The control region of the pdu/cob regulon in Salmonella typhimurium

Abstract

The pdu operon encodes proteins for the catabolism of 1,2-propanediol; the nearby cob operon encodes enzymes for the biosynthesis of adenosyl-cobalamin (vitamin B12), a cofactor required for the use of propanediol.These operons are transcribed divergently from distinct promoters separated by several kilobases. The regulation of the two operons is tightly integrated in that both require the positive activator protein PocR and both are subject to global control by the Crp and ArcA proteins. We have determined the DNA nucleotide sequences of the promoter-proximal portion of the pdu operon and the region between the pdu and cob operons. Four open reading frames have been identified, pduB, pduA, pduF, and pocR. The pduA and pduB genes are the first two genes of the pdu operon (transcribed clockwise). The pduA gene encodes a hydrophobic protein with 56% amino acid identity to a 10.9-kDa protein which serves as a component of the carboxysomes of several photosynthetic bacteria. The pduF gene encodes a hydrophobic protein with a strong similarity to the GIpF protein of Escherichia coli, which facilitates the diffusion of glycerol. The N-terminal end of the PduF protein includes a motif for a membrane lipoprotein-lipid attachment site as well as a motif characteristic of the MIP (major intrinsic protein) family of transmembrane channel proteins. We presume that the PduF protein facilitates the diffusion of propanediol. ThepocR gene encodes the positive regulatory protein of the cob andpdu operons and shares the helix-turn-helix DNA binding motif of the AraC family of regulatory proteins. The mutations cobR4 and cobR58 cause constitutive, pocR-independent expression of the cob operon under both aerobic and anaerobic conditions. Evidence that each mutation is a deletion creating a new promoter near the normal promoter site of the cob operon is presented.

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

“…AAK78412.1), and the PocR regulatory protein of Salmonella typhimurium (43). In contrast, the deduced amino acid sequence of DhaS was well conserved in the C-terminal or transmitter domain, showing the presence of a conserved ATP-binding site (HATPase-C domain, amino acids 305-405) and typical motifs, namely H, D, and N boxes (42,44).…”

Diverse Bacterial Microcompartment Organelles

“…Then, in 1994, genetic studies and sequence analyses showed that the PduA protein (which is encoded by an operon involved in B 12 -dependent 1,2-PD degradation by Salmonella) had relatively high sequence identity to the carboxysome shell protein CcmK (4). Consequently, it was proposed that a carboxysome-like structure might be involved in 1,2-PD degradation (4). A few years later, Bobik and coworkers showed that Salmonella conditionally forms polyhedral bodies similar in size and shape to carboxysomes during growth in the presence of 1,2-PD but not during growth on a variety of other carbon sources (6,22).…”

“…Further studies of carboxysome composition paved the way for the identification of diverse MCPs (3). Homologs of carboxysome shell proteins were found in diverse contexts, including operons used for 1,2-propanediol (1,2-PD) and ethanolamine degradation by Salmonella (4,5). Subsequent studies showed that Salmonella forms MCPs for the utilization of these compounds as carbon and energy sources (5)(6)(7)(8).…”

Exploiting genomic patterns to discover new supramolecular protein assemblies

“…In particular, the major shell proteins from these two microcompartments are homologous to each other. 10,11 In addition to the carboxysome and the Pdu microcompartment, other BMCs with related shells but apparently diverse functions have been identified or implicated from genomic sequence data. 12,13 The data suggest that these microcompartments are a widespread, but underappreciated subcellular structure in bacteria.…”