Search for the proteins bound to the non-coding RNAs synthesized from the uxuR gene in Escherichia coli K-12
Abstract
When studying bacterial genomes and transcriptomes, several hundred small non-coding RNAs and thousands of intragenic transcripts were found, including antisense ones. In Escherichia coli their ratio to the total number of annotated genes can reach 25%, but the functional value was established for less than two dozen small RNAs. Recently, it has also been discovered that bacteria are able to secrete RNA into the external environment, and such RNAs were called exoRNAs. The vast majority of E. coli exoRNAs were synthesised from the coding regions of metabolic regulator genes. Thus, at least three regulatory RNAs of three types:– intracellular antisense, antisense exoRNA, and co-directional RNA UxuT, were encoded at the end of the gene of the transcription factor UxuR, which controls the metabolism of hexuronates. In this work, we identified the partner proteins of these RNAs using liquid chromatography-mass spectrometry (LC/MS). Chemically synthesised RNA analogues were conjugated with biotin and immobilised onto streptavidin-coated magnetic particles. Lysate proteins of E. coli cells grown to the exponential phase in the presence of D-glucose or D-galacturonate were specifically sorbed on them. Using LC/MS spectrometry, we revealed the dependence of the spectrum of sorbed proteins on the carbon source, while hexuronate metabolism proteins and SecB chaperone were found in complexes with all small RNAs. This may indicate the participation of non-coding RNAs of the uxuR gene in the regulation of carbohydrate metabolism and a certain role of SecB in their transport.
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References
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