Part C | 18.6
486 Part C Marine Genomics
using a genetics approach, proteomics may be invaluable to population biology and structure studies, since
the proteome more accurately represents physiology
and phenotypic plasticity [18.55, 79].
Gonzalez et al. [18.79] investigated the potential of
population proteomics as a tool for detecting differences between populations of commercially important
fish. Two distinct stocks of the European hake (Merluccius merluccius, Linnaeus 1758), namely an Atlantic
Ocean and a Mediterranean Sea group, have been defined on the basis of genetic population studies. Twodimensional DIGE and MS analysis of protein expression in liver and brain tissue samples from hake
captured in the Mediterranean Sea, Cantabrian Sea,
and Atlantic Ocean identified 84 and 145 protein spots
in the liver and brain, respectively, that had significantly different expression levels between the three
groups [18.79]. Using a variety of statistical tools, Gonzalez et al. [18.79] were able to reduce the number of
proteins required to assign fish samples to a particular
population group to just three, achieving a discriminant score of 90100% accuracy. The study found
that differences in the expression of two brain proteins, involved in cell signaling and metabolism/energy,
discriminated between the three fish populations significantly better than differences in expression of the
liver proteins, suggesting that brain protein profiles
may more accurately reflect the functional adaptation
of populations [18.79]. This study clearly demonstrates
the value of population proteomics as a tool for defining
and monitoring fish populations which are at a critical point in terms of ensuring the sustainability of the
fishing industry and preserving the biodiversity of the
oceans.
18.6 Natural Products
Antibiotic discovery in the twentieth century enabled
treatment of diseases caused by previously untreatable
infectious bacteria. However, the situation has changed
dramatically over the past few decades with rapidly
emerging bacterial resistance to antibiotics as a consequence of over-prescription and inappropriate use
of antibiotics as prophylactics in farmed animals, including aquacultured fish and shellfish [18.80–82]. The
problem has been exacerbated by a steady decline in the
discovery of novel antibiotics, with just one new antibiotic class, the oxazolidinones, added to the approved list
during the 1990s [18.80]. Traditionally, drug discovery
from natural products has depended on high-throughput screening of microbial, plant, and animal extracts.
The majority of bioactive compounds with medical applications such as antibiotics, anticancer therapeutics,
anti-inflammatories, etc., have been obtained from microorganisms, particularly the filamentous bacteria belonging to the order Actinomycetales and filamentous
fungi [18.83]. However, as stated earlier, the discovery
of novel pharmaceuticals has significantly decreased
due to frequent re-isolation of the same compounds.
Since marine organisms comprise approximately half
of the total biodiversity on earth, the marine ecosystem
has the greatest potential as a source of novel bioactive
compounds [18.82–84].
Since sessile marine invertebrates such as sponges,
bryozoans, soft corals, seaweeds, and tunicates generally lack defence structures, they have developed
a broad range of secondary-metabolites with novel
molecular structures, and thus, are proving to be an invaluable source of novel pharmaceuticals [18.4, 84–87].
Interestingly, many of the bioactive compounds thought
to be produced by marine invertebrates are, indeed,
synthesized by endosymbiotic bacteria associated with
these animals [18.85, 88]. The latter has broadened the
potential of the marine environment as a source of novel
therapeutics since the biodiversity of marine microorganisms is immense, especially when one considers
that only 15% are culturable using standard laboratory techniques [18.89]. Consequently, metagenomics
is a technique that has been adopted for screening
for novel bioactive compounds from the marine environment, since it involves generating gene libraries
from DNA isolated directly from environmental samples and screening the gene sequences in the libraries
for those that may code for proteins with novel functions or structures [18.88, 90]. These candidates would
be expressed in a heterologous host in order to produce
sufficient quantities of the gene product for further analysis. Unfortunately, this approach is not simple, since
many bioactive compounds are produced via multigene
pathways, all of which would need to be cloned and expressed correctly [18.88].
A further complicating factor is that very low yields
of cloned proteins are obtained due to poor levels
of gene expression in heterologous hosts [18.89]. Although proteomics has great potential as a tool that
486 Part C Marine Genomics
using a genetics approach, proteomics may be invaluable to population biology and structure studies, since
the proteome more accurately represents physiology
and phenotypic plasticity [18.55, 79].
Gonzalez et al. [18.79] investigated the potential of
population proteomics as a tool for detecting differences between populations of commercially important
fish. Two distinct stocks of the European hake (Merluccius merluccius, Linnaeus 1758), namely an Atlantic
Ocean and a Mediterranean Sea group, have been defined on the basis of genetic population studies. Twodimensional DIGE and MS analysis of protein expression in liver and brain tissue samples from hake
captured in the Mediterranean Sea, Cantabrian Sea,
and Atlantic Ocean identified 84 and 145 protein spots
in the liver and brain, respectively, that had significantly different expression levels between the three
groups [18.79]. Using a variety of statistical tools, Gonzalez et al. [18.79] were able to reduce the number of
proteins required to assign fish samples to a particular
population group to just three, achieving a discriminant score of 90100% accuracy. The study found
that differences in the expression of two brain proteins, involved in cell signaling and metabolism/energy,
discriminated between the three fish populations significantly better than differences in expression of the
liver proteins, suggesting that brain protein profiles
may more accurately reflect the functional adaptation
of populations [18.79]. This study clearly demonstrates
the value of population proteomics as a tool for defining
and monitoring fish populations which are at a critical point in terms of ensuring the sustainability of the
fishing industry and preserving the biodiversity of the
oceans.
18.6 Natural Products
Antibiotic discovery in the twentieth century enabled
treatment of diseases caused by previously untreatable
infectious bacteria. However, the situation has changed
dramatically over the past few decades with rapidly
emerging bacterial resistance to antibiotics as a consequence of over-prescription and inappropriate use
of antibiotics as prophylactics in farmed animals, including aquacultured fish and shellfish [18.80–82]. The
problem has been exacerbated by a steady decline in the
discovery of novel antibiotics, with just one new antibiotic class, the oxazolidinones, added to the approved list
during the 1990s [18.80]. Traditionally, drug discovery
from natural products has depended on high-throughput screening of microbial, plant, and animal extracts.
The majority of bioactive compounds with medical applications such as antibiotics, anticancer therapeutics,
anti-inflammatories, etc., have been obtained from microorganisms, particularly the filamentous bacteria belonging to the order Actinomycetales and filamentous
fungi [18.83]. However, as stated earlier, the discovery
of novel pharmaceuticals has significantly decreased
due to frequent re-isolation of the same compounds.
Since marine organisms comprise approximately half
of the total biodiversity on earth, the marine ecosystem
has the greatest potential as a source of novel bioactive
compounds [18.82–84].
Since sessile marine invertebrates such as sponges,
bryozoans, soft corals, seaweeds, and tunicates generally lack defence structures, they have developed
a broad range of secondary-metabolites with novel
molecular structures, and thus, are proving to be an invaluable source of novel pharmaceuticals [18.4, 84–87].
Interestingly, many of the bioactive compounds thought
to be produced by marine invertebrates are, indeed,
synthesized by endosymbiotic bacteria associated with
these animals [18.85, 88]. The latter has broadened the
potential of the marine environment as a source of novel
therapeutics since the biodiversity of marine microorganisms is immense, especially when one considers
that only 15% are culturable using standard laboratory techniques [18.89]. Consequently, metagenomics
is a technique that has been adopted for screening
for novel bioactive compounds from the marine environment, since it involves generating gene libraries
from DNA isolated directly from environmental samples and screening the gene sequences in the libraries
for those that may code for proteins with novel functions or structures [18.88, 90]. These candidates would
be expressed in a heterologous host in order to produce
sufficient quantities of the gene product for further analysis. Unfortunately, this approach is not simple, since
many bioactive compounds are produced via multigene
pathways, all of which would need to be cloned and expressed correctly [18.88].
A further complicating factor is that very low yields
of cloned proteins are obtained due to poor levels
of gene expression in heterologous hosts [18.89]. Although proteomics has great potential as a tool that