Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

Choi, Jaeyoung; Park, Jongsun; Kim, Donghan; Jung, Ki Won; Kang, Seogchan; Lee, Yong Hwan

doi:10.1186/1471-2164-11-105

Cited by 177 publications

(178 citation statements)

References 94 publications

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“…Of the total number of different proteins in the extracellular proteome of P. chrysogenum, 102 out of 131 were predicted to contain either classical or nonclassical signal sequences using the SignalP and SecretomeP programs. Prediction of secretory proteins has been improved by the implementation of the Fungal Secretome Database (20), which is based on nine prediction programs (including SignalP and SecretomeP) and has been used to identify putative secretory proteins in 158 fungal/ oomycete genomes. The presence of proteins with nonpredicted signal sequences in the secreted fraction has also been described in the filamentous fungus Botrytis cinerea (19).…”

Section: Discussionmentioning

confidence: 99%

“…However, because of the availability of several fungal genomes and diverse prediction programs for secretory proteins, an integrated platform for annotation of fungal secretomes (Fungal Secretome Database) has been established and implemented in a web-based database (20). This database has been proposed as an integrated environment for the study of secretory proteins in the fungal kingdom.…”

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confidence: 99%

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The Penicillium Chrysogenum Extracellular Proteome. Conversion from a Food-rotting Strain to a Versatile Cell Factory for White Biotechnology

Jami

Garcı́a-Estrada

Barreiro

et al. 2010

Molecular & Cellular Proteomics

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The filamentous fungus Penicillium chrysogenum is wellknown by its ability to synthesize ␤-lactam antibiotics as well as other secondary metabolites. Like other filamentous fungi, this microorganism is an excellent host for secretion of extracellular proteins because of the high capacity of its protein secretion machinery. In this work, we have characterized the extracellular proteome reference map of P. chrysogenum

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

The Penicillium Chrysogenum Extracellular Proteome. Conversion from a Food-rotting Strain to a Versatile Cell Factory for White Biotechnology

Jami

Garcı́a-Estrada

Barreiro

et al. 2010

Molecular & Cellular Proteomics

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“…Typical signal peptides that facilitate translocation have been located in the majority of filamentous pathogen effectors identified to date (1239,1258,1260). Cysteine-rich domains may also play a role in translocation signaling, as translocated apoplastic effectors and host-translocated effec-tors are both small cysteine-rich proteins (1247).…”

Section: Common Features Of Known Effector Proteinsmentioning

confidence: 99%

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

165

195

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SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.

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“…Like transcriptomics, proteomics has a big problem with unknown proteins. In fungi, 208,883 putative secretory proteins have been identified (Choi et al, 2010), but only a small fraction of them have been studied, and so far, nobody knows the biological/ecological role of most of them. On the other hand, there are many reports describing the use of plant mutants, pathogenic bacteria, and symbiotic microbes that highlight the vast diversity of proteins or even the function of a group of proteins during plant-microbe interaction (De-la-Peña et al, 2008;Afroz et al, 2013;Alberton et al, 2013;Dam et al, 2014).…”

Section: Proteomicsmentioning

confidence: 99%

Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity

De‐la‐Peña

Loyola‐Vargas

2014

PLANT PHYSIOLOGY

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Microbes and plants have evolved biochemical mechanisms to communicate with each other. The molecules responsible for such communication are secreted during beneficial or harmful interactions. Hundreds of these molecules secreted into the rhizosphere have been identified, and their functions are being studied in order to understand the mechanisms of interaction and communication among the different members of the rhizosphere community. The importance of root and microbe secretion to the underground habitat in improving crop productivity is increasingly recognized, with the discovery and characterization of new secreting compounds found in the rhizosphere. Different omic approaches, such as genomics, transcriptomics, proteomics, and metabolomics, have expanded our understanding of the first signals between microbes and plants. In this review, we highlight the more recent discoveries related to molecules secreted into the rhizosphere and how they affect plant productivity, either negatively or positively. In addition, we include a survey of novel approaches to studying the rhizosphere and emerging opportunities to direct future studies.

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Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

Cited by 177 publications

References 94 publications

The Penicillium Chrysogenum Extracellular Proteome. Conversion from a Food-rotting Strain to a Versatile Cell Factory for White Biotechnology

The Penicillium Chrysogenum Extracellular Proteome. Conversion from a Food-rotting Strain to a Versatile Cell Factory for White Biotechnology

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity

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