Engineering of microorganisms towards recovery of rare metal ions

The bioadsorption of metal ions using microorganisms is an attractive technology for the recovery of rare metal ions as well as removal of toxic heavy metal ions from aqueous solution. In initial attempts, microorganisms with the ability to accumulate metal ions were isolated from nature and intracellular accumulation was enhanced by the overproduction of metal-binding proteins in the cytoplasm. As an alternative, the cell surface design of microorganisms by cell surface engineering is an emerging strategy for bioadsorption and recovery of metal ions. Cell surface engineering was firstly applied to the construction of a bioadsorbent to adsorb heavy metal ions for bioremediation. Cell surface adsorption of metal ions is rapid and reversible. Therefore, adsorbed metal ions can be easily recovered without cell breakage, and the bioadsorbent can be reused or regenerated. These advantages are suitable for the recovery of rare metal ions. Actually, the cell surface display of a molybdate-binding protein on yeast led to the enhanced adsorption of molybdate, one of the rare metal ions. An additional advantage is that the cell surface display system allows high-throughput screening of protein/peptide libraries owing to the direct evaluation of the displayed protein/peptide without purification and concentration. Therefore, the creation of novel metal-binding protein/peptide and engineering of microorganisms towards the recovery of rare metal ions could be simultaneously achieved.     

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.     

Facilitated beam-walking recovery during acute phase by kynurenic acid treatment in a rat model of photochemically induced thrombosis causing focal cerebral ischemia

We previously demonstrated the presence of activated areas in the non-injured contralateral sensorimotor cortex in addition to the ipsilateral sensorimotor cortex of the area surrounding a brain infarction, using a rat model of focal photochemically induced thrombosis (PIT) and functional magnetic resonance imaging. Using this model, we next applied gene expression profiling to screen key molecules upregulated in the activated area. RNA was extracted from the ipsilateral and contralateral sensorimotor cortex to the focal brain infarction and from the sham controlled cortex, and hybridized to gene-expression profiling arrays containing 1,322 neurology-related genes. Results showed that glycine receptors were upregulated in both the ipsilateral and contralateral cortex to the focal ischemic lesion. To prove the preclinical significance of upregulated glycine receptors, kynurenic acid, an endogenous antagonist to glycine receptors on neuronal cells, was administered intrathecally. As a result, the kynurenic acid significantly improved behavioral recovery within 10 days from paralysis induced by the focal PIT (p < 0.0001), as evaluated with beam walking. These results suggest that intrathecal administration of a glycine receptor antagonist may facilitate behavioral recovery during the acute phase after brain infarction.     

Generation of medaka gene knockout models by target-selected mutagenesis

We have established a reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts. A cryopreserved library of N-ethyl-N-nitrosourea (ENU) mutagenized fish was screened by high-throughput resequencing for induced point mutations. Nonsense and splice site mutations were retrieved for the Blm, Sirt1, Parkin and p53 genes and functional characterization of p53 mutants indicated a complete knockout of p53 function. The current cryopreserved resource is expected to contain knockouts for most medaka genes.     

Cribriform-morular variant of papillary thyroid carcinoma. Report of a case showing morules with peculiar nuclear clearing

BACKGROUND: There have been only 4 reported cases of cribriform-morular variant of papillary thyroid carcinoma (CMVPTC) with cytologic findings from fine needle aspiration. In these reports, the cytologic findings do not fully reflect the histologic characteristics of this entity. We report a case of CMVPTC in which a cribriform pattern without colloid and epithelial morules with peculiar nuclear clearing (PNC) were present in smears, thus fulfilling the criteria for a cytologic diagnosis of CMVPTC. Protein truncation tests for APC molecule abnormality indicated the presence of germline mutation in the patient's APC gene. CASE: A 30-year-old woman had multiple thyroid tumors. Aspiration cytology revealed a large number of round to spindle-shaped atypical-cells showing sheet-like, cribriform, follicular, whorl-like and solid, 3-dimensional arrangements. The cribriform and follicular arrangements did not contain colloid in the lumen. The powdery chromatin pattern characteristic of papillary carcinoma was not observed, but there were scattered intranuclear cytoplasmic pseudoinclusions and grooved nuclei. The nuclei of the atypical cells presenting in the whorl formations showed enlargement, thickened nuclear membranes and entirely clear contents, consistent with PNC. Hyalinelike necrotic cells were also observed in the cell clusters or in the background. Histologic and immunohistochemical findings were typical of CMVPTC. CONCLUSION: The cribriform pattern without colloid, fascicular or whorl formation of spindle cells, and morules with PNC are identifiable on cytologic smears and are sufficiently distinctive to allow a cytologic diagnosis of CMVPTC.     

Oxidative stress-induced cell death of human oral neutrophils

Polymorphonuclear leukocytes (PMN) playcrucial roles in protecting hosts against invading microbes and in thepathogenesis of inflammatory tissue injury. Although PMN migrate intomucosal layers of digestive and respiratory tracts, only limitedinformation is available of their fate and function in situ. Wepreviously reported that, unlike circulating PMN (CPMN), PMN in theoral cavity spontaneously generate superoxide radical and nitric oxide (NO) in the absence of any stimuli. When cultured for 12 h under physiological conditions, oral PMN (OPMN) showed morphological changesthat are characteristic of those of apoptosis. Upon agarose gelelectrophoresis, nuclear DNA samples isolated from OPMN revealed ladder-like profiles characteristic of nucleosomal fragmentation. L-cysteine, reduced glutathione (GSH), and herbimycin A, aprotein tyrosine kinase inhibitor, suppressed the activation ofcaspase-3 and apoptosis of OPMN. Neither thiourea, superoxidedismutase (SOD), nor catalase inhibited the activation of caspase-3 and apoptosis. Moreover,N-acetyl-Asp-Glu-Val-Asp-aldehyde (Ac-DEVD-CHO), inhibitorfor caspase-3, inhibited the fragmentation of DNA. These resultssuggested that oxidative stress and/or tyrosine-kinase-dependent pathway(s) activated caspase-3 in OPMN, thereby inducing their apoptosis.

     

(+)-Menthol and its hydroxy derivatives,novel fungal monoterpenols from the fusicoccin-producing fungi,Phomopsis amygdali F6a and Niigata 2

In our search for new fusicoccins of unique diterpene glucosides from Phomopsis amygdali, we found that a fragrant substance was formed in the early stage of fusicoccin fermentation. This fragrant constituent was isolated and identified as (+)-menthol, which is a novel fungal metabolite as the enantiomer of well-known peppermint (-)-menthol. (+)-7-Hydroxymenthol and new (+)-(6S)-hydroxymenthol were also isolated and identified as fungal metabolites. In addition, p-menthanetriol, which has been reported as the first fungal monoterpene from the fungus, was also isolated. The possible biosynthetic relationship of these metabolites is discussed.     

Nucleotide and deduced amino acid sequences of a high-molecular-mass subtilisin from an alkaliphilic Bacillus isolate

A high-molecular-mass subtilisin was found in culture broth of the alkaliphilic Bacillus sp. strain KSM-KP43. The gene encoding the enzyme (FT protease) was determined using a mixed primer designed from the N-terminal amino acid (aa) sequence of the purified enzyme. The determined nucleotide sequence of the gene consisted of a 2427-bp open reading frame (ORF) that encoded a putative prepro-peptide (152 aa) and a mature enzyme (656 aa; 68,506 Da). The deduced aa of the mature enzyme revealed a moderate homology to a subtilisin-type proteinase from Bacillus halodurans and a minor extracellular protease, Vpr, from Bacillus subtilis with 64% and 57% identity, respectively. The molecular mass of the purified recombinant FT protease was approximately 72 kDa as judged by both SDS-polyacrylamide gel electrophoresis (PAGE) and gel filtration. FT protease showed maximal activity toward glutaryl-Ala-Ala-Pro-Leu-p-nitroanilide at pH 10.5 and at 45 degrees C. The enzyme was rapidly inactivated by incubation over 45 degrees C for 15 min at both pH 7 and 10. Calcium ions were slightly protective for thermoinactivation of the enzyme.     

c-Jun N-terminal kinase negatively regulates lipopolysaccharide-induced IL-12 production in human macrophages: role of mitogen-activated protein kinase in glutathione redox regulation of IL-12 production

Although c-Jun N-terminal kinase (JNK) plays an important role in cytokine expression, its function in IL-12 production is obscure. The present study uses human macrophages to examine whether the JNK pathway is required for LPS-induced IL-12 production and defines how JNK is involved in the regulation of IL-12 production by glutathione redox, which is the balance between intracellular reduced (GSH) and oxidized glutathione (GSSG). We found that LPS induced IL-12 p40 protein and mRNA in a time- and concentration-dependent manner in PMA-treated THP-1 macrophages, and that LPS activated JNK and p38 mitogen-activated protein (MAP) kinase, but not extracellular signal-regulated kinase, in PMA-treated THP-1 cells. Inhibition of p38 MAP kinase activation using SB203580 dose dependently repressed LPS-induced IL-12 p40 production, as described. Conversely, inhibition of JNK activation using SP600125 dose dependently enhanced both LPS-induced IL-12 p40 production from THP-1 cells and p70 production from human monocytes. Furthermore, JNK antisense oligonucleotides attenuated cellular levels of JNK protein and LPS-induced JNK activation, but augmented IL-12 p40 protein production and mRNA expression. Finally, the increase in the ratio of GSH/GSSG induced by glutathione reduced form ethyl ester (GSH-OEt) dose dependently enhanced LPS-induced IL-12 p40 production in PMA-treated THP-1 cells. GSH-OEt augmented p38 MAP kinase activation, but suppressed the JNK activation induced by LPS. Our findings indicate that JNK negatively affects LPS-induced IL-12 production from human macrophages, and that glutathione redox regulates LPS-induced IL-12 production through the opposite control of JNK and p38 MAP kinase activation.