GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii

Abstract

DeoR-type helix-turn-helix (HTH) domain proteins are transcriptional regulators of sugar and nucleoside metabolism in diverse bacteria and occur in select archaea. In the model archaeon , previous work implicated GlpR, a DeoR-type transcriptional regulator, in transcriptional repression of and the gene encoding the fructose-specific phosphofructokinase () during growth on glycerol. However, the global regulon governed by GlpR remained unclear. Here we compared transcriptomes of wild type and Δ mutant strains grown on glycerol and glucose to detect significant transcript level differences for nearly 50 new genes regulated by GlpR. By coupling computational prediction of GlpR binding sequences with and DNA binding experiments, we determined that GlpR directly controls genes encoding enzymes in fructose degradation, including fructose bisphosphate aldolase, a central control point in glycolysis. GlpR also directly controls other transcription factors. In contrast, other metabolic pathways appear to be under indirect influence of GlpR. experiments demonstrated that GlpR purifies as a tetramer that binds the effector molecule fructose-1-phosphate (F1P). These results suggest that GlpR functions as a direct negative regulator of fructose degradation during growth on carbon sources other than fructose, such as glucose and glycerol, and that GlpR bears striking functional similarity to bacterial DeoR-type regulators.Many archaea are extremophiles, able to thrive in habitats of extreme salinity, pH and temperature. These biological properties are ideal for applications in biotechnology. However, limited knowledge of archaeal metabolism is a bottleneck that prevents broad use of archaea as microbial factories for industrial products. Here we characterize how sugar uptake and use is regulated in a species that lives in high salinity. We demonstrate that a key sugar regulatory protein in this archaeal species functions using molecular mechanisms conserved with distantly related bacterial species.

Conserved principles of transcriptional networks controlling metabolic flexibility in archaea

“…The mechanism of action for all three of these TMnets regulating central carbon metabolism appears to resemble that of the SurR switch described here: a ligand disrupts the TF-DNA-binding interaction, derepressing genes encoding enzymes of one pathway, but de-activating a second pathway [13,36,66,67]. However, in each case, additional complexities may be at play.…”

“…The field of transcriptional regulation in archaea is currently poised to answer these questions: experimental evidence now exists to support the functional knowledge for ∼50 archaeal TFs [5,19]. Notable examples of putative switch-like TMnets include TFs that regulate central carbon metabolism (TrmB [41], GlpR [67], and XacR [36]), which are discussed in the ensuing section.…”

“…The GlpR TF of Haloferax volcanii functions in catabolite repression [69]. In the presence of glucose and glycerol, GlpR represses genes whose products function in fructose uptake and oxidation, and induces those involved in glycerol degradation [67,69]. When fructose is available, it is transported through the phosphotransferase system and converted to fructose-1-phosphate (F-1-P) [70].…”

“…with DNA, derepressing gene-encoding enzymes in the modified Embden-Meyerhoff pathway that oxidizes fructose [24,67]. XacR of H. volcanii activates an unusual pentose degradation pathway that is promiscuous for both xylose and arabinose [36,71,72].…”

“…How gene expression changes over time remains unknown in some cases (e.g. GlpR [67]). Therefore, viewing TMnets from a dynamic modeling perspective aids in pinpointing important knowledge gaps, prioritizing experiments.…”