RNA regulation in Lactococcus lactis

This thesis reports the first transcriptome landscape of the genome of Lactococcus lactis. This lactic acid bacterium is of great importance for the dairy industry and serves as an important model organism. Differential RNA sequencing (RNA-seq) was used to detect transcription start sites of known coding genes, of long 5'-UTRs and of new putative RNA regulator molecules. The presence and size of 15 small RNAs (sRNAs) were validated by Northern hybridization, and the expression of all new RNAs under various industrially relevant stress conditions was determined by RNA-seq. In order to be able to analyze the large amounts of data generated during this work, a fully automated pipeline for the analysis of transcriptome data has been set up. This Transcriptome analysis webserver for RNA-seq Expression data (T-REx) allows biologists to perform statistical analyses and visualize their data, with a choice of tables, figures and matrices. From the hundreds of identified RNAs, a number of sRNAs have been studied in more detail. LLMGnc_147 was found to induce/stabilize an operon involved in carbon uptake and metabolism, while ArgX regulates the arginine catabolic arc operon in conjunction with the transcription factor protein ArgR. Several potential RNA targets of the cold stress-induced sRNA CisR have been identified, including tRNAs, a class of RNAs that so far escaped the repertoire of sRNA targets. The hundreds of new RNAs discovered here offer an excellent starting point for the further characterization of a new level of (gene) regulation in L. lactis.