scholarly journals Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation

2004 ◽  
Vol 33 (Database issue) ◽  
pp. D338-D343 ◽  
Author(s):  
G. L. Winsor
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Annotation ◽  
Community Based ◽  
Genome Database

scholarly journals Bovine Genome Database: integrated tools for genome annotation and discovery

2010 ◽  
Vol 39 (suppl_1) ◽  
pp. D830-D834 ◽  
Author(s):  
Christopher P. Childers ◽  
Justin T. Reese ◽  
Jaideep P. Sundaram ◽  
Donald C. Vile ◽  
C. Michael Dickens ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Bovine Genome ◽  
Genome Database

scholarly journals Bovine Genome Database: new annotation tools for a new reference genome

2019 ◽  
Author(s):  
Md Shamimuzzaman ◽  
Justin J Le Tourneau ◽  
Deepak R Unni ◽  
Colin M Diesh ◽  
Deborah A Triant ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Genome Annotation ◽  
Reference Genome ◽  
Gene Annotation ◽  
Bovine Genome ◽  
Data Retrieval ◽  
Genome Database ◽  
Ruminant Species ◽  
Search Tool ◽  
Efficient Data

Abstract The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

scholarly journals Complete Genome Sequence of Pseudomonas aeruginosa XN-1, Isolated from the Sputum of a Severe Pneumonia Patient

2020 ◽  
Vol 9 (36) ◽  
Author(s):  
Chen Gao ◽  
Ying Wang ◽  
Yi Zhang ◽  
Jinning Wei ◽  
Xin Cheng ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Genome Annotation ◽  
Complete Genome ◽  
Severe Pneumonia ◽  
Opportunistic Pathogen ◽  
Coding Sequences ◽  
Content Type ◽  
Pneumonia Patient

ABSTRACT Pseudomonas aeruginosa is an important opportunistic pathogen with strong virulence and an invasive nature. Here, we report the complete genome of strain XN-1, which was isolated from the sputum of a severe pneumonia patient. The complete genome consists of one chromosome with 6,340,573 bp. Genome annotation predicts 5,974 coding sequences, 64 tRNAs, and 12 rRNAs.

scholarly journals Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding

2020 ◽  
Vol 70 (2) ◽  
pp. 200-211 ◽  
Author(s):  
Yoshihiro Kawahara ◽  
Tomoko Endo ◽  
Mitsuo Omura ◽  
Yumiko Teramoto ◽  
Takeshi Itoh ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Molecular Breeding ◽  
Genomic Diversity ◽  
Caps Marker ◽  
Genome Database ◽  
Marker Information

Risk Factor Assessment for the Acquisition of Fluoroquinolone-Resistant Isolates of Pseudomonas aeruginosa in a Community-Based Hospital

1995 ◽  
Vol 1 (3) ◽  
pp. 219-222 ◽  
Author(s):  
LARRY M. BADDOUR ◽  
DEREK V. HICKS ◽  
MANDANA M. TAYIDI ◽  
SHANNON K. ROBERTS ◽  
ESTEBAN WALKER ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Risk Factor ◽  
Community Based ◽  
Risk Factor Assessment

scholarly journals fleN, a Gene That Regulates Flagellar Number in Pseudomonas aeruginosa

2000 ◽  
Vol 182 (2) ◽  
pp. 357-364 ◽  
Author(s):  
Nandini Dasgupta ◽  
Shiwani K. Arora ◽  
Reuben Ramphal
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Binding Motif ◽  
Gene Promoters ◽  
Wild Type ◽  
Electron Microscopic ◽  
Genome Database ◽  
Reading Frame ◽  
Mutant Strains ◽  
In The Wild ◽  
Flagellar Genes

ABSTRACT The single polar flagellum of Pseudomonas aeruginosaplays an important role in the pathogenesis of infection by this organism. However, regulation of the assembly of this organelle has not been delineated. In analyzing the sequence available at thePseudomonas genome database, an open reading frame (ORF), flanked by flagellar genes flhF and fliA, that coded for a protein (280 amino acids) with an ATP-binding motif at its N terminus was found. The ORF was inactivated by inserting a gentamicin cassette in P. aeruginosa PAK and PAO1. The resulting mutants were nonmotile on motility agar plates, but under a light microscope they exhibited random movement and tumbling behavior. Electron microscopic studies of the wild-type and mutant strains revealed that the mutants were multiflagellate, with three to six polar flagella per bacterium as rather than one as in the wild type, indicating that this ORF was involved in regulating the number of flagella and chemotactic motility in P. aeruginosa. The ORF was named fleN. An intact copy of fleN on a plasmid complemented the mutant by restoring motility and monoflagellate status. The β-galactosidase activities of eight flagellar operon or gene promoters in the wild-type andfleN mutant strains revealed a direct correlation between six promoters that were upregulated in the fleN mutant (fliLMNOPQ, flgBCDE, fliEFG,fliDS orf126, fleSR, and fliC) and positive regulation by FleQ, an NtrC-like transcriptional regulator for flagellar genes. Based on these results, we propose a model where FleN influences FleQ activity (directly or indirectly) in regulating flagellar number in P. aeruginosa.

scholarly journals Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mingju Hao ◽  
Wanshan Ma ◽  
Xiutao Dong ◽  
Xiaofeng Li ◽  
Fang Cheng ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Analysis ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Genomic Islands ◽  
Genome Database ◽  
Genomic Features ◽  
Wide Range ◽  
Complete Genomes

Abstract Background The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalities. Although hundreds of complete genomes of clinical P. aeruginosa isolates have been sequenced, only a few complete genomes of mucoid strains are available, limiting a comprehensive understanding of this important group of opportunistic pathogens. Herein, the complete genome of a clinically isolated mucoid strain P. aeruginosa JNQH-PA57 was sequenced and assembled using Illumina and Oxford nanopore sequencing technologies. Genomic features, phylogenetic relationships, and comparative genomics of this pathogen were comprehensively analyzed using various bioinformatics tools. A series of phenotypic and molecular-genetic tests were conducted to investigate the mechanisms of carbapenem resistance in this strain. Results Several genomic features of MDR P. aeruginosa JNQH-PA57 were identified based on the whole-genome sequencing. We found that the accessory genome of JNQH-PA57 including several prophages, genomic islands, as well as a PAPI-1 family integrative and conjugative element (ICE), mainly contributed to the larger genome of this strain (6,747,067 bp) compared to other popular P. aeruginosa strains (with an average genome size of 6,445,223 bp) listed in Pseudomonas Genome Database. Colony morphology analysis and biofilm crystal staining assay respectively demonstrated an enhanced alginate production and a thicker biofilm formation capability of JNQH-PA57. A deleted mutation at nt 424 presented in mucA gene, resulted in the upregulated expression of a sigma-factor AlgU and a GDP mannose dehydrogenase AlgD, which might explain the mucoid phenotype of this strain. As for the carbapenem resistance mechanisms, our results revealed that the interplay between impaired OprD porin, chromosomal β-lactamase OXA-488 expression, MexAB-OprM and MexXY-OprM efflux pumps overexpression, synergistically with the alginates-overproducing protective biofilm, conferred the high carbapenem resistance to P. aeruginosa JNQH-PA57. Conclusion Based on the genome analysis, we could demonstrate that the upregulated expression of algU and algD, which due to the truncation variant of MucA, might account for the mucoid phenotype of JNQH-PA57. Moreover, the resistance to carbapenem in P. aeruginosa JNQH-PA57 is multifactorial. The dataset presented in this study provided an essential genetic basis for the comprehensive cognition of the physiology, pathogenicity, and carbapenem resistance mechanisms of this clinical mucoid strain.

scholarly journals Identification of the Pseudomonas aeruginosa glmM Gene, Encoding Phosphoglucosamine Mutase

2000 ◽  
Vol 182 (16) ◽  
pp. 4453-4457 ◽  
Author(s):  
Isabel M. Tavares ◽  
Laure Jolly ◽  
Frédérique Pompeo ◽  
Jorge H. Leitão ◽  
Arsénio M. Fialho ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Open Reading Frame ◽  
Expression Vectors ◽  
Gene Encoding ◽  
Genome Database ◽  
Reading Frame ◽  
Peptidoglycan Biosynthesis ◽  
Essential Step ◽  
Residue Polypeptide

ABSTRACT A search for a potential algC homologue within thePseudomonas aeruginosa PAO1 genome database has revealed an open reading frame (ORF) of unknown function, ORF540 in contig 54 (July 1999 Pseudomonas genome release), that theoretically coded for a 445-amino-acid-residue polypeptide (I. M. Tavares, J. H. Leitão, A. M. Fialho, and I. Sá-Correia, Res. Microbiol. 150:105–116, 1999). The product of this gene is here identified as the phosphoglucosamine mutase (GlmM) which catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate, an essential step in the formation of the cell wall precursor UDP-N-acetylglucosamine. The P. aeruginosa gene has been cloned into expression vectors and shown to restore normal peptidoglycan biosynthesis and cell growth of a glmM Escherichia coli mutant strain. The GlmM enzyme from P. aeruginosa has been overproduced to high levels and purified to homogeneity in a six-histidine-tagged form. Beside its phosphoglucosamine mutase activity, the P. aeruginosaenzyme is shown to exhibit phosphomannomutase and phosphoglucomutase activities, which represent about 20 and 2% of its GlmM activity, respectively.

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