Integrated Response to Inducers by Communication between a Catabolic Pathway and Its Regulatory System

Abstract

Efficient gene regulation of metabolic pathways implies that the profile of molecules inducing the pathway matches that of the molecules that are metabolized. Gratuitous induction, a well-known phenomenon in catabolic pathways, is the consequence of differences in the substrate and inducer profiles. This phenomenon is particularly evident in pathways for biodegradation of organic contaminants that can be induced by a variety of molecules similar to the real substrates. Analysis of the regulation of tetralin biodegradation genes in mutant strains with mutations that affect each component of the initial dioxygenase enzymatic complex indicated that the response of the regulatory system to potential inducers is altered differently depending on the mutated component. Based on the expression phenotypes of a number of single or double mutants, we propose a model that represents an unprecedented way of communication between a catabolic pathway and its regulatory system to prevent efficient induction by a molecule that is not a real substrate. This communication allows a better fit of the substrate and inducer profiles, thus minimizing gratuitous induction, without a requirement for optimal coevolution to match the specificity of catabolic enzymes and their regulatory systems. Modulation of the regulatory system in this way not only provides a more appropriate response to potential inducers recognized by the regulatory system but also may properly adjust the levels of gene expression to the substrate availability.

Tetralin-Induced and ThnR-Regulated Aldehyde Dehydrogenase and β-Oxidation Genes in Sphingomonas macrogolitabida Strain TFA

“…The only intergenic region that failed to yield an amplified product was thnL-thnM, which suggests that genes from thnM to thnP are organized in a completely different operon. Expression of this new operon seems to also be dependent on the transcriptional activator ThnR (20,21) because no amplification of the thnM-thnN intergenic region was obtained using cDNA from the mutant T1032 that bears a deletion of thnR (Fig. 3).…”

“…Expression of the thn operons is tetralin inducible and subject to catabolite repression. In addition, a singular and unprecedented method of communication between the tetralin catabolic pathway and its regulatory system has recently been described that prevents gratuitous induction of the thn genes by molecules that cannot be metabolized through the meta-cleavage pathway (20). The key protein in this communication is ThnA3, the ferredoxin that transports electrons to the initial dioxygenase complex, ThnA1A2.…”

ThnY Is a Ferredoxin Reductase-like Iron-Sulfur Flavoprotein That Has Evolved to Function as a Regulator of Tetralin Biodegradation Gene Expression

“…Although most LysR type regulators directly sense the environmental signals to which they respond, a number of examples have been reported in which auxiliary proteins are also required to regulate transcription (18,(42)(43)(44)(45); such a two-component composition allows the regulatory system to respond to additional signals. In the case of the thn genes, transcription is subjected to carbon catabolite repression and is also responding to a modulation system exerted by the reduced form of the ferredoxin ThnA3, which prevents thn gene induction if the inducer molecule cannot be efficiently metabolized by the tetralin biodegradation pathway, thus preventing gratuitous induction (11). These additional signals may be integrated in the regulatory system by affecting the functional state of ThnY, presumably by modifying its redox state.…”

“…in the absence of a suitable substrate for the dioxygenase or in a mutant lacking tetralin dioxygenase), reduced ThnA3 would accumulate, and thn gene expression would be prevented. It has been proposed that this system will avoid gratuitous induction by potential inducers that are not substrates of the terminal oxygenase (11).…”

Integration of Metabolic Reactions and Gene Regulation

“…These changes of a metabolic pathway can be achieved by altering the activities of enzymes or by modulating the expression of the genes encoding them. One example of such feedback system is the regulation of enzymes in the tetralin degradation pathway of E. coli [86]. The input substrate (tetralin) induces the enzyme gene expression along the pathway, whereas an intermediate product (reduced ferredoxin) inhibits transcription of the gene(s) encoding the key the enzyme(s).…”