Article
Microbiology
Stephen Dela Ahator, Yang Liu, Jianhe Wang, Lian-Hui Zhang
Summary: Pseudomonas aeruginosa has a network of regulatory components, including the virulence factor regulator (Vfr), for effective response to stress factors. Vfr influences the expression of the CRISPR-Cas system through two signaling pathways in response to changes in calcium levels. Mutation of vfr reduces the CRISPR-Cas spacer acquisition and interference of horizontal gene transfer (HGT). The findings may facilitate the development of phage therapies against P. aeruginosa infections.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Anoop Singh, Mohita Gaur, Vishal Sharma, Palak Khanna, Ankur Bothra, Asani Bhaduri, Anupam Kumar Mondal, Debasis Dash, Yogendra Singh, Richa Misra
Summary: This study conducted a comparative analysis of 141 mycobacterial genomes and found the exclusive presence of the CRISPR-Cas III-A system in the Mycobacterium tuberculosis complex. Phylogenetic evidence suggests that this system was acquired through horizontal gene transfer from a Firmicutes bacterium. The variations in CRISPR-Cas organization in M. tuberculosis lineages, particularly due to IS6110 transposition, were also identified.
Article
Biochemistry & Molecular Biology
Rafael Pinilla-Redondo, Jakob Russel, David Mayo-Munoz, Shiraz A. Shah, Roger A. Garrett, Joseph Nesme, Jonas S. Madsen, Peter C. Fineran, Soren J. Sorensen
Summary: Research shows that CRISPR-Cas systems are common accessory components of many plasmids, with plasmid CRISPRs displaying a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers, highlighting the genetic independence of plasmids and suggesting a major role in mediating plasmid-plasmid conflicts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Jeniffer C. Kerber-Diaz, Mario A. Leos-Ramirez, Andony A. Flores-Ceron, Alejandro Ponce-Mendoza, Paulina de los Santos, J. Antonio Ibarra
Summary: CRISPR-Cas systems consist of repeated and non-repeated sequences, with only 8.4% of Burkholderiaceae family members harboring complete systems. Spacer sequences mostly show identity to the same genomes, with a few having identities with plasmids or phages, and this study is the first to uncover the CRISPR-Cas system for the entire Burkholderiaceae family.
ARCHIVES OF MICROBIOLOGY
(2022)
Review
Infectious Diseases
Shuan Tao, Huimin Chen, Na Li, Wei Liang
Summary: This article discusses the potential importance of the CRISPR-Cas system in controlling antibiotic resistance and its application prospects in preventing and controlling the spread of bacterial drug resistance.
INFECTION AND DRUG RESISTANCE
(2022)
Review
Biotechnology & Applied Microbiology
Rupali Chowdhry, Steven Z. Lu, Seungheon Lee, Shivudu Godhulayyagari, Sasha B. Ebrahimi, Devleena Samanta
Summary: Integrating nanotechnology with CRISPR/Cas systems has the potential to overcome limitations, enhance applications in disease diagnostics and therapeutics, and enable faster, more sensitive, and convenient readouts in detection platforms.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Microbiology
Travis G. Wentz, Benjamin J. M. Tremblay, Marite Bradshaw, Andrew C. Doxey, Shashi K. Sharma, John-Demian Sauer, Sabine Pellett
Summary: This study used bioinformatic analysis to investigate the CRISPR-Cas systems of 241 strains of C. botulinum and C. sporogenes. The results showed that the CRISPR-Cas systems mainly prevent the transfer of botulinum toxin gene clusters, rather than directly targeting the toxin gene clusters themselves. Additionally, comparative genomics analysis revealed that these genomic features often occupy the same hypervariable loci in both species.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Bridget N. J. Watson, Jurre A. Steens, Raymond H. J. Staals, Edze R. Westra, Stineke van Houte
Summary: CRISPR-Cas systems offer adaptive, heritable immunity to bacteria and archaea against their viruses, but the diversity of these systems and their importance in phage defense are still being understood. This review discusses the evolution of CRISPR-Cas immunity against phages, how this leads to immune evasion by phages, and the potential coevolution between CRISPR-Cas systems and phages.
CELL HOST & MICROBE
(2021)
Review
Biotechnology & Applied Microbiology
Jie Huang, Yitong Zhou, Jie Li, Aiping Lu, Chao Liang
Summary: The CRISPR/Cas system is an adaptive immune system in prokaryotes that prevents infection from viruses, phages, and other foreign substances. It cuts the DNA from invading viruses or phages into short fragments that integrate into the CRISPR array, allowing for rapid DNA cutting at the specified target location to protect the host. The CRISPR/Cas system has become one of the most popular gene editing technologies due to its high efficiency, versatility, and simplicity.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Plant Sciences
Irene Guzman-Benito, Natalia Patricia Achkar, Nicolas G. Bologna, Robertas Ursache
Summary: This paper reviews recent advances in CRISPR/Cas-mediated gene targeting in plants, discusses their potential applications, and suggests further improvements to achieve higher efficiency.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Microbiology
Richard Bauer, Dorina Haider, Aline Grempels, Rebecca Roscher, Stefanie Mauerer, Barbara Spellerberg
Summary: This study analyzed the CRISPR-Cas systems in Streptococcus anginosus and found two types of CRISPR-Cas II systems. One type contained a long csn2 gene, similar to Streptococcus thermophilus, while the other type contained a short csn2 gene, similar to S. pyogenes.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Faranak Hejabi, Mohammad Sadegh Abbaszadeh, Shirinsadat Taji, Andrew O'Neill, Fatemeh Farjadian, Mohammad Doroudian
Summary: CRISPR/Cas has become a promising genome-editing tool, but the safe and effective delivery remains a major challenge. Nanotechnology can be employed to overcome the delivery issue. This review discusses different types of CRISPR/Cas systems and delivery systems, focusing on the use of viral nanocarriers.
FRONTIERS IN CHEMISTRY
(2022)
Article
Plant Sciences
Michelle Roenspies, Holger Puchta
Summary: A major challenge in plant breeding is the establishment or breakage of genetic linkages through random meiotic recombination. This problem can be addressed by utilizing CRISPR-Cas-mediated chromosome engineering. Researchers found that by inverting a segment of chromosome 2 in Arabidopsis thaliana, they were able to effectively suppress genetic crossovers in that region.
Review
Pharmacology & Pharmacy
Guillermo Aquino-Jarquin
Summary: Comparative genomics has led to the discovery of small CRISPR bacterial immune system effectors that have the potential to manipulate eukaryotic genomes. Recently, smaller Cas proteins, such as miniature Cas9, Cas12, and Cas13 proteins, have been identified and shown to be efficient tools for genome and base editing in human cells. These small CRISPR-Cas systems offer a compact size, making them ideal for generating CRISPR-based therapeutics that can overcome in vivo delivery constraints. They provide a promising opportunity for editing pathogenic mutations and targeting RNAs in human cells without causing chromosomal insertions or genome alterations. Therefore, these tiny CRISPR-Cas systems represent new and highly programmable, specific, and efficient platforms that expand the CRISPR toolkit for potential therapeutic applications.
DRUG DISCOVERY TODAY
(2023)
Article
Biophysics
Nanyang Tang, Qian Ning, Zewei Wang, Yifang Tao, Xuhong Zhao, Shengsong Tang
Summary: Intelligent delivery systems incorporating sensitive materials in response to endogenous stimuli of the tumor microenvironment have shown potential for tumor-specific genome editing and reduced side effects of CRISPR/Cas in cancer gene therapy.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Biology
Jorge A. Moura de Sousa, Eduardo P. C. Rocha
Summary: This study reveals the widespread presence of P4-like phage satellites in the genomes of Enterobacterales, especially in Escherichia coli. These elements have an independent evolutionary origin, are scattered across chromosomes, and may have broad host ranges. These findings provide important insights into the molecular evolution of antagonistic interactions between phages and their satellites.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Eduardo P. C. Rocha, David Bikard
Summary: Prokaryotes possess mobile genetic elements that enable horizontal gene transfer between cells. These elements contain defense systems to filter, control, or inactivate other elements. The abundance of defense systems in these mobile genetic elements sheds new light on their role as tools of intragenomic conflict.
Editorial Material
Biochemistry & Molecular Biology
Jean Cury, Aude Bernheim
Summary: Bacteria have various defense systems against phages, and two of the most common systems, CRISPR-Cas and restriction-modification, interact to enhance bacterial defense in the long term.
TRENDS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Florian Tesson, Alexandre Herve, Ernest Mordret, Marie Touchon, Camille d'Humieres, Jean Cury, Aude Bernheim
Summary: Bacteria and archaea have developed multiple antiviral mechanisms. Researchers have introduced a tool called DefenseFinder that can automatically detect known antiviral systems in prokaryotic genomes, and have shown that variations in antiviral strategies correlate with genome size, viral threat, and lifestyle traits.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Jeremy Garb, Anna Lopatina, Aude Bernheim, Mindaugas Zaremba, Virginijus Siksnys, Sarah Melamed, Azita Leavitt, Adi Millman, Gil Amitai, Rotem Sorek
Summary: DSR proteins defend bacteria from phage infection by degrading NAD(+) and acting as active NADases, with DSR2 directly identifying phage proteins. Some phages express anti-DSR2 proteins to block bacterial immunity. This study establishes the general role of SIR2 domains in bacterial immunity against phages.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Manuel Ares-Arroyo, Charles Coluzzi, Eduardo P.C. Rocha
Summary: Plasmids can be transferred between cells by conjugation, driving bacterial evolution. By studying plasmids in Escherichia coli and Staphylococcus aureus, we have solved the mystery of plasmid transfer mechanisms and revealed the functional dependencies between plasmids. These findings are important for understanding the evolutionary relationships of plasmids and the spread of antibiotic resistance genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Francesca D'Angelo, Eduardo P. C. Rocha, Olaya Rendueles
Summary: The extracellular capsule, a virulence factor found in many pathogens, has a controversial role in antimicrobial resistance. Our study found that noncapsulated strains of Klebsiella pneumoniae exhibited increased resistance to polymyxins, but not to other antibiotics. These findings caution against the use of therapeutic agents targeting the capsule, as it may lead to its inactivation.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Liam P. Shaw, Eduardo P. C. Rocha, R. Craig MacLean
Summary: Restriction-modification systems (R-M systems) are important defense systems in bacteria, and their distribution and impact on plasmid evolution and host range have been studied. It was found that plasmid genes are more likely to avoid R-M targets than core genes, and this avoidance is stronger in smaller plasmids with broader host ranges. Two evolutionary strategies for plasmids were identified: small plasmids adapt through sequence composition, while large plasmids adapt through carrying additional genes for protection. These findings provide evidence of the importance of R-M systems as barriers to plasmid transfer.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
William Rostain, Theophile Grebert, Danylo Vyhovskyi, Paula Thiel Pizarro, Gatwa Tshinsele-Van Bellingen, Lun Cui, David Bikard
Summary: Off-target binding of Cas9 to essential gene promoters can occur with as little as 4 nt of identity in the PAM-proximal sequence, leading to toxicity. This potential for off-target effects must be considered in CRISPR-Cas experiments in bacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jorge A. Moura de Sousa, Alfred Fillol-Salom, Jose R. Penades, Eduardo P. C. Rocha
Summary: We developed SatelliteFinder to identify satellites in bacterial genomes, detecting a vast number of them, with some found in novel taxa. The gene repertoires and genomic organizations of satellites are variable but relatively conserved. The independent evolution of hijacking modules suggests that phage satellites have ancient, diverse origins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Olaya Rendueles, Jorge A. M. de Sousa, Eduardo P. C. Rocha
Summary: Many bacterial genomes carry prophages that can eliminate competitors, and bacteria can develop resistance through various mechanisms, such as surface receptor modification or lysogenization. The adaptation process of phage resistance involves both genetic and non-genetic changes. Our study showed that the frequency of capsulated cells in phage-sensitive populations increased over time, indicating the fine-tuning of capsule production as an adaptation to reduce phage absorption.
Article
Biochemistry & Molecular Biology
Charles Coluzzi, Martin Guillemet, Fanny Mazzamurro, Marie Touchon, Maxime Godfroid, Guillaume Achaz, Philippe Glaser, Eduardo P. C. Rocha
Summary: Horizontal gene transfer has a significant impact on the evolution of core genes, with mutations providing resistance to antibiotics and shaping the emergence of adaptive mutations. The rapid accumulation of these mutations increases the acquisition rate of other antibiotic resistances, leading to multidrug resistance.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Microbiology
Heloise Georjon, Aude Bernheim
Summary: In this review, the authors provide an overview of the molecular diversity of recently discovered bacterial antiphage defence systems and discuss their evolution and ecological impact.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Lee Call, Simon Roux, Stephen Nayfach, Marcel Huntemann, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Supratim Mukherjeep, T. B. K. Reddy, I-Min A. Chen, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Tanja Woyke, David A. Baltrus, Salvador Castaneda-Barba, Fernando de la Cruz, Barbara E. Funnell, James P. J. Hall, Aindrila Mukhopadhyay, Eduardo P. C. Rocha, Thibault Stalder, Eva Top, Nikos C. Kyrpides
Summary: This study introduces the IMG/PR database, which collects a large number of plasmid sequences from various microbiome samples and provides rich metadata and multiple browsing methods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Alonso Felipe-Ruiz, Alberto Marina, Eduardo P. C. Rocha
Summary: The RRNPPA family of receptors plays an important role in bacterial communication and regulates various processes. This study provides insights into the origin and diversification of RRNPPA proteins and reveals the existence of multiple subfamilies with distinct functions. The analysis also uncovers intriguing mechanisms of communication, such as eavesdroppers and chatterers. These findings contribute to our understanding of microbial communication and its implications.