Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects

详细信息    查看全文

• 作者：Fenfei Leng
• 关键词：DNA linking number change (ΔLk) ; lac repressor (LacI) ; cAMP receptor protein (CRP) ; λ O ; DNA ; bending ; DNA topological barrier
• 刊名：Biophysical Reviews
• 出版年：2016
• 出版时间：September 2016
• 年：2016
• 卷：8
• 期：3
• 页码：197-207
• 全文大小：1,439 KB
• 刊物类别：Physics and Astronomy
• 刊物主题：Physics
  Biophysics and Biomedical Physics
  Cell Biology
  Biochemistry
  Biological Techniques
  Biomedicine
  Nanotechnology
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1867-2469
• 卷排序：8

文摘

Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI–lac O1 complexes if (−) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (−) supercoils within the 401-bp DNA loop. These constrained (−) supercoils enhance LacI’s binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.