Abstract
Outside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is also able to grow and survive in stressful nature. The major organic substance in nature is plant, but the genetic system of E. coli how to utilize plant-derived materials as nutrients is poorly understood. Here we describe the set of regulatory targets for uncharacterized IclR-family transcription factor YiaJ on the E. coli genome, using gSELEX screening system. Among a total of 18 high-affinity binding targets of YiaJ, the major regulatory target was identified to be the yiaLMNOPQRS operon for utilization of ascorbate from fruits and galacturonate from plant pectin. The targets of YiaJ also include the genes involved in the utilization for other plant-derived materials as nutrients such as fructose, sorbitol, glycerol and fructoselysine. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function. These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. PlaR was also suggested to play protecting roles of E. coli under stressful environments in nature, including the formation of biofilm. We then propose renaming YiaJ to PlaR (regulator of plant utilization).
Highlights
Outside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is able to grow and survive in stressful nature
In order to identify the regulatory targets of PlaR, we employed the gSELEX screening system[8,9] using purified His-tagged PlaR and a mixture of 200– 300 bp-long genome fragments from E. coli K-12 W3110 as the DNA substrate
After 5 cycles of gSELEX, more than 25 high-level peaks were identified (Fig. 1a), but after 6 cycles, the DNA fragments with weak affinity to PlaR were eliminated, resulting in about nine major peaks (Fig. 1b), which were all identified in the SELEX pattern after the 5th gSELEX cycle
Summary
Outside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is able to grow and survive in stressful nature. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. The yiaMNO genes located in the middle of this operon have been proposed as encoding the periplasmic transporter for uptake of unidentified osmoprotectants[13] or the rare pentose L-xylulose (L-threo-2-pentulose or 2,3-dioxo-L-gulonate)[14] Based on these observations, we predicted the involvement of the yiaKLMNOPQRS operon in the catabolism of ascorbate, a major product of plant fruits, and the participation of YiaJ in regulation of this operon. We propose to rename YiaJ to PlaR (regulator of plant utilization)
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