The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner

被引：38

作者：

Antipov, S. S. ^{[1
,2
,3
,4
]}

Tutukina, M. N. ^{[1
,5
,6
,7
,8
]}

Preobrazhenskaya, E. V. ^{[1
]}

Kondrashov, F. A. ^{[5
,6
,9
]}

Patrushev, M. V. ^{[4
]}

Toshchakov, S. V. ^{[4
]}

Dominova, I. ^{[4
]}

Shvyreva, U. S. ^{[1
]}

Vrublevskaya, V. V. ^{[10
]}

Morenkov, O. S. ^{[10
]}

Sukharicheva, N. A. ^{[1
]}

Panyukov, V. V. ^{[7
,8
,11
]}

Ozoline, O. N. ^{[1
,2
,7
,8
]}

机构：

[1] Russian Acad Sci, Inst Cell Biophys, Dept Funct Genom & Cellular Stress, Moscow, Russia

[2] Pushchino State Inst Nat Sci, Dept Cell Biol, Moscow, Russia

[3] Voronezh State Univ, Dept Biophys & Biotechnol, Voronezh, Russia

[4] Immanuel Kant Balt Fed Univ, Dept Genom Microorg, Kaliningrad, Russia

[5] Ctr Genom Regulat, Bioinformat & Genom Programme, Barcelona, Spain

[6] Univ Pompeu Fabra, Dept Evolutionary Gen, Barcelona, Spain

[7] Russian Acad Sci, Dept Struct, Moscow, Russia

[8] Russian Acad Sci, Funct Gen Pushchino Res Ctr, Moscow, Russia

[9] 23 Pg Llurs Companys, ICREA, Barcelona, Spain

[10] Russian Acad Sci, Inst Cell Biophys, Dept Cell Culture & Cell Engn, Moscow, Russia

[11] Russian Acad Sci, Keldysh Inst Appl Math, Inst Math Problems Biol Branch, Dept Bioinformat, Moscow, Russia

来源：

PLOS ONE | 2017年 / 12卷 / 08期

基金：

欧洲研究理事会; 俄罗斯基础研究基金会; 俄罗斯科学基金会;

关键词：

H-NS; GENE-EXPRESSION; OXIDATIVE STRESS; STARVED CELLS; FERRITIN; PROMOTER; IRON; FIS; PROTECTION; GROWTH;

D O I：

10.1371/journal.pone.0182800

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.

引用

页数：27