Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus – Contributors to Cellular Detoxification
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{"title"=>"Glutathione S-transferase (GST) gene diversity in the crustacean Calanus finmarchicus - Contributors to cellular detoxification", "type"=>"journal", "authors"=>[{"first_name"=>"Vittoria", "last_name"=>"Roncalli", "scopus_author_id"=>"36455018700"}, {"first_name"=>"Matthew C.", "last_name"=>"Cieslak", "scopus_author_id"=>"55928572600"}, {"first_name"=>"Yale", "last_name"=>"Passamaneck", "scopus_author_id"=>"6506117932"}, {"first_name"=>"Andrew E.", "last_name"=>"Christie", "scopus_author_id"=>"7103003926"}, {"first_name"=>"Petra H.", "last_name"=>"Lenz", "scopus_author_id"=>"7103014113"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"604276922", "sgr"=>"84929179830", "issn"=>"19326203", "pmid"=>"25945801", "scopus"=>"2-s2.0-84929179830", "doi"=>"10.1371/journal.pone.0123322", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)"}, "id"=>"72b3cf2d-ee73-38d5-91cd-3b47ab700574", "abstract"=>"Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multiple gene duplications, with over 40 GST genes reported in some insects. However, less is known about the GST superfamily in marine organisms, including crustaceans. The availability of two de novo transcriptomes for the copepod, Calanus finmarchicus, provided an opportunity for an in depth study of the GST superfamily in a marine crustacean. The transcriptomes were searched for putative GST-encoding transcripts using known GST proteins from three arthropods as queries. The identified transcripts were then translated into proteins, analyzed for structural domains, and annotated using reciprocal BLAST analysis. Mining the two transcriptomes yielded a total of 41 predicted GST proteins belonging to the cytosolic, mitochondrial or microsomal classes. Phylogenetic analysis of the cytosolic GSTs validated their annotation into six different subclasses. The predicted proteins are likely to represent the products of distinct genes, suggesting that the diversity of GSTs in C. finmarchicus exceeds or rivals that described for insects. Analysis of relative gene expression in different developmental stages indicated low levels of GST expression in embryos, and relatively high expression in late copepodites and adult females for several cytosolic GSTs. A diverse diet and complex life history are factors that might be driving the multiplicity of GSTs in C. finmarchicus, as this copepod is commonly exposed to a variety of natural toxins. Hence, diversity in detoxification pathway proteins may well be key to their survival.", "link"=>"http://www.mendeley.com/research/glutathione-stransferase-gst-gene-diversity-crustacean-calanus-finmarchicus-contributors-cellular-de", "reader_count"=>20, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>7, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>7, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Medicine and Dentistry"=>1, "Agricultural and Biological Sciences"=>6, "Pharmacology, Toxicology and Pharmaceutical Science"=>3, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>3}}, "reader_count_by_country"=>{"United States"=>1, "India"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2057474"], "description"=>"<p>Relative expression measured in 2011 (black bars) and 2012 (grey bars) for nine GSTs are shown for embryos, early nauplii (NI-II), late nauplii (NV-VI), early copepodites (CI-II), late copepodites (CV), and adult females as RPKM (reads per kilobase per million mapped reads) in Log<sub>2.</sub> (A) Cytosolic GSTs belonging to the Delta (A1-A2), Mu (A3), Omega (A4) and Sigma (A5-A6) subclasses. (B) Mitochondrial Kappa GST class. (C) Microsomal GST subclass 1 (C1) and subclass 3 (C2). Error bars in 2011 (black) are standard deviations of two technical replicates for each stage, while in 2012 (gray) error bars are standard deviations of three biological replicates.</p>", "links"=>[], "tags"=>["GST proteins", "GST superfamily", "cytosolic GSTs", "stress defense mechanism", "40 GST genes", "detoxification pathway proteins", "blast", "Cellular Detoxification Detoxification"], "article_id"=>1406869, "categories"=>["Biological Sciences"], "users"=>["Vittoria Roncalli", "Matthew C. Cieslak", "Yale Passamaneck", "Andrew E. Christie", "Petra H. Lenz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123322.g004", "stats"=>{"downloads"=>0, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_expression_of_selected_Calanus_finmarchicus_cytosolic_mitochondrial_and_microsomal_GST_encoding_transcripts_across_six_developmental_stages_/1406869", "title"=>"Relative expression of selected <i>Calanus finmarchicus</i> cytosolic, mitochondrial and microsomal GST-encoding transcripts across six developmental stages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-06 04:37:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2057475"], "description"=>"<p>BLAST searches were limited to NCBI non-redundant protein database for arthropods (taxid: 6656).</p><p>†Length in amino acids.</p><p>* Predicted full-length protein flanked by “stop” codons at both N- and C-terminals.</p><p>** Putative full-length protein flanked by a “methionine” at the N-terminal, and a “stop” codon at the C-terminal. Identification of full-length is based on presence of expected structural domains and similarity to full-length proteins.</p><p>*** Partial protein with either the N-terminal “methionine” or C-terminal “stop” codon missing.</p><p>**** Protein originally identified as full-length, but prediction corrected to partial after alignment with their most similar transcript in the Norwegian Sea transcriptome (see text).</p><p>Abbreviations: GSTN, GST amino (N)-terminal domain; GSTC, GST carboxyl (C)-terminal domain; THX, thioredoxin-like domain; MAPEG, membrane-associated proteins in eicosanoid and glutathione metabolism domain.</p><p>Annotation of putative glutathione S-transferase-encoding transcripts from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123322#pone.0123322.t001\" target=\"_blank\">Table 1</a>, using reciprocal BLAST results and protein domain analysis.</p>", "links"=>[], "tags"=>["GST proteins", "GST superfamily", "cytosolic GSTs", "stress defense mechanism", "40 GST genes", "detoxification pathway proteins", "blast", "Cellular Detoxification Detoxification"], "article_id"=>1406870, "categories"=>["Biological Sciences"], "users"=>["Vittoria Roncalli", "Matthew C. Cieslak", "Yale Passamaneck", "Andrew E. Christie", "Petra H. Lenz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123322.t002", "stats"=>{"downloads"=>2, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_of_putative_glutathione_S_transferase_encoding_transcripts_from_Table_1_using_reciprocal_BLAST_results_and_protein_domain_analysis_/1406870", "title"=>"Annotation of putative glutathione S-transferase-encoding transcripts from Table 1, using reciprocal BLAST results and protein domain analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-06 04:37:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2057472"], "description"=>"<p>(A) Alignment of <i>C</i>. <i>finmarchicus</i> putative microsomal GST-1 proteins (Calfi-mGST-1-I and Calfi-mGST-1-II) with the <i>T</i>. <i>japonicus</i> query used in their discovery (Tigja-mGST-1; <b>Accession No.</b><u><b>ACE81248</b></u>). Highlighted in green are amino acids in the conserved MAPEG structural domain identified using SMART software. The abbreviation “TM” indicates predicted transmembrane regions in the <i>C</i>. <i>finmarchicus</i> mGST-1 proteins. The ‘‘*” located beneath each alignment indicates residues that are identical in the two sequences, while ‘‘:” and ‘‘.” indicate conservatively substituted (similar) amino acids shared between the protein pairs. (B) Multiple alignments of <i>C</i>. <i>finmarchicus</i> microsomal GST-1 proteins (Calfi-mGST-1-I and Calfi-mGST-1-II) with publicly available mGST-1s from the crustaceans <i>C</i>. <i>clemensi</i> (Calcl), <i>C</i>. <i>rogercresseyi</i> (Calro), <i>L</i>. <i>salmonis</i> (Lepsa), <i>T</i>. <i>japonicus</i> (Tigja) and <i>D</i>. <i>pulex</i> (Dappu). The conserved motif consisting of 16 amino acids (VERVRR<i>X</i>HLND<i>X</i>ENI<i>X</i>, where the three <i>X</i>s represent variable residues) is highlighted in blue. The non-conservative substitution found only in <i>C</i>. <i>finmarchicus</i> is highlighted in pink.</p>", "links"=>[], "tags"=>["GST proteins", "GST superfamily", "cytosolic GSTs", "stress defense mechanism", "40 GST genes", "detoxification pathway proteins", "blast", "Cellular Detoxification Detoxification"], "article_id"=>1406867, "categories"=>["Biological Sciences"], "users"=>["Vittoria Roncalli", "Matthew C. Cieslak", "Yale Passamaneck", "Andrew E. Christie", "Petra H. Lenz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123322.g002", "stats"=>{"downloads"=>1, "page_views"=>54, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_Calanus_finmarchicus_microsomal_glutathione_S_transferase_subclass_1_proteins_with_mGST_1s_from_other_crustaceans_/1406867", "title"=>"Alignment of <i>Calanus finmarchicus</i> microsomal glutathione S-transferase subclass 1 proteins with mGST-1s from other crustaceans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-06 04:37:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2057473"], "description"=>"<p>The consensus Bayesian likelihood tree shows the relationships between cytosolic GSTs from <i>C</i>. <i>finmarchicus</i> (Cf, in color) and those from the insect <i>D</i>. <i>melanogaster</i> (Dm), the copepod <i>T</i>. <i>japonicus</i> (Tj), and the cladoceran <i>D</i>. <i>pulex</i> (Dp). The tree was built using an analysis of 10,000,000 generations in MrBayes, excluding the initial 2,500,000 generations as burn-in. Bootstrap values were calculated using RAxML with 1,000 interactions. For 73 branches, Bayesian posterior probabilities were grater than P>0.5, 68% of those with P between 0.9 and 1 (data not shown). 73 branches had bootstrap values greater than 50% (color-coded circles).</p>", "links"=>[], "tags"=>["GST proteins", "GST superfamily", "cytosolic GSTs", "stress defense mechanism", "40 GST genes", "detoxification pathway proteins", "blast", "Cellular Detoxification Detoxification"], "article_id"=>1406868, "categories"=>["Biological Sciences"], "users"=>["Vittoria Roncalli", "Matthew C. Cieslak", "Yale Passamaneck", "Andrew E. Christie", "Petra H. Lenz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123322.g003", "stats"=>{"downloads"=>0, "page_views"=>48, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_for_cytosolic_GSTs_from_the_crustacean_Calanus_finmarchicus_and_other_selected_crustacean_and_insect_species_/1406868", "title"=>"Phylogenetic tree for cytosolic GSTs from the crustacean <i>Calanus finmarchicus</i> and other selected crustacean and insect species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-06 04:37:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2057470"], "description"=>"<p>(A) Alignment of <i>D</i>. <i>pulex</i> Delta GST (Dappu-Delta) (<b>Accession No.</b><u><b>EFX81633</b></u>; 222 amino acids long) and Calfi-Delta-IV (220 amino acids long). (B) Alignment of the <i>T</i>. <i>japonicus</i> Mu GST (Tigja-Mu; <b>Accession No.</b><u><b>ACE81254</b></u>; 221 amino acids long) and Calfi-Mu-III (222 amino acids long). In each panel, ‘‘*” located beneath the alignment indicates residues that are identical in the two sequences, while ‘‘:” and ‘‘.” indicate conservatively substituted (similar) amino acids shared between the protein pairs. Amino acids highlighted in black are the ones predicted by SMART analysis to form the conserved amino (N)-terminal domain (GSTN), amino acids highlighted in red represent the conserved carboxyl (C)-terminal domain (GSTC).</p>", "links"=>[], "tags"=>["GST proteins", "GST superfamily", "cytosolic GSTs", "stress defense mechanism", "40 GST genes", "detoxification pathway proteins", "blast", "Cellular Detoxification Detoxification"], "article_id"=>1406865, "categories"=>["Biological Sciences"], "users"=>["Vittoria Roncalli", "Matthew C. Cieslak", "Yale Passamaneck", "Andrew E. Christie", "Petra H. Lenz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123322.g001", "stats"=>{"downloads"=>0, "page_views"=>46, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_selected_Calanus_finmarchicus_Delta_GST_Calfi_Delta_IV_and_Mu_GST_Calfi_Mu_III_proteins_with_their_top_arthropod_protein_BLAST_hits_/1406865", "title"=>"Alignment of selected <i>Calanus finmarchicus</i> Delta GST (Calfi-Delta-IV) and Mu GST (Calfi-Mu-III) proteins with their top arthropod protein BLAST hits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-06 04:37:02"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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