{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE313nnn/GSE313102/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313102"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Standalone RNA-seq from Direct regulation of a tRNA modification enzyme by ppGpp links stress signaling to translational control and biofilm development","description":"tRNA modifications influence decoding efficiency and translational fidelity, yet how they are integrated into bacterial signaling networks remains poorly understood. Here, we identify a direct connection between stress signaling and codon-specific translational regulation. We show that the alarmone ppGpp directly inhibits MnmE (TrmE), a conserved GTPase required for wobble uridine modification. High-resolution ribosome profiling in Bacillus subtilis revealed that loss of MnmE selectively increases ribosome pausing at AAG codons and reprograms translation of a subset of genes, including small open reading frames. Among these is a previously unrecognized AAG-containing leader peptide that controls expression of the biofilm repressor AbrB. Consistent with this mechanism, mnmE mutants exhibit constitutive extracellular matrix production and bypass the biofilm defect of a relA mutant. Together, these findings establish a pathway linking ppGpp signaling, tRNA modification, codon-specific translation, and multicellular development.","dates":{"publication":"2026/09/25"},"accession":"GSE313102","cross_references":{"GSM":["GSM9361019","GSM9361018","GSM9361017","GSM9361001","GSM9361023","GSM9361022","GSM9361000","GSM9361021","GSM9361020","GSM9361005","GSM9361004","GSM9361003","GSM9361024","GSM9361002","GSM9361009","GSM9360997","GSM9360998","GSM9361008","GSM9360995","GSM9361007","GSM9361006","GSM9360996","GSM9360999","GSM9361012","GSM9361011","GSM9361010","GSM9361016","GSM9361015","GSM9361014","GSM9361013"],"GPL":["32075","36404"],"GSE":["313102"],"taxon":["Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10"]}}