The Botrytis cinerea aspartic proteinase family

Have, Arjen ten; Espino, José J.; Dekkers, Ester; Sluyter, Steven C. Van; Brito, Nélida; Kay, John; González, Celedonio; Kan, Jan A.L. van

doi:10.1016/j.fgb.2009.10.008

Cited by 85 publications

(65 citation statements)

References 56 publications

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“…Sequences of 26 APs with determined X-ray structures were retrieved from the PDB database (supplementary table S1 B , Supplementary Material online) (Berman et al 2000) and added to the reduced, scrutinized sequence set, yielding a final set of 728 sequences. This subset of sequences, from which nonhomologous N- and C- terminal extensions were removed (according to Ten Have et al [2010]), is available in supplementary datafile S1 (fasta), Supplementary Material online.…”

Section: Resultsmentioning

confidence: 99%

“…Clade VI includes the sequences with determined structures of polyporopepsin and mucorpepsin as well as the recently described BcAP8, which is the most abundant secreted proteinase of B. cinerea (Ten Have et al 2010). …”

Section: Resultsmentioning

confidence: 99%

“…There appears to be no obvious common feature of the fungi that have a homolog in clade VI. As an example, the Ascomycete phytopathogen B. cinerea secretes a highly expressed clade VI ortholog (known as BcAP8) whereas the taxonomically closely related phytopathogen, Sclerotinia sclerotiorum, lacks this ortholog (Ten Have et al 2010), despite a similar lifestyle and infection strategy (Amselem et al 2011). …”

Section: Discussionmentioning

confidence: 99%

“…All sequences identified by the matrices with a full sequence E value smaller than the HMMER exclusion threshold were considered as AP homologs. First and for identification purposes only, the N- and C-terminal regions of the sequences were trimmed according to the MSA published by Ten Have et al (2010). Basically, this consists in the removal of nonhomologous extensions beyond the mature polypeptide, which would generate noise in subsequent sequence filtering.…”

Section: Methodsmentioning

confidence: 99%

“…Fungi have a relatively high complement of APs that show a large sequence diversity and interspecific clustering (Ten Have et al 2004, 2010; Monod et al 2011; Xiao et al 2011), indicating that the AP gene family in fungi has undergone a process of birth and death rather than concerted evolution (Eirín-López et al 2012). Fungal-secreted APs used in industrial processes such as aspergillopepsin (Cho et al 2001), mucorpepsin (Newman et al 1993), and penicillopepsin (Fraser et al 1992) have been well-characterized in biochemical terms butlittle is known about their physiological functions.…”

Section: Introductionmentioning

confidence: 99%

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Extensive Expansion of A1 Family Aspartic Proteinases in Fungi Revealed by Evolutionary Analyses of 107 Complete Eukaryotic Proteomes

Revuelta

Kan²,

Kay

et al. 2014

Genome Biology and Evolution

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The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the fungal AP sequence space and to obtain an in-depth understanding of fungal AP evolution. Using a comprehensive phylogeny of approximately 700 AP sequences from the complete proteomes of 87 fungi and 20 nonfungal eukaryotes, 11 major clades of APs were defined of which clade I largely corresponds to the A1A subfamily of pepsin-archetype APs. Clade II largely corresponds to the A1B subfamily of nepenthesin-archetype APs. Remarkably, the nine other clades contain only fungal APs, thus indicating that fungal APs have undergone a large sequence diversification. The topology of the tree indicates that fungal APs have been subject to both “birth and death” evolution and “functional redundancy and diversification.” This is substantiated by coclustering of certain functional sequence characteristics. A meta-analysis toward the identification of Cluster Determining Positions (CDPs) was performed in order to investigate the structural and biochemical basis for diversification. Seven CDPs contribute to the secondary structure of the enzyme. Three other CDPs are found in the vicinity of the substrate binding cleft. Tree topology, the large sequence variation among fungal APs, and the apparent functional diversification suggest that an amendment to update the current A1 AP classification based on a comprehensive phylogenetic clustering might contribute to refinement of the classification in the MEROPS peptidase database.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Extensive Expansion of A1 Family Aspartic Proteinases in Fungi Revealed by Evolutionary Analyses of 107 Complete Eukaryotic Proteomes

Revuelta

Kan²,

Kay

et al. 2014

Genome Biology and Evolution

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Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus,Alternaria solani

Chandrasekaran

Chandrasekar

et al. 2013

J. Basic Microbiol.

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Serine proteases are involved in an enormous number of biological processes. The present study aims at characterizing three‐dimensional (3D) molecular architecture of serine proteases from early blight pathogen, Alternaria solani that are hypothesized to be markers of phytopathogenicity. A serine protease was purified to homogeneity and MALDI‐TOF‐MS/MS analysis revealed that protease produced by A. solani belongs to alkaline serine proteases (AsP). AsP is made up of 403 amino acid residues with molecular weight of 42.1 kDa (Isoelectric point – 6.51) and its molecular formula was C1859H2930N516O595S4. AsP structure model was built based on its comparative homology with serine protease using the program, MODELER. AsP had 16 β‐sheets and 10 α‐helices, with Ser350 (G347–G357), Asp158 (D158–H169), and His193 (H193–G203) in separate turn/coil structures. Biological metal binding region situated near 6th‐helix and His193 residue is responsible for metal binding site. Also, calcium ion (Ca2+) is coordinated by the carboxyl groups of Lys84, Ile85, Lys86, Asp87, Phe88, Ala89, Ala90 (K84–A90) for first Ca2+ binding site and carbonyl oxygen atom of Lys244, Gly245, Arg246, Thr247, Lys248, Lys249, and Ala250 (K244–A250), for second Ca2+ binding site. Moreover, Ramachandran plot analysis of protein residues falling into most favored secondary structures were determined (83.3%). The predicted molecular 3D structural model was further verified using PROCHECK, ERRAT, and VADAR servers to confirm the geometry and stereo‐chemical parameters of the molecular structural design. The functional analysis of AsP 3D molecular structure predictions familiar in the current study may provide a new perspective in the understanding and identification of antifungal protease inhibitor designing.

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The Botrytis cinerea early secretome

et al. 2010

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The extracellular proteome, or secretome, of phytopathogenic fungi is presumed to be a key element of their infection strategy. Especially interesting constituents of this set are those proteins secreted at the beginning of the infection, during the germination of conidia on the plant surfaces or wounds, since they may play essential roles in the establishment of a successful infection. We have germinated Botrytis cinerea conidia in conditions that resemble the plant environment, a synthetic medium enriched with low-molecular weight plant compounds, and we have collected the proteins secreted during the first 16 hours by a double precipitation protocol. 2D electrophoresis of the precipitated secretome showed a spot pattern similar for all conditions evaluated and for the control medium without plant extract. The proteins in 16 of these spots were identified by PMF and corresponded to 11 different polypeptides. Alternative determination of secretome composition by liquid chromatography-tandem mass spectrometry of tryptic fragments rendered a much larger number, 105 proteins, which included all previously identified by PMF. All proteins were functionally classified according to their putative function in the infection process. Key features of the early secretome include a large number of proteases, the abundance of proteins involved in the degradation of plant defensive barriers, and plenty of proteins with unknown function.

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The Botrytis cinerea aspartic proteinase family

Cited by 85 publications

References 56 publications

Extensive Expansion of A1 Family Aspartic Proteinases in Fungi Revealed by Evolutionary Analyses of 107 Complete Eukaryotic Proteomes

Extensive Expansion of A1 Family Aspartic Proteinases in Fungi Revealed by Evolutionary Analyses of 107 Complete Eukaryotic Proteomes

Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus,Alternaria solani

The Botrytis cinerea early secretome

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