Direct regulation of topoisomerase activity by a nucleoid-associated protein

Ghosh, Soumitra; Mallick, Bratati; Nagaraja, Valakunja

doi:10.1093/nar/gku804

Cited by 45 publications

(43 citation statements)

References 60 publications

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“…This clustering suggests that distant genomic loci are colocalized in 3D space, as has been observed for H-NS-bound loci in E. coli (37). In addition to H-NS, multiple NAPs are known to promote long-range intrachromosomal interactions through DNA bending, looping, compaction, and the stabilization of discrete subdomains (4,(55)(56)(57)(58)(59)(60)(61)(62)(63). It may be that the self-association of GapR molecules links together noncontiguous loci that contain AT-rich sequences.…”

Section: Discussionmentioning

confidence: 74%

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

Ricci

Melfi

Lasker

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Faithful cell cycle progression in the dimorphic bacterium Caulobacter crescentus requires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required for Caulobacter growth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter. The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed in E. coli, suggesting that GapR and H-NS have distinct functions. We propose that Caulobacter has co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.

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Section: Discussionmentioning

confidence: 74%

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

Ricci

Melfi

Lasker

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Considering that in bacteria, histone-like proteins and topoisomerases work together in spatial genome organization (13)(14)(15)21), and knowing that ASFV also codes for a type II DNA topoisomerase (pP1192R), we aimed to investigate whether this phenomenon is maintained in ASFV. For this purpose, increasing concentrations of pA104R (0.01, 0.05, 0.1, 0.25, and 0.5 M) were incubated with 150 ng of relaxed pBR322 DNA, in the presence or absence of ASFV topoisomerase II (0.01 M), for 30 min at 37°C in a reaction volume of 20 l. When pA104R was incubated alone with the relaxed plasmid, no supercoiling activity was detected.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, pA104R possesses the signature of histone-like proteins at residues 57 to 76 of its sequence (PROSITE PS00045), including 8 amino acid residues responsible for DNA interaction and conserved in bacterial histone-like proteins. In prokaryotes, these nucleoid-associated proteins are involved in DNA supercoiling and also play an important role in DNA replication, repair, recombination, and transcription (9)(10)(11)(12) by interacting with topoisomerases (13)(14)(15)(16). Besides their structural and sequence similarities to eukaryotic histones, these bacterial proteins are often termed histones due to their DNA-binding properties, low molecular weights, and high bending capacities (17)(18)(19).…”

mentioning

confidence: 99%

DNA-Binding Properties of African Swine Fever Virus pA104R, a Histone-Like Protein Involved in Viral Replication and Transcription

Frouco

Freitas

Coelho

et al. 2017

J Virol

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African swine fever virus (ASFV) codes for a putative histone-like protein (pA104R) with extensive sequence homology to bacterial proteins that are implicated in genome replication and packaging. Functional characterization of purified recombinant pA104R revealed that it binds to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) over a wide range of temperatures, pH values, and salt concentrations and in an ATP-independent manner, with an estimated binding site size of about 14 to 16 nucleotides. Using site-directed mutagenesis, the arginine located in pA104R's DNA-binding domain, at position 69, was found to be relevant for efficient DNA-binding activity. Together, pA104R and ASFV topoisomerase II (pP1192R) display DNA-supercoiling activity, although none of the proteins by themselves do, indicating that the two cooperate in this process. In ASFV-infected cells, A104R transcripts were detected from 2 h postinfection (hpi) onward, reaching a maximum concentration around 16 hpi. pA104R was detected from 12 hpi onward, localizing with viral DNA replication sites and being found exclusively in the Tritoninsoluble fraction. Small interfering RNA (siRNA) knockdown experiments revealed that pA104R plays a critical role in viral DNA replication and gene expression, with transfected cells showing lower viral progeny numbers (up to a reduction of 82.0%), lower copy numbers of viral genomes (Ϫ78.3%), and reduced transcription of a late viral gene (Ϫ47.6%). Taken together, our results strongly suggest that pA104R participates in the modulation of viral DNA topology, probably being involved in viral DNA replication, transcription, and packaging, emphasizing that ASFV mutants lacking the A104R gene could be used as a strategy to develop a vaccine against ASFV.IMPORTANCE Recently reintroduced in Europe, African swine fever virus (ASFV) causes a fatal disease in domestic pigs, causing high economic losses in affected countries, as no vaccine or treatment is currently available. Remarkably, ASFV is the only known mammalian virus that putatively codes for a histone-like protein (pA104R) that shares extensive sequence homology with bacterial histone-like proteins. In this study, we characterized the DNA-binding properties of pA104R, analyzed the functional importance of two conserved residues, and showed that pA104R and ASFV topoisomerase II cooperate and display DNA-supercoiling activity. Moreover, pA104R is expressed during the late phase of infection and accumulates in viral DNA replication sites, and its downregulation revealed that pA104R is required for viral DNA replication and transcription. These results suggest that pA104R participates in the modulation of viral DNA topology and genome packaging, indicating that A104R deletion mutants may be a good strategy for vaccine development against ASFV.

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“…DNA is negatively supercoiled in vivo, and a number of nucleoid-associated proteins have been implicated in the organization of bacterial chromatin, with additional roles in transcription, recombination, and replication [11][12][13][14][15][16][17][18]. In E. coli, the four most abundant nucleoid-associated proteins are factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) [19][20][21][22][23][24][25].…”

mentioning

confidence: 99%

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

Talukder

Ishihama

2015

Sci. China Life Sci.

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The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase. In addition to factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Q Hfq) and suppressor of td  phenotype A (StpA). Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, StpA and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli. growth phase, sucrose gradient, bacterial nucleoid, DNA binding protein, DNA compaction Citation:Talukder AA, Ishihama A. Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli. Sci China Life Sci, 2015, 58: 902 -911,

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Direct regulation of topoisomerase activity by a nucleoid-associated protein

Cited by 45 publications

References 60 publications

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

DNA-Binding Properties of African Swine Fever Virus pA104R, a Histone-Like Protein Involved in Viral Replication and Transcription

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

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