First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (DSM 50071
            <sup>T</sup>
            ), Determined Using PacBio Single-Molecule Real-Time Technology

Nakano, Kazuma; Terabayashi, Yasunobu; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

doi:10.1128/genomea.00932-15

Cited by 9 publications

(6 citation statements)

References 13 publications

(14 reference statements)

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“…Third-generation sequencing through single molecule real-time sequencing technology (SMRT) 14 15 produces considerably longer (up to 30 kb) unbiased DNA sequences without PCR amplification 16 . This technology has previously been used in de novo assembly through the PacBio RS II platform 17 18 19 20 21 .…”

mentioning

confidence: 99%

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

Gui

Zhang

et al. 2016

Sci Rep

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Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots.

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confidence: 99%

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

Gui

Zhang

et al. 2016

Sci Rep

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“…We used P. aeruginosa (CCUG241, Culture Collection University of Gothenburg) ( Nakano et al, 2015 ) (PAO1) cultured in Luria-Bertani (LB) broth. Bioluminescence assays for the detection of the production of AHLs by P. aeruginosa were conducted with two different Vibrio harveyi strains ( Henke and Bassler, 2004 ).…”

Section: Methodsmentioning

confidence: 99%

A novel phenolic derivative inhibits AHL-dependent quorum sensing signaling in Pseudomonas aeruginosa

et al. 2022

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Increasing antibiotic resistance and the decline in the pharmaceutical industry’s investments have amplified the need for novel treatments for multidrug-resistant bacteria. Quorum sensing (QS) inhibitors reduce pathogens’ virulence without selective pressure on bacteria and provide an alternative to conventional antibiotic-based therapies. P. aeruginosa uses complex QS signaling to control virulence and biofilm formation. We aimed to identify inhibitors of P. aeruginosa QS acting on acyl-homoserine lactones (AHL)-mediated circuits. Bioluminescence and qRT-PCR assays were employed to screen a library of 81 small phenolic derivatives to reduce AHL-dependent signaling. We identified GM-50 as the most active compound inhibiting the expression of AHL-regulated genes but devoid of cytotoxic activity in human epithelial cells and biocidal effects on bacteria. GM-50 reduces virulence factors such as rhamnolipids, pyocyanin, elastase secretion, and swarming motility in P. aeruginosa PAO1 laboratory strain. By molecular docking, we provide evidence that GM-50 highly interacts with RhlR. GM-50 significantly improved aztreonam-mediated biofilm disruption. Moreover, GM-50 prevents adhesion of PAO1 and inflammatory damage in the human A549 cell line and protects Galleria mellonella from PAO1-mediated killing. GM-50 significantly reduces virulence factors in 20 P. aeruginosa clinical isolates from patients with respiratory tract infections. In conclusion, GM-50 inhibits AHL-signaling, reduces virulence factors, enhances the anti-biofilm activity of aztreonam, and protects G. mellonella larvae from damage induced by P. aeruginosa. Since GM-50 is active on clinical strains, it represents a starting point for identifying and developing new phenolic derivatives acting as QS-inhibitors in P. aeruginosa infections.

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“…enterica serovar Typhimurium strain ATCC 13311PacBioChromosome4,793,29952.205420-bp identical sequence pairCP0091022014 [41]Plasmid38,45740.70CP009103 Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231 T )PacBioChromosome2,755,07232.8629 sets of >1000-bp identical sequence pairs (,063-bp maximum), tandem repeats (384 bp × 5 copies)CP0115262015 [42]Plasmid27,49030.69CP011527 Pseudomonas aeruginosa DSM 50071 T PacBioChromosome6,317,05066.525288-bp identical pair, 183 tandem repeats (246 bp × 20.7 copies)CP0120012015 [43] Clostridium sporogenes DSM 795 T PacBioChromosome4,142,99027.9886 sets of >1000-bp identical sequence pairs (4911-bp maximum), 380 tandem repeats (369 bp × 8.5 copies maximum), variable number tandem repeatCP0116632015 [44]CM-SJS/TEN-associated IKZF1 SNPs region of Japanese reference, Japanese SJS, and healthy subjectsPacBioTargeted long ampliconData not publishedData not publishedTargeted region (17 kb) of diploid genomeData not publishedThis article …”

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

“…We reported the first complete genome sequence of P. aeruginosa DSM 50071 T determined by PacBio RS II [ 43 ]. A single circular contig representing a chromosome was obtained (6,317,050 bp, average G+C content of 66.52%, and 843_coverage).…”

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

et al. 2017

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PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

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First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (DSM 50071 ^T ), Determined Using PacBio Single-Molecule Real-Time Technology

Cited by 9 publications

References 13 publications

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

A novel phenolic derivative inhibits AHL-dependent quorum sensing signaling in Pseudomonas aeruginosa

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

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First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (DSM 50071 T ), Determined Using PacBio Single-Molecule Real-Time Technology

Cited by 9 publications

References 13 publications

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

A novel phenolic derivative inhibits AHL-dependent quorum sensing signaling in Pseudomonas aeruginosa

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Contact Info

Product

Resources

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First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (DSM 50071 ^T ), Determined Using PacBio Single-Molecule Real-Time Technology