Seed coats serve as protective tissue to the enclosed embryo. As well as mechanical there are also chemical defence functions. During domestication, the property of the seed coat was altered including the removal of the seed dormancy.We used a range of genetic, transcriptomic, proteomic and metabolomic approaches to determine the function of the pea seed polyphenol oxidase (PPO) gene. Sequencing analysis revealed one nucleotide insertion or deletion in the PPO gene, with the functional PPO allele found in all wild pea samples, while most cultivated peas have one of the three nonfunctional ppo alleles. PPO functionality cosegregates with hilum pigmentation. PPO gene and protein expression, as well as enzymatic activity, was downregulated in the seed coats of cultivated peas.The functionality of the PPO gene relates to the oxidation and polymerisation of gallocatechin in the seed coat. Additionally, imaging mass spectrometry supports the hypothesis that hilum pigmentation is conditioned by the presence of both phenolic precursors and sufficient PPO activity.Taken together these results indicate that the nonfunctional polyphenol oxidase gene has been selected during pea domestication, possibly due to better seed palatability or seed coat visual appearance.

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Because of ongoing climate change, drought is becoming the major factor limiting productivity of all plants, including legumes. As these protein-rich crops form symbiotic associations with rhizobial bacteria — root nodules — they readily lose their productivity under drought conditions. Understanding the underlying molecular mechanisms might give access to new strategies to preserve the productivity of legume crops under dehydration. As was shown recently, development of drought response is accompanied by alterations in the patterns of protein glycation and formation of advanced glycation end products (AGEs) that might be a part of unknown regulatory mechanisms. Therefore, here we address the effects of moderate drought on protein dynamics and AGE patterns in pea (Pisum sativum) root nodules. For this, plants inoculated with rhizobial culture were subjected to osmotic stress for one week, harvested, the total protein fraction was isolated from root nodules by phenol extraction, analyzed by bottom-up LC-MS-based proteomics, and AGE patterns were characterized. Surprisingly, despite the clear drought-related changes in phenotype and stomatal conductivity, only minimal accompanying expressional changes (14 rhizobial and 14 pea proteins, mostly involved in central metabolism and nitrogen fixation) could be observed. However, 71 pea and 97 rhizobial proteins (mostly transcription factors, ABC transporters and effector enzymes) were glycated, with carboxymethylation being the major modification type. Thereby, the numbers of glycated sites in nodule proteins dramatically decreased upon stress application. It might indicate an impact of glycation in regulation of transport, protein degradation, central, lipid and nitrogen metabolism. The data are available at Proteome Xchange (accession: PXD024042).

Phaeophyceae (brown algae) essentially contribute to biotopes of cold and temperate seas. Their thalli are rich in biologically active natural products, which are strongly and universally dominated with phlorotannins—polyphenols of complex and diverse structure based on multiple differently arranged phloroglucinol units and well known as strong antioxidants with a broad spectrum of biological activities. In the algal cells, phlorotannins can either accumulate in the cytoplasm or can be secreted into the cell wall (CW). The biological activities of extractable intracellular phlorotannins have been comprehensively characterized, whereas the properties of the CW-bound polyphenol fraction are still mostly unknown. Recently, we identified dibenzodioxin bonding as the principal structural feature of the CW-bound phlorotannins in fucoid algae, whereas soluble intracellular phlorotannins rely on aryl and ether bonds. However, profiles of biological activity associated with these structural differences are still unknown. Therefore, to the best of our knowledge, for the first time we address the antioxidant, cytotoxic, neuroprotective, and antibacterial properties of the CW-bound phlorotannin fractions isolated from two representatives of the order Fucales—Fucus vesiculosus and Pelvetia canaliculata. The CW-bound phlorotannins appeared to be softer antioxidants, stronger antibacterial agents and were featured with essentially less cytotoxicity in comparison to the intracellular fraction. However, the neuroprotective effects of both sub-cellular phlorotannin fractions of F. vesiculosus and P. canaliculata were similar. Thus, due to their lower cytotoxicity, CW-bound phlorotannins can be considered as promising antioxidants and neuroprotectors.

The Phaeophyceae (brown algae) essentially contribute to biotopes of cold and temperate seas. Their thalli are rich in biologically active natural products which are strongly and universally dominated with phlorotannins – polyphenols of complex and diverse structure based on multiple differently arranged phloroglucinol units. These electron-rich compounds are strong antioxidants with antimicrobial, anti-inflammatory and neuroprotective activities. In the algal cells phlorotannins can either accumulate in cytoplasm or can be secreted into the cell wall (CW) with subsequent covalent binding to the alginate network. The biological activities of easily extractable intracellular phlorotannins were comprehensively characterized, whereas the properties of the CW-bound polyphenol fraction are still mostly unknown. Recently, we identified dibenzodioxin bonding as the principal structural feature of the CW-bound phlorotannins of fucoid algae, whereas soluble intracellular phlorotannins relied on aryl- and ether bonds. However, profiles of biological activity associated with these structural differences are still unknown. Therefore, here, to the best of our knowledge, for the first time, we address the antioxidant, cytotoxic, neuroprotective, and antibacterial properties of the CW-bound phlorotannin fractions isolated from two representatives of the order Fucales - Fucus vesiculosus and Pelvetia canaliculata. The CW-bound phlorotannins appeared to be softer antioxidants, stronger antibacterial agents and were featured with essentially less cytotoxicity in comparison to the intracellular fraction. However, the neuroprotective effects of both sub-cellular phlorotannin fractions of F. vesiculosus and P. canaliculata were essentially similar. Thus, due to their lower cytotoxicity, CW-bound phlorotannins can be considered as promising antioxidants and neuroprotectors.