{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T12:32:33Z","timestamp":1786537953204,"version":"build-2736575974"},"reference-count":54,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007825","name":"National Forestry and Grassland Administration","doi-asserted-by":"publisher","award":["20220104"],"award-info":[{"award-number":["20220104"]}],"id":[{"id":"10.13039\/501100007825","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Earmarked Fund for CARS","award":["CARS\u201334"],"award-info":[{"award-number":["CARS\u201334"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Curr. Issues Mol. Biol.","CIMB"],"abstract":"<jats:p>Although Alternaria gansuense causes yellow stunt and root rot (YSRR)\u2014a destructive disease of the leguminous forage Astragalus adsurgens in northern China\u2014systematic investigations of this pathogen at the protein level remain scarce. In this study, we establish an optimized proteomic workflow for A. gansuense by comparing two protein extraction methods. Using data-independent acquisition (DIA) mass spectrometry with a DIA-NN search against the Alternaria protein database, we construct the first comprehensive proteome reference map of A. gansuense, then perform functional annotation via Gene Ontology, KOG, KEGG, InterPro domain, and subcellular localization analyses. A total of 5052 proteins were identified from vegetative mycelia, and the proteome was found to be predominantly composed of proteins involved in primary metabolism, signal transduction, secondary metabolism, and stress responses. Notably, a set of putative pathogenicity-associated proteins, including two-component regulators (SSK1p), protein kinases, cytochrome P450 enzymes, and ABC transporters, was identified. These proteins are homologs of well-characterized virulence factors in other pathogenic fungi, suggesting a potential coordinated signaling\u2014metabolism\u2014defense network that may contribute to fungal virulence. Subcellular localization further shows that cytoplasmic and nuclear proteins together account for over 50% of the annotated proteome. This study presents the first comprehensive proteomic reference map for A. gansuense, providing a valuable resource for functional genomics. Subsequent experimental validation of the bioinformatically predicted candidate molecular targets presented here may help to dissect the pathogenic mechanisms of YSRR and enable the development of novel disease management strategies.<\/jats:p>","DOI":"10.3390\/cimb48080818","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T11:02:11Z","timestamp":1786532531000},"page":"818","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comprehensive Proteomic Profiling of Alternaria gansuense Provides Insights into Candidate Virulence-Associated Proteins and Core Physiological Features"],"prefix":"10.3390","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-5695-5286","authenticated-orcid":false,"given":"Huaqi","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0408-7556","authenticated-orcid":false,"given":"Tongtong","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1319-4436","authenticated-orcid":false,"given":"Yanzhong","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"4748","DOI":"10.1128\/aem.63.12.4748-4758.1997","article-title":"Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis","volume":"63","author":"Laguerre","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_2","unstructured":"Li, Y.Z. (2007). Study of Yellow Stunt and Root Rot (Embellisia astragali sp. nov. Li & Nan) of Astragalus adsurgens. [Ph.D. Thesis, Lanzhou University]."},{"key":"ref_3","first-page":"29","article-title":"Study on productivity of Astragalus adsurgens Pall. with different growth periods","volume":"5","author":"Sun","year":"1999","journal-title":"Chin. J. Grassl."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"16","DOI":"10.2111\/1551-501X-31.1.16","article-title":"Locoweed poisoning in livestock","volume":"31","author":"Cook","year":"2009","journal-title":"Rangelands"},{"key":"ref_5","first-page":"253","article-title":"Research on decline law and recovery technique of Astragalus adsurgens meadow on Kerqin sand land","volume":"8","author":"Sun","year":"2000","journal-title":"Acta Agrestia Sin."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1080\/15572536.2007.11832565","article-title":"A new species, Embellisia astragali sp. nov., causing standing milk-vetch disease in China","volume":"99","author":"Li","year":"2007","journal-title":"Mycologia"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"171","DOI":"10.3114\/sim0015","article-title":"Alternaria redefined","volume":"75","author":"Woudenberg","year":"2013","journal-title":"Stud. Mycol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1007\/s00284-015-0962-z","article-title":"A re-examination of the taxonomic status of Embellisia astragali","volume":"72","author":"Liu","year":"2016","journal-title":"Curr. Microbiol."},{"key":"ref_9","unstructured":"Liu, J.L. (2016). Study on Molecular Biology of Embellisia astragali. [Ph.D. Thesis, Lanzhou University]."},{"key":"ref_10","first-page":"39","article-title":"Distribution and Damage of Yellow Stunt and Root Rot of Astragalus adsurgens in Five Provinces of Northern China","volume":"20","author":"Li","year":"2011","journal-title":"Acta Pratacult. Sin."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1139\/B08-130","article-title":"Undifilum, a new genus for endophytic Embellisia oxytropis and parasitic Helminthosporium bornmuelleri on legumes","volume":"87","author":"Pryor","year":"2009","journal-title":"Botany"},{"key":"ref_12","first-page":"S102","article-title":"Pathogenic Embellisia astragali on Astragalus adsurgens is very closely related to locoweed endophyte","volume":"101","author":"Li","year":"2011","journal-title":"Phytopathology"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1007\/s10482-009-9310-2","article-title":"Nutritional study on Embellisia astragali, a fungal pathogen of milk vetch (Astragalus adsurgens)","volume":"95","author":"Li","year":"2009","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Yang, B., Nan, Z.B., and Li, Y.Z. (2025). Toxicity of standing milkvetch infected with Alternaria gansuense in white mice. Front. Vet. Sci., 11.","DOI":"10.3389\/fvets.2024.1477970"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.foodchem.2011.09.021","article-title":"Biological activities of flavonoids from pathogenic-infected Astragalus adsurgens","volume":"131","author":"Chen","year":"2012","journal-title":"Food Chem."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.ijfoodmicro.2011.03.021","article-title":"Proteome analysis of the fungus Aspergillus carbonarius under ochratoxin A producing conditions","volume":"147","author":"Gil","year":"2011","journal-title":"Int. J. Food Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/j.jaci.2024.03.026","article-title":"Distinct proteomes and allergen profiles appear across the life-cycle stages of Alternaria alternata","volume":"154","author":"Strader","year":"2024","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Xie, X., Yang, Z., Li, D., Liu, Z., Li, X., and Zhu, Z. (2025). Proteomics analysis revealed the activation and suppression of different host defense components challenged with mango leaf spot pathogen Alternaria alternata. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06250-1"},{"key":"ref_19","unstructured":"Zhang, L. (2006). Study on Biological Characteristics of Alternaria alternata and Electrophoresis Technique in the Classification of Alternaria. [Master\u2019s Thesis, Anhui Agricultural University]."},{"key":"ref_20","unstructured":"Yu, L.N. (2007). Molecular Identification of the Pathogen and Mechanism of Pathogenesis of the Black-Spot Disease on Zizyphus jujuba cv. Dongzao. [Master\u2019s Thesis, Hebei Agricultural University]."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1111\/j.1365-2958.2009.06689.x","article-title":"Identification of novel virulence factors associated with signal transduction pathways in Alternaria brassicicola","volume":"72","author":"Cho","year":"2009","journal-title":"Mol. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Cho, Y., Srivastava, A., Ohm, R.A., Lawrence, C.B., Wang, K.-H., Grigoriev, I.V., and Marahatta, S.P. (2012). Transcription Factor Amr1 Induces Melanin Biosynthesis and Suppresses Virulence in Alternaria brassicicola. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002974"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Jia, M., Gong, X., Fan, M., Liu, H., Zhou, H., Gu, S., Liu, Y., and Dong, J. (2023). Identification and analysis of the secretome of plant pathogenic fungi reveals lifestyle adaptation. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1171618"},{"key":"ref_24","unstructured":"Shi, M. (2019). The Effects of Yellow Stunt and Root Rot of Astragalus adsurgens on Swainsonine Content in Plants and Evaluation on New Disease Resistant Germplasms. [Master\u2019s Thesis, Lanzhou University]."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2011.02292.x","article-title":"Fungal proteomics: From identification to function","volume":"321","author":"Doyle","year":"2011","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nprot.2014.022","article-title":"Universal sample preparation method integrating trichloroacetic acid\/acetone precipitation with phenol extraction for crop proteomic analysis","volume":"9","author":"Wu","year":"2014","journal-title":"Nat. Protoc."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1038\/nbt.3681","article-title":"A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti","volume":"34","author":"Marx","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/0003-2697(76)90527-3","article-title":"A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding","volume":"72","author":"Bradford","year":"1976","journal-title":"Anal. Biochem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1002\/(SICI)1522-2683(20000401)21:6<1037::AID-ELPS1037>3.0.CO;2-V","article-title":"The current state of two-dimensional electrophoresis with immobilized pH gradients","volume":"21","author":"Obermaier","year":"2000","journal-title":"Electrophoresis"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1002\/elps.1150070108","article-title":"Technical improvements in two-dimensional electrophoresis increase the level of genetic variation detected in wheat-seedling proteins","volume":"7","author":"Damerval","year":"1986","journal-title":"Electrophoresis"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1021\/ac950914h","article-title":"Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels","volume":"68","author":"Shevchenko","year":"1996","journal-title":"Anal. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.cell.2016.05.069","article-title":"Integrated proteogenomic characterization of human high-grade serous ovarian cancer","volume":"166","author":"Zhang","year":"2016","journal-title":"Cell"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: Neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat. Methods"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"5803","DOI":"10.3390\/ijms16035803","article-title":"Methodologies and Perspectives of Proteomics Applied to Filamentous Fungi: From Sample Preparation to Secretome Analysis","volume":"16","author":"Bianco","year":"2015","journal-title":"Int. J. Mol. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1002\/elps.201200256","article-title":"2D difference gel electrophoresis reference map of a Fusarium graminearum nivalenol producing strain","volume":"34","author":"Pasquali","year":"2013","journal-title":"Electrophoresis"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1477-5956-10-30","article-title":"Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome","volume":"10","author":"Suh","year":"2012","journal-title":"Proteome Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/pmic.201300541","article-title":"Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea during exponential growth in axenic cultures","volume":"14","author":"Davanture","year":"2014","journal-title":"Proteomics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1046\/j.1364-3703.2003.00173.x","article-title":"Alternaria spp.: From general saprophyte to specific parasite","volume":"4","author":"Thomma","year":"2003","journal-title":"Mol. Plant Pathol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1111\/mpp.13180","article-title":"The essential role of fungal peroxisomes in plant infection","volume":"23","author":"Falter","year":"2022","journal-title":"Mol. Plant Pathol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.jprot.2015.11.010","article-title":"A Fusarium graminearum strain-comparative proteomic approach identifies regulatory changes triggered by agmatine","volume":"137","author":"Pasquali","year":"2016","journal-title":"J. Proteom."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Paudel, R., Muzhinji, N., Pandey, A., Panthee, D.R., Dean, R.A., Louws, F.J., and Adhikari, T.B. (2025). Genome assembly and comparative analysis of Alternaria linariae reveal novel genes associated with host colonization and virulence. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11819-z"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e02939-22","DOI":"10.1128\/spectrum.02939-22","article-title":"Transcriptome Analysis of the Necrotrophic Pathogen Alternaria brassicae Reveals Insights into Its Pathogenesis in Brassica juncea","volume":"11","author":"Rajarammohan","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Qi, C., Zeng, R., Li, G., Zhang, L., Yang, J., Liu, P., and Xie, Z. (2026). Genomic and Functional Characterization of an Alternaria brassicicola Isolate Causing Black Spot Disease on Broccoli Leaves. Life, 16.","DOI":"10.3390\/life16071099"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"635431","DOI":"10.6064\/2012\/635431","article-title":"Stress Response and Pathogenicity of the Necrotrophic Fungal Pathogen Alternaria alternata","volume":"2012","author":"Chung","year":"2012","journal-title":"Scientifica"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Yu, P.-L., Chen, L.-H., and Chung, K.-R. (2016). How the Pathogenic Fungus Alternaria alternata Copes with Stress via the Response Regulators SSK1 and SHO1. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0149153"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1038\/nrmicro3119","article-title":"Filamentous plant pathogen effectors in action","volume":"11","author":"Giraldo","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Dauda, W.P., Morumda, D., Abraham, P., Adetunji, C.O., Ghazanfar, S., Glen, E., Abraham, S.E., Peter, G.W., Ogra, I.O., and Ifeanyi, U.J. (2022). Genome-Wide Analysis of Cytochrome P450s of Alternaria Species: Evolutionary Origin, Family Expansion and Putative Functions. J. Fungi, 8.","DOI":"10.3390\/jof8040324"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s11103-025-01639-w","article-title":"Reactive oxygen species production and signal transduction in response to stress triggered by Alternaria elicitors in Brassicaceae","volume":"115","author":"Munir","year":"2025","journal-title":"Plant Mol. Biol."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Zhang, M., Zhang, Y., Li, Y., Bi, Y., Mao, R., Yang, Y., Jiang, Q., and Prusky, D. (2022). Cellular Responses Required for Oxidative Stress Tolerance of the Necrotrophic Fungus Alternaria alternata, Causal Agent of Pear Black Spot. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030621"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.jia.2025.02.014","article-title":"SsBMR1 as a putative ABC transporter is required for pathogenesis by promoting antioxidant export and antifungal resistance in Sclerotinia sclerotiorum","volume":"25","author":"Ding","year":"2026","journal-title":"J. Integr. Agric."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"134918","DOI":"10.1016\/j.ijbiomac.2024.134918","article-title":"Alternaria solani core effector Aex59 is a new member of the Alt a 1 protein family and is recognized as a PAMP","volume":"278","author":"Qiu","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Meena, M., Gupta, S.K., Swapnil, P., Zehra, A., Dubey, M.K., and Upadhyay, R.S. (2017). Alternaria Toxins: Potential Virulence Factors and Genes Related to Pathogenesis. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.01451"}],"container-title":["Current Issues in Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1467-3045\/48\/8\/818\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T11:47:26Z","timestamp":1786535246000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1467-3045\/48\/8\/818"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,12]]},"references-count":54,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["cimb48080818"],"URL":"https:\/\/doi.org\/10.3390\/cimb48080818","relation":{},"ISSN":["1467-3045"],"issn-type":[{"value":"1467-3045","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,12]]}}}