Open AccessRibosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation
Author(s) -
Jan Karlsen,
Johannes Asplund-Samuelsson,
Quentin Thomas,
Michael Jahn,
Elton P. Hudson
Publication year - 2018
Publication title -
msystems
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.931
H-Index - 39
ISSN - 2379-5077
DOI - 10.1128/msystems.00126-18
Subject(s) - ribosome profiling , synechocystis , ribosome , biology , transcriptome , translation (biology) , protein biosynthesis , gene , untranslated region , gene expression , microbiology and biotechnology , messenger rna , genetics , rna , mutant
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 cyanobacteriumSynechocystis 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 inSynechocystis. 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.