The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex

The MAGE (Melanoma-associated antigen) protein family members are structurally related to each other by a MAGE-homology domain comprised of 2 winged helix motifs WH/A and WH/B. This family specifically evolved in placental mammals although single homologs designated NSE3 (non-SMC element) exist in most eukaryotes. NSE3, together with its partner proteins NSE1 and NSE4 form a tight subcomplex of the structural maintenance of chromosomes SMC5–6 complex. Previously, we showed that interactions of the WH/B motif of the MAGE proteins with their NSE4/EID partners are evolutionarily conserved (including the MAGEA1-NSE4 interaction). In contrast, the interaction of the WH/A motif of NSE3 with NSE1 diverged in the MAGE paralogs. We hypothesized that the MAGE paralogs acquired new RING-finger-containing partners through their evolution and form MAGE complexes reminiscent of NSE1-NSE3-NSE4 trimers. In this work, we employed the yeast 2-hybrid system to screen a human RING-finger protein library against several MAGE baits. We identified a number of potential MAGE-RING interactions and confirmed several of them (MDM4, PCGF6, RNF166, TRAF6, TRIM8, TRIM31, TRIM41) in co-immunoprecipitation experiments. Among these MAGE-RING pairs, we chose to examine MAGEA1-TRIM31 in detail and showed that both WH/A and WH/B motifs of MAGEA1 bind to the coiled-coil domain of TRIM31 and that MAGEA1 interaction stimulates TRIM31 ubiquitin-ligase activity. In addition, TRIM31 directly binds to NSE4, suggesting the existence of a TRIM31-MAGEA1-NSE4 complex reminiscent of the NSE1-NSE3-NSE4 trimer. These results suggest that MAGEA1 functions as a co-factor of TRIM31 ubiquitin-ligase and that the TRIM31-MAGEA1-NSE4 complex may have evolved from an ancestral NSE1-NSE3-NSE4 complex.

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

In eukaryotic cells the stability and function of many proteins are regulated by the addition of ubiquitin or ubiquitin-like peptides. This process is dependent upon the sequential action of an E1-activating enzyme, an E2-conjugating enzyme, and an E3 ligase. Different combinations of these proteins confer substrate specificity and the form of protein modification. However, combinatorial preferences within ubiquitination networks remain unclear. In this study, yeast two-hybrid (Y2H) screens were combined with true homology modeling methods to generate a high-density map of human E2/E3-RING interactions. These data include 535 experimentally defined novel E2/E3-RING interactions and >1300 E2/E3-RING pairs with more favorable predicted free-energy values than the canonical UBE2L3-CBL complex. The significance of Y2H predictions was assessed by both mutagenesis and functional assays. Significantly, 74/80 (>92%) of Y2H predicted complexes were disrupted by point mutations that inhibit verified E2/E3-RING interactions, and a approximately 93% correlation was observed between Y2H data and the functional activity of E2/E3-RING complexes in vitro. Analysis of the high-density human E2/E3-RING network reveals complex combinatorial interactions and a strong potential for functional redundancy, especially within E2 families that have undergone evolutionary expansion. Finally, a one-step extended human E2/E3-RING network, containing 2644 proteins and 5087 edges, was assembled to provide a resource for future functional investigations.

The MIT domain of UBPY constitutes a CHMP binding and endosomal localization signal required for efficient epidermal growth factor receptor degradation

We have identified and characterized a Microtubule Interacting and Transport (MIT) domain at the N terminus of the deubiquitinating enzyme UBPY/USP8. In common with other MIT-containing proteins such as AMSH and VPS4, UBPY can interact with CHMP proteins, which are known to regulate endosomal sorting of ubiquitinated receptors. Comparison of binding preferences for the 11 members of the human CHMP family between the UBPY MIT domain and another ubiquitin isopeptidase, AMSH, reveals common interactions with CHMP1A and CHMP1B but a distinct selectivity of AMSH for CHMP3/VPS24, a core subunit of the ESCRT-III complex, and UBPY for CHMP7. We also show that in common with AMSH, UBPY deubiquitinating enzyme activity can be stimulated by STAM but is unresponsive to its cognate CHMPs. The UBPY MIT domain is dispensable for its catalytic activity but is essential for its localization to endosomes. This is functionally significant as an MIT-deleted UBPY mutant is unable to rescue its binding partner STAM from proteasomal degradation or reverse a block to epidermal growth factor receptor degradation imposed by small interfering RNA-mediated depletion of UBPY.

Characterization of a bifunctional catalase-peroxidase of Burkholderia cenocepacia

Isolates of Burkholderia cenocepacia express a putative haem-binding protein (molecular mass 97 kDa) that displays intrinsic peroxidase activity. Its role has been re-evaluated, and we now show that it is a bifunctional catalase-peroxidase, with activity against tetramethylbenzidine (TMB), o-dianisidine, pyrogallol, and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic) acid (ABTS). Both peroxidase and catalase activities are optimal at pH 5.5-6.0. The gene encoding this enzyme was cloned and expressed in Escherichia coli. We have named it katG because of its similarity to other katGs, including that from Burkholderia pseudomallei. It is substantially similar to a previously described catalase-peroxidase of B. cenocepacia (katA). MS analysis indicated that the initial katG translation product may be post-translationally modified in B. cenocepacia to give rise to the mature 97-kDa catalase-peroxidase.

Transmissible Burkholderia cepacia genomovar IIIa strains bind and convert monomeric iron(III) protoporphyrin IX into the mu-oxo oligomeric form

Burkholderia cepacia isolates of genomovar III are highly transmissible amongst patients with cystic fibrosis (CF) and express a 97 kDa putative haem-binding protein (HBP) [Smalley, J. W., Charalabous, P., Birss, A. J. & Hart, C. A. (2001). Clin Diagn Lab Immunol 8, 509-514]. An investigation of the interactions of iron(III) protoporphyrin IX with epidemic and non-epidemic strains of B. cepacia to determine the role of the above protein in haem acquisition and binding is reported herein. Spectrophotometric titrations of cell suspensions of genomovar IIIa strains BC7 and C5424 with iron(III) protoporphyrin IX, at pH 7.0, resulted in the depletion of Fe(III)PPIX.OH monomers and formation of the micro -oxo oligomeric species, [Fe(III)PPIX](2)O. Difference spectroscopy indicated a continuous conversion of the monomeric iron(III) protoporphyrin IX into micro -oxo oligomers. Incubations with Fe(III)PPIX.OH monomers at pH 6.5 also showed that cells could shift the equilibrium to generate the micro -oxo oligomeric form. Genomovar I strains ATCC 25416 and LMG 17997 were unable to mediate this conversion. SDS-PAGE of genomovar IIIa strains exposed to Fe(III)PPIX.OH at pH 6.5 followed by tetramethylbenzidine/H(2)O(2) staining revealed, in addition to the 97 kDa HBP, two proteins of 77 and 149 kDa located in the outer membrane which bound Fe(III)PPIX.OH monomers. These proteins were absent from the genomovar I strains. Genomovar IIIa strains BC7 and C5424 showed increased cellular binding of [Fe(III)PPIX](2)O, and as a consequence, displayed increased catalase activities compared to cells of the genomovar I isolates. It is concluded that, in addition to the putative 97 kDa HBP, B. cepacia genomovar IIIa strains express two outer-membrane proteins which function to bind and convert Fe(III)PPIX.OH monomers into the micro -oxo oligomeric form, [Fe(III)PPIX](2)O. The ability to perform this conversion at both neutral and slightly acidic pHs may enable epidemic strains to withstand attack from neutrophil-derived H(2)O(2) in the inflamed CF lung.

Detection of heme-binding proteins in epidemic strains of Burkholderia cepacia

A panel of 30 previously characterized strains representing five genomovars from the Burkholderia cepacia complex (E. Mahenthiralingam, T. Coenye, J. W. Chung, D. P. Speert, J. R. W. Govan, P. Taylor, and P. Vandamme, J. Clin. Microbiol. 38:910--913, 2000) were examined for their iron protoporphyrin IX-binding ability. These included B. cepacia genomovars I and III and B. stabilis (formerly B. cepacia genomovar IV), B. multivorans (formerly B. cepacia genomovar II), and B. vietnamiensis (formerly B. cepacia genomovar V). Cells were exposed to micro-oxo bisheme of iron protoporphyrin IX (micro-oxo dimers) and examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under nonreducing, nondenaturing conditions for the presence of heme-binding proteins using tetramethylbenzidine-H(2)O(2) staining. Seven of the 30 strains, each belonging to B. cepacia genomovar III and designated epidemic (in possessing the B. cepacia epidemic strain marker), expressed a 96- to 100-kDa heme-binding protein which was located in the outer membrane. The heme-binding protein of B. cepacia genomovar III epidemic strain C5424 bound iron(III) protoporphyrin IX in both the monomeric and micro-oxo bisheme forms. Cells of all strains grown on Columbia agar bound iron protoporphyrin IX in the micro-oxo bisheme (dimeric) form. There were no statistical differences between the five genomovars, or those possessing the heme-binding protein, in their micro-oxo bisheme-binding ability. Possession of the outer membrane heme-binding protein may be a pathogenicity trait in enabling the bacterium to withstand oxidative stresses in inflammatory exudates in the lung and may aid identification of invasive epidemic strains of B. cepacia.