Modular promoter evolution shapes infection-specific transcription in oomycete effectors

Effector proteins are critical determinants of pathogenicity in oomycetes, mediating complex strategies to reprogram host cellular processes and avoid immune detection. Although secreted effectors are known to be induced during infection stages, the regulatory mechanisms driving their expression remain underexplored, particularly when compared to core metabolic genes involved in biological processes. In the current study, promoter regions of secreted effector-encoding and putative intracellular secreted proteins were systematically investigated across five oomycetes ( Phytophthora infestans , Phytophthora sojae , Plasmopara halstedii , Pythium ultimum ( Globisporangium ultimum ) and Hyaloperonospora arabidopsidis ). Using a combination of known transcription factor motif scanning (JASPAR) with de novo motif discovery, cis-regulatory elements were identified. These included motifs bound by stress-responsive transcription factors such as C2H2 zinc finger, bZIP, AP2/ERF, MYB and homeodomain proteins. Effector-associated promoters displayed signatures in line with rapid transcriptional activation, including TATA-box, Initiator (Inr), FPR elements and novel diversified motifs, consistent with dynamic expression patterns observed during host-pathogen interactions. In contrast, structural genes showed promoter motifs linked to constitutive expression, such as CCAAT-box and repetitive motifs. Complementary amino acid composition analyses further revealed that several non-secreted proteins share residue-level profiles with experimentally validated effectors, suggesting potential effector-like functions that may have been overlooked due to unconventional secretion or annotation gaps. The identification of conserved regulatory signatures provides a foundation for uncovering core regulators of virulence and developing targeted pathogen control strategies.