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22 Application of Proteomics to Fish Processing and Quality 415of the highly abundant proteins were identified as muscle pro-
teins (Guðmundsdottir and Sveinsd ́ ottir 2006, Sveinsd ́ ottir and ́
Gudmundsdottir 2008, Sveinsd ́ ottir et al. 2008, 2009). Also, ́
cytoskeletal proteins were prominent among the identified pro-
teins. Removal of those proteins may increase detection of other
proteins present at low concentrations. However, it may also
result in a loss of other proteins, preventing identification of
holistic alterations in the analyzed proteomes. Various strategies
have been presented for the removal of highly abundant proteins
(Ahmed et al. 2003) or enrichment of low-abundance proteins
(Oda et al. 2001, Ahmed and Rice 2005).Tracking Quality Changes Using ProteomicsA persistent problem in the seafood industry is postmortem
degradation of fish muscle during chilled storage, which has
deleterious effects on the fish flesh texture, yielding a tender-
ized muscle. This phenomenon is thought to be primarily due to
autolysis of muscle proteins, but the details of this protein degra-
dation are still somewhat in the dark. However, degradation of
myofibrillar proteins by calpains and cathepsins (Ogata et al.
1998, Ladrat et al. 2000) and degradation of the extracellular
matrix by the matrix metalloproteases and matrix serine pro-
teases, capable of degrading collagens, proteoglycans, and other
matrix components (Woessner 1991, Lødemel and Olsen 2003),
are thought to be among the main culprits. Whatever the mecha-
nism, it is clear that these quality changes are species dependent
(Papa et al. 1996, Verrez-Bagnis et al. 1999) and, furthermore,
appear to display seasonal variations (Ingolfsd ́ ottir et al. 1998, ́
Ladrat et al. 2000). For example, whereas desmin is degraded
postmortem in sardine and turbot, no desmin degradation was
observed in sea bass and brown trout (Verrez-Bagnis et al. 1999).
Of further concern is the fact that several commercially impor-
tant fish muscle processing techniques, such as curing, fermen-
tation, and production of surimi and conserves occur under con-
ditions conducive to endogenous proteolysis (P ́erez-Borla et al.
2002). As with postmortem protein degradation during storage,
autolysis during processing seems to be somewhat specific. In-
deed, the myosin heavy chain of the Atlantic cod was shown
to be significantly degraded during processing of “salt fish”
(bacalhau) whereas actin was less affected (Thorarinsdottir et al.
2002). Problems of this kind, where differences are expected to
occur in the number, molecular mass, and pI of the protein
present in a tissue, are well suited to investigation using 2DE-
based proteomics. It is also worth noting that protein isoforms
other than proteolytic ones, whether they be encoded in struc-
tural genes or brought about by posttranslational modification,
usually have different molecular weight or pI and can, therefore,
be distinguished on 2DE gels. Thus, specific isoforms of my-
ofibrillar proteins, many of which are correlated with specific
textural properties in seafood products, can be observed using
2DE or other proteomic methods (Martinez et al. 1990, Pineiro ̃
et al. 2003).
Several 2DE studies have been performed on postmortem
changes in seafood flesh (Verrez-Bagnis et al. 1999, Morzel
et al. 2000, Martinez et al. 2001a, Kjaersgard and Jessen 2003,
2004, Martinez and Jakobsen Friis 2004, Kjaersgard et al.2006a, b) and have demonstrated the importance and complex-
ity of proteolysis in seafood during storage and processing. For
example, Martinez and Jakobsen Friis used a 2DE approach
to demonstrate different protein composition of surimi made
from prerigor versus postrigor cod (Martinez and Jakobsen Friis
2004). They found that 2DE could be used as a diagnostic tool
to indicate the freshness of the raw material used for surimi pro-
duction, a finding of considerable economic and public health
interest. Kjaersgard and Jessen, who used 2DE to study changes
in abundance of several muscle proteins during storage of the
Atlantic cod (Gadus morhua), proposed a general model for
postmortem protein degradation in fish flesh where initially cal-
pains were activated due to the increase in calcium levels in
the muscle tissue. Later, as pH decreases and ATP is depleted
with the consequent onset of rigor mortis, cathepsins and the
proteasome are activated sequentially (Kjaersgard and Jessen
2003).Antemortem Effects on Quality and
ProcessabilityMalcolm Love started his 1980 review paper on biological fac-
tors affecting fish processing (Love 1980) with a lament for the
easy life of poultry processors who, he said, had the good for-
tune to work on a product reared from hatching under strictly
controlled environmental and dietary conditions “so that plastic
bundles of almost identical foodstuff for man can be lined up
on the shelf of a shop.” Since the time of Love’s review, the
advent of aquaculture has made attainable, in theory at least,
just such a utopic vision. As every food processor knows, the
quality of the raw material is among the most crucial variables
that affect the quality of the final product. In fish processing,
therefore, the animal’s own individual physiological status will
to a large extent dictate where quality characteristics will fall
within the constraints set by the species’ physical and biochem-
ical makeup. It is well known that an organism’s phenotype,
including quality characteristics, is determined by environmen-
tal as well as genetic factors. Indeed, Huss noted in his review
(Huss 1995) that product quality differences within the same
fish species can depend on feeding and rearing conditions, dif-
ferences wherein can affect postmortem biochemical processes
in the product, which, in turn, affect the involution of qual-
ity characteristics in the fish product. The practice of rearing
fish in aquaculture, as opposed to wild-fish catching, therefore
raises the tantalizing prospect of managing quality characteris-
tics of the fish flesh antemortem, where individual physiological
characteristics, such as those governing gaping tendency, flesh
softening during storage, etc., are optimized. To achieve that
goal, the interplay between these physiological parameters and
environmental and dietary variables needs to be understood in
detail. With the ever-increasing resolving power of molecular
techniques, such as proteomics, this is fast becoming feasible.
In mammals, antemortem protease activities have been shown
to affect meat quality and texture (Vaneenaeme et al. 1994, Kris-
tensen et al. 2002). For example, an antemortem upregulation of
calpain activity in swine (Sus scrofa) will affect postmortem pro-
teolysis and, hence, meat tenderization (Kristensen et al. 2002).