1
|
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.
Collapse
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
| |
Collapse
|
2
|
Bignaud A, Cockram C, Borde C, Groseille J, Allemand E, Thierry A, Marbouty M, Mozziconacci J, Espéli O, Koszul R. Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes. Nat Struct Mol Biol 2024; 31:489-497. [PMID: 38177686 PMCID: PMC10948358 DOI: 10.1038/s41594-023-01178-2] [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] [Received: 08/29/2022] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Transcription generates local topological and mechanical constraints on the DNA fiber, leading to the generation of supercoiled chromosome domains in bacteria. However, the global impact of transcription on chromosome organization remains elusive, as the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~5-10 kb). Here we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units. We show that transcriptional units form discrete three-dimensional transcription-induced domains that impose mechanical and topological constraints on their neighboring sequences at larger scales, modifying their localization and dynamics. These results show that transcriptional domains constitute primary building blocks of bacterial chromosome folding and locally impose structural and dynamic constraints.
Collapse
Affiliation(s)
- Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Charlotte Cockram
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Céline Borde
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Justine Groseille
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Allemand
- INSERM-U1163, Unité mécanismes cellulaires et moléculaires des désordres hématologiques et implications thérapeutiques, Institut Imagine, Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Martial Marbouty
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des Génomes, UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France.
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France.
| |
Collapse
|
3
|
Fu Z, Guo MS, Zhou W, Xiao J. Differential roles of positive and negative supercoiling in organizing the E. coli genome. Nucleic Acids Res 2024; 52:724-737. [PMID: 38050973 PMCID: PMC10810199 DOI: 10.1093/nar/gkad1139] [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: 09/11/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how supercoiling correlates with the spatial contact maps obtained from chromosome conformation capture sequencing (Hi-C and 5C). We find that supercoiled chromosomal loci have overall higher Hi-C contact frequencies than sites that are not supercoiled. Surprisingly, positive supercoiling corresponds to higher spatial contact than negative supercoiling. Additionally, positive, but not negative, supercoiling could be identified from Hi-C data with high accuracy. We further find that the majority of positive and negative supercoils coincide with highly active transcription units, with a minor group likely associated with replication and other genomic processes. Our results show that both positive and negative supercoiling enhance spatial contact, with positive supercoiling playing a larger role in bringing genomic loci closer in space. Based on our results, we propose new physical models of how the E. coli chromosome is organized by positive and negative supercoils.
Collapse
Affiliation(s)
- Ziqi Fu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Monica S Guo
- Department of Microbiology, University of Washington, Seattle, WA 98198, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
4
|
Burman N, Belukhina S, Depardieu F, Wilkinson RA, Skutel M, Santiago-Frangos A, Graham AB, Livenskyi A, Chechenina A, Morozova N, Zahl T, Henriques WS, Buyukyoruk M, Rouillon C, Shyrokova L, Kurata T, Hauryliuk V, Severinov K, Groseille J, Thierry A, Koszul R, Tesson F, Bernheim A, Bikard D, Wiedenheft B, Isaev A. Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573894. [PMID: 38260645 PMCID: PMC10802454 DOI: 10.1101/2024.01.02.573894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Viruses compete with each other for limited cellular resources, and some viruses deliver defense mechanisms that protect the host from competing genetic parasites. PARIS is a defense system, often encoded in viral genomes, that is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving the host tRNALys. Phage T5 subverts PARIS immunity through expression of a tRNALys variant that prevents PARIS-mediated cleavage, and thereby restores viral infection. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids.
Collapse
Affiliation(s)
- Nathaniel Burman
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Svetlana Belukhina
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - Florence Depardieu
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, 75015 Paris, France
| | - Royce A. Wilkinson
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Mikhail Skutel
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - Andrew Santiago-Frangos
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Ava B. Graham
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Alexei Livenskyi
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Chechenina
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - Natalia Morozova
- Peter the Great St Petersburg State Polytechnic University, St. Petersburg, Russia
| | - Trevor Zahl
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - William S. Henriques
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Murat Buyukyoruk
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Christophe Rouillon
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, 75015 Paris, France
| | - Lena Shyrokova
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
- Science for Life Laboratory, Lund, Sweden
| | | | - Justine Groseille
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Sorbonne Université, College Doctoral
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Florian Tesson
- Institut Pasteur, Université Paris Cité, Molecular Diversity of Microbes, 75015 Paris, France
| | - Aude Bernheim
- Institut Pasteur, Université Paris Cité, Molecular Diversity of Microbes, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, 75015 Paris, France
| | - Blake Wiedenheft
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| |
Collapse
|
5
|
Badel C, Bell SD. Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins. Nat Microbiol 2024; 9:263-273. [PMID: 38110698 PMCID: PMC10769869 DOI: 10.1038/s41564-023-01540-6] [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: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/20/2023]
Abstract
Proteins in the structural maintenance of chromosomes (SMC) superfamily play key roles in chromosome organization and are ubiquitous across all domains of life. However, SMC proteins are notably absent in the Desulfurococcales of phylum Crenarchaeota. Intrigued by this observation, we performed chromosome conformation capture experiments in the model Desulfurococcales species Aeropyrum pernix. As in other archaea, we observe chromosomal interaction domains across the chromosome. The boundaries between chromosomal interaction domains show a dependence on transcription and translation for their definition. Importantly, however, we reveal an additional higher-order, bipartite organization of the chromosome-with a small high-gene-expression and self-interacting domain that is defined by transcriptional activity and loop structures. Viewing these data in the context of the distribution of SMC superfamily proteins in the Crenarchaeota, we suggest that the organization of the Aeropyrum genome represents an evolutionary antecedent of the compartmentalized architecture observed in the Sulfolobus lineage.
Collapse
Affiliation(s)
- Catherine Badel
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA.
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, Strasbourg, France.
| | - Stephen D Bell
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA.
- Biology Department, Indiana University, Bloomington, IN, USA.
| |
Collapse
|
6
|
Chromosome organization affects genome evolution in Sulfolobus archaea. Nat Microbiol 2022; 7:820-830. [PMID: 35618771 DOI: 10.1038/s41564-022-01127-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.
Collapse
|