Dynamic structure of E. coli cytoplasm: supramolecular complexes and cell aging impact spatial distribution and mobility of proteins.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
27 Apr 2024
27 Apr 2024
Historique:
received:
06
12
2023
accepted:
18
04
2024
medline:
28
4
2024
pubmed:
28
4
2024
entrez:
27
4
2024
Statut:
epublish
Résumé
Protein diffusion is a critical factor governing the functioning and organization of a cell's cytoplasm. In this study, we investigate the influence of (poly)ribosome distribution, cell aging, protein aggregation, and biomolecular condensate formation on protein mobility within the E. coli cytoplasm. We employ nanoscale single-molecule displacement mapping (SMdM) to determine the spatial distribution of the proteins and to meticulously track their diffusion. We show that the distribution of polysomes does not impact the lateral diffusion coefficients of proteins. However, the degradation of mRNA induced by rifampicin treatment leads to an increase in protein mobility within the cytoplasm. Additionally, we establish a significant correlation between cell aging, the asymmetric localization of protein aggregates and reduced diffusion coefficients at the cell poles. Notably, we observe variations in the hindrance of diffusion at the poles and the central nucleoid region for small and large proteins, and we reveal differences between the old and new pole of the cell. Collectively, our research highlights cellular processes and mechanisms responsible for spatially organizing the bacterial cytoplasm into domains with different structural features and apparent viscosity.
Identifiants
pubmed: 38678067
doi: 10.1038/s42003-024-06216-3
pii: 10.1038/s42003-024-06216-3
doi:
Substances chimiques
Escherichia coli Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
508Subventions
Organisme : Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
ID : NWA.1292.19.170
Organisme : Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
ID : NWA.1292.19.170
Informations de copyright
© 2024. The Author(s).
Références
Śmigiel, W. M. et al. Protein diffusion in Escherichia coli cytoplasm scales with the mass of the complexes and is location dependent. Sci. Adv. 8, eabo5387 (2022).
pubmed: 35960807
pmcid: 9374337
doi: 10.1126/sciadv.abo5387
Mantovanelli, L. et al. Simulation-based reconstructed diffusion unveils the effect of aging on protein diffusion in Escherichia coli. PLoS Comput Biol. 19, e1011093 (2023).
pubmed: 37695774
pmcid: 10513214
doi: 10.1371/journal.pcbi.1011093
Parry, B. R. et al. The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156, 183–194 (2014).
pubmed: 24361104
doi: 10.1016/j.cell.2013.11.028
Bakshi, S., Bratton, B. P. & Weisshaar, J. C. Subdiffraction-limit study of kaede diffusion and spatial distribution in live Escherichia coli. Biophys. J. 101, 2535–2544 (2011).
pubmed: 22098753
pmcid: 3218334
doi: 10.1016/j.bpj.2011.10.013
Golding, I. & Cox, E. C. Physical nature of bacterial cytoplasm. Phys. Rev. Lett. 96, 098102 (2006).
pubmed: 16606319
doi: 10.1103/PhysRevLett.96.098102
Azaldegui, C. A., Vecchiarelli, A. G. & Biteen, J. S. The emergence of phase separation as an organizing principle in bacteria. Biophys. J. 120, 1123–1138 (2021).
pubmed: 33186556
doi: 10.1016/j.bpj.2020.09.023
Holmes, J. A. et al. Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles. Proc. Natl. Acad. Sci. USA 113, 12490–12495 (2016).
pubmed: 27791060
pmcid: 5098656
doi: 10.1073/pnas.1602380113
Monterroso, B. et al. Bacterial FtsZ protein forms phase‐separated condensates with its nucleoid‐associated inhibitor SlmA. EMBO Rep. 20, e45946 (2019).
pubmed: 30523075
doi: 10.15252/embr.201845946
Racki, L. R. et al. Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 114, E2440–E2449 (2017).
pubmed: 28265086
pmcid: 5373386
doi: 10.1073/pnas.1615575114
Ladouceur, A.-M. et al. Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid–liquid phase separation. Proc. Natl. Acad. Sci. USA 117, 18540–18549 (2020).
pubmed: 32675239
pmcid: 7414142
doi: 10.1073/pnas.2005019117
Guilhas, B. et al. ATP-driven separation of liquid phase condensates in bacteria. Mol. Cell 79, 293–303.e4 (2020).
pubmed: 32679076
doi: 10.1016/j.molcel.2020.06.034
Al-Husini, N., Tomares, D. T., Bitar, O., Childers, W. S. & Schrader, J. M. α-proteobacterial RNA degradosomes assemble liquid-liquid phase-separated RNP bodies. Mol. Cell 71, 1027–1039.e14 (2018).
pubmed: 30197298
doi: 10.1016/j.molcel.2018.08.003
Heinkel, F. et al. Phase separation and clustering of an ABC transporter in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 116, 16326–16331 (2019).
pubmed: 31366629
pmcid: 6697873
doi: 10.1073/pnas.1820683116
Laloux, G. & Jacobs-Wagner, C. How do bacteria localize proteins to the cell pole? J. Cell Sci. 138628 https://doi.org/10.1242/jcs.138628 . (2014).
Sanamrad, A. et al. Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid. Proc. Natl Acad. Sci. USA 111, 11413–11418 (2014).
pubmed: 25056965
pmcid: 4128099
doi: 10.1073/pnas.1411558111
Coquel, A.-S. et al. Localization of protein aggregation in escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect. PLoS Comput. Biol. 9, e1003038 (2013).
pubmed: 23633942
pmcid: 3636022
doi: 10.1371/journal.pcbi.1003038
Reyes-Lamothe, R. et al. High-copy bacterial plasmids diffuse in the nucleoid-free space, replicate stochastically and are randomly partitioned at cell division. Nucleic Acids Res. 42, 1042–1051 (2014).
pubmed: 24137005
doi: 10.1093/nar/gkt918
Hunke, S. & Betton, J.-M. Temperature effect on inclusion body formation and stress response in the periplasm of Escherichia coli: Temperature effect on inclusion body formation. Mol. Microbiol. 50, 1579–1589 (2003).
pubmed: 14651640
doi: 10.1046/j.1365-2958.2003.03785.x
Strandberg, L. & Enfors, S. O. Factors influencing inclusion body formation in the production of a fused protein in Escherichia coli. Appl Environ. Microbiol. 57, 1669–1674 (1991).
pubmed: 1908208
pmcid: 183450
doi: 10.1128/aem.57.6.1669-1674.1991
Baneyx, F. & Mujacic, M. Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol. 22, 1399–1408 (2004).
pubmed: 15529165
doi: 10.1038/nbt1029
Lindner, A. B., Madden, R., Demarez, A., Stewart, E. J. & Taddei, F. Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc. Natl Acad. Sci. USA. 105, 3076–3081 (2008).
pubmed: 18287048
pmcid: 2268587
doi: 10.1073/pnas.0708931105
Maisonneuve, E., Ezraty, B. & Dukan, S. Protein aggregates: An aging factor involved in cell death. J. Bacteriol. 190, 6070–6075 (2008).
pubmed: 18621895
pmcid: 2546795
doi: 10.1128/JB.00736-08
Nyström, T. A bacterial kind of aging. PLoS Genet 3, e224 (2007).
pubmed: 18085827
pmcid: 2134940
doi: 10.1371/journal.pgen.0030224
Książek, K. Bacterial aging: from mechanistic basis to evolutionary perspective. Cell. Mol. Life Sci. 67, 3131–3137 (2010).
pubmed: 20526791
doi: 10.1007/s00018-010-0417-4
Stewart, E. J., Madden, R., Paul, G. & Taddei, F. Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol. 3, e45 (2005).
pubmed: 15685293
pmcid: 546039
doi: 10.1371/journal.pbio.0030045
Banzhaf, M. et al. Cooperativity of peptidoglycan synthases active in bacterial cell elongation: Bacterial peptidoglycan synthesis. Mol. Microbiol. 85, 179–194 (2012).
pubmed: 22606933
doi: 10.1111/j.1365-2958.2012.08103.x
Typas, A. et al. Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell 143, 1097–1109 (2010).
pubmed: 21183073
pmcid: 3060616
doi: 10.1016/j.cell.2010.11.038
Lenarcic, R. et al. Localisation of DivIVA by targeting to negatively curved membranes. EMBO J. 28, 2272–2282 (2009).
pubmed: 19478798
pmcid: 2690451
doi: 10.1038/emboj.2009.129
Renner, L. D. & Weibel, D. B. Cardiolipin microdomains localize to negatively curved regions of Escherichia coli membranes. Proc. Natl Acad. Sci. USA 108, 6264–6269 (2011).
pubmed: 21444798
pmcid: 3076878
doi: 10.1073/pnas.1015757108
Romantsov, T. et al. Cardiolipin promotes polar localization of osmosensory transporter ProP in Escherichia coli: Cardiolipin and osmoregulation in Escherichia coli. Mol. Microbiol. 64, 1455–1465 (2007).
pubmed: 17504273
doi: 10.1111/j.1365-2958.2007.05727.x
Romantsov, T., Battle, A. R., Hendel, J. L., Martinac, B. & Wood, J. M. Protein Localization in Escherichia coli Cells: Comparison of the cytoplasmic membrane proteins ProP, LacY, ProW, AqpZ, MscS, and MscL. J. Bacteriol. 192, 912–924 (2010).
pubmed: 20008071
doi: 10.1128/JB.00967-09
Mileykovskaya, E. et al. Effects of phospholipid composition on mind-membrane interactions in vitro and in vivo. J. Biol. Chem. 278, 22193–22198 (2003).
pubmed: 12676941
doi: 10.1074/jbc.M302603200
Renner, L. D. & Weibel, D. B. MinD and MinE interact with anionic phospholipids and regulate division plane formation in Escherichia coli. J. Biol. Chem. 287, 38835–38844 (2012).
pubmed: 23012351
pmcid: 3493925
doi: 10.1074/jbc.M112.407817
Xiang, L., Chen, K., Yan, R., Li, W. & Xu, K. Single-molecule displacement mapping unveils nanoscale heterogeneities in intracellular diffusivity. Nat. Methods 17, 524–530 (2020).
pubmed: 32203387
pmcid: 7205592
doi: 10.1038/s41592-020-0793-0
Schavemaker, P. E., Śmigiel, W. M. & Poolman, B. Ribosome surface properties may impose limits on the nature of the cytoplasmic proteome. eLife 6, e30084 (2017).
pubmed: 29154755
pmcid: 5726854
doi: 10.7554/eLife.30084
Bellotto, N. et al. Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth. eLife 11, e82654 (2022).
pubmed: 36468683
pmcid: 9810338
doi: 10.7554/eLife.82654
Bakshi, S., Siryaporn, A., Goulian, M. & Weisshaar, J. C. Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells: Superresolution imaging of ribosome and RNAP. Mol. Microbiol. 85, 21–38 (2012).
pubmed: 22624875
pmcid: 3383343
doi: 10.1111/j.1365-2958.2012.08081.x
Rosen, R. et al. Protein aggregation in Escherichia coli: role of proteases. FEMS Microbiol. Lett. 207, 9–12 (2002).
pubmed: 11886743
doi: 10.1111/j.1574-6968.2002.tb11020.x
Bailey, M. W., Bisicchia, P., Warren, B. T., Sherratt, D. J. & Männik, J. Evidence for divisome localization mechanisms independent of the min system and SlmA in Escherichia coli. PLoS Genet 10, e1004504 (2014).
pubmed: 25101671
pmcid: 4125044
doi: 10.1371/journal.pgen.1004504
Chai, Q. et al. Organization of ribosomes and nucleoids in escherichia coli cells during growth and in quiescence. J. Biol. Chem. 289, 11342–11352 (2014).
pubmed: 24599955
pmcid: 4036271
doi: 10.1074/jbc.M114.557348
Wang, P. et al. Robust growth of Escherichia coli. Curr. Biol. 20, 1099–1103 (2010).
pubmed: 20537537
pmcid: 2902570
doi: 10.1016/j.cub.2010.04.045
Saxton, M. J. Lateral diffusion in an archipelago. Dependence on tracer size. Biophys. J. 64, 1053–1062 (1993).
pubmed: 8494970
pmcid: 1262423
doi: 10.1016/S0006-3495(93)81471-1
Losa, J. et al. Perspective: a stirring role for metabolism in cells. Mol. Syst. Biol. 18, e10822 (2022).
pubmed: 35362256
pmcid: 8972047
doi: 10.15252/msb.202110822
Grenier, F., Matteau, D., Baby, V. & Rodrigue, S. Complete genome sequence of Escherichia coli BW25113. Genome Announc 2, e01038–14 (2014).
pubmed: 25323716
pmcid: 4200154
doi: 10.1128/genomeA.01038-14
Hanahan, D., Jessee, J. & Bloom, F. R. [4] Plasmid transformation of Escherichia coli and other bacteria. in Methods in Enzymology 204 63–113 (Elsevier, 1991).
Neidhardt, F. C., Bloch, P. L. & Smith, D. F. Culture medium for enterobacteria. J. Bacteriol. 119, 736–747 (1974).
pubmed: 4604283
pmcid: 245675
doi: 10.1128/jb.119.3.736-747.1974
Tran, B. M. et al. Super-resolving microscopy reveals the localizations and movement dynamics of stressosome proteins in Listeria monocytogenes. Commun. Biol. 6, 51 (2023).
pubmed: 36641529
pmcid: 9840623
doi: 10.1038/s42003-023-04423-y
MembraneEnzymology. MembraneEnzymology/smdm: SMdM analysis in Escherichia coli cytoplasm. Zenodo https://doi.org/10.5281/ZENODO.5911836 (2022).