Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression

Abstract

Escherichia coli strains defective in the rpiA gene, encoding ribose phosphate isomerase A, are ribose auxotrophs, despite the presence of the wild-type rpiB gene, which encodes ribose phosphate isomerase B. Ribose prototrophs of an rpiA genetic background were isolated by two different approaches. Firstly, spontaneous ribose-independent mutants were isolated. The locus for this lesion, rpiR, was mapped to 93 min on the linkage map, and the gene order zje::Tn10-rpiR-mel-zjd::Tn10-psd-purA was established. Secondly, ribose prototrophs resulted from the cloning of the rpiB gene on a multicopy plasmid. The rpiB gene resided on a 4.6-kbp HindIII-EcoRV DNA fragment from phage 10H5(642) of the Kohara gene library and mapped at 92.85 min. Consistent with this map position, the cloned DNA fragment contained two divergent open reading frames of 149 and 296 codons, encoding ribose phosphate isomerase B (molecular mass, 16,063 Da) and a negative regulator of rpiB gene expression, RpiR (molecular mass, 32,341 Da), respectively. The 5 ends of rpiB-and rpiR-specified transcripts were located by primer extension analysis. No significant amino acid sequence similarity was found between ribose phosphate isomerases A and B, but ribose phosphate isomerase B exhibited high-level similarity to both LacA and LacB subunits of the galactose 6-phosphate isomerases of several gram-positive bacteria. Analyses of strains containing rpiA, rpiB, or rpiA rpiB mutations revealed that both enzymes were equally efficient in catalyzing the isomerization step in either direction and that the construction of rpiA rpiB double mutants was a necessity to fully prevent this reaction.

Agmatine deiminase pathway genes in Lactobacillus brevis are linked to the tyrosine decarboxylation operon in a putative acid resistance locus

“…The aguA2 gene is followed by 132 bp of the 59-end of a putative regulator gene aguR. The aguR-encoded protein contains a helix-turn-helix domain involved in DNA binding at the N-terminal extremity and shares similarities with regulators of the RpiR family (Sorensen & Hove-Jensen, 1996). The gene clusters present in these bacteria differ from the previously characterized AgDI gene clusters in S. mutans and Ent.…”

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

“…Furthermore, genes involved in the utilization of plant polymers like a-and b-glucosides as well as genes involved in uronic acid metabolism display decreased transcription levels in NZ5521, NZ5522, and IL594, which is in agreement with their redundancy in a dairy environment. Additionally, a transcriptional regulator of the RpiR family, which has been described to regulate phospho-sugar metabolism in E. coli (Sorensen and Hove-Jensen 1996), as well as a transcriptional regulator involved in fructose/lactose transport were down-regulated in the adapted strains and in IL594.…”

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

“…Another response regulator, TM0126, displayed lower overall expression levels but also showed up-regulation on mannose. Whereas the transcriptional regulators described above were largely mannose-specific, the ROK family protein TM1224 and the ribose phosphate isomerase family protein TM1228 (44) were expressed on mannose and mannan polysaccharides. Both TM1224 and TM1228 lie in the same gene string as the endoglycoside hydrolase gene, TM1227 (man5).…”