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123 results on '"Hou, Xi-Miao"'

2. RQC helical hairpin in Bloom's syndrome helicase regulates DNA unwinding by dynamically intercepting nascent nucleotides

Author

Ma, Jianbing, Xu, Chunhua, Li, Jinghua, Hou, Xi-Miao, Da, Lin-Tai, Jia, Qi, Huang, Xingyuan, Yu, Jin, Xi, Xuguang, Lu, Ying, and Li, Ming

Subjects
Biochemistry and Cell Biology, Biological Sciences, Rare Diseases, Pediatric, Genetics, Biotechnology, Analytical chemistry instrumentation, Biochemistry, Biological sciences, Structural biology
Abstract

The RecQ family of helicases are important for maintenance of genomic integrity. Although functions of constructive subdomains of this family of helicases have been extensively studied, the helical hairpin (HH) in the RecQ-C-terminal domain (RQC) has been underappreciated and remains poorly understood. Here by using single-molecule fluorescence resonance energy transfer, we found that HH in the human BLM transiently intercepts different numbers of nucleotides when it is unwinding a double-stranded DNA. Single-site mutations in HH that disrupt hydrogen bonds and/or salt bridges between DNA and HH change the DNA binding conformations and the unwinding features significantly. Our results, together with recent clinical tests that correlate single-site mutations in HH of human BLM with the phenotype of cancer-predisposing syndrome or Bloom's syndrome, implicate pivotal roles of HH in BLM's DNA unwinding activity. Similar mechanisms might also apply to other RecQ family helicases, calling for more attention to the RQC helical hairpin.

Published
2022

4. DHX36-mediated G-quadruplex unfolding is ATP-independent?

Author

Guo, Hai-Lei, Chen, Wei-Fei, Rety, Stephane, Liu, Na-Nv, Song, Ze-Yu, Dai, Yan-Xue, Hou, Xi-Miao, Dou, Shuo-Xing, and Xi, Xu-Guang

Subjects
Quantitative Biology - Biomolecules, Physics - Biological Physics
Abstract

Chen et al. solved the crystal structure of bovine DHX36 bound to a DNA with a G-quadruplex (G4) and a single-stranded DNA segment. They believed that the mechanism they proposed may represent a general model for describing how a G4-unfolding helicase recognizes and unfolds G4 DNA. Their conclusion is interesting, however, we noticed that their linear DNA substrate (DNAMyc) that harbors a Myc-promoter-derived G4-forming sequence was directly used without pre-folding. This raises the question whether the structure they obtained really reflects DHX36-mediated G4 recognition and unfolding, or just only represents a DHX36-binding-induced quasi-folded G4 structure. By a combination of polymerase extension, DMS footprinting, stopped-flow, and smFRET assays, we obtained clear evidences that do not support their ATP-independent one-base translocation structural model. We further revealed that the oscillation of FRET signal they observed should correspond to a repetitive G4 binding, but not unfolding, by DHX36.

Published
2019

12. Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G‐Quadruplex.

Author

Guo, Lijuan, Bao, Yanling, Zhao, Yilin, Ren, Zhiyun, Bi, Lulu, Zhang, Xia, Liu, Cong, Hou, Xi‐Miao, Wang, Michelle D., and Sun, Bo

Subjects
DNA synthesis, DNA structure, DNA-binding proteins, DNA replication, SINGLE-stranded DNA, REPLISOMES, DNA polymerases, DNA helicases
Abstract

G‐quadruplex (G4) is a four‐stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single‐molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging‐strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single‐stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading‐strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome. [ABSTRACT FROM AUTHOR]

Published
2024
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15. The catalytic triad of rice NARROW LEAF1involves H234

Author

Huang, Ling-Yun, Liu, Na-Nv, Chen, Wei-Fei, Ai, Xia, Li, Hai-Hong, Zhang, Ze-Lin, Hou, Xi-Miao, Fossé, Philippe, Mauffret, Olivier, Lei, Dong-Sheng, Rety, Stephane, and Xi, Xu-Guang

Abstract

NARROW LEAF1(NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1’s proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.

Published
2024
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37. Direct Measurement of Sequential Folding Pathway and Energy Landscape of Human Telomeric G-quadruplex Structures

Author

Li, Wei, Hou, Xi-Miao, Wang, Peng-Ye, Xi, Xu-Guang, and Li, Ming

Abstract

Single-stranded guanine-rich sequences fold into compact G-quadruplexes. Although G-triplexes have been proposed and demonstrated as intermediates in the folding of G-quadruplexes, there is still a debate on their folding pathways. In this work, we employed magnetic tweezers to investigate the folding kinetics of single human telomeric G-quadruplexes in 100 mM Na+buffer. The results are consistent with a model in which the G-triplex is an in-pathway intermediate in the folding of the G-quadruplex. By finely tuning the force exerted on the G-quadruplex, we observed reversible transitions from the G-quadruplex to the G-triplex as well as from the G-triplex to the unfolded coil when the force was increased from 26 to 39 pN. The energy landscape derived from the probability distribution shows clearly that the G-quadruplex goes through an intermediate when it is unfolded, and vice versa.

Published
2024
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46. Study of cisplatin-induced DNA compaction using single molecule magnetic tweezers

Author

Wang Peng-Ye, Xiao Bin, Xu Chun-Hua, Hou Xi-Miao, Zhang Xinghua, and Li Ming

Subjects
Cisplatin, Magnetic tweezers, Chemistry, Kinetics, Compaction, General Physics and Astronomy, DNA condensation, chemistry.chemical_compound, Crystallography, Biophysics, medicine, DNA supercoil, Molecule, DNA, medicine.drug
Abstract

We report a single molecule study on cisplatin-induced DNA compaction. It is found that, at a small external tension （

Published
2009

47. Dynamics and statistics in few-body hard-ball systems

Author

Hou Xi-Miao, Zheng Zhi-Gang, He Li-Xia, and Fu Wen-Yu

Subjects
Mean squared displacement, Classical mechanics, Distribution function, Ballistic conduction, Mathematical analysis, Ergodicity, Ball (bearing), General Physics and Astronomy, Configuration space, Critical value, Brownian motion, Mathematics
Abstract

The dynamic and statistical properties of several hard balls restricted in a box are studied.The collision distribution in configuration space is main object of the research. Numerical simulations indicate that the distribution function is uniform (horizontal line) when the radius of balls is very small. This uniform p art decreases with increasing size of the balls, and a double-peak distribution is found when the radius exceeds a critical value. Brownian motion is simulated by using hard-ball systems. It can be found that the mean square displacement is proportional to the square of time, i.e., the transport process is dominated by ballistic transport, rather than a diffusion behavior.

Published
2005

48. Endogenous Bos taurusRECQL is predominantly monomeric and more active than oligomers

Author

Liu, Na-Nv, Song, Ze-Yu, Guo, Hai-Lei, Yin, Hu, Chen, Wei-Fei, Dai, Yang-Xue, Xin, Ben-Ge, Ai, Xia, Ji, Lei, Wang, Qing-Man, Hou, Xi-Miao, Dou, Shuo-Xing, Rety, Stephane, and Xi, Xu-Guang

Abstract

There is broad consensus that RecQ family helicase is a high-order oligomer that dissociates into a dimer upon ATP binding. This conclusion is based mainly on studies of highly purified recombinant proteins, and the oligomeric states of RecQ helicases in living cells remain unknown. We show here that, in contrast to current models, monomeric RECQL helicase is more abundant than oligomer/dimer forms in living cells. Further characterization of endogenous BtRECQL and isolated monomeric BtRECQL using various approaches demonstrates that both endogenous and recombinant monomeric BtRECQL effectively function as monomers, displaying higher helicase and ATPase activities than dimers and oligomers. Furthermore, monomeric BtRECQL unfolds intramolecular G-quadruplex DNA as efficiently as human RECQL and BLM helicases. These discoveries have implications for understanding endogenous RECQL oligomeric structures and their regulation. It is worth revisiting oligomeric states of the other members of the RecQ family helicases in living cells.

Published
2021
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49. DEAD-box RNA helicase Dbp2 binds to G-quadruplex nucleic acids and regulates different conformation of G-quadruplex DNA.

Author

Song, Qin-Xia, Lai, Chang-Wei, Liu, Na-Nv, Hou, Xi-Miao, and Xi, Xu-Guang

Subjects
*QUADRUPLEX nucleic acids, *RNA helicase, *NUCLEIC acids, *DNA-binding proteins, *DNA, *DNA replication
Abstract

G-quadruplexes (G4s) are important in regulating DNA replication, repair and RNA transcription through interactions with specialized proteins. Dbp2 has been identified as a G4 DNA binding protein from Saccharomyces cerevisiae cell lysates. The majority of G4 motifs in Saccharomyces cerevisiae display 5–50 nt loops, only a few have 1–2 nt loops. Human DDX5 could unfold MycG4 DNA, whether Dbp2 also participates in remodeling G4 motifs with short loops in Saccharomyces cerevisiae remains elusive. Here we find that Dbp2 prefers G-rich substrates and binds MycG4 with a high affinity. Dbp2 possesses a dual function for different conformations of MycG4, destabilizing the folded MycG4 and inducing further folding of the unfolded MycG4. Similarly, DDX5 can unfold MycG4, but it exhibits a weaker MycG4 folding-promoting activity relative to Dbp2. Furthermore, Dbp2 facilitates DNA annealing activity in the absence of ATP, suggesting that Dbp2 can work on DNA substrates and possibly participate in DNA metabolism. Our results demonstrate that Dbp2 plays an important role in regulating the folding and unfolding activities of MycG4. • Dbp2 prefers G-rich ssDNA and ssRNA substrates. • Dbp2 destabilized the folded MycG4 DNA. • Dbp2 induced further folding of the unfolded MycG4 DNA. • RNA helicase Dbp2 could anneal DNA and DNA substrates. [ABSTRACT FROM AUTHOR]

Published
2022
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50. RQC helical hairpin in Bloom's syndrome helicase regulates DNA unwinding by dynamically intercepting nascent nucleotides.

Author

Ma J, Xu C, Li J, Hou XM, Da LT, Jia Q, Huang X, Yu J, Xi X, Lu Y, and Li M

Abstract

The RecQ family of helicases are important for maintenance of genomic integrity. Although functions of constructive subdomains of this family of helicases have been extensively studied, the helical hairpin (HH) in the RecQ-C-terminal domain (RQC) has been underappreciated and remains poorly understood. Here by using single-molecule fluorescence resonance energy transfer, we found that HH in the human BLM transiently intercepts different numbers of nucleotides when it is unwinding a double-stranded DNA. Single-site mutations in HH that disrupt hydrogen bonds and/or salt bridges between DNA and HH change the DNA binding conformations and the unwinding features significantly. Our results, together with recent clinical tests that correlate single-site mutations in HH of human BLM with the phenotype of cancer-predisposing syndrome or Bloom's syndrome, implicate pivotal roles of HH in BLM's DNA unwinding activity. Similar mechanisms might also apply to other RecQ family helicases, calling for more attention to the RQC helical hairpin., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)

Published
2021
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