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DNA methylation in Ensifer species during free-living growth and during nitrogen-fixing symbiosis with Medicago spp.

View ORCID ProfileGeorge C. diCenzo, View ORCID ProfileLisa Cangioli, Quentin Nicoud, View ORCID ProfileJanis H.T. Cheng, View ORCID ProfileMatthew J. Blow, Nicole Shapiro, View ORCID ProfileTanja Woyke, View ORCID ProfileEmanuele G Biondi, View ORCID ProfileBenoît Alunni, View ORCID ProfileAlessio Mengoni, View ORCID ProfilePeter Mergaert
doi: https://doi.org/10.1101/2021.03.08.434416
George C. diCenzo
aDepartment of Biology, Queen’s University, Kingston ON, K7L 3N6, Canada
bDepartment of Biology, University of Florence, Florence, 50019, Italy
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  • For correspondence: george.dicenzo@queensu.ca
Lisa Cangioli
bDepartment of Biology, University of Florence, Florence, 50019, Italy
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Quentin Nicoud
cUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, 91198, France
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Janis H.T. Cheng
aDepartment of Biology, Queen’s University, Kingston ON, K7L 3N6, Canada
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Matthew J. Blow
dU.S. Department of Energy Joint Genome Institute, Berkeley CA, 94720, USA
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Nicole Shapiro
dU.S. Department of Energy Joint Genome Institute, Berkeley CA, 94720, USA
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Tanja Woyke
dU.S. Department of Energy Joint Genome Institute, Berkeley CA, 94720, USA
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  • ORCID record for Tanja Woyke
Emanuele G Biondi
cUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, 91198, France
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Benoît Alunni
cUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, 91198, France
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Alessio Mengoni
bDepartment of Biology, University of Florence, Florence, 50019, Italy
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Peter Mergaert
cUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, 91198, France
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ABSTRACT

Methylation of specific DNA sequences is ubiquitous in bacteria and has known roles in immunity and regulation of cellular processes, such as the cell cycle. Using single-molecule real-time sequencing, six genome-wide methylated motifs were identified across four Ensifer strains, five of which were strain-specific. Only the GANTC motif, recognized by the cell cycle-regulated CcrM methyltransferase, was methylated in all strains. In actively dividing cells, methylation of GANTC motifs increased progressively from the ori to ter regions in each replicon, in agreement with a cell cycle-dependent regulation of CcrM. In contrast, there was near full genome-wide GANTC methylation in the early stage of symbiotic differentiation. This was followed by a moderate decrease in the overall extent methylation and a progressive decrease in chromosomal GANTC methylation from the ori to ter regions in later stages of differentiation. We interpret these observations as evidence of dysregulated and constitutive CcrM activity during terminal differentiation, and we hypothesize that it is a driving factor for endoreduplication of terminally differentiated bacteroids.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/diCenzo-Lab/003_2021_Ensifer_DNA_methylation

  • https://genome.jgi.doe.gov/portal/Epianamicrobtool/Epianamicrobtool.info.html

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted August 24, 2021.
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DNA methylation in Ensifer species during free-living growth and during nitrogen-fixing symbiosis with Medicago spp.
George C. diCenzo, Lisa Cangioli, Quentin Nicoud, Janis H.T. Cheng, Matthew J. Blow, Nicole Shapiro, Tanja Woyke, Emanuele G Biondi, Benoît Alunni, Alessio Mengoni, Peter Mergaert
bioRxiv 2021.03.08.434416; doi: https://doi.org/10.1101/2021.03.08.434416
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DNA methylation in Ensifer species during free-living growth and during nitrogen-fixing symbiosis with Medicago spp.
George C. diCenzo, Lisa Cangioli, Quentin Nicoud, Janis H.T. Cheng, Matthew J. Blow, Nicole Shapiro, Tanja Woyke, Emanuele G Biondi, Benoît Alunni, Alessio Mengoni, Peter Mergaert
bioRxiv 2021.03.08.434416; doi: https://doi.org/10.1101/2021.03.08.434416

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