Single-molecule tracking reveals that the nucleoid-associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA.
Bacterial Proteins
/ metabolism
Chromosomes, Bacterial
/ genetics
DNA
/ metabolism
DNA, Bacterial
/ metabolism
DNA-Binding Proteins
/ metabolism
Escherichia coli
/ metabolism
Escherichia coli Proteins
/ metabolism
Gene Expression Regulation, Bacterial
/ genetics
Histones
/ metabolism
Single Molecule Imaging
/ methods
HU
chromosome organization
nucleoid size
single molecule imaging
Journal
Molecular microbiology
ISSN: 1365-2958
Titre abrégé: Mol Microbiol
Pays: England
ID NLM: 8712028
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
24
06
2020
revised:
02
07
2020
accepted:
02
07
2020
pubmed:
9
7
2020
medline:
24
8
2021
entrez:
9
7
2020
Statut:
ppublish
Résumé
HU (Histone-like protein from Escherichia coli strain U93) is the most conserved nucleoid-associated protein in eubacteria, but how it impacts global chromosome organization is poorly understood. Using single-molecule tracking, we demonstrate that HU exhibits nonspecific, weak, and transitory interactions with the chromosomal DNA. These interactions are largely mediated by three conserved, surface-exposed lysine residues (triK), which were previously shown to be responsible for nonspecific binding to DNA. The loss of these weak, transitory interactions in a HUα(triKA) mutant results in an over-condensed and mis-segregated nucleoid. Mutating a conserved proline residue (P63A) in the HUα subunit, deleting the HUβ subunit, or deleting nucleoid-associated naRNAs, each previously implicated in HU's high-affinity binding to kinked or cruciform DNA, leads to less dramatically altered interacting dynamics of HU compared to the HUα(triKA) mutant, but highly expanded nucleoids. Our results suggest HU plays a dual role in maintaining proper nucleoid volume through its differential interactions with chromosomal DNA. On the one hand, HU compacts the nucleoid through specific DNA structure-binding interactions. On the other hand, it decondenses the nucleoid through many nonspecific, weak, and transitory interactions with the bulk chromosome. Such dynamic interactions may contribute to the viscoelastic properties and fluidity of the bacterial nucleoid to facilitate proper chromosome functions.
Identifiants
pubmed: 32640056
doi: 10.1111/mmi.14572
pmc: PMC8655832
mid: NIHMS1621675
doi:
Substances chimiques
Bacterial Proteins
0
DNA, Bacterial
0
DNA-Binding Proteins
0
Escherichia coli Proteins
0
Histones
0
histone-like protein HU, bacteria
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
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
12-27Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM008403
Pays : United States
Informations de copyright
© 2020 John Wiley & Sons Ltd.
Références
Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12225-12230
pubmed: 29087325
J Bacteriol. 1992 Jul;174(14):4583-93
pubmed: 1624447
Proc Natl Acad Sci U S A. 2004 May 4;101(18):6969-74
pubmed: 15118104
Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16397-402
pubmed: 16258062
Mol Microbiol. 2002 Apr;44(1):205-16
pubmed: 11967080
Nucleic Acids Res. 2007;35(12):3988-4000
pubmed: 17553830
Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2131-2136
pubmed: 28202730
J Bacteriol. 1999 Jan;181(1):197-203
pubmed: 9864330
Histochem Cell Biol. 2014 Jun;141(6):629-38
pubmed: 24522395
EMBO J. 1992 Dec;11(12):4489-96
pubmed: 1425583
Cell. 2018 Feb 8;172(4):771-783.e18
pubmed: 29358050
Biophys J. 1993 Nov;65(5):2021-40
pubmed: 8298032
Nucleic Acids Res. 2012 Apr;40(8):3524-37
pubmed: 22180530
Biophys J. 2017 Feb 28;112(4):568-574
pubmed: 28256217
DNA Repair (Amst). 2005 Jul 28;4(8):939-50
pubmed: 15905138
J Mol Biol. 1986 Jan 5;187(1):47-60
pubmed: 3514923
EMBO J. 1997 Jun 16;16(12):3666-74
pubmed: 9218807
J Bacteriol. 1999 Oct;181(20):6361-70
pubmed: 10515926
Science. 1997 Sep 5;277(5331):1453-62
pubmed: 9278503
Sci Adv. 2016 Jul 29;2(7):e1600650
pubmed: 27482541
Nat Commun. 2016 Mar 30;7:11055
pubmed: 27025941
Science. 2011 Sep 9;333(6048):1445-9
pubmed: 21903814
Mol Microbiol. 2001 Feb;39(4):1069-79
pubmed: 11251825
J Microsc. 2000 May;198(Pt 2):82-7
pubmed: 10810003
Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8452-7
pubmed: 24912163
Mol Microbiol. 2005 Jul;57(1):9-16
pubmed: 15948945
EMBO J. 2003 Jul 15;22(14):3749-60
pubmed: 12853489
J Mol Biol. 2005 Jun 17;349(4):716-30
pubmed: 15893770
J Bacteriol. 2009 Jul;191(13):4180-5
pubmed: 19395497
Nat Commun. 2019 Aug 23;10(1):3815
pubmed: 31444361
J Biol Chem. 1984 Feb 10;259(3):1616-21
pubmed: 6363413
Nucleic Acids Res. 2007;35(3):951-61
pubmed: 17259223
J Bacteriol. 1998 Aug;180(15):3750-6
pubmed: 9683467
Structure. 2000 Oct 15;8(10):1015-23
pubmed: 11080623
J Bacteriol. 1997 Jun;179(11):3494-9
pubmed: 9171392
Gene. 2006 Sep 1;379:109-15
pubmed: 16750601
J Microsc. 2010 Dec;240(3):249-58
pubmed: 21077885
J Mol Biol. 1996 Feb 16;256(1):66-76
pubmed: 8609614
Mol Microbiol. 2003 Dec;50(5):1493-505
pubmed: 14651633
Science. 2007 May 25;316(5828):1191-4
pubmed: 17525339
J Bacteriol. 1989 Jul;171(7):3704-12
pubmed: 2544551
Curr Opin Microbiol. 2010 Dec;13(6):773-80
pubmed: 20951079
Chembiochem. 2013 Oct 11;14(15):1954-7
pubmed: 24000171
Nat Commun. 2016 Aug 26;7:12568
pubmed: 27562541
mBio. 2015 Aug 25;6(4):
pubmed: 26307168
Methods Mol Biol. 2007;398:193-219
pubmed: 18214382
Science. 2015 Mar 20;347(6228):1371-4
pubmed: 25792329
Gene. 1995 May 26;158(1):9-14
pubmed: 7789817
EMBO J. 2000 Dec 1;19(23):6527-35
pubmed: 11101525
J Mol Biol. 1988 Dec 5;204(3):581-91
pubmed: 3066907
Mol Microbiol. 2003 Aug;49(3):731-43
pubmed: 12864855
J Biol Chem. 1998 Apr 17;273(16):9570-6
pubmed: 9545287
Genes Cells. 1996 Feb;1(2):179-88
pubmed: 9140062
Annu Rev Cell Dev Biol. 2015;31:171-99
pubmed: 26566111
Proc Natl Acad Sci U S A. 1984 Jan;81(2):424-8
pubmed: 6364143
J Mol Biol. 1999 Apr 2;287(3):485-97
pubmed: 10092454
Nucleic Acids Res. 2013 Sep;41(17):8280-8
pubmed: 23828037
Biochem Biophys Res Commun. 2008 Jun 20;371(1):79-84
pubmed: 18413230
PLoS Biol. 2013;11(6):e1001591
pubmed: 23853547
Mol Microbiol. 2014 Nov;94(4):871-87
pubmed: 25250841
Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4309-14
pubmed: 17360520
Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4390-9
pubmed: 26224838
J Biol Chem. 2002 Aug 2;277(31):27622-8
pubmed: 12006568
J Mol Biol. 1997 Oct 17;273(1):93-104
pubmed: 9367749
Nat Methods. 2013 Mar;10(3):265-9
pubmed: 23396281
EMBO J. 2004 Oct 27;23(21):4330-41
pubmed: 15470498
Biophys J. 2010 Feb 17;98(4):552-9
pubmed: 20159151
Proc Natl Acad Sci U S A. 1981 Jan;78(1):224-8
pubmed: 6165987
Cell. 2013 May 9;153(4):882-95
pubmed: 23623305
Gene. 1992 Oct 12;120(1):11-6
pubmed: 1327969
J Bacteriol. 2012 Nov;194(22):6046-55
pubmed: 22942248
Nat Commun. 2013;4:3003
pubmed: 23764719
Nat Methods. 2008 Aug;5(8):695-702
pubmed: 18641657
Cell. 1979 Jun;17(2):265-74
pubmed: 222478