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{"title"=>"Origin of saxitoxin biosynthetic genes in cyanobacteria", "type"=>"journal", "authors"=>[{"first_name"=>"Ahmed", "last_name"=>"Moustafa", "scopus_author_id"=>"55251149600"}, {"first_name"=>"Jeannette E.", "last_name"=>"Loram", "scopus_author_id"=>"16646493000"}, {"first_name"=>"Jeremiah D.", "last_name"=>"Hackett", "scopus_author_id"=>"7102250019"}, {"first_name"=>"Donald M.", "last_name"=>"Anderson", "scopus_author_id"=>"7410018378"}, {"first_name"=>"F. Gerald", "last_name"=>"Plumley", "scopus_author_id"=>"6603530923"}, {"first_name"=>"Debashish", "last_name"=>"Bhattacharya", "scopus_author_id"=>"7201931909"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0005758", "sgr"=>"66749091566", "issn"=>"19326203", "pui"=>"354694317", "isbn"=>"1932-6203", "pmid"=>"19484122", "scopus"=>"2-s2.0-66749091566"}, "id"=>"e7afd5df-b9e0-33f1-a3fa-72b4e5c2ca4b", "abstract"=>"Paralytic shellfish poisoning (PSP) is a potentially fatal syndrome associated with the consumption of shellfish that have accumulated saxitoxin (STX). STX is produced by microscopic marine dinoflagellate algae. Little is known about the origin and spread of saxitoxin genes in these under-studied eukaryotes. Fortuitously, some freshwater cyanobacteria also produce STX, providing an ideal model for studying its biosynthesis. Here we focus on saxitoxin-producing cyanobacteria and their non-toxic sisters to elucidate the origin of genes involved in the putative STX biosynthetic pathway.", "link"=>"http://www.mendeley.com/research/origin-saxitoxin-biosynthetic-genes-cyanobacteria", "reader_count"=>128, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>10, "Student > Doctoral Student"=>9, "Researcher"=>32, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>11, "Other"=>6, "Student > Bachelor"=>15, "Lecturer"=>2, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>10, "Student > Doctoral Student"=>9, "Researcher"=>32, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>11, "Other"=>6, "Student > Bachelor"=>15, "Lecturer"=>2, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Engineering"=>1, "Environmental Science"=>9, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>85, "Medicine and Dentistry"=>2, "Chemistry"=>12, "Earth and Planetary Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>12}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>85}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>9}}, "reader_count_by_country"=>{"Argentina"=>1, "Uruguay"=>1, "United States"=>2, "Philippines"=>1, "Egypt"=>2, "Brazil"=>1, "Chile"=>2, "France"=>2, "Portugal"=>2, "Switzerland"=>1, "India"=>1, "French Polynesia"=>1}, "group_count"=>2}

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/bc4e84ed-3588-424c-a10c-bb851d03e1c6", "title"=>"Data availability", "body"=>"The cyanobacterial partial genome data described in this paper are available for download at: \nhttp://dblab.rutgers.edu/home/downloads/index.php \nin the \"Supplemental Material\" section. These data will also be available at NCBI under the BioProject number PRJNA69805.\n\nThe web site for reference 10 (RAST) in this paper is: \nhttp://rast.nmpdr.org/\nand the reference is:\n\nAziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75.", "isRemoved"=>false, "created"=>"2012-02-01T14:53:37Z", "lastModified"=>"2012-02-01T14:53:37Z", "creator"=>{"userId"=>"67087"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0005758", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2012-02-01T14:53:37Z", "replies"=>[]}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/896219"], "description"=>"<p>ML phylogenetic tree of sxtN (sulfotransferase) that represents saxitoxin-related genes of cyanobacterial origin that is potentially from members of the Oscillatoriales. ML bootstrap values (when ≥50%) are indicated at the nodes. The branch lengths are proportional to the number of substitutions per site (see scale in the figure). Cyanobacterial taxa are shown in blue text, non-cyanobacterial prokaryotes in black text, and eukaryotes (Plantae) in green. The tree has been rooted on the branch leading to the non-cyanobacterial prokaryotes.</p>", "links"=>[], "tags"=>["Evolutionary biology", "evolutionary biology/bioinformatics", "evolutionary biology/evolutionary ecology", "evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/genomics", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/comparative genomics", "genetics and genomics/microbial evolution and genomics", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics"], "article_id"=>566656, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_sxtN_/566656", "title"=>"Phylogeny of sxtN.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-01 01:50:56"}
• {"files"=>["https://ndownloader.figshare.com/files/896394"], "description"=>"<p>Venn diagram showing the genome-wide distribution of genes in the STX+ cyanobacterium <i>Anabaena circinalis</i> ACBU02 with respect to sequences shared with other prokaryotes and viruses.</p>", "links"=>[], "tags"=>["acbu02"], "article_id"=>566851, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.g005", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Origin_of_ACBU02_genes_/566851", "title"=>"Origin of ACBU02 genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-01 01:54:11"}
• {"files"=>["https://ndownloader.figshare.com/files/443536"], "description"=>"<div><h3>Background</h3><p>Paralytic shellfish poisoning (PSP) is a potentially fatal syndrome associated with the consumption of shellfish that have accumulated saxitoxin (STX). STX is produced by microscopic marine dinoflagellate algae. Little is known about the origin and spread of saxitoxin genes in these under-studied eukaryotes. Fortuitously, some freshwater cyanobacteria also produce STX, providing an ideal model for studying its biosynthesis. Here we focus on saxitoxin-producing cyanobacteria and their non-toxic sisters to elucidate the origin of genes involved in the putative STX biosynthetic pathway.</p><h3>Methodology/Principal Findings</h3><p>We generated a draft genome assembly of the saxitoxin-producing (STX+) cyanobacterium <em>Anabaena circinalis</em> ACBU02 and searched for 26 candidate saxitoxin­genes (named <em>sxtA</em> to <em>sxtZ</em>) that were recently identified in the toxic strain <em>Cylindrospermopsis raciborskii</em> T3. We also generated a draft assembly of the non-toxic (STX−) sister <em>Anabaena circinalis</em> ACFR02 to aid the identification of saxitoxin-specific genes. Comparative phylogenomic analyses revealed that nine putative STX genes were horizontally transferred from non-cyanobacterial sources, whereas one key gene (<em>sxtA</em>) originated in STX+ cyanobacteria <em>via</em> two independent horizontal transfers followed by fusion. In total, of the 26 candidate saxitoxin-genes, 13 are of cyanobacterial provenance and are monophyletic among the STX+ taxa, four are shared amongst STX+ and STX-cyanobacteria, and the remaining nine genes are specific to STX+ cyanobacteria.</p><h3>Conclusions/Significance</h3><p>Our results provide evidence that the assembly of STX genes in ACBU02 involved multiple HGT events from different sources followed presumably by coordination of the expression of foreign and native genes in the common ancestor of STX+ cyanobacteria. The ability to produce saxitoxin was subsequently lost multiple independent times resulting in a nested relationship of STX+ and STX− strains among <em>Anabaena circinalis</em> strains.</p></div>", "links"=>[], "tags"=>["saxitoxin", "biosynthetic", "genes", "cyanobacteria"], "article_id"=>147432, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Origin_of_Saxitoxin_Biosynthetic_Genes_in_Cyanobacteria/147432", "title"=>"Origin of Saxitoxin Biosynthetic Genes in Cyanobacteria", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-01 02:03:52"}
• {"files"=>["https://ndownloader.figshare.com/files/896286"], "description"=>"<p>(a) Schematic diagram illustrating the fusion event that resulted in sxtA (polyketide synthase) in STX+ cyanobacteria. (b) ML phylogenetic tree of sxtA after dividing it into its two phylogenetic components; i.e., sxtA1 (a gene encoding acyl-CoA N-acyltransferase and phosphopantetheine binding domain-containing protein) and sxtA2 (a gene encoding aminotransferase class I and II). ML bootstrap values (when ≥50%) are indicated at the nodes. The branch lengths are proportional to the number of substitutions per site (see scale in the figure). Cyanobacterial taxa are shown in blue text, actinobacteria in brown text, proteobacteria in red text, and other non-cyanobacterial prokaryotes in black. The tree was rooted on the branch separating the two gene fusion partners.</p>", "links"=>[], "tags"=>["fusion"], "article_id"=>566740, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_fusion_origin_of_sxtA_/566740", "title"=>"Gene fusion origin of sxtA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-01 01:52:20"}
• {"files"=>["https://ndownloader.figshare.com/files/896454"], "description"=>"<p>Unrooted ML phylogenetic tree of a putative STX+ specific S-adenosyl-L-methionine (SAM)-dependent methyltransferase that has a potential <i>Bacillus</i>-like origin. ML bootstrap values (when ≥50%) are indicated at the nodes. The branch lengths are proportional to the number of substitutions per site (see scale in the figure). Cyanobacterial taxa are shown in blue text, non-cyanobacterial prokaryotes in black text, and eukaryotes (Plantae) in green.</p>", "links"=>[], "tags"=>["sam-dependent"], "article_id"=>566910, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_SAM_dependent_methyltransferase_/566910", "title"=>"Phylogeny of SAM-dependent methyltransferase.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-01 01:55:10"}
• {"files"=>["https://ndownloader.figshare.com/files/896101"], "description"=>"<p>ML phylogenetic trees of (a) sxtY (phosphate uptake regulator) and (b) sxtZ (histidine kinase). These represent the class of saxitoxin-related genes of cyanobacterial origin in which taxa most closely related to the STX+ strains are members of the Nostocaceae. ML bootstrap values (when ≥50%) are indicated at the nodes. The branch lengths are proportional to the number of substitutions per site (see scales in the figure). Cyanobacterial taxa are shown in blue text, non-cyanobacterial prokaryotes in black text, and eukaryotes (Plantae) in green except for the photosynthetic filose amoeba <i>Paulinella chromatophora</i> in red. The trees have been rooted arbitrarily.</p>", "links"=>[], "tags"=>["sxty"], "article_id"=>566555, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_sxtY_and_sxtZ_/566555", "title"=>"Phylogeny of sxtY and sxtZ.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-01 01:49:15"}
• {"files"=>["https://ndownloader.figshare.com/files/895951"], "description"=>"<p>Unrooted ML phylogenetic trees inferred from small subunit (16S) rRNA that include (a) different cyanobacterial orders and (b) only saxitoxin-producing (STX+) and STX− strains of <i>Anabaena circinalis</i>. ML bootstrap values (when ≥50%) are indicated at the nodes. The branch lengths are proportional to the number of substitutions per site (see scales in the figure). The toxic and non-toxic strains are indicated by the plus sign (+) and minus sign (−), respectively.</p>", "links"=>[], "tags"=>["16s", "rrna"], "article_id"=>566398, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_16S_rRNA_from_cyanobacteria_/566398", "title"=>"Phylogenetic tree of 16S rRNA from cyanobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-01 01:46:38"}
• {"files"=>["https://ndownloader.figshare.com/files/896512"], "description"=>"<p>The rows are grouped based on the origin of the genes and the monophyly of the STX+ taxa for the respective gene as following: I = Cyanobacteria and not monophyletic, II = Cyanobacteria and monophyletic, III = Proteobacteria, IV = Firmicutes, V = Unknown, VI = Chimeric.</p>", "links"=>[], "tags"=>["biosynthesis", "saxitoxin", "putative"], "article_id"=>566965, "categories"=>["Evolutionary Biology", "Microbiology", "Genetics"], "users"=>["Ahmed Moustafa", "Jeannette E. Loram", "Jeremiah D. Hackett", "Donald M. Anderson", "F. Gerald Plumley", "Debashish Bhattacharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005758.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_involved_in_the_biosynthesis_of_saxitoxin_in_cyanobacteria_their_putative_functional_annotation_and_origin_/566965", "title"=>"Genes involved in the biosynthesis of saxitoxin in cyanobacteria, their putative functional annotation, and origin", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-01 01:56:05"}

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Relative Metric

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F1000Prime