Site-specific DNA transesterification by vaccinia topoisomerase: effects of benzo[alpha]pyrene-dA, 8-oxoguanine, 8-oxoadenine and 2-aminopurine modifications

Vaccinia DNA topoisomerase forms a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate at a specific target site 5'-C+5C+4C+3T+2T+1p downward arrow N-1 in duplex DNA. Here we study the effects of base modifications on the rate and extent of single-turnover DNA transesterification. Chiral trans opened C-10 R and S adducts of benzo[a]pyrene (BP) 7,8-diol 9,10-epoxide were introduced at single N6-deoxyadenosine (dA) positions within the 3'-G+5G+4G+3A+2A+1T-1A-2 sequence of the nonscissile DNA strand. The R and S BPdA adducts intercalate from the major groove on the 5' and 3' sides of the modified base, respectively, and perturb local base stacking. We found that R and S BPdA modifications at +1A reduced the transesterification rate by a factor of 700-1000 without affecting the yield of the covalent topoisomerase-DNA complex. BPdA modifications at +2A reduced the extent of transesterification and elicited rate decrements of 200- and 7000-fold for the S and R diastereomers, respectively. In contrast, BPdA adducts at the -2 position had no effect on the extent of the reaction and relatively little impact on the rate of cleavage. A more subtle probe of major groove contacts entailed substituting each of the purines of the nonscissile strand with its 8-oxo analog. The +3 oxoG modification slowed transesterification 35-fold, whereas other 8-oxo modifications were benign. 8-Oxo substitutions at the -1 position in the scissile strand slowed single-turnover cleavage by a factor of six but had an even greater slowing effect on religation, which resulted in an increase in the cleavage equilibrium constant. 2-Aminopurine at positions +3, +4, or +5 in the nonscissile strand had no effect on transesterification per se but had synergistic effects when combined with 8-oxoA at position -1 in the scissile strand. These findings illuminate the functional interface of vaccinia topoisomerase with the DNA major groove.     

Variation in the protocadherin gamma A gene cluster

We screened for variation in the 12 protocadherin gamma A (PCDHGA) genes of the protocadherin cluster on chromosome 5q31. We used denaturing high-performance liquid chromatography followed by sequencing to identify changes in the DNA sequence. We identified 24 nonsynonymous changes, 24 synonymous SNPs, and 9 polymorphisms in the 5' flanking regions. The variant with the greatest predicted impact on the encoded protein was a frameshift polymorphism in PCDHGA8, caused by a deletion of one C base (Pro174fsdelC). The del variant was more common in 512 controls compared to 506 schizophrenic (SZ) cases (10.6% vs 7.2%, p=0.007) but this trend was not replicated in an independent sample of 403 trios, in which it was transmitted 47 times and not transmitted 55 times from heterozygous parents (p=0.43). We screened 10 of the common polymorphisms for association with schizophrenia by genotyping pooled DNA from 540 SZ cases and 540 controls, but none of them showed a significant difference. It will be important to identify the phenotype associated with the loss of the PCDHGA8 gene.     

Multifrequency cw-EPR investigation of the catalytic molybdenum cofactor of polysulfide reductase from<Emphasis Type="Italic"> Wolinella succinogenes</Emphasis>

Electron paramagnetic resonance (EPR) spectra of the molybdenum centre in polysulfide reductase (Psr) from Wolinella succinogenes with unusually high G-tensor values have been observed for the first time. Three different Mo(V) states have been generated (by the addition of the substrate polysulfide and different redox agents) and analysed by their G- and hyperfine tensors using multifrequency (S-, X- and Q-band) cw-EPR spectroscopy. The unusually high G-tensor values are attributed to a large number of sulfur ligands. Four sulfur ligands are assumed to arise from two pterin cofactors; one additional sulfur ligand was identified from mutagenesis studies to be a cysteine residue of the protein backbone. One further sulfur ligand is proposed for two of the Mo(V) states, based on the experimentally observed shift of the g(av) value. This sixth sulfur ligand is postulated to belong to the polysulfide substrate consumed within the catalytic reaction cycle of the enzyme. The influence of the co-protein sulfur transferase on the Mo(V) G-tensor supports this assignment.     

Localization of serotonin and its possible role in early embryos of Tritonia diomedea(Mollusca: Nudibranchia)

A classical neurotransmitter serotonin (5-HT) was detected immunochemically using laser scanning microscopy at the early stages of Tritonia diomedea development. At the one- to eight-cell stages, immunolabeling suggested the presence of 5-HT in the cytoplasm close to the animal pole. At the morula and blastula stages, a group of micromeres at the animal pole showed immunoreactivity. At the gastrula stage no immunoreactive cells were detected, but they arose again at the early veliger stage. Antagonists of 5-HT(2) receptors, ritanserin and cyproheptadine, as well as lipophilic derivatives of dopamine blocked cleavage divisions or distorted their normal pattern. These effects were prevented by 5-HT and its highly lipophilic derivates, serotoninamides of polyenoic fatty acids, but not by the hydrophilic (quaternary) analog of 5-HT, 5-HTQ. The results confirm our earlier suggestion that endogenous 5-HT in pre-nervous embryos acts as a regulator of cleavage divisions in nudibranch molluscs.     

Lewis base interaction with gallium hydrides: a computational study

The recent synthesis and structural characterization of the complex of 3,5-dimethyl-4-hydropyridyl-gallane 1 with the Lewis base 3,5-dimethylpyridine revealed an unusually large angle α = H-Ga-H, 127(2)°, at variance with expected steric effects of the bulky substituents at the tetrahedrally coordinated Ga center. This finding prompted us to study computationally gallium hydrides using density functional and post-Hartree-Fock methods. For 1, we estimated α at 131° from a calculation on 4-hydropyridyl-gallane, GaH₂(Hpy). This value is reduced by 3° due to the interaction with Lewis base pyridine, to yield α = 128°, in excellent agreement with experiment. With an analysis of orbital interactions and a natural bond orbital analysis, we rationalized structural variations of donor-acceptor adducts LGaH₂X where X is a substituent and L is a Lewis base. Angle α is mainly determined by the polarity of the Ga-X bond: the more electronegative substituent X, the larger α and the stronger the interaction of GaH₂X with L. Interaction with a weak base L slightly distorts the initially planar geometry of the dihydride to a trigonal pyramidal form; for a strong base, the structure can become pseudo-tetrahedral.     

Genetic regulation of canine skeletal traits: trade-offs between the hind limbs and forelimbs in the fox and dog

Genetic variation in functionally integrated skeletal traitscan be maintained over 10 million years despite bottlenecksand stringent selection. Here, we describe an analysis of thegenetic architecture of the canid axial skeleton using populationsof the Portuguese Water Dog Canis familiaris) and silver fox(Vulpes vulpes). Twenty-one skeletal metrics taken from radiographsof the forelimbs and hind limbs of the fox and dog were usedto construct separate anatomical principal component (PC) matricesof the two species. In both species, 15 of the 21 PCs exhibitedsignificant heritability, ranging from 25% to 70%. The secondPC, in both species, represents a trade-off in which limb-bonewidth is inversely correlated with limb-bone length. PC2 accountsfor approximately 15% of the observed skeletal variation, 30%of the variation in shape. Many of the other significant PCsaffect very small amounts of variation (e.g., 0.2–2%)along trade-off axes that partition function between the forelimbsand hind limbs. These PCs represent shape axes in which an increasein size of an element of the forelimb is associated with a decreasein size of an element of the hind limb and vice versa. In mostcases, these trade-offs are heritable in both species and geneticloci have been identified in the Portuguese Water Dog for manyof these. These PCs, present in both the dog and the fox, includeones that affect lengths of the forelimb versus the hind limb,length of the forefoot versus that of the hind foot, musclemoment (i.e., lever) arms of the forelimb versus hind limb,and cortical thickness of the bones of the forelimb versus hindlimb. These inverse relationships suggest that genetic regulationof the axial skeleton results, in part, from the action of genesthat influence suites of functionally integrated traits. Theirpresence in both dogs and foxes suggests that the genes controllingthe regulation of these PCs of the forelimb versus hind limbmay be found in other tetrapod taxa.     

Enhancer elements in the mouse CYP1A2 gene: a comparative sequencing among different inbred mouse strains

CYP1A2 expression is constitutively high in mouse liver and is well known for metabolizing several drugs and many procarcinogens to reactive intermediates that can cause toxicity or cancer. In the present study, the basal level of hepatic CYP1A2 activity was shown to vary among different inbred mouse strains. The highest methoxyresorufin-O-demethylase activity (261+/-52pmol/mgprotein/min) was registered in CC57BR and the lowest (82+/-11pmol/mgprotein/min) in C3H/a. We have tested the hypothesis that possible polymorphisms in regulatory elements in the 5'-upstream region of the mouse CYP1A2 gene could cause the differences in CYP1A2 enzyme activity among different inbred strains. We have performed a study on the CYP1A2 gene by sequencing the regulatory region from -4675 to -4204 where two enhancer elements were recently identified. The absence of mutation prescribing the phenotype in the CYP1A2 gene was found. The region studied seems to be a highly conserved in mice and not to be associated with interstrain differences in constitutive CYP1A2 enzyme activity.     

Alternate Bearing in Citrus: Changes in the Expression of Flowering Control Genes and in Global Gene Expression in ON- versus OFF-Crop Trees

Alternate bearing (AB) is the process in fruit trees by which cycles of heavy yield (ON crop) one year are followed by a light yield (OFF crop) the next. Heavy yield usually reduces flowering intensity the following year. Despite its agricultural importance, how the developing crop influences the following year''s return bloom and yield is not fully understood. It might be assumed that an ‘AB signal’ is generated in the fruit, or in another organ that senses fruit presence, and moves into the bud to determine its fate—flowering or vegetative growth. The bud then responds to fruit presence by altering regulatory and metabolic pathways. Determining these pathways, and when they are altered, might indicate the nature of this putative AB signal. We studied bud morphology, the expression of flowering control genes, and global gene expression in ON- and OFF-crop buds. In May, shortly after flowering and fruit set, OFF-crop buds were already significantly longer than ON-crop buds. The number of differentially expressed genes was higher in May than at the other tested time points. Processes differentially expressed between ON- and OFF-crop trees included key metabolic and regulatory pathways, such as photosynthesis and secondary metabolism. The expression of genes of trehalose metabolism and flavonoid metabolism was validated by nCounter technology, and the latter was confirmed by metabolomic analysis. Among genes induced in OFF-crop trees was one homologous to SQUAMOSA PROMOTER BINDING-LIKE (SPL), which controls juvenile-to-adult and annual phase transitions, regulated by miR156. The expression pattern of SPL-like, miR156 and other flowering control genes suggested that fruit load affects bud fate, and therefore development and metabolism, a relatively long time before the flowering induction period. Results shed light on some of the metabolic and regulatory processes that are altered in ON and OFF buds.     

In vitro effects of dentin matrix protein-1 on hydroxyapatite formation provide insights into in vivo functions

Dentin matrix protein-1 (DMP1) is a mineralized tissue matrix protein synthesized by osteoblasts, hypertrophic chondrocytes, and ameloblasts as well as odontoblasts. DMP1 is believed to have multiple in vivo functions, acting both as a signaling molecule and a regulator of biomineralization. Using a cell-free system in vitro, we evaluated the action of DMP1 in the regulation of hydroxylapatite (HA) formation and crystal growth. The non-phosphorylated recombinant protein acted as an HA nucleator, increasing the amount of mineral formed in a gelatin gel HA growth system relative to protein-free controls. The recombinant protein phosphorylated in vitro had no detectable effect on HA formation and growth. In contrast, phosphorylated bovine DMP1 expressed in marrow stromal cells with an adenovirus vector containing 29.7 phosphates/mol was an effective inhibitor of HA formation and growth. The native full-length protein appeared to be absent or present in only small amounts in the extracellular matrix of bones and teeth. However, two highly phosphorylated fragments representing the N- and C-terminal portions of DMP1 have been identified, apparently arising from proteolytic cleavage of four X-Asp bonds. The highly phosphorylated C-terminal 57-kDa fragment (containing 42 phosphates/mol), like the non-phosphorylated DMP1, was an HA nucleator. These data suggest that, in its native form, DMP1 inhibits mineralization, but when cleaved or dephosphorylated, it initiates mineralization. These in vitro data are consistent with the findings in the DMP1 knockout mouse.