Thermotoga maritima transcription during exponential and stationary phase growth on 1 and 5 g/l yeast extract

Although proteins and peptides encoded in small open reading frames (ORFs < 100 AA) in microbial genomes can play critical roles as toxins, bacteriocins, transcriptional regulators, signaling molecules, and chaperones, many such ORFs remain annotated as “hypothetical proteins”. In the genome of the hyperthermophilic bacterium, Thermotoga maritima, nearly 2/3 of the 167 small ORFs have no known function. As a strategy for investigating the potential significance of specific small ORFs, growth conditions that could trigger the expression of genes encoding small ORFs were sought. A defined medium supplemented with either 1 or 5 g/L yeast extract was used to track transcriptional response during the transition from exponential to stationary phase. RNA derived from exponential (1E) and stationary (1S) phase cultures grown on 1 g/l yeast extract was compared to RNA derived from exponential (5E) and stationary (5S) phase cultures grown on 5 g/l yeast extract using a four-slide loop design.