Enhancement of RecET-mediated in vivo linear DNA assembly by a xonA mutation

Assembly of intact, replicating plasmids from linear DNA fragments introduced into bacterial cells, i.e. in vivo cloning, is a facile genetic engineering technology that avoids many of the problems associated with standard in vitro cloning. Here we report characterization of various parameters of in vivo linear DNA assembly mediated by either the RecET recombination system or the bacteriophage λ Red recombination system. As previously observed, RecET is superior to Red for this reaction when the terminal homology is 50 bases. Deletion of the E. coli xonA gene, encoding Exonuclease I, a 3′→5′ single-strand DNA exonuclease, substantially improves the efficiency of in vivo linear DNA assembly for both systems. Deletion of ExoI function allowed robust RecET assembly of six DNA segments to create a functional plasmid. The linear DNAs are joined accurately with very few errors. This discovery provides a significant improvement to previously reported in vivo linear DNA assembly technologies.

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Direct preparation of Cas9 ribonucleoprotein from E. coli for PCR-free seamless DNA assembly

10.1101/328468 ◽

2018 ◽

Cited By ~ 3

Author(s):

Wenqiang Li ◽

Shuntang Li ◽

Jie Qiao ◽

Fei Wang ◽

Yang Liu ◽

...

Keyword(s):

Large Scale ◽

Genome Engineering ◽

Restriction Enzymes ◽

General Strategy ◽

Dna Assembly ◽

E Coli ◽

Assembly Method ◽

Direct Preparation

AbstractCRISPR-Cas9 is a versatile and powerful genome engineering tool. Recently, Cas9 ribonucleoprotein (RNP) complexes have been used as promising biological tools with plenty of in vivo and in vitro applications, but there are by far no efficient methods to produce Cas9 RNP at large scale and low cost. Here, we describe a simple and effective approach for direct preparation of Cas9 RNP from E. coli by co-expressing Cas9 and target specific single guided RNAs. The purified RNP showed in vivo genome editing ability, as well as in vitro endonuclease activity that combines with an unexpected superior stability to enable routine uses in molecular cloning instead of restriction enzymes. We further develop a RNP-based PCR-free method termed Cas-Brick in a one-step or cyclic way for seamless assembly of multiple DNA fragments with high fidelity up to 99%. Altogether, our findings provide a general strategy to prepare Cas9 RNP and supply a convenient and cost-effective DNA assembly method as an invaluable addition to synthetic biological toolboxes.

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Curcumin Oxidation Is Required for Inhibition of Helicobacter pylori Growth, Translocation and Phosphorylation of Cag A

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.765842 ◽

2021 ◽

Vol 11 ◽

Author(s):

Ashwini Kumar Ray ◽

Paula B. Luis ◽

Surabhi Kirti Mishra ◽

Daniel P. Barry ◽

Mohammad Asim ◽

...

Keyword(s):

Helicobacter Pylori ◽

Growth Inhibition ◽

Mrna Expression ◽

Host Protein ◽

Dependent Manner ◽

Gene Encoding ◽

E Coli ◽

H Pylori

Curcumin is a potential natural remedy for preventing Helicobacter pylori-associated gastric inflammation and cancer. Here, we analyzed the effect of a phospholipid formulation of curcumin on H. pylori growth, translocation and phosphorylation of the virulence factor CagA and host protein kinase Src in vitro and in an in vivo mouse model of H. pylori infection. Growth of H. pylori was inhibited dose-dependently by curcumin in vitro. H. pylori was unable to metabolically reduce curcumin, whereas two enterobacteria, E. coli and Citrobacter rodentium, which efficiently reduced curcumin to the tetra- and hexahydro metabolites, evaded growth inhibition. Oxidative metabolism of curcumin was required for the growth inhibition of H. pylori and the translocation and phosphorylation of CagA and cSrc, since acetal- and diacetal-curcumin that do not undergo oxidative transformation were ineffective. Curcumin attenuated mRNA expression of the H. pylori virulence genes cagE and cagF in a dose-dependent manner and inhibited translocation and phosphorylation of CagA in gastric epithelial cells. H. pylori strains isolated from dietary curcumin-treated mice showed attenuated ability to induce cSrc phosphorylation and the mRNA expression of the gene encoding for IL-8, suggesting long-lasting effects of curcumin on the virulence of H. pylori. Our work provides mechanistic evidence that encourages testing of curcumin as a dietary approach to inhibit the virulence of CagA.

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Conserved mechanism of cell-wall synthase regulation revealed by the identification of a new PBP activator inPseudomonas aeruginosa

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1717925115 ◽

2018 ◽

Vol 115 (12) ◽

pp. 3150-3155 ◽

Cited By ~ 20

Author(s):

Neil G. Greene ◽

Coralie Fumeaux ◽

Thomas G. Bernhardt

Keyword(s):

Cell Wall ◽

Drug Targets ◽

Bacterial Cells ◽

Acinetobacter Baylyi ◽

Gram Negative ◽

E Coli ◽

Outer Membrane Lipoprotein ◽

Synthase Regulation

Penicillin-binding proteins (PBPs) are synthases required to build the essential peptidoglycan (PG) cell wall surrounding most bacterial cells. The mechanisms regulating the activity of these enzymes to control PG synthesis remain surprisingly poorly defined given their status as key antibiotic targets. Several years ago, the outer-membrane lipoproteinEcLpoB was identified as a critical activator ofEscherichia coliPBP1b (EcPBP1b), one of the major PG synthases of this organism. Activation ofEcPBP1b is mediated through the association ofEcLpoB with a regulatory domain onEcPBP1b called UB2H. Notably,Pseudomonas aeruginosaalso encodes PBP1b (PaPBP1b), which possesses a UB2H domain, but this bacterium lacks an identifiable LpoB homolog. We therefore searched for potentialPaPBP1b activators and identified a lipoprotein unrelated to LpoB that is required for the in vivo activity ofPaPBP1b. We named this protein LpoP and found that it interacts directly withPaPBP1b in vitro and is conserved in many Gram-negative species. Importantly, we also demonstrated thatPaLpoP-PaPBP1b as well as an equivalent protein pair fromAcinetobacter baylyican fully substitute forEcLpoB-EcPBP1b inE. colifor PG synthesis. Furthermore, we show that amino acid changes inPaPBP1b that bypass thePaLpoP requirement map to similar locations in the protein as changes promotingEcLpoB bypass inEcPBP1b. Overall, our results indicate that, although different Gram-negative bacteria activate their PBP1b synthases with distinct lipoproteins, they stimulate the activity of these important drug targets using a conserved mechanism.

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Escherichia coliZipA Organizes FtsZ Polymers into Dynamic Ring-Like Protofilament Structures

mBio ◽

10.1128/mbio.01008-18 ◽

2018 ◽

Vol 9 (3) ◽

Cited By ~ 15

Author(s):

Marcin Krupka ◽

Marta Sobrinos-Sanguino ◽

Mercedes Jiménez ◽

Germán Rivas ◽

William Margolin

Keyword(s):

Cell Division ◽

High Surface ◽

Bacterial Cells ◽

Content Type ◽

E Coli ◽

Membrane Attachment ◽

Lipid Surface ◽

Confocal Fluorescence Imaging

ABSTRACTZipA is an essential cell division protein inEscherichia coli. Together with FtsA, ZipA tethers dynamic polymers of FtsZ to the cytoplasmic membrane, and these polymers are required to guide synthesis of the cell division septum. This dynamic behavior of FtsZ has been reconstituted on planar lipid surfacesin vitro, visible as GTP-dependent chiral vortices several hundred nanometers in diameter, when anchored by FtsA or when fused to an artificial membrane binding domain. However, these dynamics largely vanish when ZipA is used to tether FtsZ polymers to lipids at high surface densities. This, along with somein vitrostudies in solution, has led to the prevailing notion that ZipA reduces FtsZ dynamics by enhancing bundling of FtsZ filaments. Here, we show that this is not the case. When lower, more physiological levels of the soluble, cytoplasmic domain of ZipA (sZipA) were attached to lipids, FtsZ assembled into highly dynamic vortices similar to those assembled with FtsA or other membrane anchors. Notably, at either high or low surface densities, ZipA did not stimulate lateral interactions between FtsZ protofilaments. We also usedE. colimutants that are either deficient or proficient in FtsZ bundling to provide evidence that ZipA does not directly promote bundling of FtsZ filamentsin vivo. Together, our results suggest that ZipA does not dampen FtsZ dynamics as previously thought, and instead may act as a passive membrane attachment for FtsZ filaments as they treadmill.IMPORTANCEBacterial cells use a membrane-attached ring of proteins to mark and guide formation of a division septum at midcell that forms a wall separating the two daughter cells and allows cells to divide. The key protein in this ring is FtsZ, a homolog of tubulin that forms dynamic polymers. Here, we use electron microscopy and confocal fluorescence imaging to show that one of the proteins required to attach FtsZ polymers to the membrane duringE. colicell division, ZipA, can promote dynamic swirls of FtsZ on a lipid surfacein vitro. Importantly, these swirls are observed only when ZipA is present at low, physiologically relevant surface densities. Although ZipA has been thought to enhance bundling of FtsZ polymers, we find little evidence for bundlingin vitro. In addition, we present several lines ofin vivoevidence indicating that ZipA does not act to directly bundle FtsZ polymers.

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Growth Phase and Growth Rate Regulation of therapA Gene, Encoding the RNA Polymerase-Associated Protein RapA in Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.183.20.6126-6134.2001 ◽

2001 ◽

Vol 183 (20) ◽

pp. 6126-6134 ◽

Cited By ~ 14

Author(s):

Julio E. Cabrera ◽

Ding Jun Jin

Keyword(s):

Escherichia Coli ◽

Growth Rate ◽

Rna Polymerase ◽

Growth Phase ◽

Gene Encoding ◽

Rate Regulation ◽

E Coli ◽

Growth Rate Control

ABSTRACT The Escherichia coli rapA gene encodes the RNA polymerase (RNAP)-associated protein RapA, which is a bacterial member of the SWI/SNF helicase-like protein family. We have studied therapA promoter and its regulation in vivo and determined the interaction between RNAP and the promoter in vitro. We have found that the expression of rapA is growth phase dependent, peaking at the early log phase. The growth phase control ofrapA is determined at least by one particular feature of the promoter: it uses CTP as the transcription-initiating nucleotide instead of a purine, which is used for most E. colipromoters. We also found that the rapA promoter is subject to growth rate regulation in vivo and that it forms intrinsic unstable initiation complexes with RNAP in vitro. Furthermore, we have shown that a GC-rich or discriminator sequence between the −10 and +1 positions of the rapA promoter is responsible for its growth rate control and the instability of its initiation complexes with RNAP.

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Escherichia coliZipA organizes FtsZ polymers into dynamic ring-like protofilament structures

10.1101/319228 ◽

2018 ◽

Author(s):

Marcin Krupka ◽

Marta Sobrinos-Sanguino ◽

Mercedes Jiménez ◽

Germán Rivas ◽

William Margolin

Keyword(s):

Cell Division ◽

High Surface ◽

Bacterial Cells ◽

E Coli ◽

Daughter Cells ◽

Membrane Attachment ◽

Lipid Surface ◽

Confocal Fluorescence Imaging

ABSTRACTZipA is an essential cell division protein inEscherichia coli. Together with FtsA, ZipA tethers dynamic polymers of FtsZ to the cytoplasmic membrane, and these polymers are required to guide synthesis of the cell division septum. This dynamic behavior of FtsZ has been reconstituted on planar lipid surfacesin vitro, visible as GTP-dependent chiral vortices several hundred nm in diameter, when anchored by FtsA or when fused to an artificial membrane binding domain. However, these dynamics largely vanish when ZipA is used to tether FtsZ polymers to lipids at high surface densities. This, along with somein vitrostudies in solution, has led to the prevailing notion that ZipA reduces FtsZ dynamics by enhancing bundling of FtsZ filaments. Here, we show that this is not the case. When lower, more physiological levels of the soluble, cytoplasmic domain of ZipA (sZipA) were attached to lipids, FtsZ assembled into highly dynamic vortices similar to those assembled with FtsA or other membrane anchors. Notably, at either high or low surface densities, ZipA did not stimulate lateral interactions between FtsZ protofilaments. We also usedE. colimutants that are either deficient or proficient in FtsZ bundling to provide evidence that ZipA does not directly promote bundling of FtsZ filamentsin vivo. Together, our results suggest that ZipA does not dampen FtsZ dynamics as previously thought, and instead may act as a passive membrane attachment for FtsZ filaments as they treadmill.IMPORTANCEBacterial cells use a membrane-attached ring of proteins to mark and guide formation of a division septum at mid-cell that forms a wall separating the two daughter cells and allows cells to divide. The key protein in this ring is FtsZ, a homolog of tubulin that forms dynamic polymers. Here, we use electron microscopy and confocal fluorescence imaging to show that one of the proteins required to attach FtsZ polymers to the membrane duringE. colicell division, ZipA, can promote dynamic swirls of FtsZ on a lipid surfacein vitro. Importantly, these swirls are only observed when ZipA is present at low, physiologically relevant surface densities. Although ZipA has been thought to enhance bundling of FtsZ polymers, we find little evidence for bundlingin vitro. In addition, we present several lines ofin vivoevidence indicating that ZipA does not act to directly bundle FtsZ polymers.

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CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool

Antibiotics ◽

10.3390/antibiotics8010018 ◽

2019 ◽

Vol 8 (1) ◽

pp. 18 ◽

Cited By ~ 8

Author(s):

Alexandre Loureiro ◽

Gabriela da Silva

Keyword(s):

Genetic Engineering ◽

Genetic Manipulation ◽

State Of The Art ◽

Defence Mechanism ◽

Engineering Technology ◽

Defence System ◽

In Vivo Experiments ◽

Genetic Engineering Technology

Bacteriophages are pervasive viruses that infect bacteria, relying on their genetic machinery to replicate. In order to protect themselves from this kind of invader, bacteria developed an ingenious adaptive defence system, clustered regularly interspaced short palindromic repeats (CRISPR). Researchers soon realised that a specific type of CRISPR system, CRISPR-Cas9, could be modified into a simple and efficient genetic engineering technology, with several improvements over currently used systems. This discovery set in motion a revolution in genetics, with new and improved CRISPR systems being used in plenty of in vitro and in vivo experiments in recent years. This review illustrates the mechanisms behind CRISPR-Cas systems as a means of bacterial immunity against phage invasion and how these systems were engineered to originate new genetic manipulation tools. Newfound CRISPR-Cas technologies and the up-and-coming applications of these systems on healthcare and other fields of science are also discussed.

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ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces

10.1101/2021.01.28.428624 ◽

2021 ◽

Author(s):

Yamal Al-ramahi ◽

Akos Nyerges ◽

Yago Margolles ◽

Lidia Cerdán ◽

Gyorgyi Ferenc ◽

...

Keyword(s):

Bacterial Genome ◽

Industrial Biotechnology ◽

Bacterial Cells ◽

E Coli ◽

Immunomagnetic Capture ◽

Bacterial Surfaces ◽

Potential Applications ◽

Novel Target

SUMMARYIn vivo evolution of antibodies facilitates emergence of novel target specificities from pre-existing clones. In this work we show how mutagenic ssDNA recombineering of camel-derived nanobodies encoded in a bacterial genome enables clonal hyper-diversification and the rise of new properties. As a proof-of-principle we used a nanobody recognizing the antigen TirM from enterohaemorrhagic E. coli (EHEC) and evolved it towards the otherwise not recognized TirM antigen from enteropathogenic E. coli (EPEC). To this end, E. coli cells displaying on their surface this nanobody fused to the intimin outer membrane anchor domain were subjected to multiple rounds of mutagenic ssDNA recombineering targeted to the CDR1, CDR2 and CDR3 regions of its genomically encoded VHH sequence. Binders to the new antigen (EPEC TirM) were then selected upon immunomagnetic capture of bacteria bearing the corresponding nanobody variants. As a result, several modified nanobodies were identified which maintained recognition of EHEC TirM but acquired the ability to bind the new antigen with high affinity (Kd ~20 nM). The results highlight the power of combining evolutionary properties of bacteria in vivo with oligonucleotide synthesis in vitro for the sake of focusing diversification to specific segments of a gene (or protein thereof) of interest. Our experimental workflow empowers the evolution of nanobodies displayed on the surface of bacterial cells for a large number of potential applications in medical and industrial biotechnology.

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Reversible inhibition of bacterial growth after specific inhibition of spermidine synthase by dicyclohexylamine

Biochemical Journal ◽

10.1042/bj2230823 ◽

1984 ◽

Vol 223 (3) ◽

pp. 823-830 ◽

Cited By ~ 10

Author(s):

T Mattila ◽

T Honkanen-Buzalski ◽

H Pösö

Keyword(s):

Final Concentration ◽

Spermidine Synthase ◽

Bacterial Cells ◽

Bacterial Strains ◽

E Coli ◽

Inhibition Of Growth ◽

Streptococcus Uberis ◽

Mastitis Pathogens

The effect of dicyclohexylamine on seven freshly isolated bacterial strains of mastitis pathogens was studied. Streptococcus uberis was the most sensitive strain investigated, since 5 mM-dicyclohexylamine totally arrested its growth and 1.25 mM of the drug caused 60% growth inhibition. The Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa strains were also sensitive to the drug, but less so than Strep. uberis, since 5 mM drug caused only partial inhibition of growth. Micrococcus sp. and Klebsiella sp. grew in the presence of 10.0 mM-dicyclohexylamine, and, finally the growth of Streptococcus agalactiae was not at all affected by dicyclohexylamine. These different sensitivities towards dicyclohexylamine in vivo were paralleled by different sensitivities of the bacteria's spermidine synthase to the drug in vitro, and also by the ability of the drug to lower spermidine concentration in bacterial cells. Spermidine synthase from sensitive bacteria was inhibited by more than 90% by 50 microM-dicyclohexylamine in vitro, and the concentration of spermidine was decreased in E. coli and Ps. aeruginosa by 70% and in Strep. uberis by 95%, whereas in Strep. agalactiae 5 mM-dicyclohexylamine did not affect the concentration of spermidine at all. Dicyclohexylamine treatment led to the accumulation of putrescine in Strep. uberis. Spermidine synthesis catalysed by the extracts of Micrococcus sp. required 500 microM-dicyclohexylamine for 90% inhibition, and Strep. agalactiae contained a spermidine synthase that was still active at 1000 microM-dicyclohexylamine, The observed inhibition of growth was totally reversed by adding 50 microM-spermidine (final concentration) to the medium. Putrescine reversed the inhibition only when bacteria had a spermidine synthase activity insensitive to dicyclohexylamine. Spermine did not overcome the inhibition of growth caused by dicyclohexylamine, probably because it was not taken up by the bacterial cells used in this study. The inhibition of the growth by dicyclohexylamine (even in the case of Strep. uberis) was reversible in the sense that addition of 50 microM-spermidine 18 h after dicyclohexylamine still restored the growth rate of untreated controls.

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Role of bacteriophages in STEC infections: new implications for the design of prophylactic and treatment approaches

F1000Research ◽

10.12688/f1000research.3718.1 ◽

2014 ◽

Vol 3 ◽

pp. 74 ◽

Cited By ~ 7

Author(s):

Jaime H. Amorim ◽

Monica R. Jesus ◽

Wilson B. Luiz ◽

Bruna F.M.M. Porchia ◽

Rita C.C. Ferreira ◽

...

Keyword(s):

Shiga Toxin ◽

Fluorescent Protein ◽

Imaging System ◽

Lytic Replication ◽

Biologically Active ◽

Gene Encoding ◽

E Coli ◽

Green Fluorescent

Shiga toxin (Stx) is considered the main virulence factor in Shiga toxin-producing Escherichia coli (STEC) infections. Previously we reported the expression of biologically active Stx by eukaryotic cells in vitro and in vivo following transfection with plasmids encoding Stx under control of the native bacterial promoter. Since stx genes are present in the genome of lysogenic bacteriophages, here we evaluated the relevance of bacteriophages during STEC infection. We used the non-pathogenic E. coli K12 strain carrying a lysogenic 933W mutant bacteriophage in which the stx operon was replaced by a gene encoding the green fluorescent protein (GFP). Tracking GFP expression using an In Vivo Imaging System (IVIS), we detected fluorescence in liver, kidney, and intestine of mice infected with the recombinant E. coli strain after treatment with ciprofloxacin, which induces the lytic replication and release of bacteriophages. In addition, we showed that chitosan, a linear polysaccharide composed of D-glucosamine residues and with a number of commercial and biomedical uses, had strong anti-bacteriophage effects, as demonstrated in vitro and in vivo. These findings bring promising perspectives for the prevention and treatment of hemolytic uremic syndrome (HUS) cases.

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