Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate

Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1

Inorganic pyrophosphate (PPi) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PPi must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PPi into two orthophosphates (Pi), preventing the toxic accumulation of the PPi byproduct in cells and making Pi available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.

Insight into bacterial community profiles of oil shale and sandstone in ordos basin by culture-dependent and culture-independent methods

To promote the exploitation of unconventional oil resources by indigenous microorganisms, the bacterial community profiles of oil shale and sandstone in Ordos Basin were investigated using Illumina Miseq sequencing combined with the culture-based method, which was performed and reported in this literature for the first time. A total of 601 operational taxonomic units (OTUs) were obtained from collected samples, the predominant phylum present in all samples was Proteobacteria (76.96%-93.07%). Discriminatory bacterial community profiles existed in those samples by culture-dependent and culture-independent methods, with variations not only in diversity indices but also in the abundance of bacteria at different genus levels. The dominant genera in cultured sandstone sample (SCB), uncultured sandstone sample (SUB), cultured shale sample (YCB), uncultured shale sample (YUB) were Enhydrobacter (71.62%), Acidovorax (42.44%), Pseudomonas (40.13%), Variovorax (70.02%), respectively. Both sample sources and culturing methods were the principal factors affecting the variation, while the communities' structures were favored primarily by culture-dependent or culture-independent approaches. The high abundance of hydrocarbon degradation-related genes was exhibited in YCB, which reveals a great potential for utilization of the culture-dependent method in shale oil exploitation. This study provided guidance for the exploitation of shale oil and sandstone oil by artificial utilization of indigenous bacteria.

Covalent Adduct Formation in Methylthio-d-ribose-1-phosphate Isomerase: Reaction Intermediate or Artifact?

Methylthio-d-ribose-1-phosphate (MTR1P) isomerase (MtnA) functions in the methionine salvage pathway by converting the cyclic aldose MTR1P to its open-chain ketose isomer methylthio-d-ribulose 1-phosphate (MTRu1P). What is particularly challenging for this enzyme is that the substrate's phosphate ester prevents facile equilibration to an aldehyde, which in other aldose-ketose isomerases is known to activate the α-hydrogen for proton or hydride transfer between adjacent carbons. We speculated that MtnA could use covalent catalysis via a phosphorylated residue to permit isomerization by one of the canonical mechanisms, followed by phosphoryl transfer back to form the product. In apparent support of this mechanism, [32P]MTR1P was found by SDS-PAGE and gel-filtration chromatography to radiolabel the enzyme. Susceptibility of this adduct to strongly acidic and basic pH and nucleophilic agents is consistent with an acyl phosphate. C160S and D240N, mutants of two conserved active-site residues, however, exhibited no difference in radiolabeling despite a reduction in activity of ∼107, leading to the conclusion that phosphorylation is unrelated to catalysis. Unexpectedly, prolonged incubations with C160S revealed up to 30% accumulation of radioactivity, which was identified by 31P and 13C NMR to be the result of a second adduct─a hemiketal formed between Ser160 and the carbonyl of MTRu1P. These results are interpreted as indirect support for a mechanism involving transfer of the proton from C-2 to C-1 by Cys160.