Biology Reference
In-Depth Information
Proteome of
P. gingivalis
in a Three Species Community
To begin to investigate the mechanisms of adaptation of
P. gingivalis
to a commu-
nity environment, the proteome of non-growing
P. gingivalis
cells incorporated into a
community with
F. nucleatum
and
S. gordonii
was compared to the proteome of non-
growing
P. gingivalis
cells alone. The expressed proteome of
P. gingivalis
in a com-
munity consisted of 1,156 annotated gene products detected qualitatively. Based on
spectral counting, 271 gene products showed evidence of relative abundance change at
a
q
-value of 0.01: 109 proteins at higher relative abundance and 162 at lower relative
abundance, using
P. gingivalis
alone as a reference state. Spectral counting is a con-
servative measure of protein abundance change that tends to generate low FDRs [24-
26] but that often suffers from high false negative rates (FNRs) in studies of the kind
described here [27]. Less conservative calculations based on intensity measurements
[27] found 458 gene products with evidence of relative abundance change at a
q
-value
of 0.01: 72 proteins at higher relative abundance, and 386 proteins at lower relative
abundance. Spectral counting and protein intensity measurements were examined for
common trends. Trends tended to be consistent across both biological replicates, but
the magnitudes of the abundance ratios showed significant scatter, similar to most
published expression data at either the mRNA or protein level [27]. In most cases
the abundance ratio trends were the same, using both quantitation methods, although
not necessarily significantly so. In only eight cases were the spectral counting trend
and summed intensity trend significantly in opposite directions for the same protein
(PGN 0329, 0501, 1094, 1341, 1637, 1733, 2065). The integrated relative abundance
trends found 403 gene products with evidence of lower relative abundance change and
89 at higher relative abundance. For purposes of examining the totals for combined
trends, if an abundance change was called as significant in one measurement, it was
considered significant for the above combined totals only if the ratio of the other mea-
surement showed the same direction of abundance change, with a log
2
ratio of ± 0.1
or greater regardless of the
q
-value in the second measurement. The experimental data
for differential protein abundance are shown in Figure 2 as a pseudo M/A plot [28, 29]
with a locally weighted scatterplot smoothing (LOWESS) curve fit [30]. The same
data are plotted in Figure 3 as open reading frames according to PGN numbers from
the ATCC 33277 genome annotation [31].
To assess global sampling depth, average spectral counts were calculated by sum-
ming all spectral count numbers for all
P. gingivalis
proteins in the FileMaker script
output described under Materials and Methods and dividing by the total number of
P. gingivalis
proteins in that fi le. The average redundant spectral count number for
peptides unique to a given ORF for
P. gingivalis
alone was 80, for
P. gingivalis
in the
community it was 64. The lower number of counts observed for
P. gingivalis
proteins
in the community is consistent with the added sampling demands placed on the ana-
lytical system by sequence overlaps in the proteomes of all three microbes and thus the
smaller number of unique proteolytic fragments predicted.
