• Periplasmic Proteome of Yersinia pestis KIM 6+
• Staphylococcus aureus Cell Envelope-Associated Proteins
• Staphylococcus aureus Resistance to Vancomycin

The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.

The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.

Periplasmic Proteome of Yersinia pestis KIM 6+

Profiling the Periplasmic Proteome of Yersinia pestis, strain KIM6+

A comprehensive analysis of the periplasmic proteome of Yersinia pestis strain KIM6+ was performed. The KIM6+ strain of the plague bacterium Y. pestis is an avirulent derivative of the fully virulent KIM strain, which was cured of the pCD1 plasmid. The chromosomal pgm locus and the plasmids pMT1 and pPCP1 are present in KIM6+ [1]. Periplasmic fractions were isolated using the spheroplasting method by treating cells with lysozyme and EDTA that results in cell wall degradation and release of macromolecules present in the periplasmic space [2]. Low-level lysis of spheroplasts caused experimental contamination with cytoplasmic proteins. To discern true periplasmic from cytoplasmic contaminant proteins, differential 2-DE display comparing protein profiles of the periplasmic with a cytoplasmic fraction was applied. Proteins enriched in the periplasmic fraction were assigned to the periplasm (for further information, see Table). In addition, Mr and pI values of protein spots in 2-DE gels and sequence coverage at the N-termini of proteins were assessed to evaluate the absence of signal peptides in mature periplasmic proteins. This data was also compared with bioinformatically predicted signal peptide cleavage sites (for further information, see Table). In addition to all proteins experimentally assigned to the periplasm of Y. pestis (161 entries), ca. 50 cytoplasmic proteins are also displayed in the 2-DE gel profiles in Figures 1-3 and described in the Table. Spot numbers denoted in Figures 1-3 are equivalent to spot numbers listed in column 1 of the Table. In the Table, annotation data of proteins (KIM strain, protein database in NCBI [3]) and additional data describing protein traits (functions, conserved domains, subcellular assignments) are provided.

1. Fetherston, J.D. and R.D. Perry, The pigmentation locus of Yersinia pestis KIM6+ is flanked by an insertion sequence and includes the structural genes for pesticin sensitivity and HMWP2. Mol Microbiol, 1994. 13(4): p. 697-708.
2. Lucier, T.S., et al., Iron uptake and iron-repressible polypeptides in Yersinia pestis. Infect Immun, 1996. 64(8): p. 3023-31.
3. Deng, W., et al., Genome sequence of Yersinia pestis KIM. J Bacteriol, 2002. 184(16): p. 4601-11.

Figures

Figure 1A

Figure 1B

Figure 2

Figure 3A

Figure 3B

Figure 3C

Tables

Data

Periplasm Table 1 [.xls]

Periplasm Table 1 [.pdf]