Article
Plant Sciences
Rene Lemcke, Elisabet Sjoekvist, Stefano Visentin, Manoj Kamble, Euan K. James, Rasmus Hjortshoj, Kathryn M. Wright, Anna Avrova, Adrian C. Newton, Neil D. Havis, Simona Radutoiu, Michael F. Lyngkjaer
Summary: Ramularia collo-cygni is the causal agent of Ramularia leaf spot disease on barley, posing an increasing threat to farmers worldwide. Analysis of barley cultivars with different tolerance to RLS infected by aggressive or mild R. collo-cygni isolates revealed that fungal biomass does not correlate with tolerance, and both cultivars exhibit cell wall reinforcement at the point of contact with fungal hyphae. Transcriptome analysis showed significant transcriptional differences between cultivars early in fungal colonization, particularly in kinases, calmodulins, and defense proteins, while metabolite analysis identified defense compounds correlating with responses at transcriptome and morphological levels. These comprehensive responses provide molecular tools for improving barley tolerance to R. collo-cygni.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemical Research Methods
Wei Qin, Kelvin F. Cho, Peter E. Cavanagh, Alice Y. Ting
Summary: This article introduces the proximity labeling technology for studying and applying molecular interactions. By fusing baits with promiscuous enzymes, endogenous molecules interacting with them can be tagged and identified by mass spectrometry or nucleic acid sequencing. PL technology has been used to map protein-protein, protein-RNA, and protein-DNA interactions.
Article
Microbiology
Camilla Fagorzi, Giovanni Bacci, Rui Huang, Lisa Cangioli, Alice Checcucci, Margherita Fini, Elena Perrin, Chiara Natali, George Colin diCenzo, Alessio Mengoni
Summary: This study demonstrated that the transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.
Article
Chemistry, Multidisciplinary
Justin E. Silpe, Emily P. Balskus
Summary: The gut hosts a large number of microbes that significantly impact human health, but our understanding of the chemical compounds they produce and their effects on host biology is still in its early stages. Progress in decoding and manipulating this chemical language with diverse expertise could potentially be the key to combating certain human diseases.
ACS CENTRAL SCIENCE
(2021)
Review
Genetics & Heredity
Erick Armingol, Adam Officer, Olivier Harismendy, Nathan E. Lewis
Summary: Intercellular interactions and communication can be inferred from RNA sequencing data, such as ligand-receptor pairs, which has led to new insights and methodologies for studying cell-cell interactions.
NATURE REVIEWS GENETICS
(2021)
Article
Microbiology
Parnika Mukherjee, Gaetan Burgio, Emanuel Heitlinger
Summary: Through dual RNA sequencing and meta-analysis, this study identified common interactions between hosts and parasites, such as host immune response to the Plasmodium protein degradation system. Coexpression networks revealed known processes and individual protein associations between hosts and parasites, providing a foundation for prioritizing research in human malaria experiments.
Article
Biochemistry & Molecular Biology
Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, E. Weigao, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang Ng, Guang-Hui Liu, Guo-Cheng Yuan, Guoji Guo, Xiaoping Han
Summary: By using single-cell RNA sequencing, researchers mapped organism-level cell landscapes for mice, zebrafish, and Drosophila. They identified structural inflammation and mitochondrial dysfunction as common hallmarks of organism aging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Review
Parasitology
Xing He, Weiqing Pan
Summary: Understanding host-parasite interactions is crucial for controlling parasitic diseases, and miRNAs play a significant role in these interactions, with cross-species miRNA exchanges being common and important for host defense and parasite survival.
TRENDS IN PARASITOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Julia D. D. Meredith, Michael J. J. Gray
Summary: The pseudohypohalous acid hypothiocyanite/hypothiocyanous acid (OSCN-/HOSCN) has been widely investigated for its antimicrobial properties in mammalian immunity. Generated by peroxidase enzymes from thiocyanate (SCN-) and hydrogen peroxide (H2O2), HOSCN has potential applications in food preservation, pathogen control, and oral care. However, the mechanisms by which bacteria sense and respond to HOSCN remain largely unknown. This review summarizes the current knowledge on the role of HOSCN in host-pathogen interactions and discusses recent findings regarding bacterial responses to this antimicrobial agent, focusing on three model organisms: Escherichia coli, Streptococcus spp., and Pseudomonas aeruginosa.
MOLECULAR MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Taisuke Nakahama, Yukio Kawahara
Summary: ADAR1 is an enzyme responsible for RNA editing, with the Z alpha domain in its p150 isoform playing a critical role in preventing MDA5 activation. Studies on mutant mice have shown that mutations in the Z alpha domain can lead to AGS-like encephalopathy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Article
Genetics & Heredity
Jingge Kuang, Yufei Wang, Kangshan Mao, Richard Milne, Mingcheng Wang, Ning Miao
Summary: Comparing gene expressions among parasitic plants infecting different host species can provide valuable insights into host-parasite interactions. In this study, the transcriptomes of Taxillus nigrans individuals parasitizing four host species were sequenced, and a large number of differentially expressed genes were identified. The results shed light on the molecular mechanisms involved in plant parasitism.
Article
Microbiology
Bartosz Czech, Yachun Wang, Kai Wang, Hanpeng Luo, Lirong Hu, Joanna Szyda
Summary: Climate change affects animal physiology by reducing animal vitality due to heat stress. This study analyzed the interaction between gene expression and microbiota to identify genes and microbiota associated with physiological changes in cattle under heat stress. These genes and microbiota can be used as biomarkers for heat stress in cattle.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Xin Dong, Ke Chen, Wenbo Chen, Jun Wang, Liuping Chang, Jin Deng, Lei Wei, Leng Han, Chunhua Huang, Chunjiang He
Summary: This article introduces a novel algorithm, circRIP, for identifying circRNA-RBP interactions from RIP-Seq and eCLIP data. The algorithm successfully identified multiple circRNAs binding to different RBPs, which is of great significance for further exploring the functions of circRNAs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Cindrilla Chumduri, Rajendra Kumar Gurumurthy, Hilmar Berger, Oliver Dietrich, Naveen Kumar, Stefanie Koster, Volker Brinkmann, Kirstin Hoffmann, Marina Drabkina, Panagiota Arampatzi, Dajung Son, Uwe Klemm, Hans-Joachim Mollenkopf, Hermann Herbst, Mandy Mangler, Jorg Vogel, Antoine-Emmanuel Saliba, Thomas F. Meyer
Summary: The transition zones of squamous and columnar epithelia are prone to cancer, often associated with metaplasia. Through mouse models and single-cell RNA sequencing, it was discovered that the cervical epithelial cells in the endo- and ectocervix have distinct origins from stem cells regulated by opposing Wnt signals from the stroma. Additionally, a mouse model of cervical metaplasia showed that the stroma in the endocervix undergoes remodeling and increases expression of the Wnt inhibitor DKK2, promoting the outgrowth of ectocervical stem cells.
NATURE CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Gianluca Prezza, Daniel Ryan, Gohar Maedler, Sarah Reichardt, Lars Barquist, Alexander J. Westermann
Summary: This study investigates the functional roles of noncoding RNA in gut bacteria through comparative genomics, focusing on Bacteroides thetaiotaomicron as a representative member. While technical hurdles hinder analogous analyses in anaerobic gut microbiota, computational tools and comparative genomics can provide insight into RNA biology. The research demonstrates the power of RNA informatics in studying anaerobic microbiota members.
MOLECULAR MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Francois Halloy, Annabelle Biscans, Katherine E. Bujold, Alexandre Debacker, Alyssa C. Hill, Aurelie Lacroix, Olivia Luige, Roger Stromberg, Linda Sundstrom, Jorg Vogel, Alice Ghidini
Summary: RNA-based therapeutics are emerging as a powerful platform for treating multiple diseases. There are currently two main types of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), which achieve their therapeutic effects through gene silencing, splicing modulation, or microRNA binding. Ongoing research aims to expand the scope of RNA-based drugs, including more complex templates such as messenger RNA. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs.
Editorial Material
Biochemistry & Molecular Biology
Elise Bornet, Alexander J. Westermann
Summary: This article discusses the increasing use of Bacteroides spp. as model gut commensals in cocolonization studies and their divergent roles in protecting against or promoting infection. It also explores the potential of cutting-edge transcriptomics in unraveling the molecular basis of these roles.
TRENDS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Miguel V. Gomez-Raya-Vilanova, Katarzyna Leskinen, Arnab Bhattacharjee, Pasi Virta, Petja Rosenqvist, Jake L. R. Smith, Oliver W. Bayfield, Christina Homberger, Tobias Kerrinnes, Joerg Vogel, Maria Pajunen, Mikael Skurnik
Summary: YerA41 is an unconventional phage that packages thymidine-modified genomic DNA into its capsids along with its own DNAP.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Linda Popella, Jakob Jung, Phuong Thao Do, Regan J. Hayward, Lars Barquist, Joerg Vogel
Summary: This study systematically analyzed peptide nucleic acids (PNAs) targeting essential genes in uropathogenic Escherichia coli (UPEC) and found that PNAs have bactericidal effects on UPEC. The study also revealed that transcript abundance does not predict target vulnerability and that PNA-mediated growth inhibition is not universally associated with target mRNA depletion.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Yael Yair, Charlotte Michaux, Dvora Biran, Joerg Bernhard, Joerg Vogel, Lars Barquist, Eliora Z. Ron
Summary: The RNA chaperones CspC and CspE play important roles in stress response and adaptation. In this study, we investigated their involvement in the pathogenesis of a virulent strain of Escherichia coli. Using CLIP-seq, we identified numerous transcripts that interact with these cold shock proteins and found that many of these transcripts are involved in protein synthesis, transcription, energy metabolism, and virulence-related processes. Further experiments showed that deleting either CspC or CspE significantly decreased the levels of certain virulence-associated transcripts and resulted in a loss of serum resistance, a key requirement for sepsis. These findings highlight the essential role of these RNA chaperones in the virulence of E. coli.
Article
Biochemistry & Molecular Biology
Jens Hoer, Jakob Jung, Svetlana Durica-Mitic, Lars Barquist, Joerg Vogel
Summary: INRI-seq is an in vitro method for analyzing the translational landscape of a synthetic transcriptome in a comprehensive manner. It eliminates the need for extracting ribosomes from living cells and allows for the analysis of translation initiation sites and the effects of translation inhibitors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Falk Ponath, Yan Zhu, Valentina Cosi, Jorg Vogel
Summary: Fusobacterium nucleatum, a common oral microbe, has been found to colonize tissues and tumors in the human body and is associated with several major cancer types. However, little is known about gene regulation in F. nucleatum. This study characterizes a global stress-response network governed by the sigma(E) factor and develops genetic tools to study regulatory networks in this bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Chunlei Jiao, Claas Reckstadt, Fabian Koenig, Christina Homberger, Jiaqi Yu, Joerg Vogel, Alexander J. Westermann, Cynthia M. Sharma, Chase L. Beisel
Summary: We developed a method called TIGER (transcribed RNAs inferred by genetically encoded records) to capture the transcriptional history of individual bacterial cells. This method utilizes reprogrammed tracrRNAs (Rptrs) to convert selected cellular transcripts into stored DNA edits, allowing for future sequencing and analysis. TIGER can record and quantify heterologous and endogenous transcripts, distinguish single-nucleotide differences, and read out single-cell phenomena, providing insights into complex cellular responses.
NATURE BIOTECHNOLOGY
(2023)
Article
Gastroenterology & Hepatology
Thomas Daeullary, Fabian Imdahl, Oliver Dietrich, Laura Hepp, Tobias Krammer, Christina Fey, Winfried Neuhaus, Marco Metzger, Joerg Vogel, Alexander J. Westermann, Antoine-Emmanuel Saliba, Daniela Zdzieblo
Summary: Traditional cell culture and mouse models have limitations in infection research. Modern tissue engineering approaches provide alternatives for reconstructing functional tissue models in vitro. We established an in vitro model of the human small intestinal epithelium using a biological extracellular matrix and primary tissue-derived enteroids, which accurately recapitulated the key steps of epithelial infection by Salmonella enterica serovar Typhimurium and revealed a previously unrecognized host response to Salmonella infection.
Review
Biochemistry & Molecular Biology
Anke Sparmann, Joerg Vogel
Summary: RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. This review presents an overview of different RNA-based strategies, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Three rare genetic diseases are used as examples to highlight the opportunities and challenges of this class of drugs.
Review
Microbiology
Falk Ponath, Jens Hoer, Joerg Vogel
Summary: In the past two decades, a new type of bacterial sRNA, processed 3' end fragments of mRNAs, has been discovered. These sRNAs are involved in stress responses and regulatory circuits in bacteria, interacting with RNA-binding proteins and playing unexpected and conserved roles.
FEMS MICROBIOLOGY REVIEWS
(2022)