The Mycobacterial MsDps2 Protein Is a Nucleoid-Forming DNA Binding Protein Regulated by Sigma Factors σA and σB

Saraswathi, R.; Chowdhury, Rebecca; Williams, Sunanda Margrett; Ghatak, Payel; Chatterji, Dipankar

doi:10.1371/journal.pone.0008017

Cited by 18 publications

(20 citation statements)

References 24 publications

(51 reference statements)

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“…Due to the increase in the number of fully sequenced microbial genomes, many Dps homologs were found, and their structures and functions were clarified [21,22]. It is common amongst bacteria to have more than one Dps gene per genome [23]. A number of studies have demonstrated the Dps expression control at the transcription level [23,24].…”

Section: Introductionmentioning

confidence: 99%

Polymorphic Protective Dps–DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering

et al. 2019

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Rapid increase of intracellular synthesis of specific histone-like Dps protein that binds DNA to protect the genome against deleterious factors leads to in cellulo crystallization—one of the most curious processes in the area of life science at the moment. However, the actual structure of the Dps–DNA co-crystals remained uncertain in the details for more than two decades. Cryo-electron tomography and small-angle X-ray scattering revealed polymorphous modifications of the co-crystals depending on the buffer parameters. Two different types of the Dps–DNA co-crystals are formed in vitro: triclinic and cubic. Three-dimensional reconstruction revealed DNA and Dps molecules in cubic co-crystals, and the unit cell parameters of cubic lattice were determined consistently by both methods.

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Section: Introductionmentioning

confidence: 99%

Polymorphic Protective Dps–DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering

et al. 2019

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“…Here we used pure proteins and added plasmid DNA. We reported earlier, that MsDps2 is purified from cells in DNA bound form [20]. Hence we used only purified Dps2 protein, and, on the other hand, we added plasmid pGEM-7Zf(+) to pure Dps1 protein to generate toroids (Figure 5D and 5E respectively).…”

Section: Resultsmentioning

confidence: 99%

“…We know that the transcription of MsDps2 is regulated by σ B , which is analogous to σ s in E.coli [20]. The rpos gene, that is sensitive to post-transcriptional modification, regulates the sigma factor σ s [7], [43].…”

Section: Discussionmentioning

confidence: 99%

Unveiling the Role of Dps in the Organization of Mycobacterial Nucleoid

et al. 2011

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In order to preserve genetic information in stress conditions, bacterial DNA is organized into higher order nucleoid structure. In this paper, with the help of Atomic Force Microscopy, we show the different structural changes in mycobacterial nucleoid at different points of growth in the presence of different concentrations of glucose in the medium. We also observe that in Mycobacterium smegmatis, two different Dps proteins (Dps1 and Dps2) promote two types of nucleoid organizations. At the late stationary phase, under low glucose availability, Dps1 binds to DNA to form a very stable toroid structure. On the other hand, under the same condition, Dps2-DNA complex forms an incompletely condensed toroid and finally forms a further stable coral reef structure in the presence of RNA. This coral reef structure is stable in high concentration of bivalent ion like Mg2+.

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“…With increasing numbers of completely sequenced microbial genomes, multiple dps homologs within the same species are now being identified and their structures and functions elucidated [24], [25], [26]. Having more than one dps gene per genome is common amongst bacteria [27]. However, for many genera, variation in the number of dps per genome amongst closely related species is yet to be satisfactorily explained.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, more intricate studies are now characterizing the control of dps at the transcriptional level [27], [30] and, not only is there evidence for multiple sigma factor complexes contributing to the transcription of dps [30], [31] but, it also appears that expression of these genes may be driven by suites of different sigma factors e.g. msdps1 [31] and msdps2 [27]. Together, this suggests that the evolutionary history of dps in many genera contains duplications, losses and possible lateral acquisitions.…”

Section: Introductionmentioning

confidence: 99%

The Evolution of an Osmotically Inducible dps in the Genus Streptomyces

et al. 2013

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Dps proteins are found almost ubiquitously in bacterial genomes and there is now an appreciation of their multifaceted roles in various stress responses. Previous studies have shown that this family of proteins assemble into dodecamers and their quaternary structure is entirely critical to their function. Moreover, the numbers of dps genes per bacterial genome is variable; even amongst closely related species - however, for many genera this enigma is yet to be satisfactorily explained. We reconstruct the most probable evolutionary history of Dps in Streptomyces genomes. Typically, these bacteria encode for more than one Dps protein. We offer the explanation that variation in the number of dps per genome among closely related Streptomyces can be explained by gene duplication or lateral acquisition, and the former preceded a subsequent shift in expression patterns for one of the resultant paralogs. We show that the genome of S. coelicolor encodes for three Dps proteins including a tailless Dps. Our in vivo observations show that the tailless protein, unlike the other two Dps in S. coelicolor, does not readily oligomerise. Phylogenetic and bioinformatic analyses combined with expression studies indicate that in several Streptomyces species at least one Dps is significantly over-expressed during osmotic shock, but the identity of the ortholog varies. In silico analysis of dps promoter regions coupled with gene expression studies of duplicated dps genes shows that paralogous gene pairs are expressed differentially and this correlates with the presence of a sigB promoter. Lastly, we identify a rare novel clade of Dps and show that a representative of these proteins in S. coelicolor possesses a dodecameric quaternary structure of high stability.

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The Mycobacterial MsDps2 Protein Is a Nucleoid-Forming DNA Binding Protein Regulated by Sigma Factors σA and σB

Cited by 18 publications

References 24 publications

Polymorphic Protective Dps–DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering

Polymorphic Protective Dps–DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering

Unveiling the Role of Dps in the Organization of Mycobacterial Nucleoid

The Evolution of an Osmotically Inducible dps in the Genus Streptomyces

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