Non-specific and specific DNA binding modes of bacterial histone, HU, separately regulate distinct physiological processes through different mechanisms.
HU
non-specific binding
nucleoid architecture
structure-specific binding
transcription regulation
Journal
Molecular microbiology
ISSN: 1365-2958
Titre abrégé: Mol Microbiol
Pays: England
ID NLM: 8712028
Informations de publication
Date de publication:
04 2023
04 2023
Historique:
revised:
24
01
2023
received:
21
06
2022
accepted:
25
01
2023
pmc-release:
01
04
2024
medline:
14
4
2023
pubmed:
29
1
2023
entrez:
28
1
2023
Statut:
ppublish
Résumé
The histone-like protein HU plays a diverse role in bacterial physiology from the maintenance of chromosome structure to the regulation of gene transcription. HU binds DNA in a sequence-non-specific manner via two distinct binding modes: (i) random binding to any DNA through ionic bonds between surface-exposed lysine residues (K3, K18, and K83) and phosphate backbone (non-specific); (ii) preferential binding to contorted DNA of given structures containing a pair of kinks (structure-specific) through conserved proline residues (P63) that induce and/or stabilize the kinks. First, we show here that the P63-mediated structure-specific binding also requires the three lysine residues, which are needed for a non-specific binding. Second, we demonstrate that substituting P63 to alanine in HU had no impact on non-specific binding but caused differential transcription of diverse genes previously shown to be regulated by HU, such as those associated with the organonitrogen compound biosynthetic process, galactose metabolism, ribosome biogenesis, and cell adhesion. The structure-specific binding also helps create DNA supercoiling, which, in turn, may influence directly or indirectly the transcription of other genes. Our previous and current studies show that non-specific and structure-specific HU binding appear to have separate functions- nucleoid architecture and transcription regulation- which may be true in other DNA-binding proteins.
Identifiants
pubmed: 36708073
doi: 10.1111/mmi.15033
pmc: PMC10120378
mid: NIHMS1883732
doi:
Substances chimiques
Histones
0
Bacterial Proteins
0
Lysine
K3Z4F929H6
DNA-Binding Proteins
0
DNA
9007-49-2
DNA, Bacterial
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
439-455Subventions
Organisme : Intramural NIH HHS
ID : Z01 BC008751
Pays : United States
Organisme : Intramural NIH HHS
ID : ZIA BC008751
Pays : United States
Organisme : NCI NIH HHS
ID : 75N91019D00024
Pays : United States
Informations de copyright
Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
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