c Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solventtolerant cyanobacteria strains that could be the foundation for a more productive biofuel host. C yanobacteria are attractive biochemical production platforms due to their minimal nutrient requirements, ease of genetic manipulation, and wide natural diversity. Several model cyanobacteria have been engineered as hosts for production of chemicals and biofuels such as hydrogen (1), ethanol (2), isobutanol (3, 4), and n-butanol (5). The modified cyanobacterial strains contained enzymes from fermentative organisms, such as Clostridium, Lactococcus, and Zymomonas species. The alcohols were produced at levels (up to 450 mg/liter) that were detectable but well below the titers of 10 to 20 g/liter achieved by industrial Clostridium and Saccharomyces strains (6). In addition to restrictions on metabolic flux (7,8), hosts may suffer from product inhibition even at low levels of product (9). Biofuel hosts that are more tolerant to the product may be more efficient producers even at levels below toxicity (10, 11), though this phenomenon is not universal (12).The deleterious effects of solvents on a wide range of microbes have been reported and recently reviewed (13). Solvents compromise the cell membrane and alter membrane fluidity (14). A compromised cell membrane can leak metabolites, resulting in loss of the transmembrane electrochemical gradient and hence of the proton-motive force. Reactive oxygen species (ROS) may accumulate as the cell modulates respiration to recover lost ATP (9, 15). These effects have been observed for bacteria, archaea, and yeast. Recent studies have begun to describe the complex response of cyanobacteria to solvents such as ethanol (16), n-butanol (17), and hexane (...