89 (3) ◽  
pp. 453-465
Author(s):  
Barry G Hall
Keyword(s):  
Escherichia Coli ◽  
Carbon Source ◽  
Gene Duplication ◽  
Experimental Evolution ◽  
Evolutionary Pathway ◽  
Multiple Functions ◽  
E Coli ◽  
Enzymatic Function

ABSTRACT The evolution of ebgo enzyme of Escherichia coli, an enzyme which is unable to hydrolyze lactose, lactulose, lactobionate, or galactose-arabinoside effectively, has been directed in successive steps so that the evolved enzyme is able to hydrolyze these galactosides effectively. I show that in order for a strain of E. coli with a lacZ deletion to evolve the ability to use lactobionate as a carbon source, a series of mutations must occur in the ebg genes, and that these mutations must be selected in a particular order. The ordered series of mutations constitutes an obligatory evolutionary pathway for the acquisition of a new function for ebgo enzyme. A comparison of newly evolved strains with parental strains shows that when ebg enzyme acquires a new function, its old functions often suffer; but that in several cases old functions are either unaffected or are improved. I conclude that divergence of functions catalyzed by an enzyme need not require gene duplication.

scholarly journals Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Madeline Tong ◽  
Shawn French ◽  
Sara S. El Zahed ◽  
Wai kit Ong ◽  
Peter D. Karp ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Carbon Source ◽  
High Throughput ◽  
Carbon Metabolism ◽  
Gene Deletion ◽  
Carbon Sources ◽  
Central Metabolism ◽  
Content Type ◽  
E Coli ◽  
Growth Phenotype

ABSTRACT Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growth kinetics of each of 3,796 E. coli single-gene deletion mutants in 30 different carbon sources. In total, there were 342 genes (9.01%) encompassing a breadth of biological functions that showed a growth phenotype on at least 1 carbon source, demonstrating that carbon metabolism is closely linked to a large number of processes in the cell. We identified 74 genes that showed low growth in 90% of conditions, defining a set of genes which are essential in nutrient-limited media, regardless of the carbon source. The data are compiled into a Web application, Carbon Phenotype Explorer (CarPE), to facilitate easy visualization of growth curves for each mutant strain in each carbon source. Our experimental data matched closely with the predictions from the EcoCyc metabolic model which uses flux balance analysis to predict growth phenotypes. From our comparisons to the model, we found that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates. We also identified 51 poorly annotated genes that showed a low growth phenotype in at least 1 carbon source, which allowed us to form hypotheses about the functions of these genes. From this list, we further characterized the ydhC gene and demonstrated its role in adenosine efflux. IMPORTANCE While there has been much study of bacterial gene dispensability, there is a lack of comprehensive genome-scale examinations of the impact of gene deletion on growth in different carbon sources. In this context, a lot can be learned from such experiments in the model microbe Escherichia coli where much is already understood and there are existing tools for the investigation of carbon metabolism and physiology (1). Gene deletion studies have practical potential in the field of antibiotic drug discovery where there is emerging interest in bacterial central metabolism as a target for new antibiotics (2). Furthermore, some carbon utilization pathways have been shown to be critical for initiating and maintaining infection for certain pathogens and sites of infection (3–5). Here, with the use of high-throughput solid medium phenotyping methods, we have generated kinetic growth measurements for 3,796 genes under 30 different carbon source conditions. This data set provides a foundation for research that will improve our understanding of genes with unknown function, aid in predicting potential antibiotic targets, validate and advance metabolic models, and help to develop our understanding of E. coli metabolism.

A Study of Fermentation for Human Interleukin-11 with Recombinant E. Coli

2005 ◽  
Vol 3 (1) ◽  
Author(s):  
Kaili Zhao ◽  
Yiru Gan ◽  
Zisheng Jason Zhang
Keyword(s):  
Carbon Source ◽  
Batch Fermentation ◽  
Carbon Sources ◽  
Biological Properties ◽  
Operational Parameters ◽  
Fed Batch ◽  
E Coli ◽  
Dry Cell Weight ◽  
Fed Batch Fermentation ◽  
Interleukin 11

Recombinant human interleukin-11(rhIL-11) is still the only therapy drug for thrombocytopenia. Although the biological properties and clinical behaviors of rhIL-11 have been studied extensively, its bioprocess development data have rarely been reported. In this work, fermentation conditions for recombinant E. coli, which expressed interleukin-11 as a fusion protein, were investigated. Batch and fed-batch fermentation experiments were performed in shake flasks and in a BioFlo fermenter with different medium and carbon sources under different operational parameters. Based on the results of the study, M9Ca medium was shown as the better medium and glycerol was identified to be a better carbon source than glucose for the expression of rhIL-11. When glycerol was used as the carbon source in fed-batch fermentation, a dry cell weight of 9.2 g/L and a rhIL-11 expression of 22%, were achieved. The results could be used as references in the optimization of the fermentation process.

scholarly journals Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates

2011 ◽  
Vol 77 (22) ◽  
pp. 7915-7923 ◽  
Author(s):  
Sarah M. Chiang ◽  
Tao Dong ◽  
Thomas A. Edge ◽  
Herb E. Schellhorn
Keyword(s):  
Escherichia Coli ◽  
Phenotypic Diversity ◽  
Carbon Sources ◽  
Enteric Bacteria ◽  
Environmental Isolates ◽  
Bacterial Populations ◽  
Content Type ◽  
Phenotypic Differences ◽  
Adaptive Mutations ◽  
E Coli

ABSTRACTEnteric bacteria deposited into the environment by animal hosts are subject to diverse selective pressures. These pressures may act on phenotypic differences in bacterial populations and select adaptive mutations for survival in stress. As a model to study phenotypic diversity in environmental bacteria, we examined mutations of the stress response sigma factor, RpoS, in environmentalEscherichia coliisolates. A total of 2,040 isolates from urban beaches and nearby fecal pollution sources on Lake Ontario (Canada) were screened for RpoS function by examining growth on succinate and catalase activity, two RpoS-dependent phenotypes. TherpoSsequence was determined for 45 isolates, including all candidate RpoS mutants, and of these, six isolates were confirmed as mutants with the complete loss of RpoS function. Similarly to laboratory strains, the RpoS expression of these environmental isolates was stationary phase dependent. However, the expression of RpoS regulon members KatE and AppA had differing levels of expression in several environmental isolates compared to those in laboratory strains. Furthermore, after platingrpoS+isolates on succinate, RpoS mutants could be readily selected from environmentalE. coli. Naturally isolated and succinate-selected RpoS mutants had lower generation times on poor carbon sources and lower stress resistance than theirrpoS+isogenic parental strains. These results show that RpoS mutants are present in the environment (with a frequency of 0.003 among isolates) and that, similarly to laboratory and pathogenic strains, growth on poor carbon sources selects forrpoSmutations in environmentalE. coli. RpoS selection may be an important determinant of phenotypic diversification and, hence, the survival ofE. coliin the environment.

Effect of carbon source on Phenobarbital metabolism by Rhizopus stolonifer

2010 ◽  
Vol 3 (2) ◽  
pp. 1022-1027
Author(s):  
Kavitha K ◽  
Asha S ◽  
Hima Bindu T.V.L ◽  
Vidyavathi M
Keyword(s):  
Carbon Source ◽  
High Performance ◽  
Carbon Sources ◽  
In Vitro Models ◽  
Rhizopus Stolonifer ◽  
Safety And Efficacy ◽  
Alternative Systems ◽  
Toxicological Studies ◽  
Microbial Model

The safety and efficacy of a drug is based on its metabolism or metabolite formed. The metabolism of drugs can be studied by different in vitro models, among which microbial model became popular. In the present study, eight microbes were screened for their ability to metabolize phenobarbital in a manner comparable to humans with a model to develop alternative systems to study human drug metabolism. Among the different microbes screened, a filamentous fungi Rhizopus stolonifer metabolized phenobarbital to its metabolite which is used for further pharmacological and toxicological studies. The transformation of phenobarbital was identified by high- performance liquid chromatography (HPLC). Interestingly, Rhizopus stolonifer sample showed an extra metabolite peak at 3.11min. compared to its controls. The influence of different carbon sources in media used for growth of fungus, on metabolite production was studied, to find its effect in production of metabolite as the carbon source may influence the growth of the cell.

scholarly journals Denitrification Control in a Recirculating Aquaculture System—A Simulation Study

Processes ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. 1306
Author(s):  
Pedro Almeida ◽  
Laurent Dewasme ◽  
Alain Vande Wouwer
Keyword(s):  
Carbon Source ◽  
Carbon Sources ◽  
Aquatic Organisms ◽  
Operating Conditions ◽  
Toxic Substances ◽  
Recirculating Aquaculture System ◽  
Treatment Technology ◽  
Tuning Method ◽  
Recirculating Aquaculture ◽  
Aquaculture System

The recirculating aquaculture system (RAS) is a land-based water treatment technology, which allows for farming aquatic organisms, such as fish, by reusing the water in the production (often less than 5%). This technology is based on the use of filters, either mechanical or biological, and can, in principle, be used for any species grown in aquaculture. Due to the low recirculation rate, ammonia accumulates in the system and must be converted into nitrate using nitrification reactors. Although less toxic for fish, nitrate can also be further reduced into nitrogen gas by the use of denitrification biofilters which may create several issues, such as incomplete denitrification, resulting in toxic substances, such as nitrite and nitric oxide, or a waste of carbon source in excess. Control of the added quantity of carbon source in the denitrification biofilter is then mandatory to keep nitrate/nitrite concentrations under toxic levels for fish and in accordance with local effluent regulations, and to reduce costs related to wasted organic carbon sources. This study therefore investigates the application of different control methodologies to a denitrification reactor in a RAS. To this end, a numerical simulator is built to predict the RAS behavior and to allow for the comparison of different control approaches, in the presence of changes in the operating conditions, such as fish density and biofilter removal efficiency. First, a classical proportional-integral-derivative (PID) controller was designed, based on an SIMC tuning method depending on the amount of ammonia excreted by fish. Then, linearizing and cascade controllers were considered as possible alternatives.

scholarly journals Kinetic analysis and modeling of L-valine production in fermentation batch from E. coli using glucose, lactose and whey as carbon sources

2021 ◽  
Vol 31 ◽  
pp. e00642
Author(s):  
Darwin Carranza-Saavedra ◽  
Claudia Patricia Sánchez Henao ◽  
José Edgar Zapata Montoya
Keyword(s):  
Kinetic Analysis ◽  
Carbon Sources ◽  
E Coli
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