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Background Frame-shifted genes results in non-functional peptides. Because of this complete loss of function, frame-shifted genes have never been used in constructing synthetic gene circuits. Results Here we report that the function of gene circuits is rescued by a frame-shifted gene, which functions by translating from a non-natural start codon. We report a single nucleotide deletion mutation that developed in the λ-repressor cI within a synthetic genetic NOT gate in Escherichia coli during growth and through this mutation, a non-functional synthetic gene circuit became functional. This mutation resulted in a frame-shifted cI, which showed effective functionality among genetic NOT-gates in Escherichia coli with high regulatory ranges (> 300) and Hill coefficient (> 6.5). The cI worked over a large range of relative copy numbers between the frame-shifted gene and its target promoter. These properties make this frame-shifted gene an excellent candidate for building synthetic gene circuits. We hypothesized a new operating mechanism and showed evidence that frame-shifted cI was translated from non-natural start codon. We have engineered and tested a series of NOT gates made from a library of cI genes, each of which starts from a different codon within the first several amino acids of the frame-shifted cI. It is found that one form with start codon ACA, starting from the 3rd codon had similar repression behavior as the whole frame-shifted gene. We demonstrated synthetic genetic NAND and NOR logic-gates with frame-shifted cI. This is the first report of synthetic-gene-circuits made from a frame-shifted gene. Conclusions This study inspires a new view on frame-shifted gene and may serve as a novel way of building and optimizing synthetic-gene-circuits. This work may also have significance in the understanding of non-directed evolution of synthetic genetic circuits. Electronic supplementary material The online version of this article (10.1186/s13036-019-0151-x) contains supplementary material, which is available to authorized users.

Bioengineering solutions to human space travel must consider microgravity as an important component. Thus, one of the fundamental challenges of space bioengineering is to create cellular microgravity responsive device, which integrate microgravity as a signal within biochemical and cellular processes. Here, we designed, fabricated and characterized the first biochemical and cellular microgravity responsive device using an engineered genetic circuit in E.coli, which responded to microgravity by changing the expression of a target enhanced green fluorescent gene (EGFP). Our device design was based on the deregulation of HfQ protein in E.coli in microgravity, which was translated through HfQ mediated silencing of EGFP by anti-EGFP synthetic small regulatory RNAs. This resulted a reduced silencing (~28 times) of the EGFP in microgravity. We demonstrated that the basic design of the device is universal in nature for E.coli, by creating multiple successful devices, where target genes (EGFP, TdTomato, and FtsZ) and the promoters (inducible and constitutive) were altered. Further, we applied this device to control the cell division process by microgravity. Here we targeted the cell division regulator FtsZ, which resulted an elongated cell shape in normal gravity and this deformed cell shape got rescued to normal one by applying microgravity. The work showed for the first time, a way to integrate microgravity as a physical signal within biochemical processes of a living cell in a human designed way and thus, may have significance in space bioengineering and synthetic biology.