A Substrate Preference for the Rough Endoplasmic Reticulum Resident Protein FKBP22 during Collagen Biosynthesis

The biosynthesis of collagens occurs in the rough endoplasmic reticulum and requires a large numbers of molecular chaperones, foldases, and post-translational modification enzymes. Collagens contain a large number of proline residues that are post-translationally modified to 3-hydroxyproline or 4-hydroxyproline, and the rate-limiting step in formation of the triple helix is the cis-trans isomerization of peptidyl-proline bonds. This step is catalyzed by peptidyl-prolyl cis-trans isomerases. There are seven peptidyl-prolyl cis-trans isomerases in the rER, and so far, two of these enzymes, cyclophilin B and FKBP65, have been shown to be involved in collagen biosynthesis. The absence of either cyclophilin B or FKBP65 leads to a recessive form of osteogenesis imperfecta. The absence of FKBP22 leads to a kyphoscoliotic type of Ehlers-Danlos syndrome (EDS), and this type of EDS is classified as EDS type VI, which can also be caused by a deficiency in lysyl-hydroxylase 1. However, the lack of FKBP22 shows a wider spectrum of clinical phenotypes than the absence of lysyl-hydroxylase 1 and additionally includes myopathy, hearing loss, and aortic rupture. Here we show that FKBP22 catalyzes the folding of type III collagen and interacts with type III collagen, type VI collagen, and type X collagen, but not with type I collagen, type II collagen, or type V collagen. These restrictive interactions might help explain the broader phenotype observed in patients that lack FKBP22.     

Vitronectin Induces Phosphorylation of Ezrin/Radixin/Moesin Actin-binding Proteins through Binding to Its Novel Neuronal Receptor Telencephalin

Vitronectin (VN) is an extracellular matrix protein abundantly present in blood and a wide variety of tissues and plays important roles in a number of biological phenomena mainly through its binding to αV integrins. However, its definite function in the brain remains largely unknown. Here we report the identification of telencephalin (TLCN/ICAM-5) as a novel VN receptor on neuronal dendrites. VN strongly binds to TLCN, a unique neuronal member of the ICAM family, which is specifically expressed on dendrites of spiny neurons in the mammalian telencephalon. VN-coated microbeads induce the formation of phagocytic cup-like plasma membrane protrusions on dendrites of cultured hippocampal neurons and trigger the activation of TLCN-dependent intracellular signaling cascade including the phosphorylation of ezrin/radixin/moesin actin-binding proteins and recruitment of F-actin and phosphatidylinositol 4,5-bisphosphate for morphological transformation of the dendritic protrusions. These results suggest that the extracellular matrix molecule VN and its neuronal receptor TLCN play a pivotal role in the phosphorylation of ezrin/radixin/moesin proteins and the formation of phagocytic cup-like structures on neuronal dendrites.     

Ranging patterns of Japanese macaques in the coniferous forest of Yakushima: Home range shift and travel rate

Ranging is one of the most important behavioral adaptations for coping with seasonally fluctuating food and thermal conditions. We studied the ranging patterns, in particular home range shift and travel rate of Japanese macaques (Macaca fuscata) in the coniferous forest of Yakushima by tracking a group for 17 months. We also supplemented our data with records collected every August over a 5-year annual census. The macaque group used the eastern part of their home range from May to September and the western part during the rest of the year. The eastern part of the home range was largely primary forest in the national park, and the altitude was higher than in the western part. When they used the western part, the macaques ate more herbs and fruits from small-sized trees, the availability of which was higher in the logged forest. This east–west home range shift occurred repeatedly over multiple years. A neighboring group occupied the western part of the focal group's home range in summer, which the focal group did not use in that season. Both temperature and diet affected seasonal changes in the monthly average travel rate. Animals need more energy for thermoregulation when the temperature is low, so the macaques decreased their ranging efforts to save energy at times of low temperature. They increased their ranging distance to eat fungi, since their encounters with this food would increase with the total distance walked. They also increased their travel rate when eating flowers, which had lower food patch (tree) density than other foods such as fruits. The data supported the hypothesis that the macaques capitalize on habitat heterogeneity in a seasonally fluctuating habitat by shifting their home range and modifying their travel rate.     

An approach towards artificial quinone pools by use of photo- and redox-active dendritic molecules

Molecules with one porphyrin and multiple quinone groups are described. The molecules are based on dendritic frameworks, with the quinone groups attached at the “internal” positions and the porphyrin attached at the focal point, leading to a characteristic layer architecture. When irradiated with visible light in the presence of 4-tert-butylthiophenol, the quinones were converted to quinols. Such a behavior mimics the function of quinone pools in photosynthesis.     

Analysis of changes of insect-plant ratio-improvement of key-factor analysis for evaluating bottom-up effects in insect population dynamics

A revised key-factor analysis was presented for analyzing the temporal changes in the ratio of insect absolute number to plant resource. Ten data sets for 5 insect species were then analyzed. In this key-factor analysis, the key factor is defined as the factor contributing highly to between-year variation inR _r , the log rate of the inter-year change of the insect-plant ratio. The yearly change of plant resource was handled as a separate factor, expressed byr _pl , log ratio of plant resource in yearn to plant resource in yearn+1. The following was revealed: 1) In 7 of the 10 data sets examined,r _pl influenced variations ofR _r ; in particular in 3 casesr _pl was the main key factor. 2) Generation-to-generation fluctuations of absolute insect densities showed density dependence in 4 cases, while those of insect-plant ratios, in 8 cases. 3) The Royama model or a linear model, explained well the relationship between log insect-plant ratio (X _r ) andR _r and the relationship betweenX _r and log yearly change rate of absolute insect density (R _abs ). However, in the 7 cases in whichr _pl was a critical factor for variations ofR _r , with, increase ofX _r ,R _r showed a steeper, decrease around the equilibrium point (the point for whichR _r is 0) thanR _abs . This occurred becauser _pl tended to be negatively correlated withX _r . Consequently, in two casesX _r fluctuated cyclicly or chaotically although without the changes in plant resource, fluctuations ofX _r would be damped oscillations approaching equilibrium.     

Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean

Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B₁₂-independent MetE and B₁₂-dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.     

CNDO/2 calculation of the relative stability of poly(γ-hydroxy-l-proline)

The CNDO/2 method using the tight-binding approximation for polymers was applied to poly(γ-hydroxy-l-prolines) (PHP). The calculations were carried out for PHPs which have the same backbone structure as those of poly(l-proline I) (Pro-I) and poly(l-proline II)(Pro-II). The results obtained show the preferred orientation of the OH group at the γ-position, which is in agreement with the experimental results. The calculations were also carried out for the B form (PHP-B). The conformational stability between the A form (PHP-A) and PHP-B was explained by using the calculated results in connection with the previous experimental and theoretical treatments. From the analysis of the total energy, the dominant stabilizing factors for the two forms are discussed.     

High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus

Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the products of defective translation, to recycle the tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its activity is essential for bacterial viability. Here, we have determined the crystal structure of Pth from Thermus thermophilus (TtPth) at 1.00 Å resolution. This is the first structure of a Pth from a thermophilic bacterium and the highest resolution Pth structure reported so far. The present atomic resolution data enabled the calculation of anisotropic displacement parameters for all atoms, which revealed the directionality of the fluctuations of key regions for the substrate recognition. Comparisons between TtPth and mesophilic bacterial Pths revealed that their structures are similar overall. However, the structures of the N- and C-terminal, loop-helix α4, and helix α6 regions are different. In addition, the helix α1 to strand β4 region of TtPth is remarkably different from those of the mesophilic bacterial Pths, because this region is 9 or 10 amino acid residues shorter than those of the mesophilic bacterial Pths. This shortening seems to contribute to the thermostability of TtPth. To further understand the determinants for the thermostability of TtPth, we compared various structural factors of TtPth with those of mesophilic bacterial Pths. The data suggest that the decreases in accessible surface area and thermolabile amino acid residues, and the increases in ion pairs, hydrogen bonds, and proline residues cooperatively contribute to the thermostability of TtPth.     

Purification and properties of mangano-superoxide dismutase from a strain of alkaliphilic Bacillus

A mangano-superoxide dismutase (EC 1.15.1.1) was purified to homogeneity from a strain of alkaliphilic Bacillus for the first time. The purified protein, with an isoelectric point of pH 4.5, had a molecular mass of approximately 50 kDa and consisted of two identical subunits (25 kDa). The N-terminal amino acid sequence was Ala-Tyr-Lys-Leu-Pro-Glu-Leu-Pro-Tyr-Ala-Ala-Asn-Ala-Leu-Glu-Pro-His-Ile-Asp-Glu-Ala. The optimum pH and temperature for the reaction were 7.5 and 35°C, respectively. The properties of the superoxide dismutase were compared with those of the enzyme from thermophilic Bacillus stearothermophilus. Received: September 3, 1996 / Accepted: October 4, 1996