Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

TL;DR

This study reveals how Escherichia coli can use certain sugars and nucleosides for growth when glucose is scarce, through a pathway called the DHAP shunt.

Contribution

The study identifies MtnR and CRP as regulators of the DHAP shunt, revealing its role as a functional carbon metabolism pathway in E. coli.

Findings

The DHAP shunt operon is regulated by MtnR and CRP, depending on substrate and glucose availability.

The DHAP shunt allows E. coli to use 5′-deoxynucleosides and 5-deoxypentose sugars as carbon sources.

The regulatory mechanism is conserved in pathogenic E. coli lineages like ST131.

Abstract

The dihydroxyacetone phosphate (DHAP) shunt is a multifunctional pathway for the metabolism of 5′-deoxynucleosides and 5-deoxypentose sugars, such as 5′-methylthioadenosine (MTA) and 5′-deoxyadenosine (5dAdo), into DHAP and an aldehyde species depending on the substrate. Previous work revealed that Escherichia coli strains with the DHAP shunt can utilize exogenous MTA, 5dAdo, and derivatives thereof as sole carbon and energy sources for growth. However, if and how the DHAP shunt was regulated for 5′-deoxynucleoside and 5-deoxypentose sugar metabolism remained unknown. In the present work, the DHAP shunt genes (mtnK, mtnA, and ald2) and a putative transporter gene of E. coli ATCC 25922 are observed to form an operon, which can be expressed from two separate transcription start sites (TSSs). The distal, low-activity TSS appears to be constitutive, while the proximal primary TSS is regulated based on the identity of available growth substrates by at least two transcriptional regulators. First, YjhU, a deoxyribonucleoside operon repressor family regulator previously of unknown function that we designate as MtnR, functions as a repressor of the DHAP shunt operon when DHAP shunt substrates are absent. Further, the cyclic AMP receptor protein imposes carbon catabolite repression while glucose is available. Based on comparative sequence analysis, the E. coli DHAP shunt promoter region is highly conserved, including strains of the globally disseminated ST131 lineage of extraintestinal pathogenic E. coli, indicating a similar regulatory paradigm. Thus, the E. coli DHAP shunt is a previously unrecognized pathway for the use of 5′-deoxynucleosides and 5-deoxypentose sugars as alternative carbon sources when glucose is scarce.

While not found in all Escherichia coli strains, the dihydroxyacetone phosphate (DHAP) shunt pathway is present in multiple lineages of extraintestinal pathogenic E. coli. The DHAP shunt allows E. coli strains to use a range of 5′-deoxynucleosides and 5-deoxypentose sugars as carbon and energy sources. These metabolites were previously considered waste products of cellular metabolism. This study identifies two transcriptional regulators that regulate the DHAP shunt operon, only allowing full expression when a DHAP shunt substrate is present and when glucose, a more-preferred carbon substrate, is absent. This demonstrates that the DHAP shunt is a genuine carbon metabolism pathway in E. coli and is placed under the hierarchy of carbon catabolite repression.

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