Posttranslational modifications in proteins: resources, tools and prediction methods. Ramazi Shahin,Zahiri Javad Database : the journal of biological databases and curation Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well. 10.1093/database/baab012

Proteomics of stress responses in wheat and barley-search for potential protein markers of stress tolerance. Frontiers in plant science Wheat (Triticum aestivum; T. durum) and barley (Hordeum vulgare) agricultural production is severely limited by various abiotic and biotic stress factors. Proteins are directly involved in plant stress response so it is important to study proteome changes under various stress conditions. Generally, both abiotic and biotic stress factors induce profound alterations in protein network covering signaling, energy metabolism (glycolysis, Krebs cycle, ATP biosynthesis, photosynthesis), storage proteins, protein metabolism, several other biosynthetic pathways (e.g., S-adenosylmethionine metabolism, lignin metabolism), transport proteins, proteins involved in protein folding and chaperone activities, other protective proteins (LEA, PR proteins), ROS scavenging enzymes as well as proteins affecting regulation of plant growth and development. Proteins which have been reported to reveal significant differences in their relative abundance or posttranslational modifications between wheat, barley or related species genotypes under stress conditions are listed and their potential role in underlying the differential stress response is discussed. In conclusion, potential future roles of the results of proteomic studies in practical applications such as breeding for an enhanced stress tolerance and the possibilities to test and use protein markers in the breeding are suggested. 10.3389/fpls.2014.00711

Methodological evaluation of 2-DE to study root proteomics during nematode infection in cotton and coffee plants. Franco Octavio L,Pereira Jackeline L,Costa Paulo H A,Rocha Thales L,Albuquerque Erika V S,Grossi-de-Sá Maria F,Carneiro Regina M D G,Carneiro Rui G,Mehta Angela Preparative biochemistry & biotechnology The identification of plant proteins expressed in response to phytopathogens is a remaining challenge to proteome methodology. Proteomic methods, such as electrophoresis and mass spectrometry have been extensively used for protein differential expression studies in several plants including Arabidopsis thaliana, rice, and wheat. However, in coffee (Coffea canephora) and cotton (Gossypium hirsutum), bidimensional electrophoresis (2-DE) analysis has been rarely employed. Moreover, global protein expression in both agricultural plants in response to biotic stress conditions had not been reported until now. In this study, Meloidogyne paranaensis and M. incognita, two devastating phytonematodes for numerous crop cultures, were used to infect resistant genotypes of coffee and cotton plants. The protein expression of infected- and non-infected roots were evaluated by 2-DE following in silico experiments. Additionally, gels were stained with silver nitrate and/or Coomassie brilliant blue in order to obtain an optimized method for proteomic analysis of plant-nematode interaction. The 2-DE analysis revealed an enhanced number of protein spots, as well as differentially expressed proteins, when Coomassie brilliant blue was used. The results obtained here could be extended to other plant species, providing valuable information to root-nematode interactions. 10.1080/10826060903558976