scholarly journals In vivo selection for formate dehydrogenases with high efficiency and specificity towards NADP+

2020 ◽  
Author(s):  
Liliana Calzadiaz Ramirez ◽  
Carla Calvó-Tusell ◽  
Gabriele M. M. Stoffel ◽  
Steffen N. Lindner ◽  
Sílvia Osuna ◽  
...  
Keyword(s):  
High Efficiency ◽  
Screening Methods ◽  
Nadph Regeneration ◽  
E Coli ◽  
Multiple Parameters ◽  
Naturally Occurring ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Enzyme Variant

AbstractEfficient regeneration of cofactors is vital for the establishment of continuous biocatalytic processes. Formate is an ideal electron donor for cofactor regeneration due to its general availability, low reduction potential, and benign byproduct (CO2). However, formate dehydrogenases (FDHs) are usual specific to NAD+, such that NADPH regeneration with formate is challenging. Previous studies reported naturally occurring FDHs or engineered FDHs that accept NADP+, but these enzymes show low kinetic efficiencies and specificities. Here, we harness the power of natural selection to engineer FDH variants to simultaneously optimize three properties: kinetic efficiency with NADP+, specificity towards NADP+, and affinity towards formate. By simultaneously mutating multiple residues of FDH from Pseudomonas sp. 101, which exhibits no initial activity towards NADP+, we generate a library of >106 variants. We introduce this library into an E. coli strain that cannot produce NADPH. By selecting for growth with formate as sole NADPH source, we isolate several enzyme variants that support efficient NADPH regeneration. We find that the kinetically superior enzyme variant, harboring five mutations, has 5-fold higher efficiency and 13-fold higher specificity than the best enzyme previously engineered, while retaining high affinity towards formate. By using molecular dynamics simulations, we reveal the contribution of each mutation to the superior kinetics of this variant. We further determine how non-additive epistatic effects improve multiple parameters simultaneously. Our work demonstrates the capacity of in vivo selection to identify superior enzyme variants carrying multiple mutations which would be almost impossible to find using conventional screening methods.

Combinatorial Synthesis of Novel 3/5(3,5)-(Di)nitro/chloropaeonol Carbonyl Hydrazone Derivatives as Nematicidal Agents

2021 ◽  
Vol 24 ◽  
Author(s):  
Genqiang Chen ◽  
Lina Zhu ◽  
Yanfei Xia ◽  
Jinming Yang ◽  
Song Zhang ◽  
...  
Keyword(s):  
High Efficiency ◽  
Biological Activities ◽  
Science Research ◽  
Nematicidal Activity ◽  
Effective Control ◽  
Root Bark ◽  
Naturally Occurring ◽  
Whole Plant ◽  
Wide Range

Background: Developing the high-efficiency and low-risk small-molecule green-nematocide is the key of effective control of the nematodes. Paeonol, is a naturally occurring phenolic compound, isolated from the root bark of Paeonia suffruticosa and the whole plant of Cynanchum paniculatum. Due to its crucial phenolic ketone skeleton, modern biological science research has indicated that paeonol has a wide range of biological activities. The structural modification of paeonol into paeonol carbonyl hydrazone derivatives is a potential approach for the development of novel nematodes, which showed more toxicity than paeonol. However, there are no reports on the nematicidal activity of paeonol carbonyl hydrazone derivatives to control Heterodera glycines. Results: We always endeavor to discover and develop biorational natural products-based pesticidal agents, 4 significant intermediates and 21 novel 3/5(3,5)-(di)nitro/chloropaeonol carbonyl hydrazone derivatives were prepared, and their structures well characterized by 1H NMR, HRMS, MS, and mp. Due to the steric hindrance, the substituents on the C=N double bond of all hydrazine compounds adopted E configuration. Results of nematicidal activity revealed that, among all compounds, especially 5-nitropaeonol (5) and 3,5-dinitropaeonol (7) displayed the most potent nematicidal activity H. glycines in vivo with LC50 values of 0.0323 and 0.0367 mg/mL, respectively. Conclusion: It suggested that for the 3/5(3,5)-(di)nitro/chloropaeonol carbonyl hydrazone derivatives, a nitro group introduced at C5 position of 1 was necessary for obtaining the potent compound as nematicidal agents. These preliminary results will pave the way for further modification of paeonol in the development of potential new nematicides.

scholarly journals Click-chemistry enabled directed evolution of glycosynthases for bespoke glycans synthesis

2020 ◽  
Author(s):  
Ayushi Agrawal ◽  
Chandra Kanth Bandi ◽  
Tucker Burgin ◽  
Youngwoo Woo ◽  
Heather B. Mayes ◽  
...  
Keyword(s):  
Single Cell ◽  
Click Chemistry ◽  
Directed Evolution ◽  
Cell Sorting ◽  
Screening Methods ◽  
Carbohydrate Active Enzymes ◽  
E Coli ◽  
Highly Sensitive ◽  
Increased Activity

AbstractEngineering of carbohydrate-active enzymes like glycosynthases for chemoenzymatic synthesis of bespoke oligosaccharides has been limited by the lack of suitable directed evolution based protein engineering methods. Currently there are no ultrahigh-throughput screening methods available for rapid and highly sensitive single cell-based screening of evolved glycosynthase enzymes employing azido sugars as substrates. Here, we report a fluorescence-based approach employing click-chemistry for the selective detection of glycosyl azides (versus free inorganic azides) that facilitated ultrahigh-throughput in-vivo single cell-based assay of glycosynthase activity. This discovery has led to the development of a directed evolution methodology for screening and sorting glycosynthase mutants for synthesis of desired fucosylated oligosaccharides. Our screening technique facilitated rapid fluorescence activated cell sorting of a large library of glycosynthase variants (>106 mutants) expressed in E. coli to identify several novel mutants with increased activity for β-fucosyl-azide activated donor sugars towards desired acceptor sugars, demonstrating the broader applicability of this methodology.

scholarly journals Kinetics of Targeted Phage Rescue in a Mouse Model of SystemicEscherichia coliK1

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
György Schneider ◽  
Nikolett Szentes ◽  
Marianna Horváth ◽  
Ágnes Dorn ◽  
Alysia Cox ◽  
...  
Keyword(s):  
Capsular Polysaccharide ◽  
Protective Efficacy ◽  
Lytic Bacteriophage ◽  
E Coli ◽  
Causative Agents ◽  
High Level ◽  
Systemic Infections ◽  
Kinetics Of

Escherichia (E.) coliK1 strains remain common causative agents of neonatal sepsis and meningitis. We have isolated a lytic bacteriophage (ΦIK1) againstE. colistrain IHE3034 and tested its specificityin vitro, as well as distribution and protective efficacyin vivo. The phage was shown to be specific to the K1 capsular polysaccharide. In the lethal murine model, a high level of protection was afforded by the phage with strict kinetics. A single dose of 1 x 108phage particles administered 10 and 60 minutes following the bacterial challenge elicited 100 % and 95 % survival, respectively. No mice could be rescued if phage administration occurred 3 hours postinfection. Tissue distribution surveys in the surviving mice revealed that the spleen was the primary organ in which accumulation of active ΦIK1 phages could be detected two weeks after phage administration. These results suggest that bacteriophages have potential as therapeutic agents in the control of systemic infections.

scholarly journals Creating Hybrid Genes by Homologous Recombination

2000 ◽  
Vol 16 (1-2) ◽  
pp. 3-13 ◽  
Author(s):  
Peter L. Wang
Keyword(s):  
Directed Evolution ◽  
High Efficiency ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Strand Breaks ◽  
E Coli ◽  
Hybrid Genes ◽  
Distinct Features

Recombination of homologous genes is a powerful mechanism for generating sequence diversity, and can be applied to protein analysis and directed evolution.In vitrorecombination methods such as DNA shuffling are very flexible and can give hybrid genes with multiple crossovers; they have been used extensively to evolve proteins with improved and novel properties.In vivorecombination in bothE. coliand yeast is greatly enhanced by double-strand breaks; forE. coli, mutant strains are often necessary to obtain high efficiency. Intra- and inter-molecular recombinationIn vivohave distinct features; both give hybrids with one or two crossovers, and have been used to study structure-function relationships of many proteins. Recentlyin vivorecombination has been used to generate diversity for directed evolution, creating a large phage display antibody library. Recombination methods will become increasingly useful in light of the explosion in genomic sequence data and potential for engineered proteins.

scholarly journals Escherichia coli Survival in, and Release from, White-Tailed Deer Feces

2014 ◽  
Vol 81 (3) ◽  
pp. 1168-1176 ◽  
Author(s):  
Andrey K. Guber ◽  
Jessica Fry ◽  
Rebecca L. Ives ◽  
Joan B. Rose
Keyword(s):  
Escherichia Coli ◽  
Fate And Transport ◽  
Exponential Model ◽  
Temperature Correction ◽  
Content Type ◽  
E Coli ◽  
Naturally Occurring ◽  
Different Temperatures ◽  
Kinetics Of ◽  
Source Materials

ABSTRACTWhite-tailed deer are an important reservoir for pathogens that can contribute a large portion of microbial pollution in fragmented agricultural and forest landscapes. The scarcity of experimental data on survival of microorganisms in and release from deer feces makes prediction of their fate and transport less reliable and development of efficient strategies for environment protection more difficult. The goal of this study was to estimate parameters for modelingEscherichia colisurvival in and release from deer (Odocoileus virginianus) feces. Our objectives were as follows: (i) to measure survival ofE. coliin deer pellets at different temperatures, (ii) to measure kinetics ofE. colirelease from deer pellets at different rainfall intensities, and (iii) to estimate parameters of models describing survival and release of microorganisms from deer feces. Laboratory experiments were conducted to studyE. colisurvival in deer pellets at three temperatures and to estimate parameters of Chick's exponential model with temperature correction based on the Arrhenius equation. Kinetics ofE. colirelease from deer pellets were measured at two rainfall intensities and used to derive the parameters of Bradford-Schijven model of bacterial release. The results showed that parameters of the survival and release models obtained forE. coliin this study substantially differed from those obtained by using other source materials, e.g., feces of domestic animals and manures. This emphasizes the necessity of comprehensive studies of survival of naturally occurring populations of microorganisms in and release from wildlife animal feces in order to achieve better predictions of microbial fate and transport in fragmented agricultural and forest landscapes.

scholarly journals Inhibition of isoleucyl-transfer ribonucleic acid synthetase in Echerichia coli by pseudomonic acid

1978 ◽  
Vol 176 (1) ◽  
pp. 305-318 ◽  
Author(s):  
Julia Hughes ◽  
Graham Mellows
Keyword(s):  
Rna Synthesis ◽  
Inhibitory Effect ◽  
Trna Synthetase ◽  
Threonine Deaminase ◽  
Trna Synthetases ◽  
E Coli ◽  
Naturally Occurring ◽  
Pseudomonic Acid

The mode of action of the antibiotic pseudomonic acid has been studied in Escherichia coli. Pseudomonic acid strongly inhibits protein and RNA synthesis in vivo. The antibiotic had no effect on highly purified DNA-dependent RNA polymerase and showed only a weak inhibitory effect on a poly(U)-directed polyphenylalanine-forming ribosomal preparation. Chloramphenicol reversed inhibition of RNA synthesis in vivo. Pseudomonic acid had little effect on RNA synthesis in a regulatory mutant, E. coli B AS19 RCrel, whereas protein synthesis was strongly inhibited. In pseudomonic acid-treated cells, increased concentrations of ppGpp, pppGpp and ATP were observed, but the GTP pool size decreased, suggesting that inhibition of RNA synthesis is a consequence of the stringent control mechanism imposed by pseudomonic acid-induced deprivation of an amino acid. Of the 20 common amino acids, only isoleucine reversed the inhibitory effect in vivo. The antibiotic was found to be a powerful inhibitor of isoleucyl-tRNA synthetase both in vivo and in vitro. Of seven other tRNA synthetases assayed, only a weak inhibitory effect on phenylalanyl-tRNA synthetase was observed; this presumably accounted for the weak effect on polyphenylalanine formation in a ribosomal preparation. Pseudomonic acid also significantly de-repressed threonine deaminase and transaminase B activity, but not dihydroxyacid dehydratase (isoleucine-biosynthetic enzymes) by decreasing the supply of aminoacylated tRNAIle. Pseudomonic acid is the second naturally occurring inhibitor of bacterial isoleucyl-tRNA synthetase to be discovered, furanomycin being the first.

scholarly journals Deep Sequencing Reveals New Roles for MuB in Transposition Immunity and Target-capture, and Redefines the Insular Ter Region of E. coli

2020 ◽  
Author(s):  
David M Walker ◽  
Rasika Harshey
Keyword(s):  
High Efficiency ◽  
Active Regions ◽  
Minor Role ◽  
Entire Genome ◽  
E Coli ◽  
Target Capture ◽  
Mu Transposition ◽  
A Minor

Abstract Background The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the E. coli genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (cis-immunity) as well as the entire ~37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for cis-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo.Results We tracked Mu transposition from six different starting locations on the E. coli genome, in the presence and absence of MuB. The data reveal that Mu’s ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for cis-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the E. coli genome.Conclusions The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.

scholarly journals Investigation of the in vitro and in vivo activity of the type IV pilus extension ATPase BfpD

2020 ◽  
Author(s):  
Jinlei Zhao ◽  
Shahista Nisa ◽  
Michael S. Donnenberg
Keyword(s):  
Atpase Activity ◽  
Loss Of Function ◽  
Wild Type ◽  
Multifunctional Protein ◽  
Mutant Proteins ◽  
E Coli ◽  
Type Iv ◽  
Kinetics Of

AbstractType IV pili (T4Ps) are multifunctional protein fibers found in many bacteria and archaea. All T4P systems have an extension ATPase, which provides the energy required to push structural subunits out of the membrane. We previously reported that the BfpD T4P ATPase from enteropathogenic E. coli (EPEC) has the expected hexameric structure and ATPase activity, the latter enhanced by the presence of the N-terminal cytoplasmic domains of its partner proteins BfpC and BfpE. In this study, we further investigated the kinetics of the BfpD ATPase. Despite high purity of the proteins, the reported enhanced ATPase activity was found to be from (an) ATPase(s) contaminating the N-BfpC preparation. Furthermore, although two mutations in highly conserved bfpD sites led to loss of function in vivo, the purified mutant proteins retained some ATPase activity, albeit less than the wild-type protein. Therefore, the observed ATPase activity of BfpD was also affected by (a) contaminating ATPase(s). Expression of the mutant bfpD alleles did not interfere with BfpD function in bacteria that also expressed wild-type BfpD. However, a similar mutation of bfpF, which encodes the retraction ATPase, blocked the function of wild-type BfpF when both were present. These results highlight similarities and differences in function and activity of T4P extension and retraction ATPases in EPEC.

Triglyceride kinetics, tissue lipoprotein lipase, and liver lipogenesis in septic rats

1990 ◽  
Vol 258 (4) ◽  
pp. E678-E685 ◽  
Author(s):  
S. Lanza-Jacoby ◽  
A. Tabares
Keyword(s):  
Adipose Tissue ◽  
Lipoprotein Lipase ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
E Coli ◽  
Inbred Rats ◽  
Peripheral Clearance ◽  
Vldl Triglyceride ◽  
Kinetics Of

The mechanism for the development of hypertriglyceridemia during gram-negative sepsis was studied by examining liver production and clearance of very-low-density lipoprotein (VLDL) triglyceride (TG). To assess liver output and peripheral clearance the kinetics of VLDL-TG were determined by a constant iv infusion of [2-3H]glycerol-labeled VLDL. Clearance of VLDL-TG was also evaluated by measuring activities of lipoprotein lipase (LPL) in heart, soleus muscle, and adipose tissue from fasted control, fasted E. coli-treated, fed control, and fed E. coli-treated rats. Lewis inbred rats, 275-300 g, were made septic with 8 x 10(7) live E. coli colonies per 100 g body wt. Twenty-four hours after E. coli injection, serum TG, free fatty acids (FFA), and cholesterol of fasted E. coli-treated rats were elevated by 170, 76, and 16%, respectively. The elevation of serum TG may be attributed to the 67% decrease in clearance rate of VLDL-TG in fasted E. coli-treated rats compared with their fasted controls. The suppressed activities of LPL in adipose tissue, skeletal muscle, and heart were consistent with reduced clearance of TG. Secretion of VLDL-TG declined by 31% in livers of fasted E. coli-treated rats, which was accompanied by a twofold increase in the composition of liver TG. Rates of in vivo TG synthesis in livers of the fasted E. coli-treated rats were twofold higher than in those of fasted control rats. Decreased rate of TG appearance along with the increase in liver synthesis of TG contributed to the elevation of liver lipids in the fasted E. coli-treated rats.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Host Immune Status Influences the Development of Attaching and Effacing Lesions in Weaned Pigs

2005 ◽  
Vol 73 (9) ◽  
pp. 5514-5523 ◽  
Author(s):  
Francis Girard ◽  
Isabelle P. Oswald ◽  
Ionélia Taranu ◽  
Pierre Hélie ◽  
Greg D. Appleyard ◽  
...  
Keyword(s):  
Body Weight ◽  
Immune Status ◽  
Natural Resistance ◽  
Weaned Pigs ◽  
Challenge Strain ◽  
E Coli ◽  
Newborn Piglets ◽  
Reverse Transcription Pcr ◽  
Naturally Occurring

ABSTRACT Attaching and effacing Escherichia coli (AEEC) has been associated with naturally occurring attaching and effacing (A/E) lesions in weaned pigs, and although A/E lesions have been experimentally reproduced in newborn piglets, such lesions have been much more difficult to induce in older conventional pigs. Hence, the aim of this study was to examine the effect of oral administration of dexamethasone on the development of A/E lesions in weaned pigs challenged with a porcine enteropathogenic E. coli (PEPEC) strain and to investigate the involvement of local intestinal cytokine response. Dexamethasone, given orally at a dosage of 3 mg kg of body weight−1, significantly enhanced both the colonization of the challenge strain and the prevalence of foci of intimately adherent bacteria, resulting in extensive A/E lesions in the ileum, cecum, and colon of challenged pigs. We also confirmed the expression of both intimin and Tir by PEPEC strain ECL1001 in A/E lesions in vivo, which is, to our knowledge, the first report of the involvement of the latter proteins in any AEEC infections in vivo. Moreover, semiquantitative reverse transcription-PCR demonstrated that interleukin 1β (IL-1β), IL-6, IL-8, and, to a lesser extent, IL-12p40 are significantly upregulated in the ileum following challenge with strain ECL1001, whereas dexamethasone blocks such upregulation. Taken together, our results strongly suggested that host immune status influences the development of A/E lesions in weaned pigs, and it appears that IL-1β, IL-6, IL-8, and, to a lesser extent, IL-12p40 are expressed during infection of weaned pigs by PEPEC and may contribute to the natural resistance of the host against PEPEC infection.

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