binding dynamics of Rok from bacillus subtilis

Introduction

Rok (YkuW) is a nucleoid-associated protein in Bacillus subtilis that plays a significant role in regulating genetic competence, gene expression, and chromosomal architecture. It acts primarily as a repressor, binding to A+T-rich DNA regions, often associated with horizontally acquired genes. Understanding the binding dynamics of Rok is crucial for comprehending its regulatory mechanisms and its impact on bacterial physiology.

Key Insights

Repression of comK and Competence Regulation:
- Rok represses the transcription of comK, a key competence transcription factor, by binding directly to the comK promoter .
- Rok limits the size of the subpopulation that develops competence by inhibiting comK expression.
Binding Preferences and Mechanisms:
- Rok binds preferentially to A+T-rich DNA regions, often associated with horizontally transferred genes .
- The C-terminal domain of Rok adopts a winged helix fold, binding the DNA minor groove through specific amino acid interactions.
Role in Chromosomal Architecture:
- Rok is involved in the global organization of the B. subtilis genome by binding in clusters and promoting chromosomal loop formation .
- Rok's DNA bridging ability is not affected by changes in physico-chemical conditions, unlike other H-NS-like proteins .
Interaction with Other Proteins:
- Rok interacts with DnaA, a bacterial replication initiator, to repress transcription of certain operons, suggesting a cooperative role in nucleoid architecture.
- Rok and ComK can individually repress rok transcription, establishing feedback loops.
Regulation of Gene Expression:
- Rok represses a family of genes encoding membrane-localized and secreted proteins, including those with antibiotic activity.
- Rok inactivation increases chromosomal transformation and affects the integration of homologous DNA in recombination-deficient strains.
Evolutionary and Functional Analogies:
- Rok is functionally analogous to H-NS in Gram-negative bacteria and Lsr2 in Mycobacteria, serving to repress expression of A+T-rich genes .
- Rok's role as a xenogeneic silencer helps distinguish foreign from self DNA, buffering against potential fitness consequences of misregulated expression.

Conclusion

Rok from Bacillus subtilis is a multifaceted protein that primarily acts as a repressor of competence development and gene expression by binding to A+T-rich DNA regions. It plays a crucial role in chromosomal organization and interacts with other proteins to modulate gene expression. Unlike other H-NS-like proteins, Rok's DNA binding and bridging abilities are not influenced by changes in physico-chemical conditions, highlighting its unique regulatory mechanisms. Understanding Rok's binding dynamics provides valuable insights into its regulatory functions and evolutionary significance in bacterial genomes.

Binding dynamics of Rok from bacillus subtilis

Summary

Introduction

Key Insights

Conclusion

Sources and full results

Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK

Rok protein in Bacillus subtilis regulates genetic competence by directly repressing comK, affecting comK stability but not stability of the competence transcription factor.

The Rok Protein of Bacillus subtilis Represses Genes for Cell Surface and Extracellular Functions

Rok protein in Bacillus subtilis plays a role in repressing membrane-localized and secreted proteins, including antibiotic-active genes, and has been introduced into the B. subtilis-B. licheniformis-B. amyloliquefaciens group by horizontal transmission.

The Transcriptional Regulator Rok Binds A+T-Rich DNA and Is Involved in Repression of a Mobile Genetic Element in Bacillus subtilis

Rok is a transcriptional regulator that binds to A+T-rich DNA and helps repress expression of acquired genes in Bacillus subtilis, similar to H-NS in Gram negative bacteria and Lsr2 in high G+C Mycobacteria.

Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid‐associated protein Rok in Bacillus subtilis

DnaA and Rok in Bacillus subtilis cooperate to repress transcription of yxaJ, yybNM, and sunA-bdbB operons, potentially impacting nucleoid architecture.

Rok Regulates yuaB Expression during Architecturally Complex Colony Development of Bacillus subtilis 168

Rok indirectly regulates yuaB expression during Bacillus subtilis colony development, affecting complex colony structure formation.

Inhibition of Bacillus subtilis natural competence by a native, conjugative plasmid-encoded comK repressor protein.

Bacillus subtilis can develop natural competence by repressing the comK gene, with rok(LS20) being the prototype of a newly identified subgroup of nine rok genes.

Nucleoid-associated Rok differentially affects chromosomal transformation on Bacillus subtilis recombination-deficient cells.

Rok inactivation increases chromosomal transformation in Bacillus subtilis, but differentially reduces it in transformation-deficient cells, potentially by altering nucleoid architecture.

How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome

Bacillus subtilis' Rok xenogeneic silencer prefers DNA sequences with AACTA, TACTA, and flexible multiple TpA steps, suggesting it and its resident genome may have evolved cooperatively.

The B. subtilis Rok protein compacts and organizes DNA by bridging

Rok, a DNA bridging protein in Bacillus subtilis, is not affected by changes in physico-chemical conditions, suggesting other protein-mediated mechanisms could relieve gene silencing in response to environmental changes.

The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues

The B. subtilis Rok protein is an atypical H-NS-like protein that is unaffected by changes in physico-chemical conditions, suggesting it may not directly respond to environmental stimuli.

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