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Comparative Study
. 2009 Jun;7(1-2):37-46.
doi: 10.1016/S1672-0229(08)60031-5.

Bioinformatic comparison of bacterial secretomes

Catharine Song  1 , Aseem Kumar, Mazen Saleh
Affiliations
Comparative Study

Bioinformatic comparison of bacterial secretomes

Catharine Song et al. Genomics Proteomics Bioinformatics. 2009 Jun.

Abstract

The rapid increasing number of completed bacterial genomes provides a good opportunity to compare their proteomes. This study was undertaken to specifically compare and contrast their secretomes-the fraction of the proteome with predicted N-terminal signal sequences, both type I and type II. A total of 176 theoretical bacterial proteomes were examined using the ExProt program. Compared with the Gram-positives, the Gram-negative bacteria were found, on average, to contain a larger number of potential Sec-dependent sequences. In the Gram-negative bacteria but not in the others, there was a positive correlation between proteome size and secretome size, while there was no correlation between secretome size and pathogenicity. Within the Gram-negative bacteria, intracellular pathogens were found to have the smallest secretomes. However, the secretomes of certain bacteria did not fit into the observed pattern. Specifically, the secretome of Borrelia burgdoferi has an unusually large number of putative lipoproteins, and the signal peptides of mycoplasmas show closer sequence similarity to those of the Gram-negative bacteria. Our analysis also suggests that even for a theoretical minimal genome of 300 open reading frames, a fraction of this gene pool (up to a maximum of 20%) may code for proteins with Sec-dependent signal sequences.

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Figures

Figure 1
Figure 1
Secretome size in relation to proteome size in Gram-negative and Gram-positive bacteria. Proteomes are represented by the total number of ORFs, and the number of secreted proteins (the secretome) predicted by ExProt is represented as a fraction (percent) of the proteome. The value of R2 for the line fit is 0.24 for the Gram-negative and 0.21 for the Gram-positive data.
Figure 2
Figure 2
Comparison of secretome size between pathogenic (∘) and non-pathogenic (•) Gram-negative bacteria (right two columns) as well as between pathogenic (⋄) and non-pathogenic (♦) Gram-positive bacteria (left two columns). Numbers beside the columns indicate the median for each of the groups.
Figure 3
Figure 3
Secretome size in relation to proteome size in Gram-positive bacteria excluding the mycoplasmas (R2=0.08).
See this image and copyright information in PMC

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