Genetic mapping with a thiamine-requiring auxotroph of Escherichia coli K-12 defective in thiamine phosphate pyrophosphorylase

Engineering yeast endosymbionts as a step toward the evolution of mitochondria

It has been hypothesized that mitochondria evolved from a bacterial ancestor that initially became established in an archaeal host cell as an endosymbiont. Here we model this first stage of mitochondrial evolution by engineering endosymbiosis between Escherichia coli and Saccharomyces cerevisiae An ADP/ATP translocase-expressing E. coli provided ATP to a respiration-deficient cox2 yeast mutant and enabled growth of a yeast-E. coli chimera on a nonfermentable carbon source. In a reciprocal fashion, yeast provided thiamin to an endosymbiotic E. coli thiamin auxotroph. Expression of several SNARE-like proteins in E. coli was also required, likely to block lysosomal degradation of intracellular bacteria. This chimeric system was stable for more than 40 doublings, and GFP-expressing E. coli endosymbionts could be observed in the yeast by fluorescence microscopy and X-ray tomography. This readily manipulated system should allow experimental delineation of host-endosymbiont adaptations that occurred during evolution of the current, highly reduced mitochondrial genome.

The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies

The metabolism of a cell can be viewed as a weighted sum of elementary modes. Due to the multiplicity of modes the identification of the individual weights represents a non-trivial problem. To enable the determination of weighting factors we have identified and implemented two gene deletions in combination with defined growth conditions that limit the metabolism from 4374 original elementary modes to 24 elementary modes for a non-PHB synthesizing control and 40 modes for a PHB synthesizing strain. These remaining modes can be further grouped into five families that have the same overall stoichiometry. Thus, the complexity of the problem is significantly reduced, and weighting factors for each family of modes could be determined from the measurement of accumulation rates of metabolites. Moreover, it is shown that individual weights are inversely correlated with the entropy generated by the operation of the used pathways defined in elementary modes. This suggests that evolution developed cellular regulatory patterns that permit diversity of pathways while favoring efficient pathways with low entropy generation. Furthermore, such correlation provides a rational way of estimating metabolic fluxes based on the thermodynamic properties of elementary modes. This is demonstrated with an example in which experimentally determined, intracellular fluxes are shown to be highly correlated with fluxes computed based on elementary modes and reaction entropies. The analysis suggests that the set of elementary modes can be interpreted analogous to a metabolic ensemble of quantum states of a macroscopic system.

Effect of adaptation to ethanol on cytoplasmic and membrane protein profiles of Oenococcus oeni

The practical application of commercial malolactic starter cultures of Oenococcus oeni surviving direct inoculation in wine requires insight into mechanisms of ethanol toxicity and of acquired ethanol tolerance in this organism. Therefore, the site-specific location of proteins involved in ethanol adaptation, including cytoplasmic, membrane-associated, and integral membrane proteins, was investigated. Ethanol triggers alterations in protein patterns of O. oeni cells stressed with 12% ethanol for 1 h and those of cells grown in the presence of 8% ethanol. Levels of inosine-5'-monophosphate dehydrogenase and phosphogluconate dehydrogenase, which generate reduced nicotinamide nucleotides, were decreased during growth in the presence of ethanol, while glutathione reductase, which consumes NADPH, was induced, suggesting that maintenance of the redox balance plays an important role in ethanol adaptation. Phosphoenolpyruvate:mannose phosphotransferase system (PTS) components of mannose PTS, including the phosphocarrier protein HPr and EII(Man), were lacking in ethanol-adapted cells, providing strong evidence that mannose PTS is absent in ethanol-adapted cells, and this represents a metabolic advantage to O. oeni cells during malolactic fermentation. In cells grown in the presence of ethanol, a large increase in the number of membrane-associated proteins was observed. Interestingly, two of these proteins, dTDT-glucose-4,6-dehydratase and D-alanine:D-alanine ligase, are known to be involved in cell wall biosynthesis. Using a proteomic approach, we provide evidence for an active ethanol adaptation response of O. oeni at the cytoplasmic and membrane protein levels.

Thiamine transport in Escherichia coli: the mechanism of inhibition by the sulfhydryl-specific modifier N-ethylmaleimide

Active transport of thiamin (vitamin B(1)) into Escherichia coli occurs through a member of the superfamily of transporters known as ATP-binding cassette (ABC) transporters. Although it was demonstrated that the sulfhydryl-specific modifier N-ethylmaleimide (NEM) inhibited thiamin transport, the exact mechanism of this inhibition is unknown. Therefore, we have carried out a kinetic analysis of thiamin transport to determine the mechanism of inhibition by NEM. Thiamin transport in vivo exhibits Michaelis-Menten kinetics with K(M)=15 nM and V(max)=46 U mg(-1). Treatment of intact E. coli KG33 with saturating NEM exhibited apparent noncompetitive inhibition, decreasing V(max) by approximately 50% without effecting K(M) or the apparent first-order rate constant (k(obsd)). Apparent noncompetitive inhibition is consistent with an irreversible covalent modification of a cysteine(s) that is critical for the transport process. A primary amino acid analysis of the subunits of the thiamin permease combined with our kinetic analysis suggests that inhibition of thiamin transport by NEM is different from other ABC transporters and occurs at the level of protein-protein interactions between the membrane-bound carrier protein and the ATPase subunit.

Overexpression, purification, and characterization of the periplasmic space thiamin-binding protein of the thiamin traffic ATPase in Escherichia coli

Thiamin (Vitamin B(1)) transport in Escherichia coli occurs by the superfamily of traffic ATPases in which the initial receptor is the periplasmic binding protein. We have cloned the periplasmic thiamin-binding protein (TBP) of the E. coli periplasmic thiamin transport system and purified the overexpressed protein to apparent homogeneity. A subsequent biochemical characterization demonstrates that TBP is a 34.205kDa monomer. TBP also contains one tightly bound thiamin species [thiamin, thiamin monophosphate (TMP), or thiamin diphosphate (TDP)] per monomer (K(D)=0.8 microM) when isolated under conditions that would remove any loosely bound ligands. We also demonstrate that thiamin is readily exchangeable in the presence of exogenous thiamin with a k(off)=0.12s(-1). The biochemical characteristics of the overexpressed, plasmid-derived TBP are indistinguishable from those determined for endogenous TBP purified from E. coli. The overexpression and purification of TBP that we present here allows the rapid isolation of large amounts of pure protein that are required for further mechanistic and structural studies and demonstrates a vast improvement over previously reported purifications.

A Brassica cDNA clone encoding a bifunctional hydroxymethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase involved in thiamin biosynthesis

We report the characterization of a Brassica napus cDNA clone (pBTHI) encoding a protein (BTHI) with two enzymatic activities in the thiamin biosynthetic pathway, thiamin-phosphate pyrophosphorylase (TMP-PPase) and 2-methyl-4-amino-5-hydroxymethylpyrimidine-monophosphate kinase (HMP-P kinase). The cDNA clone was isolated by a novel functional complementation strategy employing an Escherichia coli mutant deficient in the TMP-PPase activity. A biochemical assay showed the clone to confer recovery of TMP-PPase activity in the E. coli mutant strain. The cDNA clone is 1746 bp long and contains an open reading frame encoding a peptide of 524 amino acids. The C-terminal part of BTH1 showed 53% and 59% sequence similarity to the N-terminal TMP-PPase region of the bifunctional yeast proteins Saccharomyces THI6 and Schizosaccharomyces pombe THI4, respectively. The N-terminal part of BTH1 showed 58% sequence similarity to HMP-P kinase of Salmonella typhimurium. The cDNA clone functionally complemented the S. typhimurium and E. coli thiD mutants deficient in the HMP-P kinase activity. These results show that the clone encodes a bifunctional protein with TMP-PPase at the C-terminus and HMP-P kinase at the N-terminus. This is in contrast to the yeast bifunctional proteins that encode TMP-PPase at the N-terminus and 4-methyl-5-(2-hydroxyethyl)thiazole kinase at the C-terminus. Expression of the BTH1 gene is negatively regulated by thiamin, as in the cases for the thiamin biosynthetic genes of microorganisms. This is the first report of a plant thiamin biosynthetic gene on which a specific biochemical activity is assigned. The Brassica BTH1 gene may correspond to the Arabidopsis TH-1 gene.

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.

Copurification of hydroxyethylthiazole kinase and thiamine-phosphate pyrophosphorylase of Saccharomyces cerevisiae: characterization of hydroxyethylthiazole kinase as a bifunctional enzyme in the thiamine biosynthetic pathway

Mutants of Saccharomyces cerevisiae resistant to 2-amino-4-methyl-5-beta-hydroxyethylthiazole, an antimetabolite of 4-methyl-5-beta-hydroxyethylthiazole (hydroxyethylthiazole), which are deficient in the activities of both hydroxyethylthiazole kinase and thiamine-phosphate pyrophosphorylase, involved in the pathway of de novo synthesis of thiamine in S. cerevisiae, have been isolated. Genetic analysis revealed that the mutation occurs at a single gene in the nucleus. The two enzyme activities were copurified to apparent homogeneity, and the molecular masses of the purified proteins were found to be approximately 470 and 60 kDa, as determined by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively. Hydroxyethylthiazole kinase was specific for ATP and Mg2+, although to a lesser extent a combination with other nucleoside triphosphates or divalent cations could replace them. p-Chloromercuribenzoate was a potent inhibitor of the enzyme, and the inhibition was prevented by the addition of 2-mercaptoethanol. These findings indicate that yeast hydroxyethylthiazole kinase is a bifunctional enzyme with thiamine-phosphate pyrophosphorylase activity, which is an octamer of identical 60-kDa subunits.

Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12

Escherichia coli K-12 synthesizes thiamine pyrophosphate (vitamin B1) de novo. Two precursors [4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate and 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate] are coupled to form thiamine monophosphate, which is then phosphorylated to make thiamine pyrophosphate. Previous studies have identified two classes of thi mutations, clustered at 90 min on the genetic map, which result in requirements for the thiazole or the hydroxymethylpryimidine. We report here our initial molecular genetic analysis of the thi cluster. We cloned the thi cluster genes and examined their organization, structure, and function by a combination of phenotypic testing, complementation analysis, polypeptide expression, and DNA sequencing. We found five tightly linked genes, designated thiCEFGH. The thiC gene product is required for the synthesis of the hydroxymethylpyrimidine. The thiE, thiF, thiG, and thiH gene products are required for synthesis of the thiazole. These mutants did not respond to 1-deoxy-D-threo-2-pentulose, indicating that they are blocked in the conversion of this precursor compound to the thiazole itself.

The thiM locus and its relation to phosphorylation of hydroxyethylthiazole in Escherichia coli

A mutant of Escherichia coli lacking hydroxyethylthiazole kinase (EC 2.7.1.50) was produced by a further mutation of a temperature-sensitive, auxotrophic mutant for hydroxyethylthiazole. The parent cells possessed two distinct enzymes capable of phosphorylating hydroxyethylthiazole: one was hydroxyethylthiazole kinase, and the other was a phosphotransferase species that required p-nitrophenylphosphate as a phosphoryl donor. Osmotic shock fluid prepared from the mutant cells phosphorylated hydroxyethylthiazole to an extent comparable to that observed with shock fluid from the parent cells, whereas extracts from shocked cells were unable to catalyze the kinase reaction. Shock fluid from a mutant of the other type obtained as a reduced phosphatase activity against p-nitrophenylphosphate did not show any appreciable activity for the phosphotransferase reaction, while extracts from shocked cells showed full kinase activity. The former mutant had lost its ability to grow on hydroxyethylthiazole at high temperature, but the latter mutant still responded to it. It thus appears that the kinase is an enzyme which might play a role in the biosynthesis of thiamine PPi in situ. By conjugation and P1 transduction, a gene governing hydroxyethylthiazole kinase activity, for which we propose the designation thiM, was mapped on the chromosome close to thiD, a gene specifying phosphomethylpyrimidine kinase activity.

Purification and properties of hydroxymethylpyrimidine kinase from Escherichia coli

Hydroxymethylpyrimidine kinase, which catalyzes the conversion of 2-methyl-4-amino-5-hydroxymethylpyrimidine (hydroxymethylpyrimidine) to its monophosphate, is purified about 3300-fold to apparent homogeneity from the cell-free extracts of E. coli K-12 through four successive steps of column chromatographies. The purified enzyme gave a single protein band on polyacrylamide gel electrophoresis and its molecular weight is estimated to be 43 000-44 000. The enzyme phosphorylated each of the pyridoxine substrates, pyridoxine, pyridoxal and pyridoxamine as well as hydroxymethylpyrimidine, and the reaction gave rise to a corresponding 5'-phosphate compound. The Km values of the purified enzyme for hydroxymethylpyrimidine and for pyridoxine are 1.1.10(-4) and 6.6.10(-5) M, respectively. Pyridoxine inhibits competitively the phosphorylation of hydroxymethylpyrimidine with a Ki value of 2.7.10(-6) M and hydroxymethylpyrimidine shows the same for that of pyridoxine with a Ki value of 9.0.10(-5) M. A similarity in enzymic properties between the hydroxymethylpyrimidine kinase and an enzyme which has been characterized as pyridoxal kinase leads to the assumption that both hydroxymethylpyrimidine and pyridoxine might be phosphorylated by the same enzyme species.

A th-1 Mutant of Arabidopsis thaliana Is Defective for a Thiamin-Phosphate-Synthesizing Enzyme: Thiamin Phosphate Pyrophosphorylase

We have examined the activity of the thiamin phosphate pyrophosphorylase in Arabidopsis thaliana wild type and in a mutant (th-1) which requires exogenous thiamin for growth. Mutant and wild-type plants grown in 1 x 10(-7) molar thiamin were used for the examination of the production of thiamin and thiamin monophosphate (TMP) using 4-methyl-5-hydroxyethylthiazole phosphate and 2-methyl-4-amino-5-hydroxymethylpyrimidine pyrophosphate as substrates. While the wild-type strain formed both thiamin and TMP, the th-1 mutant did not. When TMP was added to the extracts, the th-1 mutant, as well as wild type, produced thiamin. Accordingly, it was concluded that the th-1 mutant was defective in the activity of TMP pyrophosphorylase. Some of the characteristics of the enzyme from the wild-type plant were examined. The optimum temperature for the reaction is 45 degrees C, and the K(m) values for the substrates are 2.7 x 10(-6) molar for 4-methyl-5-hydroxyethylthiazole phosphate and 1.8 x 10(-6) molar for 2-methyl-4-amino-5-hydroxymethylpyrimidine pyrophosphate.

Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes

Using physical and genetic data, we have demonstrated that Rhizobium meliloti SU47 has a symbiotic megaplasmid, pRmeSU47b, in addition to the previously described nod-nif megaplasmid pRmeSU47a. This plasmid includes four loci involved in exopolysaccharide (exo) synthesis as well as two loci involved in thiamine biosynthesis. Mutations at the exo loci have previously been shown to result in the formation of nodules which lack infection threads (Inf-) and fail to fix nitrogen (Fix-). Thus, both megaplasmids contain genes involved in the formation of nitrogen-fixing root nodules. Mutations at two other exo loci were not located on either megaplasmid. To mobilize the megaplasmids, the oriT of plasmid RK2 was inserted into them. On alfalfa, Agrobacterium tumefaciens strains containing pRmeSU47a induced marked root hair curling with no infection threads and Fix- nodules, as reported by others. This plant phenotype was not observed to change with A. tumefaciens strains containing both pRmeSU47a and pRmeSU47b megaplasmids, and strains containing pRmeSU47b alone failed to curl root hairs or form nodules.

A mutation in Escherichia coli K-12 results in a requirement for thiamine and a decrease in L-serine deaminase activity

Mutants of Escherichia coli K-12 deficient in L-serine deaminase (L-SD) activity have been isolated. These strains required thiamine and grew normally when it was provided. The decrease in L-SD activity caused no obvious metabolic deficiency. A study of revertants and transductants showed that a single mutation was responsible for the thiamine requirement and for the decrease in L-SD activity.

thiK and thiL loci of Escherichia coli

Mutants of Escherichia coli K-12 auxotrophic for thiamine phosphates were produced in stepwise fashion from the polyauxotrophic F- strain JC1552, via intermediate production of thiamine auxotrophs that had lost the enzymatic activity of either phosphomethylpyrimidine kinase or thiamine phosphate pyrophosphorylase. They include two types: one responds to thiamine monophosphate or thiamine pyrophosphate, and the other responds to thiamine pyrophosphate only; the former lacks thiamine kinase activity, and the latter lacks thiamine monophosphate kinase activity, in addition to the enzymatic defects caused by the first mutations. We found two genes, for which we propose the designations thiK and thiL, which govern the activities of thiamine kinase and thiamine monophosphate kinase, respectively. By conjugation and P1 transduction, the thiK locus was mapped at about 25 min, between pyrC and purB and close to fabD. The relative order of thiK with respect to nearby genes was tentatively established as pyrC-ptsG-fabD-thiK-purB. In the case of thiL, the locus was situated at about 9 min, between tsx and acrA and probably 0.2 min clockwise from the former.

Properties of the thiamine transport system in Escherichia coli

Thiamine transport was studied with a mutant (KG1976) of Escherichia coli K-12 deficient in thiamine kinase (EC 2.7.1.89), which catalyzes the formation of thiamine monophosphate from thiamine. Mutant cells accumulated thiamine 390-fold as the free form against a concentration gradient in the absence of added carbon sources at the steady state. Thiamine taken up from the medium, or thiamine preloaded in the absence of glucose, was expelled into the medium when glucose, d-lactate, or succinate was added, whereas exit in the absence of glucose was very slow. The rate of thiamine entry was therefore determined in the absence of glucose, and that of thiamine exit was followed by the addition of glucose to thiamine-preloaded cells. The activities of thiamine entry and exit were optimal at 42 and 37 degrees C, respectively. Hyperbolic saturation kinetics were obtained for the entry rate with a K(m) value of 5.9 nM. The exit rate showed a sigmoidal dependence on cellular thiamine concentrations, and a half-maximal velocity was observed at 31 muM. The rates of both entry and exit were lowered by electron transport inhibitors and uncouplers, suggesting that the energy coupled to both processes was provided through substrate oxidation. Thiamine exit from K(+)-depleted cells was enhanced by K(+) alone and by Na(+) to a much lesser extent, and K(+) and glucose were found to be synergistic for thiamine exit. These cations had no effect on the entry of thiamine into KG1676 cells in the absence of glucose. These properties of the entry and exit of thiamine in KG1676 are discussed from the standpoint of the possible involvement of different membrane components or different sites of identical thiamine carrier protein.

Pathway of thiamine pyrophosphate synthesis in Micrococcus denitrificans

The pathway of thiamine pyrophosphate (TPP) biosynthesis, which is formed either from exogeneously added thiamine or from the pyrimidine and thiazole moieties of thiamine, in Micrococcus denitrificans was investigated. The following indirect evidence shows that thiamine pyrophosphokinase (EC 2.7.6.2) catalyzes the synthesis of TPP from thiamine: (i) [35S]thiamine incubated with cells of this microorganism was detected in the form of [35S]thiamine; (ii) thiamine gave a much faster rate of TPP synthesis than thiamine monophosphate (TMP) when determined with the extracts; and (iii) a partially purified preparation of the extracts can use thiamine, but not TMP, as the substrate. The activities of the four enzymes involved in TMP synthesis from pyrimidine and thiazole moieties of thiamine were detected in the extracts of M. denitrificans. The extracts contained a high activity of the phosphatase, probably specific for TMP. After M. denitrificans cells were grown on a minimal medium containing 3 mM adenosine, which causes derepression of de novo thiamine biosynthesis in Escherichia coli, the activities of the four enzymes involved with TMP synthesis, the TMP phosphatase, and the thiamine pyrophosphokinase were enhanced two- to threefold. These results indicate that TPP is synthesized directly from thiamine without forming TMP as an intermediate and that de novo synthesis of TPP from the pyrimidine and thiazole moieties involves the formation of TMP, followed by hydrolysis to thiamine, which is then converted to TPP directly. Thus, the pathway of TPP synthesis from TMP synthesized de novo in M. denitrificans is different from that found in E. coli, in which TMP synthesized de novo is converted directly to TPP without producing thiamine.

Transductional mapping of gene trmA responsible for the production of 5-methyluridine in transfer ribonucleic acid of Escherichia coli

The gene trmA, responsible for the production of 5-methyluridine (ribothymidine) in transfer ribonucleic acid, has been located at 79 min on the chromosomal map of Escherichia coli K-12. In five-factor crosses the gene order was shown to be argH-trmA-rif-thiA-metA. The co-transduction frequency between argH and trmA was 65%. Furthermore, the trmA5 mutation was shown to be recessive, in agreement with the notion that the trmA gene is the structural gene for the transfer tibonucleic acid (5-methyluridine) methyltransferase.

Hydroxyethylthiazole uptake in Escherichia coli: general properties and relationship between uptake and thiamine biosynthesis

Uptake of (35)S-hydroxyethylthiazole (4-methyl-5-hydroxyethylthiazole) by Escherichia coli intact cells was studied. Hydroxyethylthiazole was taken up in the presence and absence of glucose at the same rate. The uptake was almost proportional to a hydroxyethylthiazole concentration gradient up to 0.1 mM with no tendency of saturation, and reached a steady state within 2 min. When the cells were treated with 1 mM N-ethylmaleimide, about 50% inhibition of hydroxyethylthiazole uptake was observed. Hydroxyethylthiazole uptake was stimulated by the addition of hydroxymethylpyrimidine (2-methyl-4-amino-5-hydroxymethylpyrimidine), and this effect was further enhanced in the presence of glucose. For full activation of hydroxyethylthiazole uptake, 1 muM hydroxymethylpyrimidine was necessary in the presence of glucose. The rate of hydroxyethylthiazole uptake was almost linear up to 60 min in the presence of hydroxymethylpyrimidine and glucose. Hydroxymethylpyrimidine monophosphate and its pyrophosphate could not stimulate the uptake. Thiamine and 2-amino-hydroxyethylthiazole were inhibitory on hydroxyethylthiazole uptake in the presence of hydroxymethylpyrimidine and glucose. N-ethylmaleimide and 2, 4-dinitrophenol were also inhibitory. No stimulatory effect of hydroxymethylpyrimidine on hydroxyethylthiazole uptake was observed in mutant cells lacking either thiaminephosphate pyrophosphorylase or hydroxymethylpyrimidine monophosphate kinase. The possibility of direct participation of thiamine-synthesizing enzymes in hydroxyethylthiazole uptake was discussed.