The Escherichia coli chromosome moves to the replisome.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
17 Jul 2024
17 Jul 2024
Historique:
received:
21
09
2023
accepted:
28
06
2024
medline:
18
7
2024
pubmed:
18
7
2024
entrez:
17
7
2024
Statut:
epublish
Résumé
In Escherichia coli, it is debated whether the two replisomes move independently along the two chromosome arms during replication or if they remain spatially confined. Here, we use high-throughput fluorescence microscopy to simultaneously determine the location and short-time-scale (1 s) movement of the replisome and a chromosomal locus throughout the cell cycle. The assay is performed for several loci. We find that (i) the two replisomes are confined to a region of ~250 nm and ~120 nm along the cell's long and short axis, respectively, (ii) the chromosomal loci move to and through this region sequentially based on their distance from the origin of replication, and (iii) when a locus is being replicated, its short time-scale movement slows down. This behavior is the same at different growth rates. In conclusion, our data supports a model with DNA moving towards spatially confined replisomes at replication.
Identifiants
pubmed: 39019870
doi: 10.1038/s41467-024-50047-z
pii: 10.1038/s41467-024-50047-z
doi:
Substances chimiques
DNA, Bacterial
0
Escherichia coli Proteins
0
DNA synthesome
EC 2.7.7.-
DNA-Directed DNA Polymerase
EC 2.7.7.7
Multienzyme Complexes
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6018Informations de copyright
© 2024. The Author(s).
Références
Mäkelä, J. & Sherratt, D. J. Organization of the escherichia coli chromosome by a MukBEF axial core. Mol. Cell 78, 250–260.e5 (2020).
pubmed: 32097603
pmcid: 7163298
doi: 10.1016/j.molcel.2020.02.003
Kavenoff, R. & Ryder, O. A. Electron microscopy of membrane-associated folded chromosomes of Escherichia coli. Chromosoma 55, 13–25 (1976).
pubmed: 767075
doi: 10.1007/BF00288323
Le, T. B. K., Imakaev, M. V., Mirny, L. A. & Laub, M. T. High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342, 731–734 (2013).
pubmed: 24158908
pmcid: 3927313
doi: 10.1126/science.1242059
O’Donnell, M. Replisome architecture and dynamics in Escherichia coli. J. Biol. Chem. 281, 10653–10656 (2006).
pubmed: 16421093
doi: 10.1074/jbc.R500028200
Kurth, I. & O’Donnell, M. Replisome dynamics during chromosome duplication. EcoSal Plus 3, 2 (2009).
Lemon, K. P. & Grossman, A. D. Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science 282, 1516–1519 (1998).
pubmed: 9822387
doi: 10.1126/science.282.5393.1516
Molina, F. & Skarstad, K. Replication fork and SeqA focus distributions in Escherichia coli suggest a replication hyperstructure dependent on nucleotide metabolism. Mol. Microbiol. 52, 1597–1612 (2004).
pubmed: 15186411
doi: 10.1111/j.1365-2958.2004.04097.x
Jensen, R. B., Wang, S. C. & Shapiro, L. A moving DNA replication factory in Caulobacter crescentus. EMBO J. 20, 4952–4963 (2001).
pubmed: 11532959
pmcid: 125615
doi: 10.1093/emboj/20.17.4952
Hiraga, S., Ichinose, C., Onogi, T., Niki, H. & Yamazoe, M. Bidirectional migration of SeqA-bound hemimethylated DNA clusters and pairing of oriC copies in Escherichia coli. Genes Cells 5, 327–341 (2000).
pubmed: 10886362
doi: 10.1046/j.1365-2443.2000.00334.x
Kongsuwan, K., Dalrymple, B. P., Wijffels, G. & Jennings, P. A. Cellular localisation of the clamp protein during DNA replication. FEMS Microbiol. Lett. 216, 255–262 (2002).
pubmed: 12435511
doi: 10.1111/j.1574-6968.2002.tb11444.x
Espeli, O., Mercier, R. & Boccard, F. DNA dynamics vary according to macrodomain topography in the E. coli chromosome. Mol. Microbiol. 68, 1418–1427 (2008).
pubmed: 18410497
doi: 10.1111/j.1365-2958.2008.06239.x
Bates, D. & Kleckner, N. Chromosome and replisome dynamics in E. coli: loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation. Cell 121, 899–911 (2005).
pubmed: 15960977
pmcid: 2973560
doi: 10.1016/j.cell.2005.04.013
Niki, H., Yamaichi, Y. & Hiraga, S. Dynamic organization of chromosomal DNA in Escherichia coli. Genes Dev. 14, 212–223 (2000).
pubmed: 10652275
pmcid: 316355
doi: 10.1101/gad.14.2.212
Li, Y., Sergueev, K. & Austin, S. The segregation of the Escherichia coli origin and terminus of replication. Mol. Microbiol. 46, 985–996 (2002).
pubmed: 12421305
doi: 10.1046/j.1365-2958.2002.03234.x
Lau, I. F. et al. Spatial and temporal organization of replicating Escherichia coli chromosomes: Escherichia coli chromosome dynamics. Mol. Microbiol. 49, 731–743 (2004).
doi: 10.1046/j.1365-2958.2003.03640.x
Nielsen, H. J., Ottesen, J. R., Youngren, B., Austin, S. J. & Hansen, F. G. The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves. Mol. Microbiol. 62, 331–338 (2006).
pubmed: 17020576
doi: 10.1111/j.1365-2958.2006.05346.x
Wang, X., Liu, X., Possoz, C. & Sherratt, D. J. The two Escherichia coli chromosome arms locate to separate cell halves. Genes Dev. 20, 1727–1731 (2006).
pubmed: 16818605
pmcid: 1522069
doi: 10.1101/gad.388406
Youngren, B., Nielsen, H. J., Jun, S. & Austin, S. The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer. Genes Dev. 28, 71–84 (2014).
pubmed: 24395248
pmcid: 3894414
doi: 10.1101/gad.231050.113
Badrinarayanan, A., Le, T. B. K. & Laub, M. T. Bacterial chromosome organization and segregation. Annu. Rev. Cell Dev. Biol. 31, 171–199 (2015).
pubmed: 26566111
pmcid: 4706359
doi: 10.1146/annurev-cellbio-100814-125211
Sadhir, I. & Murray, S. M. Mid-cell migration of the chromosomal terminus is coupled to origin segregation in Escherichia coli. Nat. Commun. 14, 7489 (2023).
pubmed: 37980336
pmcid: 10657355
doi: 10.1038/s41467-023-43351-7
Sunako, Y., Onogi, T. & Hiraga, S. Sister chromosome cohesion of Escherichia coli. Mol. Microbiol. 42, 1233–1241 (2001).
pubmed: 11886555
doi: 10.1046/j.1365-2958.2001.02680.x
Wang, X., Reyes-Lamothe, R. & Sherratt, D. J. Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV. Genes Dev. 22, 2426–2433 (2008).
pubmed: 18765793
pmcid: 2532930
doi: 10.1101/gad.487508
Espéli, O. et al. A MatP–divisome interaction coordinates chromosome segregation with cell division in E. coli. EMBO J. 31, 3198–3211 (2012).
pubmed: 22580828
pmcid: 3400007
doi: 10.1038/emboj.2012.128
Javer, A. et al. Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization. Nat. Commun. 4, 3003 (2013).
pubmed: 23764719
doi: 10.1038/ncomms3003
Reyes-Lamothe, R., Possoz, C., Danilova, O. & Sherratt, D. J. Independent positioning and action of escherichia coli replisomes in live cells. Cell 133, 90–102 (2008).
pubmed: 18394992
pmcid: 2288635
doi: 10.1016/j.cell.2008.01.044
Cass, J. A., Kuwada, N. J., Traxler, B. & Wiggins, P. A. Escherichia coli chromosomal loci segregate from midcell with universal dynamics. Biophys. J. 110, 2597–2609 (2016).
pubmed: 27332118
pmcid: 4919604
doi: 10.1016/j.bpj.2016.04.046
Mangiameli, S. M., Veit, B. T., Merrikh, H. & Wiggins, P. A. The replisomes remain spatially proximal throughout the cell cycle in bacteria. PLoS Genet. 13, e1006582 (2017).
pubmed: 28114307
pmcid: 5293282
doi: 10.1371/journal.pgen.1006582
Wallden, M., Fange, D., Lundius, E. G., Baltekin, Ö. & Elf, J. The synchronization of replication and division cycles in individual E. coli cells. Cell 166, 729–739 (2016).
pubmed: 27471967
doi: 10.1016/j.cell.2016.06.052
Knöppel, A., Broström, O., Gras, K., Elf, J. & Fange, D. Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle. Proc. Natl Acad. Sci. USA 120, e2213795120 (2023).
pubmed: 37220276
pmcid: 10235992
doi: 10.1073/pnas.2213795120
Japaridze, A., Gogou, C., Kerssemakers, J. W. J., Nguyen, H. M. & Dekker, C. Direct observation of independently moving replisomes in Escherichia coli. Nat. Commun. 11, 3109 (2020).
pubmed: 32561741
pmcid: 7305307
doi: 10.1038/s41467-020-16946-7
Moolman, M. C. et al. Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells. Nat. Commun. 5, 5820 (2014).
pubmed: 25520215
doi: 10.1038/ncomms6820
Baltekin, Ö., Boucharin, A., Tano, E., Andersson, D. I. & Elf, J. Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging. Proc. Natl Acad. Sci. USA 114, 9170–9175 (2017).
pubmed: 28790187
pmcid: 5576829
doi: 10.1073/pnas.1708558114
Jaqaman, K. et al. Robust single-particle tracking in live-cell time-lapse sequences. Nat. Methods 5, 695–702 (2008).
pubmed: 18641657
pmcid: 2747604
doi: 10.1038/nmeth.1237
Mangiameli, S. M., Cass, J. A., Merrikh, H. & Wiggins, P. A. The bacterial replisome has factory-like localization. Curr. Genet. 64, 1029–1036 (2018).
pubmed: 29632994
doi: 10.1007/s00294-018-0830-z
Chen, P. J. et al. Interdependent progression of bidirectional sister replisomes in E. coli. Elife 12, e82241 (2023).
Steiner, W., Liu, G., Donachie, W. D. & Kuempel, P. The cytoplasmic domain of FtsK protein is required for resolution of chromosome dimers. Mol. Microbiol. 31, 579–583 (1999).
pubmed: 10027974
doi: 10.1046/j.1365-2958.1999.01198.x
Hojgaard, A., Szerlong, H., Tabor, C. & Kuempel, P. Norfloxacin-induced DNA cleavage occurs at the dif resolvase locus in Escherichia coli and is the result of interaction with topoisomerase IV. Mol. Microbiol. 33, 1027–1036 (1999).
pubmed: 10476036
doi: 10.1046/j.1365-2958.1999.01545.x
Lemon, K. P. & Grossman, A. D. The extrusion-capture model for chromosome partitioning in bacteria. Genes Dev. 15, 2031–2041 (2001).
pubmed: 11511534
doi: 10.1101/gad.913301
Sawitzke, J. & Austin, S. An analysis of the factory model for chromosome replication and segregation in bacteria. Mol. Microbiol. 40, 786–794 (2001).
pubmed: 11401686
doi: 10.1046/j.1365-2958.2001.02350.x
Nielsen, H. J., Youngren, B., Hansen, F. G. & Austin, S. Dynamics of Escherichia coli chromosome segregation during multifork replication. J. Bacteriol. 189, 8660–8666 (2007).
pubmed: 17905986
pmcid: 2168957
doi: 10.1128/JB.01212-07
Lesterlin, C., Gigant, E., Boccard, F. & Espéli, O. Sister chromatid interactions in bacteria revealed by a site-specific recombination assay. EMBO J. 31, 3468–3479 (2012).
pubmed: 22820946
pmcid: 3419930
doi: 10.1038/emboj.2012.194
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. 97, 6640–6645 (2000).
pubmed: 10829079
pmcid: 18686
doi: 10.1073/pnas.120163297
Thomason, L. C., Costantino, N. & Court, D. L. E. coli genome manipulation by P1 transduction. Curr. Protoc. Mol. Biol. Chapter 1, 1.17.1–1.17.8 (2007).
Camsund, D. et al. Time-resolved imaging-based CRISPRi screening. Nat. Methods 17, 86–92 (2020).
pubmed: 31740817
doi: 10.1038/s41592-019-0629-y
Ronneberger, O., Fischer, P. & Brox, T. U-Net: Convolutional Networks for Biomedical Image Segmentation. in Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015. MICCAI 2015. Lecture Notes in Computer Science() Vol. 9351 (eds Navab, N., Hornegger, J., Wells, W. & Frangi, A.) (Springer, Cham, 2015). https://doi.org/10.1007/978-3-319-24574-4_28 .
Magnusson, K. E. G., Jalden, J., Gilbert, P. M. & Blau, H. M. Global linking of cell tracks using the Viterbi algorithm. IEEE Trans. Med. Imaging 34, 911–929 (2015).
pubmed: 25415983
doi: 10.1109/TMI.2014.2370951
Olivo-Marin, J.-C. Extraction of spots in biological images using multiscale products. Pattern Recognit. 35, 1989–1996 (2002).
doi: 10.1016/S0031-3203(01)00127-3
Lindén, M., Ćurić, V., Amselem, E. & Elf, J. Pointwise error estimates in localization microscopy. Nat. Commun. 8, 15115 (2017).
pubmed: 28466844
pmcid: 5418599
doi: 10.1038/ncomms15115