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A novel bifunctional histone protein in Streptomyces: a candidate for structural coupling between DNA conformation and transcription during development and stress?

Aldridge M, Facey P, Francis L, Bayliss S, Del Sol R, Dyson P - Nucleic Acids Res. (2013)

Bottom Line: Here, we describe a novel developmentally regulated nucleoid-associated protein, DdbA, of the genus that consists of an N-terminal DNA-binding histone H1-like domain and a C-terminal DksA-like domain that can potentially modulate RNA polymerase activity in conjunction with ppGpp.The mutant is also sensitive to oxidative stress owing to impaired upregulation of transcription of sigR, encoding an alternative sigma factor.Consequently, we propose this bifunctional histone-like protein as a candidate that could structurally couple changes in DNA conformation and transcription during the streptomycete life-cycle and in response to stress.

View Article: PubMed Central - PubMed

Affiliation: Institute of Life Science, College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK.

ABSTRACT
Antibiotic-producing Streptomyces are complex bacteria that remodel global transcription patterns and their nucleoids during development. Here, we describe a novel developmentally regulated nucleoid-associated protein, DdbA, of the genus that consists of an N-terminal DNA-binding histone H1-like domain and a C-terminal DksA-like domain that can potentially modulate RNA polymerase activity in conjunction with ppGpp. Owing to its N-terminal domain, the protein can efficiently bind and condense DNA in vitro. Loss of function of this DNA-binding protein results in changes in both DNA condensation during development and the ability to adjust DNA supercoiling in response to osmotic stress. Initial analysis of the DksA-like activity of DdbA indicates that overexpression of the protein suppresses a conditional deficiency in antibiotic production of relA mutants that are unable to synthesise ppGpp, just as DksA overexpression in Escherichia coli can suppress ppGpp(0) phenotypes. The mutant is also sensitive to oxidative stress owing to impaired upregulation of transcription of sigR, encoding an alternative sigma factor. Consequently, we propose this bifunctional histone-like protein as a candidate that could structurally couple changes in DNA conformation and transcription during the streptomycete life-cycle and in response to stress.

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Related in: MedlinePlus

DdbA contributes to nucleoid condensation during sporulation. Panel A: representative images of live-stained nucleoids from S.coelicolor M145 and the ddbA mutant. Bars indicate 10 µm. Panel B: histogram showing distribution of nucleoid sizes in these strains (a minimum of 400 nucleoids measured per strain). The histogram was generated by plotting the percentage of nucleoids per 0.1 mm size intervals, across the 0.1–3 mm size interval.
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gkt180-F3: DdbA contributes to nucleoid condensation during sporulation. Panel A: representative images of live-stained nucleoids from S.coelicolor M145 and the ddbA mutant. Bars indicate 10 µm. Panel B: histogram showing distribution of nucleoid sizes in these strains (a minimum of 400 nucleoids measured per strain). The histogram was generated by plotting the percentage of nucleoids per 0.1 mm size intervals, across the 0.1–3 mm size interval.

Mentions: The association of DdbA with compacting chromosomes during sporulation led us to compare the nucleoids of the mutant and wild-type. The dimensions of 400 pre-spore nucleoids stained with Syto9 were determined for each strain, including the genetically complemented mutant (Figure 3). Average nucleoid lengths were 0.78 µm, 0.89 µm and 0.8 µm for the wild-type, the mutant and the complemented mutant (not shown), respectively, with the length differences between nucleoids of the mutant and the other strains being statistically significant (using Kruskall–Wallis tests and pair-wise Mann–Whitney tests). Aside from the apparent length difference, the less condensed nucleoids of the mutant often appeared ‘boxier’ or ‘bilobed’ compared with those of the other strains (Figure 3). No differences were seen for either the dimensions of pre-spore compartments or the frequency of anulceate cells between these strains.Figure 3.


A novel bifunctional histone protein in Streptomyces: a candidate for structural coupling between DNA conformation and transcription during development and stress?

Aldridge M, Facey P, Francis L, Bayliss S, Del Sol R, Dyson P - Nucleic Acids Res. (2013)

DdbA contributes to nucleoid condensation during sporulation. Panel A: representative images of live-stained nucleoids from S.coelicolor M145 and the ddbA mutant. Bars indicate 10 µm. Panel B: histogram showing distribution of nucleoid sizes in these strains (a minimum of 400 nucleoids measured per strain). The histogram was generated by plotting the percentage of nucleoids per 0.1 mm size intervals, across the 0.1–3 mm size interval.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643593&req=5

gkt180-F3: DdbA contributes to nucleoid condensation during sporulation. Panel A: representative images of live-stained nucleoids from S.coelicolor M145 and the ddbA mutant. Bars indicate 10 µm. Panel B: histogram showing distribution of nucleoid sizes in these strains (a minimum of 400 nucleoids measured per strain). The histogram was generated by plotting the percentage of nucleoids per 0.1 mm size intervals, across the 0.1–3 mm size interval.
Mentions: The association of DdbA with compacting chromosomes during sporulation led us to compare the nucleoids of the mutant and wild-type. The dimensions of 400 pre-spore nucleoids stained with Syto9 were determined for each strain, including the genetically complemented mutant (Figure 3). Average nucleoid lengths were 0.78 µm, 0.89 µm and 0.8 µm for the wild-type, the mutant and the complemented mutant (not shown), respectively, with the length differences between nucleoids of the mutant and the other strains being statistically significant (using Kruskall–Wallis tests and pair-wise Mann–Whitney tests). Aside from the apparent length difference, the less condensed nucleoids of the mutant often appeared ‘boxier’ or ‘bilobed’ compared with those of the other strains (Figure 3). No differences were seen for either the dimensions of pre-spore compartments or the frequency of anulceate cells between these strains.Figure 3.

Bottom Line: Here, we describe a novel developmentally regulated nucleoid-associated protein, DdbA, of the genus that consists of an N-terminal DNA-binding histone H1-like domain and a C-terminal DksA-like domain that can potentially modulate RNA polymerase activity in conjunction with ppGpp.The mutant is also sensitive to oxidative stress owing to impaired upregulation of transcription of sigR, encoding an alternative sigma factor.Consequently, we propose this bifunctional histone-like protein as a candidate that could structurally couple changes in DNA conformation and transcription during the streptomycete life-cycle and in response to stress.

View Article: PubMed Central - PubMed

Affiliation: Institute of Life Science, College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK.

ABSTRACT
Antibiotic-producing Streptomyces are complex bacteria that remodel global transcription patterns and their nucleoids during development. Here, we describe a novel developmentally regulated nucleoid-associated protein, DdbA, of the genus that consists of an N-terminal DNA-binding histone H1-like domain and a C-terminal DksA-like domain that can potentially modulate RNA polymerase activity in conjunction with ppGpp. Owing to its N-terminal domain, the protein can efficiently bind and condense DNA in vitro. Loss of function of this DNA-binding protein results in changes in both DNA condensation during development and the ability to adjust DNA supercoiling in response to osmotic stress. Initial analysis of the DksA-like activity of DdbA indicates that overexpression of the protein suppresses a conditional deficiency in antibiotic production of relA mutants that are unable to synthesise ppGpp, just as DksA overexpression in Escherichia coli can suppress ppGpp(0) phenotypes. The mutant is also sensitive to oxidative stress owing to impaired upregulation of transcription of sigR, encoding an alternative sigma factor. Consequently, we propose this bifunctional histone-like protein as a candidate that could structurally couple changes in DNA conformation and transcription during the streptomycete life-cycle and in response to stress.

Show MeSH
Related in: MedlinePlus