Variation and<i>in vitro</i>splicing of group I introns in rRNA genes of<i>Pneumocystis carinii</i>

Liu, Yong; Leibowitz, Michael J.

doi:10.1093/nar/21.10.2415

Cited by 72 publications

(92 citation statements)

References 34 publications

(77 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…hominis has only one copy of the rRNA gene (22), our sequence analysis indicated the presence of two different bases at one position in strains from 36 (60%) specimens and provides evidence in support of infection with more than one type of P. carinii (14). An incidence of 33% mixed infections has previously been reported for AIDS patients (23) and from analysis of the mt LSU rRNA and ITS loci (10,11,14). In this study, we found mixed infections in 60% of the specimens that we analyzed.…”

Section: Discussionmentioning

confidence: 64%

“…The 5S rRNA gene also has limited sequence variation, with polymorphisms reported at five positions. Analysis of the sequence of a portion of the nuclear rRNA operon of the organism from BAL samples from five HIV-infected patients in the United States failed to show any differences (14). It is also possible, however, that the polymorphism could be explained in part by the presence of heterozygosity in diploid-stage organisms in the sample.…”

Section: Discussionmentioning

confidence: 91%

See 1 more Smart Citation

Genetic Diversity of Pneumocystis carinii f. sp. hominis Based on Variations in Nucleotide Sequences of Internal Transcribed Spacers of rRNA Genes

Nimri¹,

Moura²,

Huang

et al. 2002

J Clin Microbiol

View full text Add to dashboard Cite

A variety of genes have been used to type Pneumocystis carinii. In the present study, nucleotide sequence variations in the ITS1 and ITS2 internal transcribed spacer (ITS) regions of the rRNA genes were used to type Pneumocystis carinii f. sp. hominis DNA obtained from the lungs of 60 human immunodeficiency virus-infected individuals. These regions were amplified by PCR, cloned, and sequenced. Multibase polymorphisms were identified among samples. Several new genotypes are reported on the basis of the nucleotide sequence variations at previously unreported positions of both the ITS1 and the ITS2 regions. Twelve new ITS1 sequences were observed, in addition to the nine sequence types reported previously. The most common was type E, which was observed in 60.5% of the samples. The sequence variations in the ITS1 region were mainly located at positions 5, 12, 23, 24, 45, 53, and 54. Sixteen new ITS2 types were also identified, in addition to the 13 types reported previously. The most common was type g (26.6%). The sequences of the ITS2 regions in most specimens were different from the previously published sequence at bases 120 and 166 through 183. The most common variations observed were deletions at positions 177 through 183. The presence of more than one sequence type in some patients (60%) suggested the occurrence of coinfection with multiple P. carinii strains. The genetic polymorphism observed demonstrates the degree of diversity of Pneumocystis strains that infect humans. Furthermore, the high degree of polymorphism suggests that these genes are evolving faster than other genes. Consequently, the sequence information derived is useful for purposes such as examination of the potential of person-to-person transmission and recurrent infections but perhaps not for other genotyping applications that rely on more stable genetic loci.Pneumocystis carinii is an opportunistic pathogen that causes potentially fatal pneumonia in immunocompromised or immunosuppressed patients. Despite the decrease in the incidence of the disease in human immunodeficiency virus HIV-infected patients (3), P. carinii pneumonia (PCP) continues to be a common AIDS-defining illness associated with significant mortality in both adults (8%) (3) and children (30%) (19).Although recent research has clarified our understanding of certain biological aspects of the organism, no standard method for the typing of P. carinii has emerged. Pure isolates of the organism are difficult to obtain in large amounts due to the lack of a standardized method of in vitro cultivation of humanderived P. carinii. Standard methods of typing have similarly been slow to develop (24).Despite evidence of genetic variations among human P. carinii isolates (12,20), the degree of diversity among strains that infect humans still lacks clarification. The existence of multiple strains of P. carinii that infect humans was first demonstrated by examination of the restriction fragment length polymorphisms (RFLPs) of P. carinii genomes from three patients (21). However, RFLP analyses...

show abstract

Section: Discussionmentioning

confidence: 64%

Section: Discussionmentioning

confidence: 91%

Genetic Diversity of Pneumocystis carinii f. sp. hominis Based on Variations in Nucleotide Sequences of Internal Transcribed Spacers of rRNA Genes

Nimri¹,

Moura²,

Huang

et al. 2002

J Clin Microbiol

View full text Add to dashboard Cite

show abstract

“…To date, the mtLSU rRNA sequence has been reported from P. carinii organisms infecting nine different mammalian species: human, rat (two divergent sequence types), mouse, rabbit, pig, horse, shrew, ferret (five divergent sequence types), and rhesus macaque (17,23,37,46). The genetic diversity of P. carinii was examined at other loci such as the mitochondrial small subunit of rRNA (28), the nuclear ribosomal RNA operon (32,46), ␣-and ␤-tubulin (18,43), arom (5), thymidilate synthetase (30,35), DHPS (31), and more recently manganese-dependent superoxide dismutase (16). However, only a small variety of mammalian hosts with P. carinii were examined in former analyses.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny of Pneumocystis carinii from 18 Primate Species Confirms Host Specificity and Suggests Coevolution

Demanche

Berthelemy

Petit³

et al. 2001

J Clin Microbiol

113

114

View full text Add to dashboard Cite

Primates are regularly infected by fungal organisms identified as Pneumocystis carinii. They constitute a valuable population for the confirmation of P. carinii host specificity. In this study, the presence of P. carinii was assessed by direct examination and nested PCR at mitochondrial large subunit (mtLSU) rRNA and dihydropteroate synthetase (DHPS) genes in 98 lung tissue samples from captive or wild nonhuman primates. Fifty-nine air samples corresponding to the environment of different primate species in zoological parks were also examined. Cystic forms of P. carinii were detected in smears from 7 lung tissue samples corresponding to 5 New World primate species. Amplifications at the mtLSU rRNA gene were positive for 29 lung tissue samples representing 18 different primate species or subspecies and 2 air samples corresponding to the environment of two simian colonies. Amplifications at the DHPS gene were positive for 8 lung tissue samples representing 6 different primate species. Direct sequencing of nested PCR products demonstrated that a specific mtLSU rRNA and DHPS sequence could be attributed to each primate species or subspecies. No nonhuman primate harbored the human type of P. carinii (P. carinii f. sp. hominis). Genetic divergence in primate-derived P. carinii organisms varied in terms of the phylogenetic divergence existing among the corresponding host species, suggesting coevolution.

show abstract

“…The NJ tree (Fig. 3) reflects a close relationship between GP-D and the P. carinii group I introns (Liu and Leibowitz, 1993). So it should not be interpreted, however, that all introns occurring at a particular site are necessarily closely related or that introns at different sites in the same organisms cannot be homologous (Hibbett, 1996).…”

mentioning

confidence: 99%

Detection of multiple insertions of group I introns in the nuclear small subunit ribosomal RNA gene from the ustilaginomycete Graphiola phoenicis parasitic on palm.

Sjamsuridzal

Sugiyama

1998

J. Gen. Appl. Microbiol.

View full text Add to dashboard Cite

Variation andin vitrosplicing of group I introns in rRNA genes ofPneumocystis carinii

Cited by 72 publications

References 34 publications

Genetic Diversity of Pneumocystis carinii f. sp. hominis Based on Variations in Nucleotide Sequences of Internal Transcribed Spacers of rRNA Genes

Genetic Diversity of Pneumocystis carinii f. sp. hominis Based on Variations in Nucleotide Sequences of Internal Transcribed Spacers of rRNA Genes

Phylogeny of Pneumocystis carinii from 18 Primate Species Confirms Host Specificity and Suggests Coevolution

Detection of multiple insertions of group I introns in the nuclear small subunit ribosomal RNA gene from the ustilaginomycete Graphiola phoenicis parasitic on palm.

Contact Info

Product

Resources

About