A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

Lebreton, Annie; Bonnardel, François; Dai, Yu-Cheng; Martin, Francis; Lisacek, Frédérique

doi:10.3390/jof7060453

Cited by 23 publications

(16 citation statements)

References 48 publications

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“…We here provide an overview of lectin copy numbers in the examined Agaricomycetes in the context of 8 main families, but note that more recent classifications(Lebreton et al 2021) significantly reorganized lectin families and may provide a more nuanced view on lectin repertoires. Lectin copy numbers and expression patterns were summarized in the context of 6 Agaricomycetes species by Krizsan et al(Krizsán et al 2019) with lectins showing the RicinB fold (which includes protease inhibitors too, see above and(J et al 2016)) being most diverse and present in all species, whereas other families are more patchy.…”

Section: Results: Developmentally Expressed Gene Classes In the Agari...mentioning

confidence: 99%

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Nagy

Vonk

Künzler

et al. 2021

Preprint

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Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Key words: functional annotation; comparative genomics; cell wall remodeling; development; fruiting body morphogenesis; mushroom; transcriptome

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Section: Results: Developmentally Expressed Gene Classes In the Agari...mentioning

confidence: 99%

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Nagy

Vonk

Künzler

et al. 2021

Preprint

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“…As Polyporales is an important group of wood decayers, we investigated the decay ability of these species by analyzing their secretome. The current evolution was posited that early Agaricomycetes were saprotrophic and different lifestyles were derived from it [ 75 , 76 ]. It also supported that the white-rot lifestyle is linked to the ability to degrade lignin.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

Sun

Lebreton

Xing

et al. 2022

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The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

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“…Several β-PFTs have a lectin-type membrane-binding domain, such as CEL-III in the sea cucumber, including 35 binding sites for galactose in its hemolytic heptameric form 11 . The fungal β-PFT from L. sulfureus has a lectin domain specific for lactose that also occurs in many other fungi 51 . Plant β-trefoil lectins of the Amaranthin class were also predicted to be associated with aerolysin in many plants 24 .…”

Section: Discussionmentioning

confidence: 99%

A pore-forming β-trefoil lectin with specificity for the tumor-related glycosphingolipid Gb3

Notova

Bonnardel

Rosato

et al. 2022

Preprint

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Lectins are efficient multivalent glycan receptors, deciphering the glyco-code on cell surfaces. The β-trefoil fold, characterized by three lobe-shaped repeats, is adopted by several classes of lectins, often associated with other domains having enzymatic or toxic activity. Based on the UniLectin3D database classification, the sequence signature of trefoil lobes was defined and used to predict 44714 lectins from 4497 species. Among them, SaroL-1 from the lower eukaryote Salpingoeca rosetta was predicted to contain both β-trefoil and aerolysin-like pore-forming domain. Recombinant SaroL-1 binds to galactose and derivatives, with a stronger affinity for cancer-related α-galactosylated epitopes such as glycosphingolipid Gb3 embedded in giant unilamellar vesicles or cell membranes. Crystal structures in complex with Gb3 trisaccharide and GalNAc show similarity with pore-forming toxins. Recognition of the αGal epitope on glycolipids was necessary for hemolysis of rabbit erythrocytes and toxicity on cancer cells through carbohydrate-dependent pore-formation.

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A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

Cited by 23 publications

References 48 publications

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

A pore-forming β-trefoil lectin with specificity for the tumor-related glycosphingolipid Gb3

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