PT - JOURNAL ARTICLE AU - Robert W. Read AU - Paul M. Berube AU - Steven J. Biller AU - Iva Neveux AU - Andres Cubillos-Ruiz AU - Sallie W. Chisholm AU - Joseph J. Grzymski TI - Nitrogen cost minimization is promoted by structural changes in the transcriptome of N deprived <em>Prochlorococcus</em> cells AID - 10.1101/087643 DP - 2016 Jan 01 TA - bioRxiv PG - 087643 4099 - http://biorxiv.org/content/early/2016/11/14/087643.short 4100 - http://biorxiv.org/content/early/2016/11/14/087643.full AB - Prochlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might be used to further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions. Of 64 genes with primary and internal TSSs in both conditions, N-deprived cells initiated transcription downstream of primary TSSs more frequently than N-replete cells. Additionally, 117 genes with only an internal TSS demonstrated increased internal transcription under N-deprivation. These shortened transcripts encode predicted proteins with ~5-20% less N content compared to full-length transcripts. We hypothesized that low translation rates, which afford greater control over protein abundances, would be beneficial to relatively slow-growing organisms like Prochlorococcus. Consistent with this idea, we found that Prochlorococcus exhibits greater usage of glycine-glycine motifs, which cause translational pausing, when compared to faster growing microbes. Our findings indicate that structural changes occur within the Prochlorococcus MED4 transcriptome during N-deprivation, potentially altering the size and structure of proteins expressed under nutrient limitation.