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Background  The unicellular model cyanobacterium  Synechocystis  sp. PCC 6803 is considered a promising microbial chassis for biofuel production. However, its low tolerance to biofuel toxicity limits its potential application. Although recent studies showed that bacterial small RNAs (sRNAs) play important roles in regulating cellular processes in response to various stresses, the role of sRNAs in resisting exogenous biofuels is yet to be determined.    Results  Based on genome-wide sRNA sequencing combined with systematic analysis of previous transcriptomic and proteomic data under the same biofuel or environmental perturbations, we report the identification of 133  trans -encoded sRNA transcripts with high-resolution mapping of sRNAs in  Synechocystis , including 23 novel sRNAs identified for the first time. In addition, according to quantitative expression analysis and sRNA regulatory network prediction, sRNAs potentially involved in biofuel tolerance were identified and functionally confirmed by constructing sRNA overexpression or suppression strains of  Synechocystis . Notably, overexpression of sRNA Nc117 revealed an improved tolerance to ethanol and butanol, while suppression of Nc117 led to increased sensitivity.    Conclusions  The study provided the first comprehensive responses to exogenous biofuels at the sRNA level in  Synechocystis  and opens an avenue to engineering sRNA regulatory elements for improved biofuel tolerance in the cyanobacterium  Synechocysti s.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-017-0743-y) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803