Efficient utilization of lignocellulose is an economically relevant practice for improving the financial prospects of biorefineries. Lignocellulose contains significant levels of xylose that can be converted into valuable xylonic acid. However, some inhibitors of bioconversion processes are produced after pretreatment. Xylonic acid production in bacteria, such asGluconobacter oxydans, is hindered by poor bacterial tolerance to contaminants. Therefore, in order to enhance bacterial resistance to inhibitors, a recombinant strain ofG.oxydanswas created by the introduction of the thioredoxin gene. Thioredoxin is a key protein responsible for maintaining cellular redox potential and is critical to the conversion of xylose to xylonate. Overexpression of thioredoxin was confirmed at the enzymatic level, while the recombinant strain showed increased catalytic activity when inhibitors, such as formic acid or p-hydroxybenzaldehyde (PHBA), were added to the synthetic xylose medium (17% and 7% improvement in xylonic acid yield, respectively). To probe the molecular mechanism behind the recombinant strain response to inhibitors, the expression levels of various genes were analyzed by qRT-PCR, which revealed five differentially expressed genes (DEGs) upon exposure to formic acid or PHBA.