Microbial hydantoinases – industrial enzymes from the origin of life?

Hydantoinases are valuable enzymes for the production of optically pure d- and l-amino acids. They catalyse the reversible hydrolytic ring cleavage of hydantoin or 5′-monosubstituted hydantoins and are therefore classified in the EC nomenclature as cyclic amidases (EC 3.5.2.). In the EC nomenclature, four different hydantoin-cleaving enzymes are described: dihydropyrimidinase (3.5.2.2), allantoinase (EC 3.5.2.5), carboxymethylhydantoinase (EC 3.5.2.4), and N-methylhydantoinase (EC 3.5.2.14). Beside these, other hydantoinases with known metabolic functions, such as imidase and carboxyethylhydantoinase and enzymes with unknown metabolic function, are described in the literature and have not yet been classified. An important question is whether the distinct hydantoinases, which are frequently classified as l-, d-, and non-selective hydantoinases depending on their substrate specificity and stereoselectivity, are related to each other. In order to investigate the evolutionary relationship, amino acid sequence data can be used for a phylogenetic analysis. Although most of these enzymes only share limited sequence homology (identity<15%) and therefore are only distantly related, it can be shown (i) that most of them are members of a broad set of amidases with similarities to ureases and build a protein superfamily, whereas ATP-dependent hydantoinases are not related, (ii) that the urease-related amidases have evolved divergently from a common ancestor and (iii) that they share a metal-binding motif consisting of conserved histidine residues. The difference in enantioselectivity used for the classification of hydantoinases on the basis of their biotechnological value does not reflect their evolutionary relationship, which is to a more diverse group of enzymes than was assumed earlier. This protein superfamily probably has its origin in the prebiotic conditions of the primitive earth. Received: 24 August 1998 / Received revision: 9 November 1998 / Accepted: 21 November 1998     

The occurrence of ochratoxin A in dust collected from a problem household

Accumulated dust samples were collected from the heating ducts in a household where signs resembling ochratoxin poisoning in animals occurred. Several Penicillium spp. and Aspergillus ochraceous had been identified previously from air samples taken from this house. A composite sample from six collected samples was examined by HPLC, and it was determined that 58 ppb of ochratoxin A was present in this sample. A second set of six samples was collected and determinations were made by HPLC of the ochratoxin content in each sample. All samples, including one sample of dirt from a crawl space, yielded at least a trace of ochratoxin A; however, one sample of dust collected from the heating ducts yielded over 1500 ppb of ochratoxin A, and another sample of dust from a different heating duct yielded 306 ppb of ochratoxin A. Ochratoxin A was confirmed in all samples by LC-MS, and ochratoxin was evident in the samples by TLC analysis. This is believed to be the first report of finding ochratoxin inhouse dust. This revised version was published online in June 2006 with corrections to the Cover Date.     

Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm

We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.     

Turnover in an amphibian metacommunity: the role of local and regional factors

Ecologists have long realized that stable species richness values can mask rapid turnover in species composition. Because turnover occurs as a consequence of both local and regional processes, understanding the responsible factors provides insight on processes influencing community structure at different scales. Despite the insights to be gained from data on species turnover, they remain relatively uncommon. We present data on the interannual turnover in species composition of larval amphibian communities in 37 ponds over seven years. Species composition of a given pond community was highly dynamic; about half of the species that could be found breeding in a particular pond were actually present in a given year. All species participated in this community turnover, but to different degrees. Using a model selection approach, we show that a statistical model including local environmental factors (pond area, hydroperiod, and canopy cover) and pond connectivity on the landscape provided the best predictions of turnover. Averaged parameter estimates were significant for area, hydroperiod, and connectivity and these same variables were identified by hierarchical partitioning as having significant independent effects on turnover. Area and hydroperiod were negatively related to turnover, whereas connectivity was positively related to turnover. Additionally, the average fraction of years a species was present in a pond was positively correlated with average local population size, but even more strongly correlated with regional population size, suggesting both local and regional influences on turnover. Of the measured biotic factors (biomass of fish, invertebrate predators, anuran and caudate larvae), presence of fish was the only factor that significantly affected rates of turnover. Several mechanism could be responsible for changes in species composition (species extinctions, skipped breeding and movement of choruses), but extinctions appear to be the major cause of turnover. These results have important implications to understanding long‐term persistence of species on landscapes and the causes of patterns in species richness on environmental gradients.     

Expression of p16INK4A in Pap smears containing atypical glandular cells from the uterine cervix

OBJECTIVE: To verify one of the diagnostic dilemmas concerning atypical glandular cells (AGC) by immunocytochemical detection of p16INK4A (p16) applied to routine Pap smears with correlation of follow-up biopsies for improvement of cytologic diagnoses. STUDY DESIGN: The study included 36 Pap smears in AGC diagnostic categories, all of which were correlated histologically. The cytologic diagnoses of AGC were further classified according to the 2001 Bethesda System. All Pap smears were decolorized and immunostained with the primary anti-p16 antibody, clone E6H4. Immunoreactivity for p16 was correlated with histologic sections in a semiblind fashion. RESULTS: Of the 36 smears containing AGC, 22 (61%) were reclassified as general AGC and 14 (39%) as AGC--favor neoplasia. Follow-up biopsies revealed that 15 (42%) cervixes had no obvious abnormalities and that 21 (58%) cases had different cervical lesions. More than half the cases (19/36, 53%) of follow-up biopsies concerning AGC-containing smears represented significant lesions. There was a much higher proportion of significant lesions (13/14, 93%) in AGC--favor neoplasia than those (6/22, 27%) in general AGC cases. Fifteen of 36 (36%) AGC-containing cases were actually squamous abnormalities on follow-up biopsies. p16 Immunocytochemical stain was reactive in 22 (61%) of 36 smears, either weakly/sporadically (2 cases, 6%) or strongly positively (20 cases, 55%). Conversely, 14 (39%) of the smears were negative for p16 and displayed predominantly reactive changes. However, there was 1 case of high grade squamous intraepithelial lesion showing negative immunostaining for p16. From the view-point of clinical significance, this analysis was highly sensitive (sensitivity, 95%) and specific (specificity, 88%) and had favorable positive (90%) and negative (94%) predictive values. CONCLUSION: On the basis of both morphologic and immunostaining patterns, there was a clear association between strong p16 immunostaining of atypical cells in smears and the presence of significant lesions in the cervix except in 1 patient. Similarly, there was a clear association between lack of p16 expression and absence of cervical lesions. p16 Immunocytochemical stain can be applied successfully to conventional Pap smears and may serve as a useful biomarker in diagnoses of AGC-containing smears. This may offer a more objective parameter to help clarify this ambiguous area of gynecologic cytopathology.     

Nitric oxide-induced oxidant stress in endothelial cells: amelioration by ascorbic acid

Nitric oxide has multiple beneficial effects in the blood vessel wall. However, high concentrations of nitric oxide in the presence of hydroperoxides have been shown to damage cultured cells. In this work, the effect of relatively high concentrations of nitric oxide alone on the function and antioxidant status of a human endothelial cell line (EA.hy926) was tested. Nitric oxide generated from 0.1 to 0.5mM spermine NONOate generated reactive species in the cells detected by triazole formation from diaminofluorescein and by oxidation of dihydrofluorescein. Intracellular ascorbic acid decreased this oxidant stress. Spermine NONOate also decreased intracellular ascorbate concentrations, although reduced glutathione was not affected unless cells had also been caused to reduce dehydroascorbic acid to ascorbate. Nitric oxide predictably inhibited both endothelial nitric oxide synthase and glyceraldehyde 3-phosphate dehydrogenase, and ascorbate partially prevented inhibition of the latter enzyme. These results suggest that relatively high concentrations of nitric oxide can cause oxidant stress in endothelial cells that is ameliorated by ascorbic acid.     

Synthesis and Characterization of Tripodal Iron(II) Complexes Prepared from 2-Pyridinecarboxaldehyde and 1-Methyl-2-Imidazolecarboxaldehyde. Stabilization of Iron(II) Cations with N(6) Donor Sets

Reaction in air of iron(III) salts with tripodal ligands formed from the condensation of tris-(2-aminoethyl)amine (tren) with three equivalents of 2-pyridinecarboxaldehyde (py) or 1-methyl-2-imidazolecarboxaldehyde (NCH₃Im) yielded exclusively the iron(II) complexes, [Fetren(py)₃]X₂ (X=ClO₄ ⁻ or PF₆ ⁻) or [Fetren(NCH₃Im)₃](ClO₄)₂. The complexes were characterized by EA, IR, UV, Mössbauer, and mass spectroscopy. The structure of [Fetren(py)₃](ClO₄)₂ was determined at 100 and 290 K. The structures are essentially the same and feature an octahedral iron with facial coordination of pyridine and imine nitrogen atoms with average bond distances of 1.9747 and 1.9523 Å, respectively, at 290 K. The short Fe-N bond distances and lack of variation with temperature support a low spin, ¹A, assignment for the iron atom. The center nitrogen atom of the tren is essentially planar and is outside of bonding interaction with the iron, 3.45 Å. The low spin assignment is supported by Mössbauer spectroscopy, which reveals the presence of two low spin forms that are not in thermal equilibrium. In contrast, the Mössbauer spectrum of [Fetren(NCH₃Im)₃](ClO₄)₂ reveals the presence of both high spin, ⁵T, and low spin, ¹A, forms at room temperature, which on cooling to 77 K simplify to the low spin form.     

Analysis of the cytoplasmic domains of Salmonella FlhA and interactions with components of the flagellar export machinery

Most flagellar proteins are exported via a type III export apparatus which, in part, consists of the membrane proteins FlhA, FlhB, FliO, FliP, FliQ, and FliR and is housed within the membrane-supramembrane ring formed by FliF subunits. Salmonella FlhA is a 692-residue integral membrane protein with eight predicted transmembrane spans. Its function is not understood, but it is necessary for flagellar export. We have created mutants in which potentially important sequences were deleted. FlhA lacking the amino-terminal sequence prior to the first transmembrane span failed to complement and was dominant negative, suggesting that the sequence is required for function. Similar effects were seen in a variant lacking a highly conserved domain (FHIPEP) within a putative cytoplasmic loop. Scanning deletion analysis of the cytoplasmic domain (FlhAc) demonstrated that substantially all of FlhAc is required for efficient function. Affinity blotting showed that FlhA interacts with several other export apparatus membrane proteins. The implications of these findings are discussed, and a model of FlhA within the export apparatus is presented.     

Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons

The iron- and manganese-containing superoxide dismutases (Fe/Mn-SOD) share the same chemical function and spatial structure but can be distinguished according to their modes of oligomerization and their metal ion specificity. They appear as homodimers or homotetramers and usually require a specific metal for activity. On the basis of 261 aligned SOD sequences and 12 superimposed x-ray structures, two phenetic trees were constructed, one sequence-based and the other structure-based. Their comparison reveals the imperfect correlation of sequence and structural changes; hyperthermophilicity requires the largest sequence alterations, whereas dimer/tetramer and manganese/iron specificities are induced by the most sizable structural differences within the monomers. A systematic investigation of sequence and structure characteristics conserved in all aligned SOD sequences or in subsets sharing common oligomeric and/or metal specificities was performed. Several residues were identified as guaranteeing the common function and dimeric conformation, others as determining the tetramer formation, and yet others as potentially responsible for metal specificity. Some form cation-pi interactions between an aromatic ring and a fully or partially positively charged group, suggesting that these interactions play a significant role in the structure and function of SOD enzymes. Dimer/tetramer- and iron/manganese-specific fingerprints were derived from the set of conserved residues; they can be used to propose selected residue substitutions in view of the experimental validation of our in silico derived hypotheses.