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Journal of Bacteriology, December 2008, p. 7939-7946, Vol. 190, No. 24
0021-9193/08/$08.00+0     doi:10.1128/JB.01055-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

A Unique Combination of Genetic Systems for the Synthesis of Trehalose in Rubrobacter xylanophilus: Properties of a Rare Actinobacterial TreT ^,

Ana Nobre,¹ Susana Alarico,¹ Chantal Fernandes,¹ Nuno Empadinhas,^1,2 and Milton S. da Costa^1,2*

Centro de Neurociências e Biologia Celular, Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal,¹ Departamento de Bioquímica, Universidade de Coimbra, 3001-401 Coimbra, Portugal²

Received 29 July 2008/ Accepted 25 September 2008

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Trehalose is the primary organic solute in Rubrobacter xylanophilus under all conditions tested, including those for optimal growth. We detected genes of four different pathways for trehalose synthesis in the genome of this organism, namely, the trehalose-6-phosphate synthase (Tps)/trehalose-6-phosphate phosphatase (Tpp), TreS, TreY/TreZ, and TreT pathways. Moreover, R. xylanophilus is the only known member of the phylum Actinobacteria to harbor TreT. The Tps sequence is typically bacterial, but the Tpp sequence is closely related to eukaryotic counterparts. Both the Tps/Tpp and the TreT pathways were active in vivo, while the TreS and the TreY/TreZ pathways were not active under the growth conditions tested and appear not to contribute to the levels of trehalose observed. The genes from the active pathways were functionally expressed in Escherichia coli, and Tps was found to be highly specific for GDP-glucose, a rare feature among these enzymes. The trehalose-6-phosphate formed was specifically dephosphorylated to trehalose by Tpp. The recombinant TreT synthesized trehalose from different nucleoside diphosphate-glucose donors and glucose, but the activity in R. xylanophilus cell extracts was specific for ADP-glucose. The TreT could also catalyze trehalose hydrolysis in the presence of ADP, but with a very high K_m. Here, we functionally characterize two systems for the synthesis of trehalose in R. xylanophilus, a representative of an ancient lineage of the actinobacteria, and discuss a possible scenario for the exceptional occurrence of treT in this extremophilic bacterium.

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The disaccharide trehalose serves several roles in archaea, bacteria, yeast, fungi, plants, and invertebrates. However, trehalose is best known for its role as a universal protector molecule, protecting cells and biomolecules from stress imposed by low water activity, heat, oxidation, desiccation, and freezing (9). Five different pathways for the synthesis of trehalose have been examined (2, 27), the most common of which involves a trehalose-6-phosphate synthase (Tps) that converts nucleoside diphosphate (NDP)-glucose and glucose-6-phosphate (Glc6P) into trehalose-6-phosphate (T6P) that is then dephosphorylated to trehalose by a trehalose-6-phosphate phosphatase (Tpp) (34). Other pathways for trehalose biosynthesis involve trehalose synthase (TreS) and the maltooligosyltrehalose synthase/hydrolase (TreY/TreZ) system, which catalyze the conversion of maltose and maltooligosaccharides into trehalose, respectively (24). Additionally, the TreS from Mycobacterium smegmatis can also convert glycogen into trehalose via maltose (26). A trehalose phosphorylase (TreP) can also catalyze trehalose synthesis in the presence of Glc1P and glucose in fungi and a few bacteria (2). A less common and recently discovered pathway involves a trehalose glycosyltransferring synthase (TreT) that converts NDP-glucose and glucose into trehalose. This enzyme has been examined only in the hyperthermophilic archaea Thermococcus litoralis, Pyrococcus horikoshii, and Thermoproteus tenax (17, 29, 33).

Many organisms have one or two, or less frequently three, pathways for trehalose synthesis (7, 38). Mycobacteria and corynebacteria, for example, can accumulate trehalose or incorporate it into mycolic acids of the cell wall and generally possess three pathways for the synthesis of trehalose (38). In many organisms osmoregulated trehalose synthesis appears to involve Tps and Tpp; however, the accumulation of trehalose during osmotic adjustment in Corynebacterium glutamicum, which also possess TreS, is linked to the TreY/TreZ pathway (38). Propionibacterium freudenreichii, on the other hand, depends on the Tps/Tpp pathway for the synthesis of trehalose in response to osmotic, oxidative, and acid stresses, while TreS is involved in trehalose degradation (4).

Rubrobacter xylanophilus is a thermophilic, halotolerant, and extremely radiation- and desiccation-resistant bacterium that constitutively accumulates trehalose as the major organic solute under optimal growth conditions and under salt and thermal stresses (10). In this work, we examined the synthesis of trehalose by Tps/Tpp and TreT, two active pathways for the synthesis of this disaccharide in R. xylanophilus cell extracts, and characterized the properties of the corresponding recombinant enzymes.

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Strains, culture conditions, and DNA isolation. Rubrobacter xylanophilus PRD-1^T (DSM 9941) was our laboratory strain. Cells were grown in Thermus medium without or with 2.5% NaCl at 60 or 67°C in a medium containing 1.0 g/liter tryptone and 1.0 g/liter yeast extract (10). The cultures were also grown in a medium containing 2.0 g/liter maltose as a single carbon source, 1 g/liter NH₄Cl, and 0.25 g/liter yeast extract. Chromosomal DNA was isolated as previously described (32). All chemicals were obtained from Sigma.

Enzyme assays for detection of trehalose synthesis in cell extracts. R. xylanophilus cells were recovered by centrifugation; extracts were obtained using a French pressure cell and dialyzed (20 mM Tris-HCl, pH 7.5). To provide evidence of the activities of the TreP, Tps/Tpp, TreT, TreS, and TreY/TreZ pathways in the cell extracts, the assays were performed as previously described, with slight modifications (4, 7, 29, 37). The mixtures contained 15 µg of protein of R. xylanophilus extract (1 µg/µl) and the appropriate substrates in a final volume of 50 µl. The reactions were performed at 60°C for 30 min in 25 mM bis-Tris propane buffer at pH 7.0 with 4 mM MgCl₂ and then stopped on ice. Reaction products were visualized by thin-layer chromatography (TLC) on Silica Gel 60 plates (Merck) with a solvent system composed of chloroform, methanol, acetic acid, and water (30:50:8:4, vol/vol) (11).

TreP activity was examined with - or β-Glc1P and glucose added to the cell extracts, and the reverse reaction was examined by the addition of trehalose and inorganic phosphate. For determination of the activity of Tps, the substrates were ADP-, GDP-, UDP-, or TDP-glucose and Glc6P. The T6P formed was dephosphorylated with 2 µg of the recombinant Tpp from Thermus thermophilus RQ-1 for trehalose detection on TLC (34). Tpp activity was examined after incubation of extracts with T6P, the TreT activity was examined by the addition of NDP-glucose donors and glucose, and the TreS activity was examined with maltose or trehalose. For the examination of the TreY/TreZ pathway, the substrates maltotriose, maltoheptaose, starch, glycogen, and amylopectin were added. Sugars and sugar derivatives were added at a concentration of 10 mM and polysaccharides at 1% (wt/vol).

Detection of genes for trehalose synthesis in the R. xylanophilus genome and sequence analyses. BLAST searches were performed with the Tps (EC 2.4.1.15/EC 2.4.1.36), Tpp (EC 3.1.3.12), trehalose (maltose-converting) synthase (TreS) (EC 5.4.99.16), maltooligosyltrehalose synthase (TreY) (EC 5.4.99.15), maltooligosyltrehalose trehalohydrolase (TreZ) (EC 3.2.1.141), trehalose glycosyltransferring synthase (TreT), and trehalose phosphorylase (TreP) (EC 2.4.1.64/EC 2.4.1.231) sequences.

We analyzed the sequences of seven genes, including treT, for the levels of AGA/AGG (AGR) codons for arginine (Arg) (http://www.sysbio.muohio.edu/CodonO), which are used frequently in hyperthermophiles but rarely in mesophiles. We also determined the G+C ratio in each of these genes and compared it to that in the overall genome sequences to deduce the origins of these genes in the genome by possible lateral gene transfer events (8, 20, 21). Genes tps, tpp, and treT were selected because they represent the two active pathways for the synthesis of trehalose in R. xylanophilus growing under the conditions described. We also selected gene glnA, encoding type I glutamine synthetase (EC 6.3.1.2, Rxyl_1125), because it is a housekeeping gene that has been proposed to be a good molecular clock (18), and the conserved ubiquitous gene fusA for elongation factor EF-G (EC 3.6.5.3, Rxyl_2158), which is an informational gene thus less likely to be laterally transferred (14, 16). We also selected the ino1 gene for inositol-3-phosphate synthase (EC 5.5.1.4, Rxyl_1213) and the dippS gene (GenBank accession number EF523341, Rxyl_1212), both of which are involved in the synthesis of di-myo-inositol-phosphate (DIP), a compatible solute detected so far in hyperthermophilic prokaryotes and in R. xylanophilus and thus likely to have been acquired from a hyperthermophile (10, 32). For comparison, and because the G+C compositions of genomes might influence the synonymous codon usage (22), we analyzed the above-mentioned genes in organisms that possess treT and have different G+C genomic compositions (http://archaea.ucsc.edu/), different optimal growth temperatures, and different phylogenetic positions. We selected three hyperthermophiles: the euryarchaeon Pyrococcus horikoshii (41.9% G+C in the genome) because it also has the genes for DIP synthesis; the crenarchaeon Pyrobaculum calidifontis (57.2% G+C), which possesses tps/tpp; and the bacterium Thermotoga maritima (46.2% G+C), which contains the genes for DIP synthesis. We also analyzed the genes from mesophiles: the deltaproteobacterium Myxococcus xanthus (68.9% G+C), which, in addition to treT, also contains the tps/tpp genes; the methanogen Methanoculleus marisnigri (62.1% G+C), which contains three copies of treT and the tps/tpp pair; and the synthrophic deltaproteobacterium Syntrophus aciditrophicus, which contains the tps/tpp pair but has a moderate G+C content in the genome (51.5%).

Gene amplification and cloning. For sequence confirmation, and based on the draft genome sequence (www.jgi.doe.gov), several primers were designed to hybridize to the sequences immediately upstream and downstream from the putative tps, tpp, treT, ino1, fusA, and glnA genes. PCRs were carried out with the GC-RICH PCR system (Invitrogen). Products were cloned into pGEM-T Easy vector (Promega) with Escherichia coli DH5 as the host and sequenced (AGOWA GmbH, Berlin, Germany). For heterologous gene expression, the tps, tpp, and treT genes were amplified with the forward primers TPSNco, TPPNcoF, and TreTNde and reverse primers TPSXba, RubTPP2, and TreTBam, respectively (see Table S1 in the supplemental material). Genes tps and tpp were cloned into the expression vector pET30b, leading to production of His-tagged recombinant proteins. However, treT was cloned into the expression vector pET11a, yielding a protein without a His tag. E. coli BL21(DE3) was used as the host (Novagen).

Gene expression and purification of recombinant enzymes. Cells carrying pET30b-tps, pET30b-tpp, or pET11a-treT were grown to an optical density at 610 nm of 1.0 at 37°C in LB medium (2 liters) containing kanamycin (30 µg/ml) or ampicillin (100 µg/ml) for selection, and IPTG (isopropyl-β-D-thiogalactopyranoside) (1 mM) was added to induce gene expression. Cells carrying (His)₆-Tps and (His)₆-Tpp were allowed to grow for 6 h, harvested, and suspended in 20 mM sodium phosphate buffer with 0.5 M NaCl and 10 mM MgCl₂, DNase (4 µg/ml), and a protease inhibitor cocktail (Roche). Cells carrying the recombinant TreT were allowed to grow for a further 10 h at 30°C, suspended in 20 mM Tris-HCl at pH 7.6, and disrupted in a French pressure cell, and debris was removed by centrifugation. The extracts were heated for 10 min at 60°C, cooled, and centrifuged to remove host precipitated proteins. Supernatants with Tps and Tpp were supplemented with 20 mM imidazole and loaded onto a nickel HisTrap column equilibrated with 20 mM sodium phosphate buffer with 0.5 M NaCl and 20 mM imidazole at pH 7.4. His-tagged proteins were eluted at 5 ml/min with the same buffer containing 500 mM imidazole in a three-step gradient (30, 50, and 80%). His tags were removed by enterokinase digestion according to the supplier's instructions (Novagen).

TreT was partially purified with two sequential Q-Sepharose fast-flow columns (Hi-Load 16/10) equilibrated with 20 mM Tris-HCl, pH 7.6. Elution was carried out with linear NaCl gradients (0.0 to 1.0 M). Active fractions were dialyzed, concentrated, and loaded onto a Superdex 200 column equilibrated with 50 mM Tris-HCl and 200 mM NaCl, pH 7.6.

Fractions with active recombinant Tps, Tpp, or TreT were pooled, concentrated and dialyzed, and the purity and the molecular masses were estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (not shown) and by gel filtration chromatography, as previously described (11). The protein content of all samples was determined as previously described (34).

Enzyme assays during purification of recombinant enzymes. The activities of Tps, Tpp, and TreT were examined with the assays for detection of trehalose synthesis in cell extracts. Tps activity was detected with GDP-glucose and Glc6P followed by 20 min of incubation with 2 U of alkaline phosphatase (Roche) at 37°C to release trehalose, which was visualized by TLC. Tpp activity was examined with T6P, and TreT activity was determined with ADP-glucose and glucose as previously described (29, 34).

Tps characterization. The recombinant Tps activity was measured by the specific dephosphorylation of the T6P formed with the recombinant Tpp (2 µg) from T. thermophilus RQ-1 (34). Reaction mixtures (100 µl) containing 0.4 µg Tps and 10 mM of each substrate were stopped by the addition of 40 µl of 20% trichloroacetic acid, incubated on ice, centrifuged, and neutralized with 1 M NaOH, and the volume was adjusted to 200 µl with H₂O. A 50-µl aliquot was incubated with the T. thermophilus Tpp for 5 min at 70°C, the reaction was stopped on ice-ethanol, and the phosphate released was measured (1). The substrate specificity was examined with different sugar donors and acceptors (34), the temperature profile was determined between 30 and 90°C, the thermal stabilities at 60 and 70°C were assessed in 25 mM bis-Tris-propane buffer at pH 7.0 and residual activity determined at 40°C, the pH dependence was determined between pH 4.0 and 9.0 (11, 34), the effect of divalent cations was tested, and the V_max and K_m were determined with various substrate concentrations and calculated from the Michaelis-Menten equation (34).

Tpp characterization. The Tpp activity was measured by quantification of the phosphate released from T6P (1). Reaction mixtures (50 µl) contained 50 ng of pure recombinant Tpp and 10 mM T6P. Substrate specificity was determined using several phosphorylated compounds (34). Other parameters studied were those described above for Tps. The temperature profile was determined between 10 and 80°C. Thermal stability was evaluated in 25 mM Tris-HCl buffer (pH 7.5) containing 2 mM MgCl₂ and residual activity measured at 40°C. The pH dependence was determined between pH 5.0 and 10.5.

TreT characterization. The trehalose-forming activity of the recombinant TreT was examined by the quantification of NDP released from the condensation of NDP-glucose and glucose into trehalose. Reactions were initiated by the addition of TreT and stopped at different times by cooling on ice-ethanol, and the amount of NDP was determined (11). The substrate specificity was examined with different sugar donors and acceptors, the temperature profile was determined between 20 and 80°C, the thermal stability was determined as described above, the pH dependence was examined between pH 4.0 and 10.5, reactions in the presence of divalent cations or with EDTA (5 mM) were performed to examine cation dependence, and V_max and K_m were determined as previously described (29). The reverse activity of TreT (trehalose hydrolysis in the presence of ADP) was measured with the glucose oxidase assay kit (Sigma). The substrates ,-, ,β-, and β,β-trehalose alone or in the presence of ADP or ATP were also tested. The K_m and V_max values were determined with various concentrations of trehalose and ADP.

Nucleotide sequence accession numbers. A 4,020-bp sequence containing the treT, tps, and tpp genes from R. xylanophilus and additional 1,368-, 2,148-, and 1,332-bp sequences for the inositol-3-phosphate synthase (ino1), the elongation factor G (fusA), and the type I glutamine synthetase (glnA) genes from the same organism have been deposited in GenBank under accession numbers EU881704, EU881705, EU881706, and EU881707, respectively.

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Detection of trehalose synthesis in cell extracts. From an array of experiments on cell extracts using several glucose donors and acceptors, the combination of GDP-glucose and Glc6P resulted in the synthesis of T6P via the Tps/Tpp pathway, which was partially dephosphorylated by a native Tpp activity (Fig. 1). Full dephosphorylation of the T6P formed was achieved only after the addition of a recombinant Tpp from T. thermophilus RQ-1 (not shown). The synthesis of trehalose also occurred with ADP-glucose and glucose via the TreT pathway (Fig. 1). We did not detect either TreS activity from maltose or the reverse reaction (not shown). We were also unable to detect trehalose synthesis from maltooligosaccharides or from -1,4-linked polysaccharides via the TreY/TreZ pathway or trehalose phosphorylase (TreP) activity from Glc1P and glucose (Fig. 1).

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FIG. 1. TLC analysis of reaction products obtained with R. xylanophilus cell extracts. Lane 1, TreP activity with Glc1P and glucose; lanes 2 to 5, Tps activity with Glc6P and ADP-glucose, GDP-glucose, UDP-glucose, or TDP-glucose, respectively (reactions dephosphorylated with the Tpp from T. thermophilus RQ-1); lanes 6 and 7, Tpp activity with T6P and Glc6P; lanes 8 to 11, TreT activity with glucose and ADP-glucose, GDP-glucose, UDP-glucose, or TDP-glucose, respectively; lane 12, cell extracts incubated with glucose; lane 13, TreS activity with maltose; lanes 14 to 18, TreY/TreZ activity with maltotriose, maltoheptaose, starch, glycogen, and amylopectin, respectively; lane 19, glucose (Glc) and trehalose (Trea) standards.

Identification of genes and genetic organization. BLAST searches led to the detection of genes of four putative pathways for the synthesis of trehalose in the R. xylanophilus genome, namely, the Tps/Tpp (Rxyl_2972/Rxyl_2971), TreT (Rxyl_2973), TreS (Rxyl_0315), and TreY/TreZ (Rxyl_0319/Rxyl_0318) pathways. Primer design for amplification of the region containing the treT, tps, and tpp genes was based on the draft genome sequence. However, our own sequences confirmed that the genome contains several errors in these genes (6 to 14% at the nucleotide level). A second putative treT gene (Rxyl_3082) encoding a protein with high amino acid identity (52%) to the product of the treT gene examined in this study (Rxyl_2973) was detected in the genome, but we could not amplify it, after several attempts, with multiple primers designed from the surrounding genes. Due to the errors detected in the draft genome sequence, we are not certain that this is an authentic gene. To corroborate this view, the draft genome sequence also contains two copies of a putative ino1 gene encoding inositol-3-phosphate synthase (Rxyl_0688 and Rxyl_1213) that share 100% identity (except in the nucleotides corresponding to the C-terminal 8 amino acids) but different genetic surroundings. In this case, we could amplify only one copy (Rxyl_1213) with primers based on the flanking genes and found that as much as 19% of the nucleotide sequence of this gene in the genome was incorrect.

The treT and tps genes are sequentially arranged, with an intergenic region of 32 nucleotides (Fig. 2). A unique promoter sequence was detected upstream from treT. The tpp gene is in the opposite direction and under the control of a different promoter, which appears to be located upstream of the putative adjacent peptidase (ORF1) (Fig. 2). The TreS and TreY/TreZ pathways appear to be part of an operon-like structure with a single promoter and containing genes (Rxyl_0314 to Rxyl_0319) possibly involved in the synthesis/degradation of glycogen/maltooligosaccharides (not shown). A typical gene for TreP was not detected in the genome.

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FIG. 2. Genomic organization of the R. xylanophilus tps, tpp, and treT genes. Arrows represent genes and their directions. The putative promoter elements (boxed) upstream of treT were detected with prokaryotic promoter prediction tools at http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php and at www.fruitfly.org/seq_tools/promoter.html. RBS, putative ribosome binding site; treT, trehalose glycosyltransferring synthase gene; tps, Tps gene; tpp, Tpp gene; ORF1, putative peptidase; aa, amino acids.

Protein and nucleotide sequence analyses. The tps gene has 1,452 bp coding for a polypeptide of 483 amino acids with a deduced molecular mass of 53.9 kDa, which was shown to be a dimer. The Tps sequence has a high level of amino acid identity (>40%) with many bacterial Tps proteins, the archaeal Tps from Methanothermobacter thermautotrophicus (43%), and several sequences from fungi (30 to 35% amino acid identity) (Fig. 3). The tpp gene has 795 bp and codes for a polypeptide of 264 amino acids with 29.4 kDa, which behaved as a monomer. The Tpp sequence had no close homologues, with its closest relatives being from the green nonsulfur bacterium Herpetosiphon aurantiacus (37%), the archaeon M. thermautotrophicus (37%), and several eukaryotic organisms, namely, insects of the genera Drosophila, Culex and Anopheles (36%) (Fig. 3). The Tpp proteins from the related actinobacteria of the genera Streptomyces and Mycobacterium share even lower overall amino acid identity (31 to 35%) with the enzyme from R. xylanophilus. The treT gene contains 1,251 bp coding for a 416-amino-acid polypeptide of 46.7 kDa that also behaved as a dimer. BLAST results indicate that TreT had a few archaeal homologues, mostly crenarchaeotes, but very few bacterial homologues. The phylogenetic tree shows that archaeal and bacterial TreT sequences do not form clearly distinct clusters (Fig. 3).

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FIG. 3. Unrooted phylogenetic trees based on available amino acid sequences of TreT, Tps, and Tpp homologues. The MEGA4 program was used for sequence alignments and to generate the phylogenetic trees (36). The bootstrap values and accession numbers for proteins are indicated. For R. xylanophilus sequences, GenBank accession numbers are indicated. Bar, 0.1 changes/site.

The levels of AGA and AGG (AGR) codons (preferred by hyperthermophiles and rare in mesophiles) in the R. xylanophilus genes tps, treT, glnA, fusA, and dippS are low (3.4 to 16%), although the frequency of the AGR codon in tpp is slightly higher (25%) (Fig. 4). On the other hand, the AGR codon level in the ino1 gene (56.7%) is much higher, approaching those in the hyperthermophilic homologues. Moreover, five of the seven R. xylanophilus genes analyzed in this work, have a high G+C content (65.8 to 70.4%), similar to the experimentally determined 67.0% G+C in the R. xylanophilus chromosome (5). However, the G+C content of the ino1 gene is only 61.1%, which, along with its atypical AGR codon content, suggests a foreign origin (Fig. 4). The G+C content in the dippS gene is also higher (73.2%) than the average R. xylanophilus genomic G+C content.

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FIG. 4. Analysis of G+C content and of Arg codons AGG and AGA (AGR) in the tps, tpp, treT, glnA, fusA, ino1 and dippS genes in organisms harboring treT genes. tps, Tps gene; tpp, Tpp gene; treT, trehalose glycosyltransferring synthase gene; ino1, inositol-3-phosphate synthase gene; glnA, glutamine synthetase (type I) gene; fusA, elongation factor G gene; dippS, di-inositol-phosphate-phosphate synthase gene. M. marisnigri has two copies of glnA and three copies of treT (>42% amino acid identity). The tps and tpp genes from P. calidifontis and from M. xanthus are fused. S. aciditrophicus has fused tps/tpp, isolated tps and tpp, and three copies of fusA. M. xanthus has three copies of fusA. When multiple copies of the same gene are present in a genome, the average G+C content and AGR ratios are represented, as well as the corresponding standard deviations. Codon usage was determined with the CodonO software at http://www.sysbio.muohio.edu/CodonO. Vertical black lines indicate the overall genomic G+C level in each of the organisms examined (http://archaea.ucsc.edu/).

Properties of Tps and Tpp. Tps showed high substrate specificity for the combination of GDP-glucose and Glc6P (Table 1). The enzyme was active at between 30 and 90°C, with maximum activity at around 60°C. The recombinant enzyme exhibited Michaelis-Menten kinetics and K_m values of 0.7 ± 0.1 mM for GDP-glucose and 2.9 ± 1.2 mM for Glc6P. The V_max for Tps was 22 ± 6 µmol/min·mg protein. Within the pH range examined, the activity of the enzyme at 60°C was maximal at pH 7.0. Tps was active without cations, but maximum activation was obtained with 2 mM of Mg²⁺. The specific activity of Tps without cations was 36% of maximal activity. The enzyme had half-lives of 1.7 ± 0.2 h at 60°C and 0.7 ± 0.1 h at 70°C (Table 1).

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TABLE 1. Biochemical properties of the recombinant enzymes Tps, Tpp, and TreT and kinetic parameters for the substrates involved in the synthesis of trehalose (see Fig. S2 to S5 in the supplemental material)

Among the phosphorylated compounds tested, the recombinant Tpp was specific for T6P. Tpp had maximal activity at 60°C, and no activity was detected at 80°C. The optimum pH for activity was around 7.5. The recombinant Tpp was dependent on divalent cations for activity, and 2 mM Mg²⁺ or Co²⁺ was required for maximal activity. Other cations tested, namely, Ni²⁺, Ca²⁺, and Fe³⁺, did not stimulate enzyme activity. Tpp exhibited typical Michaelis-Menten kinetics, a K_m value for T6P of 6.1 ± 1.5 mM, and a V_max of 225 ± 18 µmol/min·mg protein. The half-lives for thermal inactivation were 3.2 ± 0.9 h at 60°C and 1.0 ± 0.1 h at 70°C (Table 1).

Properties of TreT. Of the sugar donors examined, ADP-glucose (100.0%), GDP-glucose (48.2%), and UDP-glucose (32.7%) served as substrates for the recombinant TreT, but only glucose served as an acceptor (Table 1). However, the TreT activity in cell extracts appeared to be specific for ADP-glucose and glucose (Fig. 1). Maximum activity was reached at 60°C, but the enzyme was active at between 20 and 80°C. Within the pH range examined, the activity of the enzyme remained nearly constant between pH 8.0 and 10.0. TreT was not dependent on divalent cations, but the activity was slightly enhanced by 2 mM Fe³⁺, Mn²⁺, Ca²⁺, or Li⁺ and by 20 mM Mg²⁺, Ca²⁺, or Li⁺. Curiously, no activity was detected after the addition of 20 mM of Fe³⁺ and Mn²⁺. Other cations tested, namely, Zn²⁺ and Ni²⁺, gradually inhibited TreT activity at the concentrations tested (2 to 20 mM). The half-lives for inactivation at 60°C and at 70°C were 309 ± 89 and 4.1 ± 0.3 h, respectively. TreT exhibited Michaelis-Menten kinetics: the K_m values for ADP-glucose and glucose were 0.8 ± 0.1 and 1.3 ± 0.2 mM, respectively, and the V_max was 37 ± 3 µmol/min·mg protein. TreT could also catalyze the hydrolysis of trehalose, but 150 mM trehalose was required for a measurable reaction rate (5.0 ± 3.1 µmol/min·mg). The high K_m values for trehalose (82 ± 18 mM) and for ADP (6.8 ± 0.8 mM) indicate that the formation of trehalose was highly favored (Table 1).

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Prokaryotes have the highest diversity of pathways for trehalose biosynthesis, and all five known pathways can be found in the bacterial domain. While some of these organisms can have two or even three pathways for trehalose synthesis, most bacteria as well as plants and animals have only the Tps/Tpp pathway (2, 38, 39). The TreS pathway is found almost exclusively in bacteria, and the TreT pathway is present mainly in hyperthermophilic bacteria and archaea (7, 17, 29, 33). Occasionally, more than one copy of those genes exists in the same organism: Ralstonia solanacearum, for example, has two tps genes; Thermoanaerobacter tengcongensis has two treP genes; and Methanoculleus marisnigri has three copies of treT. The genes of four pathways for trehalose synthesis were detected in the genome of R. xylanophilus: the Tps/Tpp and the TreT pathways, which we have shown to be functional in cell extracts, as well as the TreS and the TreY/TreZ pathways, which were not active under the conditions tested. This pathway multiplicity is unique among the organisms examined, strongly suggesting an essential role for this disaccharide in R. xylanophilus (9, 39). The sequential organization of treT and tps with an opposing tpp gene is also unique. Since our studies indicate that both TreT and Tps are active, this apparent redundancy could reflect maximization of substrate availability to ensure trehalose production. It also suggests that the expression of tpp is independently regulated, and our data indicate that the T6P formed is not fully dephosphorylated in R. xylanophilus cell extracts, leading to the hypothesis of an alternative role for the phosphorylated compound. In fact, T6P has been found to play important signaling roles in the regulation of sugar metabolism in Saccharomyces cerevisiae, by inhibiting hexokinase, and in Arabidopsis thaliana, where it activates ADP-glucose pyrophosphorylase (27). T6P is also a precursor of complex structures found in actinobacteria, such as mycolic acids, although R. xylanophilus lacks these trehalose-containing structures (5, 35).

The organization of the TreS and TreY/TreZ genes in a different and unique operon-like structure containing other genes for glycogen metabolism and the lack of activity in cell extracts from cultures grown on tryptone and yeast extract led us to hypothesize that these genes may be expressed only when maltose or maltooligosaccharides are used as carbon sources, as is the case with the TreS from Corynebacterium glutamicum (38). However, we did not detect TreS activity when the organism was grown on maltose. It is also possible that these pathways may be activated by other environmental stimuli such as desiccation, which induces Tps/Tpp and TreS in Bradyrhizobium japonicum (6).

The Tps from Rubrobacter xylanophilus preferred GDP-glucose as a glycosyl donor, unlike the majority of Tps proteins characterized so far, which utilize all natural glucose diphosphate nucleosides as donors for T6P synthesis or are specific for UDP-glucose (9, 13, 34). Two classes of Tps proteins, reflecting their substrate preference, have been proposed, namely, the UDP-forming (EC 2.4.1.15) and the GDP-forming (EC 2.4.1.36) enzymes. The R. xylanophilus enzyme is of the second and rarer type. This Tps has maximum activity at 60°C, which slowly decreases to undetectable levels at around 90°C. While this is not common for the majority of enzymes, the glucosylglycerate synthase from Persephonella marina and the Tpp from Thermus thermophilus have similar profiles, as their activities gradually decrease at above the optimum temperature (11, 34). It is possible that at higher temperatures they acquire more stable conformational changes (like the alpha-glucosidase from Thermotoga maritima, for example) which allow lower but stable activity for longer periods of time at temperatures above the optimum (30).

The Tpp from R. xylanophilus has high sequence similarity to eukaryal orthologues, mostly from insects, followed by some actinobacterial sequences. Similarly, some cyclases from Mycobacterium tuberculosis and the citrate synthase from Geobacter sulfurreducens are more similar to eukaryotic than to bacterial cyclases, and it has been suggested that the bacteria acquired these genes from eukaryotes (3, 28). Although we did not trace the origin of the tpp gene in R. xylanophilus, the high sequence identity with the insect homologues suggests gene transfers between these two domains. The Tpp from R. xylanophilus is, like the majority of Tpp proteins, highly specific for T6P (9). In fact, the dephosphorylation of compounds other than T6P is extremely rare, and only the enzymes from the insect Phormia regina and from T. thermophilus have also been shown to use Glc6P at lower rates (12, 34).

The TreT from R. xylanophilus catalyzes a reaction similar to that of the homofunctional enzymes from Thermococcus litoralis and Pyrococcus horikoshii, including the hydrolysis of trehalose with ADP as a cosubstrate (resembling the former), but it does not have the trehalase activity of the latter (29, 33). Interestingly, the TreT from Thermoproteus tenax could catalyze only the formation and not the hydrolysis of trehalose (17). The recombinant TreT from R. xylanophilus used ADP-glucose as well as other NDP-glucose donors, like the euryarchaeal enzymes but not the crenarchaeal TreT, which preferred UDP-glucose. However, the TreT activity in R. xylanophilus extracts appeared to be specific for ADP-glucose. Likewise, the Tps activity in Propionibacterium freudenreichii extracts is specific for ADP-glucose, unlike the recombinant enzyme, which used other NDP-glucose donors in addition to ADP-glucose (4). This may be due to an interaction with an unknown regulatory protein present in cell extracts or to slight differences in folding between the native and recombinant proteins.

The presence of treT in the R. xylanophilus genome was surprising, since among all the actinobacterial genomes sequenced (>50), only that of this organism possesses a treT gene. With the exception of hyperthermophilic bacteria and a few deltaproteobacteria, treT is not found in most bacterial genomes. This gene is also present in a few euryarchaeal genomes but is frequent in those from hyperthermophilic crenarchaeotes (17, 29, 33). Such a scattered distribution suggests that treT has been involved in lateral gene transfer events and that R. xylanophilus may have acquired it from hyperthermophiles (8, 31). However, the R. xylanophilus treT AGR codon usage, the G+C composition, and the phylogenetic analysis failed to confirm this origin (21). For example, and corroborating previous studies, our sequence analysis also supports the acquisition of the R. xylanophilus ino1 gene from a hyperthermophile (8, 25). However, the key gene (dippS) for the synthesis of the "hyperthermophilic" solute DIP in R. xylanophilus lacks a hyperthermophilic-type AGR codon usage. Although the distribution of dippS and treT suggests a hyperthermophilic origin for both, we could not detect the lateral transfer because hints of such an event seem to have been erased by amelioration to the recipient's genome (8, 19, 20). On the other hand, the phylogenetic clustering of the R. xylanophilus TreT sequence with the TreT from Myxococcus xanthus and the apparent clustering with other deltaproteobacterial (syntroph) TreT sequences and with those from methanogens suggest an archaeal origin for the bacterial TreT proteins, possibly from methanogens that coexist with bacteria in some environments (15). This hypothetical methanogenic origin is further strengthened by the detection in the R. xylanophilus genome of the key gene for the synthesis of cyclic bisphosphoglycerate, an organic solute found only in methanogens (23). This gene is extremely rare, being found only in a few Thermococcales and methanogens and in R. xylanophilus, where it lacks the hyperthermophilic AGR-type codon usage (unpublished results). Altogether, these results seem to suggest a very ancient origin for treT. The ubiquity of intracellular trehalose and the unprecedented detection of four putative pathways for its synthesis in R. xylanophilus, a desiccation- and extremely gamma-radiation-resistant organism, encourage further research into the roles of this disaccharide in the metabolism and extreme phenotype of this ancient lineage of the actinobacteria.

 
This work was supported by Fundação para a Ciência e a Tecnologia (FCT), Portugal, and by FEDER, project POCI/BIA-MIC/56511/2004. A. Nobre, S. Alarico, and C. Fernandes acknowledge scholarships from FCT (SFRH/BD/28907/2006, SFRH/BD/14140/2003, and SFRH/BD/19599/2004).

 
* Corresponding author. Mailing address: Departamento de Bioquímica, Universidade de Coimbra, 3001-401 Coimbra, Portugal. Phone: 351-239-824024. Fax: 351-239-855789. E-mail: milton{at}ci.uc.pt

Published ahead of print on 3 October 2008.

Supplemental material for this article may be found at http://jb.asm.org/.

Top ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION REFERENCES

 

1
1. Ames, B. N. 1966. Assay of inorganic phosphate, total phosphate and phosphatases. Methods Enzymol. 8:115-118.[CrossRef]
2
2. Avonce, N., A. Mendoza-Vargas, E. Morett, and G. Iturriaga. 2006. Insights on the evolution of trehalose biosynthesis. BMC Evol. Biol. 6:109.[CrossRef][Medline]
3
3. Bond, D. R., T. Mester, C. L. Nesbø, A. V. Izquierdo-Lopez, F. L. Collart, and D. R. Lovley. 2005. Characterization of citrate synthase from Geobacter sulfurreducens and evidence for a family of citrate synthases similar to those of eukaryotes throughout the Geobacteraceae. Appl. Environ. Microbiol. 71:3858-3865.[Abstract/Free Full Text]
4
4. Cardoso, F. S., R. F. Castro, N. Borges, and H. Santos. 2007. Biochemical and genetic characterization of the pathways for trehalose metabolism in Propionibacterium freudenreichii, and their role in stress response. Microbiology 153:270-280.[Abstract/Free Full Text]
5
5. Carreto, L., E. Moore, M. F. Nobre, R. Wait, P. W. Riley, R. J. Sharp, and M. S. da Costa. 1996. Rubrobacter xylanophilus sp. nov., a new thermophilic species isolated from a thermally polluted effluent. Int. J. Syst. Bacteriol. 46:460-465.[Abstract/Free Full Text]
6
6. Cytryn, E. J., D. P. Sangurdekar, J. G. Streeter, W. L. Franck, W. S. Chang, G. Stacey, D. W. Emerich, T. Joshi, D. Xu, and M. J. Sadowsky. 2007. Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J. Bacteriol. 189:6751-6762.[Abstract/Free Full Text]
7
7. De Smet, K. A. L., A. Weston, I. N. Brown, D. B. Young, and B. D. Robertson. 2000. Three pathways for trehalose biosynthesis in mycobacteria. Microbiology 146:199-208.[Abstract/Free Full Text]
8
8. Eisen, J. A. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10:606-611.[CrossRef][Medline]
9
9. Elbein, A. D., Y. T. Pan, I. Pastuszak, and D. Carroll. 2003. New insight on trehalose: a multifunctional molecule. Glycobiology 13:17R-27R.[Abstract/Free Full Text]
10
10. Empadinhas, N., V. Mendes, C. Simões, M. S. Santos, A. Mingote, P. Lamosa, H. Santos, and M. S. da Costa. 2007. Organic solutes in Rubrobacter xylanophilus: the first example of di-myo-inositol-phosphate in a thermophile. Extremophiles 11:667-673.[Medline]
11
11. Fernandes, C., N. Empadinhas, and M. S. da Costa. 2007. Single-step pathway for synthesis of glucosylglycerate in Persephonella marina. J. Bacteriol. 189:4014-4019.[Abstract/Free Full Text]
12
12. Friedman, S., and S. Alexander. 1971. Multiple forms of trehalase in Phormia regina. Biochem. Biophys. Res. Commun. 42:818-823.[CrossRef][Medline]
13
13. Giaever, H. M., O. B. Styryold, I. A. Kassen, and R. Ström. 1988. Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J. Bacteriol. 170:2841-2849.[Abstract/Free Full Text]
14
14. Hashimoto, T., and M. Hasegawa. 1996. Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G. Adv. Biophys. 32:73-120.[CrossRef][Medline]
15
15. Jackson, B. E., V. K. Bhupathiraju, R. S. Tanner, C. R. Woese, and M. J. McInerney. 1999. Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms. Arch. Microbiol. 171:107-114.[CrossRef][Medline]
16
16. Jain, R., M. C. Rivera, and J. A. Lake. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:3801-3806.[Abstract/Free Full Text]
17
17. Kouril, T., M. Zaparty, J. Marrero, H. Brinkmann, and B. Siebers. 2008. A novel trehalose synthesizing pathway in the hyperthermophilic Crenarchaeon Thermoproteus tenax: the unidirectional TreT pathway. Arch. Microbiol. doi10.1007/s00203-008-0377-3.
18
18. Kumada, Y., D. R. Benson, D. Hillemann, T. J. Hosted, D. A. Rochefort, C. J. Thompson, W. Wohlleben, and Y. Tateno. 1993. Evolution of the glutamine synthetase gene, one of the oldest existing and functioning genes. Proc. Natl. Acad. Sci. USA 90:3009-3013.[Abstract/Free Full Text]
19
19. Lake, J. A., C. W. Herbold, M. C. Rivera, J. A. Servin, and R. G. Skophammer. 2007. Rooting the tree of life using nonubiquitous genes. Mol. Biol. Evol. 24:130-136.[Abstract/Free Full Text]
20
20. Lawrence, J. G., and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:383-397.[CrossRef][Medline]
21
21. Lobry, J. R., and A. Necçsulea. 2006. Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes. Gene 385:128-136.[CrossRef][Medline]
22
22. Lynn, D. J., G. A. C. Singer, and D. A. Hickey. 2002. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30:4272-4277.[Abstract/Free Full Text]
23
23. Matussek, K., P. Moritz, N. Brunner, C. Eckerskorn, and R. Hensel. 1998. Cloning, sequencing, and expression of the gene encoding cyclic 2,3-diphosphoglycerate synthetase, the key enzyme of cyclic 2,3-diphosphoglycerate metabolism in Methanothermus fervidus. J. Bacteriol. 180:5997-6004.[Abstract/Free Full Text]
24
24. Nakada, T., K. Maruta, K. Tsusaki, M. Kubota, H. Chaen, T. Sugimoto, M. Kurimoto, and Y. Tsujisaka. 1995. Purification and properties of a novel enzyme, maltooligosyl trehalose synthase, from Arthrobacter sp. Q36. Biosci. Biotechnol. Biochem. 59:2210-2214.
25
25. Nesbo, C. L., S. L'Haridon, K. O. Stetter, and W. F. Doolittle. 2001. Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria. Mol. Biol. Evol. 18:362-375.[Abstract/Free Full Text]
26
26. Pan, Y. T., J. D. Carroll, N. Asano, I. Pastuszak, V. K. Edavana, and A. D. Elbein. 2008. Trehalose synthase converts glycogen to trehalose. FEBS J. 275:3408-3420.[CrossRef][Medline]
27
27. Paul, M. J., L. F. Primavesi, D. Jhurreea, and Y. Zhang. 2008. Trehalose metabolism and signaling. Annu. Plant Biol. 59:417-441.[CrossRef]
28
28. Ponting, C. P., L. Aravind, J. Schultz, P. Bork, and E. V. Koonin. 1999. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289:729-745.[CrossRef][Medline]
29
29. Qu, Q., S. J. Lee, and W. Boos. 2004. TreT, a novel trehalose glycosyltransferring synthase of the hyperthermophilic archaeon Thermococcus litoralis. J. Biol. Chem. 279:47890-47897.[Abstract/Free Full Text]
30
30. Raasch, C., W. Streit, J. Schanzer, M. Bibel, U. Gosslar, and W. Liebl. 2000. Thermotoga maritima AglA, an extremely thermostable NAD⁺-, Mn²⁺-, and thiol-dependent --glucosidase. Extremophiles 4:189-200.[CrossRef][Medline]
31
31. Ragan, M. A. 2001. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11:620-626.[CrossRef][Medline]
32
32. Rodrigues, M. V., N. Borges, M. Henriques, P. Lamosa, R. Ventura, C. Fernandes, N. Empadinhas, C. Maycock, M. S. da Costa, and H. Santos. 2007. Bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles. J. Bacteriol. 189:5405-5412.[Abstract/Free Full Text]
33
33. Ryu, S. I., C. S. Park, J. Cha, E. J. Woo, and S. B. Lee. 2005. A novel trehalose-synthesizing glycosyltransferase from Pyrococcus horikoshii: molecular cloning and characterization. Biochem. Biophys. Res. Commun. 329:429-436.[CrossRef][Medline]
34
34. Silva, Z., S. Alarico, and M. S. da Costa. 2005. Trehalose biosynthesis in Thermus thermophilus RQ-1: biochemical properties of the trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase. Extremophiles 9:29-36.[CrossRef][Medline]
35
35. Takayama, K., C. Wang, and G. S. Besra. 2005. Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. Clin. Microbiol. Rev. 18:81-101.[Abstract/Free Full Text]
36
36. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.[Abstract/Free Full Text]
37
37. Wannet, W. J. B., H. J. M. Op den Camp, H. W. Wisselink, C. van der Drift, L. J. L. D. Van Griensven, and G. D. Vogels. 1998. Purification and characterization of trehalose phosphorylase from the commercial mushroom Agaricus bisporus. Biochim. Biophys. Acta 1425:177-188.[Medline]
38
38. Wolf, A., R. Krämer, and S. Morbach. 2003. Three pathways for trehalose metabolism in Corynebacterium glutamicum ATCC 13032 and their significance in response to osmotic stress. Mol. Microbiol. 49:1119-1134.[CrossRef][Medline]
39
39. Woodruff, P. J., B. L. Carlson, B. Siridechadilok, M. R. Pratt, R. H. Senaratne, J. D. Mougous, L. W. Riley, S. J. Williams, and C. R. Bertozzi. 2004. Trehalose is required for growth of Mycobacterium smegmatis. J. Biol. Chem. 279:28835-28843.[Abstract/Free Full Text]

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Journal of Bacteriology, December 2008, p. 7939-7946, Vol. 190, No. 24
0021-9193/08/$08.00+0     doi:10.1128/JB.01055-08
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