Article
Plant Sciences
Amey Redkar, Volkan Cevik, Kate Bailey, He Zhao, Dae Sung Kim, Zhou Zou, Oliver J. Furzer, Sebastian Fairhead, M. Hossein Borhan, Eric B. Holub, Jonathan D. G. Jones
Summary: The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Different races of A. candida have different capacities to infect host plant species, which are associated with the polymorphic secreted proteins with a CX(2)CX(5)G ('CCG') motif. The resistance genes WRR4A and WRR4B in Arabidopsis thaliana confer resistance to multiple A. candida races and are triggered by specific CCG effector proteins, suggesting a potential mechanism for broad-spectrum resistance. This study provides insights into the interaction between Arabidopsis and A. candida.
Article
Biochemistry & Molecular Biology
Vassiliki A. Michalopoulou, Glykeria Mermigka, Konstantinos Kotsaridis, Andriani Mentzelopoulou, Patrick H. N. Celie, Panagiotis N. Moschou, Jonathan D. G. Jones, Panagiotis F. Sarris
Summary: This article investigates the mechanism by which Xanthomonas campestris evades host defense responses by targeting the plant exocyst complex through its core effector XopP. XopP inhibits exocytosis and suppresses plant immune responses, promoting successful infection.
Article
Biochemistry & Molecular Biology
Hee-Kyung Ahn, Xiao Lin, Andrea Carolina Olave-Achury, Lida Derevnina, Mauricio P. Contreras, Jiorgos Kourelis, Chih-Hang Wu, Sophien Kamoun, Jonathan D. G. Jones
Summary: Plant pathogens affect crop yields. Plants have evolved innate immunity based on NLR immune receptors that detect pathogen-derived effectors. Helper NLRs support the function of sensor NLRs, but the mechanism is not fully understood. This study uncovers the formation of resistosomes by Rpi-amr3 sensor NLR and helper NLRs NRC2 and NRC4, highlighting the importance of NRC resistosome formation in developing disease-resistant crops.
Article
Infectious Diseases
Michael B. Hall, Marie Sylvianne Rabodoarivelo, Anastasia Koch, Anzaan Dippenaar, Sophie George, Melanie Grobbelaar, Robin Warren, Timothy M. Walker, Helen Cox, Sebastien Gagneux, Derrick Crook, Tim Peto, Niaina Rakotosamimanana, Simon Grandjean Lapierre, Zamin Iqbal
Summary: This study aimed to determine whether Nanopore sequencing data can provide equivalent information to Illumina for transmission clustering and genotypic drug susceptibility testing (DST) of Mycobacterium tuberculosis. The results showed that Nanopore can achieve comparable performance with Illumina in clustering transmission and genotypic DST of M.tb. Therefore, public health laboratories can choose to use either or both technologies based on cost, batching, and turnaround time.
Article
Microbiology
Kayzad Nilgiriwala, Marie-Sylvianne Rabodoarivelo, Michael B. Hall, Grishma Patel, Ayan Mandal, Shefali Mishra, Fanantenana Randria Andrianomanana, Kate Dingle, Gillian Rodger, Sophie George, Derrick W. Crook, Sarah Hoosdally, Nerges Mistry, Niaina Rakotosamimanana, Zamin Iqbal, Simon Grandjean Lapierre, Timothy M. Walker
Summary: Universal access to drug susceptibility testing is recommended for newly diagnosed tuberculosis patients. Improved protocols for direct-from-sample sequencing of Mycobacterium tuberculosis are needed to accelerate drug susceptibility testing and molecular typing. Analysis of sputum samples using Illumina and MinION technologies showed variability in sequencing performance based on smear positivity level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Emily R. Larson, Emily May Armstrong, Helen Harper, Sandra Knapp, Keith J. Edwards, Don Grierson, Guy Poppy, Mark W. Chase, Jonathan D. G. Jones, Ruth Bastow, Graham Jellis, Steve Barnes, Paul Temple, Matthew Clarke, Giles Oldroyd, Claire S. Grierson
Article
Biochemistry & Molecular Biology
Xia Yan, Bozeng Tang, Lauren S. Ryder, Dan MacLean, Vincent M. Were, Alice Bisola Eseola, Neftaly Cruz-Mireles, Weibin Ma, Andrew J. Foster, Miriam Oses-Ruiz, Nicholas J. Talbot
Summary: The rice blast fungus is a major threat to global rice production. This study provides a detailed understanding of the biology behind the invasion of plant tissues during the disease. Through transcriptional profiling, the study identifies specific gene expression changes and a repertoire of effectors critical for successful infection.
Article
Plant Sciences
Shuta Asai, Volkan Cevik, Jonathan D. G. Jones, Ken Shirasu
Summary: A translating ribosome affinity purification system is used to analyze gene expression in pathogen-infected host cells and identify host genes whose expression is induced in infected cells. The study found that host genes are specifically induced during infection by the pathogen. This method can help us better understand the interaction between plants and pathogens.
Article
Multidisciplinary Sciences
Michelle T. Hulin, Lionel Hill, Jonathan D. G. Jones, Wenbo Ma
Summary: NAD+ is a key component in immune systems and TIR proteins function as NAD+ hydrolases. This study identified 13 T3Es with potential NADase activity, including a T3E named HopBY which promotes bacterial virulence. The research highlights the importance of NAD+ metabolism in host-pathogen interactions and provides insight into NAD+-derived molecules involved in plant immunity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Mariana G. Lopez, Ma Isolina Campos-Herrero, Manuela Torres-Puente, Fernando Canas, Jessica Comin, Rodolfo Copado, Penelope Wintringer, Zamin Iqbal, Eduardo Lagarejos, Miguel Moreno-Molina, Laura Perez-Lago, Berta Pino, Laura Sante, Dario Garcia de Viedma, Sofia Samper, Inaki Comas
Summary: By combining large genomic data sets and phylodynamic approaches, we accurately traced the origin, spread, and epidemiological parameters of an outbreak strain of Mycobacterium tuberculosis in the Canary Islands. Our study reveals the high success of the GC strain within the local region, but limited expansion abroad, and suggests that social determinants rather than intrinsic bacterial transmissibility explain its success.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Anthony Duncan, Kerrie Barry, Chris Daum, Emiley Eloe-Fadrosh, Simon Roux, Katrin Schmidt, Susannah G. Tringe, Klaus U. Valentin, Neha Varghese, Asaf Salamov, Igor Grigoriev, Richard M. Leggett, Vincent Moulton, Thomas Mock
Summary: This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can be used for genomic comparisons between environments.
Article
Infectious Diseases
Lindsay Sonnenkalb, Joshua James Carter, Andrea Spitaleri, Zamin Iqbal, Martin Hunt, Kerri Marie Malone, Christian Utpatel, Daniela Maria Cirillo, Camilla Rodrigues, Kayzad Soli Nilgiriwala, Philip William Fowler, Matthias Merker, Stefan Niemann
Summary: This study identified genetic variations that confer resistance to bedaquiline and clofazimine, and established a mutation catalogue using experimental evolution, protein modelling, genome sequencing, and phenotypic data analysis. The findings advance the understanding of drug resistance mechanisms in Mycobacterium tuberculosis complex strains and provide important genetic testing evidence for the design of effective treatments.
Article
Genetics & Heredity
Michael B. Hall, Leandro Lima, Lachlan J. M. Coin, Zamin Iqbal
Summary: Tuberculosis, a global pandemic disease, is facing an increasing challenge of antimicrobial resistance. The World Health Organization (WHO) aims to achieve universal access to drug susceptibility testing (DST), and whole-genome sequencing followed by genotype-based prediction of DST is a promising approach. In this study, we developed DrPRG (Drug resistance Prediction with Reference Graphs) by constructing a reference graph for Mycobacterium tuberculosis drug resistance using a global dataset of isolates. We compared DrPRG with existing graph-based and haplotype-based tools and found that DrPRG performs better in terms of sensitivity, specificity, computational memory usage, and runtime.
MICROBIAL GENOMICS
(2023)
Article
Biochemical Research Methods
Samuel Martin, Martin Ayling, Livia Patrono, Mario Caccamo, Pablo Murcia, Richard M. Leggett
Summary: MetaCortex is a metagenome assembler that captures intra-species diversity by searching for local variation along assembled sequences in the assembly graph and outputting these sequences in sequence graph format. It outperforms other popular metagenomic assemblers in accurately assembling mock viral communities and simulated communities with high levels of strain-level diversity.
Article
Plant Sciences
Sanu Arora, Andrew Steed, Rachel Goddard, Kumar Gaurav, Tom O'Hara, Adam Schoen, Nidhi Rawat, Ahmed F. F. Elkot, Andrey V. V. Korolev, Catherine Chinoy, Martha H. H. Nicholson, Soichiro Asuke, Rea Antoniou-Kourounioti, Burkhard Steuernagel, Guotai Yu, Rajani Awal, Macarena Forner-Martinez, Luzie Wingen, Erin Baggs, Jonathan Clarke, Diane G. O. Saunders, Ksenia V. V. Krasileva, Yukio Tosa, Jonathan D. G. Jones, Vijay K. K. Tiwari, Brande B. H. Wulff, Paul Nicholson
Summary: Since 1985, wheat blast has spread throughout South America, Bangladesh, and Zambia. Two wheat resistance genes, Rwt3 and Rwt4, have been identified as barriers against non-Triticum blast pathotypes. These genes provide molecular targets for studying the interaction between pathogen effector and host resistance genes, and can potentially improve wheat resistance to blast fungus.