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1. A photo-cross-linking approach to monitor protein dynamics in living cells

Author:
Miyazaki, Ryoji; Akiyama, Yoshinori; Mori, Hiroyuki
Source:
Biochimica et biophysica acta 2019
ISSN:
0304-4165
Subject:
Escherichia coli,   etc   ; biogenesis; cells; proteins;     Show all 4 Subjects
Abstract:
... Proteins, which comprise one of the major classes of biomolecules that constitute a cell, interact with other cellular factors during both their biogenesis and functional states. Studying not only static but also transient interactions of proteins is important to understand their physiological roles and regulation mechanisms. However, only a limited number of methods are available to analyze the d ...
DOI:
10.1016/j.bbagen.2019.03.003

2. Resistance of various shiga-toxin producing Escherichia coli (STEC) strains and serogroups to infra-red and pulsed UV radiation and effect of nalidixic acid adaptation

Author:
Chintagari, Sailaja; Jadeja, Raviraj; Hung, Yen-Con
Source:
Lebensmittel-Wissenschaft + [i.e. und] Technologie 2019 v.102 pp. 356-363
ISSN:
0023-6438
Subject:
Escherichia coli O104; Escherichia coli O157; Escherichia coli O26,   etc   ; acid tolerance; nalidixic acid; serotypes; ultraviolet radiation;     Show all 7 Subjects
Abstract:
... The efficacy of Infra-red radiation (IR) and Pulsed UV (PUV) for the inactivation of parent (Par) and Nalidixic acid adapted (Nal) strains of Escherichia coli O157:H7, top six shiga-toxin producing E. coli (E. coli O26, E. coli O45, E. coli O103, E. coli O111, E. coli O121, and E. coli O145 and E. coli O104) along with nonpathogenic surrogates were evaluated. It was observed that significant (P <  ...
DOI:
10.1016/j.lwt.2018.11.094

3. High‐affinity l‐malate transporter DcuE of Actinobacillus succinogenes catalyses reversible exchange of C4‐dicarboxylates

Author:
Rhie, Mi Na; Cho, Young Bin; Lee, Yeon Joo; Kim, Ok Bin
Source:
Environmental microbiology reports 2019 v.11 no.2 pp. 129-139
ISSN:
1758-2229
Subject:
Escherichia coli,   etc   ; Actinobacillus succinogenes; antiporters; catalytic activity;     Show all 4 Subjects
Abstract:
... Actinobacillus succinogenes is a natural succinate producer, which is the result of fumarate respiration. Succinate production from anaerobic growth with C₄‐dicarboxylates requires transporters catalysing uptake and efflux of C₄‐dicarboxylates. Transporter Asuc_1999 (DcuE) found in A. succinogenes belongs to the Dcu family and was considered the main transporter for fumarate respiration. However, ...
DOI:
10.1111/1758-2229.12719

4. Correction: Directed evolution of mevalonate kinase in Escherichia coli by random mutagenesis for improved lycopene

Author:
Chen, Hailin; Liu, Changqing; Li, Meijie; Zhang, Haibo; Xian, Mo; Liu, Huizhou
Source:
RSC advances 2019 v.9 no.16 pp. 8934
ISSN:
2046-2069
Subject:
Escherichia coli,   etc   ; directed evolution; enzymes; lycopene; mutagenesis;     Show all 5 Subjects
Abstract:
... Correction for ‘Directed evolution of mevalonate kinase in Escherichia coli by random mutagenesis for improved lycopene’ by Hailin Chen et al., RSC Adv., 2018, 8, 15021–15028. ...
DOI:
10.1039/c9ra90021g

5. Modular Engineering of Tyrosol Production in Escherichia coli

Author:
Yang, Haiquan; Xue, Yuxiang; Yang, Cui; Shen, Wei; Fan, You; Chen, Xianzhong
Source:
Journal of agricultural and food chemistry 2019 v.67 no.14 pp. 3900-3908
ISSN:
1520-5118
Subject:
Escherichia coli,   etc   ; engineering; genes; industrial applications;     Show all 4 Subjects
Abstract:
... In this study, we investigated the effects of the different critical genes in the three modules on tyrosol production in Escherichia coli. Coexpression of the yahK and ARO10 genes increased the yield of tyrosol by 10% compared to that of the control. Tyrosol production by E. coli BFPT1 and E. coli BFPA1 was higher by 15.0% and 17.8% than that by the control, respectively, via coordinated expressio ...
DOI:
10.1021/acs.jafc.9b00227

6. Center Finding in E. coli and the Role of Mathematical Modeling: Past, Present and Future

Author:
Murray, Seán M.; Howard, Martin
Source:
Journal of molecular biology 2019 v.431 no.5 pp. 928-938
ISSN:
0022-2836
Subject:
Escherichia coli,   etc   ; DNA; mathematical models; microbiology;     Show all 4 Subjects
Abstract:
... We review the key role played by mathematical modeling in elucidating two center-finding patterning systems in Escherichia coli: midcell division positioning by the MinCDE system and DNA partitioning by the ParABS system. We focus particularly on how, despite much experimental effort, these systems were simply too complex to unravel by experiments alone, and instead required key injections of quan ...
DOI:
10.1016/j.jmb.2019.01.017

7. An improved plasmid size standard, 39R861+

Author:
Moran, Robert A.; Anantham, Sashindran; Hall, Ruth M.
Source:
Plasmid 2019 v.102 pp. 6-9
ISSN:
0147-619X
Subject:
Escherichia coli,   etc   ; genetic conjugation; nucleotide sequences; plasmids;     Show all 4 Subjects
Abstract:
... The four plasmids in E. coli 39R861 have been used as size standards for closed-circular plasmid DNA since the 1980s. However, their sizes had only been estimated. Here, the complete sequence of the 61.3 kb cryptic FII plasmid p39R861–3 is reported, and the sizes of p39R861–4, pSa and NTP168 were determined to be 155.8, 40.1 and 6.8 kb, respectively. An improved size standard, 39R861+, was created ...
DOI:
10.1016/j.plasmid.2019.01.002

8. Extent of adaptation is not limited by unpredictability of the environment in laboratory populations of Escherichia coli

Author:
Karve, Shraddha M.; Bhave, Devika; Dey, Sutirth
Source:
Journal of evolutionary biology 2018 v.31 no.9 pp. 1420-1426
ISSN:
1010-061X
Subject:
Escherichia coli,   etc   ; pH; temperature;     Show all 3 Subjects
Abstract:
... Environmental variability is on the rise in different parts of the earth, and the survival of many species depends on how well they cope with these fluctuations. Our current understanding of how organisms adapt to unpredictably fluctuating environments is almost entirely based on studies that investigate fluctuations among different values of a single environmental stressor such as temperature or ...
DOI:
10.1111/jeb.13338

9. Histamine H1 receptor antagonists enhance the efficacy of antibacterials against Escherichia coli

Author:
Bruer, G. G.; Hagedorn, P.; Kietzmann, M.; Tohamy, A. F.; Filor, V.; Schultz, E.; Mielke-Kuschow, S.; Meissner, J.
Source:
BMC veterinary research 2019 v.15 no.1 pp. 55
ISSN:
1746-6148
Subject:
Escherichia coli,   etc   ; antagonists; antihistamines; histamine; microorganisms; minimum inhibitory concentration;     Show all 6 Subjects
Abstract:
... BACKGROUND: H₁ receptor antagonists are commonly used for the treatment of allergic diseases. The aim of this study was to find out, if antihistaminic compounds like mepyramine have the ability to influence the activity of antibacterials. Therefore, the checkerboard method was chosen to detect these possible effects in vitro. Studies were performed with two different Escherichia coli (E. coli) str ...
DOI:
10.1186/s12917-019-1797-9

10. Ultrabright fluorescent microsphere and its novel application for improving the sensitivity of immunochromatographic assay

Author:
Zhang, Gang-gang; Xu, Shao-lan; Xiong, Yong-hua; Duan, Hong; Chen, Wen-yao; Li, Xiang-min; Yuan, Mei-fang; Lai, Wei-hua
Source:
Biosensors & bioelectronics 2019 v.135 pp. 173-180
ISSN:
0956-5663
Subject:
Escherichia coli O157,   etc   ; biosensors; detection limit; fluorescence; immunoaffinity chromatography; microparticles;     Show all 6 Subjects
Abstract:
... Fluorescent microsphere (FM) is widely used as probe in immunochromatographic assay (ICA). However, the performance of conventional FM is limited because of the aggregation-caused quenching effect. Herein, we compared a kind of conventional FM (DMFFM, loading DMF) with novel aggregation-induced emission FM (AIEFM, loading TCBPE). The fluorescence intensity of DMFFM initially increased and then dec ...
DOI:
10.1016/j.bios.2019.04.023

11. Recent advancements in fungal-derived fuel and chemical production and commercialization

Author:
Ekas, Holly; Deaner, Matthew; Alper, Hal S
Source:
Current opinion in biotechnology 2019 v.57 pp. 1-9
ISSN:
0958-1669
Subject:
Escherichia coli,   etc   ; animals; commercialization; fermentation; petroleum; synthetic biology; yeasts;     Show all 7 Subjects
Abstract:
... Due to unsustainable petroleum supply and poor yields from plant and animal sources, there is an increased effort to engineer microbial hosts for renewable chemical production. When compared to microbes such as Escherichia coli, fungal hosts show advantages due to their natural robust tolerance for industrial fermentation. Synthetic biology has focused on implementing heterologous pathways and man ...
DOI:
10.1016/j.copbio.2018.08.014

12. Near Saturation of Ribosomal L7/L12 Binding Sites with Ternary Complexes in Slowly Growing E. coli

Author:
Mustafi, Mainak; Weisshaar, James C.
Source:
Journal of molecular biology 2019 v.431 no.12 pp. 2343-2353
ISSN:
0022-2836
Subject:
Escherichia coli,   etc   ; amino acids; binding sites; enzyme kinetics; osmolality; ribosomes;     Show all 6 Subjects
Abstract:
... For Escherichia coli growing rapidly in rich medium at 37 °C, the doubling time can be as short as ~20 min and the average rate of translation (ktrl) can be as fast as ~20 amino acids/s. For slower growth arising from poor nutrient quality or from higher growth osmolality, ktrl decreases significantly. In earlier work from the Hwa lab, a simplified Michaelis–Menten model suggested that the decreas ...
DOI:
10.1016/j.jmb.2019.04.037

13. Production of 8S- and 10S-hydroxy polyunsaturated fatty acids by recombinant Escherichia coli cells expressing mouse arachidonate 8S-lipoxygenase

Author:
Shin, Kyung-Chul; Kang, Woo-Ri; Seo, Min-Ju; Kim, Dae Wook; Oh, Deok-Kun
Source:
Biotechnology letters 2019 v.41 no.4-5 pp. 575-582
ISSN:
0141-5492
Subject:
Escherichia coli,   etc   ; arachidonic acid; eicosapentaenoic acid; enzymes; hydroxylation; mice; pH;     Show all 7 Subjects
Abstract:
... OBJECTIVE: To quantitatively hydroxylate 8S- and 10S-positions on polyunsaturated fatty acids by recombinant Escherichia coli cells expressing mouse arachidonate 8S-lipoxygenase (8S-LOX). RESULTS: Hydroxylated products gained from the conversion of arachidonic acid (20:4Δ⁵Z,⁸Z,¹¹Z,¹⁴Z, AA), eicosapentanoic acid (20:5Δ⁵Z,⁸Z,¹¹Z,¹⁴Z,¹⁷Z, EPA), and (22:6Δ⁴Z,⁷Z,¹⁰Z,¹³Z,¹⁶Z,¹⁹Z, DHA) by recombinant E. ...
DOI:
10.1007/s10529-019-02659-5

14. Assembly of TALE-based DNA scaffold for the enhancement of exogenous multi-enzymatic pathway

Author:
Xie, Si-si; Qiu, Xin-yuan; Zhu, Lv-yun; Zhu, Chu-shu; Liu, Chuan-yang; Wu, Xiao-min; Zhu, Lingyun; Zhang, Dong-yi
Source:
Journal of biotechnology 2019 v.296 pp. 69-74
ISSN:
0168-1656
Subject:
Escherichia coli,   etc   ; biochemical pathways; enzymes; plasmids; transcription (genetics);     Show all 5 Subjects
Abstract:
... Synthetic scaffold systems, which exhibit enzyme clustering effect, have been considered as an important parallel approach for metabolic flux control and pathway enhancement. Here, we described an improved DNA-based scaffold system for synthetic tri-enzymatic pathway in Escherichia coli. With plasmid DNA serving as scaffold and exogenous enzymes fused with rationally designed transcription activat ...
DOI:
10.1016/j.jbiotec.2019.03.008

15. Pif1-Family Helicases Support Fork Convergence during DNA Replication Termination in Eukaryotes

Author:
Deegan, Tom D.; Baxter, Jonathan; Ortiz Bazán, María Ángeles; Yeeles, Joseph T.P.; Labib, Karim P.M.
Source:
Molecular cell 2019 v.74 no.2 pp. 231-244.e9
ISSN:
1097-2765
Subject:
Escherichia coli,   etc   ; DNA helicases; DNA replication; eukaryotic cells; plasmids; yeasts;     Show all 6 Subjects
Abstract:
... The convergence of two DNA replication forks creates unique problems during DNA replication termination. In E. coli and SV40, the release of torsional strain by type II topoisomerases is critical for converging replisomes to complete DNA synthesis, but the pathways that mediate fork convergence in eukaryotes are unknown. We studied the convergence of reconstituted yeast replication forks that incl ...
DOI:
10.1016/j.molcel.2019.01.040

16. The Unique Lifestyle of Crohn's Disease-Associated Adherent-Invasive Escherichia coli

Author:
Shaler, Christopher R.; Elhenawy, Wael; Coombes, Brian K.
Source:
Journal of molecular biology 2019
ISSN:
0022-2836
Subject:
Escherichia coli,   etc   ; Crohn disease; bacteria; host-pathogen relationships; phylogeny;     Show all 5 Subjects
Abstract:
... Escherichia coli is one of the most genetically and phenotypically diverse species of bacteria. This remarkable diversity produces a plethora of clinical outcomes following infection and has informed much of what we currently know about host–pathogen interactions for a wide range of bacteria–host relationships. In studying the role of microbes in disease, adherent-invasive E. coli (AIEC) has emerg ...
DOI:
10.1016/j.jmb.2019.04.023

17. The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase

Author:
Imashimizu, Masahiko; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Shimamoto, Nobuo
Source:
Journal of molecular biology 2019
ISSN:
0022-2836
Subject:
Escherichia coli,   etc   ; DNA-directed RNA polymerase; RNA; nucleotides;     Show all 4 Subjects
Abstract:
... RNA polymerase can cleave a phosphodiester bond at the 3′ end of a nascent RNA in the presence of pyrophosphate producing NTP. Pyrophosphorolysis has been characterized during elongation steps of transcription where its rate is significantly slower than the forward rate of NMP addition. In contrast, we report here that pyrophosphorolysis can occur in a millisecond time scale during the transition ...
DOI:
10.1016/j.jmb.2019.04.020

18. Mechanisms of Bacterial Transcription Termination

Author:
Roberts, Jeffrey W.
Source:
Journal of molecular biology 2019
ISSN:
0022-2836
Subject:
Escherichia coli,   etc   ; DNA; enzymes; messenger RNA; torque; transcription termination;     Show all 6 Subjects
Abstract:
... Bacterial transcription termination, described mostly for Escherichia coli, occurs in three recognized ways: intrinsic termination, an activity only of the core RNAP enzyme and transcript sequences that encode an RNA hairpin and terminal uridine-rich segment; termination by the enzyme Rho, an ATP-dependent RNA translocase that releases RNA by forcing uncharacterized structural changes in the elong ...
DOI:
10.1016/j.jmb.2019.04.003

19. Nonnatural biosynthetic pathway for 2-hydroxylated xanthophylls with C50-carotenoid backbone

Author:
Li, Ling; Furubayashi, Maiko; Otani, Yusuke; Maoka, Takashi; Misawa, Norihiko; Kawai-Noma, Shigeko; Saito, Kyoichi; Umeno, Daisuke
Source:
Journal of bioscience and bioengineering 2019
ISSN:
1389-1723
Subject:
Escherichia coli,   etc   ; Brevundimonas; biochemical pathways; biosynthesis; enzymes; xanthophylls;     Show all 6 Subjects
Abstract:
... Carotenoids are structurally diverse pigments with various important biological functions. There has been a large interest in the search for novel carotenoid structures, since only a slight structural changes can result in a drastic difference in their biological functions. Carotenoid-modifying enzymes show remarkable substrate promiscuity, allowing rapid access to a vast set of novel carotenoids ...
DOI:
10.1016/j.jbiosc.2019.04.002

20. Effects of sound elements on growth, viability and protein production yield in Escherichia coli

Author:
Acuña‐González, Edgar; Ibarra, David; Benavides, Jorge
Source:
Journal of chemical technology and biotechnology 2019 v.94 no.4 pp. 1100-1113
ISSN:
0268-2575
Subject:
Escherichia coli,   etc   ; biomass; protein synthesis; recombinant proteins; viability;     Show all 5 Subjects
Abstract:
... BACKGROUND: The effect of sound on biological systems has been addressed previously in the literature. However, most studies addressing this topic focus on the characterization of the effect of frequency on biological systems. In this regard the effect of other soundwave elements has been overlooked. In the present work, the effects of frequency, amplitude, duration, intermittence and pulse – indi ...
DOI:
10.1002/jctb.5857