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Computational Molecular Biology
8
3 Comparative Analysis of Secretomes
Complete comparative evolutionary analyses of plant
secretomes or other sub-proteomes were beyond the
scope of this study. However, as complete secretome
or other sub-proteome sequences can be downloaded
directly from our database, it would facilitate further
detailed comparative study of these sub-proteomes in
different species. As an example, we performed a
comparative analysis of secretomes using a set of
representative plants including three monocots
(
Brachypodium distachyon
,
Oryza sativa
subsp.
japonica,
Zea mays
), three dicots (
Arabidopsis
thaliana
,
Populus
trichocarpa
,
Solanum
lycopersicum
), and two mosses (
Physcomitrella
patens
subsp. patens,
Selaginella moellendorffii
)
(Table 4 and Table 5). We used the blastclust tool in
the BLAST package with a cutoff of 95% identities in
the aligned pair to remove or reduce redundancy. Thus
non- or less redundant secreteomes were used for
comparisons. To provide an overview of the
functionalities of secretomes in plants, we carried
out Gene Ontology (GO) analysis of representative
secretomes of the 8 selected plant species. The
secretomes were used to search the
UniProt/Swiss-Prot dataset with BLASTP with a
cutoff E-value of 1e-10. GO information was
retrieved from UniProt ID mapping data
(http://www.uniprot.org/downloads) and analyzed
using GO SlimViewer with plant specific GO terms
(McCarthy et al., 2006). Comparison of GO biological
process and molecular function classification of
secretomes of the selected species was summarized in
Table 4. Plant secreted proteins are involved in more
than 40 different biological processes including
metabolic and catabolic processes, response to stress
and biotic or abiotic stimulus, carbohydrate, lipid and
protein metabolic processes, multicellular organismal
development, etc. Molecular function classification
revealed that plant secretomes consist of a large
number of hydrolases (~30%) and tranferases
(7%~9%), and that a large proportion of them have
various binding activity (~40%) or catalytic activity
(12%~15%). It should be noted that GO classification
was only an estimate of the distributions of each
category as many secreted proteins have not been
classified in GO.
Table 4 Gene Ontology classification of secreted proteins in different plant species
(a) Biological Process
At (%)
Pt (%) Sl (%)
Bd (%) Osj (%) Zm (%) Pp (%) Sm (%)
GO:0008152 metabolic process
673 (16) 379(21) 439 (22) 393 (20) 544 (20) 429 (20) 155 (23) 282 (21)
GO:0006950 response to stress
579 (14) 170 (9) 200 (10) 188 (10) 260 (9) 188 (9) 59 (9)
99 (7)
GO:0009056 catabolic process
386 (9) 182 (10) 242 (12) 200 (10) 269 (10) 216 (10) 71 (10) 137 (10)
GO:0009607 response to biotic stimulus
353 (9) 61 (3)
65 (3)
49 (3)
65 (2)
54 (3)
16 (2)
29 (2)
GO:0005975 carbohydrate metabolic process 313 (8) 156 (9) 190 (9) 183 (9) 247 (9) 165 (8) 56 (8)
97 (7)
GO:0007275 multicellularorganismal development 161 (4) 64 (4)
74 (4)
78 (4)
120 (4) 93 (4)
30 (4)
69 (5)
GO:0016043 cellular component organization 150 (4) 66 (4)
65 (3)
71 (4)
121 (4) 75 (4)
19 (3)
46 (3)
GO:0019538 protein metabolic process
143 (3) 98 (5)
90 (4)
98 (5)
109 (4) 91 (4)
40 (6)
71 (5)
GO:0006629 lipid metabolic process
140 (3) 65 (4)
68 (3)
72 (4)
102 (4) 83 (4)
16 (2)
61 (4)
GO:0009628 response to abiotic stimulus
111 (3)
39 (2)
39 (2)
56 (3)
82 (3)
71 (3)
14 (2)
36 (3)
GO:0007165 signal transduction
107 (3) 29 (2)
33 (2)
28 (1)
44 (2)
30 (1)
8 (1)
16 (1)
GO:0000003 reproduction
99 (2)
52 (3)
52 (3)
68 (4)
102 (4) 68 (3)
17 (2)
44 (3)
GO:0006810 transport
89 (2)
56 (3)
48 (2)
36 (2)
65 (2)
43 (2)
10 (1)
32 (2)
GO:0009058 biosynthetic process
86 (2)
66 (4)
70 (3)
62 (3)
102 (4) 89 (4)
40 (6)
60 (4)
GO:0030154 cell differentiation
86 (2)
16 (1)
20 (1)
23 (1)
44 (2)
23 (1)
8 (1)
17 (1)
others
636 (15) 316(17) 309 (15) 322 (17) 505 (18) 385 (18) 125 (18) 268 (20)
total
4112
1815 2004 1927 2780 2103 684
1364
(b) Molecular Function
At (%)
Pt (%) Sl (%)
Bd (%) Osj (%) Zm (%) Pp (%) Sm (%)
GO:0016787 hydrolase activity
649 (32) 328 (23) 380 (29) 398 (29) 533 (24) 362 (28) 114 (28) 243 (29)
GO:0005488 binding
595 (29) 435 (31) 408 (31) 434 (32) 711 (33) 407 (31) 139 (34) 263 (31)
GO:0003824 catalytic activity
249 (12) 186 (13) 158 (12) 194 (14) 272 (12) 169 (13) 59 (15)
115 (14)
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