Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution.
Background Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strai...
Published in: | PLOS Neglected Tropical Diseases |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2019
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pntd.0007463 https://doaj.org/article/2b648f1ed7a94d04acc68916ef08ece0 |
id |
ftdoajarticles:oai:doaj.org/article:2b648f1ed7a94d04acc68916ef08ece0 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:2b648f1ed7a94d04acc68916ef08ece0 2023-05-15T15:14:17+02:00 Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. Denisa Maděránková Lenka Mikalová Michal Strouhal Šimon Vadják Ivana Kuklová Petra Pospíšilová Lenka Krbková Pavlína Koščová Ivo Provazník David Šmajs 2019-06-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0007463 https://doaj.org/article/2b648f1ed7a94d04acc68916ef08ece0 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0007463 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007463 https://doaj.org/article/2b648f1ed7a94d04acc68916ef08ece0 PLoS Neglected Tropical Diseases, Vol 13, Iss 6, p e0007463 (2019) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pntd.0007463 2022-12-31T05:48:39Z Background Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14, Chicago), four T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), one T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPeC) were tested for the presence of positively selected genes. Methodology/principal findings A total of 1068 orthologous genes annotated in all 11 genomes were tested for the presence of positively selected genes using both site and branch-site models with CODEML (PAML package). Subsequent analyses with sequences obtained from 62 treponemal draft genomes were used for the identification of positively selected amino acid positions. Synthetic biotinylated peptides were designed to cover positively selected protein regions and these peptides were tested for reactivity with the patient's syphilis sera. Altogether, 22 positively selected genes were identified in the TP genomes and TPA sets of positively selected genes differed from TPE genes. While genetic variability among TPA strains was predominantly present in a number of genetic loci, genetic variability within TPE and TEN strains was distributed more equally along the chromosome. Several syphilitic sera were shown to react with some peptides derived from the protein sequences evolving under positive selection. Conclusions/significance The syphilis-, yaws-, and bejel-causing strains differed relative to sets of positively selected genes. Most of the positively selected chromosomal loci were identified among the TPA treponemes. The local accumulation of genetic variability suggests that the diversification of TPA strains took place predominantly in a limited number of genomic regions compared to the more dispersed ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Gauthier ENVELOPE(-63.583,-63.583,-64.833,-64.833) PLOS Neglected Tropical Diseases 13 6 e0007463 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Denisa Maděránková Lenka Mikalová Michal Strouhal Šimon Vadják Ivana Kuklová Petra Pospíšilová Lenka Krbková Pavlína Koščová Ivo Provazník David Šmajs Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
Background Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14, Chicago), four T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), one T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPeC) were tested for the presence of positively selected genes. Methodology/principal findings A total of 1068 orthologous genes annotated in all 11 genomes were tested for the presence of positively selected genes using both site and branch-site models with CODEML (PAML package). Subsequent analyses with sequences obtained from 62 treponemal draft genomes were used for the identification of positively selected amino acid positions. Synthetic biotinylated peptides were designed to cover positively selected protein regions and these peptides were tested for reactivity with the patient's syphilis sera. Altogether, 22 positively selected genes were identified in the TP genomes and TPA sets of positively selected genes differed from TPE genes. While genetic variability among TPA strains was predominantly present in a number of genetic loci, genetic variability within TPE and TEN strains was distributed more equally along the chromosome. Several syphilitic sera were shown to react with some peptides derived from the protein sequences evolving under positive selection. Conclusions/significance The syphilis-, yaws-, and bejel-causing strains differed relative to sets of positively selected genes. Most of the positively selected chromosomal loci were identified among the TPA treponemes. The local accumulation of genetic variability suggests that the diversification of TPA strains took place predominantly in a limited number of genomic regions compared to the more dispersed ... |
format |
Article in Journal/Newspaper |
author |
Denisa Maděránková Lenka Mikalová Michal Strouhal Šimon Vadják Ivana Kuklová Petra Pospíšilová Lenka Krbková Pavlína Koščová Ivo Provazník David Šmajs |
author_facet |
Denisa Maděránková Lenka Mikalová Michal Strouhal Šimon Vadják Ivana Kuklová Petra Pospíšilová Lenka Krbková Pavlína Koščová Ivo Provazník David Šmajs |
author_sort |
Denisa Maděránková |
title |
Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
title_short |
Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
title_full |
Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
title_fullStr |
Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
title_full_unstemmed |
Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
title_sort |
identification of positively selected genes in human pathogenic treponemes: syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pntd.0007463 https://doaj.org/article/2b648f1ed7a94d04acc68916ef08ece0 |
long_lat |
ENVELOPE(-63.583,-63.583,-64.833,-64.833) |
geographic |
Arctic Gauthier |
geographic_facet |
Arctic Gauthier |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 13, Iss 6, p e0007463 (2019) |
op_relation |
https://doi.org/10.1371/journal.pntd.0007463 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007463 https://doaj.org/article/2b648f1ed7a94d04acc68916ef08ece0 |
op_doi |
https://doi.org/10.1371/journal.pntd.0007463 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
13 |
container_issue |
6 |
container_start_page |
e0007463 |
_version_ |
1766344750250590208 |