Limits...
Comparative genomics and transcriptomics analyses reveal divergent lifestyle features of nematode endoparasitic fungus Hirsutella minnesotensis.

Lai Y, Liu K, Zhang X, Zhang X, Li K, Wang N, Shu C, Wu Y, Wang C, Bushley KE, Xiang M, Liu X - Genome Biol Evol (2014)

Bottom Line: Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota).Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi.Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China.

Show MeSH

Related in: MedlinePlus

Phylogenetic tree of nematophagous and insect fungal proteinases containing peptidase S8/S53-subtilisin/kexin/sedolisin domains annotated by Pfam. Proteinase genes from one nematode endoparasitic fungus, three nematode-trapping fungi, and five insect fungi are labeled in branch with red, green, and blue color, respectively. Phylogeny was estimated using RAxML (see Materials and Methods). Five clades were identified according to the different domain architecture of proteinase genes. Genes in Clade A contain peptidase S53 domains in combination with the peptidase S8/S53-subtilisin/kexin/sedolisin domains. This combination is found mainly in insect fungi. Most of proteinase genes in nematode endoparasitic fungus are located in Clades B–E. They have more close relationship with those of insect fungi than with trapping fungi. Clades B and C have longer peptidase S8/S53-subtilisin/kexin/sedolisin domains compared with other clades and contain DUF1034 C-terminal and proprotein convertase P domains closest to the conserved domain, respectively. Specially nine genes in Clade B contain PA signature (protease-associated domain) embedded within the peptidase S8/S53 domain. Clade D may have arisen differently; as the majority of proteins belong to nematode-trapping fungi do not have any other domains in combination with the peptidase S8/S53 domain. Half of the genes in Clade D do not carry a signal peptide, thus they do not seem to function extracellularly. Clade E is an expanded group of genes that contain signal peptide and proteinase inhibitor I9 domain on the N-terminal of proteins.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4255773&req=5

evu241-F3: Phylogenetic tree of nematophagous and insect fungal proteinases containing peptidase S8/S53-subtilisin/kexin/sedolisin domains annotated by Pfam. Proteinase genes from one nematode endoparasitic fungus, three nematode-trapping fungi, and five insect fungi are labeled in branch with red, green, and blue color, respectively. Phylogeny was estimated using RAxML (see Materials and Methods). Five clades were identified according to the different domain architecture of proteinase genes. Genes in Clade A contain peptidase S53 domains in combination with the peptidase S8/S53-subtilisin/kexin/sedolisin domains. This combination is found mainly in insect fungi. Most of proteinase genes in nematode endoparasitic fungus are located in Clades B–E. They have more close relationship with those of insect fungi than with trapping fungi. Clades B and C have longer peptidase S8/S53-subtilisin/kexin/sedolisin domains compared with other clades and contain DUF1034 C-terminal and proprotein convertase P domains closest to the conserved domain, respectively. Specially nine genes in Clade B contain PA signature (protease-associated domain) embedded within the peptidase S8/S53 domain. Clade D may have arisen differently; as the majority of proteins belong to nematode-trapping fungi do not have any other domains in combination with the peptidase S8/S53 domain. Half of the genes in Clade D do not carry a signal peptide, thus they do not seem to function extracellularly. Clade E is an expanded group of genes that contain signal peptide and proteinase inhibitor I9 domain on the N-terminal of proteins.

Mentions: The most enriched secreted protease family in H. minnesotensis and other reference fungi are the serine proteases, which comprise approximately 50% of all secreted proteases (supplementary table S8, Supplementary Material online). Serine proteases, especially the subtilases (affiliated into two families: The subtilisin-like protease S8 and the serine-carboxyl protease S53), are involved in lethal activity and the infection process of nematodes (Yang et al. 2005; Wang et al. 2007, 2009). They also assist in the infection processes of entomopathogenic fungi by degrading host cuticles, providing nutrition and disabling antimicrobial peptides (Bagga et al. 2004; Gao et al. 2011). Fewer secreted subtilase coding genes were identified in H. minnesotensis compared with the insect pathogen Me. robertsii and trapping fungi A. oligospora and Mo. haptotylum. A phylogenetic tree based on the conserved enzymatic S8/S53-subtilisin/kexin/sedolisin domains (PF00082) revealed that subtilase genes in the endoparasitic fungus diverged from those of insect fungi, supporting the origin of endoparasitic species from insect fungi and their similar functions in protein degradation. Compared with insect fungi, S53 serine proteases, which adapt to the specific insect hosts coupled with S8 proteases (Muszewska et al. 2011), have been lost from nematode-trapping and endoparasitic fungi (fig. 3, Clade A). Although they both belong to the cuticle degrading proteases, the subtilases from nematode-trapping and endoparasitic fungus are not grouped together. Most of the subtilases from trapping fungi only contain the enzymatic domain, whereas subtilases from the endoparasitic fungus contain other functional domains (fig. 3, Clades B–E), such as an N-terminal subtilisin propeptide (proteinase inhibitor I9, PF05922), the cleavage of which activates the enzyme; or the DUF1034 domain (Domain of Unknown Function 1034, PF06280) embedded with proteinase associated (PA, PF02225) domain, which may be involved in recognition of the protein by vacuolar sorting mechanisms (Luo and Hofmann 2001). Therefore, subtilases of nematode endoparasitic fungus and trapping fungi have evolved different functional domain architectures.Fig. 3.—


Comparative genomics and transcriptomics analyses reveal divergent lifestyle features of nematode endoparasitic fungus Hirsutella minnesotensis.

Lai Y, Liu K, Zhang X, Zhang X, Li K, Wang N, Shu C, Wu Y, Wang C, Bushley KE, Xiang M, Liu X - Genome Biol Evol (2014)

Phylogenetic tree of nematophagous and insect fungal proteinases containing peptidase S8/S53-subtilisin/kexin/sedolisin domains annotated by Pfam. Proteinase genes from one nematode endoparasitic fungus, three nematode-trapping fungi, and five insect fungi are labeled in branch with red, green, and blue color, respectively. Phylogeny was estimated using RAxML (see Materials and Methods). Five clades were identified according to the different domain architecture of proteinase genes. Genes in Clade A contain peptidase S53 domains in combination with the peptidase S8/S53-subtilisin/kexin/sedolisin domains. This combination is found mainly in insect fungi. Most of proteinase genes in nematode endoparasitic fungus are located in Clades B–E. They have more close relationship with those of insect fungi than with trapping fungi. Clades B and C have longer peptidase S8/S53-subtilisin/kexin/sedolisin domains compared with other clades and contain DUF1034 C-terminal and proprotein convertase P domains closest to the conserved domain, respectively. Specially nine genes in Clade B contain PA signature (protease-associated domain) embedded within the peptidase S8/S53 domain. Clade D may have arisen differently; as the majority of proteins belong to nematode-trapping fungi do not have any other domains in combination with the peptidase S8/S53 domain. Half of the genes in Clade D do not carry a signal peptide, thus they do not seem to function extracellularly. Clade E is an expanded group of genes that contain signal peptide and proteinase inhibitor I9 domain on the N-terminal of proteins.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255773&req=5

evu241-F3: Phylogenetic tree of nematophagous and insect fungal proteinases containing peptidase S8/S53-subtilisin/kexin/sedolisin domains annotated by Pfam. Proteinase genes from one nematode endoparasitic fungus, three nematode-trapping fungi, and five insect fungi are labeled in branch with red, green, and blue color, respectively. Phylogeny was estimated using RAxML (see Materials and Methods). Five clades were identified according to the different domain architecture of proteinase genes. Genes in Clade A contain peptidase S53 domains in combination with the peptidase S8/S53-subtilisin/kexin/sedolisin domains. This combination is found mainly in insect fungi. Most of proteinase genes in nematode endoparasitic fungus are located in Clades B–E. They have more close relationship with those of insect fungi than with trapping fungi. Clades B and C have longer peptidase S8/S53-subtilisin/kexin/sedolisin domains compared with other clades and contain DUF1034 C-terminal and proprotein convertase P domains closest to the conserved domain, respectively. Specially nine genes in Clade B contain PA signature (protease-associated domain) embedded within the peptidase S8/S53 domain. Clade D may have arisen differently; as the majority of proteins belong to nematode-trapping fungi do not have any other domains in combination with the peptidase S8/S53 domain. Half of the genes in Clade D do not carry a signal peptide, thus they do not seem to function extracellularly. Clade E is an expanded group of genes that contain signal peptide and proteinase inhibitor I9 domain on the N-terminal of proteins.
Mentions: The most enriched secreted protease family in H. minnesotensis and other reference fungi are the serine proteases, which comprise approximately 50% of all secreted proteases (supplementary table S8, Supplementary Material online). Serine proteases, especially the subtilases (affiliated into two families: The subtilisin-like protease S8 and the serine-carboxyl protease S53), are involved in lethal activity and the infection process of nematodes (Yang et al. 2005; Wang et al. 2007, 2009). They also assist in the infection processes of entomopathogenic fungi by degrading host cuticles, providing nutrition and disabling antimicrobial peptides (Bagga et al. 2004; Gao et al. 2011). Fewer secreted subtilase coding genes were identified in H. minnesotensis compared with the insect pathogen Me. robertsii and trapping fungi A. oligospora and Mo. haptotylum. A phylogenetic tree based on the conserved enzymatic S8/S53-subtilisin/kexin/sedolisin domains (PF00082) revealed that subtilase genes in the endoparasitic fungus diverged from those of insect fungi, supporting the origin of endoparasitic species from insect fungi and their similar functions in protein degradation. Compared with insect fungi, S53 serine proteases, which adapt to the specific insect hosts coupled with S8 proteases (Muszewska et al. 2011), have been lost from nematode-trapping and endoparasitic fungi (fig. 3, Clade A). Although they both belong to the cuticle degrading proteases, the subtilases from nematode-trapping and endoparasitic fungus are not grouped together. Most of the subtilases from trapping fungi only contain the enzymatic domain, whereas subtilases from the endoparasitic fungus contain other functional domains (fig. 3, Clades B–E), such as an N-terminal subtilisin propeptide (proteinase inhibitor I9, PF05922), the cleavage of which activates the enzyme; or the DUF1034 domain (Domain of Unknown Function 1034, PF06280) embedded with proteinase associated (PA, PF02225) domain, which may be involved in recognition of the protein by vacuolar sorting mechanisms (Luo and Hofmann 2001). Therefore, subtilases of nematode endoparasitic fungus and trapping fungi have evolved different functional domain architectures.Fig. 3.—

Bottom Line: Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota).Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi.Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China.

Show MeSH
Related in: MedlinePlus