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Xinhua  Ji, Ph.D.

Xinhua Ji, Ph.D.

  • Center for Cancer Research
  • National Cancer Institute
  • Building 538, Room 207
  • Frederick, MD 21702
  • 301-846-5035
  • 301-846-6073
  • jix@mail.nih.gov
Center for Structural Biology

RESEARCH SUMMARY

The major focus of Dr. Ji’s basic research is the structural biology of RNA biogenesis, with an emphasis on RNA-processing proteins, especially the ribonuclease III (RNase III) enzymes. He pioneered structural analysis of RNase IIIs in complex with double-stranded RNA (dsRNA) molecules. His bacterial RNase III:dsRNA structures provided the first view of dsRNA processing, revealing structural basis for substrate selection, RNA sequence specificity, and two-magnesium(II)-ion catalysis. His yeast RNase III (Rnt1p):dsRNA structures established a double-ruler mechanism for substrate selection and provided further insights into RNA sequence specificity. Together, his structures showed that substrate selection by RNase IIIs is independent of cleavage, allowing the recognition of substrates with different structures while preserving the basic mechanism of cleavage, the two-magnesium(II)-ion catalysis, for which his structures also revealed distinct features between prokaryotes and eukaryotes. For the cleavage of each phosphodiester bond, prokaryotic catalysis involves a third magnesium(II) ion, whereas eukaryotic catalysis employs two more amino acid side chains. Dr. Ji’s post-cleavage structures determined at a stage immediately after the cleavage of scissile bonds for both prokaryotic and eukaryotic RNase IIIs provided a framework for visualizing the cleavage assembly architecture of other RNase III enzymes, including prokaryotic Mini-III and eukaryotic Dcr1, Drosha, and Dicer.

Areas of Expertise

RNA-Processing Proteins
RNase III
Structure-Based Drug Design
Folate Biosynthesis Pathway Enzymes

Publications

Selected Publications

Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation

S. Abou Elela and X. Ji
Wiley Interdisciplinary Reviews-RNA. 10: e1527, 2019. [ Journal Article ]

Structure of a Eukaryotic RNase III Postcleavage Complex Reveals a Double-Ruler Mechanism for Substrate Selection

Y.-H. Liang, M. Lavoie, M.-A. Comeau, S. Abou Elela, and X. Ji
Molecular Cell. 54: 431-444, 2014. [ Journal Article ]

RNase III: Genetics and Function; Structure and Mechanism

D.L. Court, J. Gan, Y.-H. Liang, G.X. Shaw, J.E. Tropea, N. Costantino, D.S. Waugh, and X. Ji
Annual Review of Genetics. 47: 405-431, 2013. [ Journal Article ]

Structural Insight into the Mechanism of Double-Stranded RNA Processing by Ribonuclease III

J. Gan, J.E. Tropea, B.P. Austin, D.L. Court, D.S. Waugh, and X. Ji
Cell. 124: 355-366, 2006. [ Journal Article ]

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Team

Photo of Sudhaker Dharavath, NCI-CCR-CSB-BSS
Postdoctoral Fellow (Visiting)
Sudhaker Dharavath, Ph.D.

News

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Sudhaker
Sudhaker Dharavath, Ph.D.
  • Winner of the NIH Fellows Award for Research Excellence (FARE) 2024 competition, “Cooperative unwinding of RNA duplex by DEAD-box helicase DDX3X, a new paradigm of division of labor,” Frederick, MD (2023).
  • Invited speaker, the NIH RNA Club, "Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis," Bethesda, MD (2023).
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Genbin's photo
Genbin Shi, Ph.D.
  • Recipient of the Federal Technology Transfer Award, "Structure-based development of HPPK inhibitors useful as antibacterial agents," Frederick, MD (2021).
  • Invited speaker, the 17th Annual Congress of International Drug Discovery Science & Technology, “Structure-Based Design and Synthesis of HPPK Inhibitors," Kyoto, Japan (2019).
  • Invited speaker, the International Conference on Translational Medicine, "Linked Purine Pterin HPPK Inhibitors Useful as Antibacterial Agents," San Antonio, Texas (2012).

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Gary Shaw's photo
Gary Shaw, Ph.D.
  • Recipient of the Federal Technology Transfer Award, "Structure-based development of HPPK inhibitors useful as antibacterial agents," Frederick, MD (2021).
  • Invited speaker, the Shanxi Normal University, “Structure based drug design”, Xian, China (2013).
  • Invited speaker, the Institute of Salt Lakes, Chinese Academy of Science, “Crystal structures of 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase and its reaction trajectory,” Xining, China (2007).
  • Invited speaker, the Shanxi Normal University, “Crystal structures of Glutathione S-Transferase and its detoxification mechanism,” Xian, China (2004).
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Xiaomei's photo
Xiaomei Zhou, Ph.D.
  • Featured article on the front cover of the Journal of Bacteriology, “Overproduction of a dominant mutant of the conserved Era GTPase inhibits cell division in Escherichia coli," PMID: 32817092 (2020).
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Joshua's photo
Joshua Rose, Ph.D.
  • Recipient of the Taylor & Francis Biomolecular Crystallography Poster Prize, the 70th Annual Meeting of the American Crystallographic Association, “Development of a model protein for HIV Tat structural study and drug development,” Virtual Meeting (2020).
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Praba's photo
Prabakaran Ponraj, Ph.D.
  • Representing a critical advance in coronavirus research, his article, “Structure of Severe Acute Respiratory Syndrome Coronavirus Receptor-binding Domain Complexed with Neutralizing Antibody" (PMID: 16597622), has been highlighted in a special virtue issue Coronaviruses (2020).

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Lan Jin's photo
Lan Jin, Ph.D.
  • Invited speaker, the III International Conference on Advanced Genetics, “The Molecular Mechanism of dsRNA Processing by a Bacterial Dicer,” Baltimore, MD (2019).
  • Recipient of the Poster Award, the NCI Structural Biology Retreat, “The Molecular Mechanism of dsRNA Processing by a Bacterial Dicer,” Frederick, MD (2018).
  • Invited speaker, the NIH RNA Club, "Characterization of dsRNA cleavage by the inside-out mechanism of ribonuclease III," Bethesda, MD (2016).
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Chao's photo
Chao Wang, Ph.D.

  • Featured journal article on the front cover of MedChemComm, “Design, synthesis, and anticancer activity evaluation of irreversible allosteric inhibitors of ubiquitin-conjugating enzyme Ube2g2," PMID: 30542531 (2018).

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He Song's photo
He Song, Ph.D.
 
  • Invited speaker, the NIH RNA Club, “A Stepwise Model for Double-stranded RNA Processing by a Eukaryotic Ribonuclease III,” Bethesda, MD (2016).
  • Invited speaker, the 2nd NCI Structural Biology Retreat, “RNA Recognition by hnRNP A1 and Its Regulatory Roles in MicroRNA Biogenesis,” Camp Greentop, Catoctin Mountain, MD (2016).

 

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Smita's photo
Smita Kakar, Ph.D.
  • Recipient of the Poster Award, the NCI Structural Biology Retreat, “Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies," Frederick, MD (2015). 
  • Winner of the NIH Fellows Award for Research Excellence (FARE) 2016 competition, “Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies,” Frederick, MD (2015).

 

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Yu-He's photo
Yu-He Liang, Ph.D.
 
  • Featured journal article on the front cover of Molecular Cell, “Structure of a eukaryotic RNase III post-cleavage complex reveals a double-ruler mechanism for substrate selection," PMID: 24703949 (2014).
  • Recipient of the Young Investigator Award, Young Investigator Travel Grant, and Finn World Travel Award, the 26th Annual Symposium of the Protein Society, “Structural Basis for Sequence Specificity and Product Length of Yeast Ribonuclease III,” San Diego, CA (2012).
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Jason Stagno's photo
Jason Stagno, Ph.D.
  • Winner of the NIH Fellows Award for Research Excellence (FARE) 2013 competition, “Structural Basis for NusB in the Initiation of Transcription Antitermination and dsRNA Supercoiling,” Frederick, MD (2012).
  • Recipient of the American Crystallographic Association Travel Award, the 62nd Annual Meeting of the American Crystallographic Association, “Crystal structure of a plectonemic RNA supercoil,” Boston, MA (2012).
  • Recipient of the Young Investigator Award,  the SER-CAT Annual Symposium, “Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination," Lexington, KY (2012).
  • Invited speaker, the NIH Lambda Lunch Gala, “Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination,” Frederick, MD (2011).
  • Invited speaker, the American Crystallographic Association Annual Meeting, “Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination,” New Orleans, LA (2011).
  • Invited speaker, the NCI Structural Biophysics Laboratory, “Structural analysis of NusB-NusE-BoxA complexes reveals insight into antitermination complex assembly,” Frederick, MD (2010).
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Chao Tu's photo
Chao Tu, Ph.D.
  • Winner of the NIH Fellows Award for Research Excellence (FARE) 2010 competition, “Structure of ERA in complex with the 3′ end of 16S rRNA: Implications for ribosome biogenesis,” Frederick, MD (2009).
  • Recipient of the Outstanding Scientific Presentation Award, the Spring Research Festival, “ERA: a GTP-dependent Molecular Switch Recognizes the 3’ End of 16S rRNA,” Frederick, MD (2009).
  • Plenary speaker, the 17th Annual Microbial Genomics Conference, "Structure and dynamics of Era: a GTPase-dependent molecular switch recognizing the 3' end of 16S rRNA," Rocky Gap, MD (2009).
  • Recipient of the Young Investigator Award, Young Investigator Travel Grant, and Finn World Travel Award, the 23rd Annual Symposium of the Protein Society, “Structure of ERA in complex with the 3′ end of 16S rRNA: Implications for ribosome biogenesis,” Boston, MA (2009).
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Jianhua Gan's photo
Jianhua Gan, Ph.D.
 
  • Recipient of the Poster Award, the Spring Research Festival, “The art of dsRNA processing by RNase III," Frederick, MD (2007).
  • Recipient of the Young Investigator Award, the SER-CAT Annual Symposium, “Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III," Atlanta, GA (2006).
  • Winner of the NIH Fellows Award for Research Excellence (FARE) 2007 competition, "The Mechanism of Double-Stranded RNA Cleavage by Ribonuclease III: How Dicer Dices,” Frederick, MD (2006).
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Bing Xiao's photo
Bing Xiao, Ph.D.
  • Textbook contribution: Figure 3 in her article, “Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents" (PMID: 10378268), has been reproduced in the college textbook BIOCHEMISTRY, starting from the 3rd edition, Donald Voet and Judith Voet (since 2002).
 
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Jarek Blaszczyk's photo
Jaroslaw Blaszczyk, Ph.D.
  • Featured journal article on the front cover of Structure, “Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage," PMID: 11738048 (2001).

Covers

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Overproduction of a Dominant Mutant of the Conserved Era GTPase Inhibits Cell Division in Escherichia coli

Published Date

On the cover: Fluorescence microscopic image of Escherichia coli cells overproducing Era647, a dominant negative mutant mutant of the conserved GTPase Era. After several hours of Era647 overproduction, the cells cease dividing but continue to replicate and segregate their chromosomes (stained with 4ʹ,6-diamidino-2-phenylindole [DAPI], false-colored magenta). Nonfunctional aggregates of the cell division protein FtsZ (immunostained in green) localize exclusively to chromosome-free spaces in the cytoplasm. The inset shows one such cell, magnified x2, in which the magenta and green channels are offset to highlight the mutually specific localization of DNA and FtsZ under these conditions.

Citation

X. Zhou, H. Peters III, X. Li, N. Costantino, V. kumari, G. Shi, C. Tu, T. Cameron, D. Haeusser, D. Vega, X. Ji, W. Margolin, and D.L. Court, J. Bacteriol. 202, e00342-20 (2020). PMID: 32817092; PMCID: PMC7549363.

Cover-3-margin3

Design, synthesis, and anticancer activity evaluation of irreversible allosteric inhibitors of ubiquitin-conjugating enzyme Ube2g2

Published Date

On the cover: The arrow represents an irreversible inhibitor, CW3. In the middle of the target is the thiol group of a cystine side chain at one edge of CW3-binding site in a ubiquitin-conjugating enzyme (E2), Ube2g2, the cognate E2 of the RING finger-dependent ubiquitin ligase (E3) gp78. Known as the tumor autocrine motility factor receptor, gp78 contributes to tumor progression. It interacts with Ube2g2 via two structural motifs in a stepwise, allosteric fashion. Forming a covalent bond with the cystine side chain, CW3 irreversibly blocks such allosteric interactions and thereby eliminates the tumorigenic effect of gp78. Among 19 compounds screened with the NCI 60 tumor cell lines, CW3 exhibited outstanding anticancer activities. At 10 μM, it caused >50% growth inhibition to 40% of the cell lines; at 100 μM, it showed lethiferous activity against most cell lines.

Citation

C. Wang, G. Shi, and X. Ji, MedChemComm 9, 1771-1974 (2018). PMID: 30542531; PMCID: PMC6238722.

Picking Motifs in Structured RNA

Structure of a Eukaryotic RNase III Postcleavage Complex Reveals a Double- Ruler Mechanism for Substrate Selection

Published Date

On the cover: The yeast RNase III (Rnt1p) selectively processes stem-loop RNAs with a guanine nucleotide in the second position of the capping tetraloop. In this issue, Liang et al. (pp. 431-444) show that Rnt1p recognizes the guanine nucleotide by a G clamp motif at the C terminus of dsRBD, that the guanine base is also recognized by the NTD, and that the G clamp is required for substrate binding and cleavage, whereas the NTD is required for the accuracy of processing. The cover illustrates guanine-specific substrate identification by the G clamp motif of Rnt1p as the cherry-picking hand that selectively harvests guanine-containing fruits. The hand, fingers, and cherries represent Rnt1p, G clamp, and different nucleotides in the second position of the tetraloop, respectively.

Citation

Y.-H. Liang, M. Lavoie, M.-A. Comeau, S. Abou Elela, and X. Ji, Mol. Cell 54, 431-444 (2014). PMID: 24703949; PMCID: PMC4019767.

Model of RNase III:dsRNA Complex

Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage

Published Date

On the Cover: Model of a bacterial ribonuclease III (RNase III) in complex with a product of double-stranded RNA cleavage. The protein is shown as a surface representation with positive potential indicated in blue and negative in red. The product, shown as a stick model in green, has a total length of 13 nucleotides (9+2+2) created by two overlapping strands of 11 nucleotides each. The typical 2-nucleotide 3' overhang is seen at each end of the product. 

Citation

J. Blaszczyk, J. E. Tropea, K. M. Routzahn, D. S. Waugh, M. Bubunenko, D. L. Court, and X. Ji, Structure 9, 1225-1236 (2001). PMID: 11738048.