The Spectrum of Major Seed Storage Genes and Proteins in Oats (Avena sativa)
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{"title"=>"The spectrum of major seed storage genes and proteins in oats (Avena sativa)", "type"=>"journal", "authors"=>[{"first_name"=>"Olin D.", "last_name"=>"Anderson", "scopus_author_id"=>"7101972387"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84904598781", "doi"=>"10.1371/journal.pone.0083569", "pui"=>"373596225", "pmid"=>"25054628", "scopus"=>"2-s2.0-84904598781", "issn"=>"19326203"}, "id"=>"b003158b-8ef2-3886-82d9-b47069593fcf", "abstract"=>"BACKGROUND: The oat seed storage proteins are mainly composed of two classes: the globulins and avenins. Among the major cereals, the globulins are the major seed protein class in rice and oats, and along with the higher protein content of oats is the basis for the relative higher nutrition content in oats compared to the other cereals. The second major class of oat seed proteins is the avenins; also classified as prolamins - seed proteins high in proline and glutamine amino acids. The prolamins are associated with celiac disease, an autoimmune disorder of the gastrointestinal tract. In spite of their importance, neither the oat globulins nor the avenins have been completely analyzed and described for any single germplasm.\\n\\nRESULTS: Using available EST resources for a single hexaploid oat cultivar, the spectrum of avenin and globulin sequences are described for the gene coding regions and the derived protein sequences. The nine unique avenin sequences are suggested to be divided into 3-4 distinct subclasses distributed in the hexaploid genome. The globulins from the same germplasm include 24 distinct sequences. Variation in globulin size results mainly from a glutamine-rich domain, similar to as in the avenins, and to variation in the C-terminal sequence domain. Two globulin genes have premature stop codons that shorten the resulting polypeptides by 9 and 17 amino acids, and eight of the globulin sequences form a branch of the globulins not previously reported.\\n\\nCONCLUSIONS: A more complete description of the major oat seed proteins should allow a more thorough analysis of their contributions to those oat seed characteristics related to nutritional value, evolutionary history, and celiac disease association.", "link"=>"http://www.mendeley.com/research/spectrum-major-seed-storage-genes-proteins-oats-avena-sativa", "reader_count"=>43, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>6, "Other"=>4, "Student > Bachelor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>6, "Other"=>4, "Student > Bachelor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>14, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>17, "Chemistry"=>5, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>1, "Paraguay"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1607017"], "description"=>"<p>The repetitive units for domains II and IV are arrayed vertically for four of the CDC Dancer avenins.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "repetitive"], "article_id"=>1116032, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Avenin_repetitive_units_/1116032", "title"=>"Avenin repetitive units.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607015"], "description"=>"<p>The avenin polypeptide structure is shown divided into regions labeled by Roman numerals (I to VI). The signal peptide is SIG. Two glutamine plus proline/leucine regions are indicated and shaded. Cysteine residue positions are indicated by an S (representing the cysteine sulfhydryl group) and lines connecting the cysteines are intramolecular bonds previously determined for an oat avenin <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083569#pone.0083569-Egorov2\" target=\"_blank\">[16]</a>. (S) represents the additional cysteine in some avenins.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "avenin", "polypeptide"], "article_id"=>1116030, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.g002", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_of_oat_avenin_polypeptide_organization_/1116030", "title"=>"Model of oat avenin polypeptide organization.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607020"], "description"=>"1<p>Number of amino acid residues in mature polypeptide.</p>2<p>Calcultated Daltons to the first stop codon.</p>3<p>Number of assigned ESTs in contig.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "cv", "cdc", "avenin", "globulin"], "article_id"=>1116035, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.t001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oat_cv_CDC_Dancer_avenin_and_globulin_protein_characteristics_/1116035", "title"=>"Oat cv CDC Dancer avenin and globulin protein characteristics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607019"], "description"=>"<p>Sixteen of the CDC Dancer globulin derived amino acid sequences are aligned by ClustalW. Sequences are labeled by number only; i.e., “2” indicates sequence Glo-2. Not shown are eight sequences that are either C-terminal truncated or almost identical to shown sequences. The horizontal red line separates two main classes of oat globulins. The vertical red line indicates the end of the signal peptide. Amino acid residue positions conserved in all sixteen sequences are shaded blue. Conservation is defined as the same amino acid or amino acids with similar characteristics; i.e., D/E, F/Y, K/R, L/I/V/A, S/T. Cysteine residues are shaded yellow. The arrowhead following position 326 indicates site of the post-translational cleavage generating two disulfide crosslinked polypeptides. Premature stop codons are indicated by boxed periods in Glo-10 and Glo-15.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "globulin", "amino"], "article_id"=>1116034, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.g006", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_oat_globulin_amino_acid_sequences_/1116034", "title"=>"Alignment of oat globulin amino acid sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607014"], "description"=>"<p>The derived amino acid sequences of the nine cv CDC Dancer avenins are aligned with ClustalW. Positions within the total alignment are noted above the sequences. Domains of the polypeptides are indicated below the sequences in Roman numerals. Amino acid residue positions conserved in all nine sequences are shaded blue. Conservation being defined as the same amino acid or amino acids with similar characteristics; i.e., D/E, F/Y, K/R, L/I/V/A, S/T. Cysteine residues are shaded yellow. Horizontal red lines separate major subclasses. The vertical red line indicates the site of cleavage of the signal peptide during post-translational processing.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "avenin", "amino"], "article_id"=>1116029, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_avenin_amino_acid_sequences_/1116029", "title"=>"Alignment of avenin amino acid sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607021", "https://ndownloader.figshare.com/files/1607022", "https://ndownloader.figshare.com/files/1607023", "https://ndownloader.figshare.com/files/1607024", "https://ndownloader.figshare.com/files/1607025", "https://ndownloader.figshare.com/files/1607026"], "description"=>"<div><p>Background</p><p>The oat seed storage proteins are mainly composed of two classes: the globulins and avenins. Among the major cereals, the globulins are the major seed protein class in rice and oats, and along with the higher protein content of oats is the basis for the relative higher nutrition content in oats compared to the other cereals. The second major class of oat seed proteins is the avenins; also classified as prolamins – seed proteins high in proline and glutamine amino acids. The prolamins are associated with celiac disease, an autoimmune disorder of the gastrointestinal tract. In spite of their importance, neither the oat globulins nor the avenins have been completely analyzed and described for any single germplasm.</p><p>Results</p><p>Using available EST resources for a single hexaploid oat cultivar, the spectrum of avenin and globulin sequences are described for the gene coding regions and the derived protein sequences. The nine unique avenin sequences are suggested to be divided into 3–4 distinct subclasses distributed in the hexaploid genome. The globulins from the same germplasm include 24 distinct sequences. Variation in globulin size results mainly from a glutamine-rich domain, similar to as in the avenins, and to variation in the C-terminal sequence domain. Two globulin genes have premature stop codons that shorten the resulting polypeptides by 9 and 17 amino acids, and eight of the globulin sequences form a branch of the globulins not previously reported.</p><p>Conclusions</p><p>A more complete description of the major oat seed proteins should allow a more thorough analysis of their contributions to those oat seed characteristics related to nutritional value, evolutionary history, and celiac disease association.</p></div>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "genes", "oats"], "article_id"=>1116036, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0083569.s001", "https://dx.doi.org/10.1371/journal.pone.0083569.s002", "https://dx.doi.org/10.1371/journal.pone.0083569.s003", "https://dx.doi.org/10.1371/journal.pone.0083569.s004", "https://dx.doi.org/10.1371/journal.pone.0083569.s005", "https://dx.doi.org/10.1371/journal.pone.0083569.s006"], "stats"=>{"downloads"=>6, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Spectrum_of_Major_Seed_Storage_Genes_and_Proteins_in_Oats_Avena_sativa_/1116036", "title"=>"The Spectrum of Major Seed Storage Genes and Proteins in Oats (<i>Avena sativa</i>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607018"], "description"=>"<p>Shown is a phylogenetic tree oat avenin amino acid sequences constructed by the Neighbor-joining algorithm from a ClustalW alignment of all 24 CDC Dancer globulins (in bold) and the eight oat globulin sequences currently available in Genbank (labeled by accession numbers). Astericks indicate partial sequences. Tree validity was checked by bootstrap using 500 iterations.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "cdc"], "article_id"=>1116033, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.g005", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_CDC_Dancer_globulins_/1116033", "title"=>"Phylogenetic tree of CDC Dancer globulins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 05:08:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1607016"], "description"=>"<p>The avenin amino acid alignment in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083569#pone-0083569-g001\" target=\"_blank\">Figure 1</a> is used to generate a phylogenetic tree by the Neighbor-joining algorithm. Tree validity was checked by bootstrap using 500 iterations.</p>", "links"=>[], "tags"=>["agriculture", "crops", "Cereal crops", "oat", "Biochemistry", "proteins", "Nutrient and storage proteins", "protein structure", "Plant biochemistry", "Protein chemistry", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "genomics", "Plant genetics", "Plant science", "Plant physiology", "Gastroenterology and hepatology", "cdc"], "article_id"=>1116031, "categories"=>["Biological Sciences"], "users"=>["Olin D. Anderson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083569.g003", "stats"=>{"downloads"=>4, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_CDC_Dancer_avenins_/1116031", "title"=>"Phylogenetic tree of CDC Dancer avenins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 05:08:16"}

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Relative Metric

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