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Journal articles on the topic 'Nucleoid-associated Protein HU'

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Published: 6 September 2023

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1

Ali Azam, Talukder, Akira Iwata, Akiko Nishimura, Susumu Ueda, and Akira Ishihama. "Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid." Journal of Bacteriology 181, no. 20 (October 15, 1999): 6361–70. http://dx.doi.org/10.1128/jb.181.20.6361-6370.1999.

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ABSTRACT The genome DNA of Escherichia coli is associated with about 10 DNA-binding structural proteins, altogether forming the nucleoid. The nucleoid proteins play some functional roles, besides their structural roles, in the global regulation of such essential DNA functions as replication, recombination, and transcription. Using a quantitative Western blot method, we have performed for the first time a systematic determination of the intracellular concentrations of 12 species of the nucleoid protein in E. coli W3110, including CbpA (curved DNA-binding protein A), CbpB (curved DNA-binding protein B, also known as Rob [right origin binding protein]), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversion stimulation), Hfq (host factor for phage Qβ), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor oftd mutant phenotype A). Intracellular protein levels reach a maximum at the growing phase for nine proteins, CbpB (Rob), DnaA, Fis, Hfq, H-NS, HU, IciA, Lrp, and StpA, which may play regulatory roles in DNA replication and/or transcription of the growth-related genes. In descending order, the level of accumulation, calculated in monomers, in growing E. coli cells is Fis, Hfq, HU, StpA, H-NS, IHF*, CbpB (Rob), Dps*, Lrp, DnaA, IciA, and CbpA* (stars represent the stationary-phase proteins). The order of abundance, in descending order, in the early stationary phase is Dps*, IHF*, HU, Hfq, H-NS, StpA, CbpB (Rob), DnaA, Lrp, IciA, CbpA, and Fis, while that in the late stationary phase is Dps*, IHF*, Hfq, HU, CbpA*, StpA, H-NS, CbpB (Rob), DnaA, Lrp, IciA, and Fis. Thus, the major protein components of the nucleoid change from Fis and HU in the growing phase to Dps in the stationary phase. The curved DNA-binding protein, CbpA, appears only in the late stationary phase. These changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genome functions.
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2

Qian, Zhong, Victor B. Zhurkin, and Sankar Adhya. "DNA–RNA interactions are critical for chromosome condensation inEscherichia coli." Proceedings of the National Academy of Sciences 114, no. 46 (October 30, 2017): 12225–30. http://dx.doi.org/10.1073/pnas.1711285114.

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Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA–DNA contacts (DNA condensation). We demonstrate that naRNA4 uniquely acts by forming complexes that may not involve long stretches of DNA–RNA hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA–RNA interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the naRNA4-mediated DNA condensation process.
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3

Yee, Benjamin, Evgeny Sagulenko, and John A. Fuerst. "Making heads or tails of the HU proteins in the planctomycete Gemmata obscuriglobus." Microbiology 157, no. 7 (July 1, 2011): 2012–21. http://dx.doi.org/10.1099/mic.0.047605-0.

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Gemmata obscuriglobus has a highly condensed nucleoid which is implicated in its resistance to radiation. However, the mechanisms by which such compaction is achieved, and the proteins responsible, are still unknown. Here we have examined the genome of G. obscuriglobus for the presence of proteins homologous to those that have been associated with nucleoid condensation. We found two different proteins homologous to the bacterial nucleoid-associated protein HU, one with an N-terminal and one with a C-terminal extension relative to the amino acid sequence of the HU found in Escherichia coli. Sequence analysis revealed that one of these HU homologues represents a novel type with a high number of prolines in its C-terminal extension, whereas the other one has motifs similar to the N terminus of the HU homologue from the radio-resistant bacterium Deinococcus radiodurans. The occurrence of two such HU homologue proteins with these two different terminal extensions in one organism appears to be unique among the Bacteria.
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4

Hammel, Michal, Dhar Amlanjyoti, Francis E. Reyes, Jian-Hua Chen, Rochelle Parpana, Henry Y. H. Tang, Carolyn A. Larabell, John A. Tainer, and Sankar Adhya. "HU multimerization shift controls nucleoid compaction." Science Advances 2, no. 7 (July 2016): e1600650. http://dx.doi.org/10.1126/sciadv.1600650.

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Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasiveEscherichia coliinto an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.
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5

Salerno, Paola, Jessica Larsson, Giselda Bucca, Emma Laing, Colin P. Smith, and Klas Flärdh. "One of the Two Genes Encoding Nucleoid-Associated HU Proteins in Streptomyces coelicolor Is Developmentally Regulated and Specifically Involved in Spore Maturation." Journal of Bacteriology 191, no. 21 (August 28, 2009): 6489–500. http://dx.doi.org/10.1128/jb.00709-09.

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ABSTRACT Streptomyces genomes encode two homologs of the nucleoid-associated HU proteins. One of them, here designated HupA, is of a conventional type similar to E. coli HUα and HUβ, while the other, HupS, is a two-domain protein. In addition to the N-terminal part that is similar to that of HU proteins, it has a C-terminal domain that is similar to the alanine- and lysine-rich C termini of eukaryotic linker histones. Such two-domain HU proteins are found only among Actinobacteria. In this phylum some organisms have only a single HU protein of the type with a C-terminal histone H1-like domain (e.g., Hlp in Mycobacterium smegmatis), while others have only a single conventional HU. Yet others, including the streptomycetes, produce both types of HU proteins. We show here that the two HU genes in Streptomyces coelicolor are differentially regulated and that hupS is specifically expressed during sporulation, while hupA is expressed in vegetative hyphae. The developmental upregulation of hupS occurred in sporogenic aerial hyphal compartments and was dependent on the developmental regulators whiA, whiG, and whiI. HupS was found to be nucleoid associated in spores, and a hupS deletion mutant had an average nucleoid size in spores larger than that in the parent strain. The mutant spores were also defective in heat resistance and spore pigmentation, although they possessed apparently normal spore walls and displayed no increased sensitivity to detergents. Overall, the results show that HupS is specifically involved in sporulation and may affect nucleoid architecture and protection in spores of S. coelicolor.
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6

Peraman, Ramalingam, Geethavani Meka, Naresh Babu Chilamakuru, Vinay Kumar Kutagulla, Saloni Malla, Charles R. Ashby, Amit K. Tiwari, and Padmanabha Reddy Yiragamreddy. "Novel stilbene scaffolds efficiently target Mycobacterium tuberculosis nucleoid-associated protein, HU." New Journal of Chemistry 45, no. 24 (2021): 10683–92. http://dx.doi.org/10.1039/d0nj05947a.

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7

Boyko, Konstantin, Marina Gorbacheva, Tatiana Rakitina, Dmitry Korzhenevskiy, Anna Vanyushkina, Dmitry Kamashev, Alexey Lipkin, and Vladimir Popov. "Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the histone-like HU protein fromSpiroplasma melliferumKC3." Acta Crystallographica Section F Structural Biology Communications 71, no. 1 (January 1, 2015): 24–27. http://dx.doi.org/10.1107/s2053230x14025333.

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HU proteins belong to the nucleoid-associated proteins (NAPs) that are involved in vital processes such as DNA compaction and reparation, gene transcriptionetc.No data are available on the structures of HU proteins from mycoplasmas. To this end, the HU protein from the parasitic mycoplasmaSpiroplasma melliferumKC3 was cloned, overexpressed inEscherichia coliand purified to homogeneity. Prismatic crystals of the protein were obtained by the vapour-diffusion technique at 4°C. The crystals diffracted to 1.36 Å resolution (the best resolution ever obtained for a HU protein). The diffraction data were indexed in space groupC2 and the structure of the protein was solved by the molecular-replacement method with one monomer per asymmetric unit.
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8

Thakur, Bhishem, Archit Gupta, and Purnananda Guptasarma. "A novel protein-engineered dsDNA-binding protein (HU-Simulacrum) inspired by HU, a nucleoid-associated DNABII protein." Biochemical and Biophysical Research Communications 534 (January 2021): 47–52. http://dx.doi.org/10.1016/j.bbrc.2020.11.088.

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9

Lin, Szu-Ning, Gijs J. L. Wuite, and Remus T. Dame. "Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU." International Journal of Molecular Sciences 21, no. 24 (December 15, 2020): 9553. http://dx.doi.org/10.3390/ijms21249553.

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HU is a nucleoid-associated protein expressed in most eubacteria at a high amount of copies (tens of thousands). The protein is believed to bind across the genome to organize and compact the DNA. Most of the studies on HU have been carried out in a simple in vitro system, and to what extent these observations can be extrapolated to a living cell is unclear. In this study, we investigate the DNA binding properties of HU under conditions approximating physiological ones. We report that these properties are influenced by both macromolecular crowding and salt conditions. We use three different crowding agents (blotting grade blocker (BGB), bovine serum albumin (BSA), and polyethylene glycol 8000 (PEG8000)) as well as two different MgCl2 conditions to mimic the intracellular environment. Using tethered particle motion (TPM), we show that the transition between two binding regimes, compaction and extension of the HU protein, is strongly affected by crowding agents. Our observations suggest that magnesium ions enhance the compaction of HU–DNA and suppress filamentation, while BGB and BSA increase the local concentration of the HU protein by more than 4-fold. Moreover, BGB and BSA seem to suppress filament formation. On the other hand, PEG8000 is not a good crowding agent for concentrations above 9% (w/v), because it might interact with DNA, the protein, and/or surfaces. Together, these results reveal a complex interplay between the HU protein and the various crowding agents that should be taken into consideration when using crowding agents to mimic an in vivo system.
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10

Phan, Ngoc Quang, Takashi Uebanso, Takaaki Shimohata, Mutsumi Nakahashi, Kazuaki Mawatari, and Akira Takahashi. "DNA-Binding Protein HU Coordinates Pathogenicity in Vibrio parahaemolyticus." Journal of Bacteriology 197, no. 18 (July 6, 2015): 2958–64. http://dx.doi.org/10.1128/jb.00306-15.

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ABSTRACTHU is one of the most abundant nucleoid-associated proteins in bacterial cells and regulates the expression of many genes involved in growth, motility, metabolism, and virulence. It is known thatVibrio parahaemolyticuspathogenicity is related to its characteristic rapid growth and that type III secretion system 1 (T3SS1) contributes to its cytotoxicity. However, it is not known if HU plays a role in the pathogenicity ofV. parahaemolyticus. In the present study, we investigated the effect of HU proteins HU-2 (HUα) (V. parahaemolyticus2911 [vp2911]) and HUβ (vp0920) on the pathogenicity ofV. parahaemolyticus. We found that a deletion of both HU subunits (yielding the ΔHUs [Δvp0920Δvp2911] strain), but not single deletions, led to a reduction of the growth rate. In addition, expression levels of T3SS1-related genes, includingexsA(positive regulator),exsD(negative regulator),vp1680(cytotoxic effector), andvp1671(T3SS1 apparatus), were reduced in the ΔHUs strain compared to the wild type (WT). As a result, cytotoxicity to HeLa cells was decreased in the ΔHUs strain. The additional deletion ofexsDin the ΔHUs strain restored T3SS1-related gene expression levels and cytotoxicity but not the growth rate. These results suggest that the HU protein regulates the levels of T3SS1 gene expression and cytotoxicity in a growth rate-independent manner.IMPORTANCENucleoid-binding protein HU regulates cellular behaviors, including nucleoid structuring, general recombination, transposition, growth, replication, motility, metabolism, and virulence. It is thought that both the number of bacteria and the number of virulence factors may affect the pathogenicity of bacteria. In the present study, we investigated which factor(s) has a dominant role during infection in one of the most rapidly growing bacterial species,Vibrio parahaemolyticus. We found thatV. parahaemolyticuscytotoxicity is regulated, in a growth rate-independent manner, by the HU proteins through regulation of a number of virulence factors, including T3SS1 gene expression.
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11

Le Meur, Rémy, Françoise Culard, Virginie Nadan, Stéphane Goffinont, Franck Coste, Martine Guerin, Karine Loth, Céline Landon, and Bertrand Castaing. "The nucleoid-associated protein HU enhances 8-oxoguanine base excision by the formamidopyrimidine-DNA glycosylase." Biochemical Journal 471, no. 1 (September 21, 2015): 13–23. http://dx.doi.org/10.1042/bj20150387.

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The major E. coli histone-like HU protein is identified as a strong stimulator of the DNA glycosylase Fpg by inducing enzyme product release. According to an active molecular process, HU acts as a molecular partner for an efficient DNA-repair process.
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12

Lee, Steven F., Michael A. Thompson, Monica A. Schwartz, Lucy Shapiro, and W. E. Moerner. "Super-Resolution Imaging of the Nucleoid-Associated Protein HU in Caulobacter crescentus." Biophysical Journal 100, no. 7 (April 2011): L31—L33. http://dx.doi.org/10.1016/j.bpj.2011.02.022.

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13

Takeda, Toshiharu, Choong-Soo Yun, Masaki Shintani, Hisakazu Yamane, and Hideaki Nojiri. "Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids." International Journal of Evolutionary Biology 2011 (January 24, 2011): 1–30. http://dx.doi.org/10.4061/2011/685015.

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Bacterial nucleoid-associated proteins (NAPs) form nucleoprotein complexes and influence the expression of genes. Recent studies have shown that some plasmids carry genes encoding NAP homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. In this study, we determined the distributions of the well-known NAPs Fis, H-NS, HU, IHF, and Lrp and the newly found NAPs MvaT and NdpA among the whole-sequenced 1382 plasmids found in Gram-negative bacteria. Comparisons between NAP distributions and plasmid features (size, G+C content, and putative transferability) were also performed. We found that larger plasmids frequently have NAP gene homologs. Plasmids with H-NS gene homologs had less G+C content. It should be noted that plasmids with the NAP gene homolog also carried the relaxase gene involved in the conjugative transfer of plasmids more frequently than did those without the NAP gene homolog, implying that plasmid-encoded NAP homologs positively contribute to transmissible plasmids.
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14

Mangan, Michael W., Sacha Lucchini, Tadhg Ó Cróinín, Stephen Fitzgerald, Jay C. D. Hinton, and Charles J. Dorman. "Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium." Microbiology 157, no. 4 (April 1, 2011): 1075–87. http://dx.doi.org/10.1099/mic.0.046359-0.

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The role of the HU nucleoid-associated proteins in gene regulation was examined in Salmonella enterica serovar Typhimurium. The dimeric HU protein consists of different combinations of its α and β subunits. Transcriptomic analysis was performed with cultures growing at 37 °C at 1, 4 and 6 h after inoculation with mutants that lack combinations of HU α and HU β. Distinct but overlapping patterns of gene expression were detected at each time point for each of the three mutants, revealing not one but three regulons of genes controlled by the HU proteins. Mutations in the hup genes altered the expression of regulatory and structural genes in both the SPI1 and SPI2 pathogenicity islands. The hupA hupB double mutant was defective in invasion of epithelial cell lines and in its ability to survive in macrophages. The double mutant also had defective swarming activity and a competitive fitness disadvantage compared with the wild-type. In contrast, inactivation of just the hupB gene resulted in increased fitness and correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures. Our data show that HU coordinates the expression of genes involved in central metabolism and virulence and contributes to the success of S. enterica as a pathogen.
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15

Kamagata, Kiyoto, Yuji Itoh, Cheng Tan, Eriko Mano, Yining Wu, Sridhar Mandali, Shoji Takada, and Reid C. Johnson. "Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo." Nucleic Acids Research 49, no. 15 (August 5, 2021): 8642–64. http://dx.doi.org/10.1093/nar/gkab658.

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Abstract Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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16

Berger, Michael, Anca Farcas, Marcel Geertz, Petya Zhelyazkova, Klaudia Brix, Andrew Travers, and Georgi Muskhelishvili. "Coordination of genomic structure and transcription by the main bacterial nucleoid‐associated protein HU." EMBO reports 11, no. 1 (November 13, 2009): 59–64. http://dx.doi.org/10.1038/embor.2009.232.

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17

de Vasconcelos Junior, Antonio A., Jose M. Tirado-Vélez, Antonio J. Martín-Galiano, Diego Megias, María-José Ferrándiz, Pablo Hernández, Mónica Amblar, and Adela G. de la Campa. "StaR Is a Positive Regulator of Topoisomerase I Activity Involved in Supercoiling Maintenance in Streptococcus pneumoniae." International Journal of Molecular Sciences 24, no. 6 (March 22, 2023): 5973. http://dx.doi.org/10.3390/ijms24065973.

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The DNA topoisomerases gyrase and topoisomerase I as well as the nucleoid-associated protein HU maintain supercoiling levels in Streptococcus pneumoniae, a main human pathogen. Here, we characterized, for the first time, a topoisomerase I regulator protein (StaR). In the presence of sub-inhibitory novobiocin concentrations, which inhibit gyrase activity, higher doubling times were observed in a strain lacking staR, and in two strains in which StaR was over-expressed either under the control of the ZnSO4-inducible PZn promoter (strain ΔstaRPZnstaR) or of the maltose-inducible PMal promoter (strain ΔstaRpLS1ROMstaR). These results suggest that StaR has a direct role in novobiocin susceptibility and that the StaR level needs to be maintained within a narrow range. Treatment of ΔstaRPZnstaR with inhibitory novobiocin concentrations resulted in a change of the negative DNA supercoiling density (σ) in vivo, which was higher in the absence of StaR (σ = −0.049) than when StaR was overproduced (σ = −0.045). We have located this protein in the nucleoid by using super-resolution confocal microscopy. Through in vitro activity assays, we demonstrated that StaR stimulates TopoI relaxation activity, while it has no effect on gyrase activity. Interaction between TopoI and StaR was detected both in vitro and in vivo by co-immunoprecipitation. No alteration of the transcriptome was associated with StaR amount variation. The results suggest that StaR is a new streptococcal nucleoid-associated protein that activates topoisomerase I activity by direct protein-protein interaction.
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18

Nishida, Yuya, Teppei Ikeya, Tsutomu Mikawa, Jin Inoue, Yutaka Ito, Yasunori Shintani, Ryoji Masui, Seiki Kuramitsu, and Seiji Takashima. "A specific single-stranded DNA induces a distinct conformational change in the nucleoid-associated protein HU." Biochemistry and Biophysics Reports 8 (December 2016): 318–24. http://dx.doi.org/10.1016/j.bbrep.2016.09.014.

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19

O'Neil, Pierce, Scott Lovell, Nurjahan Mehzabeen, Kevin Battaile, and Indranil Biswas. "Crystal structure of histone-like protein fromStreptococcus mutansrefined to 1.9 Å resolution." Acta Crystallographica Section F Structural Biology Communications 72, no. 4 (March 16, 2016): 257–62. http://dx.doi.org/10.1107/s2053230x1600217x.

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Nucleoid-associated proteins (NAPs) in prokaryotes play an important architectural role in DNA bending, supercoiling and DNA compaction. In addition to architectural roles, some NAPs also play regulatory roles in DNA replication and repair, and act as global transcriptional regulators in many bacteria. Bacteria encode multiple NAPs and some of them are even essential for survival.Streptococcus mutans, a dental pathogen, encodes one such essential NAP called histone-like protein (HLP). Here, the three-dimensional structure ofS. mutansHLP has been determined to 1.9 Å resolution. The HLP structure is a dimer and shares a high degree of similarity with other bacterial NAPs, including HU. Since HLPs are essential for the survival of pathogenic streptococci, this structure determination is potentially beneficial for future drug development against these pathogens.
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Giangrossi, Mara, Anna Maria Giuliodori, Claudio O. Gualerzi, and Cynthia L. Pon. "Selective expression of the β-subunit of nucleoid-associated protein HU during cold shock in Escherichia coli." Molecular Microbiology 44, no. 1 (April 20, 2002): 205–16. http://dx.doi.org/10.1046/j.1365-2958.2002.02868.x.

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21

Suzuki-Minakuchi, Chiho, Ryusuke Hirotani, Masaki Shintani, Toshiharu Takeda, Yurika Takahashi, Kazuhiro Matsui, Delyana Vasileva, et al. "Effects of Three Different Nucleoid-Associated Proteins Encoded on IncP-7 Plasmid pCAR1 on Host Pseudomonas putida KT2440." Applied and Environmental Microbiology 81, no. 8 (February 13, 2015): 2869–80. http://dx.doi.org/10.1128/aem.00023-15.

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ABSTRACTNucleoid-associated proteins (NAPs), which fold bacterial DNA and influence gene transcription, are considered to be global transcriptional regulators of genes on both plasmids and the host chromosome. Incompatibility P-7 group plasmid pCAR1 carries genes encoding three NAPs: H-NS family protein Pmr, NdpA-like protein Pnd, and HU-like protein Phu. In this study, the effects of single or double disruption ofpmr,pnd, andphuwere assessed in hostPseudomonas putidaKT2440. Whenpmrandpndorpmrandphuwere simultaneously disrupted, both the segregational stability and the structural stability of pCAR1 were markedly decreased, suggesting that Pmr, Pnd, and Phu act as plasmid-stabilizing factors in addition to their established roles in replication and partition systems. The transfer frequency of pCAR1 was significantly decreased in these double mutants. The segregational and structural instability of pCAR1 in the double mutants was recovered by complementation ofpmr, whereas no recovery of transfer deficiency was observed. Comprehensive phenotype comparisons showed that the host metabolism of carbon compounds, which was reduced by pCAR1 carriage, was restored by disruption of the NAP gene(s). Transcriptome analyses of mutants indicated that transcription of genes for energy production, conversion, inorganic ion transport, and metabolism were commonly affected; however, how their products altered the phenotypes of mutants was not clear. The findings of this study indicated that Pmr, Pnd, and Phu act synergistically to affect pCAR1 replication, maintenance, and transfer, as well as to alter the host metabolic phenotype.
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Ringwald, Kenneth, and Jeffrey Gardner. "The Bacteroides thetaiotaomicron Protein Bacteroides Host Factor A Participates in Integration of the Integrative Conjugative Element CTnDOT into the Chromosome." Journal of Bacteriology 197, no. 8 (February 2, 2015): 1339–49. http://dx.doi.org/10.1128/jb.02198-14.

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ABSTRACTCTnDOT is a conjugative transposon found inBacteroidesspecies. It encodes multiple antibiotic resistances and is stimulated to transfer by exposure to tetracycline. CTnDOT integration into the host chromosome requires IntDOT and a previously unknown host factor. We have identified a protein, designated BHFa (Bacteroideshost factor A), that participates in integrative recombination. BHFa is the first host factor identified for a site-specific recombination reaction in the CTnDOT family of integrative and conjugative elements. Based on the amino acid sequence of BHFa, the ability to bind specifically to 4 sites in theattDOTDNA, and its activity in the integration reaction, BHFa is a member of the IHF/HU family of nucleoid-associated proteins. Other DNA bending proteins that bind DNA nonspecifically can substitute for BHFa in the integration reaction.IMPORTANCEBacteroidesspecies are normal members of the human colonic microbiota. These species can harbor and spread self-transmissible genetic elements (integrative conjugative elements [ICEs]) that contain antibiotic resistance genes. This work describes the role of a protein, BHFa, and its importance in the integration reaction required for the element CTnDOT to persist inBacteroideshost cells.
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Shiga, Yasuyuki, Yasuhiko Sekine, Yasunobu Kano, and Eiichi Ohtsubo. "Involvement of H-NS in Transpositional Recombination Mediated by IS1." Journal of Bacteriology 183, no. 8 (April 15, 2001): 2476–84. http://dx.doi.org/10.1128/jb.183.8.2476-2484.2001.

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ABSTRACT IS1, the smallest active transposable element in bacteria, encodes a transposase that promotes inter- and intramolecular transposition. Host-encoded factors, e.g., histone-like proteins HU and integration host factor (IHF), are involved in the transposition reactions of some bacterial transposable elements. Host factors involved in the IS1 transposition reaction, however, are not known. We show that a plasmid with an IS1 derivative that efficiently produces transposase did not generate miniplasmids, the products of intramolecular transposition, in mutants deficient in a nucleoid-associated DNA-binding protein, H-NS, but did generate them in mutants deficient in histone-like proteins HU, IHF, Fis, and StpA. Nor did IS1 transpose intermolecularly to the target plasmid in the H-NS-deficient mutant. The hns mutation did not affect transcription from the indigenous promoter of IS1 for the expression of the transposase gene. These findings show that transpositional recombination mediated by IS1 requires H-NS but does not require the HU, IHF, Fis, or StpA protein in vivo. Gel retardation assays of restriction fragments of IS1-carrying plasmid DNA showed that no sites were bound preferentially by H-NS within the IS1 sequence. The central domain of H-NS, which is involved in dimerization and/or oligomerization of the H-NS protein, was important for the intramolecular transposition of IS1, but the N- and C-terminal domains, which are involved in the repression of certain genes and DNA binding, respectively, were not. The SOS response induced by the IS1 transposase was absent in the H-NS-deficient mutant strain but was present in the wild-type strain. We discuss the possibility that H-NS promotes the formation of an active IS1 DNA-transposase complex in which the IS1 ends are cleaved to initiate transpositional recombination through interaction with IS1 transposase.
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Dadinova, Liubov A., Maxim V. Petoukhov, Alexander M. Gordienko, Valentin A. Manuvera, Vassili N. Lazarev, Tatiana V. Rakitina, Andrey A. Mozhaev, Georgy S. Peters, and Eleonora V. Shtykova. "Nucleoid-Associated Proteins HU and IHF: Oligomerization in Solution and Hydrodynamic Properties." Biochemistry (Moscow) 88, no. 5 (May 2023): 640–54. http://dx.doi.org/10.1134/s0006297923050073.

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Molan, Katja, and Darja Žgur Bertok. "Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity throughout the Life Cycle." International Journal of Molecular Sciences 23, no. 7 (April 4, 2022): 4008. http://dx.doi.org/10.3390/ijms23074008.

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Genomes of all organisms are persistently threatened by endogenous and exogenous assaults. Bacterial mechanisms of genome maintenance must provide protection throughout the physiologically distinct phases of the life cycle. Spore-forming bacteria must also maintain genome integrity within the dormant endospore. The nucleoid-associated proteins (NAPs) influence nucleoid organization and may alter DNA topology to protect DNA or to alter gene expression patterns. NAPs are characteristically multifunctional; nevertheless, Dps, HU and CbpA are most strongly associated with DNA protection. Archaea display great variety in genome organization and many inhabit extreme environments. As of yet, only MC1, an archaeal NAP, has been shown to protect DNA against thermal denaturation and radiolysis. ssDNA are intermediates in vital cellular processes, such as DNA replication and recombination. Single-stranded binding proteins (SSBs) prevent the formation of secondary structures but also protect the hypersensitive ssDNA against chemical and nuclease degradation. Ionizing radiation upregulates SSBs in the extremophile Deinococcus radiodurans.
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Dilweg, Ivar W., and Remus T. Dame. "Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria?" Biochemical Society Transactions 46, no. 5 (October 4, 2018): 1381–92. http://dx.doi.org/10.1042/bst20180488.

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Post-translational modification (PTM) of histones has been investigated in eukaryotes for years, revealing its widespread occurrence and functional importance. Many PTMs affect chromatin folding and gene activity. Only recently the occurrence of such modifications has been recognized in bacteria. However, it is unclear whether PTM of the bacterial counterparts of eukaryotic histones, nucleoid-associated proteins (NAPs), bears a comparable significance. Here, we scrutinize proteome mass spectrometry data for PTMs of the four most abundantly present NAPs in Escherichia coli (H-NS, HU, IHF and FIS). This approach allowed us to identify a total of 101 unique PTMs in the 11 independent proteomic studies covered in this review. Combined with structural and genetic information on these proteins, we describe potential effects of these modifications (perturbed DNA-binding, structural integrity or interaction with other proteins) on their function.
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Dey, Debayan, Valakunja Nagaraja, and Suryanarayanarao Ramakumar. "Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF." Molecular Phylogenetics and Evolution 107 (February 2017): 356–66. http://dx.doi.org/10.1016/j.ympev.2016.11.014.

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Datta, Chandreyee, Rajiv Kumar Jha, Wareed Ahmed, Sohini Ganguly, Soumitra Ghosh, and Valakunja Nagaraja. "Physical and functional interaction between nucleoid‐associated proteins HU and Lsr2 ofMycobacterium tuberculosis: altered DNA binding and gene regulation." Molecular Microbiology 111, no. 4 (February 11, 2019): 981–94. http://dx.doi.org/10.1111/mmi.14202.

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29

Prieto, Ana I., Christina Kahramanoglou, Ruhi M. Ali, Gillian M. Fraser, Aswin S. N. Seshasayee, and Nicholas M. Luscombe. "Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12." Nucleic Acids Research 40, no. 8 (December 16, 2011): 3524–37. http://dx.doi.org/10.1093/nar/gkr1236.

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30

Kim, Do-Hee, Hookang Im, Jun-Goo Jee, Sun-Bok Jang, Hye-Jin Yoon, Ae-Ran Kwon, Sung-Min Kang, and Bong-Jin Lee. "β-Arm flexibility of HU fromStaphylococcus aureusdictates the DNA-binding and recognition mechanism." Acta Crystallographica Section D Biological Crystallography 70, no. 12 (November 28, 2014): 3273–89. http://dx.doi.org/10.1107/s1399004714023931.

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HU, one of the major nucleoid-associated proteins, interacts with the minor groove of DNA in a nonspecific manner to induce DNA bending or to stabilize bent DNA. In this study, crystal structures are reported for both free HU fromStaphylococcus aureusMu50 (SHU) and SHU bound to 21-mer dsDNA. The structures, in combination with electrophoretic mobility shift assays (EMSAs), isothermal titration calorimetry (ITC) measurements and molecular-dynamics (MD) simulations, elucidate the overall and residue-specific changes in SHU upon recognizing and binding to DNA. Firstly, structural comparison showed the flexible nature of the β-sheets of the DNA-binding domain and that the β-arms bend inwards upon complex formation, whereas the other portions are nearly unaltered. Secondly, it was found that the disruption and formation of salt bridges accompanies DNA binding. Thirdly, residue-specific free-energy analyses using the MM-PBSA method with MD simulation data suggested that the successive basic residues in the β-arms play a central role in recognizing and binding to DNA, which was confirmed by the EMSA and ITC analyses. Moreover, residue Arg55 resides in the hinge region of the flexible β-arms, exhibiting a remarkable role in their flexible nature. Fourthly, EMSAs with various DNAs revealed that SHU prefers deformable DNA. Taken together, these data suggest residue-specific roles in local shape and base readouts, which are primarily mediated by the flexible β-arms consisting of residues 50–80.
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Qian, Zhong, Mirjana Macvanin, Emilios K. Dimitriadis, Ximiao He, Victor Zhurkin, and Sankar Adhya. "A New Noncoding RNA Arranges Bacterial Chromosome Organization." mBio 6, no. 4 (August 25, 2015). http://dx.doi.org/10.1128/mbio.00998-15.

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ABSTRACTRepeated extragenic palindromes (REPs) in the enterobacterial genomes are usually composed of individual palindromic units separated by linker sequences. A total of 355 annotatedREPs are distributed along theEscherichia coligenome. RNA sequence (RNAseq) analysis showed that almost 80% of theREPs inE. coliare transcribed. The DNA sequence ofREP325showed that it is a cluster of six repeats, each with two palindromic units capable of forming cruciform structures in supercoiled DNA. Here, we report that components of theREP325element and at least one of its RNA products play a role in bacterial nucleoid DNA condensation. These RNA not only are present in the purified nucleoid but bind to the bacterial nucleoid-associated HU protein as revealed by RNA IP followed by microarray analysis (RIP-Chip) assays. Deletion ofREP325resulted in a dramatic increase of the nucleoid size as observed using transmission electron microscopy (TEM), and expression of one of theREP325RNAs, nucleoid-associated noncoding RNA 4 (naRNA4), from a plasmid restored the wild-type condensed structure. Independently, chromosome conformation capture (3C) analysis demonstrated physical connections among variousREPelements around the chromosome. These connections are dependent in some way upon the presence of HU and theREP325element; deletion of HU genes and/or theREP325element removed the connections. Finally, naRNA4 together with HU condensed DNAin vitroby connectingREP325or other DNA sequences that contain cruciform structures in a pairwise manner as observed by atomic force microscopy (AFM). On the basis of our results, we propose molecular models to explain connections of remote cruciform structures mediated by HU and naRNA4.IMPORTANCENucleoid organization in bacteria is being studied extensively, and several models have been proposed. However, the molecular nature of the structural organization is not well understood. Here we characterized the role of a novel nucleoid-associated noncoding RNA, naRNA4, in nucleoid structures bothin vivoandin vitro. We propose models to explain how naRNA4 together with nucleoid-associated protein HU connects remote DNA elements for nucleoid condensation. We present the first evidence of a noncoding RNA together with a nucleoid-associated protein directly condensing nucleoid DNA.
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Stojkova, Pavla, and Petra Spidlova. "Bacterial nucleoid-associated protein HU as an extracellular player in host-pathogen interaction." Frontiers in Cellular and Infection Microbiology 12 (August 23, 2022). http://dx.doi.org/10.3389/fcimb.2022.999737.

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HU protein is a member of nucleoid-associated proteins (NAPs) and is an important regulator of bacterial virulence, pathogenesis and survival. NAPs are mainly DNA structuring proteins that influence several molecular processes by binding the DNA. HU´s indispensable role in DNA-related processes in bacteria was described. HU protein is a necessary bacterial transcription factor and is considered to be a virulence determinant as well. Less is known about its direct role in host-pathogen interactions. The latest studies suggest that HU protein may be secreted outside bacteria and be a part of the extracellular matrix. Moreover, HU protein can be internalized in a host cell after bacterial infection. Its role in the host cell is not well described and further studies are extremely needed. Existing results suggest the involvement of HU protein in host cell immune response modulation in bacterial favor, which can help pathogens resist host defense mechanisms. A better understanding of the HU protein’s role in the host cell will help to effective treatment development.
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Zhang, Peipei, Xiaohui Zhao, Yawen Wang, Ke Du, Zhihao Wang, Jianfeng Yu, Gang Chang, Steve Matthews, Hongliang Wang, and Bing Liu. "Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins." Proceedings of the National Academy of Sciences 119, no. 9 (February 22, 2022). http://dx.doi.org/10.1073/pnas.2116278119.

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Significance Histone-like protein from Escherichia coli strain U93 (HU) protein is the most abundant nucleoid-associated protein in bacteria, which plays a fundamental role in chromosomal compaction and organization. It is essential for most bacteria as well as Apicomplexans, thus an important target for the development of antimicrobial and antimalaria drugs. We report Gp46 as a phage protein HU inhibitor. It inhibits HU of Bacillus subtilis by occupying its DNA binding site, thus preventing chromosome segregation during cell division. As key residues for the interaction are highly conserved, Gp46 interacts with HUs of a broad range of pathogens, including many pathogenic bacteria and Apicomplexan parasites like Plasmodium falciparum. Thus, this cross-species property could benefit antibiotic and antimalaria drug development that targets HU.
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34

Schramm, Frederic D., and Heath Murray. "HU Knew? Bacillus subtilis HBsu Is Required for DNA Replication Initiation." Journal of Bacteriology, July 11, 2022. http://dx.doi.org/10.1128/jb.00151-22.

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The prokaryotic nucleoid-associated protein (NAP) HU is both highly conserved and ubiquitous. Deletion of HU causes pleiotropic phenotypes, making it difficult to uncover the critical functions of HU within a bacterial cell.
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35

Bhowmick, Tuhin, Soumitra Ghosh, Karuna Dixit, Varsha Ganesan, Udupi A. Ramagopal, Debayan Dey, Siddhartha P. Sarma, Suryanarayanarao Ramakumar, and Valakunja Nagaraja. "Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors." Nature Communications 5, no. 1 (June 11, 2014). http://dx.doi.org/10.1038/ncomms5124.

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36

Anand, Chinmay, Meghna Santoshi, Prakruti R. Singh, and Valakunja Nagaraja. "Rv0802c is an acyltransferase that succinylates and acetylates Mycobacterium tuberculosis nucleoid-associated protein HU." Microbiology 167, no. 7 (July 5, 2021). http://dx.doi.org/10.1099/mic.0.001058.

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Among the nucleoid-associated proteins (NAPs), HU is the most conserved in eubacteria, engaged in overall chromosome organization and regulation of gene expression. Unlike other bacteria, HU from Mycobacterium tuberculosis (MtHU), has a long carboxyl terminal domain enriched in basic amino acids, resembling eukaryotic histone N-terminal tails. As with histones, MtHU undergoes post-translational modifications and we have previously identified interacting kinases, methyltransferases, an acetyltransferase and a deacetylase. Here we show that Rv0802c interacts and succinylates MtHU. Although categorized as a succinyltransferase, we show that this GNAT superfamily member can catalyse both succinylation and acetylation of MtHU with comparable kinetic parameters. Like acetylation of MtHU, succinylation of MtHU caused reduced interaction of the NAP with DNA, determined by electrophoretic mobility shift assay and surface plasmon resonance. However, in vivo expression of Rv0802c did not significantly alter the nucleoid architecture. Although such succinylation of NAPs is rare, these modifications of the archetypal NAP may provide avenues to the organism to compensate for the underrepresentation of NAPs in its genome to control the dynamics of nucleoid architecture and cellular functions.
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37

Agapova, Yuliya K., Dmitry A. Altukhov, Vladimir I. Timofeev, Victor S. Stroylov, Vitaly S. Mityanov, Dmitry A. Korzhenevskiy, Anna V. Vlaskina, Eugenia V. Smirnova, Eduard V. Bocharov, and Tatiana V. Rakitina. "Structure-based inhibitors targeting the alpha-helical domain of the Spiroplasma melliferum histone-like HU protein." Scientific Reports 10, no. 1 (September 15, 2020). http://dx.doi.org/10.1038/s41598-020-72113-4.

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Abstract Here we report bisphenol derivatives of fluorene (BDFs) as a new type of chemical probes targeting a histone-like HU protein, a global regulator of bacterial nucleoids, via its dimerization interface perturbation. BDFs were identified by virtual screening and molecular docking that targeted the core of DNA-binding β-saddle-like domain of the HU protein from Spiroplasma melliferum. However, NMR spectroscopy, complemented with molecular dynamics and site-directed mutagenesis, indicated that the actual site of the inhibitors’ intervention consists of residues from the α-helical domain of one monomer and the side portion of the DNA-binding domain of another monomer. BDFs inhibited DNA-binding properties of HU proteins from mycoplasmas S. melliferum, Mycoplasma gallicepticum and Escherichia coli with half-maximum inhibitory concentrations in the range between 5 and 10 µM. In addition, BDFs demonstrated antimicrobial activity against mycoplasma species, but not against E. coli, which is consistent with the compensatory role of other nucleoid-associated proteins in the higher bacteria. Further evaluation of antimicrobial effects of BDFs against various bacteria and viruses will reveal their pharmacological potential, and the allosteric inhibition mode reported here, which avoids direct competition for the binding site with DNA, should be considered in the development of small molecule inhibitors of nucleoid-associated proteins as well as other types of DNA-binding multimeric proteins.
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38

Hołówka, Joanna, Damian Trojanowski, Mateusz Janczak, Dagmara Jakimowicz, and Jolanta Zakrzewska-Czerwińska. "The Origin of Chromosomal Replication Is Asymmetrically Positioned on the Mycobacterial Nucleoid, and the Timing of Its Firing Depends on HupB." Journal of Bacteriology 200, no. 10 (March 12, 2018). http://dx.doi.org/10.1128/jb.00044-18.

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ABSTRACTThe bacterial chromosome undergoes dynamic changes in response to ongoing cellular processes and adaptation to environmental conditions. Among the many proteins involved in maintaining this dynamism, the most abundant is the nucleoid-associated protein (NAP) HU. In mycobacteria, the HU homolog, HupB, possesses an additional C-terminal domain that resembles that of eukaryotic histones H1/H5. Recently, we demonstrated that the highly abundant HupB protein occupies the entirety of theMycobacterium smegmatischromosome and that the HupB-binding sites exhibit a bias from the origin (oriC) to the terminus (ter). In this study, we used HupB fused with enhanced green fluorescent protein (EGFP) to perform the first analysis of chromosome dynamics and to track theoriCand replication machinery directly on the chromosome during the mycobacterial cell cycle. We show that the chromosome is located in an off-center position that reflects the unequal division and growth of mycobacterial cells. Moreover, unlike the situation inE. coli, the sisteroriCregions ofM. smegmatismove asymmetrically along the mycobacterial nucleoid. Interestingly, in this slow-growing organism, the initiation of the next round of replication precedes the physical separation of sister chromosomes. Finally, we show that HupB is involved in the precise timing of replication initiation.IMPORTANCEAlthough our view of mycobacterial nucleoid organization has evolved considerably over time, we still know little about the dynamics of the mycobacterial nucleoid during the cell cycle. HupB is a highly abundant mycobacterial nucleoid-associated protein (NAP) with an indispensable histone-like tail. It was previously suggested as a potential target for antibiotic therapy against tuberculosis. Here, we fused HupB with enhanced green fluorescent protein (EGFP) to study the dynamics of the mycobacterial chromosome in real time and to monitor the replication process directly on the chromosome. Our results reveal that, unlike the situation inEscherichia coli, the nucleoid of an apically growing mycobacterium is positioned asymmetrically within the cell throughout the cell cycle. We show that HupB is involved in controlling the timing of replication initiation. Since tuberculosis remains a serious health problem, studies concerning mycobacterial cell biology are of great importance.
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Stojkova, Pavla, Petra Spidlova, and Jiri Stulik. "Nucleoid-Associated Protein HU: A Lilliputian in Gene Regulation of Bacterial Virulence." Frontiers in Cellular and Infection Microbiology 9 (May 10, 2019). http://dx.doi.org/10.3389/fcimb.2019.00159.

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40

Hołówka, Joanna, Damian Trojanowski, Katarzyna Ginda, Bartosz Wojtaś, Bartłomiej Gielniewski, Dagmara Jakimowicz, and Jolanta Zakrzewska-Czerwińska. "HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail." mBio 8, no. 6 (November 7, 2017). http://dx.doi.org/10.1128/mbio.01272-17.

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ABSTRACT In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones. In this study, we analyzed the in vivo binding of HupB on the chromosome scale. By using PALM (photoactivated localization microscopy) and ChIP-Seq (chromatin immunoprecipitation followed by deep sequencing), we observed that the C-terminal domain is indispensable for the association of HupB with the nucleoid. Strikingly, the in vivo binding of HupB displayed a bias from the origin (oriC) to the terminus (ter) of the mycobacterial chromosome (numbers of binding sites decreased toward ter). We hypothesized that this binding mode reflects a role for HupB in organizing newly replicated oriC regions. Thus, HupB may be involved in coordinating replication with chromosome segregation. IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development. IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development.
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41

Hołówka, Joanna, Tomasz Łebkowski, Helge Feddersen, Giacomo Giacomelli, Karolina Drużka, Łukasz Makowski, Damian Trojanowski, Natalia Broda, Marc Bramkamp, and Jolanta Zakrzewska-Czerwińska. "Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin." Frontiers in Microbiology 14 (March 7, 2023). http://dx.doi.org/10.3389/fmicb.2023.1146406.

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Nucleoid-associated proteins (NAPs) crucially contribute to organizing bacterial chromatin and regulating gene expression. Among the most highly expressed NAPs are the HU and integration host factor (IHF) proteins, whose functional homologues, HupB and mycobacterial integration host factor (mIHF), are found in mycobacteria. Despite their importance for the pathogenicity and/or survival of tubercle bacilli, the role of these proteins in mycobacterial chromosome organization remains unknown. Here, we used various approaches, including super-resolution microscopy, to perform a comprehensive analysis of the roles of HupB and mIHF in chromosome organization. We report that HupB is a structural agent that maintains chromosome integrity on a local scale, and that the lack of this protein alters chromosome morphology. In contrast, mIHF is a highly dynamic protein that binds DNA only transiently, exhibits susceptibility to the chromosomal DNA topology changes and whose depletion leads to the growth arrest of tubercle bacilli. Additionally, we have shown that depletion of Mycobacterium smegmatis integration host factor (msIHF) leads to chromosome shrinkage and replication inhibition.
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42

Berger, Michael, Veneta Gerganova, Petya Berger, Radu Rapiteanu, Viktoras Lisicovas, and Ulrich Dobrindt. "Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli." Scientific Reports 6, no. 1 (August 22, 2016). http://dx.doi.org/10.1038/srep31512.

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43

Bettridge, Kelsey, Subhash Verma, Xiaoli Weng, Sankar Adhya, and Jie Xiao. "Single‐molecule tracking reveals that the nucleoid‐associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA." Molecular Microbiology, August 3, 2020. http://dx.doi.org/10.1111/mmi.14572.

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44

Hocher, Antoine, Guillaume Borrel, Khaled Fadhlaoui, Jean-François Brugère, Simonetta Gribaldo, and Tobias Warnecke. "Growth temperature and chromatinization in archaea." Nature Microbiology, October 20, 2022. http://dx.doi.org/10.1038/s41564-022-01245-2.

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AbstractDNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.
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Norris, Vic, Clara Kayser, Georgi Muskhelishvili, and Yoan Konto-Ghiorghi. "The Roles of Nucleoid-Associated Proteins and Topoisomerases in Chromosome Structure, Strand Segregation and the Generation of Phenotypic Heterogeneity in Bacteria." FEMS Microbiology Reviews, December 22, 2022. http://dx.doi.org/10.1093/femsre/fuac049.

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Abstract How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organise their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the Nucleoid-Associated Proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes and hence in the phenotypes of daughter cells.
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Gupta, Archit, Ashish Joshi, Kanika Arora, Samrat Mukhopadhyay, and Purnananda Guptasarma. "The bacterial nucleoid-associated proteins, HU, and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates." Journal of Biological Chemistry, March 2023, 104637. http://dx.doi.org/10.1016/j.jbc.2023.104637.

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