Nuclear Genome Assembly of the Microalga Nannochloropsis salina CCMP1776.

Nannochloropsis salina is a halotolerant, high-lipid-producing microalga that is being explored as a biofuel production species. Here, we report an improved high-quality draft assembly and annotation for the nuclear genome of N. salina strain CCMP1776.

Dual Active Site in the Endolytic Transglycosylase gp144 of Bacteriophage phiKZ.

Lytic transglycosylases are abundant peptidoglycan lysing enzymes that degrade the heteropolymers of bacterial cell walls in metabolic processes or in the course of a bacteriophage infection. The conventional catalytic mechanism of transglycosylases involves only the Glu or Asp residue. Endolysin gp144 of Pseudomonas aeruginosa bacteriophage phiKZ belongs to the family of Gram-negative transglycosylases with a modular composition and C-terminal location of the catalytic domain. Glu115 of gp144 performs the predicted role of a catalytic residue. However, replacement of this residue does not completely eliminate the activity of the mutant protein. Site-directed mutagenesis has revealed the participation of Tyr197 in the catalytic mechanism, as well as the presence of a second active site involving Glu178 and Tyr147. The existence of the dual active site was supported by computer modeling and monitoring of the molecular dynamics of the changes in the conformation and surface charge distribution as a consequence of point mutations.

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC 49132.

The pleomorphic swarming bacilli of the genus Proteus are common human gut commensal organisms but also the causative agents of recurrent urinary tract infections and bacteremia. We sequenced and assembled the 3.99-Mbp genome of Proteus mirabilis ATCC 7002 (accession no. JOVJ00000000) and the 3.97-Mbp genome of Proteus vulgaris ATCC 49132 (accession no. JPIX00000000), both of which are commonly used reference strains.

Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01.

The Enterobacteriaceae are environmental and enteric microbes. We sequenced the genomes of two Enterobacter reference strains, E. aerogenes CDC 6003-71 and E. cloacae CDC 442-68, as well as one near neighbor used as an exclusionary reference for diagnostics, Pantoea agglomerans CDC UA0804-01. The genome sizes range from 4.72 to 5.55 Mbp and have G+C contents from 54.6 to 55.1%.

Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672.

A member of the normal human gut microflora, Providencia stuartii is of clinical interest due to its role in nosocomial infections of the urinary tract and because it readily acquires antibiotic resistance. Here, we present the complete genome of P. stuartii strain ATCC 33672, consisting of a 4.28-Mbp chromosome and a 48.9-kbp plasmid.

Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ.

Salmonella enterica constitutes a group of enteric pathogens with a broad host range, including humans, reptiles, and birds. S. enterica subsp. enterica is a common cause of inflammatory diarrhea in humans. We present the draft genome of S. enterica subsp. enterica serovar Enteritidis strain SEJ, including a 59-kbp plasmid.

Draft Genome Assembly of Neisseria lactamica Type Strain A7515.

We present the scaffolded genome assembly of Neisseria lactamica type strain A7515 (ATCC 23970) as submitted to NCBI under accession no. JOVI00000000. This type strain of the lactose-fermenting Neisseria species is often used in quality control testing and intra-genus phylogenetic analyses. The assembly includes four contigs placed into a single scaffold.

Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687.

Ochrobactrum anthropi is an occasional cause of nosocomial infections; however, interest in the organism lies in its phylogenetic proximity to the genus Brucella. Here, we present the 4.9-Mb finished genome of Ochrobactrum anthropi ATCC 49687, most commonly used as an exclusionary reference organism.

Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain.

Enterococcus faecalis is a nonmotile Gram-positive coccus, found both as a commensal organism in healthy humans and animals and as a causative agent of multiple diseases, in particular endocarditis. We sequenced the genome of E. faecalis ATCC 29212, a commonly used reference strain in laboratory studies, to complete "finished" annotated assembly (3 Mb).

Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference Strain.

We present the complete genome assembly of Escherichia coli ATCC 25922 as submitted to NCBI under accession no. CP009072. This strain was originally isolated from a clinical sample in Seattle, Washington (1946), and is often used in quality control testing. The assembled genome is 5.20 Mb (50.4% G+C content) and includes two plasmids.

Draft Genome Assembly of Pseudomonas aeruginosa Quality Control Reference Strain Boston 41501.

We present the scaffolded genome assembly of Pseudomonas aeruginosa Boston 41501, now publicly available in GenBank (JOVK00000000) in 10 contigs placed into a single scaffold. The 6.82-Mbp genome contains 66.1% G+C content and 6,295 coding sequences, including type 4 pilus and type 3 secretion system production genes.

Complete Genome Assembly of Streptococcus pyogenes ATCC 19615, a Group A ß-Hemolytic Reference Strain.

We present the complete genome assembly of Streptococcus pyogenes ATCC 19615 (Rosenbach) as submitted to GenBank under accession number CP008926. This group A nonmotile ß-hemolytic clinical isolate is used for quality control in a variety of commercially available tests. The assembled genome is 1.84 Mb (38.5% G+C content) and contains 1,788 coding regions.

Whole-genome sequences of 24 Brucella strains.

Brucella species are intracellular zoonotic pathogens which cause, among other pathologies, increased rates of abortion in ruminants. Human infections are generally associated with exposure to contaminated and unpasteurized dairy products; however Brucellae have been developed as bioweapons. Here we present 17 complete and 7 scaffolded genome assemblies of Brucella strains.

[Molecular mechanisms of transcription through a nuclesome by RNA polymerase II].

The Pol II-type mechanism is conserved from yeast to human. After initiation of transcription, Pol II can be paused within the early transcribed region of a gene. Then Pol II overcomes the initial nucleosomal barrier, and efficiently proceeds through chromatin. At low- to moderate-level transcription progression of Pol II is characterized by displacement/exchange of only H2A/H2B dimer(s) and hexasome survival, likely mediated through formation of small intranucleosomal DNA loops. This mechanism helps to preserve the "histone" code during transcription. As the transcription rate is increased, the distance between transcribing Pol II complexes becomes shorter, and trailing Pol II complexes may encounter the hexasome formed after previous transcription round, before the H2A/H2B dimer re-binds to the hexasome. In this case an unstable intermediate with a smaller number of DNA-histone contacts is formed, resulting in eviction of the histone hexamer from DNA in vitro; therefore here all core histones are evicted/exchanged in vivo. Various protein factors and histone chaperones are involved in chromatin transcription by Pol II in vivo.

[The properties of the Pseudomonas aeruginosa bacteriophage phiPMG1].

The properties of the isolated Pseudomonas aeruginosa bacteriophage phiPMG1 include the lytic infection cycle, and the formation of a broad halo (semi-transparent zone) around the plaques. We consider phiPMG1 as a potential member of therapeutic cocktails of live phages, and as a source of peptidoglycan and lipopolysaccharide degrading enzymes. Partial sequencing of phiPMG1 genome has revealed high similarity with known temperate P. aeruginosa phage D3. An open reading frame encoding lytic transglycosilase was identified in the genome. This enzyme PMG MUR was obtained in recombinant form, and its activity and substrate specificity has been studied.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1.

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California.

Xylella fastidiosa is a Gram-negative plant-pathogenic bacterium causing many economically important diseases, including almond leaf scorch disease (ALSD) in California. Genome information greatly facilitates research on this nutritionally fastidious organism. Here we report the complete genome sequences of two ALSD strains of this bacterium, M12 and M23.

DNA sequencing using differential extension with nucleotide subsets (DENS).

Here we describe template directed enzymatic synthesis of unique primers, avoiding the chemical synthesis step in primer walking. We have termed this conceptually new technique DENS (differential extension with nucleotide subsets). DENS works by selectively extending a short primer, making it a long one at the intended site only. The procedure starts with a limited initial extension of the primer (at 20-30 degrees C) in the presence of only two out of the four possible dNTPs. The primer is extended by 6-9 bases or longer at the intended priming site, which is deliberately selected, (as is the two-dNTP set), to maximize the extension length. The subsequent termination reaction at 60-65 degrees C then accepts the extended primer at the intended site, but not at alternative sites, where the initial extension (if any) is generally much shorter. DENS allows the use of primers as long as 8mers (degenerate in two positions) which prime much more strongly than modular primers involving 5-7mers and which (unlike the latter) can be used with thermostable polymerases, thus allowing cycle-sequencing with dye-terminators compatible with Taq DNA polymerase, as well as making double-stranded DNA sequencing more robust.