Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12

Genome-Wide Association Study on the Content of Nucleotide-Related Compounds in Korean Native Chicken Breast Meat

Meat flavor is an important factor that influences the palatability of chicken meat. Inosine 5'-monophosphate (IMP), inosine, and hypoxanthine are nucleic acids that serve as taste-active compounds, mainly enhancing flavor in muscle tissue. For this study, we performed a genome-wide association study (GWAS) using a mixed linear model to identify single-nucleotide polymorphisms (SNPs) that are significantly associated with changes in the contents of the nucleotide-related compounds of breast meat in the Korean native chicken (KNC) population. The genomic region on chicken chromosome 5 containing an SNP (rs316338889) was significantly (p < 0.05) associated with all three traits. The trait-related candidate genes located in this significant genomic region were investigated through performing a functional enrichment analysis and protein-protein interaction (PPI) database search. We found six candidate genes related to the function that possibly affected the content of nucleotide-related compounds in the muscle, namely, the TNNT3 and TNNT2 genes that regulate muscle contractions; the INS, IGF2, and DUSP8 genes associated with insulin sensitivity; and the C5NT1AL gene that is presumably related to the nucleotide metabolism process. This study is the first of its kind to find candidate genes associated with the content of all three types of nucleotide-related compounds in chicken meat using GWAS. The candidate genes identified in this study can be used for genomic selection to breed better-quality chickens in the future.

Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions

In large-scale fed-batch production processes, microbes are exposed to heterogeneous substrate availability caused by long mixing times. Escherichia coli, the most common industrial host for recombinant protein production, reacts by recurring accumulation of the alarmone ppGpp and energetically wasteful transcriptional strategies. Here, we compare the regulatory responses of the stringent response mutant strain E. coli SR and its parent strain E. coli MG1655 to repeated nutrient starvation in a two-compartment scale-down reactor. Our data show that E. coli SR can withstand these stress conditions without a ppGpp-mediated stress response maintaining fully functional ammonium uptake and biomass formation. Furthermore, E. coli SR exhibited a substantially reduced short-term transcriptional response compared to E. coli MG1655 (less than half as many differentially expressed genes). E. coli SR proceeded adaptation via more general SOS response pathways by initiating negative regulation of transcription, translation and cell division. Our results show that locally induced stress responses propagating through the bioreactor do not result in cyclical induction and repression of genes in E. coli SR, but in a reduced and coordinated response, which makes it potentially suitable for large-scale production processes.

Identification and characterization of guanosine 5'-monophosphate reductase of Trypanosoma congolense as a drug target

Trypanosoma congolense is one of the most prevalent pathogens which causes trypanosomosis in African animals, resulting in a significant economic loss. In its life cycle, T. congolense is incapable of synthesizing purine nucleotides via a de novo pathway, and thus relies on a salvage pathway to survive. In this study, we identified a gene from T. congolense, TcIL3000_5_1940, as a guanosine 5'-monophosphate reductase (GMPR), an enzyme that modulates the concentration of intracellular guanosine in the pathogen. The recombinant protein was expressed in Escherichia coli, and the gene product was enzymatically confirmed as a unique GMPR, designated as rTcGMPR. This enzyme was constitutively expressed in glycosomes at all of the parasite's developmental stages similar to other purine nucleotide metabolic enzymes. Mycophenolic acid (MPA) was found to inhibit rTcGMPR activity. Hence, it is a potential lead compound for the design of trypanocidal agents, specifically GMPR inhibitor.

Nucleotides, Nucleosides, and Nucleobases

We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.

A facile and sensitive method for quantification of cyclic nucleotide monophosphates in mammalian organs: basal levels of eight cNMPs and identification of 2',3'-cIMP

A sensitive, versatile and economical method to extract and quantify cyclic nucleotide monophosphates (cNMPs) using LC-MS/MS, including both 3',5'-cNMPs and 2',3'-cNMPs, in mammalian tissues and cellular systems has been developed. Problems, such as matrix effects from complex biological samples, are addressed and have been optimized. This protocol allows for comparison of multiple cNMPs in the same system and was used to examine the relationship between tissue levels of cNMPs in a panel of rat organs. In addition, the study reports the first identification and quantification of 2',3'-cIMP. The developed method will allow for quantification of cNMPs levels in cells and tissues with varying disease states, which will provide insight into the role(s) and interplay of cNMP signalling pathways.

DNA, cell wall and general oxidative damage underlie the tellurite/cefotaxime synergistic effect in Escherichia coli

The constant emergence of antibiotic multi-resistant pathogens is a concern worldwide. An alternative for bacterial treatment using nM concentrations of tellurite was recently proposed to boost antibiotic-toxicity and a synergistic effect of tellurite/cefotaxime (CTX) was described. In this work, the molecular mechanism underlying this phenomenon is proposed. Global changes of the transcriptional profile of Escherichia coli exposed to tellurite/CTX were determined by DNA microarrays. Induction of a number of stress regulators (as SoxS), genes related to oxidative damage and membrane transporters was observed. Accordingly, increased tellurite adsorption/uptake and oxidative injuries to proteins and DNA were determined in cells exposed to the mixture of toxicants, suggesting that the tellurite-mediated CTX-potentiating effect is dependent, at least in part, on oxidative stress. Thus, the synergistic tellurite-mediated CTX-potentiating effect depends on increased tellurite uptake/adsorption which results in damage to proteins, DNA and probably other macromolecules. Our findings represent a contribution to the current knowledge of bacterial physiology under antibiotic stress and can be of great interest in the development of new antibiotic-potentiating strategies.

Haploinsufficiency of two histone modifier genes on 6p22.3, ATXN1 and JARID2, is associated with intellectual disability

BACKGROUND

Nineteen patients with deletions in chromosome 6p22-p24 have been published so far. The syndromic phenotype is varied, and includes intellectual disability, behavioural abnormalities, dysmorphic features and structural organ defects. Heterogeneous deletion breakpoints and sizes (1-17 Mb) and overlapping phenotypes have made the identification of the disease causing genes challenging. We suggest JARID2 and ATXN1, both harbored in 6p22.3, as disease causing genes.

METHODS AND RESULTS

We describe five unrelated patients with de novo deletions (0.1-4.8 Mb in size) in chromosome 6p22.3-p24.1 detected by aCGH in a cohort of approximately 3600 patients ascertained for neurodevelopmental disorders. Two patients (Patients 4 and 5) carried non-overlapping deletions that were encompassed by the deletions of the remaining three patients (Patients 1-3), indicating the existence of two distinct dosage sensitive genes responsible for impaired cognitive function in 6p22.3 deletion-patients. The smallest region of overlap (SRO I) in Patients 1-4 (189 kb) included the genes JARID2 and DTNBP1, while SRO II in Patients 1-3 and 5 (116 kb) contained GMPR and ATXN1. Patients with deletion of SRO I manifested variable degrees of cognitive impairment, gait disturbance and distinct, similar facial dysmorphic features (prominent supraorbital ridges, deep set eyes, dark infraorbital circles and midface hypoplasia) that might be ascribed to the haploinsufficiency of JARID2. Patients with deletion of SRO II showed intellectual disability and behavioural abnormalities, likely to be caused by the deletion of ATXN1. Patients 1-3 presented with lower cognitive function than Patients 4 and 5, possibly due to the concomitant haploinsufficiency of both ATXN1 and JARID2. The chromatin modifier genes ATXN1 and JARID2 are likely candidates contributing to the clinical phenotype in 6p22-p24 deletion-patients. Both genes exert their effect on the Notch signalling pathway, which plays an important role in several developmental processes.

CONCLUSIONS

Patients carrying JARID2 deletion manifested with cognitive impairment, gait disturbance and a characteristic facial appearance, whereas patients with deletion of ATXN1 seemed to be characterized by intellectual disability and behavioural abnormalities. Due to the characteristic facial appearance, JARID2 haploinsufficiency might represent a clinically recognizable neurodevelopmental syndrome.

Direct binding targets of the stringent response alarmone (p)ppGpp

The Escherichia coli stringent response, mediated by the alarmone ppGpp, is responsible for the reorganization of cellular transcription upon nutritional starvation and other stresses. These transcriptional changes occur mainly as a result of the direct effects of ppGpp and its partner transcription factor DksA on RNA polymerase. An often overlooked feature of the stringent response is the direct targeting of other proteins by ppGpp. Here we review the literature on proteins that are known to bind ppGpp and, based on sequence homology, X-ray crystal structures and in silico docking, we propose new potential protein binding targets for ppGpp. These proteins were found to fall into five main categories: (i) cellular GTPases, (ii) proteins involved in nucleotide metabolism, (iii) proteins involved in lipid metabolism, (iv) general metabolic proteins and (v) PLP-dependent basic aliphatic amino acid decarboxylases. Bioinformatic rationale is provided for expanding the role of ppGpp in regulating the activities of the cellular GTPases. Proteins involved in nucleotide and lipid metabolism and general metabolic proteins provide an interesting set of structurally varied stringent response targets. While the inhibition of some PLP-dependent decarboxylases by ppGpp suggests the existence of cross-talk between the acid stress and stringent response systems.

The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes

The inosine monophosphate dehydrogenase (IMPDH)/guanosine monophosphate reductase (GMPR) family of (β/α)(8) enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMPDH and GMPR bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water, while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR, the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.

Recombinant Escherichia coli GMP reductase: kinetic, catalytic and chemical mechanisms, and thermodynamics of enzyme-ligand binary complex formation

Guanosine monophosphate (GMP) reductase catalyzes the reductive deamination of GMP to inosine monophosphate (IMP). GMP reductase plays an important role in the conversion of nucleoside and nucleotide derivatives of guanine to adenine nucleotides. In addition, as a member of the purine salvage pathway, it also participates in the reutilization of free intracellular bases. Here we present cloning, expression and purification of Escherichia coli guaC-encoded GMP reductase to determine its kinetic mechanism, as well as chemical and thermodynamic features of this reaction. Initial velocity studies and isothermal titration calorimetry demonstrated that GMP reductase follows an ordered bi-bi kinetic mechanism, in which GMP binds first to the enzyme followed by NADPH binding, and NADP(+) dissociates first followed by IMP release. The isothermal titration calorimetry also showed that GMP and IMP binding are thermodynamically favorable processes. The pH-rate profiles showed groups with apparent pK values of 6.6 and 9.6 involved in catalysis, and pK values of 7.1 and 8.6 important to GMP binding, and a pK value of 6.2 important for NADPH binding. Primary deuterium kinetic isotope effects demonstrated that hydride transfer contributes to the rate-limiting step, whereas solvent kinetic isotope effects arise from a single protonic site that plays a modest role in catalysis. Multiple isotope effects suggest that protonation and hydride transfer steps take place in the same transition state, lending support to a concerted mechanism. Pre-steady-state kinetic data suggest that product release does not contribute to the rate-limiting step of the reaction catalyzed by E. coli GMP reductase.

An enzymatic atavist revealed in dual pathways for water activation

Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct such a complicated catalyst? Here we employ a “Wang-Landau” metadynamics algorithm in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations to investigate the mechanism of the hydrolase reaction. These simulations show that the lowest energy pathway utilizes Arg418 as the base that activates water, in remarkable agreement with previous experiments. Surprisingly, the simulations also reveal a second pathway for water activation involving a proton relay from Thr321 to Glu431. The energy barrier for the Thr321 pathway is similar to the barrier observed experimentally when Arg418 is removed by mutation. The Thr321 pathway dominates at low pH when Arg418 is protonated, which predicts that the substitution of Glu431 with Gln will shift the pH-rate profile to the right. This prediction is confirmed in subsequent experiments. Phylogenetic analysis suggests that the Thr321 pathway was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMPDH utilized the Thr321 pathway exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery of the Arg418 pathway was installed. Thus, our simulations provide an unanticipated window into the evolution of a complex enzyme.

Many enzymes have the remarkable ability to catalyze several different chemical transformations. For example, IMP dehydrogenase catalyzes both an NAD-linked redox reaction and a hydrolase reaction. These reactions utilize distinct catalytic residues and protein conformations. How did Nature construct such a complicated catalyst? While using computational methods to investigate the mechanism of the hydrolase reaction, we have discovered that IMP dehydrogenase contains two sets of catalytic residues to activate water. Importantly, the simulations are in good agreement with previous experimental observations and are further validated by subsequent experiments. Phylogenetic analysis suggests that the simpler, less efficient catalytic machinery was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMP dehydrogenase utilized the less efficient machinery exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery evolved. The presence of the less efficient machinery could facilitate adaptation, making the evolutionary challenge of the IMPDH reaction much less formidable. Thus our simulations provide an unanticipated window into the evolution of a complex enzyme.

How does nature construct complex catalysts? Molecular simulations revealed two sets of catalytic residues in the enzyme IMPDH, one of which seems to represent a primitive catalytic machinery that may be a vestige of evolution.

Temperature modifies gene expression in subcuticular epithelial cells of white spot syndrome virus-infected Litopenaeus vannamei

Subtractive suppressive hybridization was used to identify differentially expressed genes in subcuticular tissues from white spot syndrome virus(WSSV)-infected shrimp kept at different temperatures. Subtractive libraries I and II contained genes expressed at 26 and 33 degrees C, respectively. Three hundred and seventy-nine insert positive clones were selected to confirm differential expression by dot-blot hybridization. Twenty-two clones from library I and eight from library II were sequenced. All sequences from Library I corresponded to white spot syndrome virus genes. From library II, five clones were homologous with previously reported expressed sequence tags of Litopenaeus vannamei, two had similarity with beta-actin and one transcript represented an unknown gene. Over-expression of VP15 in shrimp at 26 degrees C was further confirmed by real-time polymerase chain reaction (PCR), whereas beta-actin expression was similar in animals kept at both temperatures. Together, our results show that hyperthermia reduces the expression of WSSV genes on shrimp subcuticular epithelial cells.

Crystal structure of human guanosine monophosphate reductase 2 (GMPR2) in complex with GMP

Guanosine monophosphate reductase (GMPR) catalyzes the irreversible and NADPH-dependent reductive deamination of GMP to IMP, and plays a critical role in re-utilization of free intracellular bases and purine nucleosides. Here, we report the first crystal structure of human GMP reductase 2 (hGMPR2) in complex with GMP at 3.0 A resolution. The protein forms a tetramer composed of subunits adopting the ubiquitous (alpha/beta)8 barrel fold. Interestingly, the substrate GMP is bound to hGMPR2 through interactions with Met269, Ser270, Arg286, Ser288, and Gly290; this makes the conformation of the adjacent flexible binding region (residues 268-289) fixed, much like a door on a hinge. Structure comparison and sequence alignment analyses show that the conformation of the active site loop (residues 179-187) is similar to those of hGMPR1 and inosine monophosphate dehydrogenases (IMPDHs). We propose that Cys186 is the potential active site, and that the conformation of the loop (residues 129-133) suggests a preference for the coenzyme NADPH over NADH. This structure provides important information towards understanding the functions of members of the GMPR family.

NADPH-dependent GMP reductase isoenzyme of human (GMPR2). Expression, purification, and kinetic properties

GMP reductase (EC 1.6.6.8) is the only known metabolic step by which guanine nucleotides can be converted to the pivotal precursor of both adenine and guanine nucleotides. Human GMP reductase has been previously partially purified from erythrocytes and a chromosome 6-linked cDNA has been identified to correspond for encoding human GMP reductase. Here, we reported a distinct cDNA for human GMP reductase isoenzyme isolated from a human fetal brain library, and the GenBank accession number is AF419346. The deduced protein shows 90% identity with human GMP reductase reported (named GMPR1 compared with GMPR2 of this paper) and 69% with E. coli GMP reductase. Comparison of GMPR2 cDNA sequence with human genome indicates the corresponding gene spans about 6.6kb on chromosome 14, which encodes 348 amino acid residues. Northern hybridization analysis indicates a differential and disproportionate expression of mRNAs for GMPR1 and GMPR2, suggesting the existence of distinct molecular species of GMP reductase in human. The apparent Km of GMPR2 for NADPH and GMP are 26.6 and 17.4 microM, respectively. This is the first report suggesting the existence of two distinct types of human GMP reductase molecular species, which can be used to explain the bimodal saturation curve noted with the purified human erythrocyte GMP reductase.

Molecular cloning and characterization of a cDNA encoding soybean nodule IMP dehydrogenase

Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in de novo purine biosynthesis and is a postulated key enzyme in nitrogen assimilation in ureide-exporting nodules. A 2016 bp cDNA for IMPDH, designated as IMPDH, was cloned from a soybean nodule cDNA library. IMPDH encodes a polypeptide of 502 amino acids with a predicted molecular weight of 53000 and a pI of 5.54. The deduced IMPDH is 70.5% identical to that in Arabidopsis, with a 100% homology in the putative active-site region. Expressing the cloned cDNA in Escherichia coli mutant strain KLC381 (DeltaguaB) restored IMPDH activity, permitting bacterial growth on minimal medium. Southern blot analysis suggested a single copy of IMPDH gene in the soybean genome. Northern blot analysis showed that the expression of IMPDH gene is apparently nodule-specific.

Genetic footprinting in bacteria

In vivo genetic footprinting was developed in the yeast Saccharomyces cerevisiae to simultaneously assess the importance of thousands of genes for the fitness of the cell under any growth condition. We have developed in vivo genetic footprinting for Escherichia coli, a model bacterium and pathogen. We further demonstrate the utility of this technology for rapidly discovering genes that affect the fitness of E. coli under a variety of growth conditions. The definitive features of this system include a conditionally regulated Tn10 transposase with relaxed sequence specificity and a conditionally regulated replicon for the vector containing the transposase and mini-Tn10 transposon with an outwardly oriented promoter. This system results in a high frequency of randomly distributed transposon insertions, eliminating the need for the selection of a population containing transposon insertions, stringent suppression of transposon mutagenesis, and few polar effects. Successful footprints have been achieved for most genes longer than 400 bp, including genes located in operons. In addition, the ability of recombinant proteins to complement mutagenized hosts has been evaluated by genetic footprinting using a bacteriophage lambda transposon delivery system.

Inhibition of cellular growth by increased guanine nucleotide pools. Characterization of an Escherichia coli mutant with a guanosine kinase that is insensitive to feedback inhibition by GTP

In Escherichia coli the enzyme guanosine kinase phosphorylates guanosine to GMP, which is further phosphorylated to GDP and GTP by other enzymes. Here I report that guanosine kinase is subject to efficient feedback inhibition by the end product of the pathway, GTP, and that this regulation is abolished by a previously described mutation, gsk-3, in the structural gene for guanosine kinase (Hove-Jensen, B., and Nygaard, P. (1989) J. Gen. Microbiol. 135, 1263-1273). Consequently, the gsk-3 mutant strain was extremely sensitive to guanosine, which caused the guanine nucleotide pools to increase dramatically, thereby initiating a cascade of metabolic changes that eventually led to growth arrest. By isolation and characterization of guanosine-resistant derivatives of the gsk-3 mutant, some of the crucial steps in this deleterious cascade of events were found to include the following: first, conversion of GMP to adenine nucleotides via GMP reductase, encoded by the guaC gene; second, inhibition of phosphoribosylpyrophosphate synthetase by an adenine nucleotide, presumably ADP, causing starvation for histidine, tryptophan, and pyrimidines, all of which require PRPP for their synthesis; third, accumulation of the regulatory nucleotide guanosine 5',3'-bispyrophosphate (ppGpp), a general transcriptional inhibitor synthesized by the relA gene product in response to amino acid starvation.

Structure and organization of a 25 kbp region of the genome of the photosynthetic green sulfur bacterium Chlorobium vibrioforme containing Mg-chelatase encoding genes

A region comprising approximately 25 kbp of the genome of the strictly anaerobic and obligate photosynthetic green sulfur bacterium Chlorobium vibrioforme has been mapped, subcloned and partly sequenced. Approximately 15 kbp have been sequenced in it's entirety and three genes with significant homology and feature similarity to the bchI, -D and -H genes and the chlI, -D and -H genes of Rhodobacter and Synechocystis strain PCC6803, respectively, which encode magnesium chelatase subunits, have been identified. Magnesium chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX, and is the first enzyme unique to the (bacterio)chlorophyll specific branch of the porphyrin biosynthetic pathway. The organization of the three Mg-chelatase encoding genes is unique to Chlorobium and suggests that the magnesium chelatase of C. vibrioforme is encoded by a single operon. The analyzed 25 kbp region contains five additional open reading frames, two of which display significant homology and feature similarity to genes encoding lipoamide dehydrogenase and genes with function in purine synthesis, and another three display significant homology to open reading frames with unknown function in distantly related bacteria. Putative E. coli sigma 70-like promoter sequences, ribosome binding sequences and rho-independent transcriptional stop signals within the sequenced 15 kbp region are related to the identified genes and orfs. Southern analysis, restriction mapping and partial sequencing of the remaining ca. 10 kbp of the analyzed 25 kbp region have shown that this part includes the hemA, -C, -D and -B genes (MOBERG and AVISSAR 1994), which encode enzymes with function in the early part of the biosynthetic pathway of porphyrins.

The role of gene duplication in the evolution of purine nucleotide salvage pathways

Purine nucleotides are formed de novo by a widespread biochemical route that may be of monophyletic origin, or are synthesized from preformed purine bases and nucleosides through different salvage pathways. Three monophyletic sets of purine salvage enzymes, each of which catalyzes mechanistically similar reactions, can be identified: (a) adenine-, xanthine-, hypoxanthine- and guanine-phosphoribosyltransferases, which are all homologous among themselves, as well as to nucleoside phosphorylases; (b) adenine deaminase, adenosine deaminase, and adenosine monophophate deaminase; and (c) guanine reductase and inosine monophosphate dehydrogenase. These homologies support the idea that substrate specificity is the outcome of gene duplication, and that the purine nucleotide salvage pathways were assembled by a patchwork process that probably took place before the divergence of the three cell domains (Bacteria, Archaea, and Eucarya). Based on the ability of adenine PRTase to catalyze the condensation of PRPP with 4-aminoimidazole-5-carboxamide (AICA), a simpler scheme of purine nucleotide biosynthesis is presented. This hypothetical route requires the prior evolution of PRPP biosynthesis. Since it has been argued that PRPP, nucleosides, and nucleotides are susceptible to hydrolysis, they are very unlikely prebiotic compounds. If this is the case, it implies that many purine salvage pathways appeared only after the evolution of phosphorylated sugar biosynthetic pathways made ribosides available.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Expression, purification, and characterization of inosine 5'-monophosphate dehydrogenase from Borrelia burgdorferi

Inosine 5'-monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanine nucleotide biosynthesis. IMPDH converts IMP to xanthosine 5'-monophosphate with concomitant conversion of NAD+ to NADH. All IMPDHs characterized to date contain a 130-residue "subdomain" that extends from an N-terminal loop of the alpha/beta barrel domain. The role of this subdomain is unknown. An IMPDH homolog has been cloned from Borrelia burgdorferi, the causative agent of Lyme disease (Margolis, N., Hogan, D., Tilly, K., and Rosa, P. A. (1994) J. Bacteriol. 176, 6427-6432). This homolog has replaced the subdomain with a 50-residue segment of unrelated sequence. We have expressed and characterized the B. burgdorferi IMPDH homolog. This protein has IMPDH activity, which unequivocally demonstrates that the subdomain is not required for catalytic activity. The monovalent cation and dinucleotide binding sites of B. burgdorferi IMPDH are significantly different from those of human IMPDH. Therefore, these sites are targets for the design of specific inhibitors for B. burgdorferi IMPDH. Such inhibitors might be new treatments for Lyme disease.

Cloning and characterization of the gene encoding IMP dehydrogenase from Arabidopsis thaliana

We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Arabidopsis thaliana (At). The transcription unit of the At gene spans approximately 1900 bp and specifies a protein of 503 amino acids with a calculated relative molecular mass (M(r)) of 54,190. The gene is comprised of a minimum of four introns and five exons with all donor and acceptor splice sequences conforming to previously proposed consensus sequences. The deduced IMPDH amino-acid sequence from At shows a remarkable similarity to other eukaryotic IMPDH sequences, with a 48% identity to human Type II enzyme. Allowing for conservative substitutions, the enzyme is 69% similar to human Type II IMPDH. The putative active-site sequence of At IMPDH conforms to the IMP dehydrogenase/guanosine monophosphate reductase motif and contains an essential active-site cysteine residue.

Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus

We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Pyrococcus furiosus (Pf), a hyperthermophillic archeon. Sequence analysis of the Pf gene indicated an open reading frame specifying a protein of 485 amino acids (aa) with a calculated M(r) of 52900. Canonical Archaea promoter elements, Box A and Box B, are located -49 and -17 nucleotides (nt), respectively, upstream of the putative start codon. The sequence of the putative active-site region conforms to the IMPDH signature motif and contains a putative active-site cysteine. Phylogenetic relationships derived by using all available IMPDH sequences are consistent with trees developed for other molecules; they do not precisely resolve the history of Pf IMPDH but indicate a close similarity to bacterial IMPDH proteins. The phylogenetic analysis indicates that a gene duplication occurred prior to the division between rodents and humans, accounting for the Type I and II isoforms identified in mice and humans.

Structure and mechanism of inosine monophosphate dehydrogenase in complex with the immunosuppressant mycophenolic acid

The structure of inosine-5'-monophosphate dehydrogenase (IMPDH) in complex with IMP and mycophenolic acid (MPA) has been determined by X-ray diffraction. IMPDH plays a central role in B and T lymphocyte replication. MPA is a potent IMPDH inhibitor and the active metabolite of an immunosuppressive drug recently approved for the treatment of allograft rejection. IMPDH comprises two domains: a core domain, which is an alpha/beta barrel and contains the active site, and a flanking domain. The complex, in combination with mutagenesis and kinetic data, provides a structural basis for understanding the mechanism of IMPDH activity and indicates that MPA inhibits IMPDH by acting as a replacement for the nicotinamide portion of the nicotinamide adenine dinucleotide cofactor and a catalytic water molecule.

Cloning, sequence analysis and expression of the group A streptococcal guaB gene encoding inosine monophosphate dehydrogenase

Inosine monophosphate dehydrogenase (IMPDH) is an essential enzyme in the biosynthesis of purines. We cloned a group A streptococcal (GAS) DNA fragment containing an open reading frame similar to other bacterial guaB genes encoding IMPDH. The GAS guaB consists of 1479 nucleotides encoding a protein of 493 amino acids. Expression of the GAS guaB in an Escherichia coli guaB mutant restored IMPDH activity, confirming the function of the gene product and demonstrating that the GAS enzyme is active in a heterologous bacterial host. Restriction mapping and Southern hybridization analysis of GAS chromosomal DNA localized guaB to a site approximately 5 kb from the hasA and hasB genes which encode enzymes necessary for hyaluronic acid capsule synthesis.

Recombinant human inosine monophosphate dehydrogenase type I and type II proteins. Purification and characterization of inhibitor binding

Inosine monophosphate dehydrogenase (IMPDH) activity results from the expression of two separate genes, and the resulting proteins (type I and type II) are 84% identical at the amino acid level. Although the type II mRNA is expressed at higher levels in proliferating cells, both mRNAs, and by extrapolation both proteins, are present in normal and malignant cells. Since IMPDH is an important target for the development of drugs with both chemotherapeutic and immunosuppressive activity, we have compared the kinetic and physical properties of the two human enzymes expressed in and purified from Escherichia coli. Type I and II IMPDH had kcat values of 1.8 and 1.4 sec-1, respectively, with Km values for IMP of 14 and 9 microM and Km values for NAD of 42 and 32 microM. The two enzymes were inhibited competitively by the immunosuppressive agent mizoribine 5'-monophosphate (MMP) with Ki values of 8 and 4 nM and inhibited uncompetitively by mycophenolic acid with Ki values of 11 and 6 nM. The association of MMP to either isozyme, as monitored by fluorescence quenching, was relatively slow with kon values of 3-8 x 10(4) M-1 sec-1 and koff values of 3 x 10(-4) sec-1 (half-lives of 36-43 min). Thus, MMP is a potent, tight-binding competitive inhibitor that does not discriminate between the two IMPDH isozymes.

Identification of the hopG gene, a component of Escherichia coli K-12 type II export system, and its conservation among different pathogenic Escherichia coli and Shigella isolates

The Escherichia coli K-12 gene coding for a component of a type II export system was identified and characterized. The HopG protein contains a typical prepilin peptidase cleavage site and has a high degree of homology with proteins PulG, OutG, and ExeG, which are components of type II secretion systems from Klebsiella pneumoniae, Erwinia carotovora, and Aeromonas hydrophila.

Escherichia coli contains a set of genes homologous to those involved in protein secretion, DNA uptake and the assembly of type-4 fimbriae in other bacteria

A specialised system involved in a diverse array of functions, including the biogenesis of fimbriae, protein secretion and DNA uptake, has recently been found to be widespread in the eubacteria. These systems have in common several sets of related genes, including those encoding proteins containing leader sequences homologous to that of the type-4 fimbrial subunit (prepilin), a prepilin-type leader peptidase, a cytoplasmic nucleotide-binding protein, and other proteins located in the inner and outer membranes [Hobbs, M. and Mattick, J.S., Mol Microbiol. 10 (1993) 233-243]. Here, we show that Escherichia coli contains at least nine homologs of this system, and present complete sequence data for five of the genes involved (ppdD. hopB, hopC, hopD and pshM), as well as for an adjacent gene (nadC), which encodes quinolic acid phosphoribosyltransferase. Insertional mutagenesis of hopB and hopD failed to reveal any obvious effects on cell viability, morphogenesis of M13 phage, conjugative transfer of the F plasmid, or protein secretion.

Functions of the gene products of Escherichia coli

A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome.

Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus: a general system for the formation of surface-associated protein complexes

The Pseudomonas aeruginosa genes pilB-D and pilQ are necessary for the assembly of type 4 fimbriae. Homologues of these genes and of the subunit (pilin) gene have been described in various different bacterial species, but not always in association with type 4 fimbrial biosynthesis and function. Pil-like proteins are also involved in protein secretion, DNA transfer by conjugation and transformation, and morphogensis of filamentous bacteriophages. It seems likely that the Pil homologues function in the processing and export of proteins resembling type 4 fimbrial subunits, and in their organization into fimbrial-like structures. These may either be true type 4 fimbriae, or components of protein complexes which act in the transport of macromolecules (DNA or protein) into or out of the cell. Some PilB-like and PilQ-like proteins are apparently also involved in the assembly of non-type 4 polymeric structures (filamentous phage virions and conjugative pili). The diverse studies summarized in this review are providing insight into an extensive infrastructural system which appears to be utilized in the formation of a variety of cell surface-associated complexes.

Genomic structure and expression of human guanosine monophosphate reductase

In vitro translation in the rabbit reticulocyte system and transient expression in Cos7 cells were performed to characterize the protein encoded by a chromosome 6-linked human cDNA clone, whose nucleotide sequence is homologous to that of Escherichia coli guanosine monophosphate reductase (GMP reductase) cDNA. The molecular weight of the peptide produced by the cDNA was about 37,000 Dalton, and the protein produced in the Cos7 cells exhibited GMP reductase activity, substantiating that the cDNA is for human GMP reductase. The corresponding genomic clones were obtained from two human genomic libraries. The gene spans about 50 kb and is composed of 9 exons, which encode 345 amino acid residues. Organization of exons and introns was established by DNA sequencing of each exon and splicing junctions. The gene contains two potential SpI binding sites within exon 1, and a functional atypical polyadenylation signal in exon 9.