Detail
Article
Online article
FT
Medvik - BMC
  • Something wrong with this record ?

DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor

K. Šmídová, A. Ziková, J. Pospíšil, M. Schwarz, J. Bobek, J. Vohradsky,

. 2019 ; 47 (2) : 621-633. [pub] 20190125

Language English Country England, Great Britain

Document type Journal Article, Research Support, Non-U.S. Gov't

Persistent link   https://www.medvik.cz/link/bmc19034936

HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB-RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the -10 region and suggested the possible role of mono- or di-nucleotides upstream of the -10 element.

References provided by Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc19034936
003      
CZ-PrNML
005      
20191008112956.0
007      
ta
008      
191007s2019 enk f 000 0|eng||
009      
AR
024    7_
$a 10.1093/nar/gky1018 $2 doi
035    __
$a (PubMed)30371884
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a enk
100    1_
$a Šmídová, Klára $u Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia. First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, 12800 Prague, Czechia.
245    10
$a DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor / $c K. Šmídová, A. Ziková, J. Pospíšil, M. Schwarz, J. Bobek, J. Vohradsky,
520    9_
$a HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB-RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the -10 region and suggested the possible role of mono- or di-nucleotides upstream of the -10 element.
650    _2
$a bakteriální proteiny $x genetika $x metabolismus $7 D001426
650    _2
$a vazebná místa $7 D001665
650    _2
$a chromatinová imunoprecipitace $7 D047369
650    _2
$a DNA bakterií $x chemie $x metabolismus $7 D004269
650    _2
$a DNA vazebné proteiny $x metabolismus $7 D004268
650    _2
$a exprese genu $7 D015870
650    _2
$a regulace genové exprese u bakterií $7 D015964
650    _2
$a geny rRNA $7 D020459
650    _2
$a kinetika $7 D007700
650    _2
$a modely genetické $7 D008957
650    _2
$a promotorové oblasti (genetika) $7 D011401
650    _2
$a bakteriální RNA $x genetika $7 D012329
650    _2
$a RNA transferová $x genetika $7 D012343
650    12
$a regulon $7 D018085
650    _2
$a sekvenční analýza DNA $7 D017422
650    _2
$a sigma faktor $x metabolismus $7 D012808
650    _2
$a Streptomyces coelicolor $x genetika $x metabolismus $7 D048372
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Ziková, Alice $u Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia.
700    1_
$a Pospíšil, Jirí $u Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia.
700    1_
$a Schwarz, Marek $u Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia.
700    1_
$a Bobek, Jan $u First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, 12800 Prague, Czechia. Chemistry Department, Faculty of Science, J. E. Purkinje University, 40096 Ústí nad Labem, Czechia.
700    1_
$a Vohradsky, Jiri $u Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia.
773    0_
$w MED00003554 $t Nucleic acids research $x 1362-4962 $g Roč. 47, č. 2 (2019), s. 621-633
856    41
$u https://pubmed.ncbi.nlm.nih.gov/30371884 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20191007 $b ABA008
991    __
$a 20191008113413 $b ABA008
999    __
$a ok $b bmc $g 1451596 $s 1073486
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2019 $b 47 $c 2 $d 621-633 $e 20190125 $i 1362-4962 $m Nucleic acids research $n Nucleic Acids Res $x MED00003554
LZP    __
$a Pubmed-20191007
Back

Find record

Citation metrics

Archiving options