scholarly journals Improved pyrrolysine biosynthesis through continuous directed evolution of the complete pathway

2020 ◽  
Author(s):  
Joanne Ho ◽  
Corwin Miller ◽  
Jacob Mattia ◽  
Matthew Bennett
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Directed Evolution ◽  
Biosynthetic Pathway ◽  
Fluorescent Protein ◽  
Proteinogenic Amino Acid ◽  
E Coli ◽  
Rational Engineering ◽  
Fundamental Building Block ◽  
Green Fluorescent

Abstract Pyrrolysine (Pyl, O) exists in nature as the 22nd proteinogenic amino acid. Despite being a fundamental building block of proteins, studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, we improved Pyl biosynthesis via rational engineering and directed evolution of the entire biosynthetic pathway. To accommodate toxicity of Pyl biosynthetic genes in Escherichia coli, we devised an approach termed Alternating Phage Assisted Non-Continuous Evolution (Alt-PANCE) that alternates mutagenic and selective phage growths. The evolved pathway exhibited a 32-fold improved yield of Pyl-containing super- folder green fluorescent protein (sfGFP) compared to the rationally engineered ancestor, whereas the WT pathway produced no detectable quantities of Pyl-containing sfGFP. This study demonstrates that Alt-PANCE provides a general approach for evolving proteins exhibiting toxic side effects, and further provides an improved pathway capable of producing substantially greater quantities of Pyl- proteins in E. coli.

scholarly journals Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joanne M. L. Ho ◽  
Corwin A. Miller ◽  
Kathryn A. Smith ◽  
Jacob R. Mattia ◽  
Matthew R. Bennett
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Side Effects ◽  
Directed Evolution ◽  
Biosynthetic Pathway ◽  
Reporter Protein ◽  
Proteinogenic Amino Acid ◽  
E Coli ◽  
Rational Engineering ◽  
Fundamental Building Block

AbstractPyrrolysine (Pyl, O) exists in nature as the 22nd proteinogenic amino acid. Despite being a fundamental building block of proteins, studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, we improve Pyl biosynthesis via rational engineering and directed evolution of the entire biosynthetic pathway. To accommodate toxicity of Pyl biosynthetic genes in Escherichia coli, we also develop Alternating Phage Assisted Non-Continuous Evolution (Alt-PANCE) that alternates mutagenic and selective phage growths. The evolved pathway provides 32-fold improved yield of Pyl-containing reporter protein compared to the rationally engineered ancestor. Evolved PylB mutants are present at up to 4.5-fold elevated levels inside cells, and show up to 2.2-fold increased protease resistance. This study demonstrates that Alt-PANCE provides a general approach for evolving proteins exhibiting toxic side effects, and further provides an improved pathway capable of producing substantially greater quantities of Pyl-proteins in E. coli.

A Novel Approach To Investigate the Uptake and Internalization of Escherichia coli O157:H7 in Spinach Cultivated in Soil and Hydroponic Medium†

2009 ◽  
Vol 72 (7) ◽  
pp. 1513-1520 ◽  
Author(s):  
MANAN SHARMA ◽  
DAVID T. INGRAM ◽  
JITENDRA R. PATEL ◽  
PATRICIA D. MILLNER ◽  
XIAOLIN WANG ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Plasmid Vector ◽  
Green Fluorescent Protein Gene ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Novel Approach ◽  
Efficient Uptake ◽  
Green Fluorescent

Internalization of Escherichia coli O157:H7 into spinach plants through root uptake is a potential route of contamination. ATn7-based plasmid vector was used to insert a green fluorescent protein gene into the attTn7 site in the E. coli chromosome. Three green fluorescent protein–labeled E. coli inocula were used: produce outbreak O157:H7 strains RM4407 and RM5279 (inoculum 1), ground beef outbreak O157:H7 strain 86-24h11 (inoculum 2), and commensal strain HS (inoculum 3). These strains were cultivated in fecal slurries and applied at ca. 103 or 107 CFU/g to pasteurized soils in which baby spinach seedlings were planted. No E. coli was recovered by spiral plating from surface-sanitized internal tissues of spinach plants on days 0, 7, 14, 21, and 28. Inoculum 1 survived at significantly higher populations (P < 0.05) in the soil than did inoculum 3 after 14, 21, and 28 days, indicating that produce outbreak strains of E. coli O157:H7 may be less physiologically stressed in soils than are nonpathogenic E. coli isolates. Inoculum 2 applied at ca. 107 CFU/ml to hydroponic medium was consistently recovered by spiral plating from the shoot tissues of spinach plants after 14 days (3.73 log CFU per shoot) and 21 days (4.35 log CFU per shoot). Fluorescent E. coli cells were microscopically observed in root tissues in 23 (21%) of 108 spinach plants grown in inoculated soils. No internalized E. coli was microscopically observed in shoot tissue of plants grown in inoculated soil. These studies do not provide evidence for efficient uptake of E. coli O157:H7 from soil to internal plant tissue.

scholarly journals Inhibition of Salmonella Binding to Porcine Intestinal Cells by a Wood-Derived Prebiotic

2020 ◽  
Vol 8 (7) ◽  
pp. 1051 ◽  
Author(s):  
Aleksandar Božić ◽  
Robin C. Anderson ◽  
Tawni L. Crippen ◽  
Christina L. Swaggerty ◽  
Michael E. Hume ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Saccharomyces Boulardii ◽  
Binding Activity ◽  
Intestinal Cells ◽  
E Coli ◽  
Enteric Infections ◽  
Green Fluorescent

Numerous Salmonella enterica serovars can cause disease and contamination of animal-produced foods. Oligosaccharide-rich products capable of blocking pathogen adherence to intestinal mucosa are attractive alternatives to antibiotics as these have potential to prevent enteric infections. Presently, a wood-derived prebiotic composed mainly of glucose-galactose-mannose-xylose oligomers was found to inhibit mannose-sensitive binding of select Salmonella Typhimurium and Escherichia coli strains when reacted with Saccharomyces boulardii. Tests for the ability of the prebiotic to prevent binding of a green fluorescent protein (GFP)-labeled S. Typhimurium to intestinal porcine epithelial cells (IPEC-J2) cultured in vitro revealed that prebiotic-exposed GFP-labeled S. Typhimurium bound > 30% fewer individual IPEC-J2 cells than did GFP-labeled S. Typhimurium having no prebiotic exposure. Quantitatively, 90% fewer prebiotic-exposed GFP-labeled S. Typhimurium cells were bound per individual IPEC-J2 cell compared to non-prebiotic exposed GFP-labeled S. Typhimurium. Comparison of invasiveness of S. Typhimurium DT104 against IPEC-J2 cells revealed greater than a 90% decrease in intracellular recovery of prebiotic-exposed S. Typhimurium DT104 compared to non-exposed controls (averaging 4.4 ± 0.2 log10 CFU/well). These results suggest compounds within the wood-derived prebiotic bound to E. coli and S. Typhimurium-produced adhesions and in the case of S. Typhimurium, this adhesion-binding activity inhibited the binding and invasion of IPEC-J2 cells.

scholarly journals Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs

2017 ◽  
Vol 83 (8) ◽  
Author(s):  
Shireen Kotay ◽  
Weidong Chai ◽  
William Guilford ◽  
Katie Barry ◽  
Amy J. Mathers
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Hand Washing ◽  
Resistant Bacteria ◽  
Droplet Dispersion ◽  
Content Type ◽  
E Coli ◽  
Mode Of Transmission ◽  
Green Fluorescent

ABSTRACT There have been an increasing number of reports implicating Gammaproteobacteria as often carrying genes of drug resistance from colonized sink traps to vulnerable hospitalized patients. However, the mechanism of transmission from the wastewater of the sink P-trap to patients remains poorly understood. Herein we report the use of a designated hand-washing sink lab gallery to model dispersion of green fluorescent protein (GFP)-expressing Escherichia coli from sink wastewater to the surrounding environment. We found no dispersion of GFP-expressing E. coli directly from the P-trap to the sink basin or surrounding countertop with coincident water flow from a faucet. However, when the GFP-expressing E. coli cells were allowed to mature in the P-trap under conditions similar to those in a hospital environment, a GFP-expressing E. coli-containing putative biofilm extended upward over 7 days to reach the strainer. This subsequently resulted in droplet dispersion to the surrounding areas (<30 in.) during faucet operation. We also demonstrated that P-trap colonization could occur by retrograde transmission along a common pipe. We postulate that the organisms mobilize up to the strainer from the P-trap, resulting in droplet dispersion rather than dispersion directly from the P-trap. This work helps to further define the mode of transmission of bacteria from a P-trap reservoir to a vulnerable hospitalized patient. IMPORTANCE Many recent reports demonstrate that sink drain pipes become colonized with highly consequential multidrug-resistant bacteria, which then results in hospital-acquired infections. However, the mechanism of dispersal of bacteria from the sink to patients has not been fully elucidated. Through establishment of a unique sink gallery, this work found that a staged mode of transmission involving biofilm growth from the lower pipe to the sink strainer and subsequent splatter to the bowl and surrounding area occurs rather than splatter directly from the water in the lower pipe. We have also demonstrated that bacterial transmission can occur via connections in wastewater plumbing to neighboring sinks. This work helps to more clearly define the mechanism and risk of transmission from a wastewater source to hospitalized patients in a world with increasingly antibiotic-resistant bacteria that can thrive in wastewater environments and cause infections in vulnerable patients.

scholarly journals PVv3, a New Shuttle Vector for Gene Expression in Vibrio vulnificus

2013 ◽  
Vol 80 (4) ◽  
pp. 1477-1481 ◽  
Author(s):  
Karina Klevanskaa ◽  
Nadja Bier ◽  
Kerstin Stingl ◽  
Eckhard Strauch ◽  
Stefan Hertwig
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Vibrio Parahaemolyticus ◽  
Fluorescent Protein ◽  
Vibrio Vulnificus ◽  
Shuttle Vector ◽  
Content Type ◽  
E Coli ◽  
Green Fluorescent

ABSTRACTAn efficient electroporation procedure forVibrio vulnificuswas designed using the new cloning vector pVv3 (3,107 bp). Transformation efficiencies up to 2 × 106transformants per μg DNA were achieved. The vector stably replicated in bothV. vulnificusandEscherichia coliand was also successfully introduced intoVibrio parahaemolyticusandVibrio cholerae. To demonstrate the suitability of the vector for molecular cloning, the green fluorescent protein (GFP) gene and thevvhBAhemolysin operon were inserted into the vector and functionally expressed inVibrioandE. coli.

Transformation of Escherichia coli K-12 with a High-Copy Plasmid Encoding the Green Fluorescent Protein Reduces Growth: Implications for Predictive Microbiology†

2006 ◽  
Vol 69 (2) ◽  
pp. 276-281 ◽  
Author(s):  
T. P. OSCAR ◽  
K. DULAL ◽  
D. BOUCAUD
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Predictive Models ◽  
Fluorescent Protein ◽  
Inducible Promoter ◽  
E Coli ◽  
Contaminated Food ◽  
Green Fluorescent ◽  
K 12 ◽  
High Copy Plasmid

The green fluorescent protein (GFP) of the jellyfish Aequorea victoria has been widely used as a biomarker and has potential for use in developing predictive models for growth of pathogens on naturally contaminated food. However, constitutive production of GFP can reduce growth of transformed strains. Consequently, a high-copy plasmid with gfp under the control of a tetracycline-inducible promoter (pTGP) was constructed. The plasmid was first introduced into a tetracycline-resistant strain of Escherichia coli K-12 to propagate it for subsequent transformation of tetracycline-resistant strains of Salmonella. In contrast to transformed E. coli K-12, which only fluoresced in response to tetracycline, transformed Salmonella fluoresced maximally without tetracycline induction of gfp. Although pTGP did not function as intended in Salmonella, growth of parent and GFP E. coli K-12 was compared to test the hypothesis that induction of GFP production reduced growth. Although GFP production was not induced during growth on sterile chicken in the absence of tetracycline, maximum specific growth rate (μmax) of GFP E. coli K-12 was reduced 40 to 50% (P &lt; 0.05) at 10, 25, and 40°C compared with the parent strain. When growth of parent and GFP strains of E. coli K-12 was compared in sterile broth at 40°C, μmax and maximum population density of the GFP strain were reduced (P &lt; 0.05) to the same extent (50 to 60%) in the absence and presence of tetracycline. These results indicated that transformation reduced growth of E. coli K-12 independent of gfp induction. Thus, use of a low-copy plasmid or insertion of gfp into the chromosome may be required to construct valid strains for development of predictive models for growth of pathogens on naturally contaminated food.

scholarly journals Localization of Cell Division Protein FtsK to theEscherichia coli Septum and Identification of a Potential N-Terminal Targeting Domain

1998 ◽  
Vol 180 (5) ◽  
pp. 1296-1304 ◽  
Author(s):  
Xuan-chuan Yu ◽  
Anthony H. Tran ◽  
Qin Sun ◽  
William Margolin
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Cell Division ◽  
Green Fluorescent Protein ◽  
Late Stage ◽  
Fluorescent Protein ◽  
Mutant Protein ◽  
E Coli ◽  
Cell Division Protein ◽  
Green Fluorescent

ABSTRACT Escherichia coli cell division protein FtsK is a homolog of Bacillus subtilis SpoIIIE and appears to act late in the septation process. To determine whether FtsK localizes to the septum, we fused three N-terminal segments of FtsK to green fluorescent protein (GFP) and expressed them in E. colicells. All three segments were sufficient to target GFP to the septum, suggesting that as little as the first 15% of the protein is a septum-targeting domain. Localized fluorescence was detectable only in cells containing a visible midcell constriction, suggesting that FtsK targeting normally occurs only at a late stage of septation. The largest two FtsK-GFP fusions were able at least partially to complement the ftsK44 mutation in trans, suggesting that the N- and C-terminal domains are functionally separable. However, overproduction of FtsK-GFP resulted in a late-septation phenotype similar to that of ftsK44, with fluorescent dots localized at the blocked septa, suggesting that high levels of the N-terminal domain may still localize but also inhibit FtsK activity. Interestingly, under these conditions fluorescence was also sometimes localized as bands at potential division sites, suggesting that FtsK-GFP is capable of targeting very early. In addition, FtsK-GFP localized to potential division sites in cephalexin-induced andftsI mutant filaments, further supporting the idea that FtsK-GFP can target early, perhaps by recognizing FtsZ directly. This hypothesis was supported by the failure of FtsK-GFP to localize inftsZ mutant filaments. In ftsK44 mutant filaments, FtsA and FtsZ were usually localized to potential division sites between the blocked septa. When the ftsK44 mutation was incorporated into the FtsK-GFP fusions, localization to midcell ranged between very weak and undetectable, suggesting that the FtsK44 mutant protein is defective in targeting the septum.

Thermal Inactivation of Escherichia coli O157:H7 in Cow Manure Compost

2003 ◽  
Vol 66 (10) ◽  
pp. 1771-1777 ◽  
Author(s):  
XIUPING JIANG ◽  
JENNIE MORGAN ◽  
MICHAEL P. DOYLE
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Thermal Inactivation ◽  
Fluorescent Protein ◽  
Escherichia Coli O157 ◽  
Cow Manure ◽  
E Coli ◽  
Manure Compost ◽  
D Values ◽  
Green Fluorescent

Rates of inactivation of a five-strain mixture of green fluorescent protein–labeled Escherichia coli O157:H7 in autoclaved and unautoclaved commercial cow manure compost with a moisture content of ca. 38% were determined at temperatures of 50, 55, 60, 65, and 70°C. Trypticase soy agar with ampicillin was determined to be the best medium for the enumeration of heat-injured and uninjured cells of green fluorescent protein–labeled E. coli O157:H7. The results obtained in this study revealed that in autoclaved compost, E. coli O157:H7 reductions of ca. 4 log CFU/g occurred within 8 h, 3 h, 15 min, 2 min, and &lt;1 min at 50, 55, 60, 65, and 70°C, respectively. At 65 and 70°C, considerably less time was required to kill the pathogen in unautoclaved compost than in autoclaved compost. Decimal reduction times (D-values) for autoclaved compost at 50, 55, 60, 65, and 70°C were 137, 50.3, 4.1, 1.8, and 0.93 min, respectively, and D-values for unautoclaved compost at 50, 55, and 60°C were 135, 35.4, and 3.9 min, respectively. Considerable tailing was observed for inactivation curves, especially at 60, 65, and 70°C. These results are useful for identifying composting conditions that will reduce the risk of the transmission of E. coli O157:H7 to foods produced in the presence of animal fecal waste.

Use of Nonpathogenic, Green Fluorescent Protein–Marked Escherichia coli Biotype I Cultures To Evaluate the Self-Cleansing Capabilities of a Commercial Beef Grinding System after a Contamination Event

2014 ◽  
Vol 77 (11) ◽  
pp. 1889-1896 ◽  
Author(s):  
JENNIFER A. WAGES ◽  
JENNIFER WILLIAMS ◽  
JACQUELYN ADAMS ◽  
BRUCE GEORGE ◽  
ERIC OXFORD ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
The Self ◽  
E Coli ◽  
The Third ◽  
Contamination Event ◽  
Green Fluorescent ◽  
Grinding System

Inoculated beef trim containing a cocktail of green fluorescent protein–marked Escherichia coli biotype I cultures as surrogates for E. coli O157:H7 was introduced into two large, commercial grinding facilities capable of producing 180,000 kg of ground product in 1 day. Three repetitions were performed over 3 days. Sampling occurred at three different points within the process: postprimary grind, postsecondary grind-blender, and postpackaging. Resulting data show that, as the inoculated meat passes through the system, the presence of the marked surrogate quickly diminishes. The depletion rates are directly related to the amount of product in kilograms (represented by time) that has passed through the system, but these rates vary with each step of the process. The primary grinder appears to rid itself of the contaminant the most quickly; in all repetitions, the contaminant was not detected within 5 min of introduction of the contaminated combo bin into the system, which in all cases, was prior to the introduction of a second combo bin and within 1,800 kg of product. After the blending step and subsequent secondary grinding, the contaminant was detected in product produced from both the parent combo and the combo bin added directly after the parent combo bin; however, for those days on which three combo bins (approximately 2,700 kg) were available for sampling, the contaminant was not detected from product representing the third combo bin. Similarly, at the packaging step, the contaminant was detected in the product produced by both the parent and second combo bins; however, on those days when a third combo bin was available for sampling (repetitions 2 and 3), the contaminant was not detected from product produced from the third combo bin.

scholarly journals The Mechanism of Chlorine Damage Using Enhanced Green Fluorescent Protein-Expressing Escherichia coli

Water ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2156
Author(s):  
Mizozoe ◽  
Otaki ◽  
Aikawa
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Green Fluorescent Protein ◽  
Cell Membrane ◽  
Fluorescence Intensity ◽  
Enhanced Green Fluorescent Protein ◽  
Hypochlorous Acid ◽  
Fluorescent Protein ◽  
E Coli ◽  
Green Fluorescent

This study investigated how chlorine inactivates and damages Escherichia coli cells. E. coli that had transformed to express enhanced green fluorescent protein (EGFP) at the cytoplasm was treated with chlorine. Damage to the cell membrane and cell wall was analyzed by measuring the fluorescence intensity of the leaked EGFP, then accounting for the fluorescence deterioration. At pH 7, E. coli was lethally damaged after treatment with chlorine, but significant leakage of EGFP was not observed. In contrast, significant leakage of EGFP was observed at pH 9, even though E. coli was not as inactivated as it was at pH 7. Flow cytometry was used to confirm the fluorescence intensity of the remaining EGFP inside the cells. No significant fluorescence loss was observed in the cells at pH 7. However, at pH 9, the fluorescence intensity in the cells decreased, indicating leakage of EGFP. These results suggest that hypochlorous acid inactivates E. coli without damaging its cell membrane and cell wall, whereas the hypochlorite ion inactivates E. coli by damaging its cell membrane and cell wall. It was possible to confirm the chlorine damage mechanism on E. coli by measuring the fluorescence intensity of the leaked EGFP.

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