Article
Plant Sciences
Miguel Correa Marrero, Sylvain Capdevielle, Weijie Huang, Ali M. Al-Subhi, Marco Busscher, Jacqueline Busscher-Lange, Froukje van Der Wal, Dick de Ridder, Aalt D. J. van Dijk, Saskia A. Hogenhout, Richard G. H. Immink
Summary: This study generated a protein-protein interaction network between phytoplasma effectors and Arabidopsis thaliana transcription factors. The results showed widespread interactions between phytoplasma effectors and host transcription factors, especially those involved in host developmental processes. Comparison with other host-pathogen protein interaction networks revealed that phytoplasma effectors have unusual targets, indicating a unique and unusual infection strategy employed by phytoplasmas.
Article
Biochemical Research Methods
Shengrong Xia, Yingchun Xia, Chulei Xiang, Hui Wang, Chao Wang, Jin He, Guolong Shi, Lichuan Gu
Summary: In this study, a method for efficiently recognizing virus-target host proteins is proposed, which reduces drug resistance caused by mutated viruses and lowers the cost of disease treatment by considering the influence of protein complexes.
BMC BIOINFORMATICS
(2022)
Review
Microbiology
Gabriel Valiente
Summary: This article provides a systematic review of available virus-host protein-protein interaction database resources, evaluating their specificity, the number of interactions included, and functionality. It also analyzes the overlap of the databases and the structure of the interaction network across viruses and hosts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
James P. R. Connolly, Natasha C. A. Turner, Ester Serrano, Patricia T. Rimbi, Douglas F. Browning, Nicky O'Boyle, Andrew J. Roe
Summary: Ecologically beneficial traits in bacteria are determined by intrinsic and horizontally acquired genes. Regulatory flexibility in Escherichia coli allows for preexisting transcription factors to acquire new roles in regulating beneficial traits. This study reveals that the regulator DsdC in neonatal meningitis-associated E. coli acts as a global transcriptional regulator and does not require D-serine for controlling novel beneficial traits.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Xiaoxiao Ouyang, Xueyun Wang, Pan Li, Qin Huang, Li Zhou, Jingxiang Li, Li Gao, Qi Sun, Fangni Chai, Shupan Guo, Zhihui Zhou, Xin Liu, Lunzhi Dai, Wei Cheng, Haiyan Ren
Summary: In this study, the host protein ZPR1 was identified as an interacting partner of the EPEC effector NleE through protein crosslinking. It was found that ZPR1 regulates CHOP-mediated UPRER at the transcriptional level through liquid-liquid phase separation. Interestingly, NleE disrupts the binding ability of ZPR1 with K63-ubiquitin chains, which promotes its liquid-liquid phase separation. Further analysis showed that EPEC restricts host UPRER pathways at the transcription level in a cascade-dependent manner between NleE and ZPR1. Overall, this study reveals the mechanism by which EPEC interferes with CHOP-UPRER through regulating ZPR1 to facilitate immune evasion.
Review
Biochemistry & Molecular Biology
Hitoshi Iuchi, Junna Kawasaki, Kento Kubo, Tsukasa Fukunaga, Koki Hokao, Gentaro Yokoyama, Akiko Ichinose, Kanta Suga, Michiaki Hamada
Summary: The COVID-19 pandemic has revealed the limitations of medical and research institutions in managing emerging infectious diseases. Predicting virus-host interactions through host range prediction and protein-protein interaction prediction can enhance our understanding of infectious diseases. Although multiple algorithms have been developed for this purpose, there are still challenges that need to be addressed. Despite the difficulties, bioinformatics can play a significant role in advancing research on infectious diseases and human health.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Mar Perez-Ruiz, Mar Pulido-Cid, Juan Roman Luque-Ortega, Jose Maria Valpuesta, Ana Cuervo, Jose L. Carrascosa
Summary: The passage of viral DNA in bacteriophage T7 involves the assembly of core proteins gp15 and gp16 into a tube structure within the periplasm, allowing DNA transfer. The interaction between these proteins results in the formation of a channel for DNA translocation and also involves a transglycosylase motif for peptidoglycan layer degradation. This complex matches the structure of the phage tail and proposes a model for the assembly of the core translocation complex, elucidating the molecular mechanism of T7 viral DNA release into the bacterial cytoplasm.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Sarah K. Madden, Aline Dantas de Araujo, Mara Gerhardt, David P. Fairlie, Jody M. Mason
Summary: Direct inhibition of c-Myc, a transcription factor overexpressed in many human cancers, has shown promising results in triggering tumor regression with reversible side effects. Challenges and lessons from current inhibitors are evaluated to explore future strategies for translating c-Myc inhibitors into clinical practice, such as miniaturisation of Omomyc and targeting E-box binding.
Article
Biochemistry & Molecular Biology
Moira B. Dion, Pier-Luc Plante, Edwige Zufferey, Shiraz A. Shah, Jacques Corbeil, Sylvain Moineau
Summary: A large number of new phages have been discovered through viral metagenomics, with their host prediction based on CRISPR spacers which represent past phage-bacteria interactions. A set of tools has been developed for predicting hosts of uncharacterized phages, utilizing a database of over 11 million spacers and a program for large viral datasets. Performance evaluations show promise for gut-virome characterization using this host prediction method.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Patricia E. Sorensen, Duncan Y. K. Ng, Luc Duchateau, Hanne Ingmer, An Garmyn, Patrick Butaye
Summary: This study investigated the impact of bacteriophages on bacterial growth dynamics and identified seven distinct growth patterns, with phage species being the most influential factor. The results highlighted the importance of phage-host dynamics in determining a phage's ability to eliminate bacteria, and suggested that phage therapy development should take into consideration these dynamics. Candidates from Group 2, characterized by high bacterial killing, were identified as the most promising for phage therapy.
Review
Virology
Arpita Kar, Abhisekh Samanta, Soumyadeep Mukherjee, Subhasis Barik, Avik Biswas
Summary: Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), the most common primary liver malignancy. The study of HBV-host interactions has identified various mechanisms involved in the development and progression of HBV-associated HCC. This review provides a comprehensive summary of the existing knowledge on HBV-host interplay and highlights new therapeutic strategies for HBV-induced HCC.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Jett Liu, Alexander L. Jaffe, Linxing Chen, Batbileg Bor, Jillian F. Banfield
Summary: This study analyzed the CRISPR-Cas systems in Gracilibacteria, Absconditabacteria, and Saccharibacteria, and predicted the phages that infect these bacteria. Some phages were found to infect both standard-coded and alternatively coded CPR bacteria. Additionally, spacers encoded in Actinobacteria were predicted to target some phages of Saccharibacteria.
Article
Cell Biology
Longxiu Yang, Yuan Qin, Chongdong Jian
Summary: This study developed a classifier using RNA expression data to accurately distinguish AD patients and healthy individuals, and identified 3 core genes that may be related to the pathogenesis of AD. Analysis revealed that these core genes played a pivotal role in determining AD.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Rute Ferreira, Rui Amado, Jorge Padrao, Vania Ferreira, Nicolina M. Dias, Luis D. R. Melo, Silvio B. Santos, Ana Nicolau
Summary: This study describes the isolation and characterization of a new lytic bacteriophage, vB SnaP-R1 (SnaR1), targeting Sphaerotilus natans DSM 6575. The genome of SnaR1 is unique, with 99% of its sequences showing no homology to any other sequenced phage, and it is the first Podoviridae phage infecting this particular bacterium. Results suggest SnaR1 as a prototype of a new phage genus with potential as a non-chemical alternative for reducing S. natans DSM 6575 cells.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Plant Sciences
Masato Suzuki, Yugo Kitazawa, Nozomu Iwabuchi, Kensaku Maejima, Juri Matsuyama, Oki Matsumoto, Kenro Oshima, Shigetou Namba, Yasuyuki Yamaji
Summary: This study discovered a novel mechanism determining the degradation specificity of phyllogens through detailed analysis of a rice yellow dwarf phytoplasma homologue, and elucidated that phyllogen target specificity is regulated by both the MTF-binding ability and RAD23 recruitment ability of the MTF/phyllogen complex.
MOLECULAR PLANT PATHOLOGY
(2023)
