Functional analysis of the aefR mutation and identification of its binding site in Pseudomonas syringae pv. tabaci 11528.

The TetR family transcriptional regulator AefR contributes to the regulation of the quorum-sensing system. However, the role of AefR in the regulatory network of the phytopathogen Pseudomonas syringae pathovars is not known. In this study, the phenotype of a P. syringae pv. tabaci 11528 aefR deletion mutant strain was examined. The aefR gene expression and AefR DNA-binding affinity were examined by quantitative real-time polymerase chain reaction and electrophoretic mobility shift assay, respectively. AefR was found to control quorum-sensing genes as well as the efflux genes mexE, mexF, and oprN via an indirect mechanism. AefR binds to its own operator site as well as to the palindromic sequence between positions -28 and -2 corresponding to the transcription start site of aefR, as determined by dye primer sequencing. These results suggest that P. syringae AefR modulates quorum sensing and efflux as well as its own expression, which can be exploited by strategies developed to manage this plant parasite.

Integrated Multi-Omic Analyses Support Distinguishing Secretory Carcinoma of the Breast from Basal-Like Triple-Negative Breast Cancer.

PURPOSE: Secretory carcinoma (SC) of the breast is defined as an indolent tumor but is still categorized into a basal-like triple-negative breast cancer (BL-TNBC) subgroup that generally shows aggressive behavior according to the current classification. Despite the unique clinical behavior of SC, molecular characteristics that reflect biological behaviors of SC remain largely unknown. EXPERIMENTAL DESIGN: A combinatorial approach of whole-exome sequencing and mass spectrometry-based in-depth quantitative proteomics to determine the entire molecular landscape of SC using three SC formalin-fixed paraffin-embedded (FFPE) tissues is employed. RESULTS: Exome sequencing and proteomic analysis of SC identified 419 unique somatic mutations and 721 differentially expressed proteins as compared with triple-negative breast cancer (TNBC), respectively. Several pathways related to cancer metabolism were significantly upregulated in the SC group. Comparative analyses with multiple datasets revealed that SC shares genomic mutations and biological pathways more closely related to hormone receptor-positive breast cancer than BL-TNBC. CONCLUSION AND CLINICAL RELEVANCE: These multi-omic analyses provide evidence that SC harbors substantially different molecular genomic and proteomic landscapes compared with BL-TNBC. These results provide an entire spectrum of in-depth molecular landscapes to support the hypothesis that SC is distinct from BL-TNBC.