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Hsieh YC, Bockwoldt M, Heiland I. ProTaxoVis-protein taxonomic visualisation of presence. BMC Bioinformatics 2025; 26:128. [PMID: 40389829 PMCID: PMC12087122 DOI: 10.1186/s12859-025-06146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 04/23/2025] [Indexed: 05/21/2025] Open
Abstract
BACKGROUND Protein presence information is an essential component of biological pathway identification. Presence of certain enzymes in an organism points towards the metabolic pathways that occur within it, whereas the absence of these enzymes indicates either the existence of alternative pathways or a lack of these pathways altogether. The same inference applies to regulatory pathways such as gene regulation and signal transduction. Protein presence information therefore forms the basis for biological pathway studies, and patterns in presence-absence across multiple organisms allow for comparative pathway analyses. RESULTS Here we present ProTaxoVis, a novel bioinformatic tool that extracts protein presence information from database queries and maps it to a taxonomic tree or heatmap. ProTaxoVis generates a large-scale overview of presence patterns in taxonomic clades of interest. This overview reveals protein distribution patterns, and this can be used to deduce pathway evolution or to probe other biological questions. ProTaxoVis combines and filters sequence query results to extract information on the distribution of proteins and translates this information into two types of visual outputs: taxonomic trees and heatmaps. The trees supplement their topology with scaled pie-chart representations per node of the presence of target proteins and combinations of these proteins, such that patterns in taxonomic groups can easily be identified. The heatmap visualisation shows presence and conservation of these proteins for a user-determined set of species, allowing for a more detailed view over a larger group of proteins as compared to the trees. ProTaxoVis also allows for visual quality checks of hits based on a coverage plot and a length histogram, which can be used to determine e-value and minimum protein length cutoffs. Tabular output of resulting data from the query, combined, and heatmap building step are saved and easily accessible for further analyses. CONCLUSIONS We evaluate our tool with the phosphoribosyltransferases, a transferase enzyme family with notable distribution patterns amongst organisms of varying complexities and across Eukaryota, Bacteria, and Archaea. ProTaxoVis is open-source and available at: https://github.com/MolecularBioinformatics/ProTaxoVis .
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Affiliation(s)
- Yin-Chen Hsieh
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT Arctic University of Norway, 9037, Tromsø, Norway
| | - Mathias Bockwoldt
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT Arctic University of Norway, 9037, Tromsø, Norway
| | - Ines Heiland
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT Arctic University of Norway, 9037, Tromsø, Norway.
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2
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Tran JS, Ward RD, Iruegas-López R, Ebersberger I, Peters JM. Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii. PLoS Genet 2025; 21:e1011642. [PMID: 40153700 PMCID: PMC11975115 DOI: 10.1371/journal.pgen.1011642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 04/07/2025] [Accepted: 03/03/2025] [Indexed: 03/30/2025] Open
Abstract
The Gram-negative pathogen, Acinetobacter baumannii, poses a serious threat to human health due to its role in nosocomial infections that are resistant to treatment with current antibiotics. Despite this, our understanding of fundamental A. baumannii biology remains limited, as many essential genes have not been experimentally characterized. These essential genes are critical for bacterial survival and, thus, represent promising targets for drug discovery. Here, we systematically probe the function of essential genes by screening a CRISPR interference knockdown library against a diverse panel of chemical inhibitors, including antibiotics. We find that most essential genes show chemical-gene interactions, allowing insights into both inhibitor and gene function. For instance, knockdown of lipooligosaccharide (LOS) transport genes increased sensitivity to a broad range of chemicals. Cells with defective LOS transport showed cell envelope hyper-permeability that was dependent on continued LOS synthesis. Using phenotypes across our chemical-gene interaction dataset, we constructed an essential gene network linking poorly understood genes to well-characterized genes in cell division and other processes. Finally, our phenotype-structure analysis identified structurally related antibiotics with distinct cellular impacts and suggested potential targets for underexplored inhibitors. This study advances our understanding of essential gene and inhibitor function, providing a valuable resource for mechanistic studies, therapeutic strategies, and future key targets for antibiotic development.
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Affiliation(s)
- Jennifer Suzanne Tran
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan David Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genetics Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rubén Iruegas-López
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Jason Matthew Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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3
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Tran JS, Ward RD, Iruegas-López R, Ebersberger I, Peters JM. Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.05.627103. [PMID: 39677645 PMCID: PMC11643038 DOI: 10.1101/2024.12.05.627103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
The Gram-negative pathogen, Acinetobacter baumannii , poses a serious threat to human health due to its role in nosocomial infections that are resistant to treatment with current antibiotics. Despite this, our understanding of fundamental A. baumannii biology remains limited, as many essential genes have not been experimentally characterized. These essential genes are critical for bacterial survival and, thus, represent promising targets for drug discovery. Here, we systematically probe the function of essential genes by screening a CRISPR interference knockdown library against a diverse panel of chemical inhibitors, including antibiotics. We find that most essential genes show chemical-gene interactions, allowing insights into both inhibitor and gene function. For instance, knockdown of lipooligosaccharide (LOS) transport genes increased sensitivity to a broad range of chemicals. Cells with defective LOS transport showed cell envelope hyper-permeability that was dependent on continued LOS synthesis. Using phenotypes across our chemical-gene interaction dataset, we constructed an essential gene network linking poorly understood genes to well-characterized genes in cell division and other processes. Finally, our phenotype-structure analysis identified structurally related antibiotics with distinct cellular impacts and suggested potential targets for underexplored inhibitors. This study advances our understanding of essential gene and inhibitor function, providing a valuable resource for mechanistic studies, therapeutic strategies, and future key targets for antibiotic development.
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4
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Xu Y, Gehlot R, Capon SJ, Albu M, Gretz J, Bloomekatz J, Mattonet K, Vucicevic D, Talyan S, Kikhi K, Günther S, Looso M, Firulli BA, Sanda M, Firulli AB, Lacadie SA, Yelon D, Stainier DYR. PDGFRA is a conserved HAND2 effector during early cardiac development. NATURE CARDIOVASCULAR RESEARCH 2024; 3:1531-1548. [PMID: 39658721 PMCID: PMC11634778 DOI: 10.1038/s44161-024-00574-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/29/2024] [Indexed: 12/12/2024]
Abstract
The basic helix-loop-helix transcription factor HAND2 has multiple roles during vertebrate organogenesis, including cardiogenesis. However, much remains to be uncovered about its mechanism of action. Here, we show the generation of several hand2 mutant alleles in zebrafish and demonstrate that dimerization-deficient mutants display the null phenotype but DNA-binding-deficient mutants do not. Rescue experiments with Hand2 variants using a newly identified hand2 enhancer confirmed these observations. To identify Hand2 effectors critical for cardiogenesis, we analyzed the transcriptomes of hand2 loss- and gain-of-function embryonic cardiomyocytes and tested the function of eight candidate genes in vivo; pdgfra was most effective in rescuing myocardial migration in hand2 mutants. Accordingly, we identified a putative Hand2-binding region in the zebrafish pdgfra locus that is important for its expression. In addition, Hand2 loss- and gain-of-function experiments in mouse embryonic stem cell-derived cardiac cells decreased and increased Pdgfra expression, respectively. Altogether, these results further our mechanistic understanding of HAND2 function during early cardiogenesis.
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Affiliation(s)
- Yanli Xu
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Rupal Gehlot
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Samuel J Capon
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Marga Albu
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jonas Gretz
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Joshua Bloomekatz
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Biology, University of Mississippi, University, MS, USA
| | - Kenny Mattonet
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Dubravka Vucicevic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Sweta Talyan
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Khrievono Kikhi
- Flow Cytometry Service Group, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, IN, USA
| | - Miloslav Sanda
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, IN, USA
| | - Scott Allen Lacadie
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Deborah Yelon
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
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5
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Muelbaier H, Arthen F, Collins G, Hickler T, Hohberg K, Lehmitz R, Pauchet Y, Pfenninger M, Potapov A, Romahn J, Schaefer I, Scheu S, Schneider C, Ebersberger I, Bálint M. Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates. Mol Ecol 2024; 33:e17351. [PMID: 38712904 DOI: 10.1111/mec.17351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 05/08/2024]
Abstract
Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.
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Affiliation(s)
- Hannah Muelbaier
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Freya Arthen
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Gemma Collins
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Thomas Hickler
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Physical Geography, Goethe University, Frankfurt/Main, Germany
| | - Karin Hohberg
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Ricarda Lehmitz
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Yannick Pauchet
- Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Anton Potapov
- Senckenberg Museum for Natural History Görlitz, Görlitz, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- International Institute Zittau, TUD Dresden University of Technology, Zittau, Germany
| | - Juliane Romahn
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Giessen, Germany
| | - Ina Schaefer
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Animal Ecology, University of Goettingen, Goettingen, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Giessen, Germany
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6
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Rossier V, Train C, Nevers Y, Robinson-Rechavi M, Dessimoz C. Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families. Genome Biol Evol 2024; 16:evae100. [PMID: 38742690 PMCID: PMC11149776 DOI: 10.1093/gbe/evae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.
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Affiliation(s)
- Victor Rossier
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Clement Train
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Yannis Nevers
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Comparative Genomics, Lausanne, Switzerland
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7
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Langschied F, Leisegang MS, Brandes RP, Ebersberger I. ncOrtho: efficient and reliable identification of miRNA orthologs. Nucleic Acids Res 2023; 51:e71. [PMID: 37260093 PMCID: PMC10359484 DOI: 10.1093/nar/gkad467] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite their functional relevance, frameworks for the scalable and accurate detection of miRNA orthologs are missing. Consequently, there is still no comprehensive picture of how miRNAs and their associated regulatory networks have evolved. Here we present ncOrtho, a synteny informed pipeline for the targeted search of miRNA orthologs in unannotated genome sequences. ncOrtho matches miRNA annotations from multi-tissue transcriptomes in precision, while scaling to the analysis of hundreds of custom-selected species. The presence-absence pattern of orthologs to 266 human miRNA families across 402 vertebrate species reveals four bursts of miRNA acquisition, of which the most recent event occurred in the last common ancestor of higher primates. miRNA families are rarely modified or lost, but notable exceptions for both events exist. miRNA co-ortholog numbers faithfully indicate lineage-specific whole genome duplications, and miRNAs are powerful markers for phylogenomic analyses. Their exceptionally low genetic diversity makes them suitable to resolve clades where the phylogenetic signal is blurred by incomplete lineage sorting of ancestral alleles. In summary, ncOrtho allows to routinely consider miRNAs in evolutionary analyses that were thus far reserved to protein-coding genes.
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Affiliation(s)
- Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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8
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Iruegas R, Pfefferle K, Göttig S, Averhoff B, Ebersberger I. Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii. PLoS Genet 2023; 19:e1010646. [PMID: 37498819 PMCID: PMC10374093 DOI: 10.1371/journal.pgen.1010646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/06/2023] [Indexed: 07/29/2023] Open
Abstract
The Gram-negative bacterial pathogen Acinetobacter baumannii is a major cause of hospital-acquired opportunistic infections. The increasing spread of pan-drug resistant strains makes A. baumannii top-ranking among the ESKAPE pathogens for which novel routes of treatment are urgently needed. Comparative genomics approaches have successfully identified genetic changes coinciding with the emergence of pathogenicity in Acinetobacter. Genes that are prevalent both in pathogenic and a-pathogenic Acinetobacter species were not considered ignoring that virulence factors may emerge by the modification of evolutionarily old and widespread proteins. Here, we increased the resolution of comparative genomics analyses to also include lineage-specific changes in protein feature architectures. Using type IVa pili (T4aP) as an example, we show that three pilus components, among them the pilus tip adhesin ComC, vary in their Pfam domain annotation within the genus Acinetobacter. In most pathogenic Acinetobacter isolates, ComC displays a von Willebrand Factor type A domain harboring a finger-like protrusion, and we provide experimental evidence that this finger conveys virulence-related functions in A. baumannii. All three genes are part of an evolutionary cassette, which has been replaced at least twice during A. baumannii diversification. The resulting strain-specific differences in T4aP layout suggests differences in the way how individual strains interact with their host. Our study underpins the hypothesis that A. baumannii uses T4aP for host infection as it was shown previously for other pathogens. It also indicates that many more functional complexes may exist whose precise functions have been adjusted by modifying individual components on the domain level.
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Affiliation(s)
- Ruben Iruegas
- Applied Bioinformatics Group, Inst of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Katharina Pfefferle
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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9
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Dosch J, Bergmann H, Tran V, Ebersberger I. FAS: assessing the similarity between proteins using multi-layered feature architectures. Bioinformatics 2023; 39:btad226. [PMID: 37084276 PMCID: PMC10185405 DOI: 10.1093/bioinformatics/btad226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/23/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
MOTIVATION Protein sequence comparison is a fundamental element in the bioinformatics toolkit. When sequences are annotated with features such as functional domains, transmembrane domains, low complexity regions or secondary structure elements, the resulting feature architectures allow better informed comparisons. However, many existing schemes for scoring architecture similarities cannot cope with features arising from multiple annotation sources. Those that do fall short in the resolution of overlapping and redundant feature annotations. RESULTS Here, we introduce FAS, a scoring method that integrates features from multiple annotation sources in a directed acyclic architecture graph. Redundancies are resolved as part of the architecture comparison by finding the paths through the graphs that maximize the pair-wise architecture similarity. In a large-scale evaluation on more than 10 000 human-yeast ortholog pairs, architecture similarities assessed with FAS are consistently more plausible than those obtained using e-values to resolve overlaps or leaving overlaps unresolved. Three case studies demonstrate the utility of FAS on architecture comparison tasks: benchmarking of orthology assignment software, identification of functionally diverged orthologs, and diagnosing protein architecture changes stemming from faulty gene predictions. With the help of FAS, feature architecture comparisons can now be routinely integrated into these and many other applications. AVAILABILITY AND IMPLEMENTATION FAS is available as python package: https://pypi.org/project/greedyFAS/.
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Affiliation(s)
- Julian Dosch
- Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany
| | - Holger Bergmann
- Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany
| | - Vinh Tran
- Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, 60325, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt, 60325, Germany
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10
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Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure 2022; 30:462-475. [DOI: 10.1016/j.str.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 02/08/2023]
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11
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Ilnitskiy IS, Zharikova AA, Mironov AA. OUP accepted manuscript. Nucleic Acids Res 2022; 50:W534-W540. [PMID: 35610035 PMCID: PMC9252792 DOI: 10.1093/nar/gkac385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 11/27/2022] Open
Abstract
Extensive amounts of data from next-generation sequencing and omics studies have led to the accumulation of information that provides insight into the evolutionary landscape of related proteins. Here, we present OrthoQuantum, a web server that allows for time-efficient analysis and visualization of phylogenetic profiles of any set of eukaryotic proteins. It is a simple-to-use tool capable of searching large input sets of proteins. Using data from open source databases of orthologous sequences in a wide range of taxonomic groups, it enables users to assess coupled evolutionary patterns and helps define lineage-specific innovations. The web interface allows to perform queries with gene names and UniProt identifiers in different phylogenetic clades and supplement presence with an additional BLAST search. The conservation patterns of proteins are coded as binary vectors, i.e., strings that encode the presence or absence of orthologous proteins in other genomes. These strings are used to calculate top-scoring correlation pairs needed for finding co-inherited proteins which are simultaneously present or simultaneously absent in specific lineages. Profiles are visualized in combination with phylogenetic trees in a JavaScript-based interface. The OrthoQuantum v1.0 web server is freely available at http://orthoq.bioinf.fbb.msu.ru along with documentation and tutorial.
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Affiliation(s)
| | - Anastasia A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lomonosovsky Prospect 27, Building 10, 119991 Moscow, Russia
- Kharkevich Institute of Information Transmission Problems, Russian Academy of Sciences, Big Karetny Lane 19, Building 1, 127051 Moscow, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lomonosovsky Prospect 27, Building 10, 119991 Moscow, Russia
- Kharkevich Institute of Information Transmission Problems, Russian Academy of Sciences, Big Karetny Lane 19, Building 1, 127051 Moscow, Russia
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12
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Birikmen M, Bohnsack KE, Tran V, Somayaji S, Bohnsack MT, Ebersberger I. Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. Front Microbiol 2021; 12:739000. [PMID: 34603269 PMCID: PMC8481954 DOI: 10.3389/fmicb.2021.739000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023] Open
Abstract
Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
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Affiliation(s)
- Mehmet Birikmen
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Sharvari Somayaji
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Center (S-BIK-F), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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13
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Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol 2021; 38:3033-3045. [PMID: 33822172 PMCID: PMC8321534 DOI: 10.1093/molbev/msab098] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/07/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
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Affiliation(s)
- Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Yannis Nevers
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Department of Computer Science, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ikuo Uchiyama
- Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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14
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Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA. Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases. ACS Chem Biol 2020; 15:3167-3175. [PMID: 33249828 DOI: 10.1021/acschembio.0c00685] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.
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15
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Jiang Z, Carlantoni C, Allanki S, Ebersberger I, Stainier DYR. Tek (Tie2) is not required for cardiovascular development in zebrafish. Development 2020; 147:dev.193029. [PMID: 32928907 DOI: 10.1242/dev.193029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]
Abstract
Angiopoietin/TIE signalling plays a major role in blood and lymphatic vessel development. In mouse, Tek (previously known as Tie2) mutants die prenatally due to a severely underdeveloped cardiovascular system. In contrast, in zebrafish, previous studies have reported that although embryos injected with tek morpholinos (MOs) exhibit severe vascular defects, tek mutants display no obvious vascular malformations. To further investigate the function of zebrafish Tek, we generated a panel of loss-of-function tek mutants, including RNA-less alleles, an allele lacking the MO-binding site, an in-frame deletion allele and a premature termination codon-containing allele. Our data show that all these mutants survive to adulthood with no obvious cardiovascular defects. MO injections into tek mutants lacking the MO-binding site or the entire tek locus cause similar vascular defects to those observed in MO-injected +/+ siblings, indicating off-target effects of the MOs. Surprisingly, comprehensive phylogenetic profiling and synteny analyses reveal that Tek was lost in the largest teleost clade, suggesting a lineage-specific shift in the function of TEK during vertebrate evolution. Altogether, these data show that Tek is dispensable for zebrafish development, and probably dispensable in most teleost species.
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Affiliation(s)
- Zhen Jiang
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany .,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim 61231, Germany
| | - Claudia Carlantoni
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim 61231, Germany
| | - Srinivas Allanki
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim 61231, Germany
| | - Ingo Ebersberger
- Goethe University Frankfurt am Main, Institute of Cell Biology and Neuroscience, Frankfurt 60438, Germany .,Senckenberg Biodiversity and Climate Research Center (S-BIKF), Frankfurt 60438, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt 60438, Germany
| | - Didier Y R Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany .,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim 61231, Germany
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16
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Weidensdorfer M, Ishikawa M, Hori K, Linke D, Djahanschiri B, Iruegas R, Ebersberger I, Riedel-Christ S, Enders G, Leukert L, Kraiczy P, Rothweiler F, Cinatl J, Berger J, Hipp K, Kempf VAJ, Göttig S. The Acinetobacter trimeric autotransporter adhesin Ata controls key virulence traits of Acinetobacter baumannii. Virulence 2020; 10:68-81. [PMID: 31874074 PMCID: PMC6363060 DOI: 10.1080/21505594.2018.1558693] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen that causes a multitude of nosocomial infections. The Acinetobacter trimeric autotransporter adhesin (Ata) belongs to the superfamily of trimeric autotransporter adhesins which are important virulence factors in many Gram-negative species. Phylogenetic profiling revealed that ata is present in 78% of all sequenced A. baumannii isolates but only in 2% of the closely related species A. calcoaceticus and A. pittii. Employing a markerless ata deletion mutant of A. baumannii ATCC 19606 we show that adhesion to and invasion into human endothelial and epithelial cells depend on Ata. Infection of primary human umbilical cord vein endothelial cells (HUVECs) with A. baumannii led to the secretion of interleukin (IL)-6 and IL-8 in a time- and Ata-dependent manner. Furthermore, infection of HUVECs by WT A. baumannii was associated with higher rates of apoptosis via activation of caspases-3 and caspase-7, but not necrosis, in comparison to ∆ata. Ata deletion mutants were furthermore attenuated in their ability to kill larvae of Galleria mellonella and to survive in larvae when injected at sublethal doses. This indicates that Ata is an important multifunctional virulence factor in A. baumannii that mediates adhesion and invasion, induces apoptosis and contributes to pathogenicity in vivo.
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Affiliation(s)
- Marko Weidensdorfer
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Masahito Ishikawa
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Dirk Linke
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Bardya Djahanschiri
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Ruben Iruegas
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre Frankfurt (BIK-F), Frankfurt, Germany
| | - Sara Riedel-Christ
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Giulia Enders
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Laura Leukert
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Peter Kraiczy
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Florian Rothweiler
- Institute of Medical Virology, University Hospital, Goethe University, Frankfurt, Germany
| | - Jindrich Cinatl
- Institute of Medical Virology, University Hospital, Goethe University, Frankfurt, Germany
| | - Jürgen Berger
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Volkhard A J Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
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17
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Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Advances and Applications in the Quest for Orthologs. Mol Biol Evol 2020; 36:2157-2164. [PMID: 31241141 PMCID: PMC6759064 DOI: 10.1093/molbev/msz150] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
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Affiliation(s)
- Natasha Glover
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (BIK-F), Frankfurt, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany.,Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität u Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Maria-Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Cécile Pereira
- Eura Nova, Marseille, France.,Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Alan Sousa da Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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