Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae
Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar & Luís Serrano
Nature Communications 8, Article number: 14665 (2017)
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Chromosomes Computational models Molecular modelling
Received: 04 November 2016 Accepted: 20 January 2017 Published online: 08 March 2017
Figure 6: Models of bacterial chromosome organization.
Models of nucleoid organization with Ori and Ter represented by red and purple circles. (a) Model of the E. coli genome with the four macro-domains Ori, Ter, left, right, represented by circles in red, purple, pink and blue, respectively. (b) Model of the B. subtilis genome adapted from ref. 52. (c) 3D models of the M. pneumoniae genome conformation.
Abstract
DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.
Acknowledgements
We thank Dr Besray Ünal and Dr Ivan Junier for providing the co-expression data, and Dr Ivan Junier and Dr François Serra for helpful suggestions. We are also grateful to Dr Jae-Seong Yang for fruitful discussions and Tony Ferrar for critical manuscript revision and language editing (http://www.theeditorsite.com). The research leading to these results was funded by the European Union Seventh Framework Programme (FP7/2007-2013 to L.S.), through the European Research Council, under grant agreement 232913 to L.S. and 609989 to M.A.M-R., the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 634942 to L.S, the Fundación Botín to L.S., the Spanish Ministry of Economy and Competitiveness (BIO2007-61762 to L.S. and BFU2013–47736-P to M.A.M.-R., the National Plan of R+D+i, the ISCIII-Subdirección General de Evaluación y Fomento de la Investigación- (PI10/01702 to L.S.), the Human Frontiers Science Program (RGP0044 to M.A.M.-R.), the ERASynBio/MINECO Grant PCIN-2015-125 to L.S, and the European Regional Development Fund (ERDF) to L.S. We acknowledge support from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ (SEV-2012-0208). We acknowledge the support of the CERCA Programme / Generalitat de Catalunya. This paper reflects only the authorś views and the Union is not liable for any use that may be made of the information contained therein. Library preparation and sequencing was done in the CRG Genomics Unit and high resolution light microscopy analysis in the CRG microscopy unit.
Author information
Affiliations
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
Marie Trussart, Eva Yus, Sira Martinez, Thomas Pengo, Jim Swoger, Maria Lluch-Senar & Luís Serrano
Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
Marie Trussart, Eva Yus, Jim Swoger, Marc A. Marti-Renom, Maria Lluch-Senar & Luís Serrano
Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
Davide Baù & Marc A. Marti-Renom
CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
Davide Baù & Marc A. Marti-Renom
Department of Biology, Graduate School of Science, Osaka City University, 558-8585 Osaka, Japan
Yuhei O. Tahara & Makoto Miyata
OCU Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University, 558-8585 Osaka, Japan
Yuhei O. Tahara & Makoto Miyata
Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
Thomas Pengo
The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia
Michael Widjaja, Steven Djordjevic, Lynne Turnbull & Cynthia Whitchurch
Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
Simon Kretschmer
Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
Marc A. Marti-Renom & Luís Serrano
Contributions
M.T. performed super-resolution imaging experiments, DAPI and EM experiments, collected and analysed the data and wrote the manuscript; E.Y. designed, optimized and performed Hi-C experiments, obtained the gene expression data and reviewed the manuscript; C.M. performed Hi-C experiments and the FISH for super-resolution imaging experiments. D.B. implemented the simulation of 3D models and reviewed the manuscript. Y.O.T. performed EM experiments. T.P. designed a pipeline to analyse super-resolution images. MW cultured M. pneumoniae and performed the 3D-SIM experiments. S.K. performed initial Hi-C experiments and reviewed the manuscript. J.S. performed 3D reconstruction from EM images; SPD designed and supervised the mycoplasma imaging experiments and reviewed the manuscript. LT imaged the slides on the OMX microscope. MW, SPD, LT and CBW analysed the 3D-SIM data and generated the 3D models for the chromosome volume measurements. M.M. designed and supervised EM experiments and reviewed the manuscript. M.A.M.-R. supervised the computational 3D modelling and reviewed the manuscript. M.L.-S. designed and supervised super-resolution imaging experiments and reviewed the manuscript. and L.S. supervised the study and reviewed the manuscript.
Competing interests
The authors declare no competing financial interests.
Corresponding authors
Correspondence to Marc A. Marti-Renom or Maria Lluch-Senar or Luís Serrano.
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