Article
Biology
Jake L. Weissman, Ellinor O. Alseth, Sean Meaden, Edze R. Westra, Jed A. Fuhrman
Summary: A study has found that immune lag is extremely costly during viral outbreaks, even to completely immune hosts. This phenomenon of immune lag is only revealed by examining the early, transient dynamics of a host-virus system occurring immediately after viral challenge, and it is a basic parameter of microbial defense relevant to all post-infection antiviral defense systems.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Review
Microbiology
Veena Devi, Kusum Harjai, Sanjay Chhibber
Summary: Despite scientific and technological progress, the global health community is threatened by infectious diseases, particularly the rise of antibiotic-resistant microorganisms. The misuse of antibiotics has caused this problem, and finding a solution seems difficult. Developing new antibacterial therapies, such as CRISPR-Cas gene editing, is crucial to combat multidrug resistance. This review focuses on the development of CRISPR-Cas antimicrobials and the challenges in delivering them.
FUTURE MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Matvey V. Kolesnik, Iana Fedorova, Karyna A. Karneyeva, Daria N. Artamonova, Konstantin V. Severinov
Summary: The Type III CRISPR-Cas system, despite being among the most common, is one of the least investigated gene defense systems due to its complexity. This system recognizes and destroys foreign nucleic acids, with its effector complexes specifically targeting and cleaving RNA molecules.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Biology
Lucy Chou-Zheng, Asma Hatoum-Aslan
Summary: The CRISPR-Cas system is an adaptive immune system that protects prokaryotes from invading plasmids and viruses. This study identifies RNase R as a critical nuclease in completing crRNA maturation and its specific interactions with the type III effector complex member Csm5. The study also demonstrates the importance of RNase R and PNPase in maintaining robust anti-plasmid immunity.
Article
Biochemistry & Molecular Biology
Jorge Botas, Alvaro Rodriguez del Rio, Joaquin Giner-Lamia, Jaime Huerta-Cepas
Summary: GeCoViz is an online resource that provides fast and interactive visualization of custom genomic regions, allowing for easy investigation of the functional and evolutionary interpretation of prokaryotic genes.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Helen B. Belato, George P. Lisi
Summary: The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs), has revolutionized the field of CRISPR-Cas technology. These inhibitors have diverse structures and functions, and can act as orthosteric or allosteric inhibitors, as well as modify CRISPR-Cas components. Understanding the mechanisms of Acrs is crucial for the development of more precise and controllable CRISPR-Cas tools.
Review
Biology
Zhenxiao Yu, Suping Jiang, Yuan Wang, Xuhui Tian, Pengpeng Zhao, Jianan Xu, Mingxia Feng, Qunxin She
Summary: CRISPR-Cas systems provide adaptive immunity against invasive genetic elements in archaea and bacteria. Sulfolobales organisms usually contain both type I and type III CRISPR-Cas systems, with common subtypes including I-A, I-D, III-B, and III-D. Genetic assays have been developed to study the mechanisms of adaptation and interference, demonstrating PAM-dependent DNA interference and multiple interference activities by different CRISPR-Cas systems. Biochemical characterization of ribonucleoprotein effector complexes in Sulfolobales III-B and III-D systems has enriched our understanding of the molecular mechanisms of antiviral immune responses.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Microbiology
Pradeep Kumar Yadalam, Deepavalli Arumuganainar, Raghavendra Vamsi Anegundi, Deepti Shrivastava, Sultan Abdulkareem Ali Alftaikhah, Haifa Ali Almutairi, Muhanad Ali Alobaida, Abdullah Ahmed Alkaberi, Kumar Chandan Srivastava
Summary: Periodontal diseases, such as periodontitis, are immune-inflammatory diseases caused by multi-species bacteria that destroy tooth-supporting structures. The red complex bacteria, including Porphoromonas gingivalis, Tanerella forsythia, and Treponema denticola, have adapted immune mechanisms to counter bacteriophages and have the ability to modulate the microbiome of chronic periodontitis through the CRISPR-Cas system. This study investigated the role of red complex bacteria's CRISPR-Cas system in the dysbiosis of oral bacteriophages in periodontitis, revealing their ability to inhibit viruses and bacteriophages.
Review
Immunology
Sydney Newsom, Hari Priya Parameshwaran, Lindsie Martin, Rakhi Rajan
Summary: The CRISPR-Cas systems of bacteria and archaea provide adaptive immune protection against foreign genetic elements through RNA-DNA and/or RNA-RNA complementarity. Cas proteins play a role in various functions, such as RNA cleavage and transcriptional regulation, giving rise to powerful gene editing and biotechnological tools. Discovery of new CRISPR types holds promise for future technological innovations in precision genome medicine.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Angus Angermeyer, Stephanie G. Hays, Maria H. T. Nguyen, Fatema-Tuz Johura, Marzia Sultana, Munirul Alam, Kimberley D. Seed
Summary: This study describes the discovery of four previously unknown PLE variants and one additional variant from cholera patients in Bangladesh. A lineage sweep of PLE-negative V. cholerae was observed in recent sampling within the patient population. These findings reinforce our understanding of the successive nature of V. cholerae evolution.
Article
Microbiology
Angus Angermeyer, Stephanie G. Hays, Maria H. T. Nguyen, Fatema-Tuz Johura, Marzia Sultana, Munirul Alam, Kimberley D. Seed
Summary: Vibrio cholerae poses a significant threat to global public health due to its large-scale evolutionary sweeps, with recent discovery of unknown PLE variants and shifts in the resistance mechanisms against bacteriophage ICP1. The loss of CRISPR-Cas system in favor of Odn in V. cholerae strains and the coexistence of mixed PLE populations within patient samples suggest ongoing genetic developments in pandemic cholera. Monitoring V. cholerae, ICP1, and PLE dynamics in Bangladesh is essential for understanding temporal evolutionary changes and guiding outbreak surveillance efforts globally.
Article
Biochemistry & Molecular Biology
Shuai Zhang, Tao Li, Yangao Huo, Juwang Yang, Joy Fleming, Mingmin Shi, Ying Wang, Wenjing Wei, Shoujin Gu, Lijun Bi, Tao Jiang, Hongtai Zhang
Summary: Mycobacterium tuberculosis Csm1 shows ion-dependent polymerase activity when independent of the effector complex, but its functional relevance in vivo is unknown. Structural studies suggest that Csm1's catalytic core is similar to that of DNA polymerase, which could benefit future functional investigations and engineering efforts.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Microbiology
Prarthana Mohanraju, Chinmoy Saha, Peter van Baarlen, Rogier Louwen, Raymond H. J. Staals, John van der Oost
Summary: CRISPR-Cas systems not only play a role in adaptive immunity, but also control gene expression, serve as tools for virus attacks and transposon navigation, and allow pathogenic bacteria to evade the human immune system. Understanding the diverse functions of CRISPR-Cas systems is crucial for the development of CRISPR-based applications.
NATURE REVIEWS MICROBIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Veena Devi, Kusum Harjai, Sanjay Chhibber
Summary: CRISPR-Cas system is an adaptive immune system found in prokaryotes, which not only provides sequence-specific immunity but also plays a role in gene regulation, bacterial pathophysiology, and evolution.
FOLIA MICROBIOLOGICA
(2022)
Article
Ecology
John P. DeLong, Clayton E. Cressler
Summary: This study evaluates the impact of stochastic processes such as genetic drift on adaptation and finds that stochasticity can alter population dynamics and lead to evolutionary outcomes that are not predicted by classic eco-evolutionary modeling approaches. However, these outcomes are governed by nonequilibrium evolutionary attractors, which are maxima in lifetime reproductive success when stochasticity keeps the ecological system away from the deterministic equilibrium. These NEEAs alter the path of evolution but are not visible through the equilibrium lens of much evolutionary theory. The results reveal the importance of considering population processes during transient periods for a better understanding of the path and pace of evolution.
Article
Multidisciplinary Sciences
Lijia Yu, Deepak Kumar Tanwar, Emanuel Diego S. Penha, Yuri I. Wolf, Eugene V. Koonin, Malay Kumar Basu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Genetics & Heredity
Eugene V. Koonin, Kira S. Makarova, Yuri I. Wolf, Mart Krupovic
NATURE REVIEWS GENETICS
(2020)
Review
Microbiology
Eugene V. Koonin, Valerian V. Dolja, Mart Krupovic, Arvind Varsani, Yuri I. Wolf, Natalya Yutin, F. Murilo Zerbini, Jens H. Kuhn
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2020)
Review
Microbiology
Kira S. Makarova, Yuri Wolf, Jaime Iranzo, Sergey A. Shmakov, Omer S. Alkhnbashi, Stan J. J. Brouns, Emmanuelle Charpentier, David Cheng, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, David Scott, Shiraz A. Shah, Virginijus Siksnys, Michael P. Terns, Ceslovas Venclovas, Malcolm F. White, Alexander F. Yakunin, Winston Yan, Feng Zhang, Roger A. Garrett, Rolf Backofen, John van der Oost, Rodolphe Barrangou, Eugene Koonin
NATURE REVIEWS MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Noam Auslander, Yuri Wolf, Eugene Koonin
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Susana M. Cerritelli, Jaime Iranzo, Sushma Sharma, Andrei Chabes, Robert J. Crouch, David Tollervey, Aziz El Hage
NUCLEIC ACIDS RESEARCH
(2020)
Article
Microbiology
Eldar Yagmurov, Darya Tsibulskaya, Alexey Livenskyi, Marina Serebryakova, Yury Wolf, Sergei Borukhov, Konstantin Severinov, Svetlana Dubiley
Article
Microbiology
Jaime Iranzo, Guilhem Faure, Yuri Wolf, Eugene Koonin
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Microbiology
Mario Lopez-Perez, Jose M. Haro-Moreno, Jaime Iranzo, Francisco Rodriguez-Valera
Article
Biochemistry & Molecular Biology
Mario Rodriguez Mestre, Linyi Alex Gao, Shiraz A. Shah, Adrian Lopez-Beltran, Alejandro Gonzalez-Delgado, Francisco Martinez-Abarca, Jaime Iranzo, Modesto Redrejo-Rodriguez, Feng Zhang, Nicolas Toro
Summary: Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. A burst of research in recent years has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as Defense-associated RTs (DRTs) and Abortive Infection system (Abi) RTs. This study systematically analyzed these RTs, identifying 42 highly diverse groups belonging to the unknown RTs (UG) and Abi RTs. Most of these groups are predicted to be functionally associated with other genes or domains and are associated with defense functions and/or mobile genetic elements. Additionally, this study highlights the presence of one of these systems in novel families of human gut viruses. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Jaime Iranzo, George Gruenhagen, Jorge Calle-Espinosa, Eugene V. Koonin
Summary: A method called Coselens has been developed to quantify conditional selection on the excess of nonsynonymous substitutions in cancer genes, identifying 296 conditionally selected gene pairs. This study reveals a more complex scenario in cancer subtypes where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.
Article
Biochemical Research Methods
Jaime Iranzo, George Gruenhagen, Jorge Calle-Espinosa, Eugene V. Koonin
Summary: Studying genes that evolve under conditional selection can provide insights into the genomic basis of adaptation, including epistasis and phenotypic plasticity. This article describes how to use the Coselens package for comparing gene-level selection in two groups of samples. The protocol can be executed in less than 10 minutes on a laptop after installing Coselens and preparing the datasets. Coselens is particularly suitable for analyzing somatic mutations and data from experimental evolution with independently evolved samples available.
Article
Physics, Multidisciplinary
Jaime Iranzo, Federico Pablo-Marti, Jacobo Aguirre
PHYSICAL REVIEW RESEARCH
(2020)