Proteomics: A
475
Part C | 18.1
18. Proteomics: Applications and Advances
Vernon E. Coyne
Proteomics provides a snapshot of gene expression
in a particular cell, tissue, or organ at the time of
sampling. Since the proteome is the link between
the genotype and phenotype of an organism,
characterization of the proteome provides information regarding the adaptability and physiology
of an organism in relation to its environment. Proteomics is proving invaluable as a tool in marine
biotechnology, where it has been employed to
identify and characterize unique bioactive gene
products, characterize the function and regulation
of metabolic processes, elucidate marine biodiversity, and identify biomarkers of pollution and
disease. Aquaculture of commercially important
marine fish and shellfish has benefitted through
a proteomics approach to address issues relating
to disease, larviculture, and animal production in
order to improve the profitability and sustainability of the industry. This chapter describes a wide
variety of studies that illustrate the application
of proteomics in marine biotechnology. The rapid
improvements in proteomics technology expected
18.1 Omics .................................................. 475
18.2 Overview of Proteomics Techniques ...... 476
18.3 Proteomics and Marine Biotechnology .. 477
18.4 Aquaculture ........................................ 478
18.4.1 Disease..................................... 478
18.4.2 Reproduction ............................ 480
18.4.3 Animal Production .................... 481
18.5 Environment ....................................... 482
18.5.1 Climate Change ......................... 482
18.5.2 Pollution .................................. 483
18.5.3 Population Proteomics............... 485
18.6 Natural Products.................................. 486
18.7 Algal Toxins ......................................... 488
18.8 Conclusion........................................... 490
References................................................... 491
over the next few years are guaranteed to result in
dramatic advances in our understanding and use
of the valuable resources provided by the marine
environment.
18.1 Omics
In 1998, the nematode Caenorhabditis elegans was
the first multicellular organism to have its genome
sequenced [18.1]. Since then, the omics era has essentially transformed molecular biology in terms of the
vast volumes of data generated in our quest to better
understand the cellular processes responsible for the
evolutionary success and survival of living organisms.
Omics is a collective term for genomics, transcriptomics and proteomics, which focus on the three basic
levels of genetic expression in the cell, and is inclusive of additional technologies such as metabolomics,
metagenomics, epigenomics, lipidomics, etc.
While genomics characterizes all the genes of a particular organism in an attempt to elucidate their function
and regulation, transcriptomics and proteomics provide
a more dynamic approach to studying gene expression
and regulation at the cellular level. Whereas transcriptomics allows messenger ribonucleic acid (mRNA) levels to be assessed as a measure of gene expression,
proteomics provides more detail since it detects the
products of alternative mRNA splicing and post-translational modification of proteins [18.2, 3]. In addition
to providing a qualitative snap shot of gene expression in a particular cell, tissue or organism, proteomics
475
Part C | 18.1
18. Proteomics: Applications and Advances
Vernon E. Coyne
Proteomics provides a snapshot of gene expression
in a particular cell, tissue, or organ at the time of
sampling. Since the proteome is the link between
the genotype and phenotype of an organism,
characterization of the proteome provides information regarding the adaptability and physiology
of an organism in relation to its environment. Proteomics is proving invaluable as a tool in marine
biotechnology, where it has been employed to
identify and characterize unique bioactive gene
products, characterize the function and regulation
of metabolic processes, elucidate marine biodiversity, and identify biomarkers of pollution and
disease. Aquaculture of commercially important
marine fish and shellfish has benefitted through
a proteomics approach to address issues relating
to disease, larviculture, and animal production in
order to improve the profitability and sustainability of the industry. This chapter describes a wide
variety of studies that illustrate the application
of proteomics in marine biotechnology. The rapid
improvements in proteomics technology expected
18.1 Omics .................................................. 475
18.2 Overview of Proteomics Techniques ...... 476
18.3 Proteomics and Marine Biotechnology .. 477
18.4 Aquaculture ........................................ 478
18.4.1 Disease..................................... 478
18.4.2 Reproduction ............................ 480
18.4.3 Animal Production .................... 481
18.5 Environment ....................................... 482
18.5.1 Climate Change ......................... 482
18.5.2 Pollution .................................. 483
18.5.3 Population Proteomics............... 485
18.6 Natural Products.................................. 486
18.7 Algal Toxins ......................................... 488
18.8 Conclusion........................................... 490
References................................................... 491
over the next few years are guaranteed to result in
dramatic advances in our understanding and use
of the valuable resources provided by the marine
environment.
18.1 Omics
In 1998, the nematode Caenorhabditis elegans was
the first multicellular organism to have its genome
sequenced [18.1]. Since then, the omics era has essentially transformed molecular biology in terms of the
vast volumes of data generated in our quest to better
understand the cellular processes responsible for the
evolutionary success and survival of living organisms.
Omics is a collective term for genomics, transcriptomics and proteomics, which focus on the three basic
levels of genetic expression in the cell, and is inclusive of additional technologies such as metabolomics,
metagenomics, epigenomics, lipidomics, etc.
While genomics characterizes all the genes of a particular organism in an attempt to elucidate their function
and regulation, transcriptomics and proteomics provide
a more dynamic approach to studying gene expression
and regulation at the cellular level. Whereas transcriptomics allows messenger ribonucleic acid (mRNA) levels to be assessed as a measure of gene expression,
proteomics provides more detail since it detects the
products of alternative mRNA splicing and post-translational modification of proteins [18.2, 3]. In addition
to providing a qualitative snap shot of gene expression in a particular cell, tissue or organism, proteomics