Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga
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{"title"=>"Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga", "type"=>"journal", "authors"=>[{"first_name"=>"Michael T.", "last_name"=>"Guarnieri", "scopus_author_id"=>"7007125027"}, {"first_name"=>"Ambarish", "last_name"=>"Nag", "scopus_author_id"=>"13103774000"}, {"first_name"=>"Sharon L.", "last_name"=>"Smolinski", "scopus_author_id"=>"6603818452"}, {"first_name"=>"Al", "last_name"=>"Darzins", "scopus_author_id"=>"24178395500"}, {"first_name"=>"Michael", "last_name"=>"Seibert", "scopus_author_id"=>"7006117632"}, {"first_name"=>"Philip T.", "last_name"=>"Pienkos", "scopus_author_id"=>"35574272700"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"80054728497", "doi"=>"10.1371/journal.pone.0025851", "pui"=>"362771719", "pmid"=>"22043295", "scopus"=>"2-s2.0-80054728497", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"6f37f539-f415-3179-ab4b-ebe1b34ae2b0", "abstract"=>"Biofuels derived from algal lipids represent an opportunity to dramatically impact the global energy demand for transportation fuels. Systems biology analyses of oleaginous algae could greatly accelerate the commercialization of algal-derived biofuels by elucidating the key components involved in lipid productivity and leading to the initiation of hypothesis-driven strain-improvement strategies. However, higher-level systems biology analyses, such as transcriptomics and proteomics, are highly dependent upon available genomic sequence data, and the lack of these data has hindered the pursuit of such analyses for many oleaginous microalgae. In order to examine the triacylglycerol biosynthetic pathway in the unsequenced oleaginous microalga, Chlorella vulgaris, we have established a strategy with which to bypass the necessity for genomic sequence information by using the transcriptome as a guide. Our results indicate an upregulation of both fatty acid and triacylglycerol biosynthetic machinery under oil-accumulating conditions, and demonstrate the utility of a de novo assembled transcriptome as a search model for proteomic analysis of an unsequenced microalga.", "link"=>"http://www.mendeley.com/research/examination-triacylglycerol-biosynthetic-pathways-via-novo-transcriptomic-proteomic-analyses-unseque", "reader_count"=>191, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>53, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>55, "Student > Postgraduate"=>5, "Other"=>3, "Student > Master"=>29, "Student > Bachelor"=>11, "Lecturer"=>3, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>53, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>55, "Student > Postgraduate"=>5, "Other"=>3, "Student > Master"=>29, "Student > Bachelor"=>11, "Lecturer"=>3, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>13, "Agricultural and Biological Sciences"=>131, "Chemical Engineering"=>1, "Chemistry"=>3, "Computer Science"=>3, "Earth and Planetary Sciences"=>1, "Energy"=>1, "Engineering"=>10, "Environmental Science"=>11, "Biochemistry, Genetics and Molecular Biology"=>12, "Mathematics"=>1, "Neuroscience"=>1, "Psychology"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>13}, "Environmental Science"=>{"Environmental Science"=>11}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Engineering"=>{"Engineering"=>10}, "Chemistry"=>{"Chemistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Energy"=>{"Energy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>131}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>5, "Japan"=>1, "United Kingdom"=>2, "Malaysia"=>2, "India"=>3, "New Zealand"=>1, "Canada"=>2, "Netherlands"=>2, "Iran"=>1, "Ireland"=>1, "Brazil"=>2, "Germany"=>1}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/724092"], "description"=>"<p>Despite high sequence identity (Expect values<1e-124), ACAT was not identified using <i>Chlorophyta</i> sequence databases as search models in MS/MS analysis. Notably, underlined peptides differed by just a single amino acid substitution between <i>C. vulgaris</i> and <i>C. variabilis</i>, preventing positive identification. Using the <i>C. vulgaris</i> transcriptome as a sequence search database yielded 7 peptide identifications at a confidence interval >95%.</p>", "links"=>[], "tags"=>["alignment", "acetyl-coa", "acyltransferase", "peptides"], "article_id"=>394440, "categories"=>["Microbiology", "Inorganic Chemistry", "Biochemistry", "Plant Biology", "Biotechnology", "Genetics"], "users"=>["Michael T. Guarnieri", "Ambarish Nag", "Sharon L. Smolinski", "Al Darzins", "Michael Seibert", "Philip T. Pienkos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025851.g005", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_sequence_alignment_for_acetyl_coA_acyltransferase_ACAT_peptides_identified_via_MS_MS_analysis_/394440", "title"=>"Multiple sequence alignment for acetyl-coA acyltransferase (ACAT) peptides identified via MS/MS analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/723960"], "description"=>"<p>Functional distribution of the complete annotated <i>C. vulgaris</i> transcriptome (grey bars) and the 2,949 transcripts corresponding to proteins identified in sub-proteomic soluble fraction via MS/MS analysis (black bars). Distribution is represented as percent of total transcripts in respective fractions.</p>", "links"=>[], "tags"=>["ontology", "enrichment"], "article_id"=>394310, "categories"=>["Microbiology", "Inorganic Chemistry", "Biochemistry", "Plant Biology", "Biotechnology", "Genetics"], "users"=>["Michael T. Guarnieri", "Ambarish Nag", "Sharon L. Smolinski", "Al Darzins", "Michael Seibert", "Philip T. Pienkos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025851.g004", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_enrichment_analysis_/394310", "title"=>"Gene Ontology enrichment analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:45:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/723847"], "description"=>"<p>(A) One dimensional SDS-PAGE of <i>C. vulgaris</i> soluble fraction utilized for comparative proteomic analysis. M, Marker; N+, Nitrogen-replete; N−, Nitrogen-deplete. (B) Mass spectral analysis data for the <i>C. vulgaris</i> proteome searched against all available <i>Chlorophyta</i> genome databases (left) and the <i>C. vulgaris</i> Transcriptome (right).</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "plant biology", "biotechnology", "marine and aquatic sciences", "Biochemistry"], "article_id"=>394196, "categories"=>["Microbiology", "Inorganic Chemistry", "Biochemistry", "Plant Biology", "Biotechnology", "Genetics"], "users"=>["Michael T. Guarnieri", "Ambarish Nag", "Sharon L. Smolinski", "Al Darzins", "Michael Seibert", "Philip T. Pienkos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025851.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteomic_Analysis_of_C_vulgaris_/394196", "title"=>"Proteomic Analysis of <i>C. vulgaris</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:44:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/723747"], "description"=>"<p>Workflow for <i>de novo</i> transcriptome assembly and comparative proteomic analyses.</p>", "links"=>[], "tags"=>["transcriptome", "comparative", "proteomic"], "article_id"=>394096, "categories"=>["Microbiology", "Inorganic Chemistry", "Biochemistry", "Plant Biology", "Biotechnology", "Genetics"], "users"=>["Michael T. Guarnieri", "Ambarish Nag", "Sharon L. Smolinski", "Al Darzins", "Michael Seibert", "Philip T. Pienkos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025851.g002", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Workflow_for_de_novo_transcriptome_assembly_and_comparative_proteomic_analyses_/394096", "title"=>"Workflow for <i>de novo</i> transcriptome assembly and comparative proteomic analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:43:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/724217"], "description"=>"<p>(A) Critical components of the fatty acid and triacylglycerol (TAG) biosynthetic pathways were absent from initial MS/MS searches against all available <i>Chlorophyta</i> databases. Proteins highlighted in yellow were amongst the proteins absent from initial analyses, yet positively identified when searching against the <i>C. vulgaris</i> transcriptome database. Proteins in green (not highlighted) were identified using both <i>Chlorophyta</i> and <i>C. vulgaris</i> transcriptome databases. Numbers below proteins represent NSAF values (10<sup>5</sup>) for nitrogen replete and nitrogen deplete conditions, respectively. ACCase, acetyl-CoA carboxylase; ACP, acyl carrier protein; AMPK, AMP-activated kinase; DAGK, diacylglycerol kinase; DGAT, diacylglycerol acyltransferase; DHAP, dihydroxyacetone phosphate; ENR, enoyl-ACP reductase; FAT<sub>P</sub>, fatty acyl-ACP thioesterase (putative); G3PDH, glycerol-3-phosphate dehydrogenase; GPAT, glycerol-3-phosphate acyltransferase; HD, 3-hydroxyacyl-ACP dehydratase; KAR, 3-ketoacyl-ACP reductase; KAS, 3-ketoacyl-ACP synthase; LPAAT, lyso-phosphatidic acid acyltransferase; LPAT, lyso-phosphatidylcholine acyltransferase; MAT, malonyl-CoA:ACP transacylase; PAP, phosphatidic acid phosphatase. Adapted from Radakovits et al., 2010 and Hu et al., 2008. (B) Corresponding spectral count fold-changes for components of the FA (left panel) and TAG (right panel) biosynthetic components.</p>", "links"=>[], "tags"=>["pathway", "assembled", "transcriptome", "changes", "abundance", "nitrogen"], "article_id"=>394564, "categories"=>["Microbiology", "Inorganic Chemistry", "Biochemistry", "Plant Biology", "Biotechnology", "Genetics"], "users"=>["Michael T. Guarnieri", "Ambarish Nag", "Sharon L. Smolinski", "Al Darzins", "Michael Seibert", "Philip T. Pienkos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025851.g006", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Improved_pathway_identification_using_a_de_novo_assembled_transcriptome_database_and_changes_in_protein_abundance_under_nitrogen_depletion_/394564", "title"=>"Improved pathway identification using a <i>de novo</i> assembled transcriptome database and changes in protein abundance under nitrogen depletion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:46:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/723690"], "description"=>"<p>(A) Representative growth curves for <i>C. vulgaris</i> cultured photoautotrophically under nitrogen-replete (blue) and nitrogen-deplete (red) conditions. Harvest points utilized for all comparative analyses and images are circled. Inset: cultures grown under nitrogen-replete (green) and nitrogen-deplete (yellow) conditions. (B) Fatty acid methyl ester (FAME) analysis of <i>C. vulgaris</i> under nitrogen-replete and nitrogen-deplete conditions. (C) Average fatty acid composition (%, w/w) for <i>C. vulgaris</i> under nitrogen-replete and nitrogen-deplete conditions. (D) Epifluorescent microscopy images of BODIPY-stained <i>C. vulgaris</i> in nitrogen-replete (top panel) and nitrogen-deplete (bottom panel) medium. Red fluorescence is due to chlorophyll autofluorescence and green fluorescence is due to BODIPY-neutral lipid interaction. Magnification bar (white) equals 5 µm.</p>", "links"=>[], "tags"=>["lipid", "accumulation", "properties", "nitrogen"], "article_id"=>394034, "categories"=>["Microbiology", "Inorganic Chemistry", "Biochemistry", "Plant Biology", "Biotechnology", "Genetics"], "users"=>["Michael T. Guarnieri", "Ambarish Nag", "Sharon L. Smolinski", "Al Darzins", "Michael Seibert", "Philip T. Pienkos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025851.g001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_and_lipid_accumulation_properties_of_C_vulgaris_under_nitrogen_limitation_/394034", "title"=>"Growth and lipid accumulation properties of <i>C. vulgaris</i> under nitrogen limitation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:43:13"}

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Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[304, 568, 702, 818, 927, 1027, 1118, 1206, 1285, 1357, 1427, 1500, 1564, 1636, 1705, 1773, 1840, 1909, 1974, 2039, 2106, 2170, 2234, 2296, 2358, 2423, 2484, 2546, 2606, 2673, 2734, 2795, 2857, 2921, 2984, 3046, 3100]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[290, 559, 698, 813, 927, 1028, 1121, 1206, 1289, 1360, 1433, 1501, 1569, 1637, 1707, 1774, 1841, 1911, 1974, 2038, 2103, 2161, 2219, 2280, 2345, 2406, 2466, 2529, 2592, 2654, 2713, 2772, 2835, 2893, 2954, 3020, 3071]}]}
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