Purification and characterization of the fructose-inducible HPr-like protein, FPr, and the fructose-specific enzyme III of the phosphoenolpyruvate: sugar phosphotransferase system of Salmonella typhimurium

Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes

Salmonella enterica is a globally significant bacterial food-borne pathogen that utilizes a variety of carbon sources. We report here that Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) uses d-glucosaminate (2-amino-2-deoxy-d-gluconic acid) as a carbon and nitrogen source via a previously uncharacterized mannose family phosphotransferase system (PTS) permease, and we designate the genes encoding the permease dgaABCD (d-glucosaminate PTS permease components EIIA, EIIB, EIIC, and EIID). Two other genes in the dga operon (dgaE and dgaF) were required for wild-type growth of S. Typhimurium with d-glucosaminate. Transcription of dgaABCDEF was dependent on RpoN (σ(54)) and an RpoN-dependent activator gene we designate dgaR. Introduction of a plasmid bearing dgaABCDEF under the control of the lac promoter into Escherichia coli strains DH5α, BL21, and JM101 allowed these strains to grow on minimal medium containing d-glucosaminate as the sole carbon and nitrogen source. Biochemical and genetic data support a catabolic pathway in which d-glucosaminate, as it is transported across the cell membrane, is phosphorylated at the C-6 position by DgaABCD. DgaE converts the resulting d-glucosaminate-6-phosphate to 2-keto-3-deoxygluconate 6-phosphate (KDGP), which is subsequently cleaved by the aldolase DgaF to form glyceraldehyde-3-phosphate and pyruvate. DgaF catalyzes the same reaction as that catalyzed by Eda, a KDGP aldolase in the Entner-Doudoroff pathway, and the two enzymes can substitute for each other in their respective pathways. Examination of the Integrated Microbial Genomes database revealed that orthologs of the dga genes are largely restricted to certain enteric bacteria and a few species in the phylum Firmicutes.

Replacing the general energy-coupling proteins of the phospho-enol-pyruvate:sugar phosphotransferase system ofSalmonella typhimuriumwith fructose-inducible counterparts results in the inability to utilize nonphosphotransferase system sugars

A Salmonella typhimurium mutant lacking Enzyme I and HPr, general proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), but producing homologues EIFructoseand FPr constitutively, did not grow in minimal medium supplemented with non-PTS sugars (melibiose, glycerol, and maltose) in the absence of any trace of Luria–Bertani broth; adding cyclic AMP allowed growth. On melibiose, rapid growth began only when melibiose permease activity had reached a threshold level. Wild-type cultures reached this level within about 2 h, but the mutant only after a 12–14 h lag period, and then only when cyclic AMP had been added to the medium. On a mixture of melibiose and a PTS sugar, permease was undetectable in either the wild type or mutant until the PTS sugar had been exhausted. Permease then appeared, increasing with time, but in the mutant it never reached the threshold allowing rapid growth on melibiose unless cyclic AMP had been added. On rich medium supplemented with melibiose or glycerol, the mutant produced lower (30%) levels of melibiose permease or glycerol kinase compared with the wild type. We propose that poor phosphorylation of the regulatory protein Enzyme IIAGlucose, leading to constitutive inducer exclusion and catabolite repression in this strain, accounts for these results.

Effect of replacing the general energy-coupling proteins of the PEP:sugar phosphotransferase system of Salmonella typhimurium with their fructose-inducible counterparts on utilization of the PTS sugar glucitol

A strain of Salmonella typhimurium in which the genes encoding the general phosphoenolpyruvate:sugar phosphotransferase system (PTS) proteins HPr and Enzyme I have been deleted, the normally cryptic gene encoding the fructose-inducible Enzyme I (EI* or EI(fructose)) is expressed, and the fructose repressor protein is inactive (fruR or cra mutant) was studied. This strain lacks HPr and EI, but expresses FPr (DTP) and EI(fructose) constitutively. Since FPr and EI(fructose) can substitute for HPr and EI, the strain grew in minimal liquid medium supplemented with the PTS sugars glucose, fructose, N-acetylglucosamine, mannitol or mannose. However, it showed very poor to negligible growth on the PTS sugar glucitol. It also grew very poorly on the non-PTS sugars maltose, melibiose and especially glycerol. Adding cAMP to the medium allowed growth on glucitol, but did not affect growth on glycerol. We suggest that poor phosphorylation of the regulatory molecule Enzyme IIA(glucose) by FPr is responsible for these effects.

Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant

Two rpoN-linked delta Tn10-kan insertions suppress the conditionally lethal erats allele. One truncates rpoN while the second disrupts another gene (ptsN) in the rpoN operon and does not affect classical nitrogen regulation. Neither alter expression of era indicating that suppression is post-translational. Plasmid clones of ptsN prevent suppression by either disruption mutation indicating that this gene is important for lethality caused by erats. rpoN and six neighboring genes were sequenced and compared with sequences in the database. Two of these genes encode proteins homologous to Enzyme IIAFru and HPr of the phosphoenolpyruvate:sugar phosphotransferase system. We designate these proteins IIANtr (ptsN) and NPr (npr). Purified IIANtr and NPr exchange phosphate appropriately with Enzyme I, HPr, and Enzyme IIA proteins of the phosphoenolpyruvate: sugar phosphotransferase system. Several sugars and tricarboxylic acid cycle intermediates inhibited growth of the ptsN disruption mutant on medium containing an amino acid or nucleoside base as a combined source of nitrogen, carbon, and energy. This growth inhibition was relieved by supplying the ptsN gene or ammonium salts but was not aleviated by altering levels of exogenously supplied cAMP. These results support our previous proposal of a novel mechanism linking carbon and nitrogen assimilation and relates IIANtr to the unknown process regulated by the essential GTPase Era.

Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria

Numerous gram-negative and gram-positive bacteria take up carbohydrates through the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS). This system transports and phosphorylates carbohydrates at the expense of PEP and is the subject of this review. The PTS consists of two general proteins, enzyme I and HPr, and a number of carbohydrate-specific enzymes, the enzymes II. PTS proteins are phosphoproteins in which the phospho group is attached to either a histidine residue or, in a number of cases, a cysteine residue. After phosphorylation of enzyme I by PEP, the phospho group is transferred to HPr. The enzymes II are required for the transport of the carbohydrates across the membrane and the transfer of the phospho group from phospho-HPr to the carbohydrates. Biochemical, structural, and molecular genetic studies have shown that the various enzymes II have the same basic structure. Each enzyme II consists of domains for specific functions, e.g., binding of the carbohydrate or phosphorylation. Each enzyme II complex can consist of one to four different polypeptides. The enzymes II can be placed into at least four classes on the basis of sequence similarity. The genetics of the PTS is complex, and the expression of PTS proteins is intricately regulated because of the central roles of these proteins in nutrient acquisition. In addition to classical induction-repression mechanisms involving repressor and activator proteins, other types of regulation, such as antitermination, have been observed in some PTSs. Apart from their role in carbohydrate transport, PTS proteins are involved in chemotaxis toward PTS carbohydrates. Furthermore, the IIAGlc protein, part of the glucose-specific PTS, is a central regulatory protein which in its nonphosphorylated form can bind to and inhibit several non-PTS uptake systems and thus prevent entry of inducers. In its phosphorylated form, P-IIAGlc is involved in the activation of adenylate cyclase and thus in the regulation of gene expression. By sensing the presence of PTS carbohydrates in the medium and adjusting the phosphorylation state of IIAGlc, cells can adapt quickly to changing conditions in the environment. In gram-positive bacteria, it has been demonstrated that HPr can be phosphorylated by ATP on a serine residue and this modification may perform a regulatory function.

Evolutionary relationships among the permease proteins of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Construction of phylogenetic trees and possible relatedness to proteins of eukaryotic mitochondria

The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-beta-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.

Involvement of the histidine protein (HPr) of the phosphotransferase system in chemotactic signaling of Escherichia coli K-12

It is known that in mutants of Escherichia coli lacking the histidine protein (HPr) of the carbohydrate: phosphotransferase system, all substrates of the system can be taken up in the presence of the fructose-regulated HPr-like protein FPr (gene fruF). Although this protein fully substituted for HPr in transport and phosphorylation, we found that it was not able to complement efficiently for HPr in mediating chemotaxis toward phosphotransferase system substrates. Furthermore, transport activity and chemotaxis could be genetically dissected by the exchange of single amino acids in HPr. The results suggest a specific role of HPr in chemotactic signaling. We propose a possible link of signal transduction pathways for phosphotransferase system- and methyl chemotaxis protein-dependent substrates via HPr.

Physiological consequences of the complete loss of phosphoryl-transfer proteins HPr and FPr of the phosphoenolpyruvate:sugar phosphotransferase system and analysis of fructose (fru) operon expression in Salmonella typhimurium

Mutants of Salmonella typhimurium defective in the proteins of the fructose operon [fruB(MH)KA], the fructose repressor (fruR), the energy-coupling enzymes of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) (ptsH and ptsI), and the proteins of cyclic AMP action (cya and crp) were analyzed for their effects on cellular physiological processes and expression of the fructose operon. The fru operon consists of three structural genes: fruB(MH), which encodes the enzyme IIIFru-modulator-FPr tridomain fusion protein of the PTS; fruK, which encodes fructose-1-phosphate kinase; and fruA, which encodes enzyme IIFru of the PTS. Among the mutants analyzed were Tn10 insertion mutants and lacZ transcriptional fusion mutants. It was found that whereas a fruR::Tn10 insertion mutant, several fruB(MH)::Mu dJ and fruK::Mu dJ fusion mutants, and several ptsHI deletion mutants expressed the fru operon and beta-galactosidase at high constitutive levels, ptsH point mutants and fruA::Mu dJ fusion mutants retained inducibility. Inclusion of the wild-type fru operon in trans did not restore fructose-inducible beta-galactosidase expression in the fru::Mu dJ fusion mutants. cya and crp mutants exhibited reduced basal activities of all fru regulon enzymes, but inducibility was not impaired. Surprisingly, fruB::Mu dJ crp or cya double mutants showed over 10-fold inducibility of the depressed beta-galactosidase activity upon addition of fructose, even though this activity in the fruB::Mu dJ fusion mutants that contained the wild-type cya and crp alleles was only slightly inducible. By contrast, beta-galactosidase activity in a fruK::Mu dJ fusion mutant, which was similarly depressed by introduction of a crp or cya mutation, remained constitutive. Other experiments indicated that sugar uptake via the PTS can utilize either FPr-P or HPr-P as the phosphoryl donor, but that FPr is preferred for fructose uptake whereas HPr is preferred for uptake of the other sugars. Double mutants lacking both proteins were negative for the utilization of all sugar substrates of the PTS, were negative for the utilization of several gluconeogenic carbon sources, exhibited greatly reduced adenylate cyclase activity, and were largely nonmotile. These phenotypic properties are more extreme than those observed for tight ptsH and ptsI mutants, including mutants deleted for these genes. A biochemical explanation for this fact is proposed.

Structure and evolution of a multidomain multiphosphoryl transfer protein. Nucleotide sequence of the fruB(HI) gene in Rhodobacter capsulatus and comparisons with homologous genes from other organisms

The gene order of the fructose (fru) operon and nucleotide sequence of the first gene (fruB(HI) of Rhodobacter capsulatus are reported, analyzed and compared with homologous genes from other bacteria, and the gene products are identified. Included within the region reported is a gene encoding a multiphosphoryl transfer protein (MTP) of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). MTP consists of three moieties: a fructose-specific enzyme III (IIIfru)-like N-terminal moiety (residues 1 to 143) followed by an FPr(HPr)-like moiety (residues 157 to 245) and an enzyme I-like moiety (residues 273 to 827). The enzyme III-like moiety closely resembles the N-terminal 143 residues of the IIIfru-FPR fusion protein from Salmonella typhimurium (40.6% identity throughout its length) and the C-terminal 145 residues of the mannitol-specific enzyme II (IImtl) (37.8% identity throughout its length with the IIImtl moiety of IImtl). The FPr-like domain of MTP resembles the S. typhimurium FPr (42.4% identity) and the Escherichia coli or S. typhimurium HPr (38.8% identity). The enzyme I-like moiety resembles the E. coli enzyme I (38.9% identity). Predicted phosphorylation sites within the three functional units of MTP (His62 in the IIIfru-like moiety; His171 in the FPr-like moiety and His457 in the enzyme I-like moiety) were identified on the basis of sequence comparisons with the homologous proteins from enteric bacteria. The three functional domains of MTP are joined by two flexible "linkage" regions, rich in alanine, glycine and proline, which show 47% sequence identity with each other. They also exhibit a high degree of sequence identity with the linkage region of the mannose-specific enzyme III (IIIman) of the E. coli PTS as well as several other proteins of bacterial, eukaryotic and viral origin. At the RNA level, these linker regions formed hairpin structures with high (90%) G + C content. Analyses of the IIIfru-FPr fusion protein of S. typhimurium revealed that between the IIIfru and FPr moieties of this protein is a stretch of 142 amino acids that do not show homology to known PTS proteins. This region and the adjacent FPr-like region contain a sequence of 110 residues exhibiting 59% similarity to the receiver consensus motif defined by Kofoid and Parkinson. Because the Salmonella IIIfru-FPr fusion protein has been implicated in transcriptional regulation, this region of the Salmonella protein may prove to have regulatory significance.(ABSTRACT TRUNCATED AT 400 WORDS)

Altered transcriptional patterns affecting several metabolic pathways in strains of Salmonella typhimurium which overexpress the fructose regulon

Expression of beta-galactosidase in transcriptional fusions with the pps gene (encoding phosphoenolpyruvate [PEP] synthase), the aceBAK operon (encoding malate synthase, isocitrate lyase, and isocitrate dehydrogenase kinase, respectively), and the phs operon (encoding either thiosulfate reductase or a regulatory protein controlling its expression) was studied in Salmonella typhimurium. beta-Galactosidase synthesis in these strains was repressible either by growth in the presence of glucose or by the presence of a fruR mutation, which resulted in the constitutive expression of the fructose (fru) regulon. Five enzymes of gluconeogenesis (PEP synthase, PEP carboxykinase, isocitrate lyase, malate synthase, and fructose-1,6-diphosphatase) were shown to be repressed either by growth in the presence of glucose or the fruR mutation, while the glycolytic enzymes, enzyme I and enzymes II of the phosphotransferase system as well as phosphofructokinase, were induced either by growth in the presence of glucose or the fruR mutation. Overexpression of the cloned fru regulon genes (not including fruR) resulted in parallel repression of representative gluconeogenic, Krebs cycle, and glyoxylate shunt enzymes. Studies with temperature-sensitive mutants of S. typhimurium which synthesized heat-labile IIIFru proteins provided evidence that this protein plays a role in the regulation of gluconeogenic substrate utilization. Other mutant analyses revealed a complex relationship between fru gene expression and the expression of genes encoding gluconeogenic enzymes. Taken together, the results suggest that a number of genes encoding catabolic, biosynthetic, and amphibolic enzymes in enteric bacteria are transcriptionally regulated by a complex catabolite repression/activation mechanism which may involve enzyme IIIFru of the phosphotransferase system as one component of the regulatory system.

The PEP: fructose phosphotransferase system in Salmonella typhimurium: FPr combines enzyme IIIFru and pseudo-HPr activities

We have cloned the fru operon of Salmonella typhimurium, coding for the enzymes of the phosphoenolpyruvate: fructose phosphotransferase system (Fructose PTS). The fruFKA operon consists of three genes: fruF coding for FPr, fruK for fructose 1-phosphate kinase and fruA for Enzyme IIFru. Insertions of Tn5 in the different genes were isolated and the activities of the gene products were measured. Expression of the plasmid-encoded fru operon in the maxicell system resulted in the synthesis of three proteins with molecular weights of 47 kDa (fruA), 39 kDa (fruF) and 32 kDa (fruK). We have sequenced the fruF gene and the regulatory region of the fru operon. In contrast to previously published results, we have found that the fruF gene codes for a 39 kDa protein, FPr, that combines Enzyme IIIFru and pseudo-HPr activities. The N-terminal part of FPr is homologous to the cytoplasmic domain of the Escherichia coli Enzyme IIMtl, as well as several Enzymes IIIMtl from gram-positive bacteria. The C-terminal domain shows homology to HPr of E. coli and several gram-positive organisms. The fru operon is regulated by a repressor, FruR. We have constructed an operon fusion between fru and the galK gene and shown that regulation of the fru operon by FruR takes place at the level of transcription.