Studying the features of 57 confirmed CRISPR loci in 29 strains of <i>Escherichia coli</i>

Rahmatabadi, Seyyed Soheil; Nezafat, Navid; Negahdaripour, Manica; Hajighahramani, Nasim; Morowvat, Mohammad Hossein; Ghasemi, Younes

doi:10.1002/jobm.201500707

Cited by 22 publications

(9 citation statements)

References 32 publications

(58 reference statements)

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“…Cas proteins function to degrade foreign nucleic acids of bacteriophages or plasmids. The number of CRISPR loci detected vary between and within bacterial species and strains, 1–4 in Escherichia coli [ 3 ], 3 in Yersinia pestis [ 4 ], 2 in Salmonella Typhimurium [ 5 ], and 1–2 in Staphylococcus aureus [ 6 ]. CRISPR loci contain multiple direct repeat (DRs) sequences from 21 to 48 bp long separated by variable spacer sequences 21–72 bp in length [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

CRISPR-like sequences in Helicobacter pylori and application in genotyping

et al. 2017

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BackgroundMany bacteria and archaea possess a defense system called clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (CRISPR-Cas system) against invaders such as phages or plasmids. This system has not been demonstrated in Helicobacter pylori. The numbers of spacer in CRISPR array differ among bacterial strains and can be used as a genetic marker for bacterial typing.ResultsA total of 36 H. pylori isolates were collected from patients in three hospitals located in the central (PBH) and southern (SKH) regions of Thailand. It is of interest that CRISPR-like sequences of this bacterium were detected in vlpC encoded for VacA-like protein C. Virulence genes were investigated and the most pathogenic genotype (cagA vacA s1m1) was detected in 17 out of 29 (58.6%) isolates from PBH and 5 out of 7 (71.4%) from SKH. vapD gene was identified in each one isolate from PBH and SKH. CRISPR-like sequences and virulence genes of 20 isolates of H. pylori obtained in this study were analyzed and CRISPR-virulence typing was constructed and compared to profiles obtained by the random amplification of polymorphic DNA (RAPD) technique. The discriminatory power (DI) of CRISPR-virulence typing was not different from RAPD typing.ConclusionCRISPR-virulence typing in H. pylori is easy and reliable for epidemiology and can be used for inter-laboratory interpretation.Electronic supplementary materialThe online version of this article (10.1186/s13099-017-0215-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

CRISPR-like sequences in Helicobacter pylori and application in genotyping

et al. 2017

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“…Currently, vaccinology integrates immunology, systems biology, immunoinformatics, structural biology, and nanotechnology sciences, which, like pieces of a puzzle, should be put together to develop efficient vaccines. Bioinformatics provides great help for researchers aiming to generate predictions before performing lab experiments to design SAPNs, similar to some other fields Negahdaripour et al, 2017;Rahmatabadi et al, 2016;Zamani et al, 2015), which helps save time and energy Rahmatabadi et al, 2016). On the other hand, the use of computational tools in vaccine design or SAPN development seems unavoidable, considering the huge volume of data that must be compiled.…”

Section: Employing Computational Tools In Sapn Designmentioning

confidence: 99%

Harnessing self-assembled peptide nanoparticles in epitope vaccine design

Negahdaripour

Golkar

Hajighahramani

et al. 2017

Biotechnology Advances

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103

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Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.

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“…We downloaded the sequence of CRISPR loci from 10,000 bp upstream to 10,000 bp downstream from the CRISPRdb [26], which contains CRISPR arrays. CRISPR finder Program Online allowed us to acquire the numbers and sequences of repeats and spacers of CRISPRs [27].…”

Section: Analysis Methodsmentioning

confidence: 99%

Bioinformatic analysis of Listeria monocytogenes CRISPR

Qu¹,

Shen²,

Xu³

et al. 2018

Oncotarget

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Listeria monocytogenes is a leading causes of death from food-borne pathogens. Bioinformatics approach was applied to investigate the features of L. monocytogenes CRISPR structure and the relationship between CRISPR and plasmid transposase content. Among 93 L. monocytogenes genomes, 95 confirmed CRISPR structure loci were identified and classified into 5 groups based on repeat size. RNA secondary structure and minimum free energy indicated that the secondary structure of Group 5 (36 bp) was more stable than other groups. Type I-B or II-A Cas genes were found in 36 strains, and the CRISPR-Cas system of type I-B was more conserved than type II-A. Furthermore, CRISPR loci affected the enzyme transposase content of L. monocytogenes plasmid. This study examined the diversity of the CRISPR-Cas system in L. monocytogenes, classified CRISPR structure and repeats, and demonstrated the influence of the CRISPR-Cas system on the number of transposase in plasmid.

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Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli

Cited by 22 publications

References 32 publications

CRISPR-like sequences in Helicobacter pylori and application in genotyping

CRISPR-like sequences in Helicobacter pylori and application in genotyping

Harnessing self-assembled peptide nanoparticles in epitope vaccine design

Bioinformatic analysis of Listeria monocytogenes CRISPR

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