Contribution of Lysine 11-linked Ubiquitination to MIR2-mediated Major Histocompatibility Complex Class I Internalization

The polyubiquitin chain is generated by the sequential addition of ubiquitin moieties to target molecules, a reaction between specific lysine residues that is catalyzed by E3 ubiquitin ligase. The Lys⁴⁸-linked and Lys⁶³-linked polyubiquitin chains are well established inducers of proteasome-dependent degradation and signal transduction, respectively. The concept has recently emerged that polyubiquitin chain-mediated regulation is even more complex because various types of atypical polyubiquitin chains have been discovered in vivo. Here, we demonstrate that a novel complex ubiquitin chain functions as an internalization signal for major histocompatibility complex class I (MHC I) membrane proteins in vivo. Using a tetracycline-inducible expression system and quantitative mass spectrometry, we show that the polyubiquitin chain generated by the viral E3 ubiquitin ligase of Kaposi sarcoma-associated herpesvirus, MIR2, is a Lys¹¹ and Lys⁶³ mixed-linkage chain. This novel ubiquitin chain can function as an internalization signal for MHC I through its association with epsin1, an adaptor molecule containing ubiquitin-interacting motifs.     

Two isocitrate dehydrogenases from a psychrophilic bacterium, Colwellia psychrerythraea

Two structurally different monomeric and dimeric types of isocitrate dehydrogenase (IDH; EC 1.1.1.42) isozymes were confirmed to exist in a psychrophilic bacterium, Colwellia psychrerythraea, by Western blot analysis and the genes encoding them were cloned and sequenced. Open reading frames of the genes (icd-M and icd-D) encoding the monomeric and dimeric IDHs of this bacterium, IDH-M and IDH-D, were 2,232 and 1,251 bp in length and corresponded to polypeptides composed of 743 and 416 amino acids, respectively. The deduced amino acid sequences of the IDH-M and IDH-D showed high homology with those of monomeric and dimeric IDHs from other bacteria, respectively. Although the two genes were located in tandem, icd-M then icd-D, on the chromosomal DNA, a Northern blot analysis and primer extension experiment revealed that they are transcribed independent of each other. The expression of the monomeric and dimeric IDH isozyme genes in C. maris, a psychrophilic bacterium of the same genus as C. psychrerythraea, is known to be induced by low temperature and acetate, respectively, but no such induction in the expression of the C. psychrerythraea icd-M and icd-D genes was detected. IDH-M and IDH-D overexpressed in Escherichia coli were purified and characterized. In C. psychrerythraea, the IDH-M isozyme is cold-active whereas IDH-D is mesophilic, which is similar to C. maris that contains both cold-adapted and mesophilic isozymes of IDH. Experiments with chimeric enzymes between the cold-adapted monomeric IDHs of C. psychrerythraea and C. maris (IDH-M and ICD-II, respectively) suggested that the C-terminal region of the C. maris IDH-II is involved in its catalytic activity.     

Single chain antibodies that recognize the N-glycosylation site

We aimed to identify antibodies that can recognize the Asn-Xaa-Ser/Thr(NXS/T) N-glycosylation site that guides oligosaccharyltransferase (OT) activity. We used synthetic Asn-Cys-Ser/Thr(NCS/T) tripeptides conjugated to bovine serum albumin to isolate single chain antibody fragments of a variable region (scFv) from the Griffin 1 phage antibody library. Although Ser and Thr have different side chains, the scFv proteins thus isolated bound to both NCS and NCT with Kd values of the order of 10(-6) M and accepted the substitution of the Cys residue with various amino acids, including Ala, Gly, and Val. However, these proteins recognized neither Asn-Pro-Ser/Thr nor non-NXS/T tripeptides. The scFv proteins recognized NCS/T and N-glycosylation site of mutant yeast protein disulfide isomerase when they were in their native but not denatured state. These results indicate that antibody recognition of the NXS/T motif is conformation dependent and suggest that NXS/T spontaneously adopts a specific conformation that is necessary for antibody recognition. These features are likely to correlate with the known binding specificity of OT.     

Participation of a fusogenic protein,glyceraldehyde-3-phosphate dehydrogenase,in nuclear membrane assembly

We found an autoimmune serum, K199, that strongly suppresses nuclear membrane assembly in a cell-free system involving a Xenopus egg extract. Four different antibodies that suppress nuclear assembly were affinity-purified from the serum using Xenopus egg cytosol proteins. Three proteins recognized by these antibodies were identified by partial amino acid sequencing to be glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fructose-1,6-bisphosphate aldolase, and the regulator of chromatin condensation 1. GAPDH is known to be a fusogenic protein. To verify the participation of GAPDH in nuclear membrane fusion, authentic antibodies against human and rat GAPDH were applied, and strong suppression of nuclear assembly at the nuclear membrane fusion step was observed. The nuclear assembly activity suppressed by antibodies was recovered on the addition of purified chicken GAPDH. A peptide with the sequence of amino acid residues 70-94 of GAPDH, which inhibits GAPDH-induced phospholipid vesicle fusion, inhibited nuclear assembly at the nuclear membrane fusion step. We propose that GAPDH plays a crucial role in the membrane fusion step in nuclear assembly in a Xenopus egg extract cell-free system.     

Bystander effect on cell growth stimulation in neoplastic HSGc cells induced by heavy-ion irradiation

The bystander effect on unirradiated neoplastic human salivary gland (HSGc) cells was investigated by co-culturing them with HSGc cells that had been irradiated with 290 MeV/u carbon beams of different linear energy transfer (LET) values. It was found that the plating efficiency and proliferation of the unirradiated recipient cells were increased and that these increases were related to the LET as well as the radiation dose. Exposure of HSGc cells to higher LET and higher dose was much more effective in enhancing the plating efficiency and proliferation of the unirradiated cells than exposure to lower LET and lower dose. However, when PTIO, a nitric oxide (NO)-specific scavenger, was present in the co-culture medium, the cell growth capacity of the unirradiated recipients was reduced to control level, indicating that NO is involved in the bystander response. As an oxidization product of NO, nitrite was detected in the co-culture medium and its concentration depended on the LET and dose of irradiation. Using a NO-generator sper/NO, it was verified that NO at low concentrations indeed enhanced cell proliferation. Accordingly, NO plays an important role in medium-mediated bystander effects.     

Assay method for mitochondrial sterol 27-hydroxylase with 7alpha-hydroxy-4-cholesten-3-one as a substrate in the rat liver

Mitochondrial sterol 27-hydroxylase (EC 1.14.13.15) is an important enzyme, not only in the formation of bile acids from cholesterol intermediates in the liver but also in the removal of cholesterol by side chain hydroxylation in extrahepatic tissues. The enzyme has been assayed by complicated methods using radiolabeled substrates or deuterium-labeled tracers. These methods may be inaccurate for measuring enzyme activity, because the amount of electron-transferring proteins may be insufficient for maximal velocity. To solve this problem, after solubilization of the enzyme from rat liver mitochondria with n-octyl-beta-d-glucopyranoside (OGP), we measured the enzyme activity by incubating the solubilized enzyme with saturated amounts of electron-transferring proteins. In our assay system, using 7alpha-hydroxy-4-cholesten-3-one (HCO) as a substrate, we could easily measure the product, 7alpha,27-dihydroxy-4-cholesten-3-one, with HPLC monitoring absorbance at 240 nm. The product formation was proportionate to the time up to 5 min and the protein concentration up to 0.5 mg of protein/ml. The maximal velocity of the enzyme was 1.1 nmol/min/mg of protein, which was 4- to 16-fold higher than previously reported values. A simple and accurate assay method for sterol 27-hydroxylase in rat liver mitochondria is herein described.     

Growth dynamics of Bacillus circulans colony

We have investigated the growth dynamics of Bacillus circulans colony exhibiting the knotted-branching pattern by swarming on a hard agar medium. The knotted-branching pattern consists of many circular clusters, so-called subcolonies, and their trajectories. We analysed the processes of a subcolony because they are presumably the key elements for the formation of knotted-branching pattern. It was found that a subcolony has three processes, i.e. "generation", "growth", and "migration" by microscopic and time-resolved observations. An embryonic small subcolony (child subcolony) formed around an existing subcolony (parent subcolony) grows larger and migrates away from the parent subcolony. We proposed a simple model to explain the migration and the growth processes. It is assumed that the internal part of the subcolony is unfavorable for the bacteria and that the motion of the child subcolony on the agar medium can be modeled using a frictional force. The experimental data were quantitatively analysed in order to compare with models. Our models are consistent with the experimental results on following three points: (1) the radius of a subcolony increases linearly with the incubation time, (2) a subcolony stops just after formation and then starts to migrate suddenly, and (3) the trajectory of a subcolony predicted by the model agrees with the experimental one.     

Electron spin resonance studies of radicals obtained by the reaction of alpha-tocopherol and its model compound with superoxide ion.

alpha-Tocopherol (vitamin E) and its model compound, 6-hydroxy-2,2,5,7,8-pentamethylchroman, were found to be oxidized by O2- to yield free radicals which were detected at room temperature by ESR spectroscopy. The ESR spectra of these radicals showed seven main lines with additional hyperfine structure and have the same g-values at 2.0046. Assignments of the ESR spectra were done on the basis of the spectra of the free radicals of deuterated hydroxypentamethylchroman obtained from the same reaction with O2-. The radicals observed are chromanoxyls generated by the abstraction of hydrogen from the 6-hydroxy group of tocopherols.