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Background  The microbial production of fatty acids has received great attention in the last few years as feedstock for the production of renewable energy. The main advantage of using cyanobacteria over other organisms is their ability to capture energy from sunlight and to transform CO 2  into products of interest by photosynthesis, such as fatty acids. Fatty acid synthesis is a ubiquitous and well-characterized pathway in most bacteria. However, the activity of the enzymes involved in this pathway in cyanobacteria remains poorly explored.    Results  To characterize the function of some enzymes involved in the saturated fatty acid synthesis in cyanobacteria, we genetically engineered  Synechococcus elongatus  PCC 7942 by overexpressing or deleting genes encoding enzymes of the fatty acid synthase system and tested the lipid profile of the mutants. These modifications were in turn used to improve alpha-linolenic acid production in this cyanobacterium. The mutant resulting from  fabF  overexpression and  fadD  deletion, combined with the overexpression of  desA  and  desB  desaturase genes from  Synechococcus  sp. PCC 7002, produced the highest levels of this omega-3 fatty acid.    Conclusions  The fatty acid composition of  S. elongatus  PCC 7942 can be significantly modified by genetically engineering the expression of genes coding for the enzymes involved in the first reactions of fatty acid synthesis pathway. Variations in fatty acid composition of  S. elongatus  PCC 7942 mutants did not follow the pattern observed in  Escherichia coli  derivatives. Some of these modifications can be used to improve omega-3 fatty acid production. This work provides new insights into the saturated fatty acid synthesis pathway and new strategies that might be used to manipulate the fatty acid content of cyanobacteria.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1243-4) contains supplementary material, which is available to authorized users.

Engineering the fatty acid synthesis pathway in Synechococcus elongatus PCC 7942 improves omega-3 fatty acid production