Yanji Xu

Publications (3)22.48 Total impact

• Article: Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine.

  Jing Liu, Ziqing Mei, Ningning Li, Yutao Qi, Yanji Xu, Yigong Shi, Feng Wang, Jianlin Lei, Ning Gao
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  ABSTRACT: The MecA-ClpC complex is a bacterial type II AAA+ molecular machine, responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA+ proteins are long conceived, the detailed mechanistic model remains elusive. With cryo-electron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA+ rings, and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of fashions, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two NBD rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA+ rings, and suggest that concerted actions of two AAA+ rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase, and especially, lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA+ hexamers.
  Journal of Biological Chemistry 04/2013; · 4.77 Impact Factor
• Article: Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process.

  Qiang Guo, Simon Goto, Yuling Chen, Boya Feng, Yanji Xu, Akira Muto, Hyouta Himeno, Haiteng Deng, Jianlin Lei, Ning Gao
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  ABSTRACT: Ribosome biogenesis is a tightly regulated, multi-stepped process. The assembly of ribosomal subunits is a central step of the complex biogenesis process, involving nearly 30 protein factors in vivo in bacteria. Although the assembly process has been extensively studied in vitro for over 40 years, very limited information is known for the in vivo process and specific roles of assembly factors. Such an example is ribosome maturation factor M (RimM), a factor involved in the late-stage assembly of the 30S subunit. Here, we combined quantitative mass spectrometry and cryo-electron microscopy to characterize the in vivo 30S assembly intermediates isolated from mutant Escherichia coli strains with genes for assembly factors deleted. Our compositional and structural data show that the assembly of the 3'-domain of the 30S subunit is severely delayed in these intermediates, featured with highly underrepresented 3'-domain proteins and large conformational difference compared with the mature 30S subunit. Further analysis indicates that RimM functions not only to promote the assembly of a few 3'-domain proteins but also to stabilize the rRNA tertiary structure. More importantly, this study reveals intriguing similarities and dissimilarities between the in vitro and the in vivo assembly pathways, suggesting that they are in general similar but with subtle differences.
  Nucleic Acids Research 01/2013; · 8.03 Impact Factor
• Source

  Available from: Boya Feng

  Article: Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.

  Qiang Guo, Yi Yuan, Yanji Xu, Boya Feng, Liang Liu, Kai Chen, Ming Sun, Zhixiu Yang, Jianlin Lei, Ning Gao
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  ABSTRACT: The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.
  Proceedings of the National Academy of Sciences 08/2011; 108(32):13100-5. · 9.68 Impact Factor