NMR solution structures of Runella slithyformis RNA 2'-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity.

Tpt1, an essential component of the fungal and plant tRNA splicing machinery, catalyzes transfer of an internal RNA 2'-PO4 to NAD+ yielding RNA 2'-OH and ADP-ribose-1',2'-cyclic phosphate products. Here, we report NMR structures of the Tpt1 ortholog from the bacterium Runella slithyformis (RslTpt1), as apoenzyme and bound to NAD+. RslTpt1 consists of N- and C-terminal lobes with substantial inter-lobe dynamics in the free and NAD+-bound states. ITC measurements of RslTpt1 binding to NAD+ (KD ∼31 µM), ADP-ribose (∼96 µM) and ADP (∼123 µM) indicate that substrate affinity is determined primarily by the ADP moiety; no binding of NMN or nicotinamide is observed by ITC. NAD+-induced chemical shift perturbations (CSPs) localize exclusively to the RslTpt1 C-lobe. NADP+, which contains an adenylate 2'-PO4 (mimicking the substrate RNA 2'-PO4), binds with lower affinity (KD ∼1 mM) and elicits only N-lobe CSPs. The RslTpt1·NAD+ binary complex reveals C-lobe contacts to adenosine ribose hydroxyls (His99, Thr101), the adenine nucleobase (Asn105, Asp112, Gly113, Met117) and the nicotinamide riboside (Ser125, Gln126, Asn163, Val165), several of which are essential for RslTpt1 activity in vivo. Proximity of the NAD+ ß-phosphate to ribose-C1″ suggests that it may stabilize an oxocarbenium transition-state during the first step of the Tpt1-catalyzed reaction.

Substrate analogs that trap the 2'-phospho-ADP-ribosylated RNA intermediate of the Tpt1 (tRNA 2'-phosphotransferase) reaction pathway.

The enzyme Tpt1 removes an internal RNA 2'-PO4 via a two-step reaction in which: (i) the 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-(ADP-ribose) intermediate and nicotinamide; and (ii) transesterification of the ADP-ribose O2″ to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1″,2″-cyclic phosphate. Because step 2 is much faster than step 1, the ADP-ribosylated RNA intermediate is virtually undetectable under normal circumstances. Here, by testing chemically modified nucleic acid substrates for activity with bacterial Tpt1 enzymes, we find that replacement of the ribose-2'-PO4 nucleotide with arabinose-2'-PO4 selectively slows step 2 of the reaction pathway and results in the transient accumulation of high levels of the reaction intermediate. We report that replacing the NMN ribose of NAD+ with 2'-fluoroarabinose (thereby eliminating the ribose O2″ nucleophile) results in durable trapping of RNA-2'-phospho-(ADP-fluoroarabinose) as a "dead-end" product of step 1. Tpt1 enzymes from diverse taxa differ in their capacity to use ara-2″F-NAD+ as a substrate.

Structure-Function Analysis of the Phosphoesterase Component of the Nucleic Acid End-Healing Enzyme Runella slithyformis HD-Pnk.

Runella slithyformis HD-Pnk is the prototype of a family of dual 5' and 3' nucleic acid end-healing enzymes that phosphorylate 5'-OH termini and dephosphorylate 2',3'-cyclic-PO4, 3'-PO4, and 2'-PO4 ends. HD-Pnk is composed of an N-terminal HD phosphohydrolase module and a C-terminal P-loop polynucleotide kinase module. Here, we probed the phosphoesterase activity of HD-Pnk by querying its ability to hydrolyze non-nucleic acid phosphoester substrates and by conducting a mutational analysis of conserved amino acid constituents of the HD domain. We report that HD-Pnk catalyzes vigorous hydrolysis of p-nitrophenylphosphate (Km = 3.13 mM; kcat = 27.8 s-1) using copper as its metal cofactor. Mutagenesis identified Gln28, His33, His73, Asp74, Lys77, His94, His127, Asp162, and Arg166 as essential for p-nitrophenylphosphatase and DNA 3' phosphatase activities. Structural modeling places these residues at the active site, wherein His33, His73, Asp74, His94, and His127 are predicted to coordinate a binuclear metal complex and Lys77 and Arg166 engage the scissile phosphate. HD-Pnk homologs are distributed broadly (and exclusively) in bacteria, usually in a two-gene cluster with a putative ATP-dependent polynucleotide ligase (LIG). We speculate that HD-Pnk and LIG comprise the end-healing and end-sealing components of a bacterial nucleic acid repair pathway.IMPORTANCE 5'-end healing and 3'-end healing are key steps in nucleic acid break repair in which 5'-OH ends are phosphorylated by a polynucleotide kinase, and 3'-PO4 or 2',3'-cyclic-PO4 ends are hydrolyzed by a phosphoesterase to generate 5'-PO4 and 3'-OH termini needed for joining by DNA and RNA ligases. This study interrogates, biochemically and via mutagenesis, the phosphoesterase activity of Runella slithyformis HD-Pnk, a bifunctional bacterial 5'- and 3'-end-healing enzyme composed of HD phosphoesterase and P-loop kinase modules. HD-Pnk homologs are found in 129 bacterial genera from 11 phyla. In 123/129 instances, HD-Pnk is encoded in an operon-like gene cluster with a putative ATP-dependent polynucleotide ligase (LIG), suggesting that HD-Pnk and LIG are agents of a conserved bacterial nucleic acid repair pathway.

Enzymatic characteristics of D-mannose 2-epimerase, a new member of the acylglucosamine 2-epimerase superfamily.

Carbohydrate epimerases and isomerases are essential for the metabolism and synthesis of carbohydrates. In this study, Runella slithyformis Runsl_4512 and Dyadobacter fermentans Dfer_5652 were characterized from a cluster of uncharacterized proteins of the acylglucosamine 2-epimerase (AGE) superfamily. These proteins catalyzed the intramolecular conversion of D-mannose to D-glucose, whereas they did not act on ß-(1 → 4)-mannobiose, N-acetyl-D-glucosamine, and D-fructose, which are substrates of known AGE superfamily members. The kcat/Km values of Runsl_4512 and Dfer_5652 for D-mannose epimerization were 3.89 and 3.51 min-1 mM-1, respectively. Monitoring the Runsl_4512 reaction through 1H-NMR showed the formation of ß-D-glucose and ß-D-mannose from D-mannose and D-glucose, respectively. In the reaction with ß-D-glucose, ß-D-mannose was produced at the initial stage of the reaction, but not in the reaction with α-D-glucose. These results indicate that Runsl_4512 catalyzed the 2-epimerization of the ß-anomer substrate with a net retention of the anomeric configuration. Since 2H was obviously detected at the 2-C position of D-mannose and D-glucose in the equilibrated reaction mixture produced by Runsl_4512 in 2H2O, this enzyme abstracts 2-H from the substrate and adds another proton to the intermediate. This mechanism is in accordance with the mechanism proposed for the reactions of other epimerases of the AGE superfamily, that is, AGE and cellobiose 2-epimerase. Upon reaction with 500 g/L D-glucose at 50 °C and pH 8.0, Runsl_4512 and Dfer_5652 produced D-mannose with a 24.4 and 22.8% yield, respectively. These D-mannose yields are higher than those of other enzyme systems, and ME acts as an efficient biocatalyst for producing D-mannose.

Two-step mechanism and step-arrest mutants of Runella slithyformis NAD+-dependent tRNA 2'-phosphotransferase Tpt1.

Tpt1 catalyzes the transfer of an internal 2'-monophosphate moiety (2'-PO4) from a "branched" 2'-PO4 RNA splice junction to NAD+ to form a "clean" 2'-OH, 3'-5' phosphodiester junction, ADP-ribose 1″-2″ cyclic phosphate, and nicotinamide. First discovered as an essential component of the Saccharomyces cerevisiae tRNA splicing machinery, Tpt1 is widely distributed in nature, including in taxa that have no yeast-like RNA splicing system. Here we characterize the RslTpt1 protein from the bacterium Runella slithyformis, in which Tpt1 is encoded within a putative RNA repair gene cluster. We find that (i) expression of RslTpt1 in yeast complements a lethal tpt1Δ knockout, and (ii) purified recombinant RslTpt1 is a bona fide NAD+-dependent 2'-phosphotransferase capable of completely removing an internal 2'-phosphate from synthetic RNAs. The in vivo activity of RslTpt1 is abolished by alanine substitutions for conserved amino acids Arg16, His17, Arg64, and Arg119. The R64A, R119A, and H17A mutants accumulate high levels of a 2'-phospho-ADP-ribosylated RNA reaction intermediate (2'-P-ADPR, evanescent in the wild-type RslTpt1 reaction), which is converted slowly to a 2'-OH RNA product. The R16A mutant is 300-fold slower than wild-type RslTpt1 in forming the 2'-P-ADPR intermediate. Whereas wild-type RsTpt1 rapidly converts the isolated 2'-P-ADPR intermediate to 2'-OH product in the absence of NAD+, the H17A, R119A, R64A, and R16A mutant are slower by factors of 3, 33, 210, and 710, respectively. Our results identify active site constituents involved in the catalysis of step 1 and step 2 of the Tpt1 reaction pathway.

A ß-agarase with high pH stability from Flammeovirga sp. SJP92.

A novel endo-type ß-agarase, AgaB, was cloned from an agar-degrading bacterium, Flammeovirga sp. SJP92. The gene agaB consists of 2, 550 bp and encodes a protein of 849 amino acids including a 19 amino acids signal peptide. Based on the amino acid sequence similarity, AgaB belongs to the glycoside hydrolase family GH16. The recombinant AgaB was expressed in Escherichia coli and exhibited maximal activity at around 45 °C and pH 8.0, with a specific activity of 254.2 U/mg, a Km of 3.99 mg/ml and a Vmax of 700 U/mg for agarose. The agarase was stable at neutral to mildly alkaline condition, and remained 85%-90% of activity after treatment for 1 h, a characteristic much more different from other agarases reported. The recombinant enzyme was sensitive to some metal ions (Cu(2+), Co(2+) and Zn(2+)), but resistant to some denaturants (urea and SDS). It can hydrolyze the ß-1, 4-glycosidic linkages of agarose, yielding neoagarotetraose and neoagarohexaose as the main products. These properties could make AgaB has a potential application in the food, cosmetic and medical industries.

Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma-radiation resistance isolated from soil in South Korea.

A Gram-negative, rod-shaped, non-motile, gamma and UV radiation resistant bacterium Hymenobacter radioresistens DG25B was isolated from a soil sample collected in South Korea. The complete genome sequence of H. radioresistens DG25B consists of one circular chromosome (3,874,646 bp). The bacterium was isolated from gamma ray irradiated soil and contains the genomic features of enzymes involved in the nucleotide excision repair (NER) pathway that protect the damaged DNA. The genome also contains other genes involved in the efficient removal of double-strand breaks (DSB) caused by the ionizing radiations.

An inverting ß-1,2-mannosidase belonging to glycoside hydrolase family 130 from Dyadobacter fermentans.

The glycoside hydrolase family (GH) 130 is composed of inverting phosphorylases that catalyze reversible phosphorolysis of ß-D-mannosides. Here we report a glycoside hydrolase as a new member of GH130. Dfer_3176 from Dyadobacter fermentans showed no synthetic activity using α-D-mannose 1-phosphate but it released α-D-mannose from ß-1,2-mannooligosaccharides with an inversion of the anomeric configuration, indicating that Dfer_3176 is a ß-1,2-mannosidase. Mutational analysis indicated that two glutamic acid residues are critical for the hydrolysis of ß-1,2-mannotriose. The two residues are not conserved among GH130 phosphorylases and are predicted to assist the nucleophilic attack of a water molecule in the hydrolysis of the ß-D-mannosidic bond.

[Isolation, identification and agarose degradation of a polysaccharide-degrading marine bacterium Persicobacter sp. JZB09].

OBJECTIVE: To isolate and identify a versatile carbohydrate-degrading bacterium from marine environments, and characterize the extracellular agarase activity. METHODS: The I2 staining method was applied in the isolation of agarose-degrading bacteria from coastal sediments of the Jiaozhou bay nearby Qingdao city, China. The JZB09 strain was cultured in multiple media using various complex polysaccharides as the sole carbon source to test the carbohydrate utilizing abilities. The 16S rRNA gene was cloned, sequenced and analyzed to identify the taxonomic position of the strain. Crude extracellular proteins were prepared using (NH4)2SO4 precepitation method. The dialyzed enzyme extract was applied in further studies including activity testing, activity staining, and agarose degrading for oligosaccharides purifiction. Three purified oligosaccharides were individually analyzed using thin layer chromatograph (TLC) and MALDI-TOF MS method. RESULTS: The agarolytic marine bacterium, Persicobacter sp. JZB09, could use multiple complex polysaccharides as the sole carbon source and grew well on agarose, cellulose and xylan. The extracellular enzyme extract exhibits efficient and extensive degradation activity on agarose with an activity of 77.2 U/mg proteins. The extracellular agarase system (EAS) in the crude extracellular enzymes contains at least two agarose depolymerases with molecular masses of approximately 45 kDa and 70 kDa, respectively. A series of degradation products from agarose by the EAS was purified and identified as neoagaro-oligosaccharides, among which neoagarotetraose was the major product of the crude enzymatic products, which suggests that beta-agarase is the major constituent of the JZB09 EAS. CONCLUSION: The polysaccharide-degrading bacterium Persicobacter sp. JZB09 and its polysaccharide-degrading system is promising for the exploration of polysaccharide depolymerase resources including beta-agarases.

The FPase properties and morphology changes of a cellulolytic bacterium, Sporocytophaga sp. JL-01, on decomposing filter paper cellulose.

Sporocytophaga sp. JL-01 is a sliding cellulose degrading bacterium that can decompose filter paper (FP), carboxymethyl cellulose (CMC) and cellulose CF11. In this paper, the morphological characteristics of S. sp. JL-01 growing in FP liquid medium was studied by Scanning Electron Microscope (SEM), and one of the FPase components of this bacterium was analyzed. The results showed that the cell shapes were variable during the process of filter paper cellulose decomposition and the rod shape might be connected with filter paper decomposing. After incubating for 120 h, the filter paper was decomposed significantly, and it was degraded absolutely within 144 h. An FPase1 was purified from the supernatant and its characteristics were analyzed. The molecular weight of the FPase1 was 55 kDa. The optimum pH was pH 7.2 and optimum temperature was 50°C under experiment conditions. Zn(2+) and Co(2+) enhanced the enzyme activity, but Fe(3+) inhibited it.

A carotenoid synthesis gene cluster from Algoriphagus sp. KK10202C with a novel fusion-type lycopene beta-cyclase gene.

A carotenoid synthesis gene cluster was isolated from a marine bacterium Algoriphagus sp. strain KK10202C that synthesized flexixanthin. Seven genes were transcribed in the same direction, among which five of them were involved in carotenoid synthesis. This cluster had a unique gene organization, with an isoprenoid gene, ispH (previously named lytB), being present among the carotenoid synthesis genes. The lycopene beta-cyclase encoded by the crtY ( cd ) gene appeared to be a fusion of bacterial heterodimeric lycopene cyclase CrtY(c) and CrtY(d). This was the first time that a fusion-type of lycopene beta-cyclase was reported in eubacteria. Heterologous expression of the Algoriphagus crtY ( cd ) gene in lycopene-accumulating Escherichia coli produced bicyclic beta-carotene. A biosynthesis pathway for monocyclic flexixanthin was proposed in Algoriphagus sp. strain KK10202C, though several of the carotenoid synthesis genes not linked with the cluster have not yet been cloned.

[Study on the process of degrading filter paper cellulose by Sporocytophaga sp. JL-01].

Sporocytophaga is a kind of bacteria that can glide on the solid medium surface. It can decompose the cotton and filter paper after 6 days cultured. The sporocytophaga can only produce a low extracellular carboxymethylcellulase activity and no other cellulase activities. In this work, the process about degradation of filter paper fibre by a strain of Sporocytophaga was studied using scan electronmicroscopy. The morphological changes that Sporocytophaga sp. JI-01 grew on filter paper were observed. The study revealed the JL-01 adhered tightly to the surface of filter paper fibre or penetrated into interior of the fibre through its 2.5 microm - 4.0 microm bacilliform cells in the process of degrading. The bacilliform cells degrade the cellulose strongly and produced a mass of sticky polysaccharides. At the anaphase of cultured, the bacteria existed as a cycloidal dormancy body-sporocyst.

[Correlation between subgingival microflora and peptidase activity in periodontal pockets measured with synthetic substrates].

The activity of peptidases in periodontal pockets of patients were examined by using four different synthetic enzyme substrates, and surveyed their correlation with the microbial populations of subgingival plaque and clinical symptoms. The substrates were (1) alpha-N-benzoyl-DL-arginine-beta-naphthylamide (BANA), (2) N-carbobenzoxy-glycylglycyl-arginine-4-methoxy-beta-naphthylamide, (3) alpha-N-benzoyl-L-arginylglycyl-L-phenylalanyl-L-proline-4-methoxy -beta-naphthylamide and (4) N-carbobenzoxy-prolyl-L-alanylglycyl-L-proline-4-methoxy-beta naphthylamide. Whereas substrates (1) and (2) were hydrolyzed more specifically by peptidases of mainly Bacteroides gingivalis and Treponema denticola, substrates (3) and (4) were susceptible to most of the strains of black-pigmented Bacteroides, Capnocytophaga and T. denticola. Correlation between the peptidase activity and the level of Spirochetes in the plaques were observed with the substrates (1), (2) and (3). Substrate (3) had the strongest correlation also with the level of the black-pigmented Bacteroides and with the depth of the periodontal pockets, suggesting that it is a better substrate for enzymatic diagnosis than BANA which is currently used as an indicator of oral Spirochetes and the black-pigmented Bacteroides.

Comparison of the phosphatases of Lysobacter enzymogenes with those of related bacteria.

Lysobacter enzymogenes ATCC 29487 (UASM 495) produces an outer-membrane-associated phosphatase and an excreted phosphatase. The cell-associated enzyme was compared to phosphatases of nine other Gram-negative gliding bacteria and to that of Escherichia coli. The other three species of the genus Lysobacter also produce a particulate, cell-associated phosphatase. Antiserum prepared against the phosphatase from the outer membrane of L. enzymogenes effectively precipitated the phosphatases of two other L. enzymogenes strains and the enzymes of L. antibioticus, L. brunescens and L. gummosus. Some inhibition of the enzyme by the antiserum also was observed. No significant reaction could be detected between the antiserum and the cell-associated phosphatases of species of Cytophaga johnsonae, 'C. compacta', Myxococcus xanthus, E. coli and the excreted phosphatase of L. enzymogenes. The results indicate that the four species of the genus Lysobacter are closely related despite their physiological differences and that the outer-membrane-associated phosphatases of these organisms have different structural characteristics than the phosphatases of the other Gram-negative bacteria that were used. Furthermore, differences in the amino acid compositions of the cell-associated and the excreted phosphatase of L. enzymogenes confirm the immunological results and are in agreement with the physical and chemical differences noted between the two enzymes.

Enzymatic and antigenic characterization of immunoglobulin A1 proteases from Bacteroides and Capnocytophaga spp.

Bacteroides and Capnocytophaga species have been implicated as periodontal pathogens. Some of these species possess immunoglobulin A1 (IgA1) proteases that are capable of cleaving the human IgA1 molecule in the hinge region, leaving intact Fc alpha and Fab alpha fragments. The purpose of this study was to characterize this activity. In addition to IgA1 protease activity in already known species, IgA1 protease activity was a feature of Bacteroides buccalis, Bacteroides oralis, Bacteroides veroralis, Bacteroides capillus, and Bacteroides pentosaceus. Results of immunoelectrophoretic and sodium dodecyl sulfate-polyacrylamide gel electrophoretic analyses suggested that all species cleave the alpha-chain at the same peptide bond, i.e., the prolyl-seryl bond between residues 223 and 224 in the hinge region. The Bacteroides proteases could be classified as thiol proteases, which were at the same time dependent on metal ions, while the Capnocytophaga proteases were metallo enzymes. None of the proteases were inhibited by the physiologic proteases inhibitors alpha 2-macroglobulin and alpha 1-proteinase inhibitor. Investigations with enzyme-neutralizing antibodies raised in rabbits against protease preparations from the respective type strains revealed that, despite otherwise identical characteristics, the IgA1 protease of each Bacteroides species was antigenically distinct. Bacteroides buccae and the two later synonymous species B. capillus and B. pentosaceus produced identical proteases. In contrast, IgA1 proteases from Capnocytophaga ochracea and Capnocytophaga sputigena strains were apparently identical, while Capnocytophaga gingivalis had a protease that differed from those of the other Capnocytophaga species.

Phenotypic and genetic relationships of so-called Moraxella (Pasteurella) anatipestifer to the Flavobacterium/Cytophaga group.

So-called Moraxella (or Pasteurella) anatipestifer and members of the Flavobacterium/Cytophaga group exhibit remarkable common features: lack of flagellation, low guanine + cytosine content of the chromosomal DNA, production of menaquinones and branched-chain fatty acids, absence of carbohydrate fermentation, and similar patterns of hydrolytic enzymes. Using the renaturation method of DNA:DNA hybridization two urease-negative European isolates and the urease-positive type strain (which was isolated in the United States) of M. P. anatipestifer were shown to have about 85% of their genome DNA base sequences in common; they may represent two subspecies. The type strain of this species was neither measurably related to the type species of the genus Moraxella nor to selected members of the family Pasteurellaceae (Pohl 1981). On the other hand, low but significant degrees of DNA binding between selected strains of so-called M. anatipestifer, Cytophaga marinoflava, Flavobacterium meningosepticum, F. odoratum and F. pectinovorum were observed. On the basis of these findings the transfer of the so-called M. anatipestifer to the Flavobacterium/Cytophaga group (family Cytophagaceae) is proposed. More detailed investigations are required to establish its relationship at the genus level.

Eight new restriction endonucleases fröm Herpetosiphon giganteus--divergent evolution in a family of enzymes.

Characterization of eight restriction endonucleases isolated from five strains of Herpetosiphon giganteus is described. HgiCI from strain Hpg9 recognizes and cleaves the degenerate sequence: GGPyPuCC, producing 5'-hexanucleotide protruding ends. Endonucleases HgiBI, HgiCII and HgiEI are isoschizomers of AvaII; HgiCIII and HgiDII are isoschizomers of SalI; and HgiDI and HgiGI are isoschizomers of AcyI. Based upon their closely related and in part overlapping recognition specificities a close evolutionary relationship is proposed for all known Hgi restriction endonucleases.