Limits...
A New Noncoding RNA Arranges Bacterial Chromosome Organization.

Qian Z, Macvanin M, Dimitriadis EK, He X, Zhurkin V, Adhya S - MBio (2015)

Bottom Line: Deletion of REP325 resulted in a dramatic increase of the nucleoid size as observed using transmission electron microscopy (TEM), and expression of one of the REP325 RNAs, nucleoid-associated noncoding RNA 4 (naRNA4), from a plasmid restored the wild-type condensed structure.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

No MeSH data available.


Related in: MedlinePlus

Models of HU- and naRNA-mediated DNA condensation. (A) DNA-naRNA-HU-naRNA-DNA model. Cruciform DNA structures connect with a hairpin in naRNA. Two DNA-bound RNAs are then bridged together by an HU dimer. (B) DNA-naRNA(HU)-DNA data are presented similarly to the model data presented in panel A, but the stoichiometry of HU and naRNA in the complex is 1:1. HU facilitates the binding of an RNA molecule to two cruciform structures. (C) DNA-HU-naRNA-HU-DNA:HU binds to cruciform DNA structures; two bound-HU dimers are then connected by a molecule of naRNA. How naRNA interacts with DNA cruciform, if such an interaction occurs, is unknown, but HU interaction with cruciform-generating DNA has been established (31, 32). (D) DNA-HU(naRNA)-DNA data are presented similarly to the model data presented in panel C, but the stoichiometry of HU and naRNA is 1:1. naRNA binding to HU facilitates one molecule of HU binding to two DNA cruciform structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4550694&req=5

fig5: Models of HU- and naRNA-mediated DNA condensation. (A) DNA-naRNA-HU-naRNA-DNA model. Cruciform DNA structures connect with a hairpin in naRNA. Two DNA-bound RNAs are then bridged together by an HU dimer. (B) DNA-naRNA(HU)-DNA data are presented similarly to the model data presented in panel A, but the stoichiometry of HU and naRNA in the complex is 1:1. HU facilitates the binding of an RNA molecule to two cruciform structures. (C) DNA-HU-naRNA-HU-DNA:HU binds to cruciform DNA structures; two bound-HU dimers are then connected by a molecule of naRNA. How naRNA interacts with DNA cruciform, if such an interaction occurs, is unknown, but HU interaction with cruciform-generating DNA has been established (31, 32). (D) DNA-HU(naRNA)-DNA data are presented similarly to the model data presented in panel C, but the stoichiometry of HU and naRNA is 1:1. naRNA binding to HU facilitates one molecule of HU binding to two DNA cruciform structures.

Mentions: It has become clear that the organization of the chromosome in E. coli is not random. The chromosome is not merely a disordered aggregate of randomly coiled DNA. Instead, it is a dynamic but spatially organized defined entity that undergoes strictly controlled and reproducible changes when they are needed (23). Structural models of elements such as “macro domains,” “supercoiled topological loops,” “filaments,” and “remote connections” are suggested to represent structural constituents of chromosomes from observations using different approaches (19, 24–27). A number of NAPs, such as the HU, Fis, IHF, H-NS, and SMC proteins, modulate chromosome structure. We focused on HU, which binds to DNA nonspecifically but prefers distorted DNA structures such as nicks, gaps, bends, and cruciforms (28, 29). Due to its high abundance and growth-phase-dependent subunit compositions (HUαα, HUαβ, and HUββ), HU is believed to modulate chromosome structure in accordance with the growth phase of the cell (30). We confirmed that HU binds to naRNA4 and to several other RNAs by electrophoretic mobility shift assay (EMSA) (see Fig. S3 in the supplemental material), but not all HU-RNA bindings could help DNA condensation both in vivo (Fig. 2) and in vitro but bound to those which contained two hairpin structures (Fig. 4). Thus, an HU-naRNA4 interaction may be somewhat unusual and specific; the presence of at least two hairpin motifs, such as Z2 and Y, in the RNA is needed for DNA condensation. We conclude that two cruciform structures in DNA, not yet completely defined, interact with each other in a pairwise fashion for DNA condensation, which needs both HU and naRNA4. We propose four mechanisms for interactions between two DNA cruciforms mediated by HU and naRNA4 (Fig. 5). (i) For DNA-naRNA-HU-naRNA-DNA interactions, each cruciform structure binds to one hairpin of naRNA and two DNA-bound RNAs are bridged together by an HU dimer using the other hairpins of the two naRNAs (Fig. 5A). (ii) For DNA-naRNA(HU)-DNA interactions, the model is similar to model i, but the stoichiometry of HU and naRNA in the complex is 1:1. HU binding to naRNA makes the latter amenable to interaction with two cruciforms (Fig. 5B). (iii) For DNA-HU-naRNA-HU-DNA interactions, HU binds to cruciform DNA; two bound-HU dimers are then connected by a molecule of naRNA through the two hairpins (Fig. 5C). (iv) For DNA-HU(naRNA)-DNA interactions, the model is similar to model iii, but the stoichiometry of HU and naRNA in the complex is 1:1. naRNA binding to HU makes the latter potent for interactions with two cruciform structures. We note here that in models ii and iv, it is possible that the roles of naRNA and HU, respectively, could be only catalytic and that they are not involved in the complex. At this stage, we are unable to prefer one model to the others except that a specific interaction between HU and a DNA cruciform structure has been previously established (31, 32), which would support models iii and iv. Cross-linking of the condensed DNA complexes followed by fragmentation and chemical identification of the products may distinguish between the different models.


A New Noncoding RNA Arranges Bacterial Chromosome Organization.

Qian Z, Macvanin M, Dimitriadis EK, He X, Zhurkin V, Adhya S - MBio (2015)

Models of HU- and naRNA-mediated DNA condensation. (A) DNA-naRNA-HU-naRNA-DNA model. Cruciform DNA structures connect with a hairpin in naRNA. Two DNA-bound RNAs are then bridged together by an HU dimer. (B) DNA-naRNA(HU)-DNA data are presented similarly to the model data presented in panel A, but the stoichiometry of HU and naRNA in the complex is 1:1. HU facilitates the binding of an RNA molecule to two cruciform structures. (C) DNA-HU-naRNA-HU-DNA:HU binds to cruciform DNA structures; two bound-HU dimers are then connected by a molecule of naRNA. How naRNA interacts with DNA cruciform, if such an interaction occurs, is unknown, but HU interaction with cruciform-generating DNA has been established (31, 32). (D) DNA-HU(naRNA)-DNA data are presented similarly to the model data presented in panel C, but the stoichiometry of HU and naRNA is 1:1. naRNA binding to HU facilitates one molecule of HU binding to two DNA cruciform structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4550694&req=5

fig5: Models of HU- and naRNA-mediated DNA condensation. (A) DNA-naRNA-HU-naRNA-DNA model. Cruciform DNA structures connect with a hairpin in naRNA. Two DNA-bound RNAs are then bridged together by an HU dimer. (B) DNA-naRNA(HU)-DNA data are presented similarly to the model data presented in panel A, but the stoichiometry of HU and naRNA in the complex is 1:1. HU facilitates the binding of an RNA molecule to two cruciform structures. (C) DNA-HU-naRNA-HU-DNA:HU binds to cruciform DNA structures; two bound-HU dimers are then connected by a molecule of naRNA. How naRNA interacts with DNA cruciform, if such an interaction occurs, is unknown, but HU interaction with cruciform-generating DNA has been established (31, 32). (D) DNA-HU(naRNA)-DNA data are presented similarly to the model data presented in panel C, but the stoichiometry of HU and naRNA is 1:1. naRNA binding to HU facilitates one molecule of HU binding to two DNA cruciform structures.
Mentions: It has become clear that the organization of the chromosome in E. coli is not random. The chromosome is not merely a disordered aggregate of randomly coiled DNA. Instead, it is a dynamic but spatially organized defined entity that undergoes strictly controlled and reproducible changes when they are needed (23). Structural models of elements such as “macro domains,” “supercoiled topological loops,” “filaments,” and “remote connections” are suggested to represent structural constituents of chromosomes from observations using different approaches (19, 24–27). A number of NAPs, such as the HU, Fis, IHF, H-NS, and SMC proteins, modulate chromosome structure. We focused on HU, which binds to DNA nonspecifically but prefers distorted DNA structures such as nicks, gaps, bends, and cruciforms (28, 29). Due to its high abundance and growth-phase-dependent subunit compositions (HUαα, HUαβ, and HUββ), HU is believed to modulate chromosome structure in accordance with the growth phase of the cell (30). We confirmed that HU binds to naRNA4 and to several other RNAs by electrophoretic mobility shift assay (EMSA) (see Fig. S3 in the supplemental material), but not all HU-RNA bindings could help DNA condensation both in vivo (Fig. 2) and in vitro but bound to those which contained two hairpin structures (Fig. 4). Thus, an HU-naRNA4 interaction may be somewhat unusual and specific; the presence of at least two hairpin motifs, such as Z2 and Y, in the RNA is needed for DNA condensation. We conclude that two cruciform structures in DNA, not yet completely defined, interact with each other in a pairwise fashion for DNA condensation, which needs both HU and naRNA4. We propose four mechanisms for interactions between two DNA cruciforms mediated by HU and naRNA4 (Fig. 5). (i) For DNA-naRNA-HU-naRNA-DNA interactions, each cruciform structure binds to one hairpin of naRNA and two DNA-bound RNAs are bridged together by an HU dimer using the other hairpins of the two naRNAs (Fig. 5A). (ii) For DNA-naRNA(HU)-DNA interactions, the model is similar to model i, but the stoichiometry of HU and naRNA in the complex is 1:1. HU binding to naRNA makes the latter amenable to interaction with two cruciforms (Fig. 5B). (iii) For DNA-HU-naRNA-HU-DNA interactions, HU binds to cruciform DNA; two bound-HU dimers are then connected by a molecule of naRNA through the two hairpins (Fig. 5C). (iv) For DNA-HU(naRNA)-DNA interactions, the model is similar to model iii, but the stoichiometry of HU and naRNA in the complex is 1:1. naRNA binding to HU makes the latter potent for interactions with two cruciform structures. We note here that in models ii and iv, it is possible that the roles of naRNA and HU, respectively, could be only catalytic and that they are not involved in the complex. At this stage, we are unable to prefer one model to the others except that a specific interaction between HU and a DNA cruciform structure has been previously established (31, 32), which would support models iii and iv. Cross-linking of the condensed DNA complexes followed by fragmentation and chemical identification of the products may distinguish between the different models.

Bottom Line: Deletion of REP325 resulted in a dramatic increase of the nucleoid size as observed using transmission electron microscopy (TEM), and expression of one of the REP325 RNAs, nucleoid-associated noncoding RNA 4 (naRNA4), from a plasmid restored the wild-type condensed structure.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

No MeSH data available.


Related in: MedlinePlus