Multiple physiological roles of both specific and non-specific DNA binding modes of HU protein in Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA732436 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14635651_1.fastq.gz | Fastqsanger.gz | |||
| SRR14635651_2.fastq.gz | Fastqsanger.gz | |||
| SRR14635652_1.fastq.gz | Fastqsanger.gz | |||
| SRR14635652_2.fastq.gz | Fastqsanger.gz | |||
| SRR14635653_1.fastq.gz | Fastqsanger.gz |
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Project description:The histone-like protein HU is crucial for genome organization and the expression of many genes in Escherichia coli. HU binds DNA independent of any specific nucleotide sequence but exhibits two binding affinities; low-affinity to any B-DNA (non-specific) and high affinity to DNA with distortions like kinks and cruciforms (structure-specific). We validated and defined the three conserved lysine residues, K3, K18, and K83, in HU as critical amino acid residues for the non-specific binding and the conserved P63 together with the lysine residues critical for the structure-specific binding both in vitro and in vivo. By determining the effects of disrupting the two DNA binding modes on various HU-dependent physiological processes, we demonstrate that the DNA structure-specific binding regulates expression of many genes including those involved in DNA metabolic processes that control chromosome maintenance and partition. On the other hand, HU associates with the chromosome at numerous sites primarily through the lysines-mediated non-specific binding and control chromosome dynamics and structural maintenance. Thus, we demonstrate that two different DNA binding mode of HU plays separate roles: (i) The high-affinity DNA structure-specific binding regulates many distinct DNA metabolic processes, primarily through transcription regulation. (ii) Its low-affinity, non-specific binding directly helps general organization of the genome.
2021-08-01 | GSE175465 | GEO
Project description:Hydroxyurea (HU) is toxic to Sulfolobus cells. To address the basis of the HU toxicity, we performed transcriptome analyses on untreated cells and cells following exposure to 5 mM HU for 4 hours.
2016-10-05 | GSE87612 | GEO
Project description:HU is a conserved prokaryotic nucleoid-associated protein known for its role in DNA binding and maintaining negative supercoils in DNA. HU also binds to a few RNAs but the natural targets are unknown. To understand the biology of HU interactions with RNA in Escherichia coli, potential HU-RNA in vivo complexes were immunoprecipitated and bound RNAs were examined by hybridization to whole-genome tiling arrays. We observed HU associations with rRNA, multiple tRNAs, a few sRNAs and a small, distinct set of mRNAs. More importantly, we also identified associations between HU and ten intragenic non-coding (nonc) RNAs, two of which are homologous to the annotated Bacterial Interspersed Mosaic Elements (BIME) and boxC elements; the other eight RNAs have not been annotated. We confirmed binding of HU to BIME RNA in vitro. Since HU and some unidentified RNAs have been implicated in the nucleoid structure, we explored an idea that HU, along with some or all of the nonc RNA species discovered here bind to BIME and/or boxC repeats to condense chromosomal DNA in a specific fashion. We propose that nonc RNAs may interact with both HU and DNA repeats to form ternary complexes, which are the anchoring points separating different chromosomal domains.
2012-12-07 | GSE28565 | GEO
Project description:The physiological role of the various nucleoid-associated proteins in bacteria and HU in particular has been addressed in a number of studies but remains so far not fully understood. In this work, a genome-wide microarray hybridization approach, combined with in vivo genetic experimentation, has been performed in order to compare and evaluate the effect of HUalpha, HUbeta and HUalphabeta on the transcription of the Escherichia coli K12 genes as a function of growth phase. The histone-like protein HU is present in the E. coli cell under three dimeric forms (HUalphabeta, HUalpha2 and HUbeta2) in a ratio that varies with growth phase. The experimental protocol is designed to handle strain genotype and growth phase as independent variables. Keywords: genotype, growth phase
2009-01-01 | GSE11183 | GEO
Project description:DNA replication checkpiont kinase rad3 (human ATM/ATR-like kinase) and cds1 (human CHK2-like kinase) are known to restore stalled replication forks and prevent subsequent cell cycle progression during a replication block imposed by HU-treatment in fission yeast. In order to identify cell cycle-specific exression which are modulated by replication checkpoint kinase rad3 and cds1, microarray approach was used to profile asynchronous and synchronous cells of wildtype and mutants treated and untreated with HU Keywords: HU treated cells vs wildtype untreated cells
2007-12-20 | GSE4280 | GEO
Project description:DNA replication checkpiont kinase rad3 (human ATM/ATR-like kinase) and cds1 (human CHK2-like kinase) are known to restore stalled replication forks and prevent subsequent cell cycle progression during a replication block imposed by HU-treatment in fission yeast. In order to identify cell cycle-specific exression which are modulated by replication checkpoint kinase rad3 and cds1, microarray approach was used to profile asynchronous and synchronous cells of wildtype and mutants treated and untreated with HU Keywords: HU treated cells vs wildtype untreated cells
2007-12-20 | GSE4283 | GEO
Project description:Analysis of the response to hydroxyurea in a yeast aft1 mutant strain compared to wild-type strain (BY4741 or BY4742 backgrounds). Cells were grown in YPD rich medium containong 200 mM hydroxyurea (HU) for 2 hours. Analysis of the response to hydroxyurea in a yeast aft1aft2 mutant strain (Y18aft2d) compared to wild-type strain (CM3260). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes due to the aft1 mutation were also analysed in absence of HU (BY4741 background). Analysis of mid-term response to hydroxyurea in a yeast wild-type strain (W303a). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes were analysed compared to the same strain grown in the same medium without HU. Keywords: repeat sample
2005-12-01 | GSE1914 | GEO
Project description:ELAV/Hu factors are conserved RNA binding proteins that play diverse roles in mRNA processing and regulation. The founding member, Drosophila Elav, was recognized as a vital neural factor 35 years ago. Nevertheless, still little is known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3' UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. While only a few splicing targets of Drosophila are known, we find that ectopic expression of the three family members (Elav, Fne and Rbp9) induces overlapping changes to hundreds of cassette exon and dozens of alternative last exon (ALE) splicing events. Reciprocally, double mutants of elav/fne, but not elav alone, have opposite effects on both classes of regulated mRNA processing events in the larval CNS. While manipulation of Drosophila ELAV/Hu factors induces both exon skipping and inclusion, motif analysis indicates their major direct effects are to suppress cassette exon usage. Moreover, the roles of ELAV/HU factors in global promotion of distal ALE splicing are mechanistically linked to terminal 3' UTR extensions in neurons, since both involve local suppression of proximal polyadenylation signals via ELAV/Hu binding sites downstream of cleavage sites. The phenotypic impact of combined ELAV/Hu activities in neural mRNA processing is overt, since fne loss strongly enhances neuronal differentiation phenotypes in elav mutants. Finally, we provide evidence for conservation in mammalian neurons, which undergo broad programs of distal ALE and APA lengthening, linked to ELAV/Hu motifs downstream of regulated polyadenylation sites. Overall, ELAV/Hu proteins orchestrate multiple conserved programs of neuronal mRNA processing by suppressing alternative exons and polyadenylation sites.
2021-02-23 | GSE164129 | GEO
Project description:Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. By preparing and characterizing site-specifically acetylated bacterial protein for the first time, this work indicates that acetyllysine plays an important role in bacterial epigenetics and presents a promising target against bacterial infections.
2018-10-24 | PXD007289 | Pride
Project description:Hu sheep adipose RNA seq
| PRJNA576088 | ENA