The HSP70 Gene Family in <i>Pneumocystis carinii</i>: Molecular and Phylogenetic Characterization of Cytoplasmic Members

Stedman, Timothy T.; Butler, Diann R.; Buck, Gregory A.

doi:10.1111/j.1550-7408.1998.tb04554.x

Cited by 16 publications

(11 citation statements)

References 33 publications

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“…To adapt the RT-PCR viability assay developed for human P. carinii, primers were designed to target a fragment of the Phsb1 mRNA [11]. Like the gene targeted in the rat P. carinii assay, this gene is a member of the hsp70 family.…”

Section: Resultsmentioning

confidence: 99%

Development and Characterization of a Molecular Viability Assay forPneumocystis cariniif sphominis

Maher¹,

Vermund

Welsh

et al. 2001

J INFECT DIS

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Pneumocystis carinii pneumonia (PCP) remains the most common opportunistic infection among human immunodeficiency virus-infected persons. Despite this, little is known concerning the transmission dynamics of this infection. In the absence of a reliable method to isolate and culture P. carinii from environmental samples, it has not been possible to assess the importance of person-to-person transmission in the epidemiology of PCP. A molecular viability assay was developed for the human form of P. carinii (P. carinii f sp hominis) that is applicable to both clinical specimens and environmental samples. This assay will enable the evaluation of the spread and persistence of viable human P. carinii in the environment.

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Section: Resultsmentioning

confidence: 99%

Development and Characterization of a Molecular Viability Assay forPneumocystis cariniif sphominis

Maher¹,

Vermund

Welsh

et al. 2001

J INFECT DIS

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“…There are many reasons for selecting this new target: the HSP70 gene is conserved across eukaryotic organisms,22 30 yet the sequence identity is not. Phylogenetic analysis suggests this sequence is unlikely to be lost, reducing the likelihood of sensitivity being compromised.…”

Section: Discussionmentioning

confidence: 99%

“…The objective of this study was to compare real-time PCR using primers designed to hybridise to the heat shock protein 70 (HSP70) gene of P jirovecii 22 23 with conventional PCR using primers designed to the large subunit of mitochondrial rRNA (mt LSU rRNA)3 4 10 for detection of P jirovecii DNA in BAL fluid from patients undergoing diagnostic bronchoscopy. Patients had either proven PCP or confirmed alternative diagnoses.…”

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confidence: 99%

Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients

Huggett

Taylor

Kocjan

et al. 2007

Thorax

116

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Background: Pneumocystis pneumonia (PCP) is conventionally diagnosed by identifying Pneumocystis jirovecii in lower respiratory tract samples using cytochemical stains. Molecular diagnosis of PCP is potentially more sensitive. Methods: A study was undertaken to use an extensively optimised real-time polymerase chain reaction (PCR) using primers designed to hybridise with the P jirovecii heat shock protein 70 (HSP70) gene to quantify P jirovecii DNA in bronchoalveolar lavage (BAL) fluid from HIV-infected patients with and without PCP, and to compare this assay with conventional PCR targeting the P jirovecii mitochondrial large subunit rRNA gene sequence (mt LSU rRNA). Results: Sixty-one patients had 62 episodes of PCP (defined by detection of P jirovecii in BAL fluid by cytochemical stains and typical clinical presentation). Quantifiable HSP70 DNA was detected in 61/62 (range ,13-18 608 copies/reaction; median ,332) and was detectable but below the limit of quantification (,5 copies/reaction) in 1/62. Seventy-one other patients had 74 episodes with alternative diagnoses. Quantifiable HSP70 DNA was detectable in 6/74 (8%) episodes (range ,6-590 copies/reaction; median ,14) and detectable but below the limit of quantification in 34/74 (46%). Receiver-operator curve analysis (cut-off .10 copies/ reaction) showed a clinical sensitivity of 98% (95% 91% to 100%) and specificity of 96% (95% CI 87% to 99%) for diagnosis of PCP. By contrast, clinical sensitivity of mt LSU rRNA PCR was 97% (95% CI 89% to 99%) and specificity was 68% (95% CI 56% to 78%). Conclusion: The HSP70 real-time PCR assay detects P jirovecii DNA in BAL fluid and may have a diagnostic application. Quantification of P jirovecii DNA by real-time PCR may also discriminate between colonisation with P jirovecii and infection.

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“…HSP70 genes have been used for inferring the phylogenetic relationships among divergent taxa (Gupta et al, 1994(Gupta et al, , 1999Molto et al, 1994;Gupta and Golding, 1993;Borchiellini et al, 1998;Budin and Philippe, 1998;Stedman et al, 1998;Germot and Philippe, 1999;Philippe et al, 1999;Schultz et al, 1999;Rue et al, 2000;Sulaiman et al, 2000). In many cases, however, inferred organismal trees based on HSP70 data do not match traditional phylogenies or those based on other genes.…”

Section: Implications For Phylogenies Based On Hsp Genesmentioning

confidence: 96%

“…HSP70 is an ideal choice because much is known about the structure, function, phylogeny, and evolution of these genes (Lindquist and Craig, 1988;Morimoto et al, 1994;James et al, 1997;Feder and Hofmann, 1999). Moreover, HSP70 genes have been used for inferring phylogenetic relationships among divergent taxa (Gupta et al, 1994(Gupta et al, , 1999Molto et al, 1994;Gupta and Golding, 1993;Borchiellini et al, 1998;Budin and Philippe, 1998;Stedman et al, 1998;Germot and Philippe, 1999;Philippe et al, 1999;Schultz et al, 1999;Rue et al, 2000;Sulaiman et al, 2000). In some cases, HSP70 gene trees challenge conventional hypotheses (e.g., Budin and Philippe, 1998), and it is important to understand the limitations of HSP70 genes for phylogenetic inference before abandoning favored hypotheses for alternatives, no matter how interesting the alternatives may be.…”

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confidence: 99%

Perils of Paralogy: Using HSP70 Genes for Inferring Organismal Phylogenies

Martin¹,

Burg²

2002

Systematic Biology

101

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Conserved genes have found their way into the mainstream of molecular systematics. Many of these genes are members of multigene families. A difficulty with using single genes of multigene families for phylogenetic inference is that genes from one species may be paralogous to those from another taxon. We focus attention on this problem using heat shock 70 (HSP70) genes. Using polymerase chain reaction techniques with genomic DNA, we isolated and sequenced 123 distinct sequences from 12 species of sharks. Phylogenetic analysis indicated that the sequences cluster with constituitively expressed cytoplasmic heat shock-like genes. Three highly divergent gene clades were sampled. A number of similar sequences were sampled from each species within each distinct gene clade. Comparison of published species trees with an HSP70 gene tree inferred using Bayesian phylogenetic analysis revealed several cases of gene duplication and differential sorting of gene lineages within this group of sharks. Gene tree parsimony based on the objective criteria of duplication and losses showed that previously published hypotheses of species relationships and two novel hypothesis based on Bayesian phylogenetics were concordant with the history of HSP70 gene duplication and loss. By contrast, two published hypotheses based on morphological data were not significantly different from the null hypothesis of a random association between species relatedness and the HSP70 gene tree. These results suggest that gene tree parsimony using data from multigene families can be used for inferring species relationships or testing published alternative hypotheses. More importantly, the results suggest that systematic studies relying on phylogenetic inferences from HSP70 genes may by plagued by unrecognized paralogy of sampled genes. Our results underscore the distinction between gene and species trees and highlight an underappreciated source of discordance between gene trees and organismal phylogeny, i.e., unrecognized paralogy of sampled genes.

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The HSP70 Gene Family in Pneumocystis carinii: Molecular and Phylogenetic Characterization of Cytoplasmic Members

Cited by 16 publications

References 33 publications

Development and Characterization of a Molecular Viability Assay forPneumocystis cariniif sphominis

Development and Characterization of a Molecular Viability Assay forPneumocystis cariniif sphominis

Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients

Perils of Paralogy: Using HSP70 Genes for Inferring Organismal Phylogenies

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