Molecular Biology Techniques in Agriculture: Proteomics

Proteomics

Proteomics together with genomics, and metabolomics ramified from standard molecular biology due to the high demand for information on biological adaptation of a variety of biological systems. The brief outline presented here is the first in the series of articles presenting techniques that mastered by the Department of Animal Molecular Biology of the National Research Institute of Animal Production.

Proteomics is the branch of molecular biology focused on the study of all the proteins expressed by a living cell, an organ, or a living organism. It developed from the basic laboratory techniques employed for protein separation using their physical properties: electric charge (isoelectric point separation – the first dimension) and molecular mass (SDS gel electrophoresis – the second dimension).

Figure 1. The picture of 2D-gel with silver-stained protein spots of Calanus sinicus. Wiacek, M., Uddin, N., Kim, H.J. & Zubrzycki, I.Z., 2013. Proteome changes in response to ecologically viable environmental variation in Calanus sinicus. Protein and Peptide Letters 20(1): 78-87.

Employment of proteomics allows for an in-depth look into posttranslational processes occurring in the cell (the processes leading into the biosynthesis of a mature protein) and is, very often, the first step of analysis of protein structure (Zubrzycki and Gäde 1999), function, protein-protein, protein-lipid bilayer, enzyme-substrate (Zubrzycki 2002), and enzyme-product interactions.

Because one gene encodes more than one protein, it is a field of study broader and more complex than genomics. The fact that a proteome is a dynamics body determined by a vista of epigenetic mechanisms and environmental factors renders this technique more complicated than genomics. During the last twenty years, proteomics was a tool employed in a variety of different disciplines including biotechnology, physiology, oncology, immunology, animal breeding, and veterinary medicine. The use of proteomics in human (Hoffrogge et al. 2006) and veterinary medicine brings measurable benefits in the form of early diagnosis of diseases and monitoring and prediction (prognosis) of their progress. It also may be used for setting new goals for therapeutic intervention.

Implementation of proteomics grants possibility for building protein reference maps that allow for comparing protein profiles and tracking changes in protein content fluctuations rendered by changing physiological conditions and pathological processes, or influence of the experimental factors. The use of this method permits identification of new biomarkers characteristic biological “performance” of animals which is a mirror of diseases and genetic defects and to assess the environmental impact on the immune system.

The example of the application of 2D-gel electrophoresis in an animal study is well-documented in the papers Zubrzycki I.Z., et al., (Zubrzycki et al. 2012) and Wiacek et al., (Wiacek et al. 2013). The latter study is focused on an analysis of adaptation at the proteome level to the variable ocean temperature – the hot topic in the global warming era. The presented results show that observed increase in milieu temperature resulted in triggering of cell machinery involved in protein folding used in compensating for an increase in reaction rates rendered by higher surrounding (water) temperature. An increase in milieu temperature associated by a decrease in water oxygen-saturation induced an increase in potassium ion channel activity which compensates for an increase in reaction rates and kinetic transition. There is also infinitesimal adaptation in transcriptional and translational processes as a function of environmental changes and an increase in xenobiotic metabolism in response to pollution increase rendering increased cell xenobiotic recruitment.


References:

  • Hoffrogge, R., S. Mikkat, C. Scharf, S. Beyer, H. Christoph, J. Pahnke, E. Mix, M. Berth, A. Uhrmacher, I. Z. Zubrzycki, E. Miljan, U. Völker, and A. Rolfs. 2006. “2-DE proteome analysis of a proliferating and differentiating human neuronal stem cell line (ReNcell VM).” Proteomics 6 (6):1833-1847.
  • Wiacek, M., N. Uddin, H. J. Kim, and I. Z. Zubrzycki. 2013. “Proteome changes in response to ecologically viable environmental variation in Calanus sinicus .” Protein and Peptide Letters 20 (1):78-87.
  • Zubrzycki, I. Z. 2002. “Homology modeling and molecular dynamics study of NAD-dependent glycerol-3-phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for anti-sleeping sickness drug development.” Biophysical Journal 82 (6):2906-2915.
  • Zubrzycki, I. Z., and G. Gäde. 1999. “Conformational study on a representative member of the AKH/RPCH neuropeptide family, Emp-AKH, in the presence of SDS micelle.” European Journal of Entomology 96 (3):337-340.
  • Zubrzycki, I. Z., S. Lee, K. Lee, M. Wiacek, and W. Lee. 2012. “The study on highly expressed proteins as a function of an elevated ultraviolet radiation in the copepod, Tigriopus japonicus.” Ocean Science Journal 47 (2):75-82.

Author: Igor Z. Zubrzycki PhD

Department of Animal Molecular Biology
National Research Institute of Animal Production
1 Krakowska Street, 32-083 Balice, Poland


An article prepared as part of the ProBio Małopolska project