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Q&A: Jean Armengaud on the Application of Proteomics to 'Blue' Biotechnology

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Name: Jean Armengaud
Position: Researcher at French Institute of Environmental Biology and Biotechnology

NEW YORK (GenomeWeb) – Given that some 70 percent of the earth is covered in water, the marine world represents a major source of organisms and biological products of potential medical or scientific use. Indeed, so-called “blue” biotech has led to the development of products including the Taq polymerase derived from the thermophilic bacterium Thermus aquaticus, which is used in PCR as well as the agar commonly used in gel electrophoresis.

Marine organisms are also a potentially promising source of new drugs, particularly given that they have been far less thoroughly investigated than traditional sources of therapeutic agents like terrestrial microorganisms. In fact, the vast majority of marine organisms remain unexplored, marking this space as one with significant potential for the discovery of novel biomedical compounds.

Mass spec-based proteomics has emerged as an important tool in such investigations, allowing researchers to screen and characterize organisms and explore their proteomes for novel, potentially useful proteins.

Jean Armengaud, a scientist with France's Institute of Environmental Biology and Biotechnology is a leading researcher in marine proteomics and the corresponding author on a review of the field published in the journal Marine Genomics in April. This week he spoke to ProteoMonitor about the current state of marine proteomics and its future potential.

Below is an edited version of the interview.

Are there any particular organisms or research areas that marine proteomics has focused on to date? What would you say are some of the most notable successes in the field in terms of applications of its findings?

Lately, marine proteomics [has been] applied to analyze the most extreme organisms living on earth in search of new enzymatic activities and to understand the response of marine organisms to stress in general. [Our lab has] contributed to this field with several studies on the Roseobacter clade comprising [a class of] bacteria that are abundant, and that could be interesting sources of novel antibiotics.

What does proteomics bring that adds to genomic efforts in this field?

Proteins are key molecular players that should be identified and quantified to understand their function, and to exploit their activities. While genomics gives very deep insights into the potential of marine organisms or ecosystems, proteomics is crucial for understanding how these systems really work, and for transforming them into valuable biotech products.

Are there any particular challenges that are unique to marine proteomics — for instance in terms of sampling, or sample preparation, or data analysis?

I see two main challenges for marine proteomics: first, the large biodiversity encountered in marine environments and the low concentration of a given species result in the need of higher sensitivity for a direct analysis of the samples; second, the sampling of specific areas is just amazingly difficult. How to reach deep hot vents and deep salt lakes, for example, and control the quality of sampling?

How important is the growing use of sample-specific databases built via NGS to the expansion of marine proteomics?

Data interpretation in proteomics relies heavily on nucleic acid sequences and access to such databases. Large metagenomic surveys and specific organisms sequencing are thus crucial for the field to expand. However, [in a June paper in EuPA Open Proteomics] we recently pointed out the problem of data contamination in these databases for interpreting proteomic data. New initiatives are welcome in order to curate these sequence databases, and we are currently developing a new concept to considerably reduce this time-consuming process.

It seems that MALDI-TOF has been the primary mode of mass spec used in marine proteomics to date. Is that true? If so, is there any particular reasons it has been more widespread in this field than electrospray approaches?

Because of funding [considerations], proteomic platforms are mainly developing new technologies [for] human health-related programs. Microbiology and environmental fields [have] thus remained for a while with traditional 2D PAGE approaches combined with MALDI-TOF mass fingerprinting for protein identification. Today, shotgun approaches with [high-resolution] mass spectrometry are widespread, and their use is really boosting these two fields. Another important idea is the quite recent development of whole-cell MALDI-TOF MS for quickly identifying and screening organisms. This approach combined with culturomics should result in important discoveries of novel species, new products, and drugs in the next decade.

What are the major academic centers/labs doing regarding research into marine proteomics? Who are the major industry players in this area?

Academic centers/labs interested into marine proteomics or aquatic proteomics are really numerous ... If I should cite only one name, Peter Golyshin from Wales works on really interesting marine bugs with high potential for biotechnology. The industry players are also quite diverse and numerous, and all biotechnology players are looking for promising new marine products. An interesting initiative, the Bio2Mar platform launched recently in France with a cosmetic/pharma player and public partnership is worth citing as its aim is the discovery of thousands of new marine products and drugs.

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