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

Abstract

Using the Pseudomonas aeruginosa Genome Project as a test case, we have developed a database and submission system to facilitate a community-based approach to continually updated genome annotation (http://www.pseudomonas.com). Researchers submit proposed annotation updates through one of three web-based form options which are then subjected to review, and if accepted, entered into both the database and log file of updates with author acknowledgement. In addition, a coordinator continually reviews literature for suitable updates, as we have found such reviews to be the most efficient. Both the annotations database and updates-log database have Boolean search capability with the ability to sort results and download all data or search results as tab-delimited files. To complement this peer-reviewed genome annotation, we also provide a linked GBrowse view which displays alternate annotations. Additional tools and analyses are also integrated, including PseudoCyc, and knockout mutant information. We propose that this database system, with its focus on facilitating flexible queries of the data and providing access to both peer-reviewed annotations as well as alternate annotation information, may be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach. The source code is freely available under GNU General Public Licence.

Involvement of a Novel Efflux System in Biofilm-Specific Resistance to Antibiotics

“…We present the identification of a novel biofilm-specific efflux pump in P. aeruginosa. Our conclusions are based on the gene annotations of PA1874-1877 provided by the Pseudomonas genome database (42), confirmation of the importance of these genes in biofilm-specific resistance to antibiotics (Tables 1 and 2), and demonstration of the accumulation of tobramycin in the PA1874-1877 operon knockout mutant biofilm (Fig. 2).…”

“…1). The probability that these genes are cotranscribed is high (be- (40,42). On the basis of the published annotation, the PA1874 gene is predicted to encode a large outer membrane protein with sequence similarity to LapA of Pseudomonas putida and Bap of Staphylococcus aureus (42).…”

“…The other genes in this operon are predicted to encode an outer membrane protein with homology to an RND efflux pump outer membrane protein (PA1875), an ABC transporter protein (PA1876), and a membrane fusion protein predicted to be part of an ABC transporter (PA1877) (Fig. 1) (42). Given the predicted functions of the gene products of the PA1874-1877 operon and their phenotype in the initial genetic screen, we initiated this study in order to determine whether these gene products are important for biofilm-specific efflux of antibiotics.…”

A High-Throughput, Homogeneous, Bioluminescent Assay for Pseudomonas aeruginosa Gyrase Inhibitors and Other DNA-Damaging Agents

“…We tested the entire upstream region from each of 3 of the earliest genes in the cluster for the ability to drive luciferase production in a ciprofloxacin-regulated manner as follows. We fused 451 nt, 353 nt, and 150 nt of predicted noncoding sequence upstream from PA0612, PA0614, and PA0617, 18,19 respectively, to the P. luminescens luxCDABE operon in the site-specific integrating vector mini-Tn7-Gm-GW-LUX and integrated them into the chromosome of P. aeruginosa PAO-LAC (Fig. 1C).…”

Community annotation: Procedures, protocols, and supporting tools: Table 1.

“…Organized decentralized community annotation has been used for fungal, archaeal, and prokaryotic genomes (Stover et al 2000;Galagan et al 2002;McLeod et al 2004;Braun et al 2005;Tripathy et al 2006). In addition, several community annotation databases allow ongoing input for fungal and prokaryotic genomes (Glasner et al 2003;D'Ascenzo et al 2004;Winsor et al 2005;Aguero et al 2006;Tripathy et al 2006). Several model organism databases use the Distributed Annotation System (DAS) to facilitate data sharing (Dowell et al 2001), but the DAS system does not yet involve incorporating the community annotation data into an official set of gene models.…”