Parkin-catalyzed Ubiquitin-Ester Transfer Is Triggered by PINK1-dependent Phosphorylation

PINK1 and PARKIN are causal genes for autosomal recessive familial Parkinsonism. PINK1 is a mitochondrial Ser/Thr kinase, whereas Parkin functions as an E3 ubiquitin ligase. Under steady-state conditions, Parkin localizes to the cytoplasm where its E3 activity is repressed. A decrease in mitochondrial membrane potential triggers Parkin E3 activity and recruits it to depolarized mitochondria for ubiquitylation of mitochondrial substrates. The molecular basis for how the E3 activity of Parkin is re-established by mitochondrial damage has yet to be determined. Here we provide in vitro biochemical evidence for ubiquitin-thioester formation on Cys-431 of recombinant Parkin. We also report that Parkin forms a ubiquitin-ester following a decrease in mitochondrial membrane potential in cells, and that this event is essential for substrate ubiquitylation. Importantly, the Parkin RING2 domain acts as a transthiolation or acyl-transferring domain rather than an E2-recruiting domain. Furthermore, formation of the ubiquitin-ester depends on PINK1 phosphorylation of Parkin Ser-65. A phosphorylation-deficient mutation completely inhibited formation of the Parkin ubiquitin-ester intermediate, whereas phosphorylation mimics, such as Ser to Glu substitution, enabled partial formation of the intermediate irrespective of Ser-65 phosphorylation. We propose that PINK1-dependent phosphorylation of Parkin leads to the ubiquitin-ester transfer reaction of the RING2 domain, and that this is an essential step in Parkin activation.     

From Asian curiosity to eruptive American pest: Megacopta cribraria (Hemiptera: Plataspidae) and prospects for its biological control

The kudzu bug or bean plataspid, Megacopta cribraria (Fabricius), is native to Asia where it appears to be widely distributed (although the taxonomy is not entirely clear), but is infrequently a pest of legumes. This bug appeared in 2009 in the southeastern United States, where it is closely associated with kudzu, Pueraria montana Lour. [Merr.] variety lobata [Willd.] Maesen & S. Almeida. However, the insect has become a consistent economic pest of soybeans, Glycine max (L.) Merr., and some other leguminous crops in areas where large numbers can build in kudzu, in addition to being a considerable nuisance in urban landscapes where kudzu occurs. The insect has remarkable capacity for movement and has spread rapidly from nine Georgia counties in 2009 to seven states in 2012. Despite being a nuisance in urban areas and a crop pest, high populations of the bug also reduce the biomass of kudzu, which is itself a seriously problematic invasive weed, complicating the status of M. cribraria in its expanded range. Extant predators and a pathogen in the US have been observed attacking kudzu bugs in the laboratory and field, but no parasitism of eggs or nymphs has been observed to date. A single record of parasitism of an adult kudzu bug by a tachinid fly is known from the US, but no other adult parasitism has been observed in the US or elsewhere. Extant enemies may eventually significantly reduce the bug’s populations, but at present native enemies appear to be insufficient for the task, and exotic enemies from the kudzu bug’s native range may offer the best possibility for effective biological control in the US. Based on the available literature, the best option for an importation biological control program appears to be the platygastrid egg parasitoid Paratelenomus saccharalis (Dodd) because of its apparent host specificity, intimate biological linkages with M. cribraria, and wide geographic distribution in the Eastern Hemisphere. Other natural enemies may eventually emerge as good candidates for importation, but at present P. saccharalis appears to be the most promising.     

Structure-Function Relationships in Unusual Nonvertebrate Globins

Based on the literature and our own results, this review summarizes the most recent state of nonvertebrate myoglobin (Mb) and hemoglobin (Hb) research, not as a general survey of the subject but as a case study. For this purpose, we have selected here four typical globins to discuss their unique structures and properties in detail. These include Aplysia myoglobin, which served as a prototype for the unusual globins lacking the distal histidine residue; midge larval hemoglobin showing a high degree of polymorphism; Tetrahymena hemoglobin evolved with a truncated structure; and yeast flavohemoglobin carrying an enigmatic two-domain structure. These proteins are not grouped by any common features other than the fact they have globin domains and heme groups. As a matter of course, various biochemical functions other than the conventional oxygen transport or storage have been proposed so far to these primitive or ancient hemoglobins or myoglobins, but the precise in vivo activity is still unclear.

In this review, special emphasis is placed on the stability properties of the heme-bound O₂. Whatever the possible roles of nonvertebrate myoglobins and hemoglobins may be (or might have been), the binding of molecular oxygen to iron(II) must be the primary event to manifest their physiological functions in vivo. However, the reversible and stable binding of O₂ to iron(II) is not a simple process, since the oxygenated form of Mb or Hb is oxidized easily to its ferric met-form with the generation of superoxide anion. The metmyoglobin or methemoglobin thus produced cannot bind molecular oxygen and is therefore physiologically inactive. In this respect, protozoan ciliate myoglobin and yeast flavohemoglobin are of particular interest in their very unique structures. Indeed, both proteins have been found to have completely different strategies for overcoming many difficulties in the reversible and stable binding of molecular oxygen, as opposed to the irreversible oxidation of heme iron(II). Such comparative studies of the stability of MbO₂ or HbO₂ are of primary importance, not only for a full understanding of the globin evolution, but also for planning new molecular designs for synthetic oxygen carriers that may be able to function in aqueous solution and at physiological temperature.     

The State of Amino Acid Residues in Alkaline Protease Produced by Bacillus No. 221

The state of amino acid residues in alkaline protease of Bacillus No. 221 and that of subtiiisin BPN’ were compared by spectrophotometric tiiration of tyrosine residues and by several reagents: β-naphtoqumone-4,6-disulfonic acid and monochlorofluoroquinone for amino groups, H₂O₂-dioxane for tryptophan, glyoxal for arginine, and tetranitromethane for tyrosine.

The reactivity of both proteases was fairly similar to those reagents.

The helix content of alkaline protease of Bacillus No. 221 (37%) was higher than that of subtilisin BPN’ (20%).

The Km and V_max of alkaline protease of Bacillus No. 221 toward ATEE and BTEE were obtained from Lineweaver-Burk plot and compared with those of α-chymotrypsin and subtiiisin BPN’.     

Enrichment of n-Alkane Assimilation-Deficient Mutants of Candida Yeast by Synergistic Effect of Nystatin and Pyrrolnitrin

In order to clarify further the relationship between the heat stability of casein micelles and the formation of soluble casein upon heating concentrated milk, the effect of formaldehyde was examined. The addition of formaldehyde up to 20 mM markedly increased the heat stability of both concentrated skim milk and concentrated whey protein-free (WPF) milk. The stabilizing effect of formaldehyde was greater for concentrated skim milk than for concentrated WPF milk. The addition of formaldehyde depressed the formation of soluble casein upon heating concentrated milk. No soluble casein was formed on the addition of 20 mM formaldehyde. It was confirmed by Sephadex G-200 gel filtration in the presence of 6.6 M urea that cross-links among the casein components were formed in heated concentrated WPF milk containing formaldehyde. These facts suggest that formaldehyde may introduce cross-links among the casein components and prevent the formation of soluble casein accompanying the release of K-casein from micelles, thus stabilizing the casein micelles.     

Purification of Cytochrome P-450«/A from n-Alkane-grown Cells of Candida maltosa,and Cloning and Nucleotide Sequencing of the Encoding Gene

When the cells of an n-alkane-assimilating yeast, Candida maltosa I AM12247, were transferred from a glucose medium to an n-alkane medium, various enzymes are induced in the endoplasmic reticulum and peroxisome. Cytochrome P-450alk, one of these enzymes in the endoplasmic reticulum, was purified after mild solubilization of the membrane, followed by a few steps of chromatography. The enzyme was characterized spectrophotometrically and its N-terminal amino acid sequence (12 residues) was determined.

Using oligonucleotide probes prepared to match parts of the N-terminal amino acid sequence and of the partial cDNA sequence of cytochrome P-450alk of C. maltosa EH 15, we isolated from a gene library of C. maltosa I AM 12247 a clone which had a gene encoding cytochrome P-450a/Ar. By nucleotide sequencing of this gene, the amino acid sequence of this enzyme was deduced. It consisted of 523 amino acids (59,838 daltons), with a non-cleavable signal sequence in the N-terminal region. The structure of this enzyme was compared with some other members of the cytochrome P-450 superfamily.     

Occurrence of γ-(Guanylureido)butyric Acid in a Red Alga,Gymnogongrus flabelliformis

From a red alga, Gymnogongrus flabelliformis, a new guanidino compound of an empirical formula, C₆H₁₂O₃N₄ was isolated. The decomposition products identified were carbon dioxide, guanidine and γ-aminobutyric acid on hydrolysis at 120°C, succinic acid and guanylurea on oxidation with potassium permanganate, and γ-aminobutyric and γ-ureidobutyric acids on hydrolysis with barium hydroxide, respectively. These results led the authors to postulate that the substance is 1-amidino-3-(3-carboxypropyl)urea or γ-(guanylureido)butyric acid.     

Phospholipid Composition of Gluconobacter cerinus

Phospholipids of Gluconobacter cerinus were investigated. The cells of this bacterium were found to have cardiolipin, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine together with three ornithine-containing lipids. Phosphatidylcholine was the most abundant of these phospholipids, and calculated at 31.0% of total phospholipids in the cells at the late logarithmic phase. The fatty acid of this lipid was composed of palmitate, stearate and vaccenate, and there were no remarkable differences in quality among fatty acids of these four phospholipids. The phosphatidylcholine was also found in other acetic acid bacteria.     

16S rRNA-based amplicon analysis of changes in the bacterial population in the lesions of papillomatous digital dermatitis in dairy cattle after topical treatment with allyl isothiocyanate

Papillomatous digital dermatitis (PDD) is a foot disease causing lameness in dairy cattle. It is regarded as a polymicrobial infection, although its etiology is not fully understood. PDD is treated by the topical or systemic administration of antibiotics such as lincomycin (LCM); however, the milk of the cows cannot be marketed during the treatment and withdrawal period due to the residual antibiotics in milk. Allyl isothiocyanate (AITC), an extract of Wasabia japonica (known as wasabi or Japanese horseradish) widely employed as a food additive, can be used as an alternative antimicrobial agent that overcomes this problem. We previously showed that AITC is as effective as LCM in PDD treatment. Here, using the samples obtained in the previous clinical study, we analyzed changes in the bacterial population in the PDD-associated microbiota after AITC treatment and compared those with that following LCM treatment by 16S ribosomal RNA (rRNA)-based amplicon analysis. Both treatments induced major changes in the bacterial population, and Treponema species, which have been regarded as the major causative agents of PDD, were efficiently eliminated by both agents. However, the AITC-treated samples exhibited higher diversity compared with pretreatment samples, but this trend was not observed for LCM treatment, probably reflecting different antibacterial activities of the two agents. Importantly, this analysis detected population changes before morphological changes in PDD lesions (clinical signs of healing) became evident, indicating that 16S rRNA-based amplicon analysis represents an efficient strategy for analyzing and monitoring the treatment efficiency of PDD as well as other polymicrobial diseases.     

Longitudinal analysis of pre- and post-treatment measurements with equal baseline assumptions in randomized trials

For continuous variables of randomized controlled trials, recently, longitudinal analysis of pre- and posttreatment measurements as bivariate responses is one of analytical methods to compare two treatment groups. Under random allocation, means and variances of pretreatment measurements are expected to be equal between groups, but covariances and posttreatment variances are not. Under random allocation with unequal covariances and posttreatment variances, we compared asymptotic variances of the treatment effect estimators in three longitudinal models. The data-generating model has equal baseline means and variances, and unequal covariances and posttreatment variances. The model with equal baseline means and unequal variance–covariance matrices has a redundant parameter. In large sample sizes, these two models keep a nominal type I error rate and have high efficiency. The model with equal baseline means and equal variance–covariance matrices wrongly assumes equal covariances and posttreatment variances. Only under equal sample sizes, this model keeps a nominal type I error rate. This model has the same high efficiency with the data-generating model under equal sample sizes. In conclusion, longitudinal analysis with equal baseline means performed well in large sample sizes. We also compared asymptotic properties of longitudinal models with those of the analysis of covariance (ANCOVA) and t-test.