Wnt3a Promotes Hippocampal Neurogenesis by Shortening Cell Cycle Duration of Neural Progenitor Cells

The effects of Wnt signaling on neural progenitor cells have been controversial. Activation of the canonical Wnt signaling pathway either promotes neural progenitor cell proliferation or accelerates their differentiation into postmitotic neurons. This study demonstrates that activation of the Wnt signaling pathway by itself induces neural progenitor cell proliferation but does not directly affect neuronal differentiation processes. To investigate whether Wnt signaling promotes expansion and/or differentiation of neural progenitor cells in the developing hippocampus, we prepared primary mouse hippocampal progenitors and treated them with Wnt3a in a chemically defined culture medium. Wnt3a increased the total number of cells, including the numbers of Ki67⁺ proliferating cells and Tuj1⁺ differentiated neurons. This result verified that Wnt3a promoted neural progenitor cell proliferation. Meanwhile, Wnt3a did not appear to actively enhance the neuronal differentiation process itself, because (1) the ratio of Tuj1⁺ cells to the total cells, and (2) the ratio of BrdU⁺ Tuj1⁺ cells to the total BrdU⁺ cells, were both comparable between cultures with or without Wnt3a. Indeed, Wnt3a caused no significant change in either cell survival or the proportion of symmetric and asymmetric cell divisions that directly affected neuron production. We finally demonstrated that the Wnt3a treatment simply shortened cell cycle duration of neural progenitor cells by 2.9 h. The accelerated cell cycle progression without affecting the ratio of symmetric/asymmetric cell divisions explains how Wnt signaling per se leads to the expansion of both proliferative cell population and differentiated neuronal cell population.     

Leptodora kindtii: a cladoceran species highly sensitive to toxic chemicals

Leptodora kindtii is a major predator of small zooplankton in eutrophic and fish-abundant lakes. However, as it is very difficult to culture in the laboratory, information about its sensitivity to pollutants is lacking. We have successfully established a laboratory clonal culture of Leptodora. In this study, acute toxicities of an insecticide and three heavy metals to Leptodora were estimated by using laboratory-cultured individuals. Our results suggest that Leptodora is more susceptible to contamination with those chemicals than the standard test organism, Daphnia.     

Crystal structure of zinc-finger domain of Nanos and its functional implications

Nanos is an RNA-binding protein that is involved in the development and maintenance of germ cells. In combination with Pumilio, Nanos binds to the 3' untranslated region of a messenger RNA and represses its translation. Nanos has two conserved Cys-Cys-His-Cys zinc-finger motifs that are indispensable for its function. In this study, we have determined the crystal structure of the zinc-finger domain of zebrafish Nanos, for the first time revealing that Nanos adopts a novel zinc-finger structure. In addition, Nanos has a conserved basic surface that is directly involved in RNA binding. Our results provide the structural basis for further studies to clarify Nanos function.     

Essential in Vivo Roles of the C-type Lectin Receptor CLEC-2: EMBRYONIC/NEONATAL LETHALITY OF CLEC-2-DEFICIENT MICE BY BLOOD/LYMPHATIC MISCONNECTIONS AND IMPAIRED THROMBUS FORMATION OF CLEC-2-DEFICIENT PLATELETS*?

CLEC-2 has been described recently as playing crucial roles in thrombosis/hemostasis, tumor metastasis, and lymphangiogenesis. The snake venom rhodocytin is known as a strong platelet activator, and we have shown that this effect is mediated by CLEC-2 (Suzuki-Inoue, K., Fuller, G. L., García, A., Eble, J. A., Pöhlmann, S., Inoue, O., Gartner, T. K., Hughan, S. C., Pearce, A. C., Laing, G. D., Theakston, R. D., Schweighoffer, E., Zitzmann, N., Morita, T., Tybulewicz, V. L., Ozaki, Y., and Watson, S. P. (2006) Blood 107, 542–549). Podoplanin, which is expressed on the surface of tumor cells, is an endogenous ligand for CLEC-2 and facilitates tumor metastasis by inducing platelet aggregation. Mice deficient in podoplanin, which is also expressed on the surface of lymphatic endothelial cells, show abnormal patterns of lymphatic vessel formation. In this study, we report on the generation and phenotype of CLEC-2-deficient mice. These mice are lethal at the embryonic/neonatal stages associated with disorganized and blood-filled lymphatic vessels and severe edema. Moreover, by transplantation of fetal liver cells from Clec-2^−/− or Clec-2^+/+ embryos, we were able to demonstrate that CLEC-2 is involved in thrombus stabilization in vitro and in vivo, possibly through homophilic interactions without apparent increase in bleeding tendency. We propose that CLEC-2 could be an ideal novel target protein for an anti-platelet drug, which inhibits pathological thrombus formation but not physiological hemostasis.     

Deficiency of Chemokine Receptor CCR1 Causes Osteopenia Due to Impaired Functions of Osteoclasts and Osteoblasts

Chemokines are characterized by the homing activity of leukocytes to targeted inflammation sites. Recent research indicates that chemokines play more divergent roles in various phases of pathogenesis as well as immune reactions. The chemokine receptor, CCR1, and its ligands are thought to be involved in inflammatory bone destruction, but their physiological roles in the bone metabolism in vivo have not yet been elucidated. In the present study, we investigated the roles of CCR1 in bone metabolism using CCR1-deficient mice. Ccr1^−/− mice have fewer and thinner trabecular bones and low mineral bone density in cancellous bones. The lack of CCR1 affects the differentiation and function of osteoblasts. Runx2, Atf4, Osteopontin, and Osteonectin were significantly up-regulated in Ccr1^−/− mice despite sustained expression of Osterix and reduced expression of Osteocalcin, suggesting a lower potential for differentiation into mature osteoblasts. In addition, mineralized nodule formation was markedly disrupted in cultured osteoblastic cells isolated from Ccr1^−/− mice. Osteoclastogenesis induced from cultured Ccr1^−/− bone marrow cells yielded fewer and smaller osteoclasts due to the abrogated cell-fusion. Ccr1^−/− osteoclasts exerted no osteolytic activity concomitant with reduced expressions of Rank and its downstream targets, implying that the defective osteoclastogenesis is involved in the bone phenotype in Ccr1^−/− mice. The co-culture of wild-type osteoclast precursors with Ccr1^−/− osteoblasts failed to facilitate osteoclastogenesis. This finding is most likely due to a reduction in Rankl expression. These observations suggest that the axis of CCR1 and its ligands are likely to be involved in cross-talk between osteoclasts and osteoblasts by modulating the RANK-RANKL-mediated interaction.     

Identification of Novel Acetyltransferase Activity on the Thermostable Protein ST0452 from Sulfolobus tokodaii Strain 7

A 401-residue-long protein, ST0452, has been identified from a thermophilic archaeon, Sulfolobus tokodaii strain 7, as a glucose-1-phosphate thymidylyltransferase (Glc-1-P TTase) homolog with a 170-residue-long extra C-terminus portion. Functional analyses of the ST0452 protein have confirmed that the protein possessed dual sugar-1-phosphate nucleotidylyltransferase (sugar-1-P NTase) activities. The 24 repeats of a signature motif sequence which has been found in bacterial acetyltransferases, (L/I/V)-(G/A/E/D)-XX-(S/T/A/V)-X, were detected at the C terminus of the ST0452 protein. This observation prompted our group to investigate the acetyltransferase activity of the ST0452 protein. Detection of the release of coenzyme A (CoA) from acetyl-CoA and the production of UDP-N-acetyl-d-glucosamine (UDP-GlcNAc) from glucosamine-1-phosphate (GlcN-1-P) and UTP in the presence of the ST0452 protein revealed that this protein possesses the GlcN-1-P-specific acetyltransferase activity. In addition, analyses of substrate specificity showed that acetyltransferase activity of the ST0452 protein is capable of catalyzing the change of galactosamine-1-phosphate (GalN-1-P) to N-acetyl-d-galactosamine-1-phosphate (GalNAc-1-P) as well as GlcN-1-P and that its sugar-1-P NTase activity is capable of producing UDP-GalNAc from GalNAc-1-P and UTP. This is the first report of a thermostable bifunctional enzyme with GalN-1-P acetyltransferase and GalNAc-1-P uridyltransferase activities. The observation reveals that the bacteria-type UDP-GlcNAc biosynthetic pathway from fructose-6-phospate is utilized in this archaeon and represents a novel biosynthetic pathway for producing UDP-GalNAc from GalN-1-P in this microorganism.The nucleotide-sugar molecule is used as a substrate for the construction of the polymer structure of carbohydrates and as a starting material for the biosynthesis of modified-sugar-nucleotide conjugates; for example, TDP-glucose is the starting material for the construction of TDP-rhamnose (25). Several sugar-1-phosphate nucleotidylyltransferases (sugar-1-P NTases) involved in some biosynthetic reactions, such as glucose-1-phosphate thymidylyltransferase (Glc-1-P TTase), N-acetyl-d-glucosamine-1-phosphate uridyltransferase (GlcNAc-1-P UTase), and mannose-1-phosphate guanylyltransferase, have been identified from many bacteria, including pathogens, as well as from eukaryotes (5, 10, 11, 17, 25, 27, 29). However, only limited information on the archaeal enzyme with sugar-1-P NTase activity has been obtained.Our group has previously reported the first thermostable enzyme with sugar-1-P NTase activity from an acidothermophilic archaeon, Sulfolobus tokodaii strain 7 (31). The sugar-1-P NTase activity of the ST0452 protein, which was primarily identified by sequence similarity with the Escherichia coli RmlA protein, indicated the utilization of Glc-1-P and GlcNAc-1-P as a sugar-1-P substrate and all deoxynucleoside triphosphates (dNTPs) and UTP as nucleoside triphosphate (NTP) substrates, but glucosamine-1-phosphate (GlcN-1-P) was not utilized as a substrate. It was also reported that the GlcNAc-1-P UTase activity of the ST0452 protein was improved by the introduction of site-directed mutagenesis (30).The identification of GlcNAc-1-P UTase activity on the ST0452 protein suggests that the protein may have activities and features similar to those of the bacterial GlmU enzyme (19). However, the ST0452 protein exhibits only a low level of sequence identity (less than 20% identity) with E. coli GlmU (data not shown). The phylogenetic analysis of the ST0452 protein and related proteins indicates that the ST0452 protein and homologous proteins form a group independent of other related enzymes identified as RmlA or GlmU (Fig. ​(Fig.11).Open in a separate windowFIG. 1.Phylogenetic relationship among bacterial RmlA, bacterial GlmU, and ST0452 proteins. The phylogenetic positions of two bacterial RmlA proteins, two bacterial GlmU proteins, three archaeal ST0452 homologous proteins, and the ST0452 protein were determined with the ClustalW algorithm provided by the DNA Database of Japan (DDBJ). Evolutionary distance is shown by the horizontal bar. E_RmlA, S_RmlA, E_GlmU, S_GlmU, MJ1101, SSO0745, Saci0619, and ST0452 indicate the RmlA proteins from Escherichia coli (Uniprot accession number A1AHV8) and Streptococcus mutans (Uniprot accession number {"type":"entrez-protein","attrs":{"text":"P95778","term_id":"2500162"}}P95778), the GlmU proteins from E. coli (Uniprot accession number {"type":"entrez-protein","attrs":{"text":"A8A6J2","term_id":"166990434"}}A8A6J2) and Streptococcus pneumoniae (Uniprot accession number {"type":"entrez-protein","attrs":{"text":"Q04KU2","term_id":"122278758"}}Q04KU2), the MJ1101 protein from Methanocaldococcus janaschii (Uniprot accession number {"type":"entrez-protein","attrs":{"text":"Q58501","term_id":"38258700"}}Q58501), the SSO0745 protein from Sulfolobus solfataricus (Uniprot accession number Q9UXD3), the Saci0619 protein from Sulfolobus acidocaldarius (Uniprot accession number Q4JB18), and the ST0452 protein used in this work, respectively.In spite of the low level of sequence similarity of the ST0452 protein with the bacterial GlmU, GlcNAc-1-P UTase activity was detected on the protein. Twenty-four incomplete repeats of the hexapeptide repeat motif sequences with the left-handed parallel beta-helix (LβH) structural feature (22) (L/I/V)-(G/A/E/D)-XX-(S/T/A/V)-X were also detected at the C-terminal region of the ST0452 protein (Fig. ​(Fig.2).2). This motif sequence has been identified in enzymes with acetyl- or acyltransferase (22), succinyltransferase (1), and carbonic anhydrase (12) activities. Sequences with this motif are detected at the C terminus of all three archaea-related genes shown in Fig. ​Fig.1,1, Saci0619, MJ1101, and SSO0745, but there is no information on the function or activities of Saci0619 and SSO0745. For MJ1101, activities were detected but detailed analysis was not performed (18). Therefore, we hypothesized that the acetyltransferase activity was also present on the ST0452 protein.Open in a separate windowFIG. 2.Repeat motif sequences identified at the C-terminal region of the ST0452 protein. The repeat motif sequence predicted at the C-terminal region from Val235 to Gly394 of the ST0452 protein, (L/I/V)-(G/A/E/D)-XX-(S/T/A/V)-X, is shown. The conserved residues at the first, second, and fifth positions within the motif sequences detected are indicated by boxes, boldface letters, and shaded boxes, respectively. Three repeat motif sequence units, which are predicted to make up one turn of the helix structure, are shown in each row. The residues from Val341 to Phe358, the sequence of which is different from the motif consensus sequence, are shown in parentheses.In this work, we analyzed the acetyltransferase activity of the recombinant ST0452 protein and confirmed the GlcN-1-P acetylation activity by two independent experiments, i.e., detection of conversion from acetyl coenzyme A (acetyl-CoA) to CoA and construction of UDP-N-acetyl-d-glucosamine (UDP-GlcNAc). The substrate specificity analyses indicated that the ST0452 protein was capable of utilizing galactosamine-1-phosphate (GalN-1-P) as the substrate for the acetyltransferase activity and N-acetyl-d-galactosamine-1-phosphate (GalNAc-1-P) as the substrate for the sugar-1-P NTase activity of the recombinant ST0452 protein. This is the first report describing a bifunctional enzyme with both GlcN-1-P and GalN-1-P acetyltransferase activities plus GlcNAc-1-P and GalNAc-1-P NTase activities and a high degree of stability; therefore, industrial applications of this enzyme are expected.     

Genome Sequence of the Cellulosome-Producing Mesophilic Organism Clostridium cellulovorans 743B

Clostridium cellulovorans 743B was isolated from a wood chip pile and is an anaerobic and mesophilic spore-forming bacterium. This organism degrades native substrates in soft biomass such as corn fiber and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Here we report the genome sequence of C. cellulovorans 743B.The biotechnological potential of polysaccharolytic enzymes has resulted in the isolation and characterization of a large number of anaerobic, Gram-positive, spore-forming bacteria, the majority of which have been allocated to the genus Clostridium. Among clostridia, the cellulosomes produced by Clostridium species are particularly designed for efficient degradation of plant cell wall polysaccharides. The component parts of the multicomponent complex are integrated by virtue of a unique family of integrating modules, the cohesins and the dockerins, whose distribution and specificity dictate the overall cellulosome architecture (3). The cellulosome system in Clostridium cellulovorans 743B (ATCC 35296) has been studied extensively for the last 20 years and has resulted in providing basic information about mesophilic cellulosomes. This organism was isolated from a wood chip pile and is an anaerobic spore-forming bacterium whose optimal growth temperature is 37°C (9). It has the ability to utilize cellulose, xylan, pectin, cellobiose, glucose, fructose, galactose, and mannose as carbon sources for growth. Its fermentation products include H₂, CO₂, acetate, butyrate, formate, lactate, and ethanol. When it is grown in the presence of cellulose, electron micrographs have shown that large protuberances are present on its cell surface (4), while small or no protuberances are evident when cells are grown in the presence of glucose or cellobiose (5).We sequenced a total length of 101,749,598 bp and analyzed 381,514 reads by Genome Sequencer FLX 454./Roche sequencing (8) (GS-FLX version) to highly oversample the genome (20× coverage) and generated 123,892 paired-end sequence tags, to enable the assembly of all tags using the GS De Novo Assembler version 1.1.03.24 (Roche Diagnostics) and the Genome Analyzer II and sequencing kit 36-Cycle Run (Illumina). Finally, we assembled 30 scaffolds (sets of 601 ordered and oriented contigs; total length of 5,123,527 bp) to generate approximately 5.1 Mbp of nearly contiguous Clostridium botulinum E3 strain Alaska E43 (accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_010723","term_id":"188587536","term_text":"NC_010723"}}NC_010723) complete genome sequence. We analyzed a number of predicted genes included in the C. cellulovorans genome using CRITICA (version 1.05b) (2) and Glimmer 2 (version 2.10) (6) to find regions in proteins with known functions. We annotated and classified according to Gene Ontology (GO) (1). In silico Molecular Cloning Genomic Edition ver. 3.0.26 software (In Silico Biology, Co., Ltd., Japan) was used for individual genomic analysis.The C. cellulovorans 743B (ATCC 35296) genome consists of 5,123,527 bp. A total of 4,220 polypeptide-encoding open reading frames (ORFs) were identified using CRITICA, while 4,297 ORFs were identified using Glimmer 2. The number of ORFs identical between CRITICA and Glimmer 2 was 2,773. Sixty-three tRNAs and 33 anticodons were also identified using tRNAscan-SE (7). In comparison of the genome sizes among cellulosomal clostridia such as Clostridium cellulolyticum H10 (4.07 Mbp) (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"CP001348","term_id":"219997787","term_text":"CP001348"}}CP001348) and Clostridium thermocellum ATCC 27405 (3.84 Mbp) (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"CP000568","term_id":"125712750","term_text":"CP000568"}}CP000568), the C. cellulovorans genome was over 1 Mbp larger than the other genomes. Moreover, the number of predicted genes (4,220 by CRITICA) in the C. cellulovorans genome was the largest among them. On the other hand, the G+C content in C. cellulovorans was 31.1%, similar to that (30.9%) in Clostridium acetobutylicum ATCC 824 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE001437","term_id":"25168256","term_text":"AE001437"}}AE001437), while the G+C contents in C. cellulolyticum and C. thermocellum were 37.7% and 39.0%, respectively.A protein BLAST search against the database of clusters of orthologous groups (COGs) of proteins indicated that 4,171 genes were annotated by 4,220 predicted coding sequences using CRITICA while 4,098 genes were identified by 4,297 predicted coding sequences using Glimmer 2. On the other hand, a protein BLAST search against the NCBI nr database indicated that 4,184 genes were annotated by 4,220 predicted coding sequences using CRITICA while 4,071 genes were identified by 4,297 predicted coding sequences using Glimmer 2. Interestingly, 57 cellulosomal genes were found in the C. cellulovorans genome and coded for not only carbohydrate-active enzymes but also lipases, peptidases, and proteinase inhibitors. Moreover, two novel genes encoding a scaffolding protein were found in the genome. Thus, by examining genome sequences from multiple Clostridium species, comparative genomics offers new insight into genome evolution and the way in which natural selection molds functional DNA sequence evolution. Our analysis, coupled with the genome sequence data, will provide a road map for constructing enhanced cellulosome-producing Clostridium strains for industrial applications such as biofuel production.