Trichomonas Transmembrane Cyclases Result from Massive Gene Duplication and Concomitant Development of Pseudogenes
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{"title"=>"Trichomonas transmembrane cyclases result from massive gene duplication and concomitant development of pseudogenes", "type"=>"journal", "authors"=>[{"first_name"=>"Jike", "last_name"=>"Cui", "scopus_author_id"=>"36808172300"}, {"first_name"=>"Suchismita", "last_name"=>"Das", "scopus_author_id"=>"54388770600"}, {"first_name"=>"Temple F.", "last_name"=>"Smith", "scopus_author_id"=>"7405496903"}, {"first_name"=>"John", "last_name"=>"Samuelson", "scopus_author_id"=>"7006708022"}], "year"=>2010, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"pui"=>"359899890", "sgr"=>"78149248014", "isbn"=>"1935-2735", "scopus"=>"2-s2.0-78149248014", "issn"=>"1935-2735", "pmid"=>"20689771", "doi"=>"10.1371/journal.pntd.0000782"}, "id"=>"aa04fc71-6439-3e65-88be-a5adbf4318a9", "abstract"=>"Trichomonas vaginalis has an unusually large genome (approximately 160 Mb) encoding approximately 60,000 proteins. With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here a family of approximately 123 Trichomonas genes that encode transmembrane adenylyl cyclases (TMACs).", "link"=>"http://www.mendeley.com/research/trichomonas-transmembrane-cyclases-result-massive-gene-duplication-concomitant-development-pseudogen", "reader_count"=>13, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Student > Bachelor"=>2, "Student > Doctoral Student"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Student > Bachelor"=>2, "Student > Doctoral Student"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>2, "Arts and Humanities"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["http://files.figshare.com/838066/Figure_3.tif"], "pos_in_sequence"=>0, "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "users"=>["Jike Cui", "Temple F. Smith", "John Samuelson", "Suchismita Das"], "links"=>[], "tags"=>["examples", "tmac", "flanking", "repetitive", "duplication", "interrupting"], "title"=>"<p>Rare examples of gene conversion of a <i>Trichomonas</i> TMAC gene, duplication of TMAC flanking sequences, and a repetitive element interrupting a TMAC gene.</p>", "figshare_url"=>"http://figshare.com/articles/_Rare_examples_of_gene_conversion_of_a_Trichomonas_TMAC_gene_duplication_of_TMAC_flanking_sequences_and_a_repetitive_element_interrupting_a_TMAC_gene_/508421", "defined_type"=>1, "doi"=>["http://dx.doi.org/10.1371/journal.pntd.0000782.g003"], "published_date"=>"2010-08-03 02:20:21", "article_id"=>508421, "categories"=>["Biochemistry", "Medicine", "Genetics"], "description"=>"<p >In A, the so-called daughter sequence (TVAG_052960 marked in red) is composed of two parts. The major portion of the daughter (green) derives from the so-called major parent (TVAG_373640), while the minor portion of the daughter (blue) derives from the so-called minor parent (TVAG_127610). In the tree on the left (representing the major portion), the daughter is more similar to the major parent than the minor parent. Conversely, the tree on the right (representing the minor portion), the daughter is more similar to the minor parent than the major parent. In B, predicted transmembrane cyclase genes (green) on two different scaffolds have similar flanking sequences on one side (marked with yellow lines). These flanking sequences including multiple ORFs (black) as well as repetitive elements (blue). Note there is a gap in the cyclase gene in scaffold 92915. This figure shows that a small segment of the chromosome that contains a transmembrane cyclase has been duplicated. In C, a single transmembrane cyclase (green) has been interrupted by a segment of DNA that contains predicted ORFs (black), repetitive elements (blue), and an inverted repeat (d and d&#8242; at its ends).</p>"}
  • {"files"=>["http://files.figshare.com/838160/Figure_4.tif"], "pos_in_sequence"=>0, "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "users"=>["Jike Cui", "Temple F. Smith", "John Samuelson", "Suchismita Das"], "links"=>[], "tags"=>["lines", "codons", "reassortment", "tmac", "genome", "genes", "g3", "polymorphisms", "trees"], "title"=>"<p>Phylogenetic trees or lines based upon polymorphisms at stop codons in TMAC genes of the <i>Trichomonas</i> genome project strain G3 demonstrate reassortment of markers.</p>", "figshare_url"=>"http://figshare.com/articles/_Phylogenetic_trees_or_lines_based_upon_polymorphisms_at_stop_codons_in_TMAC_genes_of_the_Trichomonas_genome_project_strain_G3_demonstrate_reassortment_of_markers_/508524", "defined_type"=>1, "doi"=>["http://dx.doi.org/10.1371/journal.pntd.0000782.g004"], "published_date"=>"2010-08-03 02:22:04", "article_id"=>508524, "categories"=>["Biochemistry", "Medicine", "Genetics"], "description"=>"<p>PCR products flanking 33 stop codons in TMAC genes were sequenced from S1 and B7RC2 strains of <i>Trichomonas</i> with the results graphed as follows. A. In 22 cases that are not informative concerning the history of the three strains, S1 and B7RC2 had the same stop codon as G3. This result indicates that the pseudogene was present in the common ancestor of all three strains, and we are unable to determine the wild-type sequence. In 11 cases that are historically informative (B to D) S1 and/or B7RC2 strains did not share the stop codon with G3. In these cases, we assume that the amino acid replacing the stop is the wild-type sequence. Interestingly, tree B suggests S1 and B7RC2 are more like each other than G3; tree C suggests B7RC2 is more like G3 than S1; while tree D suggests S1 is more like G3 than B7RC2. These findings that demonstrate reassortment of markers are inconsistent with clonal reproduction by <i>Trichomonas</i>, as has been suggested <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000782#pntd.0000782-Tibayrenc1\" target=\"_blank\">[40]</a>.</p>"}
  • {"files"=>["http://files.figshare.com/837813/Figure_1.tif"], "pos_in_sequence"=>0, "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "users"=>["Jike Cui", "Temple F. Smith", "John Samuelson", "Suchismita Das"], "links"=>[], "tags"=>["genes", "cyclase"], "title"=>"<p>Transmembrane cyclase genes of <i>Trichomonas</i> form two groups.</p>", "figshare_url"=>"http://figshare.com/articles/_Transmembrane_cyclase_genes_of_Trichomonas_form_two_groups_/508181", "defined_type"=>1, "doi"=>["http://dx.doi.org/10.1371/journal.pntd.0000782.g001"], "published_date"=>"2010-08-03 02:16:21", "article_id"=>508181, "categories"=>["Biochemistry", "Medicine", "Genetics"], "description"=>"<p>A phylogenetic tree constructed by maximum likelihood methods shows the cyclase domains of representative <i>Trichomonas</i> TMACs form two groups (A and B). A subgroup of A (A′) is most recently duplicated (shows very short branch lengths that are proportional to differences between sequences). Pseudogenes (marked in red) are present in both groups A and B. Incomplete genes due to assembly issues are marked in grey. Numbers at nodes indicate boot strap support for 100 iterations, while nodes with less than 50% support are collapsed. Similar results were obtained when trees were drawn using parsimony or Bayesian methods.</p>"}
  • {"files"=>["http://files.figshare.com/838223/Figure_5.tif"], "pos_in_sequence"=>0, "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "users"=>["Jike Cui", "Temple F. Smith", "John Samuelson", "Suchismita Das"], "links"=>[], "tags"=>["rnas", "tmacs"], "title"=>"<p>Messenger RNAs for numerous <i>Trichomonas</i> TMACs are expressed at the same time.</p>", "figshare_url"=>"http://figshare.com/articles/_Messenger_RNAs_for_numerous_Trichomonas_TMACs_are_expressed_at_the_same_time_/508602", "defined_type"=>1, "doi"=>["http://dx.doi.org/10.1371/journal.pntd.0000782.g005"], "published_date"=>"2010-08-03 02:23:22", "article_id"=>508602, "categories"=>["Biochemistry", "Medicine", "Genetics"], "description"=>"<p>A. RT-PCR shows that 4 of 5 TMACs are expressed by uncloned <i>Trichomonas</i> and by two clones of <i>Trichomonas</i> isolated on soft agar. B. qRT-PCR of uncloned <i>Trichomonas</i> shows that mRNAs vary in quantity more within particular group (A or B) of TMACs than they do between groups. The average abundance of mRNAs for TMACs pseudogenes is not statistically different than those for intact genes in either group A or group B (see <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000782#pntd.0000782.s002\" target=\"_blank\">Data S2</a> for gene and primer identifications).</p>"}
  • {"files"=>["http://files.figshare.com/837949/Figure_2.tif"], "pos_in_sequence"=>0, "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "users"=>["Jike Cui", "Temple F. Smith", "John Samuelson", "Suchismita Das"], "links"=>[], "tags"=>["genes", "codons", "differs", "tmac"], "title"=>"<p>The distribution of stop codons (nonsense mutations) in TMAC genes differs from chance in multiple ways.</p>", "figshare_url"=>"http://figshare.com/articles/_The_distribution_of_stop_codons_nonsense_mutations_in_TMAC_genes_differs_from_chance_in_multiple_ways_/508315", "defined_type"=>1, "doi"=>["http://dx.doi.org/10.1371/journal.pntd.0000782.g002"], "published_date"=>"2010-08-03 02:18:35", "article_id"=>508315, "categories"=>["Biochemistry", "Medicine", "Genetics"], "description"=>"<p>A. Each transmembrane adenylyl cyclase (TMAC) has a similar topology predicted by Phobius. There is a series of N-terminal TMHs (green), followed by a conserved cytosolic domain (tan) and a C-terminal cyclase domain (grey) <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000782#pntd.0000782-Kll1\" target=\"_blank\">[23]</a>. B. With one exception that may reflect an assembly error, none of the stops and frame shifts is in the same place in 40 aligned TMAC pseudogenes. This result suggests that the stop codons and frame shifts occurred after gene duplication. Note that the alignment technique, which introduces gaps, makes the TMACs appear longer than 1600 amino acids. Green line marks the beginning of the conserved cyclase domain. C. The actual distribution of stop codons among TMAC pseudogenes differs from a Poisson distribution. This result suggests there is selection against the first stop codon (disabling the protein coding capacity of the gene) but not against subsequent stop codons. D. Average number of stops and frame shifts are calculated using a window size of 300 aa in the aligned sequences of group A and B. Stop codons are more abundant in TMAC from the more recently duplicated group A than from group B. Stop codons are also more frequent in less conserved parts of the TMAC genes.</p>"}
  • {"files"=>["http://files.figshare.com/417261/Data_S1.doc", "http://files.figshare.com/417284/Data_S2.xls", "http://files.figshare.com/417291/Figure_S1.tif", "http://files.figshare.com/417298/Figure_S2.tif", "http://files.figshare.com/417309/Figure_S3.tif"], "pos_in_sequence"=>0, "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "users"=>["Jike Cui", "Temple F. Smith", "John Samuelson", "Suchismita Das"], "links"=>[], "tags"=>["cyclases", "duplication", "pseudogenes", "concomitant", "transmembrane"], "title"=>"<em>Trichomonas</em> Transmembrane Cyclases Result from Massive Gene Duplication and Concomitant Development of Pseudogenes", "figshare_url"=>"http://figshare.com/articles/_Trichomonas_Transmembrane_Cyclases_Result_from_Massive_Gene_Duplication_and_Concomitant_Development_of_Pseudogenes/142364", "defined_type"=>4, "doi"=>["http://dx.doi.org/10.1371/journal.pntd.0000782.s001", "http://dx.doi.org/10.1371/journal.pntd.0000782.s002", "http://dx.doi.org/10.1371/journal.pntd.0000782.s003", "http://dx.doi.org/10.1371/journal.pntd.0000782.s004", "http://dx.doi.org/10.1371/journal.pntd.0000782.s005"], "published_date"=>"2010-08-03 00:39:24", "article_id"=>142364, "categories"=>["Biochemistry", "Medicine", "Genetics"], "description"=>"<div><section><h3>Background</h3><p><em>Trichomonas vaginalis</em> has an unusually large genome (&#8764;160 Mb) encoding &#8764;60,000 proteins. With the goal of beginning to understand why some <em>Trichomonas</em> genes are present in so many copies, we characterized here a family of &#8764;123 <em>Trichomonas</em> genes that encode transmembrane adenylyl cyclases (TMACs).</p></section><section><h3>Methodology/Principal Findings</h3><p>The large family of TMACs genes is the result of recent duplications of a small set of ancestral genes that appear to be unique to trichomonads. Duplicated TMAC genes are not closely associated with repetitive elements, and duplications of flanking sequences are rare. However, there is evidence for TMAC gene replacements by homologous recombination. A high percentage of TMAC genes (∼46%) are pseudogenes, as they contain stop codons and/or frame shifts, or the genes are truncated. Numerous stop codons present in the genome project G3 strain are not present in orthologous genes of two other <em>Trichomonas</em> strains (S1 and B7RC2). Each TMAC is composed of a series of N-terminal transmembrane helices and a single C-terminal cyclase domain that has adenylyl cyclase activity. Multiple TMAC genes are transcribed by <em>Trichomonas</em> cloned by limiting dilution.</p></section><section><h3>Conclusions/Significance</h3><p>We conclude that one reason for the unusually large genome of <em>Trichomonas</em> is the presence of unstable families of genes such as those encoding TMACs that are undergoing massive gene duplication and concomitant development of pseudogenes.</p></section></div>"}

PMC Usage Stats | Further Information

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Relative Metric

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