Isolation, draft genome sequence, and identification of subsp. CCS26.

To isolate the useful strain for fermentation to produce bioactive compounds, we screened oligotrophic bacteria, and then strain CCS26 was isolated from leaf soil collected in Japan. This strain was capable of growth on low-nutrient medium. To elucidate the taxonomy of strain CCS26, we determined the 16S rRNA gene and draft genome sequences, respectively.

Isolation and draft genome sequence of sp CCS19.

Here, we describe the isolation and draft genome sequence of sp. CCS19. sp.

Crystal structure of metagenomic β-glycosidase MeBglD2 in complex with various saccharides.

Metagenomic MeBglD2 is a glycoside hydrolase family 1 (GH1) β-glycosidase that has β-glucosidase, β-fucosidase, and β-galactosidase activities, and is highly activated in the presence of monosaccharides and disaccharides. The β-glucosidase activity of MeBglD2 increases in a cellobiose concentration-dependent manner and is not inhibited by a high concentration of D-glucose or cellobiose. Previously, we solved the crystal structure of MeBglD2 and designed a thermostable mutant; however, the mechanism of substrate recognition of MeBglD2 remains poorly understood.

Structural basis for the catalytic mechanism of the glycoside hydrolase family 3 isoprimeverose-producing oligoxyloglucan hydrolase from Aspergillus oryzae.

Aspergillus oryzae isoprimeverose-producing oligoxyloglucan hydrolase (IpeA) releases isoprimeverose units (α-d-xylopyranosyl-(1→6)-d-glucose) from the non-reducing end of xyloglucan oligosaccharides and belongs to glycoside hydrolase family 3. In this paper, we report the X-ray crystal structure of the IpeA complexed with a xyloglucan oligosaccharide, (XXXG: Glc Xyl ). Trp515 of IpeA plays a critical role in XXXG recognition at positive subsites.

Draft Genome Sequence of Klebsiella pneumoniae subsp. CCI2, Isolated from Leaf Soil.

Klebsiella pneumoniae subsp. CCI2 was isolated from leaf soil collected in Hiroshima Prefecture, Japan. The draft genome sequence comprises 78 contigs and contains 5,075,115 bp with a G+C content of 57.

Draft Genome Sequence of CCA3, Isolated from Leaf Soil.

CCA3 was isolated from leaf soil collected in Hiroshima Prefecture, Japan. Here, we report the draft genome sequence of CCA3. The draft genome sequence of CCA3 consists of 29 contigs of 4,425,100 bp, with a GC content of 54.

Paenibacillus glycanilyticus subsp. hiroshimensis subsp. nov., isolated from leaf soil collected in Japan.

Strain CCI5, an oligotrophic bacterium, was isolated from leaf soil collected in Japan. Strain CCI5 grew at temperatures between 25 °C and 43 °C (optimum temperature, 40 °C) and at pHs between 6.0 and 10.

Draft Genome Sequence of sp. AS-1, a Potential Eurytrophic Recombination Host.

Strain AS-1 was isolated from laboratory-scale activated sludge collected in Japan. This strain not only grows on rich medium, including R2A medium, but also forms colonies on medium lacking organic matter other than agar (water agar), indicating it could be used as a eurytrophic recombinant host in material production processes. Here, we present a draft genome sequence of sp.

Isolation, draft genome sequencing and identification of CCI9.

Strain CCI9, which was isolated from leaf soil collected in Japan, was capable of growth on poor-nutrient medium, at temperatures of 10°C to 45°C, at pHs of 4.5 to 10, and in the presence of 7.0% NaCl.

Characterization of an NAD(P)-dependent meso-diaminopimelate dehydrogenase from Thermosyntropha lipolytica.

meso-Diaminopimelate dehydrogenase (meso-DAPDH) catalyzes the reversible NADP-dependent oxidative deamination of meso-2,6-diaminopimelate (meso-DAP) to produce l-2-amino-6-oxopimelate. meso-DAPDH is divided into two major clusters, types I and II, based on substrate specificity and structural characteristic. Here, we describe a novel type II meso-DAPDH from Thermosyntropha lipolytica (TlDAPDH).

Performance of Burkholderia multivorans CCA53 for ethyl red degradation.

The discharge of industrial dyes and their breakdown products are often environmentally harmful. Here, we describe a biodegradation method using Burkholderia multivorans CCA53, which exhibits a capacity to degrade azo dyes, particularly ethyl red. Under the optimized culture conditions, 100 μM ethyl red was degraded more than 99% after incubation for 8 h.

Identification and functional characterization of NAD(P) -dependent meso-diaminopimelate dehydrogenase from Numidum massiliense.

meso-Diaminopimelate dehydrogenase (meso-DAPDH) catalyzes the reversible NADP -dependent oxidative deamination of meso-2,6-diaminopimelate (meso-DAP) to produce l-2-amino-6-oxopimelate. Moreover, d-amino acid dehydrogenase (d-AADHs) derived from protein-engineered meso-DAPDH is useful for one-step synthesis of d-amino acids with high optical purity. Here, we report the identification and functional characterization of a novel NAD(P) -dependent meso-DAPDH from Numidum massiliense (NmDAPDH).

Deinococcus kurensis sp. nov., isolated from pond water collected in Japan.

An aerobic, oligotrophic, Gram-positive, non-sporulating, motile, rod-shaped, palladium-leaching bacterial strain, Deinococcus sp. KR-1, was previously isolated from pond water collected in Japan. This strain grew at 10 °C to 40 °C (optimum 30 °C), at pH 4.

Draft genome sequence of sp KR-1, a potential strain for palladium-leaching.

Strain KR-1 was isolated from pond water collected in Japan. Because this strain was capable of adsorbing palladium particles in sterilized water, strain KR-1 will be a useful biocatalyst for palladium-leaching from metal waste. Here we present a draft genome sequence of sp.

IoGAS1, a GPI-Anchored Protein Derived from Issatchenkia orientalis, Confers Tolerance of Saccharomyces cerevisiae to Multiple Acids.

Construction of acid-tolerant strains of Saccharomyces cerevisiae is required for various bioproduction processes. We previously isolated the gene IoGAS1 from multiple stress-tolerant Issatchenkia orientalis as a gene conferring sulfuric acid resistance in S. cerevisiae, but its acid tolerance was only investigated using sulfuric acid.

Enterobacter oligotrophica sp. nov., a novel oligotroph isolated from leaf soil.

A novel oligotrophic bacterium, designated strain CCA6, was isolated from leaf soil collected in Japan. Cells of the strain were found to be a Gram-negative, non-sporulating, motile, rod-shaped bacterium. Strain CCA6 grew at 10-45°C (optimum 20°C) and pH 4.

Pseudomonas humi sp. nov., isolated from leaf soil.

An aerobic, Gram-negative, non-sporulating, motile, rod-shaped and lignin-degrading bacterial strain, Pseudomonas sp. CCA1, was isolated from leaf soil collected in Japan. This strain grew at 20-45 °C (optimum 20 °C), at pH 5.

Artificial Thermostable D-Amino Acid Dehydrogenase: Creation and Application.

Many kinds of NAD(P)-dependent L-amino acid dehydrogenases have been so far found and effectively used for synthesis of L-amino acids and their analogs, and for their sensing. By contrast, similar biotechnological use of D-amino acid dehydrogenase (D-AADH) has not been achieved because useful D-AADH has not been found from natural resources. Recently, using protein engineering methods, an NADP-dependent D-AADH was created from -diaminopimelate dehydrogenase (-DAPDH).

Production of acetoin from hydrothermally pretreated oil mesocarp fiber using metabolically engineered Escherichia coli in a bioreactor system.

Acetoin is used in the biochemical, chemical and pharmaceutical industries. Several effective methods for acetoin production from petroleum-based substrates have been developed, but they all have an environmental impact and do not meet sustainability criteria. Here we describe a simple and efficient method for acetoin production from oil palm mesocarp fiber hydrolysate using engineered Escherichia coli.

Complete Genome Sequence of A1, a Thermophilic Bacillus Isolated from Compost.

A1 was isolated from compost collected in Munakata City, Fukuoka Prefecture, Japan. Here, we report the first complete genome sequence of The complete genome of this strain consists of 3,488,104 bp with a GC content of 36.3% and comprises 3,362 predicted coding sequences.

Identification and characterization of Burkholderia multivorans CCA53.

Objective: A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp.

Production of d-lactate using a pyruvate-producing Escherichia coli strain.

To generate an organism capable of producing d-lactate, NAD-dependent d-lactate dehydrogenase was expressed in our pyruvate-producing strain, Escherichia coli strain LAFCPCPt-accBC-aceE. After determining the optimal culture conditions for d-lactate production, 18.4 mM d-lactate was produced from biomass-based medium without supplemental mineral or nitrogen sources.

Structure-Based Engineering of an Artificially Generated NADP-Dependent d-Amino Acid Dehydrogenase.

A stable NADP-dependent d-amino acid dehydrogenase (DAADH) was recently created from -diaminopimelate dehydrogenase through site-directed mutagenesis. To produce a novel DAADH mutant with different substrate specificity, the crystal structure of apo-DAADH was determined at a resolution of 1.78 Å, and the amino acid residues responsible for the substrate specificity were evaluated using additional site-directed mutagenesis.

Draft Genome Sequence of Pseudomonas sp. Strain CCA1, Isolated from Leaf Soil.

Pseudomonas sp. strain CCA1 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain.

Pyruvate production using engineered Escherichia coli.

Pyruvate plays an essential role in the central carbon metabolism of multiple organisms and is used as a raw material in the chemical, biochemical and pharmaceutical industries. To meet demand, large amounts of pyruvate are produced through fermentation processes. Here we describe a simple and efficient method for producing pyruvate in Escherichia coli.