Proteomics

Proteomics is a discipline of microbiology and molecular biology that has arisen from the gene sequencing efforts that culminated in the sequencing of the human genome in the last years of the twentieth century. In addition to the human genome, sequences of disease-causing bacteria are being deduced. Although fundamental, knowledge of the sequence of nucleotides that comprise deoxyribonucleic acid reveals only a portion of the protein structure encoded by the DNA. Because proteins are an essential element of bacterial structure and function (e.g., role in causing infection), the knowledge of the three-dimensional structure and associations of proteins is vital. Proteomics is an approach to unravel the structure and function of proteins.

The word proteomics is derived from PROTEin complement to a genOME. Essentially, this is the spectrum of proteins that are produced from the template of an organism's genetic material under a given set of conditions. Proteomics compares the protein profiles of proteomes under different conditions in order to unravel biological processes.

The origin of proteomics dates back to the identification of the double-stranded structure of DNA by Watson and Crick in 1953. More recently, the development of the techniques of protein sequencing and gel electrophoresis in the 1960s and 1970s provided the technical means to probe protein structure. In 1986, the first protein sequence database was created (SWISS-PROT, located at the University of Geneva). By the mid-1990s, the concept of the proteome and the discipline of proteomics were well established. The power of proteomics was manifest in March 2000, when the complete proteome of a whole organism was published, that of the bacterium Mycoplasma genitalium

Proteomics research often involves the comparison of the proteins produced by a bacterium (example, Escherichia coli) grown at different temperatures, or in the presence of different food sources, or a population grown in the lab versus a population recovered from an infection. Escherichia coli responds to changing environments by altering the proteins it produces. However, the full extent of the various alterations and their molecular bases are largely unknown. Proteomics research essentially attempts to provide a molecular explanation for bacterial behavior.

Proteomics can be widely applied to research of diverse microbes. For example, the yeast Saccharomyces cerevisiae is being studied to reveal the proteins produced and their functional associations with one another.

The task of sorting out all the proteins that can be produced by a bacterium or yeast cell is formidable. Targeting of the research effort is essential. For example, the comparison of the protein profile of a bacterium obtained directly from an infection (in vivo) with populations of the same microbe grown under defined conditions in the lab (in vitro) could identify proteins that are unique to the infection. Some of these could become targets for diagnosis, therapy, or for prevention of the infection.

The study of proteins is difficult. The amount of protein cannot be amplified as easily as can the amount of DNA, making the detection of minute amounts of protein challenging. The structure of proteins must be maintained, which can be difficult. For example, enzymes, heat, light, or the energy of mixing can break down some proteins.

With the advent of the so-called DNA chips, the expression of thousands of genes can be monitored simultaneously. But DNA is static. It exists and is either expressed or not. Moreover, the expression of a protein does not necessarily mean that the protein is active. Also, proteins can be modified after being produced. Proteins can adopt different shapes, which can determine different functions and levels of activity after they have been produced. These functions provide the structural and operational framework for the life of the bacterium. Proteomics represents the next step after gene expression analysis

Proteomics utilizes various techniques to probe protein expression and structure. The migration of proteins can depend on their net charge and on the size of the protein molecule. When these migrations are in two dimensions, as in 2-D polyacrylamide gel electrophoresis, thousands of proteins can be distinguished in a single experiment. A technique called mass spectrometry analyzes a trait of proteins known as the mass-to-charge ratio, which essentially enables the sequence of amino acids comprising the protein to be determined. Techniques exist that detect modifications after protein manufacture, such as the addition of phosphate groups. Analogous to DNA chips, so-called protein microarrays have been developed. In these, a solid support holds various molecules (antibodies and receptors, as two examples) that will specifically bind protein. The binding pattern of proteins to the support can help determine what proteins are being made and when they are synthesized.

Proteomics typically operates in tandem with bioinformatics, which is an integration of mathematical, statistical, and computational methods to unravel biological data. The vast amount of protein information emerging from a single experiment would be impossible to analyze by manual computation or analysis. Accordingly, comparison of the data with other databases and the use of computer modeling programs, such as those that calculate three-dimensional structures, are invaluable in proteomics.

The knowledge of protein expression and structure, and the potential changes in structure and function under different conditions, could allow the tailoring of treatment strategies. For example, in the lungs of those afflicted with cystic fibrosis, the bacterium Pseudomonas aeuruginosa forms adherent populations on the surface of the lung tissue. These populations, which are enclosed in a glycocalyx that the bacteri produce, are very resistant to treatments and directly and indirectly damage the lung tissue to a lethal extent. Presently, it is known that the bacteria change their genetic expression as they become more firmly associated with the surface. Through proteomics, more details of the proteins involved in the initial approach to the surface and the subsequent, irreversible surface adhesion could be revealed. Once the targets are known, it is conceivable that they can be blocked. Thus, biofilms would not form and the bacteria could be more expeditiously eliminated from the lungs.

See also Biotechnology; Molecular biology and molecular genetics