ProFASTA: A pipeline web server for fungal protein scanning with integration of cell surface prediction software

Groot, Piet W. J. de; Brandt, Bernd W.

doi:10.1016/j.fgb.2011.12.009

Cited by 19 publications

(17 citation statements)

References 43 publications

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“…Two programs were used for the prediction of cell wall proteins/adhesins: ProFASTA [138] and FungalRV [139]. Analysis using the fasta files of the complete genomes of S. schenckii and S. brasiliensis were performed for prediction of GPI-anchor secretion signal and transmembrane domain identification.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis

et al. 2014

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BackgroundThe fungal genus Sporothrix includes at least four human pathogenic species. One of these species, S. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in Brazil. Elsewhere, sapronoses are caused by S. schenckii and S. globosa. The major aims on this comparative genomic study are: 1) to explore the presence of virulence factors in S. schenckii and S. brasiliensis; 2) to compare S. brasiliensis, which is cat-transmitted and infects both humans and cats with S. schenckii, mainly a human pathogen; 3) to compare these two species to other human pathogens (Onygenales) with similar thermo-dimorphic behavior and to other plant-associated Sordariomycetes.ResultsThe genomes of S. schenckii and S. brasiliensis were pyrosequenced to 17x and 20x coverage comprising a total of 32.3 Mb and 33.2 Mb, respectively. Pair-wise genome alignments revealed that the two species are highly syntenic showing 97.5% average sequence identity. Phylogenomic analysis reveals that both species diverged about 3.8-4.9 MYA suggesting a recent event of speciation. Transposable elements comprise respectively 0.34% and 0.62% of the S. schenckii and S. brasiliensis genomes and expansions of Gypsy-like elements was observed reflecting the accumulation of repetitive elements in the S. brasiliensis genome. Mitochondrial genomic comparisons showed the presence of group-I intron encoding homing endonucleases (HE’s) exclusively in S. brasiliensis. Analysis of protein family expansions and contractions in the Sporothrix lineage revealed expansion of LysM domain-containing proteins, small GTPases, PKS type1 and leucin-rich proteins. In contrast, a lack of polysaccharide lyase genes that are associated with decay of plants was observed when compared to other Sordariomycetes and dimorphic fungal pathogens, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style.ConclusionsComparative genomic data suggest a unique ecological shift in the Sporothrix lineage from plant-association to mammalian parasitism, which contributes to the understanding of how environmental interactions may shape fungal virulence. . Moreover, the striking differences found in comparison with other dimorphic fungi revealed that dimorphism in these close relatives of plant-associated Sordariomycetes is a case of convergent evolution, stressing the importance of this morphogenetic change in fungal pathogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-943) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis

et al. 2014

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“…The Kyte-Doolittle hydropathy plot was generated using a webserver at the University of Virginia (http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=misc1). For pattern scanning we used ProFASTA (http://www.bioinformatics.nl/tools/profasta/) [19] and for homology searching, NCBI-Blast (http://blast.ncbi.nlm.nih.gov/Blast.cgi). …”

Section: Methodsmentioning

confidence: 99%

In Candida parapsilosis the ATC1 Gene Encodes for an Acid Trehalase Involved in Trehalose Hydrolysis, Stress Resistance and Virulence

et al. 2014

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An ORF named CPAR2-208980 on contig 005809 was identified by screening a Candida parapsilosis genome data base. Its 67% identity with the acid trehalase sequence from C. albicans (ATC1) led us to designate it CpATC1. Homozygous mutants that lack acid trehalase activity were constructed by gene disruption at the two CpATC1 chromosomal alleles. Phenotypic characterization showed that atc1Δ null cells were unable to grow on exogenous trehalose as carbon source, and also displayed higher resistance to environmental challenges, such as saline exposure (1.2 M NaCl), heat shock (42°C) and both mild and severe oxidative stress (5 and 50 mM H2O2). Significant amounts of intracellular trehalose were specifically stored in response to the thermal upshift in both wild type and mutant strains. Analysis of their antioxidant activities revealed that catalase was only triggered in response to heat shock in atc1Δ cells, whereas glutathione reductase was activated upon mild oxidative stress in wild type and reintegrant strains, and in response to the whole set of stress treatments in the homozygous mutant. Furthermore, yeast cells with double CpATC1 deletion were significantly attenuated in non-mammalian infection models, suggesting that CpATC1 is required for the pathobiology of the fungus. Our results demonstrate the involvement of CpAtc1 protein in the physiological hydrolysis of external trehalose in C. parapsilosis, where it also plays a major role in stress resistance and virulence.

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“…Therefore, although the N-terminal effector domains of proteins in different subfamilies may not show obvious similarities, these proteins do have structural (and probably functional) relationships. Interestingly, the presence of (multiple) VSHITT or SFFIT megasatellites seems specific for adhesins in C. glabrata as it does not occur in any other protein currently present in the NCBI protein database (123). Elucidation of the exact functions of the repeat regions remains largely elusive.…”

Section: Candida Glabrata Adhesinsmentioning

confidence: 99%

Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick

et al. 2013

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Understanding the pathogenesis of an infectious disease is critical for developing new methods to prevent infection and diagnose or cure disease. Adherence of microorganisms to host tissue is a prerequisite for tissue invasion and infection. Fungal cell wall adhesins involved in adherence to host tissue or abiotic medical devices are critical for colonization leading to invasion and damage of host tissue. Here, with a main focus on pathogenic Candida species, we summarize recent progress made in the field of adhesins in human fungal pathogens and underscore the importance of these proteins in establishment of fungal diseases.

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ProFASTA: A pipeline web server for fungal protein scanning with integration of cell surface prediction software

Cited by 19 publications

References 43 publications

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis

In Candida parapsilosis the ATC1 Gene Encodes for an Acid Trehalase Involved in Trehalose Hydrolysis, Stress Resistance and Virulence

Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick

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