Phenotypic and genotypic characterization of esterase-producing Ureibacillus thermosphaericus isolated from an aerobic digestor of swine waste.

Eight closely related thermophilic strains were isolated from an aerobic and thermophilic treatment of swine wastes. The pleomorphic cells (short and long rods; cocci) showed peritrichous flagella, terminally swollen sporangium, and liberated spores exhibiting hairy appendages. The Gram reaction was negative for both young (4 h) and old (48 h) cultures. Several features, such as colonial morphology, growth between 35 degrees C and 65 degrees C, presence of catalase, presence of spores, and strictly aerobic metabolism (except for one strain), are similar to those found for the genus Bacillus. The inability of the strains to use sugars, except esculin, as source of carbon and energy and the whole cell fatty acid composition are similar to those found in Bacillus thermosphaericus DSM 10633. Sequence analysis of the 16S rRNA gene revealed 99.8%-99.9% identity for seven of the thermophilic strains with this species. A new genus, Ureibacillus, was recently proposed for type strain B. thermosphaericus DSM 10633 The last strain exhibits 97.8% and 97.3% identity with Ureibacillus terrenus DSM12654 and Bacillus sp. TP-84, respectively. Esterase activities were detected for all strains, and assays on p-nitrophenyl butyrate and p-nitrophenyl caprylate revealed that strains were more active on the shorter substrate.     

Creation of a thermostable NADP+-dependent d-amino acid dehydrogenase from Ureibacillus thermosphaericus strain A1 meso-diaminopimelate dehydrogenase by site-directed mutagenesis

A thermostable, NADP(+)-dependent D: -amino acid dehydrogenase (DAADH) was created from the meso-diaminopimelate dehydrogenase of Ureibacillus thermosphaericus strain A1 by introducing five point mutations into amino acid residues located in the active site. The recombinant protein, expressed in Escherichia coli, was purified to homogeneity using a two-step separation procedure and then characterized. In the presence of NADP(+), the protein catalyzed the oxidative deamination of several D: -amino acids, including D: -cyclohexylalanine, D: -isoleucine and D: -2-aminooctanoate, but not meso-diaminopimelate, confirming the creation of a NADP(+)-dependent DAADH. For the reverse reaction, the corresponding 2-oxo acids were aminated in the presence of NADPH and ammonia. In addition, the D: -amino acid dehydrogenase showed no loss of activity at 65?°C, indicating the mutant enzyme was more thermostable than its parental meso-diaminopimelate dehydrogenase.     

内消旋-二氨基庚二酸脱氢酶不对称合成非天然手性D-氨基酸的研究进展

内消旋-二氨基庚二酸脱氢酶不对称合成非天然的手性D-氨基酸是目前生物催化领域的研究热点。内消旋-二氨基庚二酸脱氢酶具有优良的立体选择性,利用其进行酶催化不对称合成光学纯的手性D-氨基酸,被广泛用于医药、食品、化妆品、精细化学品等领域。为了促进生物催化法在合成手性D-氨基酸方向的进一步发展,本文对内消旋-二氨基庚二酸脱氢酶催化合成D-氨基酸的现状进行了综述。重点介绍了Corynebacterium glutamicum、Ureibacillus thermosphaericus、Symbiobacterium thermophilum来源的内消旋-二氨基庚二酸脱氢酶在新酶的挖掘、催化性能、晶体结构解析、分子改造、功能与催化机制、合成D-氨基酸新途径等方面的研究进展,并对内消旋-二氨基庚二酸脱氢酶的未来研究方向及策略进行了展望。本综述将进一步加深人们对内消旋-二氨基庚二酸脱氢酶的认识,也为具有挑战性的生物合成任务提供信息借鉴。     

Genome Sequence of the Rice Pathogen Dickeya zeae Strain ZJU1202

Dickeya zeae is a phytopathogenic bacterium causing soft rot diseases in a wide range of economically important crops. Here we present the draft genome sequence of strain ZJU1202, which is the causal agent of rice foot rot in China. The draft genome will contribute to epidemiological and comparative genomic studies and the quarantine of this devastating phytopathogen.     

Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43

This work describes the draft genome sequence of Lactococcus garvieae DCC43. The 2.2-Mb draft genome contains 2,227 predicted protein-coding genes, among which is a region encoding the bacteriocin garvicin ML. No antibiotic resistance genes or capsule-related virulence genes were identified. Two plasmid replication regions indicate that this strain likely contains plasmids. Comparative genomics suggests that this strain displays a high degree of sequence variation from the previously sequenced L. garvieae strains.     

Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

We report here the 6.97-Mb draft genome sequence of Pseudomonas fluorescens strain NCIMB 11764, which is capable of growth on cyanide as the sole nitrogen source. The draft genome sequence allowed the discovery of several genes implicated in enzymatic cyanide turnover and provided additional information contributing to a better understanding of this organism''s unique cyanotrophic ability. This is the first sequenced genome of a cyanide-assimilating bacterium.     

Draft genome sequence of the nontoxigenic Clostridium difficile strain CD37

Here we report the draft genome sequence of Clostridium difficile strain CD37, the first nontoxigenic strain sequenced. Every sequenced strain of Clostridium difficile has been shown to contain multiple different mobile genetic elements. The draft genome sequence of strain CD37 reveals the presence of two putative conjugative transposons.     

Draft genome sequence of Nesterenkonia sp. strain F, isolated from Aran-Bidgol Salt Lake in Iran

The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp. strain F consists of a 2,812,133-bp chromosome. This study is the first to report the shotgun-sequenced draft genome of a member of the genus Nesterenkonia.     

Genome Sequence of Hydrogenophaga sp. Strain PBC, a 4-Aminobenzenesulfonate-Degrading Bacterium

Hydrogenophaga sp. strain PBC is an effective degrader of 4-aminobenzenesulfonate isolated from textile wastewater. Here we present the assembly and annotation of its genome, which may provide further insights into its metabolic potential. This is the first announcement of the draft genome sequence of a strain from the genus Hydrogenophaga.     

Genome sequence of the phototrophic betaproteobacterium Rubrivivax benzoatilyticus strain JA2T

Herein we report the draft genome sequence of a phototrophic bacterium, Rubrivivax benzoatilyticus strain JA2(T), which apparently is the first genome sequence report of a phototrophic member belonging to the class Betaproteobacteria. The unique feature of this strain is its capability to synthesize carotenoids through both spirilloxanthin and spheroidenone pathways. Strain JA2(T) produces several novel secondary metabolites, and the genome insights help in understanding the unique machinery that the strain adapted.     

Draft genome sequence of the sulfur-oxidizing bacterium "Candidatus Sulfurovum sediminum" AR, which belongs to the Epsilonproteobacteria

Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich environments. They play important roles in the global sulfur cycle on earth. Here, we present a high-quality draft genome sequence of a sulfur-oxidizing bacterium, "Candidatus Sulfurovum sediminum" strain AR, which belongs to the class Epsilonproteobacteria and dominated an enrichment culture from a marine sediment collected off Svalbard, within the Arctic Circle. Its genome contains genes for sulfur oxidation and carbon fixation. The size of the draft genome is 2.12 Mb, and the G+C content is 39.4%.     

Draft genome sequence of the virulent strain 01-B526 of the fish pathogen Aeromonas salmonicida

Aeromonas salmonicida is an important fish pathogen, mainly of salmonids. This bacterium causes a disease named furunculosis, which is particularly detrimental for the aquaculture industry. Here, we present the draft genome sequence of A. salmonicida 01-B526, a strain isolated from a brook trout that is more virulent than A. salmonicida reference strain A449, for which a genome sequence is available.     

Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly Bemisia tabaci

We report the draft genome sequence of the Rickettsia sp. strain MEAM1, which is a facultative symbiont from an invasive species of the whitefly Bemisia tabaci. The total length of the assembled genome is approximately 1.24 Mb, with 335 scaffolds and 1,247 coding sequences predicted within the genome.     

Draft Genome Sequence of an Aeromonas sp. Strain 159 Clinical Isolate That Shows Quorum-Sensing Activity

Aeromonas is a pathogenic organism that is often found to infect humans. Here we report the draft genome of a clinical isolate in Malaysia, Aeromonas sp. strain 159, which shows N-acylhomoserine lactone production. In the draft genome of strain 159, luxI and luxR homologue genes were found to be located at contig 47, and these genes are believed to be important for the quorum-sensing system present in this pathogen.     

Draft genome sequence of salt-tolerant yeast Debaryomyces hansenii var. hansenii MTCC 234

Debaryomyces hansenii is one of the most halotolerant species of yeast, and the genome sequence of D. hansenii strain CBS767 is already available. Here we report the 11.46-Mb draft genome of D. hansenii strain MTCC 234, which is even more halotolerant than strain CBS767. Comparative analysis of these sequences would definitely provide further insight into the halotolerance of this yeast.     

Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India

Rheinheimera sp. strain A13L, which has antimicrobial activity, was isolated from alkaline brackish water of the high-altitude Pangong Lake of Ladakh, India. Here we report the draft genome sequence of Rhienheimera sp. strain A13L (4,523,491 bp with a G+C content of 46.23%). The genome is predicted to contain genes for marinocine and colicin V production, which may be responsible for the antimicrobial activity of the strain.     

Draft genome sequence of an Acinetobacter genomic species 3 strain harboring a bla(NDM-1) gene

Here we report the draft genome sequence of one Acinetobacter genomic species 3 strain, D499, which harbors the bla(NDM-1) gene. The total length of the assembled genome is 4,103,824 bp, and 3,896 coding sequences (CDSs) were predicted within the genome. A previously unreported bla(NDM-1)-bearing plasmid was identified in this strain.     

Draft genome sequence of Thermus sp. strain RL, isolated from a hot water spring located atop the Himalayan ranges at Manikaran, India

Thermus sp. strain RL was isolated from a hot water spring (90°C to 98°C) at Manikaran, Himachal Pradesh, India. Here we report the draft genome sequence (20,36,600 bp) of this strain. The draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average G+C content of 68.77%.     

Complete genome sequence of Riemerella anatipestifer reference strain

Riemerella anatipestifer is an infectious pathogen causing serositis in ducks. We had the genome of the R. anatipestifer reference strain ATCC 11845 sequenced. The completed draft genome consists of one circular chromosome with 2,164,087 bp. There are 2,101 genes in the draft, and its GC content is 35.01%.     

Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones,Isolated from Malaysian Tropical Soil

Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.