Review
Biochemistry & Molecular Biology
Saumyadeep Goswami, Dibyendu Samanta, Kheerthana Duraivelan
Summary: Viruses utilize molecular mimicry to hijack host cellular machinery, mimicking host sequences or structures to exploit host physiological interactions for their pathogenesis. Short linear motifs (SLiMs) are a common form of sequence mimicry, mediating transient interactions in host protein networks. Research on well-characterized SLiMs involved in viral entry can aid in the discovery of unknown cellular receptors used by viruses and inform the development of targeted therapeutics such as vaccines or inhibitors.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Microbiology
Heidy Elkhaligy, Christian A. Balbin, Jessica Siltberg-Liberles
Summary: Protein-protein interactions in eukaryotes are driven by short linear motifs (SLiMs). Conserved SLiMs can help identify functional SLiMs in eukaryotic protein families. However, the simplicity of eukaryotic SLiMs makes them appear by chance not only in eukaryotes but also in pathogenic bacteria and viruses. Additionally, functional eukaryotic SLiMs often exist in disordered regions. Pathogenic bacteria and viruses have less disorder in their proteomes compared to eukaryotes, but their proteins can mimic and disrupt eukaryotic SLiMs. Finding important SLiMs in pathogens is challenging but essential for understanding host-pathogen interactions. A comparative analysis of SLiMs across viruses, bacteria, and eukaryotes showed that viral SLiMs and certain motifs found in both viruses and eukaryotes have less disorder. The analysis of structural features of equivalent SLiMs from pathogens and eukaryotes revealed that some motifs are more structured in pathogens while others are more structured in eukaryotes, suggesting a varied mechanism of interaction between pathogens and their eukaryotic hosts.
Review
Biology
Sobia Idrees, Keshav Raj Paudel, Tayyaba Sadaf, Philip M. Hansbro
Summary: Viruses interact with their hosts by developing protein-protein interactions and mimic host proteins using short linear motifs. This mimicry can interfere with the function of host proteins. By studying viral mimicry, we can gain a better understanding of the mechanisms involved.
Review
Biotechnology & Applied Microbiology
Paula M. Tribelli, Nancy Lopez
Summary: This review provides an overview of temperature-response mechanisms in Pseudomonas species and highlights their relevance to human and animal health as well as agricultural applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Biology
Hajarooba Gnanagobal, Javier Santander
Summary: This review provides a comprehensive analysis of the interactions between marine Gram-positive pathogens and fish hosts, which cause economic losses in global marine fish aquaculture. Understanding these host-pathogen interactions is crucial for developing effective prophylactic measures and treatments.
Article
Biochemistry & Molecular Biology
Jordi Gomez Borrego, Marc Torrent Burgas
Summary: Adhesion and colonization of host cells by pathogenic bacteria rely on protein-protein interactions (PPIs). This study developed a filtering process to obtain a reliable list of domains and motifs participating in PPIs between bacteria and human cells. Structural analysis revealed that human proteins involved in these interactions are rich in alpha helix and disordered regions. The most significant domain-domain interactions were validated, but verifying domain-motif interactions was more challenging. Post-translational modifications, especially phosphorylation, also play a role in these interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Microbiology
Charmaine Retanal, Brianna Ball, Jennifer Geddes-McAlister
Summary: This review focuses on the role of post-translational modifications (PTMs) in fungal pathogens, such as Candida spp., Aspergillus spp., and Cryptococcus spp., in adapting to host environments, manipulating host immune responses, and developing resistance to antifungal drugs. It provides a critical evaluation of current knowledge, addresses key questions in understanding the complex roles of PTMs in fungal pathogens, and presents research opportunities for uncovering new therapeutic strategies.
Article
Biochemistry & Molecular Biology
Sonali Tayal, Venugopal Bhatia, Tanya Mehrotra, Sonika Bhatnagar
Summary: This study curated experimental host-pathogen and host-host protein-protein interactions, annotated the domains and motifs of these proteins, and proposed the concept of mimicry pairs. The results were organized in a web-based resource called ImitateDB, which allows for easy querying of a large number of identified mimicry pairs in interacting host and pathogen proteins.
Article
Microbiology
Jane Chepsergon, Celiwe Innocentia Nxumalo, Brenda S. C. Salasini, Aquillah M. Kanzi, Lucy Novungayo Moleleki
Summary: A bioinformatics study identified core RxLR effectors in Phytophthora parasitica, which contain short linear motifs (SLiMs) that may play a crucial role in effector translocation.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Mariano Martin, Franco G. Brunello, Carlos P. Modenutti, Juan P. Nicola, Marcelo A. Marti
Summary: This study combines sequence variant information and structural analysis to propose a strategy for predicting true functional short linear motifs (SLiMs) and improving the rejection of false positives, with a direct impact in clinical genomics.
Article
Microbiology
Jane Chepsergon, Celiwe Innocentia Nxumalo, Brenda S. C. Salasini, Aquillah M. Kanzi, Lucy Novungayo Moleleki
Summary: Oomycetes of the genus Phytophthora, including Phytophthora parasitica, are successful plant pathogens due to their secretion of effector proteins that alter host physiological processes. In this study, we identified 333 candidate RxLR effectors in P. parasitica and found that 71 of them are highly conserved among P. parasitica strains. These conserved effectors, designated as core RxLR effectors (CREs), exhibit enrichment of intrinsically disordered regions in the N terminus and contain important short linear motifs (SLiMs) in the C terminus. One of the CREs, PpRxLR1, was shown to interact with host defense proteins and carry a ubiquitin-like SLiM that may mediate these interactions. This research improves our understanding of Phytophthora RxLR effector function and may contribute to the development of control strategies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Ecology
Lia Schlippe Justicia, Martin Mayer, Richard Shine, Cathy Shilton, Gregory P. Brown
Summary: Coevolutionary host-parasite arms races can be disrupted by biological invasions, affecting both host and parasite densities, as well as their traits. The spread of cane toads and their parasitic lungworm across tropical Australia provides an opportunity to study a perturbed host-parasite system. Infection success was highest when toads from long-established populations were exposed to lungworms from close to the invasion front, suggesting increased parasite infectivity and host resistance over the course of invasion. Most virulence/tolerance traits have not consistently increased or decreased during invasion. Higher parasite burdens were associated with increased feeding performance in toads and faster growth in lungworms, suggesting host manipulation by the parasite.
ECOLOGY AND EVOLUTION
(2022)
Article
Immunology
Victor Garcia-Bustos, Javier Peman, Alba Ruiz-Gaitan, Marta Dafne Cabanero-Navalon, Ana Cabanilles-Boronat, Maria Fernandez-Calduch, Lucia Marcilla-Barreda, Ignacio A. Sigona-Giangreco, Miguel Salavert, Maria Angeles Tormo-Mas, Amparo Ruiz-Sauri
Summary: This study analyzes the in vivo behavior of Candida auris compared to other Candida species in G. mellonella. It reveals that C. auris exhibits higher immunogenic activity, unique invasion patterns, and inter-phenotypic tissue tropism differences. The study also highlights the importance of phenotypic identification in clinical settings.
EMERGING MICROBES & INFECTIONS
(2022)
Review
Biochemistry & Molecular Biology
Asahiro Morishita, Kyoko Oura, Tomoko Tadokoro, Koji Fujita, Joji Tani, Tsutomu Masaki
Summary: The liver is a non-immunological organ involved in metabolic activities, nutrient storage, and detoxification. Resident immune cells in the liver drive immunological reactions and certain microRNAs are associated with the immune response to pathogens, although the exact mechanism of miRNA interference in these interactions remains unclear.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Yibin Yang, Xia Zhu, Haixin Zhang, Yuhua Chen, Yi Song, Xiaohui Ai
Summary: The study on the host-pathogen interaction between channel catfish and Yersinia ruckeri revealed the dynamic regulation of the transcriptome during infection, with significant upregulation of immune-related pathways. Specifically, the infection was found to be closely related to metabolic pathways, and the pathogenesis promoted by Y. ruckeri in channel catfish was mainly through the flagellum gene fliC. This research contributes to understanding how catfish respond to infection and develop enteric red mouth disease (ERM) through a transcriptional perspective.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Katarzyna Wreczycka, Vedran Franke, Bora Uyar, Ricardo Wurmus, Selman Bulut, Baris Tursun, Altuna Akalin
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Diogo M. Ribeiro, Alexis Prod'homme, Adrien Teixeira, Andreas Zanzoni, Christine Brun
NUCLEIC ACIDS RESEARCH
(2020)
Review
Cell Biology
Bora Uyar, Daniel Palmer, Axel Kowald, Hugo Murua Escobar, Israel Barrantes, Steffen Moeller, Altuna Akalin, Georg Fuellen
AGEING RESEARCH REVIEWS
(2020)
Article
Biochemistry & Molecular Biology
Marina Kolesnichenko, Nadine Mikuda, Uta E. Hoepken, Eva Kaergel, Bora Uyar, Ahmet Bugra Tufan, Maja Milanovic, Wei Sun, Inge Krahn, Kolja Schleich, Linda Hoff, Michael Hinz, Michael Willenbrock, Sabine Jungmann, Altuna Akalin, Soyoung Lee, Ruth Schmidt-Ullrich, Clemens A. Schmitt, Claus Scheidereit
Summary: The study reveals that DNA double-strand breaks elicit two subsequent phases of NF-kappa B activation, with the first phase controlling anti-apoptotic gene expression and the second phase driving expression of senescence-associated genes.
Article
Cell Biology
Jonathan J. Froehlich, Bora Uyar, Margareta Herzog, Kathrin Theil, Petar Glazar, Altuna Akalin, Nikolaus Rajewsky
Summary: Understanding how regulatory sequences control gene expression is crucial for explaining phenotypes in health and disease. This study used inducible Cas9 and multiplexed guide RNAs to create mutations in enhancers/promoters and 3'UTRs of multiple genes in C. elegans, showing the impact on expression and fitness. The approach enabled parallel analysis of regulatory sequences directly in animals, providing insights into how specific binding sites can independently regulate gene expression.
Article
Mathematical & Computational Biology
Sebastien A. Choteau, Audrey Wagner, Philippe Pierre, Lionel Spinelli, Christine Brun
Summary: High-throughput technologies have revealed the presence of non-canonical short open reading frames (sORFs) on most eukaryotic ribonucleic acids. MetamORF provides a repository of unique sORFs identified in the human and mouse genomes for future investigations. The database offers new analyses at locus, gene, transcript, and ORF levels and is accessible through a user-friendly web interface.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Review
Microbiology
Deeya Saha, Marta Iannuccelli, Christine Brun, Andreas Zanzoni, Luana Licata
Summary: Viral infections are a major cause of human diseases, and understanding the virus-host protein-protein interactions is crucial for developing treatments. The interactions have been captured in molecular interaction databases, allowing for further bioinformatic and network studies. Network analysis of virus-host interactomes helps us understand the effects of viral infection on the host and the key proteins and pathways targeted by the virus.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Bertrand Fabre, Sebastien A. Choteau, Carine Duboe, Carole Pichereaux, Audrey Montigny, Dagmara Korona, Michael J. Deery, Mylene Camus, Christine Brun, Odile Burlet-Schiltz, Steven Russell, Jean-Philippe Combier, Kathryn S. Lilley, Serge Plaza
Summary: Recent studies have found that many small proteins are overlooked during the annotation of protein-coding genes. These alternative proteins, which have short open reading frames or are monocistronic, have failed to be properly characterized. Some of these alternative proteins have been shown to have biological activity and are involved in a wide range of functions. However, the exploration of the alternative proteome is limited to a small number of species. In this article, a deep peptidomics workflow was used to identify 401 alternative proteins in the fruit fly Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of these alternative proteins, providing insight into their specific functions. Several alternative proteins were found to have higher abundances than their canonical counterparts, suggesting that they are the main products of their corresponding genes. Additionally, 14 alternative proteins were found to have developmentally regulated expression patterns and 10 were induced upon heat-shock treatment of embryos, indicating stage or stress-specific production of alternative proteins.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dae-Kyum Kim, Benjamin Weller, Chung-Wen Lin, Dayag Sheykhkarimli, Jennifer J. Knapp, Guillaume Dugied, Andreas Zanzoni, Carles Pons, Marie J. Tofaute, Sibusiso B. Maseko, Kerstin Spirohn, Florent Laval, Luke Lambourne, Nishka Kishore, Ashyad Rayhan, Mayra Sauer, Veronika Young, Hridi Halder, Nora Marin-de la Rosa, Oxana Pogoutse, Alexandra Strobel, Patrick Schwehn, Roujia Li, Simin T. Rothballer, Melina Altmann, Patricia Cassonnet, Atina G. Cote, Lena Elorduy Vergara, Isaiah Hazelwood, Betty B. Liu, Maria Nguyen, Ramakrishnan Pandiarajan, Bushra Dohai, Patricia A. Rodriguez Coloma, Juline Poirson, Paolo Giuliana, Luc Willems, Mikko Taipale, Yves Jacob, Tong Hao, David E. Hill, Christine Brun, Jean-Claude Twizere, Daniel Krappmann, Matthias Heinig, Claudia Falter, Patrick Aloy, Caroline Demeret, Marc Vidal, Michael A. Calderwood, Frederick P. Roth, Pascal Falter-Braun
Summary: A study mapping the contactome between SARS-CoV-2 and human host proteins uncovers an inhibitor of viral replication and connects it to COVID-19 severity and human genetic architecture, providing important insights for therapy design and drug development.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Saswati Saha, Laurent Perrin, Laurence Roder, Christine Brun, Lionel Spinelli
Summary: In this article, a novel method called epiMEIF is proposed for detecting higher-order epistatic interactions from GWAS data, improving the detection of genetic architecture underlying complex phenotypes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Saswati Saha, Lionel Spinelli, Jaime A. Castro Mondragon, Anais Kervadec, Michaela Lynott, Laurent Kremmer, Laurence Roder, Sallouha Krifa, Magali Torres, Christine Brun, Georg Vogler, Rolf Bodmer, Alexandre R. Colas, Karen Ocorr, Laurent Perrin
Summary: Studying the cardiac performance variations in Drosophila reveals genetic networks associated with natural variation of cardiac traits and identifies genes related to cardiac function variations. The findings in fruit flies can potentially accelerate the discovery of heart diseases in humans.
Article
Oncology
Artem Baranovskii, Irem B. Guenduez, Vedran Franke, Bora Uyar, Altuna Akalin
Summary: Cancer is a complex disease with heterogeneous subtypes, and the current genomic analysis panels only partially reflect the tumor's response to cancer drugs. This study demonstrates that incorporating transcriptome information on top of genomic aberrations significantly improves the prediction of drug response.
