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Ponndara S, Kortebi M, Boccard F, Bury-Moné S, Lioy VS. Principles of bacterial genome organization, a conformational point of view. Mol Microbiol 2024. [PMID: 38922728 DOI: 10.1111/mmi.15290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Bacterial chromosomes are large molecules that need to be highly compacted to fit inside the cells. Chromosome compaction must facilitate and maintain key biological processes such as gene expression and DNA transactions (replication, recombination, repair, and segregation). Chromosome and chromatin 3D-organization in bacteria has been a puzzle for decades. Chromosome conformation capture coupled to deep sequencing (Hi-C) in combination with other "omics" approaches has allowed dissection of the structural layers that shape bacterial chromosome organization, from DNA topology to global chromosome architecture. Here we review the latest findings using Hi-C and discuss the main features of bacterial genome folding.
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Affiliation(s)
- Sokrich Ponndara
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Mounia Kortebi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Frédéric Boccard
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Stéphanie Bury-Moné
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Virginia S Lioy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R. Orchestrating chromosome conformation capture analysis with Bioconductor. Nat Commun 2024; 15:1072. [PMID: 38316789 PMCID: PMC10844600 DOI: 10.1038/s41467-024-44761-x] [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: 09/02/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.
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Affiliation(s)
- Jacques Serizay
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France.
| | - Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Swiss Data Science Center, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Université de Lausanne, Center for Integrative Genomics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
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3
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Lamy-Besnier Q, Garneau JR. Enrichment, Sequencing, and Identification of DNA Bacteriophages from Fecal Samples. Methods Mol Biol 2024; 2732:133-144. [PMID: 38060122 DOI: 10.1007/978-1-0716-3515-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Research on individual viruses and phages, as well as viral populations (viromes), is greatly expanding. Phages and viromes are increasingly suspected to have numerous impacts on the ecosystem in which they reside by interacting directly or indirectly with the other organisms present in their environment. In particular, phage communities of the gut microbiota have been associated with a wide range of diseases. However, properly investigating intestinal viromes is still very challenging, both experimentally and analytically. This chapter proposes a simple and reproducible protocol to separate and enrich DNA phage particles from fecal samples, to sequence them, and finally obtain a basic but robust bioinformatic characterization and classification of the global bacteriophage community.
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Affiliation(s)
- Quentin Lamy-Besnier
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, Paris, France
| | - Julian R Garneau
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France.
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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Hoareau M, Gerges E, Crémazy FGE. Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches. Methods Mol Biol 2024; 2819:3-26. [PMID: 39028499 DOI: 10.1007/978-1-0716-3930-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The complex architecture of DNA within living organisms is essential for maintaining the genetic information that dictates their functions and characteristics. Among the many complexities of genetic material organization, the folding and arrangement of DNA into chromosomes play a critical role in regulating gene expression, replication, and other essential cellular processes. Bacteria, despite their apparently simple cellular structure, exhibit a remarkable level of chromosomal organization that influences their adaptability and survival in diverse environments. Understanding the three-dimensional arrangement of bacterial chromosomes has long been a challenge due to technical limitations, but the development of Chromosome Conformation Capture (3C) methods revolutionized our ability to explore the hierarchical structure and the dynamics of bacterial genomes. Here, we review the major advances in the field of bacterial chromosome structure using 3C technology over the past decade.
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Affiliation(s)
- Marion Hoareau
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Elias Gerges
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Frédéric G E Crémazy
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France.
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Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The landscape of the histone-organized chromatin of Bdellovibrionota bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564843. [PMID: 37961278 PMCID: PMC10634947 DOI: 10.1101/2023.10.30.564843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Doughty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Arc Institute, Palo Alto, California, USA
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6
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Ye H, Borusak S, Eberl C, Krasenbrink J, Weiss AS, Chen SC, Hanson BT, Hausmann B, Herbold CW, Pristner M, Zwirzitz B, Warth B, Pjevac P, Schleheck D, Stecher B, Loy A. Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut. Nat Commun 2023; 14:5533. [PMID: 37723166 PMCID: PMC10507020 DOI: 10.1038/s41467-023-41008-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/21/2023] [Indexed: 09/20/2023] Open
Abstract
Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.
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Affiliation(s)
- Huimin Ye
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sabrina Borusak
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Claudia Eberl
- Max-von-Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
| | - Julia Krasenbrink
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna S Weiss
- Max-von-Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Buck T Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o Waitaha, University of Canterbury, Christchurch, New Zealand
| | - Manuel Pristner
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria
| | - Benjamin Zwirzitz
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria
- Exposome Austria, Research Infrastructure and National EIRENE Hub, Vienna, Austria
| | - Petra Pjevac
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - David Schleheck
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Ludwig Maximilian University Munich, Munich, Germany
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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