Editor's choice: The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale,intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat

Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria.     

Identification of a novel hedycaryol synthase gene isolated from Camellia brevistyla flowers and floral scent of Camellia cultivars

Planta - A novel terpene synthase ( Tps ) gene isolated from Camellia brevistyla was identified as hedycaryol synthase, which was shown to be expressed specifically in flowers. Camellia plants are...     

Precipitation of sword bean proteins by heating and addition of magnesium chloride in a crude extract

Sword bean (Canavalia gladiata) seeds are a traditional food in Asian countries. In this study, we aimed to determine the optimal methods for the precipitation of sword bean proteins useful for the food development. The soaking time for sword beans was determined by comparing it with that for soybeans. Sword bean proteins were extracted from dried seeds in distilled water using novel methods. We found that most proteins could be precipitated by heating the extract at more than 90 °C. Interestingly, adding magnesium chloride to the extract at lower temperatures induced specific precipitation of a single protein with a molecular weight of approximately 48 kDa. The molecular weight and N-terminal sequence of the precipitated protein was identical to that of canavalin. These data suggested that canavalin was precipitated by the addition of magnesium chloride to the extract. Our results provide important insights into the production of processed foods from sword bean.     

Phosphorylation‐dependent Akt–Inversin interaction at the basal body of primary cilia

A primary cilium is a microtubule‐based sensory organelle that plays an important role in human development and disease. However, regulation of Akt in cilia and its role in ciliary development has not been demonstrated. Using yeast two‐hybrid screening, we demonstrate that Inversin (INVS) interacts with Akt. Mutation in the INVS gene causes nephronophthisis type II (NPHP2), an autosomal recessive chronic tubulointerstitial nephropathy. Co‐immunoprecipitation assays show that Akt interacts with INVS via the C‐terminus. In vitro kinase assays demonstrate that Akt phosphorylates INVS at amino acids 864–866 that are required not only for Akt interaction, but also for INVS dimerization. Co‐localization of INVS and phosphorylated form of Akt at the basal body is augmented by PDGF‐AA. Akt‐null MEF cells as well as siRNA‐mediated inhibition of Akt attenuated ciliary growth, which was reversed by Akt reintroduction. Mutant phosphodead‐ or NPHP2‐related truncated INVS, which lack Akt phosphorylation sites, suppress cell growth and exhibit distorted lumen formation and misalignment of spindle axis during cell division. Further studies will be required for elucidating functional interactions of Akt–INVS at the primary cilia for identifying the molecular mechanisms underlying NPHP2.     

Day workers suffering from a wider range of sleep problems are more likely to experience suicidality

Both a higher suicide rate and widespread sleep problems are serious health concerns in Japan when compared with those of other countries. We investigated the relationship between suicidal ideation and sleep problems in Japanese day workers using the 3-dimensional sleep scale (3DSS), which measures three sleep elements (phase, quality, and quantity). Data from 635 Japanese day workers (461 mens and 174 womens) were included. The 3DSS was used to assess participants’ sleep condition. Participants were classified into eight sleep types based on scores of phase, quality, and quantity: All Good Sleep, Owl (poor phase), Inefficient (poor quality), Short (poor quantity), Owl + Inefficient (poor phase and quality), Owl + Short (poor phase and quantity), Inefficient + Short (poor quality and quantity), and All Poor Sleep. We assessed participants’ suicidal ideation using question 19 of the self-rating depression scale (SDS); 119 cases (18.7 %) had ratings of 2–4 for this question and were considered to have suicidal ideation. The higher the number of sleep problems, the higher the risk of suicidal ideation compared to sleep types not indicative of problems. All Poor Sleep had the highest risk of the eight sleep types. Individuals with Owl + Short, Inefficient + Short, or All Poor Sleep had a significant risk of suicidal ideation even after adjusting for hopelessness and nightmares. Our findings suggested that sleep problems assessed by the 3DSS were related to suicidal ideation. Analysis of various aspects of sleep could be helpful for suicide prevention.

     

Chromatin binding of RCC1 during mitosis is important for its nuclear localization in interphase

RCC1, a guanine nucleotide exchange factor of the small GTPase Ran, plays various roles throughout the cell cycle. However, the functions of RCC1 in biological processes in vivo are still unclear. In particular, although RCC1 has multifunctional domains, the biological significance of each domain is unclear. To examine each domain of RCC1, we established an RCC1 conditional knockout chicken DT40 cell line and introduced various RCC1 mutants into the knockout cells. We found that nuclear reformation did not occur properly in RCC1-deficient cells and examined whether specific RCC1 mutants could rescue this phenotype. Surprisingly, we found that neither the nuclear localization signal nor the chromatin-binding domain of RCC1 is essential for its function. However, codisruption of these domains resulted in defective nuclear reformation, which was rescued by artificial nuclear localization of RCC1. Our data indicate that chromatin association of RCC1 during mitosis is crucial for its proper nuclear localization in the next interphase. Moreover, proper nuclear localization of RCC1 in interphase is essential for its function through its nucleotide exchange activity.