Mining seed proteome: from protein dynamics to modification profiles

Authors

  • Andrej Frolov Department of Bioorganic Chemistry, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0003-3250-5858
  • Tatiana Mamontova Department of Bioorganic Chemistry, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0002-9794-8089
  • Christian Ihling Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Wolfgang-Langenbeck-Strasse 4, 06120 Halle/Saale DE, Martin-Luther Universität Halle-Wittenberg, Germany
  • Elena Lukasheva Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0002-0889-2395
  • Mikhail Bankin Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0002-6240-2246
  • Veronika Chantseva Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0002-3486-4232
  • Maria Vikhnina Department of Bioorganic Chemistry, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0003-0120-3435
  • Alena Soboleva Department of Bioorganic Chemistry, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation; Department of Сell and Metabolic Biology, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany https://orcid.org/0000-0002-7318-8628
  • Julia Shumilina Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0002-9747-5779
  • Gregory Mavropolo-Stolyarenko Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0001-8712-0272
  • Tatiana Grishina Department of Biochemistry, Faculty of Biology, Saint Petersburg State University, Srednii prosp., 41–43, Saint Petersburg, 199004, Russian Federation https://orcid.org/0000-0002-5306-2980
  • Natalia Osmolovskaya Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0001-8764-8552
  • Vladimir Zhukov All-Russia Research Institute for Agricultural Microbiology, Podbelsky chaussee 3, Pushkin, Saint Petersburg, 196608, Russian Federation https://orcid.org/0000-0002-2411-9191
  • Wolfgang Hoehenwarter Proteome Analytics Research Group, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany https://orcid.org/0000-0002-7669-7524
  • Andrea Sinz Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Wolfgang-Langenbeck-Strasse 4, 06120 Halle/Saale DE, Martin-Luther Universität Halle-Wittenberg, Germany https://orcid.org/0000-0003-1521-4899
  • Igor Tikhononovich All-Russia Research Institute for Agricultural Microbiology, Podbelsky chaussee 3, Pushkin, Saint Petersburg, 196608, Russian Federation; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0001-8968-854X
  • Ludger Wessjohann Department of Bioorganic Chemistry, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany https://orcid.org/0000-0003-2060-8235
  • Tatiana Bilova Department of Bioorganic Chemistry, Weinberg 3, 06120 Halle/Saale DE, Leibniz Institute of Plant Biochemistry, Germany; Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0002-6024-3667
  • Galina Smolikova Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0001-5238-1851
  • Sergei Medvedev Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 199034, Russian Federation https://orcid.org/0000-0003-1127-1343

DOI:

https://doi.org/10.21638/spbu03.2018.106

Abstract

In the modern world, crop plants represent a major source of daily consumed foods. Among them, cereals and legumes — i.e. the crops accumulating oils, carbohydrates and proteins in their seeds — dominate in European agriculture, tremendously impacting global protein consumption and biodiesel production. Therefore, the seeds of crop plants attract the special attention of biologists, biochemists, nutritional physiologists and food chemists. Seed development and germination, as well as age- and stress-related changes in their viability and nutritional properties, can be addressed by a variety of physiological and biochemical methods. In this context, the methods of functional genomics can be applied to address characteristic changes in seed metabolism, which can give access to stress-resistant genotypes. Among these methods, proteomics is one of the most effective tools, allowing mining metabolism changes on the protein level. Here we discuss the main methodological approaches of seed proteomics in the context of physiological changes related to environmental stress and ageing. We provide a comprehensive comparison of gel- and chromatographybased approaches with a special emphasis on advantages and disadvantages of both strategies in characterization of the seed proteome.

Keywords:

food safety, LC-MS, post-translational modifications, proteomics, seed quality

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2018-06-08

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Frolov, A., Mamontova, T., Ihling, C., Lukasheva, E., Bankin, M., Chantseva, V., … Medvedev, S. (2018). Mining seed proteome: from protein dynamics to modification profiles. Biological Communications, 63(1), 43–58. https://doi.org/10.21638/spbu03.2018.106

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Vol. 63 No. 1 (2018)

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