Regulation of carbamoylphosphate synthesis in Escherichia coli: an amazing metabolite at the crossroad of arginine and pyrimidine biosynthesis

Abstract

In all organisms, carbamoylphosphate (CP) is a precursor common to the synthesis of arginine and pyrimidines. In Escherichia coli and most other Gram-negative bacteria, CP is produced by a single enzyme, carbamoylphosphate synthase (CPSase), encoded by the carAB operon. This particular situation poses a question of basic physiological interest: what are the metabolic controls coordinating the synthesis and distribution of this high-energy substance in view of the needs of both pathways? The study of the mechanisms has revealed unexpected moonlighting gene regulatory activities of enzymes and functional links between mechanisms as diverse as gene regulation and site-specific DNA recombination. At the level of enzyme production, various regulatory mechanisms were found to cooperate in a particularly intricate transcriptional control of a pair of tandem promoters. Transcription initiation is modulated by an interplay of several allosteric DNA-binding transcription factors using effector molecules from three different pathways (arginine, pyrimidines, purines), nucleoid-associated factors (NAPs), trigger enzymes (enzymes with a second unlinked gene regulatory function), DNA remodeling (bending and wrapping), UTP-dependent reiterative transcription initiation, and stringent control by the alarmone ppGpp. At the enzyme level, CPSase activity is tightly controlled by allosteric effectors originating from different pathways: an inhibitor (UMP) and two activators (ornithine and IMP) that antagonize the inhibitory effect of UMP. Furthermore, it is worth noticing that all reaction intermediates in the production of CP are extremely reactive and unstable, and protected by tunneling through a 96 Å long internal channel.

Gene autoregulation by 3’ UTR-derived bacterial small RNAs

“…Similar to OppBCDF, the CarAB complex contains one subunit of CarA and one subunit of CarB. Transcriptional control of carAB is complex and controlled by several transcription factors integrating information from purine, pyrimidine, and arginine pathways ( Charlier et al, 2018 ). While the exact biological role of CarZ-mediated feedback regulation of carAB requires further investigation, transcription factor-based feedback regulation has been reported to reduce transcriptional noise ( Alon, 2007 ), which could also be an important feature of sRNA-mediated autoregulation.…”

Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology

“…Besides this complex regulation by multiple bona fide TFs and trigger enzymes, P1 is subject to stringent control (ppGpp) (Bouvier, Patte and Stragier 1984) and UTP-dependent RNAP stuttering (Han and Turnbough 1998) (see below for the mechanism of RNAP stuttering). For a complete overview of carAB regulation, see Charlier, Nguyen Le Minh and Roovers (2018).…”

Competitive Repression of the artPIQM Operon for Arginine and Ornithine Transport by Arginine Repressor and Leucine-Responsive Regulatory Protein in Escherichia coli

“…As shown above, the ARG boxes in the lrp control region are located downstream of the transcription start site. In this context, it is worth noticing that ArgR binding to the ARG boxes overlapping the E. coli car P2 promoter strongly represses transcription initiation from this promoter but does not hinder transcription initiated 67 nt more upstream at the car P1 promoter (Charlier et al, 1988, 2018). Hence, it appears that ArgR is unable to function as an efficient roadblock for an elongating RNA polymerase.…”