Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.
Cell Cycle
Chromosomes, Bacterial
/ metabolism
Crystallography, X-Ray
DNA, Bacterial
/ genetics
DNA-Binding Proteins
/ metabolism
Dimerization
Escherichia coli
/ metabolism
Escherichia coli Proteins
/ metabolism
Gene Expression Profiling
Gene Expression Regulation, Bacterial
Hydrogen-Ion Concentration
Ions
Mutation
Protein Multimerization
Tomography, X-Ray
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
09 06 2020
09 06 2020
Historique:
received:
17
12
2019
accepted:
19
05
2020
entrez:
11
6
2020
pubmed:
11
6
2020
medline:
28
8
2020
Statut:
epublish
Résumé
Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation. By imaging of near-native, unlabeled E. coli cells by soft X-ray tomography, we show that HU remodels nucleoids by promoting the formation of a dense condensed core surrounded by less condensed isolated domains. Nucleoid remodeling during cell growth and environmental adaptation correlate with pH and ionic strength controlled molecular switch that regulated HUαα dependent intermolecular DNA bundling. Through crystallographic and solution-based studies we show that these effects mechanistically rely on HUαα promiscuity in forming multiple electrostatically driven multimerization interfaces. Changes in DNA bundling consequently affects gene expression globally, likely by constrained DNA supercoiling. Taken together our findings unveil a critical function of HU-DNA interaction in nucleoid remodeling that may serve as a general microbial mechanism for transcriptional regulation to synchronize genetic responses during the cell cycle and adapt to changing environments.
Identifiants
pubmed: 32518228
doi: 10.1038/s41467-020-16724-5
pii: 10.1038/s41467-020-16724-5
pmc: PMC7283360
doi:
Substances chimiques
DNA, Bacterial
0
DNA-Binding Proteins
0
Escherichia coli Proteins
0
Ions
0
hns protein, E coli
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
2905Subventions
Organisme : NIGMS NIH HHS
ID : P30 GM138441
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103445
Pays : United States
Organisme : NIGMS NIH HHS
ID : P30 GM124169
Pays : United States
Organisme : NCI NIH HHS
ID : P01 CA092584
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM124149
Pays : United States
Références
Dorman, C. J. DNA supercoiling and environmental regulation of gene expression in pathogenic bacteria. Infect. Immun. 59, 745–749 (1991).
pubmed: 1997427
pmcid: 258322
doi: 10.1128/IAI.59.3.745-749.1991
Dorman, C. J. Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription. Biochem Soc. Trans. 41, 542–547 (2013).
pubmed: 23514151
doi: 10.1042/BST20120222
Meyer, S., Reverchon, S., Nasser, W. & Muskhelishvili, G. Chromosomal organization of transcription: in a nutshell. Curr. Genet 64, 555–565 (2018).
pubmed: 29184972
doi: 10.1007/s00294-017-0785-5
Travers, A. & Muskhelishvili, G. DNA supercoiling - a global transcriptional regulator for enterobacterial growth? Nat. Rev. Microbiol. 3, 157–169 (2005).
pubmed: 15685225
doi: 10.1038/nrmicro1088
Azam, T. A. & Ishihama, A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274, 33105–33113 (1999).
pubmed: 10551881
doi: 10.1074/jbc.274.46.33105
Berger, M. et al. Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU. EMBO Rep. 11, 59–64 (2010).
pubmed: 20010798
doi: 10.1038/embor.2009.232
Hammel, M. et al. HU multimerization shift controls nucleoid compaction. Sci. Adv. 2, e1600650 (2016).
pubmed: 27482541
pmcid: 4966879
doi: 10.1126/sciadv.1600650
Kar, S., Edgar, R. & Adhya, S. Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc. Natl Acad. Sci. USA 102, 16397–16402 (2005).
pubmed: 16258062
doi: 10.1073/pnas.0508032102
Berger, M. et al. Genes on a wire: the nucleoid-associated protein HU insulates transcription units in Escherichia coli. Sci. Rep. 6, 31512 (2016).
pubmed: 27545593
pmcid: 4992867
doi: 10.1038/srep31512
Lioy, V. S. et al. Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins. Cell 172, 771–783 (2018).
pubmed: 29358050
doi: 10.1016/j.cell.2017.12.027
Prieto, A. I. et al. Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res. 40, 3524–3537 (2012).
pubmed: 22180530
doi: 10.1093/nar/gkr1236
Wang, W., Li, G. W., Chen, C., Xie, X. S. & Zhuang, X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333, 1445–1449 (2011).
pubmed: 21903814
pmcid: 3329943
doi: 10.1126/science.1204697
Kamashev, D. & Rouviere-Yaniv, J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 19, 6527–6535 (2000).
pubmed: 11101525
pmcid: 305869
doi: 10.1093/emboj/19.23.6527
Swinger, K. K., Lemberg, K. M., Zhang, Y. & Rice, P. A. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 22, 3749–3760 (2003).
pubmed: 12853489
pmcid: 165621
doi: 10.1093/emboj/cdg351
Claret, L. & Rouviere-Yaniv, J. Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival. J. Mol. Biol. 273, 93–104 (1997).
pubmed: 9367749
doi: 10.1006/jmbi.1997.1310
Le Gros, M. A., McDermott, G. & Larabell, C. A. X-ray tomography of whole cells. Curr. Opin. Struct. Biol. 15, 593–600 (2005).
pubmed: 16153818
doi: 10.1016/j.sbi.2005.08.008
Le Gros, M. A. et al. Soft X-ray tomography reveals gradual chromatin compaction and reorganization during neurogenesis in vivo. Cell Rep. 17, 2125–2136 (2016).
pubmed: 27851973
pmcid: 5135017
doi: 10.1016/j.celrep.2016.10.060
Fisher, J. K. et al. Four-dimensional imaging of E. coli nucleoid organization and dynamics in living cells. Cell 153, 882–895 (2013).
pubmed: 23623305
pmcid: 3670778
doi: 10.1016/j.cell.2013.04.006
Robinow, C. & Kellenberger, E. The bacterial nucleoid revisited. Microbiol. Rev. 58, 211–232 (1994).
pubmed: 7521510
pmcid: 372962
doi: 10.1128/MMBR.58.2.211-232.1994
Valens, M., Penaud, S., Rossignol, M., Cornet, F. & Boccard, F. Macrodomain organization of the Escherichia coli chromosome. Embo J. 23, 4330–4341 (2004).
pubmed: 15470498
pmcid: 524398
doi: 10.1038/sj.emboj.7600434
Wang, X., Montero Llopis, P. & Rudner, D. Z. Organization and segregation of bacterial chromosomes. Nat. Rev. Genet. 14, 191–203 (2013).
pubmed: 23400100
doi: 10.1038/nrg3375
Liu, Y. et al. A model for chromosome organization during the cell cycle in live E. coli. Sci. Rep. 5, 17133 (2015).
pubmed: 26597953
pmcid: 4657085
doi: 10.1038/srep17133
Porod, G. in Small Angle X-ray Scattering (eds Glatter, O. & Kratky, O.) 17–51 (Academic Press, 1982).
Zaslaver, A. et al. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3, 623–628 (2006).
pubmed: 16862137
doi: 10.1038/nmeth895
Pin, C. et al. Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase. BMC Syst. Biol. 3, 108 (2009).
pubmed: 19917103
pmcid: 2780417
doi: 10.1186/1752-0509-3-108
Tucker, D. L., Tucker, N. & Conway, T. Gene expression profiling of the pH response in Escherichia coli. J. Bacteriol. 184, 6551–6558 (2002).
pubmed: 12426343
pmcid: 135413
doi: 10.1128/JB.184.23.6551-6558.2002
Foster, J. W. Escherichia coli acid resistance: tales of an amateur acidophile. Nat. Rev. Microbiol. 2, 898–907 (2004).
pubmed: 15494746
doi: 10.1038/nrmicro1021
Krulwich, T. A., Sachs, G. & Padan, E. Molecular aspects of bacterial pH sensing and homeostasis. Nat. Rev. Microbiol. 9, 330–343 (2011).
pubmed: 21464825
pmcid: 3247762
doi: 10.1038/nrmicro2549
Martinez, K. A. II et al. Cytoplasmic pH response to acid stress in individual cells of Escherichia coli and Bacillus subtilis observed by fluorescence ratio imaging microscopy. Appl Environ. Microbiol. 78, 3706–3714 (2012).
pubmed: 22427503
pmcid: 3346368
doi: 10.1128/AEM.00354-12
Frenkiel-Krispin, D. et al. Nucleoid restructuring in stationary-state bacteria. Mol. Microbiol. 51, 395–405 (2004).
pubmed: 14756781
doi: 10.1046/j.1365-2958.2003.03855.x
Kleckner, N. et al. The bacterial nucleoid: nature, dynamics and sister segregation. Curr. Opin. Microbiol. 22, 127–137 (2014).
pubmed: 25460806
pmcid: 4359759
doi: 10.1016/j.mib.2014.10.001
Gorkin, D. U., Leung, D. & Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14, 762–775 (2014).
pubmed: 4107214
pmcid: 4107214
doi: 10.1016/j.stem.2014.05.017
Clowney, E. J. et al. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 151, 724–737 (2012).
pubmed: 23141535
pmcid: 3659163
doi: 10.1016/j.cell.2012.09.043
Dorman, C. J. Genome architecture and global gene regulation in bacteria: making progress towards a unified model? Nat. Rev. Microbiol 11, 349–355 (2013).
pubmed: 23549066
doi: 10.1038/nrmicro3007
Badrinarayanan, A., Le, T. B. & 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
Sobetzko, P., Travers, A. & Muskhelishvili, G. Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc. Natl Acad. Sci. USA 109, E42–E50 (2012).
pubmed: 22184251
doi: 10.1073/pnas.1108229109
Wiggins, P. A., Cheveralls, K. C., Martin, J. S., Lintner, R. & Kondev, J. Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc. Natl Acad. Sci. USA 107, 4991–4995 (2010).
pubmed: 20194778
doi: 10.1073/pnas.0912062107
Berlatzky, I. A., Rouvinski, A. & Ben-Yehuda, S. Spatial organization of a replicating bacterial chromosome. Proc. Natl Acad. Sci. USA 105, 14136–14140 (2008).
pubmed: 18779567
doi: 10.1073/pnas.0804982105
Victor, T. W. et al. X-ray fluorescence nanotomography of single bacteria with a sub-15 nm beam. Sci. Rep. 8, 13415 (2018).
pubmed: 30194316
pmcid: 6128931
doi: 10.1038/s41598-018-31461-y
Dillon, S. C. & Dorman, C. J. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol. 8, 185–195 (2010).
pubmed: 20140026
doi: 10.1038/nrmicro2261
Sagi, D., Friedman, N., Vorgias, C., Oppenheim, A. B. & Stavans, J. Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes. J. Mol. Biol. 341, 419–428 (2004).
pubmed: 15276833
doi: 10.1016/j.jmb.2004.06.023
Kundukad, B., Cong, P., van der Maarel, J. R. & Doyle, P. S. Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein. Nucleic Acids Res. 41, 8280–8288 (2013).
pubmed: 23828037
pmcid: 3783175
doi: 10.1093/nar/gkt593
van Noort, J., Verbrugge, S., Goosen, N., Dekker, C. & Dame, R. T. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc. Natl. Acad. Sci. USA 101, 6969–6974 (2004).
pubmed: 15118104
doi: 10.1073/pnas.0308230101
Czapla, L., Peters, J. P., Rueter, E. M., Olson, W. K. & Maher, L. J. III Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins. J. Mol. Biol. 409, 278–289 (2011).
pubmed: 21459097
pmcid: 3095720
doi: 10.1016/j.jmb.2011.03.050
Koh, J., Shkel, I., Saecker, R. M., Record, M. T. Jr. & Nonspecific, D. N. A. binding and bending by HUalphabeta: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J. Mol. Biol. 410, 241–267 (2011).
pubmed: 21513716
pmcid: 3115508
doi: 10.1016/j.jmb.2011.04.001
Wei, J., Czapla, L., Grosner, M. A., Swigon, D. & Olson, W. K. DNA topology confers sequence specificity to nonspecific architectural proteins. Proc. Natl Acad. Sci. USA 111, 16742–16749 (2014).
pubmed: 25385626
doi: 10.1073/pnas.1405016111
Xiao, B., Zhang, H., Johnson, R. C. & Marko, J. F. Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation. Nucleic Acids Res. 39, 5568–5577 (2011).
pubmed: 21427084
pmcid: 3141252
doi: 10.1093/nar/gkr141
Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 97, 5978–5983 (2000).
pubmed: 10811905
doi: 10.1073/pnas.100127597
Datta, S., Costantino, N. & Court, D. L. A set of recombineering plasmids for gram-negative bacteria. Gene 379, 109–115 (2006).
pubmed: 16750601
doi: 10.1016/j.gene.2006.04.018
Wada, M. K., Ogawa, Y., Okazaki, T. & Imamoto, T. F. Construction and characterization of the deletion mutant of hupA and hupB genes in Escherichia coli. J. Mol. Biol. 204, 581–591 (1988).
pubmed: 3066907
doi: 10.1016/0022-2836(88)90357-9
Bazan, J. F. F. & R. J. Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc. Natl Acad. Sci. USA 85, 7872–7876 (1988).
pubmed: 3186696
doi: 10.1073/pnas.85.21.7872
Le Gros, M. A. et al. Biological soft X-ray tomography on beamline 2.1 at the advanced light source. J. Synchrotron. Radiat. 21, 1370–1377 (2014).
pubmed: 25343808
pmcid: 4211134
doi: 10.1107/S1600577514015033
Pettersen, E. F. et al. UCSF chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
doi: 10.14806/ej.17.1.200
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
pmcid: 23104886
doi: 10.1093/bioinformatics/bts635
Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
pubmed: 21816040
pmcid: 3163565
doi: 10.1186/1471-2105-12-323
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
pubmed: 19910308
pmcid: 19910308
doi: 10.1093/bioinformatics/btp616
Classen, S. et al. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the advanced light source. J. Appl Crystallogr. 46, 1–13 (2013).
pubmed: 23396808
pmcid: 3547225
doi: 10.1107/S0021889812048698
Kabsch, W. XDS. Acta Crystallogr. D. Biol. Crystallogr. 66, 125–132 (2010).
pubmed: 20124692
pmcid: 2815665
doi: 10.1107/S0907444909047337
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
pubmed: 2483472
pmcid: 2483472
doi: 10.1107/S0021889807021206
Matthews, B. W. Solvent content of protein crystals. J. Mol. Biol. 33, 491–497 (1968).
pubmed: 5700707
doi: 10.1016/0022-2836(68)90205-2
Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D. Biol. Crystallogr. 68, 352–367 (2012).
pubmed: 3322595
pmcid: 3322595
doi: 10.1107/S0907444912001308
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta. Crystallogr. D. Biol. Crystallogr. 60, 2126–2132 (2004).
pubmed: 15572765
doi: 10.1107/S0907444904019158
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665–W667 (2004).
pubmed: 15215472
pmcid: 441519
doi: 10.1093/nar/gkh381
Guinier, A. & Fournet, G. Small-Angle Scattering of X-Rays (John Wiley and Sons, Inc., New York, 1955).
Svergun, D. I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25, 495–503 (1992).
doi: 10.1107/S0021889892001663
Schneidman-Duhovny, D., Hammel, M., Tainer, J. A. & Sali, A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys. J. 105, 962–974 (2013).
pubmed: 23972848
pmcid: 3752106
doi: 10.1016/j.bpj.2013.07.020
Hammel, M. Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur. Biophys. J. 41, 789–799 (2012).
pubmed: 22639100
pmcid: 3462898
doi: 10.1007/s00249-012-0820-x
Schneidman-Duhovny, D., Hammel, M., Tainer, J. A. & Sali, A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res. 44, W424–W429 (2016).
pubmed: 27151198
pmcid: 4987932
doi: 10.1093/nar/gkw389