Cloning and sequence analysis of the heat-stable acrylamidase from a newly isolated thermophilic bacterium, Geobacillus thermoglucosidasius AUT-01.

A thermophilic bacterium capable of degrading acrylamide, AUT-01, was isolated from soil collected from a hot spring area in Montana, USA. The thermophilic strain grew with 0.2 % glucose as the sole carbon source and 1.4 mM acrylamide as the sole nitrogen source. The isolate AUT-01 was identified as Geobacillus thermoglucosidasius based on 16S rDNA sequence. An enzyme from the strain capable of transforming acrylamide to acrylic acid was purified by a series of chromatographic columns. The molecular weight of the enzyme was estimated to be 38 kDa by SDS-PAGE. The enzyme activity had pH and temperature optima of 6.2 and 70 ºC, respectively. The influence of different metals and amino acids on the ability of the purified protein to transform acrylamide to acrylic acid was evaluated. The gene from G. thermoglucosidasius encoding the acrylamidase was cloned, sequenced, and compared to aliphatic amidases from other bacterial strains. The G. thermoglucosidasius gene, amiE, encoded a 38 kDa, monomeric, heat-stable amidase that catalysed the cleavage of carbon-nitrogen bonds in acrylamide. Comparison of the amino acid sequence to other bacterial amidases revealed 99 and 82 % similarity to the amino acid sequences of Bacillus stearothermophilus and Pseudomonas aeruginosa, respectively.

Characterization of Acrylamidase isolated from a newly isolated acrylamide-utilizing bacterium, Ralstonia eutropha AUM-01.

A mesophilic bacterium capable of utilizing acrylamide was isolated, AUM-01, from soil collected from leaf litter at Picnic Point on the UW-Madison campus. In minimal medium with acrylamide as the sole carbon and nitrogen source, a batch culture of AUM-01 completely converted 28.0 mM acrylamide to acrylic acid in 8 h and reached a cell density of 0.3 (A600)). Afterward all the acrylic acid was degraded by 20 h with the cell density increasing to 1.9 (A600). The acrylamide-utilizing bacterium was identified as Ralstonia eutropha based on morphological observations, the BiOLOG GN2 MicroPlate™ identification system for Gram-negative bacteria, and additional physiological tests. An acrylamidase that hydrolyzes acrylamide to acrylic acid was purified from the strain AUM-01. The molecular weight of the enzyme from AUM-01 was determined to be 38 kDa by SDS-PAGE. The enzyme had pH and temperature optima of 6.3 and 55°C, and the influence of different metals and amino acids on the ability of the purified protein to transform acrylamide to acrylic acid was evaluated. The enzyme from AUM-01 was totally inhibited by ZnSO4 and AgNO3.

Evidence that Bacillus catabolite control protein CcpA interacts with RNA polymerase to inhibit transcription.

Summary Bacilluscatabolite control protein (CcpA) mediates carbon catabolite repression (CCR) by controlling expression of catabolite responsive (CR) genes or operons through interaction with catabolite responsive elements (cres) located within or outside of CR promoters. Here, we investigated how CcpA inhibits the transcription of CR promoters in vitro. CcpA has different affinities for different cres, but this does not correlate with its ability to inhibit transcription. In the amyE promoter, which overlaps a CcpA binding site (amyE cre centred at +4.5), CcpA does not prevent RNA polymerase (RNAP) binding to the promoter; it may even interact with RNAP. Inserting non-integral turns of helix (1.5 and 2.5) between the amyE promoter (-10 hexamer) and the amyE cre relieved CCR of amyE expression. In the xyl operon, despite the downstream location of its cre (a major cre centred at +130.5), CcpA blocked transcription initiation, not elongation (roadblock) at the site of the cre. Taken together, our results strongly suggest that CcpA requires interactions with RNAP to inhibit transcription.

Crystallization and preliminary analysis of xenobiotic reductase B from Pseudomonas fluorescens I-C.

Single crystals have been obtained of xenobiotic reductase B (XenB), a flavoenzyme isolated and cloned from Pseudomonas fluorescens I-C. The enzyme catalyzes the NADPH-dependent elimination of nitrite from nitroglycerin with an approximately fivefold kinetic preference for the middle nitro group, primarily yielding 1,3-dinitroglycerol. X-ray diffraction data sets have been collected from native crystals to 2.3 A resolution. The space group is P4(1)2(1)2, with unit-cell parameters a = b = 140, c = 95.6 A. The asymmetric unit is likely to contain at least two XenB molecules (V(M) = 3.1 A(3) Da(-1), 60% solvent) and a molecular-replacement solution has been determined in order to solve the structure.

Crystallization and preliminary analysis of xenobiotic reductase A and ligand complexes from Pseudomonas putida II-B.

Diffraction-quality crystals have been obtained of the xenobiotic reductase A (XenA) from Pseudomonas II-B, which was originally cultured from the contaminated soil of a World War II era munitions-manufacturing plant. Several complete X-ray diffraction data sets have been collected and analyzed. The native XenA data set includes reflections between 35 and 1.65 A. Four-wavelength MAD data sets from selenomethionine-enriched XenA and from three different ligand complexes are also reported. The XenA crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 84, b = 158, c = 57 A. Experimental phasing from analysis of the MAD data from selenomethionine-enriched XenA reveals the presence of two molecules in the asymmetric unit. They are related by a non-crystallographic 2(1) screw axis nearly parallel to the c axis, but offset by a quarter unit-cell translation. Thus, the local symmetry produces approximate systematic absences along the (00l) principal axis and complicates the space-group determination.

The TRTGn motif stabilizes the transcription initiation open complex.

The effect on transcription initiation by the extended -10 motif (5'-TRTG(n)-3'), positioned upstream of the -10 region, was investigated using a series of base substitution mutations in the alpha-amylase promoter (amyP). The extended -10 motif, previously referred to as the -16 region, is found frequently in Gram-positive bacterial promoters and several extended -10 promoters from Escherichia coli. The inhibitory effects of the non-productive promoter site (amyP2), which overlaps the upstream region of amyP, were eliminated by mutagenesis of the -35 region and the TRTG motif of amyP2. Removal by mutagenesis of the competitive effects of amyP2 resulted in a reduced dependence of amyP on the TRTG motif. In the absence of the second promoter, mutations in the TRTG motif of amyP destabilized the open complex and prevented the maintenance of open complexes at low temperatures. The open complex half-life was up to 26-fold shorter in the mutant TRTG motif promoters than in the wild-type promoter. We demonstrate that the amyP TRTG motif dramatically stabilizes the open complex intermediate during transcription initiation. Even though the open complex is less stable in the mutant promoters, the region of melted DNA is the same in the wild-type and mutant promoters. However, upon addition of the first three nucleotides, which trap RNAP (RNA polymerase) in a stable initiating complex, the melted DNA region contracts at the 5'-end in a TRTG motif promoter mutant but not at the wild-type promoter, indicating that the motif contributes to maintaining DNA-strand separation.