Abstract
Ribosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium Synechocystis were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when cyanobacteria are cultivated in poorly mixed bioreactors or engineered to be product-secreting cell factories. A small fraction of genes (<200), including stress response genes, showed changes in translational efficiency during carbon starvation, indicating condition-dependent translation-level regulation. We observed ribosome occupancy in untranslated regions, possibly due to an alternative translation initiation mechanism in Synechocystis. The higher proportion of ribosomes residing in untranslated regions during carbon starvation may be a mechanism to quickly inactivate superfluous ribosomes. This work provides the first ribosome profiling data for cyanobacteria and reveals new regulation strategies for coping with nutrient limitation.
Highlights
Cyanobacteria experience both rapid and periodic fluctuations in light and inorganic carbon (Ci) and have evolved regulatory mechanisms to respond to these, including extensive posttranscriptional gene regulation
Complexity was added with the discovery that cyanobacteria have a higher quantity of noncoding RNAs than other bacteria and that several prominent ncRNAs are involved in gene regulation during nutrient shifts, including Ci and light [9]
The translational efficiency (TE) of genes was largely constant between HC and LC, despite large changes in mRNA abundance
Summary
Cyanobacteria experience both rapid and periodic fluctuations in light and inorganic carbon (Ci) and have evolved regulatory mechanisms to respond to these, including extensive posttranscriptional gene regulation. At LC, total translation was reduced by 80% and ribosome pausing was increased at stop and start codons and in untranslated regions, which may be a sequestration mechanism to inactivate ribosomes in response to rapid Ci depletion. The translatome and transcriptome of the model cyanobacterium Synechocystis were compared under carbon-replete and carbon starvation conditions The latter may be experienced when cyanobacteria are cultivated in poorly mixed bioreactors or engineered to be product-secreting cell factories. A small fraction of genes (Ͻ200), including stress response genes, showed changes in translational efficiency during carbon starvation, indicating condition-dependent translation-level regulation. Further evidence of posttranscriptional regulation in cyanobacteria can be inferred from reports showing that the transcriptome oscillates strongly during the day/night cycle, while proteome oscillations are weak or nonexistent [10,11]
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