scholarly journals Exploring lowering the optimal growth temperature of Escherichia coli in biotechnology applications

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Growth Temperature ◽  
Optimal Growth ◽  
The Other ◽  
Optimal Growth Temperature ◽  
Laboratory Evolution ◽  
E Coli ◽  
Number Of Genes ◽  
Specific Temperature

Different microbes grow at different optimal growth temperature. But, what defines this metabolic adaptation at the molecular and genetic level? And, more importantly, how different metabolic and signalling networks interact to yield a cellular system able to achieve maximal growth rate at a specific temperature? Molecular knowledge of such interacting components could provide a template on which modifications could be made to help adapt a microbe to another optimal growth temperature. However, given the large number of genes, proteins and pathways involved, efforts to re-adapt a microbe to another optimal growth temperature is likely difficult through a rational design approach. On the other hand, laboratory evolution approach might do the trick, but significant efforts are needed to understand the biochemical and physiological logic of the re-adaption. Using the genetically tractable Escherichia coli as model organism, this work aims to explore the possibility of using a rational approach at lowering the optimal growth temperature of the bacterium from 37 oC to 25 oC to help reduce energy costs and carbon emissions of fermentation. To this end, population level RNA-seq would be used to understand the global transcriptome of E. coli cultivated at 25, 30 and 37 oC in LB medium. Highly transcribed genes at 37 oC would represent those that need to be activated during growth at 25 oC. On the other hand, genes transcribed at a low level at 37 oC should remain poorly expressed at 25 oC. While modern genetic engineering tools such as use of promoters and terminators with differentiated strength would allow the targeted tuning of expression of specific genes, potential need for re-engineering the expression of large number of genes might present difficulties. Thus, answers to what tune a microbe to operate optimally at a specific temperature might come from the signalling and gene regulation level where genes and proteins occupying particular nodes in the biochemical network hold sway on the expression of large number of downstream genes. Knowledge such as these could accrue from the feeding of transcriptome data into genome-scale metabolic models able to help identify critical nodes in metabolic pathways whose modulation would change cellular physiology. Given the importance of regulons governed by specific sigma factors, their modulation through altering sigma factor expression might be critical to gaining more widespread control of global gene expression at particular temperature. Collectively, developing rational approaches for tuning the optimal growth temperature of E. coli present critical challenges compared to laboratory evolution methods. As gene expression is regulated at multiple levels using a variety of mechanisms, transposing expression levels of highly transcribed genes at 37 oC to 25 oC would require the simultaneous modulation of different regulatory nodes belonging to both metabolic and signalling pathways.

scholarly journals Exploring lowering the optimal growth temperature of Escherichia coli in biotechnology applications

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Growth Temperature ◽  
Optimal Growth ◽  
The Other ◽  
Optimal Growth Temperature ◽  
Laboratory Evolution ◽  
E Coli ◽  
Number Of Genes ◽  
Specific Temperature

Different microbes grow at different optimal growth temperature. But, what defines this metabolic adaptation at the molecular and genetic level? And, more importantly, how different metabolic and signalling networks interact to yield a cellular system able to achieve maximal growth rate at a specific temperature? Molecular knowledge of such interacting components could provide a template on which modifications could be made to help adapt a microbe to another optimal growth temperature. However, given the large number of genes, proteins and pathways involved, efforts to re-adapt a microbe to another optimal growth temperature is likely difficult through a rational design approach. On the other hand, laboratory evolution approach might do the trick, but significant efforts are needed to understand the biochemical and physiological logic of the re-adaption. Using the genetically tractable Escherichia coli as model organism, this work aims to explore the possibility of using a rational approach at lowering the optimal growth temperature of the bacterium from 37 oC to 25 oC to help reduce energy costs and carbon emissions of fermentation. To this end, population level RNA-seq would be used to understand the global transcriptome of E. coli cultivated at 25, 30 and 37 oC in LB medium. Highly transcribed genes at 37 oC would represent those that need to be activated during growth at 25 oC. On the other hand, genes transcribed at a low level at 37 oC should remain poorly expressed at 25 oC. While modern genetic engineering tools such as use of promoters and terminators with differentiated strength would allow the targeted tuning of expression of specific genes, potential need for re-engineering the expression of large number of genes might present difficulties. Thus, answers to what tune a microbe to operate optimally at a specific temperature might come from the signalling and gene regulation level where genes and proteins occupying particular nodes in the biochemical network hold sway on the expression of large number of downstream genes. Knowledge such as these could accrue from the feeding of transcriptome data into genome-scale metabolic models able to help identify critical nodes in metabolic pathways whose modulation would change cellular physiology. Given the importance of regulons governed by specific sigma factors, their modulation through altering sigma factor expression might be critical to gaining more widespread control of global gene expression at particular temperature. Collectively, developing rational approaches for tuning the optimal growth temperature of E. coli present critical challenges compared to laboratory evolution methods. As gene expression is regulated at multiple levels using a variety of mechanisms, transposing expression levels of highly transcribed genes at 37 oC to 25 oC would require the simultaneous modulation of different regulatory nodes belonging to both metabolic and signalling pathways.

Optimal growth temperature of O157 and non-O157 Escherichia coli strains

2001 ◽  
Vol 33 (5) ◽  
pp. 352-356 ◽  
Author(s):  
A. Gonthier ◽  
V. Guerin-Faublee ◽  
B. Tilly ◽  
M.-L. Delignette-Muller
Keyword(s):  
Escherichia Coli ◽  
Growth Temperature ◽  
Optimal Growth ◽  
Optimal Growth Temperature

scholarly journals Characteristics of Phomopsis juglandina (Sacc.) Hohn. Associated with Dieback of Walnut in the Climatic Conditions of Southern Romania

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 46
Author(s):  
Cristina Mihaescu ◽  
Daniel Dunea ◽  
Adrian Gheorghe Bășa ◽  
Loredana Neagu Frasin
Keyword(s):  
Growth Temperature ◽  
Potential Evapotranspiration ◽  
Optimal Growth ◽  
Climatic Conditions ◽  
Cultural Characteristics ◽  
Optimal Growth Temperature ◽  
Conidial State ◽  
Optimal Ph

Phomopsis juglandina (Sacc.) Höhn., which is the conidial state of Diaporthe juglandina (Fuckel) Nitschke, and the main pathogen causing the dieback of branches and twigs of walnut was recently detected in many orchards from Romania. The symptomatological, morphological, ultrastructural, and cultural characteristics, as well as the pathogenicity of an isolate of this lignicolous fungus, were described and illustrated. The optimum periods for infection, under the conditions prevailing in Southern Romania, mainly occur in the spring (April) and autumn months (late September-beginning of October). Strong inverse correlations (p < 0.001) were found between potential evapotranspiration and lesion lengths on walnut branches in 2019. The pathogen forms two types of phialospores: alpha and beta; the role of beta phialospores is not well known in pathogenesis. In Vitro, the optimal growth temperature of mycelial hyphae was in the range of 22–26 °C, and the optimal pH is 4.4–7. This pathogen should be monitored continuously due to its potential for damaging infestations of intensive plantations.

scholarly journals Escherichia coli O157:H7 SURVIVAL IN TRADITIONAL AND LOW LACTOSE YOGURT DURING FERMENTATION AND COOLING PERIODS

2017 ◽  
Vol 18 (0) ◽  
Author(s):  
Camila Sampaio Cutrim ◽  
Raphael Ferreira de Barros ◽  
Robson Maia Franco ◽  
Marco Antonio Sloboda Cortez
Keyword(s):  
Escherichia Coli ◽  
The Other ◽  
Lactose Hydrolysis ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Gas Formation ◽  
Whole Milk ◽  
Milk Contamination ◽  
Different Types ◽  
Fermentation Period

Abstract The purpose of this study was to evaluate the behavior of E. coli O157:H7 during lactose hydrolysis and fermentation of traditional and low lactose yogurt. It also aimed to verify E. coli O157:H7 survival after 12 h of storage at 4 ºC ±1 ºC. Two different types of yogurts were prepared, two with whole milk and two with pre-hydrolyzed whole milk; in both groups one yogurt was inoculated with E. coli O157:H7 and the other one was not inoculated. The survival of E. coli and pH of yogurt were determined during fermentation and after 12-h refrigeration. The results showed that E. coli O157:H7 was able to grow during the fermentation period (from 4.34 log CFU.mL-1 to 6.13 log CFU.mL-1 in traditional yogurt and 4.34 log CFU.mL-1 to 6.16 log CFU.mL-1 in low lactose yogurt). The samples with E. coli O157:H7 showed gas formation and syneresis. Thus, E. coli O157:H7 was able to survive and grow during fermentation of traditional and low lactose yogurts affecting the manufacture technology. Moreover, milk contamination by E. coli before LAB addition reduces the growth of L. bulgaricus and S. thermophilus especially when associated with reduction of lactose content.

The correlation between genomic G + C and optimal growth temperature of prokaryotes is robust: A reply to Marashi and Ghalanbor

2005 ◽  
Vol 330 (2) ◽  
pp. 357-360 ◽  
Author(s):  
Hector Musto ◽  
Hugo Naya ◽  
Alejandro Zavala ◽  
Hector Romero ◽  
Fernando Alvarez-Valin ◽  
...  
Keyword(s):  
Growth Temperature ◽  
Optimal Growth ◽  
Optimal Growth Temperature

Genomic GC level, optimal growth temperature, and genome size in prokaryotes

2006 ◽  
Vol 347 (1) ◽  
pp. 1-3 ◽  
Author(s):  
Héctor Musto ◽  
Hugo Naya ◽  
Alejandro Zavala ◽  
Héctor Romero ◽  
Fernando Alvarez-Valín ◽  
...  
Keyword(s):  
Genome Size ◽  
Growth Temperature ◽  
Optimal Growth ◽  
Optimal Growth Temperature

scholarly journals Building a tRNA thermometer to access the world’s biochemical diversity

2020 ◽  
Author(s):  
Emre Cimen ◽  
Sarah E. Jensen ◽  
Edward S. Buckler
Keyword(s):  
Growth Temperature ◽  
Input Data ◽  
Prediction Models ◽  
Extreme Temperature ◽  
Protein Composition ◽  
Network Models ◽  
Optimal Growth ◽  
Optimal Growth Temperature ◽  
Neural Network Models ◽  
Thermophilic Organism

ABSTRACTBecause ambient temperature affects biochemical reactions, organisms living in extreme temperature conditions adapt protein composition and structure to maintain biochemical functions. While it is not feasible to experimentally determine optimal growth temperature (OGT) for every known microbial species, organisms adapted to different temperatures have measurable differences in DNA, RNA, and protein composition that allow OGT prediction from genome sequence alone. In this study, we built a model using tRNA sequence to predict OGT. We used tRNA sequences from 100 archaea and 683 bacteria species as input to train two Convolutional Neural Network models. The first pairs individual tRNA sequences from different species to predict which comes from a more thermophilic organism, with accuracy ranging from 0.538 to 0.992. The second uses the complete set of tRNAs in a species to predict optimal growth temperature, achieving a maximum r2 of 0.86; comparable with other prediction accuracies in the literature despite a significant reduction in the quantity of input data. This model improves on previous OGT prediction models by providing a model with minimum input data requirements, removing laborious feature extraction and data preprocessing steps, and widening the scope of valid downstream analyses.

scholarly journals Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Kumari Sonal Choudhary ◽  
Julia A. Kleinmanns ◽  
Katherine Decker ◽  
Anand V. Sastry ◽  
Ye Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Target Gene ◽  
Target Genes ◽  
Rna Seq ◽  
Content Type ◽  
E Coli ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems

ABSTRACT Escherichia coli uses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data were used to validate condition-specific target gene binding sites. Based on these data, we do the following: (i) identify the target genes for each TCS; (ii) show how the target genes are transcribed in response to stimulus; and (iii) reveal novel relationships between TCSs, which indicate noncognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded. IMPORTANCE E. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli’s two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in E. coli and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.

Involvement of the cgtA gene function in stimulation of DNA repair in Escherichia coli and Vibrio harveyi

Microbiology ◽  
2003 ◽  
Vol 149 (7) ◽  
pp. 1763-1770 ◽  
Author(s):  
Ryszard Zielke ◽  
Aleksandra Sikora ◽  
Rafał Dutkiewicz ◽  
Grzegorz Wegrzyn ◽  
Agata Czyż
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Dna Repair ◽  
Gene Product ◽  
Uv Irradiation ◽  
Vibrio Harveyi ◽  
Bacterial Species ◽  
Wild Type ◽  
E Coli ◽  
Stimulation Of

CgtA is a member of the Obg/Gtp1 subfamily of small GTP-binding proteins. CgtA homologues have been found in various prokaryotic and eukaryotic organisms, ranging from bacteria to humans. Nevertheless, despite the fact that cgtA is an essential gene in most bacterial species, its function in the regulation of cellular processes is largely unknown. Here it has been demonstrated that in two bacterial species, Escherichia coli and Vibrio harveyi, the cgtA gene product enhances survival of cells after UV irradiation. Expression of the cgtA gene was found to be enhanced after UV irradiation of both E. coli and V. harveyi. Moderate overexpression of cgtA resulted in higher UV resistance of E. coli wild-type and dnaQ strains, but not in uvrA, uvrB, umuC and recA mutant hosts. Overexpression of the E. coli recA gene in the V. harveyi cgtA mutant, which is very sensitive to UV light, restored the level of survival of UV-irradiated cells to the levels observed for wild-type bacteria. Moreover, the basal level of the RecA protein was lower in a temperature-sensitive cgtA mutant of E. coli than in the cgtA + strain, and contrary to wild-type bacteria, no significant increase in recA gene expression was observed after UV irradiation of this cgtA mutant. Finally, stimulation of uvrB gene transcription under these conditions was impaired in the V. harveyi cgtA mutant. All these results strongly suggest that the cgtA gene product is involved in DNA repair processes, most probably by stimulation of recA gene expression and resultant activation of RecA-dependent DNA repair pathways.

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