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298 results on '"Qimron, Udi"'

2. Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains

Author

Apjok, Gábor, Számel, Mónika, Christodoulou, Chryso, Seregi, Viktória, Vásárhelyi, Bálint Márk, Stirling, Tamás, Eszenyi, Bálint, Sári, Tóbiás, Vidovics, Fanni, Nagrand, Erika, Kovács, Dorina, Szili, Petra, Lantos, Ildikó Ilona, Méhi, Orsolya, Jangir, Pramod K., Herczeg, Róbert, Gálik, Bence, Urbán, Péter, Gyenesei, Attila, Draskovits, Gábor, Nyerges, Ákos, Fekete, Gergely, Bodai, László, Zsindely, Nóra, Dénes, Béla, Yosef, Ido, Qimron, Udi, Papp, Balázs, Pál, Csaba, and Kintses, Bálint

Published
2023
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4. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity

Author

Vialetto, Elena, primary, Miele, Solange, additional, Goren, Moran G, additional, Yu, Jiaqi, additional, Yu, Yanying, additional, Collias, Daphne, additional, Beamud, Beatriz, additional, Osbelt, Lisa, additional, Lourenço, Marta, additional, Strowig, Till, additional, Brisse, Sylvain, additional, Barquist, Lars, additional, Qimron, Udi, additional, Bikard, David, additional, and Beisel, Chase L, additional

Published
2024
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5. Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model.

Author

Yosef, Ido, Edgar, Rotem, Levy, Asaf, Amitai, Gil, Sorek, Rotem, Munitz, Ariel, and Qimron, Udi

Subjects
Escherichia coli, Bacteriophage T7, Bacteriophage lambda, DNA, Viral, Virus Replication, DNA Replication, Mutagenesis, Mutation, Stress, Physiological, Selection, Genetic, Genetics, 2.1 Biological and endogenous factors, Infection
Abstract

The emergence of mutations following growth-limiting conditions underlies bacterial drug resistance, viral escape from the immune system and fundamental evolution-driven events. Intriguingly, whether mutations are induced by growth limitation conditions or are randomly generated during growth and then selected by growth limitation conditions remains an open question(1). Here, we show that bacteriophage T7 undergoes apparent stress-induced mutagenesis when selected for improved recognition of its host's receptor. In our unique experimental set-up, the growth limitation condition is physically and temporally separated from mutagenesis: growth limitation occurs while phage DNA is outside the host, and spontaneous mutations occur during phage DNA replication inside the host. We show that the selected beneficial mutations are not pre-existing and that the initial slow phage growth is enabled by the phage particle's low-efficiency DNA injection into the host. Thus, the phage particle allows phage populations to initially extend their host range without mutagenesis by virtue of residual recognition of the host receptor. Mutations appear during non-selective intracellular replication, and the frequency of mutant phages increases by natural selection acting on free phages, which are not capable of mutagenesis.

Published
2016

8. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning

Author

Sberro, Hila, Leavitt, Azita, Kiro, Ruth, Koh, Eugene, Peleg, Yoav, Qimron, Udi, and Sorek, Rotem

Abstract

Toxin-antitoxin (TA) modules, composed of a toxic protein and a counteracting antitoxin, play important roles in bacterial physiology. We examined the experimental insertion of 1.5 million genes from 388 microbial genomes into an Escherichia coli host using over 8.5 million random clones. This revealed hundreds of genes (toxins) that could only be cloned when the neighboring gene (antitoxin) was present on the same clone. Clustering of these genes revealed TA families widespread in bacterial genomes, some of which deviate from the classical characteristics previously described for such modules. Introduction of these genes into E. coli validated that the toxin toxicity is mitigated by the antitoxin. Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage. Moreover, our experiments revealed an 'anti-defense' protein in phage T7 that neutralizes phage resistance. Our results expose active fronts in the arms race between bacteria and phage.

Published
2013

9. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author

Edwards, Robert A., Vega, Alejandro A., Norman, Holly M., Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A., Cinek, Ondrej, Aziz, Ramy K., McNair, Katelyn, Barr, Jeremy J., Bibby, Kyle, Brouns, Stan J. J., Cazares, Adrian, de Jonge, Patrick A., Desnues, Christelle, Díaz Muñoz, Samuel L., Fineran, Peter C., Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T., Nobrega, Franklin L., Reyes Muñoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander V., Vinuesa, Pablo, Wagemans, Jeroen, Zhernakova, Alexandra, Aarestrup, Frank M., Ahmadov, Gunduz, Alassaf, Abeer, Anton, Josefa, Asangba, Abigail, Billings, Emma K., Cantu, Vito Adrian, Carlton, Jane M., Cazares, Daniel, Cho, Gyu-Sung, Condeff, Tess, Cortés, Pilar, Cranfield, Mike, Cuevas, Daniel A., De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P., Dominy, Nathaniel J., Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Eren, A. Murat, Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M., Haggerty, John M., Head, Steven R., Hendriksen, Rene S., Hill, Colin, Hyöty, Heikki, Ilina, Elena N., Irwin, Mitchell T., Jeffries, Thomas C., Jofre, Juan, Junge, Randall E., Kelley, Scott T., Khan Mirzaei, Mohammadali, Kowalewski, Martin, Kumaresan, Deepak, Leigh, Steven R., Lipson, David, Lisitsyna, Eugenia S., Llagostera, Montserrat, Maritz, Julia M., Marr, Linsey C., McCann, Angela, Molshanski-Mor, Shahar, Monteiro, Silvia, Moreira-Grez, Benjamin, Morris, Megan, Mugisha, Lawrence, Muniesa, Maite, Neve, Horst, Nguyen, Nam-phuong, Nigro, Olivia D., Nilsson, Anders S., O’Connell, Taylor, Odeh, Rasha, Oliver, Andrew, Piuri, Mariana, Prussin II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A. O., Rossi, Alessandro, Santos, Ricardo, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, and Dutilh, Bas E.

Published
2019
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14. Towards T7 RNA polymerase (T7RNAP)-based expression system in yeast: challenges and opportunities

Author

David Sáez Moreno, Qimron Udi, Joana Azeredo, Lucília Domingues, and Universidade do Minho

Subjects
Science & Technology, Protein expression, Bioengineering, General Medicine, Yeast engineering, Applied Microbiology and Biotechnology, Synthetic biology, mRNA capping, T7 RNA polymerase, Biotechnology
Abstract

During the last decades, we have witnessed unprecedented advances in biological engineering and synthetic biology. These disciplines aim to take advantage of gene pathway regulation and gene expression in different organisms, to enable cells to perform desired functions. Yeast has been widely utilized as a model for the study of eukaryotic protein expression while bacteriophage T7RNAP and its promoter constitute the preferred system for prokaryotic protein expression (such as pET-based expression systems). The ability to integrate a T7RNAP-based expression system in yeast could allow for a better understanding of gene regulation in eukaryotic cells, and potentially increase the efficiency and processivity of yeast as an expression system. However, the attempts for the creation of such a system have been unsuccessful to date. This review aims to: (i) summarize the efforts that, for many years, have been devoted to the creation of a T7RNAP-based yeast expression system and ii) provide an overview of the latest advances in knowledge of eukaryotic transcription and translation that could lead to the construction of a successful T7RNAP expression system in yeast. The completion of this new expression system would allow to further expand the toolkit of yeast in synthetic biology and ultimately contribute to boost yeast usage as a key cell factory in sustainable biorefinery and circular economy., The work was supported by the Fundacao para a Ciencia e a Tecnologia [UIDB/04469/2020]; Fundacao para a Ciencia e a Tecnologia [UI/BD/151411/2021]., info:eu-repo/semantics/publishedVersion

Published
2022
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26. CRISPR adaptation biases explain preference for acquisition of foreign DNA

Author

Levy, Asaf, Goren, Moran G., Yosef, Ido, Auster, Oren, Manor, Miriam, Amitai, Gil, Edgar, Rotem, Qimron, Udi, and Sorek, Rotem

Subjects
Nucleotide sequencing, Immune response -- Identification and classification -- Genetic aspects, DNA sequencing, Adaptation (Physiology) -- Identification and classification -- Genetic aspects, Bacterial proteins -- Health aspects, Host-parasite relationships -- Identification and classification -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

CRISPR-Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids. In the process of CRISPR adaptation, short pieces of DNA ('spacers') are acquired from foreign elements and integrated into the CRISPR array. So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition. Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA. We further show that the avoidance of self is mediated by the RecBCD double-stranded DNA break repair complex. Our results suggest that, in Escherichia coli, acquisition of new spacers largely depends on RecBCD-mediated processing of double-stranded DNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA. This model explains the strong preference to acquire spacers both from high copy plasmids and from phages., CRISPR-Cas is an adaptive defence system in bacteria and archaea that provides acquired immunity against phages and plasmids (1-6). It comprises multiple cas genes, as well as an array of [...]

Published
2015
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35. The Escherichia coli CRISPR system protects from [lambda] lysogenization, lysogens, and prophage induction

Author

Edgar, Rotem and Qimron, Udi

Subjects
Escherichia coli -- Physiological aspects, Escherichia coli -- Genetic aspects, Genomes -- Physiological aspects, Lysogeny -- Research, Bacteriophages -- Physiological aspects, Biological sciences
Abstract

We show that phage lysogenization, lysogens, and prophage induction are all targeted by CRISPR. The results demonstrate that genomic DNA is not immune to the CRISPR system, that the CRISPR system does not require noncytoplasmic elements, and that the system protects from phages entering and exiting the lysogenic cycle. doi: 10.1128/JB.00644-10

Published
2010

39. Towards T7 RNA polymerase (T7RNAP)-based expression system in yeast: challenges and opportunities

Author

Sáez Moreno, David, Qimron, Udi, Azeredo, Joana, and Domingues, Lucília

Abstract

ABSTRACTDuring the last decades, we have witnessed unprecedented advances in biological engineering and synthetic biology. These disciplines aim to take advantage of gene pathway regulation and gene expression in different organisms, to enable cells to perform desired functions. Yeast has been widely utilized as a model for the study of eukaryotic protein expression while bacteriophage T7RNAP and its promoter constitute the preferred system for prokaryotic protein expression (such as pET-based expression systems). The ability to integrate a T7RNAP-based expression system in yeast could allow for a better understanding of gene regulation in eukaryotic cells, and potentially increase the efficiency and processivity of yeast as an expression system. However, the attempts for the creation of such a system have been unsuccessful to date. This review aims to: (i) summarize the efforts that, for many years, have been devoted to the creation of a T7RNAP-based yeast expression system and ii) provide an overview of the latest advances in knowledge of eukaryotic transcription and translation that could lead to the construction of a successful T7RNAP expression system in yeast. The completion of this new expression system would allow to further expand the toolkit of yeast in synthetic biology and ultimately contribute to boost yeast usage as a key cell factory in sustainable biorefinery and circular economy.

Published
2022
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47. CRISPR Inspirations

Author

Qimron, Udi, Moineau, Sylvain, Sashital, Dipali, Qimron, Udi, Moineau, Sylvain, and Sashital, Dipali

Published
2020

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