Machine Learning Predicts New Anti-CRISPR Proteins

Eitzinger, Simon; Asif, Amina; Watters, Kyle E.; Iavarone, Anthony T.; Knott, Gavin J.; Doudna, Jennifer A.; Minhas, Fayyaz ul Amir Afsar

doi:10.1101/854950

Cited by 5 publications

(4 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For every known microbial defense strategy phages evolved means for counter defense, and thus it is only a matter of time before phage encoded inhibitors of novel defense systems will be described [25,26,46]. It was pro posed that similar to the defense islands, anti defense genes tend to form clusters in phage genomes or mobile genetic elements.…”

Section: Introductionmentioning

confidence: 99%

Microbial Arsenal of Antiviral Defenses – Part I

Musharova

Severinov

2021

Biochemistry Moscow

View full text Add to dashboard Cite

Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.

show abstract

Section: Introductionmentioning

confidence: 99%

Microbial Arsenal of Antiviral Defenses – Part I

Musharova

Severinov

2021

Biochemistry Moscow

View full text Add to dashboard Cite

show abstract

“…Two types of Anti CRISPR (Acr) regions were detected from selected strains as AcrIIA21 being present in 26 strains whilst AcrIIA18 in just GBS1-NY strain. AcrIIA21 exhibits broad spectrum action by inhibiting Streptococcus pyogenes Cas9 (SpyCas9), Staphylococcus aureus Cas9 (SauCas9), and Streptococcus iniae Cas9 (SinCas9), exhibiting high efficacy against SinCas9 [30]. An in depth understanding of its mechanism remains elusive.…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics reveals the diversity of CRISPR-Cas systems among neonatal sepsis causing group BStreptococcus agalactiae

Ghate,

Rao,

Shastry

et al. 2023

Preprint

View full text Add to dashboard Cite

The pathogenStreptococcus agalactiae, or Group BStreptococcus(GBS) infection is the leading cause of neonatal sepsis and meningitis in neonates. In this study, we aimed to investigate the occurrence and diversity of the CRISPR-Cas system inS. agalactiaegenomes using computational biology approaches. A total of 51 out of 52 complete genomes (98.07%) ofS. agalactiaepossess CRISPR arrays (75 CRISPR arrays) with 17 strains possessing multiple CRISPR arrays. There were only two CRISPR-Cas systems – type II-A system and type I-C system inS. agalactiaestrains. RNA secondary structure analysis through direct repeat analysis showed that the analyzed strains could form stable secondary structures. The 16S rRNA phylogeny exhibited clustering of the strains into three major clades grouped on the type of CRISPR-Cas system. The anti-CRISPRs that contribute to CRISPR-Cas system diversity and prevent genome editing were also detected. These results provide valuable insights into elucidating the evolution, diversity, and function of CRISPR/Cas elements in this pathogen.

show abstract

“…Validated Acr are mostly short proteins (89% between 60 and 160 aa). We ran our phage proteomes in AcrHub on two different Acr prediction algorithms (PaCRISPR [42] and AcRanker [43]).…”

Section: Iii14 Prediction Of Anti-crispr Proteins (Acr)mentioning

confidence: 99%

Genetic mining of newly isolated Salmophages for phage therapy

Gendre

Ansaldi

Olivenza

et al. 2022

Preprint

View full text Add to dashboard Cite

Salmonella enterica – a Gram negative zoonotic bacterium – is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. Main reservoirs are found in poultry farms but also in wild birds. The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections. Here we aimed at deciphering and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy. We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR. We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database. We finally searched for useful functions for phage therapy such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRIPSR proteins. We thus were able to genetically characterized nine virulent phages and one temperate phage and identified putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.

show abstract

Machine Learning Predicts New Anti-CRISPR Proteins

Cited by 5 publications

References 54 publications

Microbial Arsenal of Antiviral Defenses – Part I

Microbial Arsenal of Antiviral Defenses – Part I

Comparative genomics reveals the diversity of CRISPR-Cas systems among neonatal sepsis causing group BStreptococcus agalactiae

Genetic mining of newly isolated Salmophages for phage therapy

Contact Info

Product

Resources

About