Biology Reference
In-Depth Information
2
Samples
All meaningful proteomic comparisons, whether gel-based [ 15 ] or
gel-free [ 16 ] are complicated by both technical and biological vari-
ations. It is paramount that this not be further exacerbated by sam-
ple variation. Otherwise, seemly important quantitative or
qualitative differences might simply be artifacts because of nonuni-
form starting material. This can be particularly important with
regard to studies of seeds where it is well-known that there can be
substantial developmental and physiological changes [ 3 , 17 - 19 ].
2.1 Anatomy:
The Whole, the Sum,
or Just Some
of the Parts?
Formation of the seed completes a reproductive cycle that begins
with development of fl owers, and pollination [ 4 ]. The embryo
develops from the zygote formed by the fusion of an egg and a
sperm cell, and the seed coat or testa develops from the integu-
ments of the ovule [ 20 ]. Angiosperm seeds typically have the nutri-
ents, including the SSP, stored in either the cotyledons of dicots
[ 3 ] or endosperm of monocots [ 2 ]. The SSP in Gymnosperm seeds
are stored within the endosperm-related megagametophyte [ 21 ].
During development or maturation it is typical to analyze whole
seeds, as the seed coats and embryonic axes make a relatively small
contribution to the mass of the whole seed. Thus, “seed pro-
teomics” often means proteomic analysis of the storage tissues/
organs. Post-germination the seed coat remnants generally slough
off and are discarded, and the storage organs are often separated
from the growing seedling.
Is whole-seed proteomic analysis justifi ed? It depends upon the
nature of the seeds and the intended goals of the study. For exam-
ple if focus is on the post-germination, heterotrophic to autotro-
phic transition, or mobilization of SSP, then one can reasonably
assume that the relatively small contribution of the seed coat and
axis proteins will not confound the analysis. There is also the matter
of practicality. Removal of the seed coat and embryonic axis from a
tiny A. thaliana seed is a near impossible task versus removal of the
relatively large castor oil ( Ricinus communis ) seed coat and axis.
During seed development and maturation, however, the different
organs and tissues have their own distinctive protein composition
(c.f., Fig. 1 ), which refl ects their specialized origins and roles.
In these cases it would seem that separation of the seeds into
component parts is justifi ed, if not essential. What certainly is
essential is for the Methods sections to include a description of
what was done during sample preparation!
All seeds can be separated into two categories depending upon
the nature of the storage organ; endosperm-dominant or cotyledon-
dominant [ 4 ]. Endosperm-dominant seeds typically store starch and
proteins, while cotyledon-dominant seeds seem approximately evenly
distributed among starch plus proteins and starch plus lipids groups.
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