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Here, we integrated transcriptomics, quantitative proteomics, and phosphoproteomics to analyze PKAc1-associated responses in the parental strain QM9414 and a \u0394\n                    <jats:italic>pkac1<\/jats:italic>\n                    strain cultivated under glucose or sugarcane bagasse conditions. Deletion of\n                    <jats:italic>pkac1<\/jats:italic>\n                    was associated with altered growth-related phenotypes and reduced extracellular activities of selected biomass-depolymerizing enzymes. Multi-omics profiling revealed condition-dependent changes affecting subsets of carbohydrate-active enzymes (CAZymes) genes and proteins, nutrient transporters, stress-associated proteins, and regulatory factors. Phosphoproteomics identified phosphorylation-state changes associated with\n                    <jats:italic>pkac1<\/jats:italic>\n                    deletion, including reduced phosphorylation at sites enriched for the PKA consensus motif. In silico peptide docking was used to prioritize candidate PKAc1-associated substrates for future validation, including a Sec 7-derived peptide with favorable docking behavior relative to the control peptide. Together, these data support a working model in which PKAc1 contributes to regulatory and phosphorylation-state remodeling during adaptation to sugarcane bagasse, with effects on the magnitude and\/or timing of selected CAZyme-related outputs in\n                    <jats:italic>T. reesei<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1007\/s11274-026-05252-x","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T02:14:41Z","timestamp":1788833681000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-omics analysis reveals Protein Kinase A-associated regulatory remodeling during adaptation of Trichoderma reesei to lignocellulosic substrate"],"prefix":"10.1007","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9012-4610","authenticated-orcid":false,"given":"Hermano","family":"Zenaide-Neto","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3982-0626","authenticated-orcid":false,"given":"Wellington Ramos","family":"Pedersoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8886-3083","authenticated-orcid":false,"given":"David Batista","family":"Mau\u00e9s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1537-5644","authenticated-orcid":false,"given":"Lucas Matheus Soares","family":"Pereira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5871-5506","authenticated-orcid":false,"given":"Iasmin Cartaxo","family":"Taveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-9775-1327","authenticated-orcid":false,"given":"Thiago de Andrade","family":"Simon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2052-2848","authenticated-orcid":false,"given":"Andrei S.","family":"Steindorff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3205-7944","authenticated-orcid":false,"given":"Vitor Marcel","family":"Fa\u00e7a","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6712-437X","authenticated-orcid":false,"given":"Renato Graciano","family":"de Paula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8992-7130","authenticated-orcid":false,"given":"Roberto N.","family":"Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"issue":"2","key":"5252_CR1","doi-asserted-by":"publisher","first-page":"119","DOI":"10.2174\/1389202917666151116212901","volume":"17","author":"ACC Antoni\u00eato","year":"2016","unstructured":"Antoni\u00eato ACC, de Paula RG, Castro LS, Silva-Rocha R, Persinoti GF, Silva RN (2016) Trichoderma reesei CRE1-mediated carbon catabolite repression in response to sophorose through RNA sequencing analysis. 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