scholarly journals Cross-Feeding between Cyanobacterium Synechococcus and Escherichia Coli in Artificial Autotrophic-Heterotrophic Co-Culture System Revealed by Integrated Omics Analysis

2021 ◽  
Author(s):  
Jiajia Ma ◽  
Taohong Guo ◽  
Lei Chen ◽  
Xinyu Song ◽  
Weiwen Zhang
Keyword(s):  
Escherichia Coli ◽  
Ascorbic Acid ◽  
Cell Growth ◽  
Carbon Metabolism ◽  
Culture System ◽  
Value Added ◽  
Ros Scavenging ◽  
E Coli ◽  
Omics Analysis ◽  
Integrated Omics

Abstract Background: The light-driven consortia consisted of sucrose-secreting cyanobacteria and heterotrophic species capable of producing valuable chemicals have recently attracted significant attention, and are considered as a promising strategy for green biomanufacturing. In a previous study (Zhang et al, 2020, Biotechnol Biofuel, 13:82), we achieved a one-step conversion of CO2 through sucrose derived from cyanobacteria to fine chemicals by constructing an artificial co-culture system consisting of sucrose-secreting Synechococcus elongateus cscB+ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analysis of the co-culture system showed that cyanobacterial cells were growing better than its corresponding axenic culture. To explore the underlaid mechanism and to identify the metabolic modules to further improve the co-culture system, an integrated metabolomics, transcriptomic and proteomic analysis was conducted.Results: We first explored the effect of reactive oxygen species (ROS) on cyanobacterial cell growth under co-culture system by supplementing additional ascorbic acid to scavenge ROS in CoBG-11 medium. The result showed cyanobacterial growth was obviously improved with additional 1 mM ascorbic acid under pure culture; however, cyanobacterial growth was still slower than that in the co-culture with E. coli, suggesting that the better growth of Synechococcus cscB+ might be caused by other factors more than just ROS quenching. We then investigated the intracellular metabolite levels in cyanobacteria using LC-MS based metabolomics analysis. The results showed that metabolites involved in central carbon metabolism were increased, suggesting more carbon sources were utilized by cyanobacteria in the co-culture system, which illuminating that enhanced photosynthesis attributes to the higher CO2 availability produced from co-cultivated heterotrophic partner. To further explore the interaction based on cross-feeding and metabolite exchange, quantitative transcriptomics and proteomics were applied to Synechococcus cscB+. Analysis of differentially regulated genes/proteins showed that the higher availability of carbon, nitrogen, phosphate, calcium, Cu2+, Fe3+ and co-factors was observed in co-cultivated Synechococcus cscB+ during co-cultivation, suggesting the heterotrophic partner in the system might be involved in supplementing CO2 and improving essential micronutrients necessary to maintain high photosynthetic growth of Synechococcus cscB+. Conclusion: Integrated omics analysis of the interaction mechanism between S. elongateus and E. coli showed metabolic changes such as enhanced photosynthesis, oxidative phosphorylation, essential micronutrients, and the ROS scavenging occurred at multiple levels of genes, proteins and metabolites, which might be together contributing to the better cell growth of Synechococcus cscB+ in co-cultivation. In addition, the results implicated that the co-culture system could be further improved by engineering the modules related to the ROS quenching, carbon metabolism, nitrogen metabolism, Pi transport, metal transport and co-factors biosynthesis. Finally, the light condition, which may influence the cross-feeding metabolites between phototrophic and heterotrophic species, and also affect the oxidative pressure on the E. coli strains due to the photosynthesis, could be further optimized to improve cell growth in the co-culture system, eventually leading to high productivity of value-added products.

scholarly journals Study on the isoprene-producing co-culture system of Synechococcus elongatus- Escherichia coli through omics analysis

2020 ◽  
Author(s):  
Hui Liu ◽  
Yujin Cao ◽  
Jing Guo ◽  
Xin Xu ◽  
Qi Long ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Culture System ◽  
Rational Design ◽  
Continuous Fermentation ◽  
Axenic Culture ◽  
Scientific Basis ◽  
Synechococcus Elongatus ◽  
Spatial And Temporal Scales ◽  
E Coli ◽  
Omics Analysis

Abstract Background: The majority of microbial fermentations are currently performed in the batch or fed-batch manner with the high process complexity, huge water consumption and so on. The continuous microbial production can contribute to the green sustainable development of the fermentation industry. The co-culture systems of photo-autotrophic and heterotrophic species can play important roles in establishing the continuous fermentation mode for the bio-based chemicals production. Results: In the present paper, the co-culture system of Synechococcus elongatus- Escherichia coli was established and put into operation stably for isoprene production. Compared with the axenic culture, the fermentation period of time was extended from 100h to 400h in the co-culture and the isoprene production was increased to 8-fold. For in depth understanding this novel system, the differential omics profiles were analyzed. The responses of BL21(DE3) to S. elongatus PCC 7942 were triggered by the oxidative pressure through the Fenton reaction and all these changes were linked with one another at different spatial and temporal scales. The oxidative stress mitigation pathways might contribute to the long-lasting fermentation process. The performance of this co-culture system can be further improved according to the fundamental rules discovered by the omics analysis. Conclusions: The isoprene-producing co-culture system of S. elongatus- E. coli was established and then analyzed by the omics methods. This study on the co-culture system of the model S. elongatus- E. coli is of significance to reveal the common interactions between photo-autotrophic and heterotrophic species without natural symbiotic relation, which could provide the scientific basis for rational design of microbial community.

scholarly journals Study on the isoprene-producing co-culture system of Synechococcus elongates–Escherichia coli through omics analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Hui Liu ◽  
Yujin Cao ◽  
Jing Guo ◽  
Xin Xu ◽  
Qi Long ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Culture System ◽  
Rational Design ◽  
Continuous Fermentation ◽  
Axenic Culture ◽  
Scientific Basis ◽  
Spatial And Temporal Scales ◽  
E Coli ◽  
Omics Analysis ◽  
Symbiotic Relation

Abstract Background The majority of microbial fermentations are currently performed in the batch or fed-batch manner with the high process complexity and huge water consumption. The continuous microbial production can contribute to the green sustainable development of the fermentation industry. The co-culture systems of photo-autotrophic and heterotrophic species can play important roles in establishing the continuous fermentation mode for the bio-based chemicals production. Results In the present paper, the co-culture system of Synechococcus elongates–Escherichia coli was established and put into operation stably for isoprene production. Compared with the axenic culture, the fermentation period of time was extended from 100 to 400 h in the co-culture and the isoprene production was increased to eightfold. For in depth understanding this novel system, the differential omics profiles were analyzed. The responses of BL21(DE3) to S. elongatus PCC 7942 were triggered by the oxidative pressure through the Fenton reaction and all these changes were linked with one another at different spatial and temporal scales. The oxidative stress mitigation pathways might contribute to the long-lasting fermentation process. The performance of this co-culture system can be further improved according to the fundamental rules discovered by the omics analysis. Conclusions The isoprene-producing co-culture system of S. elongates–E. coli was established and then analyzed by the omics methods. This study on the co-culture system of the model S. elongates–E. coli is of significance to reveal the common interactions between photo-autotrophic and heterotrophic species without natural symbiotic relation, which could provide the scientific basis for rational design of microbial community.

scholarly journals Staphylococcus aureus MazF Specifically Cleaves a Pentad Sequence, UACAU, Which Is Unusually Abundant in the mRNA for Pathogenic Adhesive Factor SraP

2009 ◽  
Vol 191 (10) ◽  
pp. 3248-3255 ◽  
Author(s):  
Ling Zhu ◽  
Koichi Inoue ◽  
Satoshi Yoshizumi ◽  
Hiroshi Kobayashi ◽  
Yonglong Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Cell Growth ◽  
Bioinformatics Analysis ◽  
Human Tissues ◽  
Regulatory Relationship ◽  
E Coli ◽  
Pathogenic Factors ◽  
Inhibit Cell Growth ◽  
Adhesive Factor

ABSTRACT Escherichia coli mRNA interferases, such as MazF and ChpBK, are sequence-specific endoribonucleases encoded by toxin-antitoxin (TA) systems present in its genome. A MazF homologue in Staphylococcus aureus (MazFSa) has been shown to inhibit cell growth when induced in E. coli. Here, we determined the cleavage site for MazFSa with the use of phage MS2 RNA as a substrate and CspA, an RNA chaperone, which prevents the formation of secondary structures in the RNA substrate. MazFSa specifically cleaves the RNA at a pentad sequence, U↓ACAU. Bioinformatics analysis revealed that this pentad sequence is significantly abundant in several genes, including the sraP gene in the S. aureus N315 strain. This gene encodes a serine-rich protein, which is known to play an important role in adhesion of the pathogen to human tissues and thus in endovascular infection. We demonstrated that the sraP mRNA became extremely unstable in comparison with the ompA mRNA only when MazFSa was induced in E. coli. Further bioinformatics analysis indicated that the pentad sequence is also significantly abundant in the mRNAs for all the pathogenic factors in S. aureus. This observation suggests a possible regulatory relationship between the MazEFSa TA module and the pathogenicity in S. aureus.

scholarly journals In Vivo Modulation of a DnaJ Homolog, CbpA, by CbpM

2007 ◽  
Vol 189 (9) ◽  
pp. 3635-3638 ◽  
Author(s):  
Matthew R. Chenoweth ◽  
Nancy Trun ◽  
Sue Wickner
Keyword(s):  
Escherichia Coli ◽  
Cell Growth ◽  
Stationary Phase ◽  
Specific Inhibitor ◽  
Vitro Activity ◽  
In Vitro Activity ◽  
E Coli ◽  
Hsp70 Chaperone

ABSTRACT CbpA, an Escherichia coli DnaJ homolog, can function as a cochaperone for the DnaK/Hsp70 chaperone system, and its in vitro activity can be modulated by CbpM. We discovered that CbpM specifically inhibits the in vivo activity of CbpA, preventing it from functioning in cell growth and division. Furthermore, we have shown that CbpM interacts with CbpA in vivo during stationary phase, suggesting that the inhibition of activity is a result of the interaction. These results reveal that the activity of the E. coli DnaK system can be regulated in vivo by a specific inhibitor.

scholarly journals The Role of Metabolites in the Link between DNA Replication and Central Carbon Metabolism in Escherichia coli

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 447
Author(s):  
Klaudyna Krause ◽  
Monika Maciąg-Dorszyńska ◽  
Anna Wosinski ◽  
Lidia Gaffke ◽  
Joanna Morcinek-Orłowska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Protein Interactions ◽  
Carbon Metabolism ◽  
Molecular Mechanisms ◽  
Central Carbon Metabolism ◽  
Replication Initiation ◽  
Cell Physiology ◽  
E Coli ◽  
Central Carbon

A direct link between DNA replication regulation and central carbon metabolism (CCM) has been previously demonstrated in Bacillus subtilis and Escherichia coli, as effects of certain mutations in genes coding for replication proteins could be specifically suppressed by particular mutations in genes encoding CCM enzymes. However, specific molecular mechanism(s) of this link remained unknown. In this report, we demonstrate that various CCM metabolites can suppress the effects of mutations in different replication genes of E. coli on bacterial growth, cell morphology, and nucleoid localization. This provides evidence that the CCM-replication link is mediated by metabolites rather than direct protein-protein interactions. On the other hand, action of metabolites on DNA replication appears indirect rather than based on direct influence on the replication machinery, as rate of DNA synthesis could not be corrected by metabolites in short-term experiments. This corroborates the recent discovery that in B. subtilis, there are multiple links connecting CCM to DNA replication initiation and elongation. Therefore, one may suggest that although different in detail, the molecular mechanisms of CCM-dependent regulation of DNA replication are similar in E. coli and B. subtilis, making this regulation an important and common constituent of the control of cell physiology in bacteria.

Ascorbic Acid Enhances Destruction of Escherichia coli O157:H7 during Home-Type Drying of Apple Slices

2001 ◽  
Vol 64 (8) ◽  
pp. 1244-1248 ◽  
Author(s):  
JENNIFER A. BURNHAM ◽  
PATRICIA A. KENDALL ◽  
JOHN N. SOFOS
Keyword(s):  
Escherichia Coli ◽  
Ascorbic Acid ◽  
Acid Solution ◽  
Escherichia Coli O157 ◽  
Bacterial Populations ◽  
Ascorbic Acid Solution ◽  
Initial Inoculum ◽  
E Coli ◽  
Apple Slices ◽  
Agar Media

Destruction of Escherichia coli O157:H7 was evaluated on inoculated apple slices dehydrated at two temperatures with and without application of predrying treatments. Half-ring slices (0.6 cm thick) of peeled and cored Gala apples were inoculated by immersion for 30 min in a four-strain composite inoculum of E. coli O157:H7. The inoculated slices (8.7 to 9.4 log CFU/g) either received no predrying treatment (control), were soaked for 15 min in a 3.4% ascorbic acid solution, or were steam blanched for 3 min at 88°C immediately prior to drying at 57.2 or 62.8°C for up to 6 h. Samples were plated on tryptic soy (TSA) and sorbitol MacConkey (SMAC) agar media for direct enumeration of surviving bacterial populations. Steam blanching changed initial inoculation levels by +0.3 to −0.7 log CFU/g, while immersion in the ascorbic acid solution reduced the inoculation levels by 1.4 to 1.6 log CFU/g. Dehydration of control samples for 6 h reduced mean bacterial populations by 2.9 log CFU/g (TSA or SMAC) at 57.2°C and by 3.3 (SMAC) and 3.5 (TSA) log CFU/g at 62.8°C. Mean decreases from initial inoculum levels for steam-blanched slices after 6 h of drying were 2.1 (SMAC) and 2.0 (TSA) log CFU/g at 57.2°C, and 3.6 (TSA or SMAC) log CFU/g at 62.8°C. In contrast, initial bacterial populations on ascorbic acid–pretreated apple slices declined by 5.0 (SMAC) and 5.1 (TSA) log CFU/g after 3 h of dehydration at 57.2°C, and by 7.3 (SMAC) and 6.9 (TSA) log CFU/g after 3 h at 62.8°C. Reductions on slices treated with ascorbic acid were in the range of 8.0 to 8.3 log CFU/g after 6 h of drying, irrespective of drying temperature or agar medium used. The results of immersing apple slices in a 3.4% ascorbic acid solution for 15 min prior to drying indicate that a predrying treatment enhances the destruction of E. coli O157:H7 on home-dried apple products.

Effects of Oxidative Compounds on Thermotolerance in Escherichia coli O157:H7 Strains EO139 and 380-94

2005 ◽  
Vol 68 (11) ◽  
pp. 2443-2446 ◽  
Author(s):  
ISABEL C. BLACKMAN ◽  
YOUNG W. PARK ◽  
MARK A. HARRISON
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Ascorbic Acid ◽  
Lethal Effect ◽  
Iron Chloride ◽  
Plate Count ◽  
Escherichia Coli O157 ◽  
Bacterial Cells ◽  
E Coli ◽  
Chloride Hexahydrate

An oxidative complex composed of ferric iron chloride hexahydrate, ADP, and ascorbic acid can generate hydrogen peroxide and hydroxyl radicals in fibroblasts. These compounds are naturally found in meat and meat-based products and may elicit oxidative stress on Escherichia coli O157:H7, thus conferring thermotolerance to the bacterium due to the phenomenon of the global stress response. The effect of the levels of the oxidative complex on the thermotolerance of E. coli O157:H7 was investigated. Cultures of E. coli O157:H7 strains EO139 and 380-94 were mixed in three different concentrations (10:10: 40, 15:15:60, and 20:20:80 μM) of the oxidative complex (iron III chloride, ADP, and ascorbic acid, respectively). The samples were inserted into capillary tubes and heated in a circulating water bath at 59 and 60°C for EO139 and 380-94, respectively. Tubes were removed at intervals of 5 min for up to 1 h and contents spirally plated on plate count agar that was incubated for 48 h at 37°C. The thermotolerance of both E. coli O157:H7 strains EO139 and 380-94 was influenced by the concentrations of the oxidative complex. The ratio of 10:10:40 μM enhanced thermotolerance of EO139 and 390-94 at 59 and 60°C, respectively. However, exposure to the ratios of 15:15:60 and 20:20:80 μM rendered the pathogen more sensitive to the lethal effect and did not enhance the thermotolerance of the cells. The significance of this study is twofold. This experiment proves that oxidative stress can enhance thermotolerance of bacterial cells induced by an oxidative complex if only in a specific ratio and concentration. It is possible to speculate that if the chemical compounds are present in this ratio in meats, they may enhance the thermal resistance of E. coli O157:H7 and make the bacteria more difficult to eliminate, thus increasing the risk of foodborne illness in consumers.

scholarly journals Efficient production of myo-inositol in Escherichia coli through metabolic engineering

2020 ◽  
Author(s):  
Ran You ◽  
Lei Wang ◽  
Congrong Shi ◽  
Hao Chen ◽  
Shasha Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Metabolic Engineering ◽  
Carbon Flux ◽  
Value Added ◽  
Efficient Production ◽  
Wild Type ◽  
Food Industries ◽  
E Coli ◽  
Mixed Carbon Source

Abstract Background: The biosynthesis of high value-added compounds using metabolically engineered strains has received wide attention in recent years. Myo-inositol (inositol), an important compound in the pharmaceutics, cosmetics and food industries, is usually produced from phytate via a harsh set of chemical reactions. Recombinant Escherichia coli strains have been constructed by metabolic engineering strategies to produce inositol, but with a low yield. The proper distribution of carbon flux between cell growth and inositol production is a major challenge for constructing an efficient inositol-synthesis pathway in bacteria. Construction of metabolically engineered E. coli strains with high stoichiometric yield of inositol is desirable.Results: In the present study, we designed an inositol-synthesis pathway from glucose with a theoretical stoichiometric yield of 1 mol inositol/mol glucose. Recombinant E. coli strains with high stoichiometric yield (>0.7 mol inositol/mol glucose) were obtained. Inositol was successfully biosynthesized after introducing two crucial enzymes: inositol-3-phosphate synthase (IPS) from Trypanosoma brucei, and inositol monophosphatase (IMP) from E. coli. Based on starting strains E. coli BW25113 (wild-type) and SG104 (ΔptsG::glk, ΔgalR::zglf, ΔpoxB::acs), a series of engineered strains for inositol production was constructed by deleting the key genes pgi, pfkA and pykF. Plasmid-based expression systems for IPS and IMP were optimized, and expression of the gene zwf was regulated to enhance the stoichiometric yield of inositol. The highest stoichiometric yield (0.96 mol inositol/mol glucose) was achieved from recombinant strain R15 (SG104, Δpgi, Δpgm, and RBSL5-zwf). Strain R04 (SG104 and Δpgi) reached high-density in a 1-L fermenter when using glucose and glycerol as a mixed carbon source. In scaled-up fed-batch bioconversion in situ using strain R04, 0.82 mol inositol/mol glucose was produced within 23 h, corresponding to a titer of 106.3 g/L (590.5 mM) inositol.Conclusions: The biosynthesis of inositol from glucose in recombinant E. coli was optimized by metabolic engineering strategies. The metabolically engineered E. coli strains represent a promising method for future inositol production. This study provides an essential reference to obtain a suitable distribution of carbon flux between glycolysis and inositol synthesis.

scholarly journals Possible epigenetic influence on cellular differentiation and lineage segregation in Escherichia coli

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Cell Growth ◽  
Single Cell ◽  
Cell Fate ◽  
Cellular Differentiation ◽  
Environmental Stressors ◽  
Epigenetic Markers ◽  
E Coli ◽  
Growth Chambers

Epigenetics provides the critical connection between environmental influence and gene expression, where environmental stressors could modulate expression of specific genes in particular scenarios using molecular markers etched at the genome level. Hence, epigenetics likely play important roles in potentiating the development of specific lineages, cell fate or cellular differentiation. For example, when specific environmental stressor is present, epigenetic markers in the genome receive a signal for either activating or deactivating expression of particular sets of genes, which may be linked to the developmental trajectory of the organism. Using Escherichia coli as model organism, a possible study may investigate the role of epigenetics in influencing cellular differentiation of the bacterium. Specifically, a single E. coli cell would be propagated into a consortium of 12 or more bacterial cells in a microfluidics growth chamber. Genetic material extracted would be sent for single cell genomics, transcriptomics, and chromatin immunoprecipitation sequencing (ChIP-seq). After profiling, the residual population would be diverted by microchannels to 6 different cell growth chambers, where they would be cultivated under identical conditions for understanding possible triggers to cell differentiation. At suitable time points of 2, 4, 6, 8, 10, 12 hours, single cell would be extracted from each growth chamber for profiling single cell genomics, transcriptomics, and epigenetics markers. Optical and confocal laser scanning microscopy would provide readout of cell morphologies. Comparison of the readout between the original clonal population and those of the different growth chambers may provide important points for correlating epigenetic markers with gene expression and phenotypic readout in cell lineage, fate and differentiation. In subsequent experiments, different environmental stressors such as pH, imbalance nutrient composition between carbon and nitrogen, nanoparticles or heavy metals, could be used as triggers for specific cell growth response guided by epigenetic programmes embedded within the epigenome of the bacterium. Collectively, epigenetics hold influence for cellular differentiation in view of specific environmental stressors, where epigenetic markers on the genome communicate specific environmental factor's effect on the organism through altering expression of particular sets of genes, that result in different cell fate, lineage and differentiation. Using modern single cell techniques at the genomics, transcriptomics and epigenomics level, the study hopes to elucidate epigenetic potentiators of cellular differentiation in E. coli with and without environmental stressors such as nutrient deprivation, pH and toxic metals.

scholarly journals Reproducing bench-scale cell growth and productivity

2018 ◽  
Author(s):  
Ariel Hecht ◽  
James Filliben ◽  
Sarah A. Munro ◽  
Marc Salit
Keyword(s):  
Escherichia Coli ◽  
Cell Growth ◽  
Small Molecule ◽  
Fluorescent Protein ◽  
Fractional Factorial ◽  
Red Fluorescent Protein ◽  
Factorial Experiments ◽  
Minimum Information ◽  
E Coli ◽  
Product Titer

Reproducing, exchanging, comparing, and building on each other’s work is foundational to technology advances.1Advancing biotechnology calls for reliable reuse of engineered strains.2Reliable reuse of engineered strains requires reproducible growth and productivity. To demonstrate reproducibility for biotechnology, we identified the experimental factors that have the greatest effect on the growth and productivity of our engineered strains.3–6We present a draft of a Minimum Information Standard for Engineered Organism Experiments (MIEO) based on this method. We evaluated the effect of 22 factors onEscherichia coli(E. coli) engineered to produce the small molecule lycopene, and 18 factors onE. coliengineered to produce red fluorescent protein (RFP). Container geometry and shaking had the greatest effect on product titer and yield. We reproduced our results under two different conditions of reproducibility:7conditions of use (different fractional factorial experiments), and time (48 biological replicates performed on 12 different days over four months).

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