The effects of protein solubility on the RNA Integrity Number (RIN) for recombinant Escherichia coli

• Recombinant E. coli gene expression analysis requires high quality RNA.
• RNA Integrity Number (RIN) evaluates RNA quality for gene expression analysis.
• Soluble protein production does not affect RIN values relative to uninduced cells.
• Insoluble protein production results in low RIN values.
• Further analysis of effects on RIN values are needed for recombinant E. coli.

High quality, intact messenger RNA (mRNA) is required for DNA microarray and reverse transcriptase polymerase chain reaction analysis and is generally obtained from total RNA isolations. The most widely recognized measure of RNA integrity is the RNA Integrity Number (RIN) obtained from the Agilent Bioanalyzer, as it provides sizing, quantification, and quality control measures. This work describes comparisons of the RIN values obtained for recombinant Escherichia coli. Uninduced recombinant E. coli cultures were examined, as well as induced cultures that produced either a soluble or insoluble recombinant protein. The uninduced cultures and the induced cultures producing soluble protein had higher RIN values than the induced cultures producing insoluble protein. These lower RIN values for E. coli producing the insoluble protein indicate that cellular degradation of the ribosomal RNA species is the likely cause of the lower RIN values. As the use of DNA microarrays and other gene expression tools increase in usage in the industrial recombinant protein production community, these results suggest the need for further studies to determine acceptable RIN ranges for gene expression analysis and effects of various culture conditions on RIN values for recombinant E. coli.