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Although transcriptional waves of effector expression have been described in several pathosystems, the\n                    <jats:italic>cis<\/jats:italic>\n                    \u2010regulatory elements underlying their temporal coordination remain largely unknown. Here, we investigate the temporal regulation of effector genes in the biotrophic smut fungus\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Ustilago maydis<\/jats:italic>\n                    <\/jats:styled-content>\n                    , a model organism for fungal plant pathogenesis. By integrating transcriptome reanalysis with comparative promoter motif enrichment across biotrophic fungi, we identify distinct promoter motifs associated with defined infection phases. In\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>U. maydis<\/jats:italic>\n                    <\/jats:styled-content>\n                    , three candidate\n                    <jats:italic>cis<\/jats:italic>\n                    \u2010regulatory elements correlate with early, proliferative and late infection stages, respectively. Positional enrichment relative to transcription start sites supports their regulatory relevance. Functional dissection of the native\n                    <jats:italic>pep1<\/jats:italic>\n                    ,\n                    <jats:italic>stp1<\/jats:italic>\n                    , and\n                    <jats:italic>cmu1<\/jats:italic>\n                    promoters revealed strongly context\u2010dependent contributions of these elements and synthetic promoter assays showed that the early\u2010phase motif acts as an activating and the proliferative motif as a repressive element. Together, our findings support a combinatorial\n                    <jats:italic>cis<\/jats:italic>\n                    \u2010regulatory code in which activating and repressive promoter elements are integrated in a promoter\u2010specific manner to shape temporal effector expression during\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>U. maydis<\/jats:italic>\n                    <\/jats:styled-content>\n                    infection. These elements provide a framework for engineering synthetic fungal promoters with tunable transcriptional outputs.\n                  <\/jats:p>","DOI":"10.1111\/mpp.70358","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T05:31:06Z","timestamp":1791178266000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Combinatorial\n                    <i>cis<\/i>\n                    \u2010regulatory elements shape temporal effector expression in\n                    <scp>\n                      <i>Ustilago maydis<\/i>\n                    <\/scp>"],"prefix":"10.1111","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8781-6886","authenticated-orcid":false,"given":"Georgios","family":"Saridis","sequence":"first","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6421-4783","authenticated-orcid":false,"given":"Janina","family":"Werner","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharina","family":"Stein","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luyao","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ute","family":"Meyer","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Muelhoefer","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namarta C.","family":"Singh","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7353-8456","authenticated-orcid":false,"given":"Gunther","family":"Doehlemann","sequence":"additional","affiliation":[{"name":"Institute for Plant Sciences University of Cologne  Cologne Germany"},{"name":"Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne  Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,4]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1242\/DEV.122.10.2965"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1146\/ANNUREV\u2010PHYTO\u2010080508\u2010081923"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/PPA.13398"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/J.1364\u20103703.2011.00783.X"},{"key":"e_1_2_7_6_1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-3-031-16503-0_1","volume-title":"Plant Relationships","author":"Djamei 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