Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus

Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.

The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities

A Nudix enzyme from Bacillus cereus (NCBI RefSeq accession no. NP_831800) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3'→5' RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-Å resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an "enclosed" Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.

Efficiencies of recovery of bdellovibrios from brackish- water environments by using various bacterial species as prey

A total of 44 bacterial species subdivided into 10 trial experiments have been used as prey for the recovery of bdellovibrios from samples of water from a brackish tidal pond and an aquarium saltwater tank. In an initial investigation, the recovery efficiency of each of the test bacterial species was compared with that of a designated standard prey, Vibrio parahaemolyticus P-5. The results revealed that in each case strain P-5 yielded an equal or significantly greater number of plaques of bdellovibrios than the test prey with but a single exception, strain CS5. In repeat experiments, CS5 yielded fewer plaques than P-5. To determine whether the use of multiple bacterial species compared with a single species as prey would increase the number of PFU of bdellovibrios recovered, material from plaques appearing on each of the test prey in the respective trials was sequentially subcultured onto two respective agar plates, the first containing as prey V. parahaemolyticus P-5 and the second containing the initial test organism. In nearly every case, subculture of plaques from lawns of the test prey to P-5 resulted in plaque formation. On the basis of the results, the use of several test prey and P-5 did not result in the recovery of any more bdellovibrio PFU than the use of P-5 alone. In this study, V. parahaemolyticus P-5 was observed to be the most efficient prey for the recovery of bdellovibrios from moderate salt water.

A Comparison of the Survival of Intraperiplasmic and Attack Phase Bdellovibrios with Reduced Oxygen

The ability of intraperiplasmic and attack phase bdellovibrios to survive and/or grow under anoxic and microaerobic conditions was examined. Both halotolerant and nonhalotolerant bdellovibrio strains were examined. In all instances, the bdellovibrio strains were unable to grow under anoxic conditions, but were able to survive for periods of time in both the extracellular and intraperiplasmic forms. However, the intraperiplasmic organisms were observed to survive longer. Increased temperature hastened the loss of viability of both forms of the predatory bacteria in oxic and anoxic environments. Under microaerobic conditions, halotolerant bdellovibrios were observed to grow, although at a slightly reduced rate than in atmospheric oxygen, while two nonhalotolerant isolates survived but did not grow. The ability of attack phase bdellovibrios to survive in an anoxic environment for up to nine days and their growth or survival under microaerobic conditions greatly expands the possible ecological niches in which the predators may be active members of the microbial community.

Recovery of bdellovibrios from submerged surfaces and other aquatic habitats

The distribution of bdellovibrios was investigated over a wide geographical area of the Chesapeake Bay including some tributaries and subestuaries. Bdellovibrios were recovered from five aquatic habitats; water, sediment, oyster shell surface biofilm, zooplankton, and plants over a wide range of temperature and salinity measurements. Consistently, the greatest number of the predators was recovered from samples of biofilm irrespective of temperature and salinity. A decrease in the numbers and frequency of predators recovered from all habitats was observed at temperatures below 10°C. Only the shell surface biofilm samples yielded bdellovibrios 100% of the time. The organisms were recovered from 79% of water samples and 44% of sediment samples. The results reveal that bdellovibrios are surface-associated organisms and that this association appears to provide some protection for the predators at low temperatures.

Serogrouping of Halophilic Bdellovibrios from Chesapeake Bay and Environs by Immunodiffusion and Immunoelectrophoresis

Little has been reported on the serological relationship of halophilic bdellovibrios (Bd). Immunodiffusion analysis performed with rabbit or mouse Bd antisera developed against eight halophilic Bd isolates and one terrestrial Bd isolate, when reacted with soluble antigen preparations of 45 isolates of halophilic Bd, allowed separation into seven serogroups, which were distinct from the terrestrial isolate. Soluble antigen preparations of prey bacteria, Vibrio parahaemolyticus P-5 (P-5) and Escherichia coli ML 35 (ML 35), exhibited no reactivity with the antisera by immunodiffusion. Immunoelectrophoresis revealed the presence of three distinct antigens in homologous reactions and one shared antigen in heterologous Bd reactions. Shared antigens were noted between halophilic and terrestrial Bd, in addition to between halophilic Bd strains, indicating the possible existence of an antigen(s) which may be shared among all Bd. Again, no shared antigen was noted when P-5 or ML 35 was allowed by immunoelectrophoresis to react with the antisera. Prey susceptibility testing of the seven distinct groups of halophilic Bd, using 20 test prey, produced essentially identical spectra for each group, indicating that this was not a useful technique in delineating the Bd. While immunoelectrophoresis was able to demonstrate an antigen common to all Bd tested, immunodiffusion was able to delineate strains on the basis of a “serogroup specific” antigen. This suggests that immunological tools may serve as important means to study the taxonomy of halophilic Bd, as well as in the formation of a clearer taxonomic picture of the genus Bdellovibrio.