Comparative Genomics Suggests that the Fungal Pathogen Pneumocystis Is an Obligate Parasite Scavenging Amino Acids from Its Host's Lungs
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{"title"=>"Comparative genomics suggests that the fungal pathogen Pneumocystis is an obligate parasite scavenging amino acids from its host's lungs", "type"=>"journal", "authors"=>[{"first_name"=>"Philippe M.", "last_name"=>"Hauser", "scopus_author_id"=>"7102618021"}, {"first_name"=>"Frederic X.", "last_name"=>"Burdet", "scopus_author_id"=>"8072226600"}, {"first_name"=>"Ousmane H.", "last_name"=>"Cissé", "scopus_author_id"=>"14060017700"}, {"first_name"=>"Laurent", "last_name"=>"Keller", "scopus_author_id"=>"7202066299"}, {"first_name"=>"Patrick", "last_name"=>"Taffé", "scopus_author_id"=>"35278587100"}, {"first_name"=>"Dominique", "last_name"=>"Sanglard", "scopus_author_id"=>"7005396991"}, {"first_name"=>"Marco", "last_name"=>"Pagni", "scopus_author_id"=>"6604025567"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361048258", "isbn"=>"1932-6203", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0015152", "sgr"=>"78650891904", "scopus"=>"2-s2.0-78650891904", "pmid"=>"21188143"}, "id"=>"1fdcb3ec-92af-3d59-9d5d-3799dde6ad76", "abstract"=>"Pneumocystis jirovecii is a fungus causing severe pneumonia in immuno-compromised patients. Progress in understanding its pathogenicity and epidemiology has been hampered by the lack of a long-term in vitro culture method. Obligate parasitism of this pathogen has been suggested on the basis of various features but remains controversial. We analysed the 7.0 Mb draft genome sequence of the closely related species Pneumocystis carinii infecting rats, which is a well established experimental model of the disease. We predicted 8'085 (redundant) peptides and 14.9% of them were mapped onto the KEGG biochemical pathways. The proteome of the closely related yeast Schizosaccharomyces pombe was used as a control for the annotation procedure (4'974 genes, 14.1% mapped). About two thirds of the mapped peptides of each organism (65.7% and 73.2%, respectively) corresponded to crucial enzymes for the basal metabolism and standard cellular processes. However, the proportion of P. carinii genes relative to those of S. pombe was significantly smaller for the \"amino acid metabolism\" category of pathways than for all other categories taken together (40 versus 114 against 278 versus 427, P<0.002). Importantly, we identified in P. carinii only 2 enzymes specifically dedicated to the synthesis of the 20 standard amino acids. By contrast all the 54 enzymes dedicated to this synthesis reported in the KEGG atlas for S. pombe were detected upon reannotation of S. pombe proteome (2 versus 54 against 278 versus 427, P<0.0001). This finding strongly suggests that species of the genus Pneumocystis are scavenging amino acids from their host's lung environment. Consequently, they would have no form able to live independently from another organism, and these parasites would be obligate in addition to being opportunistic. These findings have implications for the management of patients susceptible to P. jirovecii infection given that the only source of infection would be other humans.", "link"=>"http://www.mendeley.com/research/comparative-genomics-suggests-fungal-pathogen-pneumocystis-obligate-parasite-scavenging-amino-acids", "reader_count"=>42, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Other"=>1, "Student > Master"=>7, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Other"=>1, "Student > Master"=>7, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Medicine and Dentistry"=>5, "Agricultural and Biological Sciences"=>28, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Austria"=>1, "Taiwan"=>1, "Portugal"=>1, "Switzerland"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/811480"], "description"=>"<p>The <i>S. pombe</i> proteome (right box) was blasted against an intermediary set of fungal proteins, i.e. the proteome of <i>S. cerevisiae</i> in this example (middle box), and only the highest scoring blast matches were retained. By utilizing the <i>S. cerevisiae</i> mapping to the KEGG Orthologs (between the middle and left boxes), one can produce a mapping through <i>S. cerevisiae</i> of the <i>S. pombe</i> proteins to the KEGG Orthologs. The latter mapping can then be compared with the one that is actually provided by KEGG to compute precision and recall values. The experience was systematically repeated using different proteomes as intermediary data sets (or several proteomes at once), to eventually determine the optimal one.</p>", "links"=>[], "tags"=>["numerical", "optimize", "precision", "annotation"], "article_id"=>481836, "categories"=>["Biochemistry", "Medicine", "Biological Sciences", "Microbiology", "Infectious Diseases"], "users"=>["Philippe M. Hauser", "Frédéric X. Burdet", "Ousmane H. Cissé", "Laurent Keller", "Patrick Taffé", "Dominique Sanglard", "Marco Pagni"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015152.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principle_of_the_numerical_experience_used_to_optimize_the_precision_and_recall_of_the_annotation_predictions_/481836", "title"=>"Principle of the numerical experience used to optimize the precision and recall of the annotation predictions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:44:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/811561"], "description"=>"<p>The KO - <i>S. pombe</i> association pairs obtained by “blasting” an intermediary data set were evaluated <i>a posteriori</i> as true positive (TP) or false positive (FP) according to the KO - <i>S. pombe</i> mapping which is provided by KEGG. Those missed KO - <i>S. pombe</i> pairs existing in KEGG were taken as false negatives (FN). The overall quality of the obtained mapping can be expressed in terms of precision TP/(TP+FP) and recall TP/(TP+FN).</p>", "links"=>[], "tags"=>["kegg", "maps", "performing", "re-prediction", "annotation", "proteome", "intermediary", "consisting", "18", "fungal"], "article_id"=>481913, "categories"=>["Biochemistry", "Medicine", "Biological Sciences", "Microbiology", "Infectious Diseases"], "users"=>["Philippe M. Hauser", "Frédéric X. Burdet", "Ousmane H. Cissé", "Laurent Keller", "Patrick Taffé", "Dominique Sanglard", "Marco Pagni"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015152.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimation_of_the_quality_of_the_mapping_onto_KEGG_maps_by_performing_a_re_prediction_of_the_annotation_of_S_pombe_proteome_through_intermediary_data_set_consisting_of_one_two_three_or_18_fungal_proteomes_/481913", "title"=>"Estimation of the quality of the mapping onto KEGG maps by performing a re-prediction of the annotation of <i>S. pombe</i> proteome through intermediary data set consisting of one, two, three, or 18 fungal proteomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:45:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/811613"], "description"=>"<p>Proteomes investigated for transfer the KEGG annotations of the <i>P. carinii</i> predicted proteome.</p>", "links"=>[], "tags"=>["investigated", "kegg", "annotations"], "article_id"=>481974, "categories"=>["Biochemistry", "Medicine", "Biological Sciences", "Microbiology", "Infectious Diseases"], "users"=>["Philippe M. Hauser", "Frédéric X. Burdet", "Ousmane H. Cissé", "Laurent Keller", "Patrick Taffé", "Dominique Sanglard", "Marco Pagni"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015152.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteomes_investigated_for_transfer_the_KEGG_annotations_of_the_P_carinii_predicted_proteome_/481974", "title"=>"Proteomes investigated for transfer the KEGG annotations of the <i>P. carinii</i> predicted proteome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:45:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/811657"], "description"=>"a<p>The reference gene numbers of <i>S. pombe</i> are those obtained from KEGG.</p>b<p>The four enzymes are the same for Ile and Val syntheses.</p>c<p>One of the enzymes is also involved in Ile and Val syntheses.</p>", "links"=>[], "tags"=>["enzymes", "dedicated", "biosyntheses", "amino", "acids"], "article_id"=>482015, "categories"=>["Biochemistry", "Medicine", "Biological Sciences", "Microbiology", "Infectious Diseases"], "users"=>["Philippe M. Hauser", "Frédéric X. Burdet", "Ousmane H. Cissé", "Laurent Keller", "Patrick Taffé", "Dominique Sanglard", "Marco Pagni"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015152.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_enzymes_dedicated_to_the_biosyntheses_of_amino_acids_identified_in_P_carinii_and_S_pombe_a_/482015", "title"=>"Number of enzymes dedicated to the biosyntheses of amino acids identified in <i>P. carinii</i> and <i>S. pombe</i><sup>a</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:45:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/811693"], "description"=>"<p>Some features of free-living microorganisms and obligate parasites.</p>", "links"=>[], "tags"=>["free-living", "microorganisms", "obligate"], "article_id"=>482059, "categories"=>["Biochemistry", "Medicine", "Biological Sciences", "Microbiology", "Infectious Diseases"], "users"=>["Philippe M. Hauser", "Frédéric X. Burdet", "Ousmane H. Cissé", "Laurent Keller", "Patrick Taffé", "Dominique Sanglard", "Marco Pagni"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015152.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Some_features_of_free_living_microorganisms_and_obligate_parasites_/482059", "title"=>"Some features of free-living microorganisms and obligate parasites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:45:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/811749"], "description"=>"a<p>The reference gene numbers of <i>S. pombe</i> are those obtained from KEGG. Maps with less than five reference genes of <i>S. pombe</i> are not shown. KOs which are redundant in the pathways are counted only once in “OVERALL KOs”.</p>", "links"=>[], "tags"=>["kegg", "orthologs", "56", "pathways", "correspond", "basal", "metabolism", "cellular"], "article_id"=>482106, "categories"=>["Biochemistry", "Medicine", "Biological Sciences", "Microbiology", "Infectious Diseases"], "users"=>["Philippe M. Hauser", "Frédéric X. Burdet", "Ousmane H. Cissé", "Laurent Keller", "Patrick Taffé", "Dominique Sanglard", "Marco Pagni"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015152.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_KEGG_orthologs_KO_predicted_for_P_carinii_and_S_pombe_in_56_pathways_that_correspond_to_basal_metabolism_and_cellular_processes_a_/482106", "title"=>"Number of KEGG orthologs (KO) predicted for <i>P. carinii</i> and <i>S. pombe</i> in 56 pathways that correspond to basal metabolism and cellular processes<sup>a</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:46:11"}

PMC Usage Stats | Further Information

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Relative Metric

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