Biology subjects

Harris, F. E.

Publications and source records attributed to Harris, F. E..

3 recordsLinked to original sources

bioRxiv2026

Extracellular NAD(P) activates systemic acquired resistance through LecRK-VI.2-mediated phosphorylation of NPR1

Systemic acquired resistance (SAR) is a long-lasting, broad-spectrum immune response induced in distal tissues by signals generated at primary infection sites. Although numerous mobile immune signals have been implicated in SAR, how these signals are perceived and mechanistically coupled to transcriptional reprogramming in systemic tissues remains poorly understood. Extracellular NAD(P) [eNAD(P)] functions as a key integrative SAR signal that activates immunity through the plasma membrane-localized lectin receptor kinase LecRK-VI.2 and the master immune coactivator NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1). However, the mechanism linking eNAD(P) perception to activation of NPR1 has remained unknown. Here, we show that LecRK-VI.2 constitutively associates with NPR1 and directly phosphorylates NPR1 at T359 and likely S356 upon eNAD(P) perception. NADP+-induced phosphorylation of NPR1 occurs rapidly in vivo and requires LecRK-VI.2. Nonphosphorylatable NPR1 variants abolish eNADP+-induced local and systemic immunity as well as biologically induced SAR, whereas phosphomimetic variants retain NPR1 function. Mechanistically, LecRK-VI.2-mediated phosphorylation promotes NPR1 interaction with TGACG-binding transcription factors (TGAs) and the Mediator subunit MED15, thereby enhancing assembly of a transcriptional activation complex required for defense gene expression. We further demonstrate that NPR1 facilitates TGA-MED15 association in a phosphorylation-dependent manner. Together, these findings establish a receptor-to-coactivator signaling mechanism that directly links extracellular immune signal perception to transcriptional activation. This work closes a major mechanistic gap in the SAR signaling pathway and reveals receptor-mediated coactivator activation as a mechanism for rapid conversion of extracellular immune cues into coordinated transcriptional outputs during systemic immunity.

plant biology↗

bioRxiv2026

Repetitive extragenic palindrome (REP) elements are local, context-dependent, dual 3'UTR regulators in Escherichia coli

Repetitive extragenic palindromes (REPs) are the most abundant repetitive noncoding elements in the E. coli genome. Despite their abundance, the primary function of REPs has remained unclear. At different times, REPs have been proposed to contribute to chromosome organization, mRNA decay regulation, and transcription termination, among other functions. Here, we show that the model REP, REP325, does not measurably compact the chromosome but instead acts as a 3UTR-associated transcription regulator within the yjdMN operon, functioning both as a partially Rho-dependent terminator that limits transcription into the downstream yjdN gene and as an mRNA stabilizer that protects the upstream yjdM transcript from degradation. This dual role in controlling both transcriptional readthrough and susceptibility to decay provides a framework that reconciles several previously conflicting observations about REP function. Our genome-wide RNA-seq analysis further reveals that REPs with more canonical sequence and hairpin structures are more often associated with upstream-biased expression in tandem gene pairs, and that REPs positioned between convergent genes correlate with elevated expression of both genes. The large variance in expression patterns in both gene pair configurations is consistent with context-dependent termination and degradation blocking. Similarly, REPs do not uniformly affect mRNA half-lives. Because REP locations vary between E. coli strains, REPs likely contribute to regulatory diversity by tuning gene expression without altering protein-coding sequences or promoter regions, opening new avenues for modulating gene expression through REP-mediated transcription regulation.

biophysics↗

bioRxiv2025

Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

Chromosomal topology and transcription are tightly coupled, yet the quantitative impact of topological constraints on transcription, supercoiling, and the potential coupling between neighboring genes in vivo remains unclear. In this work, we constructed synthetic chromosomal domains in Escherichia coli that contained two genes inside a topology-controllable domain and a third gene outside. Using three-color single-molecule fluorescence in situ hybridization (smFISH), we measured transcription output from the three genes in individual cells under conditions in which gene orientation, domain formation state, and global chromosomal supercoiling density were varied. We found that topological domain formation repressed transcription, diminished gene orientation-dependent differences in transcription, and modulated the supercoiling sensitivity of genes located both within and near the domain. Relaxing global negative supercoiling through gyrase inhibition broadly repressed transcription; increasing global negative supercoiling level through topoisomerase I inhibition repressed highly expressed genes, while activating lowly expressed ones. Besides single-gene effects, we also observed an intrinsic coupling between neighboring genes with a non-monotonic dependence on the underlying supercoiling state, which shifted with domain topology and gene syntax. Our results establish chromosome topology as a major regulator of both transcription levels and the coupling between adjacent genes.

biophysics↗