Part C | 18.8
490 Part C Marine Genomics
termined at four time points (0, 3, 6, and 24 h posttreatment). The study identified 58 proteins that were
differentially expressed over the 24 h period which
functioned in macromolecular metabolism, cytoskeleton reorganization, signal transduction, molecular chaperoning, and oxidative stress [18.110]. Although it has
been known for some time that okadaic acid acts as
an inhibitor of types 1, 2a, and 3 serine/threonine
protein phosphatases (PPs), which results in the diarrhoeic effects as a consequence of the accumulation
of phosphorylated proteins that regulate metabolism,
transport, and secretion, the data obtained from the in
vivo proteomic study suggests that okadaic acid toxicity
in mouse intestines is complex and diverse, involving
multiple proteins other than PP in the diarrheic process [18.110]. Indeed, the proteomic analysis revealed
that okadaic acid toxicity interrupted cytoskeleton reorganization of intestinal epithelial cells, destroyed the
digestive enzyme system by affecting lipid, amino acid,
and sugar metabolism, induced oxidative stress, and
simultaneously interfered with cell signal transduction in intestinal cells [18.110]. The authors suggested
that villin 1 (cytoskeletal protein; down-regulated by
okadaic acid) and hnRNP F (RNA binding protein that
may function in apoptotic pathways; up-regulated by
okadaic acid 3 h post-administration) may be key triggers that induce diarrhoea by interrupting cytoskeleton
reorganization and cell apoptosis in the mouse small intestine, and thus, may be candidate biomarkers for acute
okadaic acid toxicity [18.110].
18.8 Conclusion
It is clear that proteomics is a tool that will strongly
influence all aspects of marine biotechnology, since it
provides information on a scale that reflects the new
omics era that is a hallmark of twenty-first century science. The technology is constantly improving, and as
such, our ability to better understand the biology of marine organisms, their interactions with each other, and
the environment will be enhanced by new developments
in proteomics that are expected to be realized in the near
future.
Goals anticipated to be achieved over the next 5
years include a 100 to 1000-fold increase in the sensitivity of MS-based protein identification that will allow
characterization of biologically relevant, low abundance proteins; increased sensitivity will reduce the
amount of sample required for proteomic analysis from
10
6 to 10
3 cells and eventually to single cells, while
enhanced throughput of proteomics assays will allow
the analysis of hundreds of specimens per day, which
would be beneficial to research areas that investigate
large numbers of samples such as in marine natural
product identification and characterization [18.112].
Nagaraj et al. [18.113] used a high-performance
benchtop quadrupole Orbitrap mass spectrometer to
identify the majority of proteins expressed in the yeast
Saccharomyces cerevisiae W303 MAT˛ (an average of
4000 proteins per run), which allowed almost complete
coverage of the yeast proteome in a few hours using
a minute amount of sample (4 g of peptide sample).
Indeed, the proteomics field is said to be moving rapidly
from a second generation state to a third generation
phase where it is expected that MS-based proteomics
will be routinely used to determine absolute protein levels as opposed to relative quantification, as is currently
the case, and to characterize the dynamic response of
entire proteomes in both space and time [18.114].
The development of new software that will allow
integration of proteomics data with that obtained from
next-generation sequencing and metabolomics will allow a systems biological approach to the study of
marine organisms. Thus, proteogenomics is expected
to provide a more holistic understanding of marine
organisms, since proteomics data can be used to validate and annotate genome sequences as well as identify
novel genes and pseudogenes which may be missed during DNA sequence annotation [18.3, 115]. The study
of marine organisms will be elevated to an unprecedented level through the detailed information that will
be gained with regard to their functional genetics,
the regulation of these processes and in turn their
metabolism, physiology, and interaction with the environment. This knowledge will significantly influence
all aspects of marine biotechnology in that the impact
of climate change and anthropogenic pollution on marine organisms will be understood in greater depth, the
discovery of novel bioactive compounds will be greatly
facilitated, aquaculture will benefit through a deeper
understanding of reproduction, metabolism and stress
leading to improved quality, survival and growth rates
in farmed species, and most importantly, a greatly improved balance between exploitation and conservation
of resources from the marine environment.
490 Part C Marine Genomics
termined at four time points (0, 3, 6, and 24 h posttreatment). The study identified 58 proteins that were
differentially expressed over the 24 h period which
functioned in macromolecular metabolism, cytoskeleton reorganization, signal transduction, molecular chaperoning, and oxidative stress [18.110]. Although it has
been known for some time that okadaic acid acts as
an inhibitor of types 1, 2a, and 3 serine/threonine
protein phosphatases (PPs), which results in the diarrhoeic effects as a consequence of the accumulation
of phosphorylated proteins that regulate metabolism,
transport, and secretion, the data obtained from the in
vivo proteomic study suggests that okadaic acid toxicity
in mouse intestines is complex and diverse, involving
multiple proteins other than PP in the diarrheic process [18.110]. Indeed, the proteomic analysis revealed
that okadaic acid toxicity interrupted cytoskeleton reorganization of intestinal epithelial cells, destroyed the
digestive enzyme system by affecting lipid, amino acid,
and sugar metabolism, induced oxidative stress, and
simultaneously interfered with cell signal transduction in intestinal cells [18.110]. The authors suggested
that villin 1 (cytoskeletal protein; down-regulated by
okadaic acid) and hnRNP F (RNA binding protein that
may function in apoptotic pathways; up-regulated by
okadaic acid 3 h post-administration) may be key triggers that induce diarrhoea by interrupting cytoskeleton
reorganization and cell apoptosis in the mouse small intestine, and thus, may be candidate biomarkers for acute
okadaic acid toxicity [18.110].
18.8 Conclusion
It is clear that proteomics is a tool that will strongly
influence all aspects of marine biotechnology, since it
provides information on a scale that reflects the new
omics era that is a hallmark of twenty-first century science. The technology is constantly improving, and as
such, our ability to better understand the biology of marine organisms, their interactions with each other, and
the environment will be enhanced by new developments
in proteomics that are expected to be realized in the near
future.
Goals anticipated to be achieved over the next 5
years include a 100 to 1000-fold increase in the sensitivity of MS-based protein identification that will allow
characterization of biologically relevant, low abundance proteins; increased sensitivity will reduce the
amount of sample required for proteomic analysis from
10
6 to 10
3 cells and eventually to single cells, while
enhanced throughput of proteomics assays will allow
the analysis of hundreds of specimens per day, which
would be beneficial to research areas that investigate
large numbers of samples such as in marine natural
product identification and characterization [18.112].
Nagaraj et al. [18.113] used a high-performance
benchtop quadrupole Orbitrap mass spectrometer to
identify the majority of proteins expressed in the yeast
Saccharomyces cerevisiae W303 MAT˛ (an average of
4000 proteins per run), which allowed almost complete
coverage of the yeast proteome in a few hours using
a minute amount of sample (4 g of peptide sample).
Indeed, the proteomics field is said to be moving rapidly
from a second generation state to a third generation
phase where it is expected that MS-based proteomics
will be routinely used to determine absolute protein levels as opposed to relative quantification, as is currently
the case, and to characterize the dynamic response of
entire proteomes in both space and time [18.114].
The development of new software that will allow
integration of proteomics data with that obtained from
next-generation sequencing and metabolomics will allow a systems biological approach to the study of
marine organisms. Thus, proteogenomics is expected
to provide a more holistic understanding of marine
organisms, since proteomics data can be used to validate and annotate genome sequences as well as identify
novel genes and pseudogenes which may be missed during DNA sequence annotation [18.3, 115]. The study
of marine organisms will be elevated to an unprecedented level through the detailed information that will
be gained with regard to their functional genetics,
the regulation of these processes and in turn their
metabolism, physiology, and interaction with the environment. This knowledge will significantly influence
all aspects of marine biotechnology in that the impact
of climate change and anthropogenic pollution on marine organisms will be understood in greater depth, the
discovery of novel bioactive compounds will be greatly
facilitated, aquaculture will benefit through a deeper
understanding of reproduction, metabolism and stress
leading to improved quality, survival and growth rates
in farmed species, and most importantly, a greatly improved balance between exploitation and conservation
of resources from the marine environment.