Biomedical subjects

Tingting Yao

Publications and source records attributed to Tingting Yao.

9 recordsLinked to original sources

PubMed2006

Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1.

Uch37 is one of the three principal deubiquitinating enzymes (DUBs), and the only ubiquitin carboxy-terminal hydrolase (UCH)-family protease, that is associated with mammalian proteasomes. We show that Uch37 is responsible for the ubiquitin isopeptidase activity in the PA700 (19S) proteasome regulatory complex. PA700 isopeptidase disassembles Lys 48-linked polyubiquitin specifically from the distal end of the chain, a property that may be used to clear poorly ubiquitinated or unproductively bound substrates from the proteasome. To better understand Uch37 function and the mechanism responsible for its specificity, we investigated how Uch37 is recruited to proteasomes. Uch37 binds through Adrm1, a previously unrecognized orthologue of Saccharomyces cerevisiae Rpn13p, which in turn is bound to the S1 (also known as Rpn2) subunit of the 19S complex. Adrm1 (human Rpn13, hRpn13) binds the carboxy-terminal tail of Uch37, a region that is distinct from the UCH catalytic domain, which we show inhibits Uch37 activity. Following binding, Adrm1 relieves Uch37 autoinhibition, accelerating the hydrolysis of ubiquitin-7-amido-4-methylcoumarin (ubiquitin-AMC). However, neither Uch37 alone nor the Uch37-Adrm1 or Uch37-Adrm1-S1 complexes can hydrolyse di-ubiquitin efficiently; rather, incorporation into the 19S complex is required to enable processing of polyubiquitin chains.

Amino Acid Sequence↗

PubMed2006

Purification and assay of the human INO80 and SRCAP chromatin remodeling complexes.

Chromatin modifying and remodeling enzymes play critical roles in many aspects of chromosome biology including transcription, replication, recombination, and repair. Our laboratory recently identified and characterized two multisubunit human chromatin remodeling enzymes designated the INO80 and SRCAP complexes. Mechanistic studies revealed that the human INO80 complex catalyzes nucleosome sliding and the SRCAP complex catalyzes ATP-dependent exchange of histone H2A/H2B dimers containing the histone variant H2A.Z into nucleosomes. Here we describe methods for purification and assay of the INO80 and SRCAP chromatin remodeling complexes.

Adenosine Triphosphatases↗

PubMed2005

A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex.

The mammalian Tip49a and Tip49b proteins belong to an evolutionarily conserved family of AAA+ ATPases. In Saccharomyces cerevisiae, orthologs of Tip49a and Tip49b, called Rvb1 and Rvb2, respectively, are subunits of two distinct ATP-dependent chromatin remodeling complexes, SWR1 and INO80. We recently demonstrated that the mammalian Tip49a and Tip49b proteins are integral subunits of a chromatin remodeling complex bearing striking similarities to the S. cerevisiae SWR1 complex (Cai, Y., Jin, J., Florens, L., Swanson, S. K., Kusch, T., Li, B., Workman, J. L., Washburn, M. P., Conaway, R. C., and Conaway, J. W. (2005) J. Biol. Chem. 280, 13665-13670). In this report, we identify a new mammalian Tip49a- and Tip49b-containing ATP-dependent chromatin remodeling complex, which includes orthologs of 8 of the 15 subunits of the S. cerevisiae INO80 chromatin remodeling complex as well as at least five additional subunits unique to the human INO80 (hINO80) complex. Finally, we demonstrate that, similar to the yeast INO80 complex, the hINO80 complex exhibits DNA- and nucleosome-activated ATPase activity and catalyzes ATP-dependent nucleosome sliding.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2005

The mammalian Mediator complex.

The multiprotein Mediator (Med) complex is an evolutionarily conserved transcriptional regulator that plays important roles in activation and repression of RNA polymerase II transcription. Prior studies identified a set of more than twenty distinct polypeptides that compose the Saccharomyces cerevisiae Mediator. Here we discuss efforts to characterize the subunit composition and associated activities of the mammalian Med complex.

Animals↗

PubMed2005

The mammalian Mediator complex and its role in transcriptional regulation.

Mediator is an essential component of the RNA polymerase II general transcriptional machinery and plays a crucial part in the activation and repression of eukaryotic mRNA synthesis. The Saccharomyces cerevisiae Mediator was the first to be defined and is a high molecular mass complex composed of >20 distinct subunits that performs multiple activities in transcription. Recent studies have defined the subunit composition and associated activities of mammalian Mediator, and revealed a striking evolutionary conservation of Mediator structure and function from yeast to man.

Animals↗

PubMed2005

Ubiquitin-ovomucoid fusion proteins as model substrates for monitoring degradation and deubiquitination by proteasomes.

Protein degradation by 26S proteasomes requires the coordinated action of multiple binding and catalytic activities to process ubiquitinated protein substrates. For the purpose of studying conjugate degradation independently of substrate targeting and unfolding steps, we have developed substrates based on an N-terminal fusion of ubiquitin to an irreversibly unfolded protein, the 83 amino acid HA epitope-tagged first domain of chicken ovomucoid. Fluorescent labeling of the six cysteines in the ovomucoid moiety (OM) with Lucifer Yellow iodoacetamide yields UbOM(LY); the ubiquitin in the fusion protein can be extended by the addition of a K48-linked polyubiquitin chain to form Ub(n)OM(LY). UbOM(LY) derivatives provide versatile substrates to monitor both protein degradation and deubiquitination by 26S proteasomes in vitro. Comparisons of polyubiquitin conjugates of unfolded OM(LY) with folded dihydrofolate reductase (DHFR) in degradation assays can help resolve and identify the rate-limiting steps in proteasome degradation.

Animals↗

PubMed2004

Simultaneous determination of cryptotanshinone, tanshinone I and tanshinone IIA in traditional Chinese medicinal preparations containing Radix salvia miltiorrhiza by HPLC.

A reversed-phase high performance liquid chromatographic method was established for the simultaneous determination of tanshinones in five kinds of traditional Chinese medicinal preparations (TCMPs) containing Radix salvia miltiorrhiza (Chinese herbal name: Danshen). Tanshinones including cryptotanshinone, tanshinone I and tanshinone IIA were successfully separated on a Diamonsil C18 column (150 mm x 4.6 mm i.d., 5 microm). The mobile phase was a mixture of methanol, tetrahydrofuran, water and glacial acetic acid (20:35:44:1, v/v/v/v), employing isocratic elution at a flow rate of 1.0 mL/min. Detection was accomplished at 254 nm. The compounds were identified by comparing their retention times and UV spectra in the 200-400 nm range with authentic standards. Regression equations revealed good linear relationship between the peak areas of the constituents and their concentrations (correlation coefficients: 0.9998 for cryptotanshinone, 0.9999 for tanshinone I and 1.0000 for tanshinone IIA). The relative standard deviations (n=6) of retention time and peak area were less than 0.25% and 1.00%, respectively. The recoveries were between 96.2% and 102.5%. The proposed method has been successfully applied to the simultaneous determination of the tanshinones in five kinds of Chinese herbal preparations containing Danshen within 20 min.

Abietanes↗

PubMed2002

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.

The ubiquitin-specific processing protease (UBP) family of deubiquitinating enzymes plays an essential role in numerous cellular processes. HAUSP, a representative UBP, specifically deubiquitinates and hence stabilizes the tumor suppressor protein p53. Here, we report the crystal structures of the 40 kDa catalytic core domain of HAUSP in isolation and in complex with ubiquitin aldehyde. These studies reveal that the UBP deubiquitinating enzymes exhibit a conserved three-domain architecture, comprising Fingers, Palm, and Thumb. The leaving ubiquitin moiety is specifically coordinated by the Fingers, with its C terminus placed in the active site between the Palm and the Thumb. Binding by ubiquitin aldehyde induces a drastic conformational change in the active site that realigns the catalytic triad residues for catalysis.

Aldehydes↗

PubMed2002

A cryptic protease couples deubiquitination and degradation by the proteasome.

The 26S proteasome is responsible for most intracellular proteolysis in eukaryotes. Efficient substrate recognition relies on conjugation of substrates with multiple ubiquitin molecules and recognition of the polyubiquitin moiety by the 19S regulatory complex--a multisubunit assembly that is bound to either end of the cylindrical 20S proteasome core. Only unfolded proteins can pass through narrow axial channels into the central proteolytic chamber of the 20S core, so the attached polyubiquitin chain must be released to allow full translocation of the substrate polypeptide. Whereas unfolding is rate-limiting for the degradation of some substrates and appears to involve chaperone-like activities associated with the proteasome, the importance and mechanism of degradation-associated deubiquitination has remained unclear. Here we report that the POH1 (also known as Rpn11 in yeast) subunit of the 19S complex is responsible for substrate deubiquitination during proteasomal degradation. The inability to remove ubiquitin can be rate-limiting for degradation in vitro and is lethal to yeast. Unlike all other known deubiquitinating enzymes (DUBs) that are cysteine proteases, POH1 appears to be a Zn(2+)-dependent protease.

Adenosine Triphosphatases↗