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Computational Molecular Biology
10
Continuing Table 5
Dicots
Monocots
Mosses
Pfam ID
At
Pt
Sl
Bd Osj
Zm Pp Sm
Pfam name
Pfam discription
pfam00314 15 22 15 25 44 24 3 9 Thaumatin
Thaumatin family
pfam00067 12 31 20 31 74 13 6 21 p450
Cytochrome P450
pfam02298 12 20 14 30 36 28 9 9 Cu_bind_like
Plastocyanin-like domain
pfam04398 12 15 9 17 23 14 2 1 DUF538
Protein of unknown function
pfam02469 10 16 10 14 20 15 1 0 Fasciclin
Fasciclin domain
pfam01453 7
30 9 3
5 2 1 20 B_lectin
D-mannose binding lectin
pfam00197 7
22 15 2
3 0 0 0 Kunitz_legume Trypsin and protease inhibitor
pfam00069 6
22 11 11 47 3 1 4 Pkinase
Protein kinase domain
pfam07714 6
19 4 3 24 4 0 1 Pkinase_Tyr
Protein tyrosine kinase
pfam00251 6
5
4 7 26 5 0 1 Glyco_hydro_32N Glycosyl hydrolases family 32
pfam13947 4
23 2 6 32 7 0 0 GUB_WAK_bind Wall-associated receptor kinase
pfam00704 2
14 8 13 31 10 1 10 Glyco_hydro_18 Glycosyl hydrolases family 18
pfam01559 0
0
0 0
0 30 0 0 Zein
Zein seed storage protein
pfam13352 0
0
0 0
0 0 61 0 DUF4100
Protein of unknown function (DUF4100)
Note:
At
:
Arabidopsis thaliana
;
Pt
:
Populus trichocarpa
;
Sl
:
Solanum lycopersicum
; Monocots -
Bd
:
Brachypodium distachyon
;
Osj
:
Oryza sativa (subsp. japonica)
;
Zm
:
Zea mays.
Mosses - Physcomitrella patens (subsp. patens);
Sm
:
Selaginella moellendorffii.
A
complete list is in Supplementary Table 1
The functionalities of secreted proteins were further
analyzed using rpsBLAST to search against Pfam in
the Conserved Domain Database (CDD)
(Marchler-Bauer et al., 2009). The results of Pfam
analysis for a species having 20 or more members in a
Pfam were summarized in Table 5. A complete list of
Pfams can be found in Supplementary Table 1. The
detailed analysis of molecular functions in secretomes
searching Pfam revealed the difference in protein
families among different species, including both
variations in the number of members in a given Pfam
and species specific Pfams (Table 5). Noticeably there
were twice as many secreted peroxidase proteins in
rice compared to Arabidopsis (Table 5). Plant
peroxidases have multiple tissue-specific functions
e.g., removal of hydrogen peroxide from chloroplasts
and cytosol, oxidation of toxic compounds,
biosynthesis of the cell wall, and defense responses
towards wounding (Sottomayor and Barceló, 2004).
The glycosyl hydrolases are suggested to have
valuable applications in modifying plant cell wall
architecture and in the development
and
characterization of new bioenergy and feedstocks
(Lopez-Casado et al., 2008). The rice secretome
consists of 31 members of Glyco-hydro-18 (GH18)
and 26 of GH32N while only two GH18 and 6
GH32N were identified in the Arabidopsis secretome.
We also observed a number of Pfams having more
members in rice than in other species. These Pfams
include dirigen-like protein, multicopper oxidase,
pollen allergen, cytochrome P450, etc (Table 5). It
should be noted that these predicted secreted
cytochrome P450 proteins most likely are false
positives as there is no secreted cytochrome P450
protein reported with experimental evidence in plants.
Wen et al. (2007) reported a cytochrome P450
presented in the pea root cap secretome. However, its
presence might represent leakage that occurs during
the cell separation process. In general, moss species
have fewer secreted proteins as well as a smaller
member number in a given Pfam due to their small
genomes. However, we noted that the lycophyte
model organism
Selaginella moellendorffii
has 20
members of D-mannose binding lectin family, while
other plant species have less than 10 members in this
Pfam, except
Populus trichocarpa
, which has 30
members. Species-specific secreted proteins are also
observed, such as corn, which has 30 members of Zein
seed storage protein and
Physcomitrella patens
(subsp.
patens), which has 61 members of a protein with an
unknown function (DUF4100).
4 Discussion
We constructed the PlantSecKB to provide a resource
for the plant research community. As the subcellular
location(s) of a given protein curated by UniProtKB
Computational
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