Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

Ma, Liang; Chen, Zehua; Huang, Da Wei; Kutty, Geetha; Ishihara, Mayumi; Wang, Honghui; Abouelleil, Amr; Bishop, Lisa R.; Davey, Emma; Deng, Rebecca; Deng, Xianwen; Lin, Fan; Fantoni, Giovanna; FitzGerald, Michael G.; Gogineni, Emile; Goldberg, Jonathan M.; Handley, Grace; Hu, Xiaojun; Huber, Charles; Jiao, Xiaoli; Jones, Kristine; Levin, Joshua Z.; Liu, Yueqin; Macdonald, Pendexter; Melnikov, Alexandre; Raley, Castle; Sassi, Monica; Sherman, Brad T.; Song, Xiaohong; Sykes, Sean M.; Tran, Bao; Walsh, Laura; Xia, Yun; Yang, Jun; Young, Sarah; Zeng, Qiandong; Zheng, Xin; Stephens, Robert M.; Nusbaum, Chad; Birren, Bruce W.; Azadi, Parastoo; Lempicki, Richard A.; Cuomo, Christina A.; Kovacs, Joseph A.

doi:10.1038/ncomms10740

Cited by 161 publications

(402 citation statements)

References 74 publications

Supporting

Mentioning

381

Contrasting

Unclassified

Order By: Relevance

“…More recently, an intriguing study by Rapaka and colleagues (15) suggested that mice infected with P. murina (Pm) could generate increased levels of IgM antibodies against fungal carbohydrates, including GlcNAc-containing carbohydrates. Recently, however, it has been shown that, although Pneumocystis species contain chitin chaperone proteins implicated in proper transportation of major chitin synthases to the cell membrane in yeast, the genomes of Pneumocystis species lack major chitin synthase or chitin-degrading chitinase enzymes (5). In this light, we initiated a comprehensive analysis of the various enzymes potentially leading to the synthesis of GlcNAc in Pneumocystis organisms.…”

mentioning

confidence: 99%

“…The cell surface of the pathogenic fungal species represented by Pneumocystis organisms have not been fully elucidated, but are known to contain b-1,3 and b-1,6 glucans, and the major surface mannoserich glycoproteins, variously termed major surface glycoprotein (MSG) or glycoprotein A (gpA) (3)(4)(5). We and others have shown that the Pneumocystis species contain b-glucan synthetases that can be inhibited by specific b-glucan inhibitors, such as the echinocandins, pneumocandins, and newly generated compounds (3,4,6,7).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Characterization of N-Acetylglucosamine Biosynthesis in Pneumocystis species. A New Potential Target for Therapy

Kottom

Hebrink

Jenson

et al. 2017

Am J Respir Cell Mol Biol

View full text Add to dashboard Cite

N-acetylglucosamine (GlcNAc) serves as an essential structural sugar on the cell surface of organisms. For example, GlcNAc is a major component of bacterial peptidoglycan, it is an important building block of fungal cell walls, including a major constituent of chitin and mannoproteins, and it is also required for extracellular matrix generation by animal cells. Herein, we provide evidence for a uridine diphospho (UDP)-GlcNAc pathway in Pneumocystis species. Using an in silico search of the Pneumocystis jirovecii and P. murina (Pm) genomic databases, we determined the presence of at least four proteins implicated in the Saccharomyces cerevisiae UDP-GlcNAc biosynthetic pathway. These genes, termed GFA1, GNA1, AGM1, and UDP-GlcNAc pyrophosphorylase (UAP1), were either confirmed to be present in the Pneumocystis genomes by PCR, or, in the case of Pm uap1 (Pmuap1), functionally confirmed by direct enzymatic activity assay. Expression analysis using quantitative PCR of Pneumocystis pneumonia in mice demonstrated abundant expression of the Pm uap1 transcript. A GlcNAc-binding recombinant protein and a novel GlcNAc-binding immune detection method both verified the presence of GlcNAc in P. carinii (Pc) lysates. Studies of Pc cell wall fractions using highperformance gas chromatography/mass spectrometry documented the presence of GlcNAc glycosyl residues. Pc was shown to synthesize GlcNAc in vitro. The competitive UDP-GlcNAc substrate synthetic inhibitor, nikkomycin Z, suppressed incorporation of GlcNAc by Pc preparations. Finally, treatment of rats with Pneumocystis pneumonia using nikkomycin Z significantly reduced organism burdens. Taken together, these data support an important role for GlcNAc generation in the cell surface of Pneumocystis organisms.

show abstract

mentioning

confidence: 99%

mentioning

confidence: 99%

Characterization of N-Acetylglucosamine Biosynthesis in Pneumocystis species. A New Potential Target for Therapy

Kottom

Hebrink

Jenson

et al. 2017

Am J Respir Cell Mol Biol

View full text Add to dashboard Cite

show abstract

“…Both stages express surface glycoproteins and mannoproteins, which may serve as pathogen-associated molecular patterns (PAMPs) that could interact with receptors on phagocytic cells (17)(18)(19). Neither life form expresses chitin or ␣-glucans (20).…”

mentioning

confidence: 99%

The Life Cycle Stages of Pneumocystis murina Have Opposing Effects on the Immune Response to This Opportunistic Fungal Pathogen

2016

View full text Add to dashboard Cite

P neumocystis species are opportunistic fungal pathogens that cause severe pneumonia in immunocompromised hosts, including AIDS patients. Clearance of Pneumocystis organisms is dependent on effective CD4ϩ T and B cell and macrophage responses (1-4). Failure to clear Pneumocystis organisms leads to severe alveolar damage due to the exaggerated inflammatory immune response (5). In spite of a reduced incidence of Pneumocystis pneumonia (PcP) in HIV-infected individuals due to improved antiviral therapies, the mortality rate for patients with PcP has not improved with the implementation of highly active antiretroviral therapy (HAART) (6). Additional studies are required to inform novel approaches to reduce morbidity and mortality due to Pneumocystis pneumonia.Outbreaks of PcP were first described in malnourished or premature infants in orphanages following the Second World War (7). Evidence suggests that immunocompetent individuals of all ages are capable of mounting protective immune responses to Pneumocystis jirovecii that prevent progression to pneumonia. Most children encounter this opportunistic fungus at a young age, as indicated by the presence of specific antibodies in the sera of 85% of individuals by the age of 3 years (8). Previous work from our lab has shown that the neonatal mouse immune response to Pneumocystis is delayed, due in part to an anti-inflammatory lung environment (9-12). The neonatal lung environment is characterized by anti-inflammatory mediators, including transforming growth factor ␤1 (TGF-␤1) and interleukin 10 (IL-10), and immature immune cells (9-12). Neonatal alveolar macrophages and T cells adoptively transferred to an adult lung environment are competent at resolving Pneumocystis murina pneumonia in mice (9, 12). In addition, neonatal alveolar macrophages are deficient in NF-B translocation following stimulation with Pneumocystis organisms (9). Neonatal alveolar CD11c ϩ cells demonstrate delayed trafficking to the draining lymph nodes (11). Together, these data indicate that both the neonatal lung environment and intrinsic immune cell deficits contribute to the delayed clearance of P. murina in neonatal mice.Pneumocystis species have a biphasic life cycle. Trophic forms are proposed to represent the asexual stage of the life cycle, whereas cysts are the ascus-like sexual stage (13). Trophic forms are single-nucleated organisms that are typically found in clusters surrounded by a biofilm-like substance consisting of a conglomeration of DNA, ␤-glucan, and other sugars (14). Cysts are ascuslike structures that consist of multiple nuclei surrounded by a fungal cell wall. ␤-1,3-Glucan and ␤-1,6-glucan serve as the structural components of the cyst wall (15, 16). Trophic forms do not express ␤-glucan (15). Both stages express surface glycoproteins and mannoproteins, which may serve as pathogen-associated molecular patterns (PAMPs) that could interact with receptors on phagocytic cells (17)(18)(19). Neither life form expresses chitin or ␣-glucans (20).Dendritic cells are the principal ant...

show abstract

“…A total of 14 and 16 MG192 variants, with 1 to 8 variants per time point, were identified from each of the two animals. It is likely that the MG192 variants detected may not represent all variants in each isolate studied and that additional variants could be detected if a larger number of plasmid clones were stud- ied or using the newly developed high-throughput long-read PacBio SMRT sequencing technology (19), though currently this technology is not widely available or affordable (20,24). Using average numbers of nucleotide and predicted amino acid changes at each time point, we observed a significant increase of sequence changes over time during an 11-to 13-week period of infection in both animals ( Table 1).…”

Section: Discussionmentioning

confidence: 99%

Kinetics of Genetic Variation of the Mycoplasma genitalium MG192 Gene in Experimentally Infected Chimpanzees

Jensen

Mancuso

et al. 2016

Infect Immun

Self Cite

View full text Add to dashboard Cite

c Mycoplasma genitalium, a human pathogen associated with sexually transmitted diseases, is capable of causing chronic infections, though mechanisms for persistence remain unclear. Previous studies have found that variation of the MgPa operon occurs by recombination of repetitive chromosomal sequences (known as MgPars) into the MG191 and MG192 genes carried on this operon, which may lead to antigenic variation and immune evasion. In this study, we determined the kinetics of MG192 sequence variation during the course of experimental infection using archived specimens from two chimpanzees infected with M. genitalium strain G37. The highly variable region of MG192 was amplified by PCR from M. genitalium isolates obtained at various time points postinfection (p.i.). Sequence analysis revealed that MG192 sequence variation began at 5 weeks p.i. With the progression of infection, sequence changes accumulated throughout the MG192 variable region. The presence of MG192 variants at specific time points was confirmed by variant-specific PCR assays and sequence analysis of single-colony cloned M. genitalium organisms. MG192 nucleotide sequence variation correlated with estimated recombination events, predicted amino acid changes, and time of seroconversion, a finding consistent with immune selection of MG192 variants. In addition, we provided evidence that MG192 sequence variation occurred during the process of M. genitalium single-colony cloning. Such spontaneous variation suggests that some MG192 variation is independent of immune selection but may form the basis for subsequent immune selection. Mycoplasma genitalium is an important etiology of urogenital tract infections in humans and can be transmitted heterosexually or homosexually. Like infections caused by other pathogenic mycoplasmas, M. genitalium infections can persist for several months to more than 2 years as has been documented in animal models (1, 2) and humans (3-5). One of the best-known potential mechanisms for persistence is antigenic variation of two immunodominant surface proteins encoded by the MG191 (mgpB or P140) and MG192 (mgpC or P110) genes in the M. genitalium MgPa operon (5-11).Genetic variation in the MG191 and MG192 genes was first described in 1995 by Peterson et al. (11), but it was not until 2007 that we (10) and others (7) confirmed that this variation resulted from the recombination of the MG191 and MG192 variable regions with chromosomal repeats outside the MgPa operon, known as MgPa repeats or MgPar sequences. While the functional consequences of genetic variation at MG191 and MG192 remain unclear, it has been hypothesized that genetic variation can either change the antigenicity of the proteins to allow immune evasion or alter the mobility and adhesion ability of the organism to adapt to diverse host microenvironments, thus facilitating persistent infection (5-13). The former hypothesis is supported by a recent study in a pig-tailed macaque model in which MG191 sequence changes lead to reduced reactivity to antibodies produced at the e...

show abstract

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

Cited by 161 publications

References 74 publications

Characterization of N-Acetylglucosamine Biosynthesis in Pneumocystis species. A New Potential Target for Therapy

Characterization of N-Acetylglucosamine Biosynthesis in Pneumocystis species. A New Potential Target for Therapy

The Life Cycle Stages of Pneumocystis murina Have Opposing Effects on the Immune Response to This Opportunistic Fungal Pathogen

Kinetics of Genetic Variation of the Mycoplasma genitalium MG192 Gene in Experimentally Infected Chimpanzees

Contact Info

Product

Resources

About