Whole Genome Sequence of Treponema pallidum ssp. pallidum, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains
Publication Date
September 20, 2012
Journal
PLOS Neglected Tropical Diseases
Authors
Helena Pětrošová, Marie Zobaníková, Darina Čejková, Lenka Mikalová, et al
Volume
6
Issue
9
Pages
e1832
DOI
https://dx.plos.org/10.1371/journal.pntd.0001832
Publisher URL
http://journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0001832
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23029591
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447947
Europe PMC
http://europepmc.org/abstract/MED/23029591
Web of Science
000309528100032
Scopus
84866945465
Mendeley
http://www.mendeley.com/research/whole-genome-sequence-treponema-pallidum-ssp-pallidum-strain-mexico-suggests-recombination-between-y
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Mendeley | Further Information

{"title"=>"Whole Genome Sequence of Treponema pallidum ssp. pallidum, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains", "type"=>"journal", "authors"=>[{"first_name"=>"Helena", "last_name"=>"Pětrošová", "scopus_author_id"=>"55370544500"}, {"first_name"=>"Marie", "last_name"=>"Zobaníková", "scopus_author_id"=>"36718450800"}, {"first_name"=>"Darina", "last_name"=>"Čejková", "scopus_author_id"=>"23099215700"}, {"first_name"=>"Lenka", "last_name"=>"Mikalová", "scopus_author_id"=>"36717991200"}, {"first_name"=>"Petra", "last_name"=>"Pospíšilová", "scopus_author_id"=>"37085412600"}, {"first_name"=>"Michal", "last_name"=>"Strouhal", "scopus_author_id"=>"23029368000"}, {"first_name"=>"Lei", "last_name"=>"Chen", "scopus_author_id"=>"56415315900"}, {"first_name"=>"Xiang", "last_name"=>"Qin", "scopus_author_id"=>"57037659400"}, {"first_name"=>"Donna M.", "last_name"=>"Muzny", "scopus_author_id"=>"6603763638"}, {"first_name"=>"George M.", "last_name"=>"Weinstock", "scopus_author_id"=>"7005387907"}, {"first_name"=>"David", "last_name"=>"Šmajs", "scopus_author_id"=>"6603422324"}], "year"=>2012, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"sgr"=>"84866945465", "pui"=>"365756046", "doi"=>"10.1371/journal.pntd.0001832", "pmid"=>"23029591", "scopus"=>"2-s2.0-84866945465", "issn"=>"19352727", "isbn"=>"1935-2735 (Electronic)\\r1935-2727 (Linking)"}, "id"=>"f428a800-bebc-3c05-a5db-ae2a8d760a6b", "abstract"=>"BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, and Treponema pallidum ssp. pertenue (TPE), the causative agent of yaws, are closely related spirochetes causing diseases with distinct clinical manifestations. The TPA Mexico A strain was isolated in 1953 from male, with primary syphilis, living in Mexico. Attempts to cultivate TPA Mexico A strain under in vitro conditions have revealed lower growth potential compared to other tested TPA strains.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: The complete genome sequence of the TPA Mexico A strain was determined using the Illumina sequencing technique. The genome sequence assembly was verified using the whole genome fingerprinting technique and the final sequence was annotated. The genome size of the Mexico A strain was determined to be 1,140,038 bp with 1,035 predicted ORFs. The Mexico A genome sequence was compared to the whole genome sequences of three TPA (Nichols, SS14 and Chicago) and three TPE (CDC-2, Samoa D and Gauthier) strains. No large rearrangements in the Mexico A genome were found and the identified nucleotide changes occurred most frequently in genes encoding putative virulence factors. Nevertheless, the genome of the Mexico A strain, revealed two genes (TPAMA_0326 (tp92) and TPAMA_0488 (mcp2-1)) which combine TPA- and TPE- specific nucleotide sequences. Both genes were found to be under positive selection within TPA strains and also between TPA and TPE strains.\\n\\nCONCLUSIONS/SIGNIFICANCE: The observed mosaic character of the TPAMA_0326 and TPAMA_0488 loci is likely a result of inter-strain recombination between TPA and TPE strains during simultaneous infection of a single host suggesting horizontal gene transfer between treponemal subspecies.", "link"=>"http://www.mendeley.com/research/whole-genome-sequence-treponema-pallidum-ssp-pallidum-strain-mexico-suggests-recombination-between-y", "reader_count"=>36, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>4, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>4, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>16, "Medicine and Dentistry"=>11, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>11}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Tanzania"=>1, "Guatemala"=>1, "Brazil"=>1, "United Kingdom"=>2, "Mexico"=>1, "Switzerland"=>1, "Spain"=>1, "Indonesia"=>1}, "group_count"=>4}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/301989", "https://ndownloader.figshare.com/files/301999", "https://ndownloader.figshare.com/files/302018", "https://ndownloader.figshare.com/files/302038"], "description"=>"<div><h3>Background</h3><p><em>Treponema pallidum</em> ssp. <em>pallidum</em> (TPA), the causative agent of syphilis, and <em>Treponema pallidum</em> ssp. <em>pertenue</em> (TPE), the causative agent of yaws, are closely related spirochetes causing diseases with distinct clinical manifestations. The TPA Mexico A strain was isolated in 1953 from male, with primary syphilis, living in Mexico. Attempts to cultivate TPA Mexico A strain under <em>in vitro</em> conditions have revealed lower growth potential compared to other tested TPA strains.</p> <h3>Methodology/Principal Findings</h3><p>The complete genome sequence of the TPA Mexico A strain was determined using the Illumina sequencing technique. The genome sequence assembly was verified using the whole genome fingerprinting technique and the final sequence was annotated. The genome size of the Mexico A strain was determined to be 1,140,038 bp with 1,035 predicted ORFs. The Mexico A genome sequence was compared to the whole genome sequences of three TPA (Nichols, SS14 and Chicago) and three TPE (CDC-2, Samoa D and Gauthier) strains. No large rearrangements in the Mexico A genome were found and the identified nucleotide changes occurred most frequently in genes encoding putative virulence factors. Nevertheless, the genome of the Mexico A strain, revealed two genes (TPAMA_0326 (<em>tp92</em>) and TPAMA_0488 (<em>mcp2-1</em>)) which combine TPA- and TPE- specific nucleotide sequences. Both genes were found to be under positive selection within TPA strains and also between TPA and TPE strains.</p> <h3>Conclusions/Significance</h3><p>The observed mosaic character of the TPAMA_0326 and TPAMA_0488 loci is likely a result of inter-strain recombination between TPA and TPE strains during simultaneous infection of a single host suggesting horizontal gene transfer between treponemal subspecies.</p> </div>", "links"=>[], "tags"=>["genome", "mexico", "suggests", "recombination", "yaws", "syphilis", "strains"], "article_id"=>119551, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.s001", "https://dx.doi.org/10.1371/journal.pntd.0001832.s002", "https://dx.doi.org/10.1371/journal.pntd.0001832.s003", "https://dx.doi.org/10.1371/journal.pntd.0001832.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Whole_Genome_Sequence_of_Treponema_pallidum_ssp_pallidum_Strain_Mexico_A_Suggests_Recombination_between_Yaws_and_Syphilis_Strains/119551", "title"=>"Whole Genome Sequence of <em>Treponema pallidum</em> ssp. <em>pallidum</em>, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-20 02:39:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/572972"], "description"=>"<p>The Mexico A sequence was compared to three TPA (Nichols, SS14, and Chicago) and three TPE CDC-2, Gauthier, Samoa D) strains. Black vertical lines represent nucleotide positions differentiating all TPA and TPE strains. Green and red vertical lines represent nucleotide changes present in all analyzed TPA and TPE strains where the TPA Mexico A sequence is identical to TPA and TPE strains, respectively. Two nucleotide positions (584, 1655) in the TP0488 locus were found only in the Nichols and Chicago strains and not in the SS14 genome (open vertical lines). The symbol Δ stands for 15-bp deletion present in the TPE and Mexico A strains in the TP0326 gene.</p>", "links"=>[], "tags"=>["schematic", "tpama_0326", "tpama_0488"], "article_id"=>243453, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_schematic_representation_of_the_TPAMA_0326_and_TPAMA_0488_loci_/243453", "title"=>"A schematic representation of the TPAMA_0326 and TPAMA_0488 loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-20 00:57:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/573026"], "description"=>"<p>TPA Mexico A, TPA SS14, TPE Samoa D and <i>Treponema paraluiscuniculi</i> strain Cuniculi A were analyzed. Colored vertical lines represent 501 bp-long windows with G+C content above the 63% or below the 41% threshold. Black vertical lines represent genome locations of <i>tpr</i> genes. Stars denote 5 kb-long DNA regions with 40 or more nucleotide positions differentiating TPA and TPE strains <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Cejkova1\" target=\"_blank\">[7]</a>. Please note that there is no clear association of DNA regions with different G+C content and regions differentiating TPA and TPE strains <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Cejkova1\" target=\"_blank\">[7]</a> or locations of <i>tpr</i> genes.</p>", "links"=>[], "tags"=>[], "article_id"=>243519, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_G_C_content_variation_in_selected_Treponema_strains_/243519", "title"=>"G+C content variation in selected <i>Treponema</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-20 00:58:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/573119"], "description"=>"<p>A. Unrooted tree constructed from restriction target site data from 25.6% of the analyzed TP genomes (modified according to Šmajs <i>et al.. </i><a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Smajs3\" target=\"_blank\">[18]</a>). TPA (Dallas, Nichols, Mexico A and SS14), TPE (CDC-2, Gauthier and Samoa D), TEN (Bosnia A) strains and unclassified simian isolate Fribourg-Blanc were analyzed. TPA strains are shown in bold. Patterns shown for the Bosnia A strain are based on the sequences of TP0326 (GenBank acc. no. JX392330.1, this sequence is identical to partial sequence published by Harper <i>et al.. </i><a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Harper1\" target=\"_blank\">[19]</a>) and TP0488 (GenBank acc. no. JX392331.1) determined by us, and on the whole genome fingerprinting data <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Smajs3\" target=\"_blank\">[18]</a>. B. Scheme illustrating hypothetical evolution of TP strains. Please note that the ancestral position of Mexico A related to other TPA strains does not explain presence of TEN-specific pattern in TP0326 (<i>tp92</i>) locus in the SS14-like group of TPA strains. C. Scheme illustrating hypothetical recombinations among TP strains. A hypothetical ancestor of TEN and Mexico A strains is marked by star.</p>", "links"=>[], "tags"=>["relationships", "tp", "strains", "hypothetical", "evolutionary"], "article_id"=>243603, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationships_among_TP_strains_and_hypothetical_evolutionary_schemes_/243603", "title"=>"Evolutionary relationships among TP strains and hypothetical evolutionary schemes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-20 01:00:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/573207"], "description"=>"<p>Green lines are nucleotide sequences specific for TPA strains (Nichols, SS14, Chicago), red ones for TPE strains (CDC-2, Gauthier, Samoa D). Vertical black lines denote corresponding positions of the TPAMA_0326 loci. A) Homologous recombination. 1. Homologous recombination between TPA and TPE loci with suggested possible recombination sites (x); arrow indicates direction of branch migration. 2. The resulting heteroduplex contains both TPA and TPE sequences; green loop denotes a 15 bp insertion present in all investigated TPA strains. 3. Recognition of mismatched DNA by MutS-MutL complex and subsequent cleavage of DNA strands by endonucleases (marked by arrows). 4. Unwinding of cleaved strands by DNA helicase (open elipse) and DNA polymerase-mediated (grey) gap filling. 5. Reparation of DNA breaks with DNA ligase. Alternatively, there is a possibility of an active DNA uptake across the cell membrane. Although no gene orthologs involved in natural competence have been identified in the TPA genomes, one cannot exclude this activity in one or several genes with unknown function. B) Gene conversion. Successive half crossing-over model. 1. First half crossing-over with suggested recombination site (x). 2. Successive second half crossing-over and the second recombination site (x). 3. Duplex recovery and degradation of both displaced ends. Please note that model B) requires the presence of two TPA-like nucleotide sequences in the donor TPE sequence.</p>", "links"=>[], "tags"=>["molecular", "mechanisms", "resulting", "mosaic", "tpama_0326"], "article_id"=>243685, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_possible_molecular_mechanisms_resulting_in_formation_of_the_mosaic_structure_of_the_TPAMA_0326_locus_/243685", "title"=>"Two possible molecular mechanisms resulting in formation of the mosaic structure of the TPAMA_0326 locus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-20 01:01:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/573282"], "description"=>"<p>Three TPA (Nichols, SS14, and Chicago) and three TPE (CDC-2, Gauthier, and Samoa D) strains were analyzed. Numbers in square brackets correspond to amino acid position in TPAMA_0488 protein. Amino acid sequence in the encoded protein is shown in brackets.</p>1)<p>Domain prediction according to the NCBI Conserved Domain Database.</p>2)<p>A (T) was identified in TPE CDC-2 strain while A (I) in TPE Gauthier and Samoa D strains.</p>3)<p>T (S) was identified in TPA Nichols and Chicago strains while A (R) in TPA SS14 strain.</p>4)<p>G (G) was identified in TPA Nichols and Chicago strains while A (D) in TPA SS14 strain.</p>5)<p>Mexico A-specific nucleotide change in the vicinity of TPA-like change causes amino acid change specific for Mexico A.</p>6)<p>G (R) was identified in TPA Nichols and Chicago strain while A (Q) in TPA SS14 strain.</p>", "links"=>[], "tags"=>["changes", "tpama_0488"], "article_id"=>243767, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_list_of_changes_found_at_the_TPAMA_0488_locus_/243767", "title"=>"A list of changes found at the TPAMA_0488 locus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-20 01:02:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/573325"], "description"=>"<p>Three TPA (Nichols, SS14, and Chicago) and three TPE (CDC-2, Gauthier, and Samoa D) strains were analyzed. The numbers in square brackets correspond to amino acid position in the TPAMA_0326 protein. The amino acid sequence of the encoded protein is shown in brackets.</p>1)<p>Domain prediction according to Desrosiers <i>et al.</i><a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Desrosiers1\" target=\"_blank\">[41]</a>.</p>2)<p>G (R) was found in TPE CDC-2 strain, G (E) in TPE Gauthier, while T (N) was found in TPE Samoa D strain.</p>3)<p>15 bp (GTAGAACCACCAGCT) encode SRTTS in TPA Nichols and Chicago strain and 15 bp (GTAGCACCACCAGCT) encode SSTTS in TPA SS14 strain.</p>", "links"=>[], "tags"=>["changes", "tpama_0326"], "article_id"=>243808, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Helena Pětrošová", "Marie Zobaníková", "Darina Čejková", "Lenka Mikalová", "Petra Pospíšilová", "Michal Strouhal", "Lei Chen", "Xiang Qin", "Donna M. Muzny", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001832.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_list_of_changes_found_in_the_TPAMA_0326_locus_/243808", "title"=>"A list of changes found in the TPAMA_0326 locus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-20 01:03:28"}

PMC Usage Stats | Further Information

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Relative Metric

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