A Sensitive Predictor for Potential GPI Lipid Modification Sites in Fungal Protein Sequences and its Application to Genome-wide Studies for Aspergillus nidulans, Candida albicans Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe

Eisenhaber, Birgit; Schneider, Georg; Wildpaner, Michael; Eisenhaber, Frank

doi:10.1016/j.jmb.2004.01.025

Cited by 265 publications

(254 citation statements)

References 53 publications

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“…Identification of conserved domains was performed using the SMART protein analysis tool (Letunic et al, 2009) and InterProScan (Quevillon et al, 2005). For signal peptide prediction, Signal P v. 4.0 (Petersen et al, 2011) was used, while analyses for transmembrane helices and glycosyl-phosphatidylinositol (GPI) plasma membrane anchors were conducted using TMHMM v. 2.0 (Krogh et al, 2001) and the big-PI Fungal Predictor program (Eisenhaber et al, 2004), respectively. Target P v. 1.1 (Emanuelsson et al, 2000) and PSORT II (Nakai & Horton, 1999) were used to analyse subcellular localization.…”

Section: Methodsmentioning

confidence: 99%

Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea

et al. 2015

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Clonostachys rosea is a mycoparasitic fungal species that is an efficient biocontrol agent against many plant diseases. During mycoparasitic interactions, one of the most crucial steps is the hydrolysis of the prey's fungal cell wall, which mainly consists of glucans, glycoproteins and chitin. Chitinases are hydrolytic enzymes responsible for chitin degradation and it is suggested that they play an important role in fungal-fungal interactions. Fungal chitinases belong exclusively to the glycoside hydrolase (GH) family 18.These GH18 proteins are categorized into three distinct phylogenetic groups (A, B and C), subdivided into several subgroups. In this study, we identified 14 GH18 genes in the C. rosea genome, which is remarkably low compared with the high numbers found in mycoparasitic Trichoderma species. Phylogenetic analysis revealed that C. rosea contains eight genes in group A, two genes in group B, two genes in group C, one gene encoding a putative ENGase (endo-b-N-acetylglucosaminidase) and the ech37 gene, which is of bacterial origin. Gene expression analysis showed that only two genes had higher transcription levels during fungal-fungal interactions, while eight out of 14 GH18 genes were triggered by chitin. Furthermore, deletion of the C group chiC2 gene decreased the growth inhibitory activity of C. rosea culture filtrates against Botrytis cinerea and Rhizoctonia solani, although the biocontrol ability of C. rosea against B. cinerea was not affected. In addition, a potential role of the CHIC2 chitinase in the sporulation process was revealed. These results provide new information about the role of GH18 proteins in mycoparasitic interactions.

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Section: Methodsmentioning

confidence: 99%

Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea

et al. 2015

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“…Of these 237 proteins, the tmHmm prediction server (http://www.cbs.dtu.dk /services/TMHMM/) identified 188 proteins without transmembrane domains. The Fungal BIG-PI server (http://mendel.imp.ac.at/gpi/fungi_server.html) was slightly more conservative and identified a subset of 149 (79%) as potential GPI-anchored proteins (18). Like the S. cerevisiae cell wall proteins, 115 of the Y. lipolytica proteins contained regions with high S and T content: Ͼ50 consecutive residues with Ͼ30% S and T.…”

Section: Methodsmentioning

confidence: 99%

Conserved Processes and Lineage-Specific Proteins in Fungal Cell Wall Evolution

et al. 2007

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The cell wall is a defining organelle that differentiates fungi from its sister clades in the opisthokont superkingdom. With a sensitive technique to align low-complexity protein sequences, we have identified 187 cell wall-related proteins in Saccharomyces cerevisiae and determined the presence or absence of homologs in 17 other fungal genomes. There were both conserved and lineage-specific cell wall proteins, and the degree of conservation was strongly correlated with protein function. Some functional classes were poorly conserved and lineage specific: adhesins, structural wall glycoprotein components, and unannotated open reading frames. These proteins are primarily those that are constituents of the walls themselves. On the other hand, glycosyl hydrolases and transferases, proteases, lipases, proteins in the glycosyl phosphatidyl-inositol-protein synthesis pathway, and chaperones were strongly conserved. Many of these proteins are also conserved in other eukaryotes and are associated with wall synthesis in plants. This gene conservation, along with known similarities in wall architecture, implies that the basic architecture of fungal walls is ancestral to the divergence of the ascomycetes and basidiomycetes. The contrasting lineage specificity of wall resident proteins implies diversification. Therefore, fungal cell walls consist of rapidly diversifying proteins that are assembled by the products of an ancestral and conserved set of genes.

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“…For protein motifs and predicted functions, the following tools were used: signal peptides were predicted using SignalP 3.0 (Bendtsen et al, 2004) at the CBS prediction server (www.cbs.dtu.dk/services/); glycosylphosphatidylinositol (GPI) modification sites were predicted with the big-PI fungal prediction server (http://mendel.imp.univie. ac.at/gpi/fungi_server.html) (Eisenhaber et al, 1998(Eisenhaber et al, , 2004; transmembrane domain prediction and protein localization were performed with the TMHMM 2.0 algorithm (Krogh et al, 2001) and TargetP 1.1 (Emanuelsson et al, 2000) at the CBS prediction server, or with ProtComp 6.0 at www.softberry.com, with the LOCSVMPSI 1.3 server (bioinformatics.ustc.edu.cn) (Xie et al, 2005) or with PA-SUB (www.cs.ualberta.ca/~bioinfo/PA/Sub/) (Lu et al, 2004).…”

Section: Methodsmentioning

confidence: 99%

MfLIP1, a gene encoding an extracellular lipase of the lipid-dependent fungus Malassezia furfur

Brunke

Hube

2006

Microbiology

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Malassezia furfur is a dimorphic fungus and a member of the normal cutaneous microflora of humans. However, it is also a facultative pathogen, associated with a wide range of skin diseases. One unusual feature of M. furfur is an absolute dependency on externally provided lipids which the fungus hydrolyses by lipolytic activity to release fatty acids necessary for both growth and pathogenicity. In this study, the cloning and characterization of the first gene encoding a secreted lipase of M. furfur possibly associated with this activity are reported. The gene, MfLIP1, shows high sequence similarity to other known extracellular lipases, but is not a member of a lipase gene family in M. furfur. MfLIP1 consists of 1464 bp, encoding a protein with a molecular mass of 54?3 kDa, a conserved lipase motif and an N-terminal signal peptide of 26 aa. By using a genomic library, two other genes were identified flanking MfLIP1, one of them encoding a putative secreted catalase, the other a putative amine oxidase. The cDNA of MfLIP1 was expressed in Pichia pastoris and the biochemical properties of the recombinant lipase were analysed. MfLip1 is most active at 40 6C and the pH optimum was found to be 5?8. The lipase hydrolysed lipids, such as Tweens, frequently used as the source of fatty acids in M. furfur media, and had minor esterase activity. Furthermore, the lipase is inhibited by different bivalent metal ions. This is the first molecular description of a secreted lipase from M. furfur.

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A Sensitive Predictor for Potential GPI Lipid Modification Sites in Fungal Protein Sequences and its Application to Genome-wide Studies for Aspergillus nidulans, Candida albicans Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe

Cited by 265 publications

References 53 publications

Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea

Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea

Conserved Processes and Lineage-Specific Proteins in Fungal Cell Wall Evolution

MfLIP1, a gene encoding an extracellular lipase of the lipid-dependent fungus Malassezia furfur

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